R/feature_categories.R
In bergerm1/GenomeDerivedDiagnosis: Identify Cancer Type using IMPACT Data only
Defines functions
mutations
truncating_mutations
hotspots
focal_cn_portal
broad_cn
fun.aggregate
Documented in
broad_cn
focal_cn_portal
hotspots
mutations
truncating_mutations
tdt <- function (inpdt){
transposed <- t(inpdt[, -1, with = F])
colnames(transposed) <- inpdt[[1]]
transposed <- data.table(transposed, keep.rownames = T)
setnames(transposed, 1, names(inpdt)[1])
return(transposed)
}
#' @name mutations
#' @title something
#' @description
#'
#' Mutations - MSK-IMPACT 341
#'
#' @param maf
#'
#' @return binary table of mutations in the 341 IMPACT gene panel
mutations = function(maf = maf){
Nonsyn_Consequences = c("missense_variant", "stop_gained", "frameshift_variant", "splice_donor_variant",
"splice_acceptor_variant", "inframe_insertion", "inframe_deletion",
"stop_lost", "exon_loss_variant", "disruptive_inframe_deletion",
"disruptive_inframe_insertion", "start_lost")
maf = as.data.table(maf)
if("Tumor_Sample_Barcode" %in% names(maf)){
setnames(maf, "Tumor_Sample_Barcode", "SAMPLE_ID")
}
setkey(maf, "SAMPLE_ID")
mutations_d = dcast.data.table(
maf[ Consequence %like% paste(collapse = "|", Nonsyn_Consequences) & Hugo_Symbol %in% MolecularDiagnosis::msk_impact_341],
SAMPLE_ID ~ Hugo_Symbol,
value.var = 'SAMPLE_ID',
fun.aggregate = function(x) {
ifelse(length(x) > 0, 1, 0)
}
)
mutations_d = as.data.table(mutations_d)
unmutated_impact_genes = setdiff(MolecularDiagnosis::msk_impact_341, colnames(mutations_d))
suppressWarnings(mutations_d[, unmutated_impact_genes := 0, with = F])
# add TERT promoter as an additional feature
mutations_d[SAMPLE_ID %in% maf[Consequence == "upstream_gene_variant" &
Hugo_Symbol == "TERT"]$SAMPLE_ID, TERTp := 1]
mutations_d[!SAMPLE_ID %in% maf[Consequence == "upstream_gene_variant" &
Hugo_Symbol == "TERT"]$SAMPLE_ID, TERTp := 0]
setcolorder(mutations_d, c("SAMPLE_ID", sort(MolecularDiagnosis::msk_impact_341), "TERTp"))
if("Tumor_Sample_Barcode" %in% names(maf)){
setnames(maf, "Tumor_Sample_Barcode", "SAMPLE_ID")
}
copy(mutations_d)
}
#' @name truncating_mutations
#' @title something
#' @description
#'
#' Truncating mutations - MSK-IMPACT341
#'
#' @param maf
#'
#' @return binary table of truncating mutations in the 341 IMPACT gene panel
truncating_mutations = function(maf = maf) {
if("Tumor_Sample_Barcode" %in% names(maf)){
setnames(maf, "Tumor_Sample_Barcode", "SAMPLE_ID")
}
setkey(maf, "SAMPLE_ID")
if("Consequence" %in% names(maf)) {
trunc <- c("stop_gained", "frameshift_variant", "splice_donor_variant",
"splice_acceptor_variant", "stop_lost", "exon_loss_variant")
mutations_d <- dcast.data.table(
maf[Consequence %like% paste(collapse = "|", trunc) &
Hugo_Symbol %in% MolecularDiagnosis::msk_impact_341],
SAMPLE_ID ~ paste0(Hugo_Symbol, "_", "TRUNC"),
value.var = 'SAMPLE_ID',
fun.aggregate = function(x) {
ifelse(length(x) > 0, 1, 0)
}
)
} else {
trunc <- c("Frame_Shift_Del", "Splice_Site", "Frame_Shift_Ins",
"Nonsense_Mutation", "Nonstop_Mutation")
mutations_d <- dcast.data.table(
maf[ Variant_Classification %like% paste(collapse = "|", trunc) & Hugo_Symbol %in% MolecularDiagnosis::msk_impact_341],
SAMPLE_ID ~ paste0(Hugo_Symbol, "_", "TRUNC"),
value.var = 'SAMPLE_ID',
fun.aggregate = function(x) {
ifelse(length(x) > 0, 1, 0)
}
)
}
mutations_d <- as.data.table(mutations_d)
unmutated_impact_genes <- setdiff(paste0(MolecularDiagnosis::msk_impact_341, "_", "TRUNC"), colnames(mutations_d))
suppressWarnings(mutations_d[, unmutated_impact_genes := 0, with = F])
setcolorder(mutations_d, c("SAMPLE_ID", paste0(
sort(MolecularDiagnosis::msk_impact_341), "_", "TRUNC"
)))
if("Tumor_Sample_Barcode" %in% names(maf)) setnames(maf, "Tumor_Sample_Barcode", "SAMPLE_ID")
copy(mutations_d)
}
#' Hotspots - MSK-IMPACT 341
#'
#' @param maf
#'
#' @return binary table of hotpots in the 341 IMPACT gene panel
#'
#' @export hotspots
hotspot_list <- c("ABCC10 R570L", "ABCC10 R570Q", "ABCC10 R570W", "ACADS R330C",
"ACADS R330H", "ACP6 V29G", "ACSBG2 I250M", "ACVR1 G328E", "ACVR1 G328V",
"ACVR1 R206H", "ACVR1 R258G", "ACVR1 R258M", "ACVR1B R485*",
"AHI1 Q294R", "AKT1 D323G", "AKT1 D323N", "AKT1 D323Y", "AKT1 E17*",
"AKT1 E17K", "AKT1 L52H", "AKT1 L52R", "AKT1 P68_C77dup", "AKT1 Q79K",
"AKT1 T65_I75dup", "AKT2 C60_I75dup", "AKT2 L78_Q79insHANTFVIRCL",
"AKT2 R67_L78dup", "AKT2 R76_I84dup", "AKT3 E17*", "AKT3 E17K",
"ALK F1174C", "ALK F1174L", "ALK F1174V", "ALK F1245I", "ALK F1245V",
"ALK R1275*", "ALK R1275L", "ALK R1275Q", "ALK R395=", "ALK R395H",
"ALK R401*", "ALK R401L", "ALK R401Q", "AMPD1 L631F", "AMPD1 L631V",
"ANKRD11 E1008_P1015del", "ANKRD11 K1012del", "ANKRD11 K1461del",
"ANKRD11 K369R", "ANKZF1 A650=", "ANKZF1 A650V", "APC E1353*",
"APC E1379*", "APC E1397*", "APC E1408*", "APC Q1294*", "APC Q1303*",
"APC Q1328*", "APC Q1338*", "APC Q1367*", "APC Q1367E", "APC Q1378*",
"APC Q1406*", "APC Q1406H", "APC Q1429*", "APC Q1429R", "APC R1114*",
"APC R1450*", "APC R213*", "APC R216*", "APC R232*", "APC R499*",
"APC R564*", "APC R876*", "APC R876Q", "APC S1315*", "APC Y935*",
"AR H875Y", "AR L702=", "AR L702H", "AR T878A", "AR T878S", "AR W742C",
"AR W742L", "ARAF P216L", "ARAF P216R", "ARAF S214=", "ARAF S214A",
"ARAF S214C", "ARAF S214F", "ARAF S214P", "ARAF S214Y", "ARHGAP28 L277P",
"ARHGAP28 L277R", "ARID1A G2087E", "ARID1A G2087R", "ARID1A Q1142*",
"ARID1A R1276*", "ARID1A R1276Q", "ARID1A R1335*", "ARID1A R1461*",
"ARID1A R1461Q", "ARID1A R1721*", "ARID1A R1722*", "ARID1A R1989*",
"ARID1A R1989Q", "ARID1A R2158*", "ARID1A R2158=", "ARID1A R2158Q",
"ARID1A R693*", "ARID1A X911_splice", "ARID1B G966D", "ARID1B Q1179*",
"ARID1B Q1179P", "ARID1B T1652=", "ARID1B T1652A", "ARID1B T1652M",
"ARID2 R314C", "ARID2 R314S", "ARID2 S297=", "ARID2 S297F", "ARID3A S557G",
"ARIH1 A409E", "ARL16 G6R", "ASF1B P21=", "ASF1B P21L", "ASXL2 E330D",
"ASXL2 E330K", "ASXL2 E330Q", "ASXL2 M1?", "ASXL2 R357*", "ATM I2888L",
"ATM I2888T", "ATM L2890P", "ATM L2890R", "ATM L2890V", "ATM N2875K",
"ATM N2875S", "ATM N2875T", "ATM R1466*", "ATM R1466P", "ATM R1466Q",
"ATM R250*", "ATM R250P", "ATM R2832C", "ATM R2832S", "ATM R3008C",
"ATM R3008H", "ATM R3008L", "ATM R337C", "ATM R337H", "ATP6V1B2 P352=",
"ATP6V1B2 P352S", "ATRX R1426*", "ATRX R1426=", "ATRX R907*",
"ATRX X199_splice", "AXIN1 X652_splice", "AXL A273P", "AXL A273V",
"AXL T443=", "B2M L12=", "B2M L12P", "B2M L12Q", "B2M L7*", "B2M L7S",
"B2M M1?", "B2M X23_splice", "BAP1 E31del", "BAP1 K25_D34delinsN",
"BAP1 K25_Q28del", "BAP1 Y33del", "BCL10 E178=", "BCL10 E178D",
"BCL10 L174*", "BCL10 N173H", "BCL2 A131D", "BCL2 A131T", "BCL2 A131V",
"BCL2 G33=", "BCL2 G33R", "BCL2 K22*", "BCL2 K22=", "BCL2 K22R",
"BCL2 N172=", "BCL2 N172Q", "BCL2 N172S", "BCL2L11 G156*", "BCL2L11 G156E",
"BCL2L11 G156R", "BCL2L12 F17=", "BCL2L12 F8=", "BCL2L12 R18W",
"BCL6 R594G", "BCL6 R594Q", "BCL6 R618C", "BCL6 R618H", "BCOR N1459S",
"BNC2 S575I", "BNC2 S575R", "BRAF D594E", "BRAF D594G", "BRAF D594H",
"BRAF D594N", "BRAF D594V", "BRAF D594Y", "BRAF G466A", "BRAF G466E",
"BRAF G466V", "BRAF G469*", "BRAF G469=", "BRAF G469A", "BRAF G469E",
"BRAF G469R", "BRAF G469S", "BRAF G469V", "BRAF G596C", "BRAF G596D",
"BRAF G596R", "BRAF G596S", "BRAF G596V", "BRAF I592_A598dup",
"BRAF K601_W604del", "BRAF K601E", "BRAF K601N", "BRAF K601T",
"BRAF L485*", "BRAF L485F", "BRAF L485S", "BRAF L485W", "BRAF L597=",
"BRAF L597Q", "BRAF L597R", "BRAF L597S", "BRAF L597V", "BRAF N486_A489delinsK",
"BRAF N486_P490del", "BRAF N581D", "BRAF N581H", "BRAF N581I",
"BRAF N581S", "BRAF N581T", "BRAF N581Y", "BRAF P490_Q494del",
"BRAF T488_P492del", "BRAF T488_Q493delinsK", "BRAF T599dup",
"BRAF V600_K601delinsE", "BRAF V600_R603del", "BRAF V600=", "BRAF V600E",
"BRAF V600G", "BRAF V600K", "BRAF V600M", "BRAF V600R", "BRAF X327_splice",
"BRCA2 S2303=", "BRCA2 S2303F", "BRD4 P1065=", "BRD4 P1065R",
"BRD7 Y455*", "BRINP1 G713=", "BTBD11 K1003M", "BTBD11 K1003R",
"BTBD11 K1003T", "C16orf80 R100C", "C16orf80 R100H", "C3orf70 S6*",
"C3orf70 S6L", "C3orf70 S6W", "C5orf49 K130T", "C6 K817R", "C6 K817T",
"CANT1 K131R", "CARD11 D357N", "CARD11 D357V", "CARD11 D401N",
"CARD11 E626*", "CARD11 E626K", "CARD11 E626Q", "CARD11 E93D",
"CARD11 E93K", "CARD11 E93Q", "CARD11 K215M", "CARD11 K215N",
"CARD11 K215T", "CARD11 L251P", "CARD11 R337*", "CARD11 R337Q",
"CARD11 R423=", "CARD11 R423Q", "CARD11 R423W", "CASP8 R127*",
"CASP8 R127Q", "CASP8 R292Q", "CASP8 R292W", "CASP8 R491*", "CASP8 R491Q",
"CASP8 R494*", "CASP8 X243_splice", "CBFB W73*", "CBL C384R",
"CBL C384W", "CCND1 C47S", "CCND1 E9=", "CCND1 E9D", "CCND1 E9K",
"CCND1 P287A", "CCND1 P287L", "CCND1 P287R", "CCND1 P287S", "CCND1 P287T",
"CCND1 T286A", "CCND1 T286I", "CCND1 Y44*", "CCND1 Y44C", "CCND1 Y44D",
"CCND1 Y44F", "CCND1 Y44H", "CCND1 Y44S", "CCND3 I290K", "CCND3 I290R",
"CCND3 Q276*", "CCT8 I86T", "CD79B X185_splice", "CD79B Y197C",
"CD79B Y197D", "CD79B Y197F", "CD79B Y197H", "CD79B Y197N", "CD79B Y197R",
"CD79B Y197S", "CDH1 D254E", "CDH1 D254N", "CDH1 D254Y", "CDH1 D288N",
"CDH1 D288V", "CDH1 Q23*", "CDH1 R335*", "CDH1 R335Q", "CDH1 R63*",
"CDH1 R63G", "CDH1 R63P", "CDH1 X177_splice", "CDH1 X278_splice",
"CDH1 X440_splice", "CDH1 X722_splice", "CDH1 Y190C", "CDK12 R890H",
"CDK4 K22M", "CDK4 K22Q", "CDK4 R24C", "CDK4 R24H", "CDK4 R24L",
"CDK4 R24S", "CDK6 L65=", "CDKN1B G72=", "CDKN1B G72A", "CDKN1B G72D",
"CDKN1B X159_splice", "CDKN2A A36_N39delinsD", "CDKN2A D108G",
"CDKN2A D108H", "CDKN2A D108N", "CDKN2A D108V", "CDKN2A D108Y",
"CDKN2A D74G", "CDKN2A D74N", "CDKN2A D74V", "CDKN2A D74Y", "CDKN2A D84A",
"CDKN2A D84G", "CDKN2A D84N", "CDKN2A D84V", "CDKN2A D84Y", "CDKN2A E120*",
"CDKN2A E120D", "CDKN2A E120K", "CDKN2A E27del", "CDKN2A E88*",
"CDKN2A E88K", "CDKN2A G35_A36del", "CDKN2A H83D", "CDKN2A H83N",
"CDKN2A H83Q", "CDKN2A H83R", "CDKN2A H83Y", "CDKN2A L130Q",
"CDKN2A L130R", "CDKN2A L130V", "CDKN2A L32_L37del", "CDKN2A N39_N42del",
"CDKN2A N42H", "CDKN2A N42I", "CDKN2A N42K", "CDKN2A N42Y", "CDKN2A P114F",
"CDKN2A P114H", "CDKN2A P114L", "CDKN2A P114S", "CDKN2A P114T",
"CDKN2A P48L", "CDKN2A P48R", "CDKN2A Q50*", "CDKN2A Q50=", "CDKN2A Q50H",
"CDKN2A Q50R", "CDKN2A R140C", "CDKN2A R170C", "CDKN2A R29_A34del",
"CDKN2A R58*", "CDKN2A R80*", "CDKN2A R80Q", "CDKN2A S114R",
"CDKN2A S12*", "CDKN2A S12L", "CDKN2A V28_E33del", "CDKN2A W110*",
"CDKN2A X153_splice", "CDKN2A X51_splice", "CDKN2A Y129*", "CDKN2A Y129C",
"CEBPA N307_E309delinsK", "CEBPA T310_Q311insKQNP", "CEBPA T310_Q311insW",
"CEBPA V308dup", "CELSR1 W1958C", "CEP63 S153=", "CEP63 S153L",
"CEP89 S153I", "CHEK2 R346C", "CHEK2 R346G", "CHEK2 R346H", "CHEK2 R346S",
"CHIT1 W358*", "CIC N205S", "CIC P203A", "CIC P203L", "CIC P203S",
"CIC R1512C", "CIC R1512H", "CIC R1512L", "CIC R1512S", "CIC R1515C",
"CIC R1515H", "CIC R201=", "CIC R201W", "CIC R202Q", "CIC R202W",
"CIC R215=", "CIC R215Q", "CIC R215W", "CIC S231G", "CIC S231I",
"CIC S231N", "CIC W238*", "CIC W238R", "CIC X151_splice", "CIZ1 L59P",
"CLEC14A R193=", "CLEC14A R193C", "CLEC14A R193H", "COBL E480D",
"CR1 R1842C", "CR1 R1842H", "CRB1 F630S", "CRB1 F630V", "CREBBP D1435G",
"CREBBP D1435H", "CREBBP D1435N", "CREBBP D1435Y", "CREBBP I1431=",
"CREBBP I1431N", "CREBBP I1431S", "CREBBP I1431V", "CREBBP L1499P",
"CREBBP L1499Q", "CREBBP L1499R", "CREBBP R1446C", "CREBBP R1446G",
"CREBBP R1446H", "CREBBP R1446L", "CREBBP R1446P", "CREBBP R1446S",
"CREBBP S1680del", "CREBBP W1472C", "CREBBP W1472G", "CREBBP W1472R",
"CREBBP W1472S", "CREBBP W1502*", "CREBBP W1502C", "CREBBP W1502L",
"CREBBP W1502R", "CREBBP Y1450C", "CREBBP Y1450D", "CREBBP Y1450N",
"CREBBP Y1482C", "CREBBP Y1482D", "CREBBP Y1482H", "CREBBP Y1482N",
"CREBBP Y1503C", "CREBBP Y1503D", "CREBBP Y1503H", "CREBBP Y1503N",
"CREBBP Y1503S", "CRLF2 S128=", "CRLF2 S128L", "CRNKL1 S128=",
"CRNKL1 S128F", "CSPG5 R365=", "CSPG5 R365Q", "CSPG5 R365W",
"CTCF H284N", "CTCF H284P", "CTCF H284Y", "CTCF H288D", "CTCF H288R",
"CTCF H288Y", "CTCF R377C", "CTCF R377H", "CTCF R448*", "CTCF S354F",
"CTCF S354Y", "CTCF Y226C", "CTNNB1 A43_P44dup", "CTNNB1 D32_I35delinsV",
"CTNNB1 D32_S33del", "CTNNB1 D32_S37delinsA", "CTNNB1 D32A",
"CTNNB1 D32G", "CTNNB1 D32H", "CTNNB1 D32N", "CTNNB1 D32V", "CTNNB1 D32Y",
"CTNNB1 G34_S71del", "CTNNB1 G34*", "CTNNB1 G34A", "CTNNB1 G34E",
"CTNNB1 G34L", "CTNNB1 G34R", "CTNNB1 G34V", "CTNNB1 G38_P44del",
"CTNNB1 H36P", "CTNNB1 H36Y", "CTNNB1 I35=", "CTNNB1 I35S", "CTNNB1 K292E",
"CTNNB1 K292T", "CTNNB1 K335I", "CTNNB1 K335T", "CTNNB1 L31_I35del",
"CTNNB1 L31_S33del", "CTNNB1 N387I", "CTNNB1 N387K", "CTNNB1 N387Y",
"CTNNB1 P44_S60del", "CTNNB1 Q26_D32delinsH", "CTNNB1 Q28_D32delinsH",
"CTNNB1 R535*", "CTNNB1 R535Q", "CTNNB1 S23_S33del", "CTNNB1 S33_A39del",
"CTNNB1 S33A", "CTNNB1 S33C", "CTNNB1 S33F", "CTNNB1 S33P", "CTNNB1 S33T",
"CTNNB1 S33Y", "CTNNB1 S37A", "CTNNB1 S37C", "CTNNB1 S37F", "CTNNB1 S37P",
"CTNNB1 S37Y", "CTNNB1 S45_P52del", "CTNNB1 S45=", "CTNNB1 S45A",
"CTNNB1 S45C", "CTNNB1 S45del", "CTNNB1 S45F", "CTNNB1 S45P",
"CTNNB1 S45Y", "CTNNB1 T41_S45del", "CTNNB1 T41_S47del", "CTNNB1 T41A",
"CTNNB1 T41I", "CTNNB1 T41N", "CTNNB1 T42_K49del", "CTNNB1 W25_D32del",
"CTNNB1 W25_H36del", "CTNNB1 W383C", "CTNNB1 W383G", "CTNNB1 W383R",
"CTNNB1 W383S", "CTNNB1 Y30_S33del", "CUL3 A20=", "CUL3 M299R",
"CUL3 M299V", "CYP2C8 P402L", "CYP2C8 P402S", "CYP4A11 I491T",
"CYP7B1 K332T", "CYSLTR2 L129Q", "DCAF13 T118=", "DDX28 S442=",
"DDX28 S442F", "DHRS4 T102M", "DICER1 D1709N", "DICER1 D1810A",
"DICER1 D1810H", "DICER1 D1810N", "DICER1 D1810V", "DICER1 D1810Y",
"DICER1 E1813A", "DICER1 E1813G", "DICER1 E1813K", "DICER1 E1813Q",
"DICER1 S1344I", "DICER1 S1344L", "DIS3 D479G", "DIS3 D479H",
"DIS3 D479V", "DIS3 D479Y", "DIS3 D488A", "DIS3 D488G", "DIS3 D488H",
"DIS3 D488N", "DIS3 D488Y", "DIS3 L767F", "DIS3 R382G", "DIS3 R382Q",
"DIS3 R689G", "DIS3 R689Q", "DIS3 R780G", "DIS3 R780K", "DIS3 R780S",
"DIS3 R780T", "DNAH9 E2368D", "DNAH9 E2368K", "DNAJB1 L190=",
"DNMT1 E432K", "DNMT1 E51K", "DNMT3A R882C", "DNMT3A R882H",
"DNMT3A R882P", "DNMT3B V229=", "DNMT3B V229L", "DNMT3B V229M",
"DUSP16 R483*", "EBF2 G444E", "EBF2 G444V", "EGFR A289D", "EGFR A289I",
"EGFR A289N", "EGFR A289T", "EGFR A289V", "EGFR A750=", "EGFR A750P",
"EGFR A767_V769dup", "EGFR D770_N771insG", "EGFR D770_N771insGF",
"EGFR D770_N771insGL", "EGFR D770_N771insY", "EGFR D770_P772dup",
"EGFR E709_T710delinsD", "EGFR E709A", "EGFR E709K", "EGFR E709Q",
"EGFR E746_A750del", "EGFR E746_T751delinsA", "EGFR G598A", "EGFR G598E",
"EGFR G598V", "EGFR G719A", "EGFR G719C", "EGFR G719D", "EGFR G719S",
"EGFR H304Y", "EGFR H773_V774dup", "EGFR H773dup", "EGFR K745_E746insVPVAIK",
"EGFR K754_I759del", "EGFR K754=", "EGFR K754E", "EGFR K754I",
"EGFR L62R", "EGFR L747_E749del", "EGFR L747_P753delinsS", "EGFR L747_S752del",
"EGFR L747_T751del", "EGFR L747=", "EGFR L747F", "EGFR L747P",
"EGFR L747S", "EGFR L833F", "EGFR L833M", "EGFR L833V", "EGFR L838M",
"EGFR L838P", "EGFR L858R", "EGFR L861Q", "EGFR N771_H773dup",
"EGFR N771_P772insH", "EGFR N771_P772insHH", "EGFR N771_P772insV",
"EGFR P596=", "EGFR P596L", "EGFR P596R", "EGFR P596S", "EGFR P772_H773dup",
"EGFR P772_H773insTPNP", "EGFR R108G", "EGFR R108K", "EGFR R222C",
"EGFR R222H", "EGFR R252C", "EGFR R252H", "EGFR R252P", "EGFR S752_I759del",
"EGFR S768_D770dup", "EGFR S768I", "EGFR S768T", "EGFR T263I",
"EGFR T263P", "EGFR T363A", "EGFR T363I", "EGFR T363N", "EGFR T751_A755del",
"EGFR T751_E758del", "EGFR T790=", "EGFR T790M", "EGFR Y764_D770dup",
"EIF1AX G15=", "EIF1AX G15D", "EIF1AX G15V", "EIF1AX G6C", "EIF1AX G6D",
"EIF1AX G6R", "EIF1AX G6S", "EIF1AX G8E", "EIF1AX G8R", "EIF1AX G9D",
"EIF1AX G9R", "EIF1AX G9V", "EIF1AX K10E", "EIF1AX K10T", "EIF1AX N4I",
"EIF1AX N4S", "EIF1AX N4Y", "EIF1AX P2=", "EIF1AX P2L", "EIF1AX P2S",
"EIF1AX R13C", "EIF1AX R13G", "EIF1AX R13H", "EIF1AX R13L", "EIF1AX R13P",
"EIF1AX X113_splice", "EIF1AX X6_splice", "ELTD1 S11=", "ELTD1 S11F",
"ELTD1 S11P", "EP300 C1164S", "EP300 C1164Y", "EP300 D1399E",
"EP300 D1399N", "EP300 D1399Y", "EP300 H1451=", "EP300 H1451L",
"EP300 H1451P", "EP300 H1451Q", "EP300 H1451R", "EP300 L415P",
"EP300 Q1455=", "EP300 Q1455H", "EP300 Q1455R", "EP300 W1466*",
"EP300 W1466C", "EP300 W1466G", "EP300 W1466L", "EP300 W1466R",
"EP300 X1429_splice", "EP300 X1539_splice", "EP300 Y1414C", "EP300 Y1414D",
"EP300 Y1467C", "EP300 Y1467D", "EP300 Y1467H", "EP300 Y1467K",
"EP300 Y1467N", "EP300 Y1467S", "EPAS1 P531A", "EPAS1 P531L",
"EPAS1 P531S", "EPAS1 Y532C", "EPHA3 R136*", "EPHA7 G656=", "EPHA7 G656E",
"EPHA7 G656R", "EPHA7 G656W", "EPHB1 R743=", "EPHB1 R743Q", "EPHB1 R743W",
"ERBB2 A293P", "ERBB2 A293T", "ERBB2 A293V", "ERBB2 D277G", "ERBB2 D277H",
"ERBB2 D277V", "ERBB2 D277Y", "ERBB2 D769H", "ERBB2 D769N", "ERBB2 D769Y",
"ERBB2 G660=", "ERBB2 G660D", "ERBB2 G660R", "ERBB2 G776S", "ERBB2 G776V",
"ERBB2 G778_P780dup", "ERBB2 I767M", "ERBB2 L755=", "ERBB2 L755A",
"ERBB2 L755M", "ERBB2 L755P", "ERBB2 L755S", "ERBB2 L755W", "ERBB2 L869R",
"ERBB2 M774dup", "ERBB2 R103Q", "ERBB2 R138Q", "ERBB2 R138W",
"ERBB2 R678Q", "ERBB2 R678W", "ERBB2 S310=", "ERBB2 S310F", "ERBB2 S310Y",
"ERBB2 T733I", "ERBB2 T862A", "ERBB2 V659=", "ERBB2 V659D", "ERBB2 V659E",
"ERBB2 V697L", "ERBB2 V777L", "ERBB2 V777M", "ERBB2 V842I", "ERBB2 Y772_A775dup",
"ERBB3 A232T", "ERBB3 A232V", "ERBB3 D297A", "ERBB3 D297H", "ERBB3 D297N",
"ERBB3 D297V", "ERBB3 D297Y", "ERBB3 E332K", "ERBB3 E332Q", "ERBB3 E928G",
"ERBB3 E928K", "ERBB3 F219C", "ERBB3 F219L", "ERBB3 G284R", "ERBB3 H228Q",
"ERBB3 H228R", "ERBB3 K329E", "ERBB3 K329R", "ERBB3 K329T", "ERBB3 M60K",
"ERBB3 M60R", "ERBB3 M91I", "ERBB3 N126I", "ERBB3 N126K", "ERBB3 R103=",
"ERBB3 R103G", "ERBB3 R103H", "ERBB3 R475W", "ERBB3 S846I", "ERBB3 T355A",
"ERBB3 T355I", "ERBB3 T355P", "ERBB3 V104L", "ERBB3 V104M", "ERBB4 F1102=",
"ERBB4 F1102C", "ERBB4 K1002R", "ERBB4 K1002T", "ERBB4 K1223M",
"ERBB4 K1223R", "ERBB4 K1223T", "ERBB4 L798=", "ERBB4 L798H",
"ERBB4 L798P", "ERBB4 L798R", "ERBB4 Q707=", "ERBB4 Q707E", "ERBB4 S1289A",
"ERBB4 S774G", "ERBB4 S774N", "ERBB4 S774R", "ERCC2 D609E", "ERCC2 D609G",
"ERCC2 E606G", "ERCC2 E606Q", "ERCC2 N238S", "ERCC2 P463L", "ERCC2 P463Q",
"ERCC2 P463S", "ERCC2 S246=", "ERCC2 S246F", "ERCC2 S246Y", "ERCC2 T484A",
"ERCC2 T484M", "ERCC2 Y14C", "ERCC2 Y24C", "ERCC2 Y72C", "ERCC3 L713=",
"ERG R354=", "ERRFI1 K116*", "ERRFI1 K409N", "ERRFI1 K409Q",
"ESR1 D538G", "ESR1 E380Q", "ESR1 L536=", "ESR1 L536H", "ESR1 L536P",
"ESR1 L536Q", "ESR1 L536R", "ESR1 V422del", "ESR1 Y537C", "ESR1 Y537D",
"ESR1 Y537N", "ESR1 Y537S", "ETV6 R369=", "ETV6 R369L", "ETV6 R369Q",
"ETV6 R369W", "ETV6 S284=", "ETV6 S284F", "ETV6 X11_splice",
"EYA4 L152H", "EYA4 L152I", "EYA4 L152P", "EYA4 L152R", "EYA4 L152V",
"EZH2 K515R", "EZH2 K665E", "EZH2 K665R", "EZH2 Y646=", "EZH2 Y646C",
"EZH2 Y646F", "EZH2 Y646H", "EZH2 Y646N", "EZH2 Y646S", "FAM46D S69G",
"FAM46D S69R", "FAM58A X141_splice", "FAT1 R1627*", "FAT1 R1627Q",
"FBXW7 D520G", "FBXW7 D520H", "FBXW7 D520N", "FBXW7 D520V", "FBXW7 D520Y",
"FBXW7 E287D", "FBXW7 E287K", "FBXW7 E287Q", "FBXW7 E287V", "FBXW7 G423*",
"FBXW7 G423A", "FBXW7 G423V", "FBXW7 G437*", "FBXW7 G437=", "FBXW7 G437E",
"FBXW7 G437V", "FBXW7 R14*", "FBXW7 R14Q", "FBXW7 R224*", "FBXW7 R224Q",
"FBXW7 R278*", "FBXW7 R367*", "FBXW7 R367P", "FBXW7 R393*", "FBXW7 R393Q",
"FBXW7 R441G", "FBXW7 R441L", "FBXW7 R441Q", "FBXW7 R441W", "FBXW7 R465C",
"FBXW7 R465G", "FBXW7 R465H", "FBXW7 R465L", "FBXW7 R465P", "FBXW7 R465S",
"FBXW7 R479*", "FBXW7 R479=", "FBXW7 R479G", "FBXW7 R479L", "FBXW7 R479P",
"FBXW7 R479Q", "FBXW7 R505C", "FBXW7 R505G", "FBXW7 R505H", "FBXW7 R505L",
"FBXW7 R505P", "FBXW7 R505S", "FBXW7 R658*", "FBXW7 R658=", "FBXW7 R658Q",
"FBXW7 R689Q", "FBXW7 R689W", "FBXW7 S546*", "FBXW7 S546L", "FBXW7 S546P",
"FBXW7 S582=", "FBXW7 S582L", "FBXW7 S582P", "FBXW7 T385I", "FBXW7 T385K",
"FBXW7 T385P", "FBXW7 T532I", "FBXW7 T532P", "FBXW7 X195_splice",
"FBXW7 Y545*", "FBXW7 Y545C", "FGFR1 K687*", "FGFR1 K687=", "FGFR1 K687E",
"FGFR1 K687N", "FGFR1 N577D", "FGFR1 N577K", "FGFR2 C382R", "FGFR2 C382Y",
"FGFR2 F276C", "FGFR2 F276I", "FGFR2 N549H", "FGFR2 N549K", "FGFR2 N549S",
"FGFR2 N549T", "FGFR2 P253L", "FGFR2 P253R", "FGFR2 R203C", "FGFR2 R203H",
"FGFR2 S252=", "FGFR2 S252L", "FGFR2 S252W", "FGFR2 Y375C", "FGFR3 G370C",
"FGFR3 G380R", "FGFR3 K650E", "FGFR3 K650M", "FGFR3 K650N", "FGFR3 K650T",
"FGFR3 L8=", "FGFR3 R248C", "FGFR3 S249C", "FGFR3 S371C", "FGFR3 Y373C",
"FGFR4 N535K", "FGFR4 V550L", "FGFR4 V550M", "FH M336I", "FH M336L",
"FLT3 D586_E596dup", "FLT3 D593_F594insSPEDNEYFYVD", "FLT3 D835E",
"FLT3 D835H", "FLT3 D835V", "FLT3 D835Y", "FLT3 E598_F612dup",
"FLT3 E598_Y599insSGSSDNEYFYVDFREYE", "FLT3 E598_Y599insVAYVDFREYE",
"FLT3 E604_F605insSPRGGNEYFYVDFREYEYDLKWE", "FLT3 F594_D600dup",
"FLT3 F594_R595insGTGSSDNEYFYVDF", "FLT3 F612_G613insQGFYVDFREYEYDLKWEFPRENLEF",
"FLT3 L601_K602insNVDFREYEYDL", "FLT3 M578_E598dup", "FLT3 N587_D600dup",
"FLT3 R595_E596insDYVDFR", "FLT3 R595_L601dup", "FLT3 S584_D600dup",
"FLT3 S584_F605dup", "FLT3 S585_F594dup", "FLT3 Y597_E598insAGSSDNEYFYVDFREY",
"FLT3 Y597_E598insDEYFYVDFREY", "FLT3 Y597_K602dup", "FLT3 Y599_D600insEYEYEYEY",
"FLT3 Y599_D600insPAPQIMSTSTLISENMNIA", "FLT3 Y599_E604dup",
"FOXA1 A323_P326del", "FOXA1 C258_R261del", "FOXA1 D226G", "FOXA1 D226N",
"FOXA1 D249_F254del", "FOXA1 D249_N252del", "FOXA1 E255_N256del",
"FOXA1 F254_E255del", "FOXA1 F254_G257delinsC", "FOXA1 F254_L260del",
"FOXA1 F254_N256delinsY", "FOXA1 F266=", "FOXA1 F266C", "FOXA1 F266I",
"FOXA1 F266L", "FOXA1 F266S", "FOXA1 F266V", "FOXA1 G251_F254del",
"FOXA1 G251_G257del", "FOXA1 G284_G290del", "FOXA1 H247L", "FOXA1 H247Q",
"FOXA1 H247R", "FOXA1 H247Y", "FOXA1 I176M", "FOXA1 I176V", "FOXA1 K264_K267del",
"FOXA1 K264dup", "FOXA1 K267dup", "FOXA1 M253_N256del", "FOXA1 M253_Y259del",
"FOXA1 M253K", "FOXA1 M253R", "FOXA1 M253T", "FOXA1 N252_C258del",
"FOXA1 N252_G257del", "FOXA1 N252_S408del", "FOXA1 N397_F400del",
"FOXA1 Q263_C268del", "FOXA1 Q263_D296delinsH", "FOXA1 Q263_G281del",
"FOXA1 Q263del", "FOXA1 R219=", "FOXA1 R219C", "FOXA1 R219G",
"FOXA1 R219S", "FOXA1 R261C", "FOXA1 R261G", "FOXA1 R261H", "FOXA1 R261S",
"FOXA1 R265_K270del", "FOXA1 S242F", "FOXA1 S242Y", "FOXA1 S250_F254del",
"FOXA1 S250_N252del", "FOXA1 S250_Y259del", "FOXA1 S250F", "FOXA1 S250Y",
"FOXA1 S282_G283dup", "FOXA1 S409del", "FOXA1 Y259C", "FOXA1 Y259F",
"FOXA1 Y259S", "FOXL2 C134W", "FOXL2 E118K", "FOXL2 E118Q", "FOXO1 S205=",
"FOXO1 S205N", "FOXO1 S22=", "FOXO1 S22P", "FOXO1 S22W", "FOXO1 T24I",
"FOXO1 T24M", "FOXP1 R514C", "FOXP1 R514H", "FOXP1 S448=", "FOXP1 S448L",
"FOXP1 X511_splice", "FRMD4B P368F", "FRMD4B P368L", "FRMD4B P368S",
"FRMD6 S17=", "FRMD6 S17C", "FRMD6 S17I", "FUBP1 R430C", "FUBP1 R430H",
"FZD10 S22R", "GATA2 C352*", "GATA2 C352=", "GATA2 C352F", "GATA2 C352R",
"GATA3 M293K", "GATA3 M293R", "GATA3 R364G", "GATA3 R364S", "GATA3 R364T",
"GATA3 R366*", "GATA3 R366Q", "GLI1 R380*", "GLI1 R380=", "GLI1 R380Q",
"GNA11 Q209H", "GNA11 Q209L", "GNA11 Q209P", "GNA11 R183=", "GNA11 R183C",
"GNA11 R183H", "GNAQ G48*", "GNAQ G48L", "GNAQ G48V", "GNAQ Q209H",
"GNAQ Q209L", "GNAQ Q209P", "GNAQ R183*", "GNAQ R183Q", "GNAS Q227H",
"GNAS Q227K", "GNAS Q227L", "GNAS R160C", "GNAS R160H", "GNAS R160P",
"GNAS R201C", "GNAS R201H", "GNAS R201L", "GNAS R201S", "GPS2 X242_splice",
"GSK3B X239_splice", "GTF2I F641C", "GTF2I L424H", "GTF2I N440S",
"H3F3A G35R", "H3F3A G35V", "H3F3A G35W", "H3F3A K28M", "H3F3A K28R",
"HGF G229A", "HGF G229D", "HIST1H1C A180=", "HIST1H1C A180P",
"HIST1H1C E115K", "HIST1H1C K23del", "HIST1H3B E106=", "HIST1H3B E106K",
"HIST1H3B E106Q", "HIST1H3B E51=", "HIST1H3B E51D", "HIST1H3B E51K",
"HIST1H3B E51Q", "HIST1H3B K28E", "HIST1H3B K28M", "HIST1H3C K37=",
"HIST1H3C K37M", "HIST1H3H K37E", "HIST1H3H K37M", "HNF1A G338=",
"HNF1A G338A", "HNF1A R114C", "HNF1A R114H", "HNF1A R114L", "HNF1A S591=",
"HNF1A S591Y", "HNMT L145=", "HOOK2 S630=", "HOOK2 S630A", "HOOK2 S630F",
"HOXB2 P335=", "HRAS G12A", "HRAS G12C", "HRAS G12D", "HRAS G12N",
"HRAS G12S", "HRAS G12V", "HRAS G13C", "HRAS G13D", "HRAS G13I",
"HRAS G13N", "HRAS G13R", "HRAS G13S", "HRAS G13V", "HRAS K117N",
"HRAS K117R", "HRAS Q61H", "HRAS Q61K", "HRAS Q61L", "HRAS Q61R",
"HSD11B1 G45=", "HSD11B1 G45E", "HSD11B1 G45R", "HSD11B1 G45V",
"HSD11B1 G45W", "IDH1 R132C", "IDH1 R132G", "IDH1 R132H", "IDH1 R132I",
"IDH1 R132L", "IDH1 R132S", "IDH2 R140L", "IDH2 R140Q", "IDH2 R140W",
"IDH2 R172=", "IDH2 R172G", "IDH2 R172K", "IDH2 R172M", "IDH2 R172S",
"IDH2 R172T", "IDH2 R172W", "IGF1R G129=", "IGF1R G129A", "IGF1R G129R",
"IKZF1 E304K", "IKZF1 E304Q", "IL7R I241F", "IL7R I241L", "IL7R I241M",
"IL7R I241V", "IL7R K395=", "IL7R K395M", "IL7R K395N", "IL7R K395R",
"IL7R K395T", "IL7R R206*", "IL7R R206Q", "ING1 R339*", "INMT S212=",
"INMT S212F", "INPPL1 R70H", "INTS12 M1?", "IRF4 C99=", "IRF4 C99R",
"IRF4 C99Y", "IRF4 K123R", "IRF4 Y428*", "IRF4 Y428H", "JAK1 L910=",
"JAK1 L910P", "JAK1 L910S", "JUN E112K", "JUN E112Q", "KAT8 R98Q",
"KAT8 R98W", "KCNH5 T147=", "KCNJ12 E430*", "KCNJ8 G417D", "KCNJ8 G417E",
"KCNJ8 G417R", "KCNQ5 G273E", "KCNQ5 G273R", "KDM6A G526*", "KDM6A G526=",
"KDM6A G526E", "KDM6A G526V", "KDM6A Q1003*", "KDM6A Q1003P",
"KDM6A Q555*", "KDM6A X1246_splice", "KDM6A X129_splice", "KDM6A X1293_splice",
"KDM6A X1336_splice", "KDM6A X76_splice", "KDR C482*", "KDR R1032*",
"KDR R1032Q", "KDR S1037=", "KDR S1037L", "KDR S1037T", "KEAP1 G333C",
"KEAP1 G333F", "KEAP1 G333S", "KEAP1 G417E", "KEAP1 G417R", "KEAP1 G417V",
"KEAP1 G417W", "KEAP1 G480=", "KEAP1 G480V", "KEAP1 G480W", "KEAP1 M110I",
"KEAP1 M110V", "KEAP1 R260*", "KEAP1 R260L", "KEAP1 R260Q", "KEAP1 R272C",
"KEAP1 R272H", "KEAP1 R272L", "KEAP1 R272P", "KEAP1 R320L", "KEAP1 R320M",
"KEAP1 R320P", "KEAP1 R320Q", "KEAP1 R320W", "KEAP1 R470C", "KEAP1 R470H",
"KEAP1 R470S", "KEAP1 R601L", "KEAP1 R601W", "KEAP1 V155A", "KEAP1 V155F",
"KIAA0020 K63R", "KIF26B R2024C", "KIF26B R2024H", "KIF26B R2024S",
"KIT A502_Y503dup", "KIT D579del", "KIT D816A", "KIT D816H",
"KIT D816V", "KIT D816Y", "KIT D820A", "KIT D820E", "KIT D820G",
"KIT D820V", "KIT D820Y", "KIT G565_T574delinsA", "KIT K550_P551del",
"KIT K558_V560del", "KIT K558_V560delinsN", "KIT K642E", "KIT K642N",
"KIT K642Q", "KIT L576_H580dup", "KIT L576del", "KIT L576P",
"KIT M552_E554delinsI", "KIT M552_V555del", "KIT M552_V555delinsI",
"KIT M552_W557del", "KIT M552_Y570del", "KIT N566_P573del", "KIT N822I",
"KIT N822K", "KIT N822Y", "KIT P551_M552delinsL", "KIT P551_V555del",
"KIT P551_Y553delinsH", "KIT Q556_D572del", "KIT Q556_V560delinsH",
"KIT Q575del", "KIT R888=", "KIT R888Q", "KIT R888W", "KIT T574_H580dup",
"KIT V559_E561del", "KIT V559_G565del", "KIT V559_N566delinsD",
"KIT V559_P573del", "KIT V559A", "KIT V559D", "KIT V559G", "KIT V560=",
"KIT V560A", "KIT V560D", "KIT V560del", "KIT V560G", "KIT V654A",
"KIT W557_E561del", "KIT W557_K558del", "KIT W557_V559delinsF",
"KIT W557C", "KIT W557G", "KIT W557R", "KIT W557S", "KIT Y553_E554del",
"KIT Y570_L576del", "KIT Y578_D579insEQQLPY", "KIT Y823C", "KIT Y823D",
"KLF4 K409N", "KLF4 K409Q", "KLF5 E419K", "KLF5 E419Q", "KMT2A R1264*",
"KMT2C R4549C", "KMT2C R4549H", "KMT2C R4549S", "KMT2C R56*",
"KMT2C R56Q", "KMT2D L1375=", "KMT2D L1375I", "KMT2D R1903*",
"KMT2D R1903=", "KMT2D R2685*", "KMT2D R2685=", "KMT2D R5179C",
"KMT2D R5179H", "KMT2D R5179L", "KMT2D R5179P", "KMT2D R5432=",
"KMT2D R5432Q", "KMT2D R5432W", "KNSTRN C22S", "KNSTRN C22Y",
"KNSTRN P28L", "KNSTRN P28S", "KNSTRN S24F", "KNSTRN V12=", "KNSTRN V12G",
"KRAS A11=", "KRAS A11T", "KRAS A146P", "KRAS A146T", "KRAS A146V",
"KRAS A59=", "KRAS A59E", "KRAS A59G", "KRAS A59T", "KRAS D33E",
"KRAS G12=", "KRAS G12A", "KRAS G12C", "KRAS G12D", "KRAS G12F",
"KRAS G12I", "KRAS G12L", "KRAS G12R", "KRAS G12S", "KRAS G12V",
"KRAS G13=", "KRAS G13A", "KRAS G13C", "KRAS G13D", "KRAS G13E",
"KRAS G13R", "KRAS G13V", "KRAS G60=", "KRAS G60D", "KRAS G60S",
"KRAS G60V", "KRAS K117N", "KRAS K117R", "KRAS K5E", "KRAS L19F",
"KRAS Q22H", "KRAS Q22K", "KRAS Q61A", "KRAS Q61E", "KRAS Q61H",
"KRAS Q61K", "KRAS Q61L", "KRAS Q61P", "KRAS Q61R", "LAMC1 P641=",
"LAMC1 P641L", "LATS2 P479_A480insPP", "LCE1A K28M", "LCE1A K28R",
"LCE1A K28T", "LCE1F P27=", "LCE1F P27L", "LCE1F P27Q", "LRP1 P1058L",
"LRP1 P1058T", "LRP5 S1609=", "LRP5 S1609P", "LRRC71 K324=",
"LSM14A R272C", "LSM14A R272H", "LST3 R709=", "LST3 R709K", "LST3 R709T",
"LTN1 S19F", "LTN1 S19Y", "LYN I364L", "LYN I364N", "MAGEC1 K1046N",
"MAGI2 L603P", "MAGI2 L603R", "MAGOH I137T", "MAP2K1 C121=",
"MAP2K1 C121S", "MAP2K1 E102_I103del", "MAP2K1 E203K", "MAP2K1 E203V",
"MAP2K1 F53C", "MAP2K1 F53I", "MAP2K1 F53L", "MAP2K1 F53V", "MAP2K1 G128D",
"MAP2K1 G128R", "MAP2K1 G128V", "MAP2K1 I103_K104del", "MAP2K1 I99_K104del",
"MAP2K1 K57E", "MAP2K1 K57N", "MAP2K1 K57T", "MAP2K1 N122D",
"MAP2K1 P105_A106del", "MAP2K1 P105_I107delinsL", "MAP2K1 P124=",
"MAP2K1 P124L", "MAP2K1 P124M", "MAP2K1 P124Q", "MAP2K1 P124R",
"MAP2K1 P124S", "MAP2K1 Q56P", "MAP2K1 T386=", "MAP2K1 Y130C",
"MAP2K1 Y130H", "MAP2K1 Y130N", "MAP2K2 F57L", "MAP2K2 F57V",
"MAP2K4 R110*", "MAP2K4 R110L", "MAP2K4 R110P", "MAP2K4 R110Q",
"MAP2K4 R134L", "MAP2K4 R134Q", "MAP2K4 R134W", "MAP2K4 S184=",
"MAP2K4 S184L", "MAP2K4 S184W", "MAP2K4 X297_splice", "MAP2K4 X347_splice",
"MAP3K1 L380S", "MAP3K1 S1330L", "MAP3K1 S1330W", "MAP3K13 X502_splice",
"MAPK1 E322*", "MAPK1 E322A", "MAPK1 E322K", "MAPK7 A501D", "MARCH10 G241=",
"MARCH10 G241E", "MARCH10 G241R", "MAX H28R", "MAX R36W", "MAX R60=",
"MAX R60Q", "MAX R60W", "MDC1 I1020_R1028del", "MDC1 K1025del",
"MED12 G44_F45del", "MED12 G44A", "MED12 G44C", "MED12 G44D",
"MED12 G44S", "MED12 G44V", "MED12 K42_N46del", "MED12 L1224F",
"MED12 L1224V", "MED12 N46_S52del", "MED12 P49_E55del", "MED12 V1223L",
"MED12 V41_S52del", "MED28 G7C", "MEF2A P99S", "MEF2B K4E", "MET D1010H",
"MET D1010N", "MET D1010Y", "MET F1200I", "MET F1200V", "MET H1094R",
"MET H1094Y", "MET M1250T", "MET T222=", "MET V1070A", "MET V1070E",
"MET V1070R", "MET X1010_splice", "MET Y1003*", "MET Y1003C",
"MET Y1003F", "MET Y1230C", "MET Y1230H", "MET Y1230S", "METTL14 R298H",
"METTL14 R298P", "MGA R1242*", "MSH2 E580*", "MTOR A1459_D1468del",
"MTOR A1459D", "MTOR A1459P", "MTOR A1459V", "MTOR A1971P", "MTOR A1971S",
"MTOR A1971T", "MTOR C1483F", "MTOR C1483R", "MTOR C1483W", "MTOR C1483Y",
"MTOR E1455_D1458dup", "MTOR E1455_E1457dup", "MTOR E1799K",
"MTOR F1888I", "MTOR F1888L", "MTOR F1888V", "MTOR I2500F", "MTOR I2500M",
"MTOR I2500N", "MTOR L1460P", "MTOR L2427Q", "MTOR L2427R", "MTOR M2327I",
"MTOR M2327V", "MTOR S2215F", "MTOR S2215T", "MTOR S2215Y", "MTOR T1977I",
"MTOR T1977K", "MTOR T1977R", "MTOR T1977S", "MTOR V2006=", "MTOR V2006F",
"MTOR V2006I", "MTOR V2006L", "MTOR W1456_L1460delinsC", "MTOR Y1450_W1456del",
"MXRA5 G792=", "MYC P74L", "MYC P74Q", "MYC P74R", "MYC P74S",
"MYC P74T", "MYC S161L", "MYC S298del", "MYC T73I", "MYC V7M",
"MYCN P44F", "MYCN P44L", "MYD88 L265P", "MYD88 M232T", "MYD88 P166=",
"MYD88 P166L", "MYD88 S243N", "MYO18A G979=", "MYO18A G979A",
"MYO18B P1018=", "MYO18B P1018L", "MYO18B P1018S", "MYO18B P1018T",
"MYO9A P1300=", "MYO9A P1300L", "MYO9A P1300S", "MYOD1 L122=",
"MYOD1 L122M", "MYOD1 L122R", "MYT1L K203R", "MYT1L K203T", "NAP1L3 K502=",
"NAP1L3 K502M", "NAP1L3 K502N", "NAP1L3 K502R", "NAP1L3 K502T",
"NCOA3 R80C", "NCOA3 R80H", "NCR1 E42=", "NCR1 E42G", "NCR1 E42K",
"NF1 R1241*", "NF1 R1870Q", "NF1 R1870W", "NF1 R2450*", "NF1 R2450Q",
"NF1 R440*", "NF1 R440Q", "NF1 R461*", "NF1 R461Q", "NFE2L2 D21_I22delinsE",
"NFE2L2 D27del", "NFE2L2 D29G", "NFE2L2 D29H", "NFE2L2 D29N",
"NFE2L2 D29Y", "NFE2L2 D77G", "NFE2L2 D77H", "NFE2L2 D77V", "NFE2L2 D77Y",
"NFE2L2 E35_R42del", "NFE2L2 E79*", "NFE2L2 E79D", "NFE2L2 E79del",
"NFE2L2 E79G", "NFE2L2 E79K", "NFE2L2 E79Q", "NFE2L2 E79V", "NFE2L2 E82A",
"NFE2L2 E82D", "NFE2L2 E82G", "NFE2L2 E82Q", "NFE2L2 F37del",
"NFE2L2 G31A", "NFE2L2 G31del", "NFE2L2 G31E", "NFE2L2 G31R",
"NFE2L2 G31V", "NFE2L2 G81A", "NFE2L2 G81C", "NFE2L2 G81D", "NFE2L2 G81R",
"NFE2L2 G81S", "NFE2L2 G81V", "NFE2L2 I22_D29del", "NFE2L2 I28dup",
"NFE2L2 I28T", "NFE2L2 L30_S33del", "NFE2L2 L30F", "NFE2L2 L30H",
"NFE2L2 L30P", "NFE2L2 L30R", "NFE2L2 L74_Q87del", "NFE2L2 L76_E82del",
"NFE2L2 Q26H", "NFE2L2 Q26K", "NFE2L2 Q26L", "NFE2L2 Q26P", "NFE2L2 Q26R",
"NFE2L2 Q73_T80del", "NFE2L2 R34_F37delinsL", "NFE2L2 R34_S40del",
"NFE2L2 R34*", "NFE2L2 R34G", "NFE2L2 R34L", "NFE2L2 R34P", "NFE2L2 R34Q",
"NFE2L2 S33_R34del", "NFE2L2 T80A", "NFE2L2 T80I", "NFE2L2 T80K",
"NFE2L2 T80P", "NFE2L2 T80R", "NFE2L2 W24_D29delinsY", "NFE2L2 W24C",
"NFE2L2 W24R", "NFE2L2 W24S", "NFIC S339P", "NOL4 L423=", "NOL4 L423M",
"NOL4 L423V", "NOTCH1 C359del", "NOTCH1 C440F", "NOTCH1 C440R",
"NOTCH1 C440S", "NOTCH1 C440W", "NOTCH1 D338del", "NOTCH1 E455=",
"NOTCH1 E455K", "NOTCH1 F357del", "NOTCH1 F853C", "NOTCH1 F853I",
"NOTCH1 G310E", "NOTCH1 G310R", "NOTCH1 I471T", "NOTCH1 R365C",
"NOTCH1 R365S", "NOTCH1 S356del", "NOTCH1 Y358del", "NOTCH2 R2400*",
"NOTCH2 T235S", "NPAS1 F159=", "NPAS1 F159L", "NRAS G12A", "NRAS G12C",
"NRAS G12D", "NRAS G12R", "NRAS G12S", "NRAS G12V", "NRAS G13C",
"NRAS G13D", "NRAS G13F", "NRAS G13R", "NRAS G13S", "NRAS G13V",
"NRAS G60=", "NRAS G60E", "NRAS G60V", "NRAS Q61*", "NRAS Q61H",
"NRAS Q61K", "NRAS Q61L", "NRAS Q61P", "NRAS Q61R", "NSD1 C1710*",
"NSD1 C1710S", "NSD1 C1710Y", "NSD1 F392=", "NUP93 E14G", "NUP93 E14K",
"NUP93 Q15*", "NUP93 Q15K", "OBP2B S133P", "OXA1L L57F", "PACS2 Q87=",
"PACS2 Q87H", "PAK7 M173I", "PARP1 G500=", "PASD1 M338I", "PAX5 V26G",
"PBRM1 R1160*", "PBRM1 R1160P", "PBRM1 R1160Q", "PBRM1 R710*",
"PBRM1 R710G", "PBRM1 R921*", "PBRM1 X856_splice", "PCBP1 L102P",
"PCBP1 L102Q", "PCBP1 L102R", "PCED1B S343F", "PCED1B S343P",
"PCED1B S343Y", "PCMTD1 P342L", "PCSK5 W924*", "PCSK5 W924L",
"PDGFRA C235R", "PDGFRA C235S", "PDGFRA C235Y", "PDGFRA D842=",
"PDGFRA D842H", "PDGFRA D842I", "PDGFRA D842V", "PDGFRA E229*",
"PDGFRA E229K", "PDGFRA E229V", "PDGFRA N659K", "PDGFRA N659S",
"PDGFRA N659Y", "PDHA1 G145D", "PDPK1 P499L", "PDPK1 P499S",
"PGR R836*", "PGR R836Q", "PIK3CA C378F", "PIK3CA C378R", "PIK3CA C378Y",
"PIK3CA C420G", "PIK3CA C420R", "PIK3CA C604R", "PIK3CA C901F",
"PIK3CA C90G", "PIK3CA C90R", "PIK3CA C90S", "PIK3CA C90Y", "PIK3CA D350G",
"PIK3CA D350N", "PIK3CA D350V", "PIK3CA D939G", "PIK3CA E110_K111dup",
"PIK3CA E110del", "PIK3CA E365K", "PIK3CA E365V", "PIK3CA E39G",
"PIK3CA E39K", "PIK3CA E453_D454del", "PIK3CA E453_P466del",
"PIK3CA E453_T462del", "PIK3CA E453D", "PIK3CA E453del", "PIK3CA E453K",
"PIK3CA E453Q", "PIK3CA E542A", "PIK3CA E542G", "PIK3CA E542K",
"PIK3CA E542Q", "PIK3CA E542V", "PIK3CA E545A", "PIK3CA E545D",
"PIK3CA E545G", "PIK3CA E545K", "PIK3CA E545Q", "PIK3CA E726A",
"PIK3CA E726K", "PIK3CA E81*", "PIK3CA E81K", "PIK3CA E970K",
"PIK3CA G1007D", "PIK3CA G1007R", "PIK3CA G1049A", "PIK3CA G1049R",
"PIK3CA G106_N107del", "PIK3CA G106_R108del", "PIK3CA G106C",
"PIK3CA G106R", "PIK3CA G106S", "PIK3CA G106V", "PIK3CA G118D",
"PIK3CA G364A", "PIK3CA G364R", "PIK3CA G451_D454del", "PIK3CA G463_N465delinsD",
"PIK3CA H1047L", "PIK3CA H1047Q", "PIK3CA H1047R", "PIK3CA H1047Y",
"PIK3CA H1065L", "PIK3CA H1065Y", "PIK3CA H419_C420del", "PIK3CA H419_L422del",
"PIK3CA H450_L455del", "PIK3CA I102_E103delinsK", "PIK3CA I102del",
"PIK3CA I112_L113del", "PIK3CA K111_I112del", "PIK3CA K111del",
"PIK3CA K111E", "PIK3CA K111N", "PIK3CA K111Q", "PIK3CA K111R",
"PIK3CA L10_M16del", "PIK3CA L113del", "PIK3CA L436_P449dup",
"PIK3CA L452_G460del", "PIK3CA L452_P458del", "PIK3CA L455_G460delinsF",
"PIK3CA M1004I", "PIK3CA M1004V", "PIK3CA M1043I", "PIK3CA M1043L",
"PIK3CA M1043T", "PIK3CA M1043V", "PIK3CA N1044K", "PIK3CA N1044Y",
"PIK3CA N107=", "PIK3CA N107I", "PIK3CA N107S", "PIK3CA N114del",
"PIK3CA N345=", "PIK3CA N345D", "PIK3CA N345H", "PIK3CA N345I",
"PIK3CA N345K", "PIK3CA N345T", "PIK3CA N345Y", "PIK3CA P104_V105del",
"PIK3CA P104L", "PIK3CA P104R", "PIK3CA P447_L455del", "PIK3CA P449_L452del",
"PIK3CA P449_L456del", "PIK3CA P471A", "PIK3CA P471L", "PIK3CA P539R",
"PIK3CA Q546E", "PIK3CA Q546H", "PIK3CA Q546K", "PIK3CA Q546L",
"PIK3CA Q546P", "PIK3CA Q546R", "PIK3CA R108del", "PIK3CA R108H",
"PIK3CA R108L", "PIK3CA R108S", "PIK3CA R115L", "PIK3CA R115P",
"PIK3CA R115Q", "PIK3CA R357*", "PIK3CA R357G", "PIK3CA R357L",
"PIK3CA R357Q", "PIK3CA R38C", "PIK3CA R38G", "PIK3CA R38H",
"PIK3CA R38L", "PIK3CA R38S", "PIK3CA R88Q", "PIK3CA R93L", "PIK3CA R93Q",
"PIK3CA R93W", "PIK3CA T1025A", "PIK3CA T1025S", "PIK3CA T1052K",
"PIK3CA V344A", "PIK3CA V344G", "PIK3CA V344M", "PIK3CA W11_H14delinsY",
"PIK3CA W11_P18del", "PIK3CA Y1021C", "PIK3CA Y1021H", "PIK3CB D1067A",
"PIK3CB D1067H", "PIK3CB D1067V", "PIK3CB D1067Y", "PIK3CB E1051G",
"PIK3CB E1051K", "PIK3CB R321Q", "PIK3CD C416R", "PIK3CD E1021K",
"PIK3CD R894=", "PIK3CD R894Q", "PIK3R1 D440_E451del", "PIK3R1 D440_K448del",
"PIK3R1 D440del", "PIK3R1 D464_E468dup", "PIK3R1 D464_Y467del",
"PIK3R1 D464_Y470dup", "PIK3R1 D560G", "PIK3R1 D560H", "PIK3R1 D560N",
"PIK3R1 D560Y", "PIK3R1 D569_L570delinsV", "PIK3R1 D569_L581delinsE",
"PIK3R1 D569dup", "PIK3R1 D578_M582delinsE", "PIK3R1 E403_L404del",
"PIK3R1 E403_L404delinsV", "PIK3R1 E439del", "PIK3R1 E451_Y452del",
"PIK3R1 E451del", "PIK3R1 E458_K459del", "PIK3R1 E458_Y463dup",
"PIK3R1 E458del", "PIK3R1 E462_R465del", "PIK3R1 E462_Y463delinsD",
"PIK3R1 E462dup", "PIK3R1 E468_E469insGEYDRLYE", "PIK3R1 E468_E469insGLYE",
"PIK3R1 E468_Y470dup", "PIK3R1 E558_K561del", "PIK3R1 E558_R562del",
"PIK3R1 F456_K459del", "PIK3R1 F456_Q457del", "PIK3R1 G376R",
"PIK3R1 G446_E451del", "PIK3R1 G446_L449delinsV", "PIK3R1 H450_E451del",
"PIK3R1 H450_E451dup", "PIK3R1 H450_E451insD", "PIK3R1 H450_E451insVH",
"PIK3R1 H450_K459del", "PIK3R1 H450_Q455dup", "PIK3R1 H450_T454del",
"PIK3R1 H450del", "PIK3R1 I405_L420del", "PIK3R1 I405del", "PIK3R1 I442_E443delinsK",
"PIK3R1 I442_N453del", "PIK3R1 I566_P568delinsT", "PIK3R1 I571_K575del",
"PIK3R1 I571_L581del", "PIK3R1 I571_Q572insR", "PIK3R1 I571_R574del",
"PIK3R1 K379del", "PIK3R1 K379E", "PIK3R1 K379N", "PIK3R1 K448_N453del",
"PIK3R1 K448_Y452del", "PIK3R1 K459del", "PIK3R1 K567_I571del",
"PIK3R1 K567_L570del", "PIK3R1 K567del", "PIK3R1 K567E", "PIK3R1 K575_L581delinsM",
"PIK3R1 K575_R577del", "PIK3R1 K575_R577dup", "PIK3R1 K575_T576del",
"PIK3R1 L380del", "PIK3R1 L449_H450insQ", "PIK3R1 L449_K459del",
"PIK3R1 L449_Q455del", "PIK3R1 L449del", "PIK3R1 L466_E469del",
"PIK3R1 L466_Y470delinsF", "PIK3R1 L466del", "PIK3R1 L570_D578del",
"PIK3R1 L570_I571insY", "PIK3R1 L573_K575del", "PIK3R1 L573_R574del",
"PIK3R1 L573del", "PIK3R1 M563_L570delinsI", "PIK3R1 M563_N564delinsI",
"PIK3R1 N378del", "PIK3R1 N441_T454del", "PIK3R1 N453_D464dup",
"PIK3R1 N453_Q455delinsK", "PIK3R1 N453_Q457del", "PIK3R1 N453_Y463del",
"PIK3R1 N453del", "PIK3R1 N564_P568delinsT", "PIK3R1 N564D",
"PIK3R1 P568_L573del", "PIK3R1 Q455_F456insL", "PIK3R1 Q455_K459del",
"PIK3R1 Q455_S460dup", "PIK3R1 Q457_E462del", "PIK3R1 Q457_S460del",
"PIK3R1 Q579_Y580delinsH", "PIK3R1 R348*", "PIK3R1 R461_E462delinsQ",
"PIK3R1 R465_Y467del", "PIK3R1 R465dup", "PIK3R1 R574del", "PIK3R1 R577_D578del",
"PIK3R1 R577_L581del", "PIK3R1 R577del", "PIK3R1 S399_L404del",
"PIK3R1 S460_D464del", "PIK3R1 T397_V401del", "PIK3R1 T576del",
"PIK3R1 V401_H407del", "PIK3R1 V401_N406del", "PIK3R1 V402_L413del",
"PIK3R1 X434_splice", "PIK3R1 X475_splice", "PIK3R1 X582_splice",
"PIK3R1 Y452_N453insF", "PIK3R1 Y452_Q457del", "PIK3R1 Y452C",
"PIK3R1 Y452dup", "PIK3R1 Y452H", "PIK3R1 Y452N", "PIK3R1 Y463_E468dup",
"PIK3R1 Y467_Y470del", "PIK3R1 Y580_L581insF", "PIK3R2 D557G",
"PIK3R2 D557H", "PIK3R2 D557N", "PIK3R2 D557Y", "PIK3R2 G373R",
"PIM1 E79=", "PIM1 E79D", "PIM1 G28A", "PIM1 G28D", "PIM1 G28V",
"PIM1 K24=", "PIM1 K24N", "PIM1 L2F", "PIM1 L2V", "PIM1 N7=",
"PIM1 Q37=", "PIM1 S97=", "PIM1 S97N", "PIM1 S97R", "PIM1 S97T",
"PLCB3 T909P", "PLK2 L208P", "PLK2 L208V", "PNLIPRP3 K431R",
"PNLIPRP3 K431T", "PODXL S22P", "POLE E18K", "POLE P286H", "POLE P286L",
"POLE P286R", "POLE P286S", "POLE P286T", "POLE V411L", "POM121 N94S",
"PPM1D E525*", "PPP2R1A P179L", "PPP2R1A P179R", "PPP2R1A R182=",
"PPP2R1A R182W", "PPP2R1A R183G", "PPP2R1A R183Q", "PPP2R1A R183W",
"PPP2R1A S256F", "PPP2R1A S256Y", "PPP6C R264C", "PPP6C S270L",
"PRDM14 F204=", "PRDM14 F204V", "PRDM14 R505C", "PRDM14 R505H",
"PREX2 L50=", "PREX2 L50V", "PRKCI R480C", "PRKCI R480H", "PRKCI R480S",
"PSG4 E263K", "PTEN A126D", "PTEN A126G", "PTEN A126S", "PTEN A126V",
"PTEN C105*", "PTEN C105G", "PTEN C105R", "PTEN C105S", "PTEN C105W",
"PTEN C105Y", "PTEN C124G", "PTEN C124R", "PTEN C124S", "PTEN C124Y",
"PTEN C136*", "PTEN C136F", "PTEN C136R", "PTEN C136Y", "PTEN C71*",
"PTEN C71F", "PTEN C71Y", "PTEN D24E", "PTEN D24G", "PTEN D24H",
"PTEN D24N", "PTEN D24V", "PTEN D92E", "PTEN D92G", "PTEN D92H",
"PTEN D92N", "PTEN D92V", "PTEN D92Y", "PTEN G127*", "PTEN G127E",
"PTEN G127R", "PTEN G127V", "PTEN G129*", "PTEN G129=", "PTEN G129E",
"PTEN G129R", "PTEN G129V", "PTEN G132A", "PTEN G132D", "PTEN G132S",
"PTEN G132V", "PTEN G165*", "PTEN G165E", "PTEN G165R", "PTEN G251A",
"PTEN G251D", "PTEN G251V", "PTEN H61N", "PTEN H61R", "PTEN H61Y",
"PTEN H93L", "PTEN H93P", "PTEN H93R", "PTEN H93Y", "PTEN I101T",
"PTEN I67K", "PTEN I67T", "PTEN I67V", "PTEN L140*", "PTEN L140F",
"PTEN L146*", "PTEN L247*", "PTEN L247F", "PTEN L320*", "PTEN L320S",
"PTEN L320V", "PTEN M35I", "PTEN M35L", "PTEN M35V", "PTEN P38F",
"PTEN P38L", "PTEN P38S", "PTEN Q171*", "PTEN Q171K", "PTEN Q171R",
"PTEN R130*", "PTEN R130=", "PTEN R130G", "PTEN R130L", "PTEN R130P",
"PTEN R130Q", "PTEN R130S", "PTEN R173C", "PTEN R173H", "PTEN R173P",
"PTEN R233*", "PTEN R233Q", "PTEN R335*", "PTEN R335G", "PTEN R335P",
"PTEN S170G", "PTEN S170I", "PTEN S170N", "PTEN T277*", "PTEN T277A",
"PTEN T277I", "PTEN T277N", "PTEN W111*", "PTEN W111G", "PTEN W111R",
"PTEN W111S", "PTEN W274*", "PTEN W274S", "PTEN X212_splice",
"PTEN X267_splice", "PTEN X268_splice", "PTEN X342_splice", "PTEN X343_splice",
"PTEN X70_splice", "PTEN X85_splice", "PTEN Y155C", "PTEN Y155H",
"PTEN Y16*", "PTEN Y16=", "PTEN Y16D", "PTEN Y174*", "PTEN Y174D",
"PTEN Y174H", "PTEN Y177*", "PTEN Y177C", "PTEN Y177D", "PTEN Y177F",
"PTEN Y178*", "PTEN Y178C", "PTEN Y178H", "PTEN Y27*", "PTEN Y27C",
"PTEN Y27D", "PTEN Y27H", "PTEN Y27N", "PTEN Y336*", "PTEN Y346*",
"PTEN Y346C", "PTEN Y346D", "PTEN Y346H", "PTEN Y65*", "PTEN Y68*",
"PTEN Y68C", "PTEN Y68H", "PTEN Y68N", "PTN K44M", "PTN K44T",
"PTPN11 A461G", "PTPN11 A461T", "PTPN11 A72D", "PTPN11 A72G",
"PTPN11 A72S", "PTPN11 A72T", "PTPN11 A72V", "PTPN11 D61N", "PTPN11 D61Y",
"PTPN11 E69D", "PTPN11 E69K", "PTPN11 E76A", "PTPN11 E76G", "PTPN11 E76K",
"PTPN11 E76Q", "PTPN11 F285S", "PTPN11 F285V", "PTPN11 G503=",
"PTPN11 G503V", "PTPN11 N308D", "PTPN11 N308S", "PTPN11 Q510E",
"PTPN11 Q510H", "PTPN11 Q510L", "PTPN11 T468=", "PTPN11 T468M",
"PTPN11 T507K", "PTPRD S431*", "PTPRD S431=", "PTPRD S431L",
"PTPRS R1492=", "PTPRS R1492Q", "PTPRS R1492W", "PTPRS Y398=",
"PTPRT E548G", "PTPRT E548K", "PTPRT L668=", "PTPRT L668V", "PTPRT L695=",
"PTPRT L695F", "PTPRT L695R", "PTPRT R364*", "PTPRT R364=", "PTPRT R364Q",
"RAC1 A178V", "RAC1 C18F", "RAC1 C18S", "RAC1 C18Y", "RAC1 G12R",
"RAC1 G12V", "RAC1 K135N", "RAC1 K135R", "RAC1 N111I", "RAC1 N111K",
"RAC1 N111S", "RAC1 P29F", "RAC1 P29L", "RAC1 P29S", "RAC1 P29T",
"RAC1 P34H", "RAC1 P34R", "RAC1 P34S", "RAC1 Q61K", "RAC1 Q61R",
"RAD50 D69N", "RAD50 D69Y", "RAD51C P21A", "RAD51C P21S", "RAD51C P21T",
"RAD51C Y224H", "RAD52 R396=", "RAD52 R396H", "RAF1 S257L", "RAF1 S257W",
"RAF1 S259=", "RAF1 S259C", "RAF1 S259F", "RAF1 S259P", "RARA F286C",
"RARA F286I", "RARA F286S", "RB1 R251*", "RB1 R251Q", "RB1 R320*",
"RB1 R445*", "RB1 R455*", "RB1 R467*", "RB1 R552*", "RB1 R579*",
"RB1 R787*", "RB1 R787Q", "RB1 X127_splice", "RB1 X203_splice",
"RB1 X405_splice", "RB1 X406_splice", "RB1 X445_splice", "RB1 X46_splice",
"RB1 X463_splice", "RB1 X474_splice", "RB1 X500_splice", "RB1 X605_splice",
"RB1 X654_splice", "RB1 X702_splice", "RB1 X776_splice", "RB1 X830_splice",
"RB1 X89_splice", "RB1 Y606*", "RB1 Y606C", "RBM10 R153*", "RBM10 R153G",
"RBM10 X91_splice", "RBM39 T353=", "RBM39 T353I", "RECQL4 X766_splice",
"RET M918T", "RHEB Y35*", "RHEB Y35C", "RHEB Y35H", "RHEB Y35N",
"RHEB Y35S", "RHOA A161T", "RHOA A161V", "RHOA E40*", "RHOA E40D",
"RHOA E40K", "RHOA E40Q", "RHOA E40V", "RHOA E47K", "RHOA G17A",
"RHOA G17E", "RHOA G17V", "RHOA G62E", "RHOA G62R", "RHOA G62V",
"RHOA L22=", "RHOA L22P", "RHOA L22R", "RHOA L57V", "RHOA L69M",
"RHOA L69P", "RHOA L69R", "RHOA R5L", "RHOA R5Q", "RHOA R5W",
"RHOA T37A", "RHOA T37I", "RHOA T37S", "RHOA Y34C", "RHOA Y34F",
"RHOA Y42C", "RHOA Y42F", "RHOA Y42I", "RHOA Y42S", "RICTOR S1101=",
"RICTOR S1101L", "RIMS1 R71=", "RIMS1 R71G", "RIMS2 S423=", "RINT1 K85N",
"RINT1 K85T", "RIPPLY2 S110*", "RIPPLY2 S110L", "RIT1 A77P",
"RIT1 A77S", "RIT1 A77T", "RIT1 F82C", "RIT1 F82L", "RIT1 M90I",
"RNF43 H86R", "RNF43 H86Y", "RNF43 R132*", "RNF43 R145*", "RNF43 R371*",
"RPL10L K156M", "RPL10L K156R", "RPL10L K156T", "RPS6KA4 R629=",
"RPS6KA4 R629C", "RPS6KA4 R629H", "RPS6KA4 S236=", "RPS6KA4 S236L",
"RPTOR R139H", "RQCD1 P131L", "RQCD1 P131S", "RQCD1 S87C", "RQCD1 S87P",
"RRAS2 Q72H", "RRAS2 Q72L", "RTKN2 R33*", "RTKN2 R33Q", "RUNX1 R162G",
"RUNX1 R162K", "RUNX1 R162S", "RUNX1 R201*", "RUNX1 R201G", "RUNX1 R201Q",
"RXRA S427F", "RXRA S427Y", "S100A3 P97=", "S100A3 P97S", "S100A8 K49R",
"SDHA L639V", "SDHA S445=", "SDHA S445L", "SDHA V644L", "SDHA V644M",
"SDHAF2 S10*", "SDHAF2 S10A", "SDHAF2 S10L", "SDHAF2 X87_splice",
"SEMA4B S231=", "SEMA4B S231F", "SESN2 I425V", "SETD2 H1603R",
"SETD2 H1603Y", "SETD2 R1625C", "SETD2 R1625H", "SETD2 R1625L",
"SETD2 R1625S", "SETD2 X1572_splice", "SETD2 Y1666*", "SETD2 Y1666C",
"SETD2 Y1666H", "SF3B1 D894A", "SF3B1 D894G", "SF3B1 D894N",
"SF3B1 D894Y", "SF3B1 E902G", "SF3B1 E902K", "SF3B1 E902Q", "SF3B1 G740E",
"SF3B1 G740V", "SF3B1 G742D", "SF3B1 K666E", "SF3B1 K666M", "SF3B1 K666N",
"SF3B1 K666Q", "SF3B1 K666T", "SF3B1 K700=", "SF3B1 K700E", "SF3B1 K700R",
"SF3B1 K741*", "SF3B1 K741E", "SF3B1 K741N", "SF3B1 K741Q", "SF3B1 K741T",
"SF3B1 N626D", "SF3B1 N626H", "SF3B1 N626Y", "SF3B1 R625C", "SF3B1 R625G",
"SF3B1 R625H", "SF3B1 R625L", "SF3B1 V701A", "SF3B1 V701F", "SF3B1 V701I",
"SF3B1 Y623C", "SF3B1 Y623H", "SF3B1 Y623S", "SHB A460T", "SHROOM1 P300T",
"SLC16A13 F158L", "SLC27A5 T554=", "SLC27A5 T554I", "SLCO1B7 E27K",
"SMAD2 C463*", "SMAD2 C463F", "SMAD2 P305L", "SMAD2 P305Q", "SMAD2 P305T",
"SMAD2 R182*", "SMAD2 R182=", "SMAD2 R321*", "SMAD2 R321Q", "SMAD2 S464*",
"SMAD2 T303I", "SMAD2 T303R", "SMAD3 R268C", "SMAD3 R268H", "SMAD3 R287Q",
"SMAD3 R287W", "SMAD4 A118V", "SMAD4 C363del", "SMAD4 C363F",
"SMAD4 C363R", "SMAD4 C363S", "SMAD4 C363Y", "SMAD4 D351A", "SMAD4 D351G",
"SMAD4 D351H", "SMAD4 D351N", "SMAD4 D351V", "SMAD4 D351Y", "SMAD4 D355G",
"SMAD4 D355V", "SMAD4 D355Y", "SMAD4 D493A", "SMAD4 D493G", "SMAD4 D493H",
"SMAD4 D493N", "SMAD4 D537_E538dup", "SMAD4 D537A", "SMAD4 D537E",
"SMAD4 D537G", "SMAD4 D537H", "SMAD4 D537V", "SMAD4 D537Y", "SMAD4 E330*",
"SMAD4 E330G", "SMAD4 E330K", "SMAD4 E330Q", "SMAD4 E526*", "SMAD4 E526A",
"SMAD4 E526D", "SMAD4 E526K", "SMAD4 E526Q", "SMAD4 E526V", "SMAD4 F362_H371del",
"SMAD4 G352*", "SMAD4 G352A", "SMAD4 G352E", "SMAD4 G352L", "SMAD4 G352R",
"SMAD4 G352V", "SMAD4 G358_D360del", "SMAD4 G365_E377del", "SMAD4 G386A",
"SMAD4 G386C", "SMAD4 G386D", "SMAD4 G386R", "SMAD4 G386S", "SMAD4 G386V",
"SMAD4 G419R", "SMAD4 G419V", "SMAD4 G419W", "SMAD4 G510*", "SMAD4 G510A",
"SMAD4 G510E", "SMAD4 G510R", "SMAD4 L536_E538delinsQ", "SMAD4 L536P",
"SMAD4 L536Q", "SMAD4 L536R", "SMAD4 L540del", "SMAD4 P356H",
"SMAD4 P356L", "SMAD4 P356R", "SMAD4 P356S", "SMAD4 Q534*", "SMAD4 Q534P",
"SMAD4 R361_G365del", "SMAD4 R361_L364del", "SMAD4 R361C", "SMAD4 R361G",
"SMAD4 R361H", "SMAD4 R361L", "SMAD4 R361P", "SMAD4 R361S", "SMAD4 R445*",
"SMAD4 R445Q", "SMAD4 S178*", "SMAD4 S357_G365del", "SMAD4 V539_A546del",
"SMAD4 W524C", "SMAD4 W524L", "SMAD4 W524R", "SMAD4 W524S", "SMAD4 Y353C",
"SMAD4 Y353D", "SMAD4 Y353N", "SMAD4 Y95*", "SMAD4 Y95C", "SMAD4 Y95H",
"SMARCA4 E821D", "SMARCA4 E821K", "SMARCA4 G1232C", "SMARCA4 G1232D",
"SMARCA4 G1232S", "SMARCA4 G1232V", "SMARCA4 K546del", "SMARCA4 M781I",
"SMARCA4 M781L", "SMARCA4 M781V", "SMARCA4 R1135Q", "SMARCA4 R1135W",
"SMARCA4 R1157Q", "SMARCA4 R1157W", "SMARCA4 R1189*", "SMARCA4 R1189G",
"SMARCA4 R1189L", "SMARCA4 R1189Q", "SMARCA4 R1192C", "SMARCA4 R1192H",
"SMARCA4 R1192P", "SMARCA4 R1243G", "SMARCA4 R1243L", "SMARCA4 R1243P",
"SMARCA4 R1243W", "SMARCA4 R973Q", "SMARCA4 R973W", "SMARCA4 T910=",
"SMARCA4 T910A", "SMARCA4 T910M", "SMARCA4 T910R", "SMARCB1 K364del",
"SMARCB1 R374Q", "SMARCB1 R374W", "SMARCB1 R377C", "SMARCB1 R377H",
"SMARCB1 R377L", "SMARCD1 R183*", "SMARCD1 R183L", "SMARCD1 R183Q",
"SMO L412=", "SMO L412F", "SMO V414=", "SMO V414A", "SMO V414G",
"SMO W535L", "SMTNL2 X244_splice", "SNRPD3 G96C", "SNRPD3 G96R",
"SNRPD3 G96S", "SNRPD3 G96V", "SOCS1 A3E", "SOCS1 A3P", "SOCS1 A3R",
"SOCS1 A3T", "SOS1 A90=", "SOS1 A90T", "SOS1 A90V", "SOS1 N233Y",
"SOX17 A96G", "SOX17 S403I", "SOX9 K167del", "SOX9 R152_K167del",
"SOX9 R152del", "SPOP F102C", "SPOP F102I", "SPOP F102L", "SPOP F102S",
"SPOP F102V", "SPOP F125C", "SPOP F125I", "SPOP F125L", "SPOP F125V",
"SPOP F133C", "SPOP F133I", "SPOP F133L", "SPOP F133S", "SPOP F133V",
"SPOP K129E", "SPOP M117V", "SPOP W131C", "SPOP W131G", "SPOP W131L",
"SPOP W131R", "SPOP W131S", "SPOP Y87C", "SPOP Y87D", "SPOP Y87N",
"SPOP Y87S", "SPRED1 R349S", "SPRED1 R349W", "SPTA1 K1732T",
"SRSF2 P95_H99del", "SRSF2 P95_R102del", "SRSF2 P95_R117del",
"SRSF2 P95H", "SRSF2 P95L", "SRSF2 P95R", "SRSF2 Y92_H100del",
"SRSF2 Y92_H99del", "SSBP3 K6R", "STAG2 R216*", "STAG2 R216=",
"STAG2 R216Q", "STAT3 D661V", "STAT3 D661Y", "STAT3 E616del",
"STAT3 F384L", "STAT3 F384V", "STAT3 F384Y", "STAT3 H410P", "STAT3 H410R",
"STAT3 S614R", "STK11 D194G", "STK11 D194H", "STK11 D194N", "STK11 D194V",
"STK11 D194Y", "STK11 E165*", "STK11 E165K", "STK11 E165Q", "STK11 E223*",
"STK11 E223K", "STK11 E223V", "STK11 G196=", "STK11 G196R", "STK11 G196V",
"STK11 G242=", "STK11 G242R", "STK11 G242V", "STK11 G242W", "STK11 G251C",
"STK11 G251R", "STK11 G251V", "STK11 H174=", "STK11 H174D", "STK11 H174L",
"STK11 H174R", "STK11 H174Y", "STK11 K84*", "STK11 N181I", "STK11 N181S",
"STK11 N181T", "STK11 N181Y", "STK11 P179L", "STK11 P179Q", "STK11 P179R",
"STK11 P221=", "STK11 P221L", "STK11 P221S", "STK11 Q220*", "STK11 Q220P",
"STK11 S216=", "STK11 S216F", "STK11 W239*", "STK11 W239C", "STK11 W239S",
"STK11 W308*", "STK11 W308C", "STK11 W308L", "STK11 X125_splice",
"STK11 X155_splice", "STK11 X199_splice", "STK11 X200_splice",
"STK11 X245_splice", "STK11 X288_splice", "STK11 X307_splice",
"STK11 X97_splice", "STK19 D89=", "STK19 D89N", "SUZ12 R101*",
"SUZ12 R101Q", "SWI5 P34S", "SYT13 P228S", "SYT13 P228T", "TACC3 P417=",
"TACC3 P417S", "TARBP2 E191*", "TARBP2 E191=", "TBX2 S192I",
"TBX3 W113*", "TBX3 W113R", "TCEB1 Y79*", "TCEB1 Y79C", "TCEB1 Y79F",
"TCEB1 Y79N", "TCEB1 Y79S", "TCF20 P815L", "TCF20 P815S", "TCF3 N551K",
"TCF7L2 R471C", "TCF7L2 R471H", "TCF7L2 R471S", "TET1 P1752=",
"TET1 P1752S", "TET2 R550*", "TGFBR1 I259=", "TGFBR1 I259N",
"TGFBR1 R487Q", "TGFBR1 R487W", "TGFBR1 S241*", "TGFBR1 S241=",
"TGFBR1 S241L", "TGFBR1 T375I", "TGFBR1 T375K", "TGFBR1 T375R",
"TGFBR2 D471N", "TGFBR2 D471V", "TGFBR2 D471Y", "TGFBR2 E544K",
"TGFBR2 R520*", "TGFBR2 R520=", "TGFBR2 R553C", "TGFBR2 R553G",
"TGFBR2 R553H", "TGFBR2 R553L", "TGFBRAP1 P824=", "TGFBRAP1 P824F",
"TGFBRAP1 P824L", "TGFBRAP1 P824S", "THBD C554=", "THRA R79H",
"THSD7B E1181K", "THSD7B G557E", "THSD7B G557R", "THSD7B G557V",
"TMEM131 E1319*", "TMEM131 E1319K", "TMEM131 E1319Q", "TMEM147 A92=",
"TMEM147 A92V", "TMEM200C R19C", "TMEM200C R19H", "TMEM200C R19S",
"TNFRSF14 C111W", "TNFRSF14 C111Y", "TOP2B R651H", "TP53 A138_L145del",
"TP53 A138_P142del", "TP53 A159=", "TP53 A159D", "TP53 A159del",
"TP53 A159P", "TP53 A159V", "TP53 A161_I162del", "TP53 A161D",
"TP53 A161S", "TP53 A161T", "TP53 A161V", "TP53 A276_C277dup",
"TP53 A276_E285del", "TP53 C135_L137delinsW", "TP53 C135*", "TP53 C135F",
"TP53 C135G", "TP53 C135R", "TP53 C135S", "TP53 C135W", "TP53 C135Y",
"TP53 C141_P142del", "TP53 C141*", "TP53 C141F", "TP53 C141G",
"TP53 C141R", "TP53 C141S", "TP53 C141W", "TP53 C141Y", "TP53 C176_H179del",
"TP53 C176*", "TP53 C176=", "TP53 C176dup", "TP53 C176F", "TP53 C176G",
"TP53 C176R", "TP53 C176S", "TP53 C176W", "TP53 C176Y", "TP53 C229_H233del",
"TP53 C229_T230del", "TP53 C238_M243del", "TP53 C238_N239delinsY",
"TP53 C238_S240del", "TP53 C238F", "TP53 C238G", "TP53 C238R",
"TP53 C238S", "TP53 C238W", "TP53 C238Y", "TP53 C242*", "TP53 C242=",
"TP53 C242F", "TP53 C242G", "TP53 C242R", "TP53 C242S", "TP53 C242W",
"TP53 C242Y", "TP53 C275_R282delinsW", "TP53 C275*", "TP53 C275F",
"TP53 C275G", "TP53 C275R", "TP53 C275S", "TP53 C275W", "TP53 C275Y",
"TP53 C277*", "TP53 C277dup", "TP53 C277F", "TP53 C277G", "TP53 C277W",
"TP53 C277Y", "TP53 D148_T150del", "TP53 D148_T155dup", "TP53 D148del",
"TP53 D208E", "TP53 D208G", "TP53 D208N", "TP53 D208V", "TP53 D259=",
"TP53 D259H", "TP53 D259N", "TP53 D259V", "TP53 D259Y", "TP53 D281_R282insP",
"TP53 D281=", "TP53 D281A", "TP53 D281E", "TP53 D281G", "TP53 D281H",
"TP53 D281N", "TP53 D281P", "TP53 D281V", "TP53 D281Y", "TP53 E180_D184del",
"TP53 E198*", "TP53 E204_L206del", "TP53 E258*", "TP53 E258=",
"TP53 E258A", "TP53 E258D", "TP53 E258G", "TP53 E258K", "TP53 E258Q",
"TP53 E258V", "TP53 E271*", "TP53 E271K", "TP53 E271Q", "TP53 E271V",
"TP53 E285_K292del", "TP53 E285*", "TP53 E285=", "TP53 E285K",
"TP53 E285Q", "TP53 E285V", "TP53 E286_E287del", "TP53 E286*",
"TP53 E286A", "TP53 E286G", "TP53 E286K", "TP53 E286Q", "TP53 E286V",
"TP53 E294*", "TP53 E298*", "TP53 E298Q", "TP53 F109C", "TP53 F109I",
"TP53 F109S", "TP53 F109V", "TP53 F113=", "TP53 F113C", "TP53 F113L",
"TP53 F113P", "TP53 F113S", "TP53 F113V", "TP53 F134C", "TP53 F134I",
"TP53 F134L", "TP53 F134S", "TP53 F134V", "TP53 F270C", "TP53 F270del",
"TP53 F270I", "TP53 F270L", "TP53 F270S", "TP53 F270V", "TP53 G105=",
"TP53 G105C", "TP53 G105D", "TP53 G105R", "TP53 G105S", "TP53 G105V",
"TP53 G154_T155del", "TP53 G154C", "TP53 G154D", "TP53 G154V",
"TP53 G199_E204del", "TP53 G244_M246delinsV", "TP53 G244=", "TP53 G244A",
"TP53 G244C", "TP53 G244D", "TP53 G244F", "TP53 G244R", "TP53 G244S",
"TP53 G244V", "TP53 G245_P250delinsA", "TP53 G245A", "TP53 G245C",
"TP53 G245D", "TP53 G245N", "TP53 G245R", "TP53 G245S", "TP53 G245V",
"TP53 G262del", "TP53 G262V", "TP53 G266*", "TP53 G266E", "TP53 G266K",
"TP53 G266R", "TP53 G266T", "TP53 G266V", "TP53 H168L", "TP53 H168P",
"TP53 H168R", "TP53 H178_S183del", "TP53 H178D", "TP53 H178N",
"TP53 H178P", "TP53 H178Q", "TP53 H179_D184del", "TP53 H179D",
"TP53 H179del", "TP53 H179L", "TP53 H179N", "TP53 H179P", "TP53 H179Q",
"TP53 H179R", "TP53 H179Y", "TP53 H193D", "TP53 H193L", "TP53 H193N",
"TP53 H193P", "TP53 H193Q", "TP53 H193R", "TP53 H193Y", "TP53 H214L",
"TP53 H214P", "TP53 H214Q", "TP53 H214R", "TP53 I162_Y163delinsN",
"TP53 I162dup", "TP53 I195_G199del", "TP53 I195=", "TP53 I195F",
"TP53 I195K", "TP53 I195M", "TP53 I195N", "TP53 I195S", "TP53 I195T",
"TP53 I232=", "TP53 I232F", "TP53 I232N", "TP53 I232S", "TP53 I232T",
"TP53 I251=", "TP53 I251F", "TP53 I251M", "TP53 I251N", "TP53 I251S",
"TP53 I254_T256del", "TP53 I254F", "TP53 I254L", "TP53 I254M",
"TP53 I254N", "TP53 I254S", "TP53 I254V", "TP53 I255=", "TP53 I255del",
"TP53 I255dup", "TP53 I255F", "TP53 I255N", "TP53 I255S", "TP53 I255T",
"TP53 K120*", "TP53 K120E", "TP53 K120M", "TP53 K120N", "TP53 K132*",
"TP53 K132E", "TP53 K132M", "TP53 K132N", "TP53 K132Q", "TP53 K132R",
"TP53 K132T", "TP53 K139_P142delinsT", "TP53 K164*", "TP53 K164E",
"TP53 L111M", "TP53 L111P", "TP53 L111Q", "TP53 L111R", "TP53 L130_A138dup",
"TP53 L130del", "TP53 L130F", "TP53 L130H", "TP53 L130P", "TP53 L130R",
"TP53 L130V", "TP53 L194F", "TP53 L194H", "TP53 L194P", "TP53 L194R",
"TP53 L252_I254del", "TP53 L252del", "TP53 L252dup", "TP53 L257=",
"TP53 L257P", "TP53 L257Q", "TP53 L257R", "TP53 L257V", "TP53 L264_N268del",
"TP53 L265=", "TP53 L265del", "TP53 L265M", "TP53 L265P", "TP53 L265R",
"TP53 M133I", "TP53 M133K", "TP53 M133R", "TP53 M133T", "TP53 M237_N239del",
"TP53 M237I", "TP53 M237K", "TP53 M237V", "TP53 M243_I255del",
"TP53 M246I", "TP53 M246K", "TP53 M246L", "TP53 M246R", "TP53 M246T",
"TP53 M246V", "TP53 N131=", "TP53 N131del", "TP53 N131I", "TP53 N131K",
"TP53 N131S", "TP53 N235_Y236dup", "TP53 N235del", "TP53 N239_S240del",
"TP53 N239_S241del", "TP53 N239D", "TP53 N239dup", "TP53 N239H",
"TP53 N239K", "TP53 N239S", "TP53 N239T", "TP53 N247=", "TP53 N247I",
"TP53 N263_N268del", "TP53 N268_R273del", "TP53 P128_L130del",
"TP53 P128del", "TP53 P142dup", "TP53 P151A", "TP53 P151F", "TP53 P151H",
"TP53 P151L", "TP53 P151R", "TP53 P151S", "TP53 P151T", "TP53 P152=",
"TP53 P152K", "TP53 P152L", "TP53 P152Q", "TP53 P152R", "TP53 P152S",
"TP53 P152T", "TP53 P153_G154del", "TP53 P153del", "TP53 P177_C182del",
"TP53 P177_H178del", "TP53 P190L", "TP53 P190R", "TP53 P190S",
"TP53 P190T", "TP53 P191_L201del", "TP53 P191del", "TP53 P250_I251delinsL",
"TP53 P250_L252del", "TP53 P250=", "TP53 P250L", "TP53 P250R",
"TP53 P278A", "TP53 P278F", "TP53 P278H", "TP53 P278L", "TP53 P278R",
"TP53 P278S", "TP53 P278T", "TP53 Q104*", "TP53 Q104H", "TP53 Q136_C141del",
"TP53 Q136*", "TP53 Q136del", "TP53 Q136E", "TP53 Q136H", "TP53 Q136L",
"TP53 Q136P", "TP53 Q144*", "TP53 Q144H", "TP53 Q144L", "TP53 Q144P",
"TP53 Q165*", "TP53 Q165H", "TP53 Q167*", "TP53 Q192*", "TP53 Q192del",
"TP53 Q192L", "TP53 Q317*", "TP53 Q331*", "TP53 Q331H", "TP53 R110C",
"TP53 R110H", "TP53 R110L", "TP53 R110P", "TP53 R156del", "TP53 R158_A159del",
"TP53 R158_A159dup", "TP53 R158C", "TP53 R158F", "TP53 R158G",
"TP53 R158H", "TP53 R158L", "TP53 R158P", "TP53 R158S", "TP53 R175C",
"TP53 R175G", "TP53 R175H", "TP53 R175L", "TP53 R181C", "TP53 R181H",
"TP53 R181P", "TP53 R196*", "TP53 R196L", "TP53 R196P", "TP53 R196Q",
"TP53 R202_L206del", "TP53 R213*", "TP53 R213G", "TP53 R213L",
"TP53 R213P", "TP53 R213Q", "TP53 R248=", "TP53 R248G", "TP53 R248L",
"TP53 R248P", "TP53 R248Q", "TP53 R248W", "TP53 R249G", "TP53 R249I",
"TP53 R249K", "TP53 R249M", "TP53 R249S", "TP53 R249T", "TP53 R249W",
"TP53 R267=", "TP53 R267G", "TP53 R267L", "TP53 R267P", "TP53 R267Q",
"TP53 R267W", "TP53 R273C", "TP53 R273G", "TP53 R273H", "TP53 R273L",
"TP53 R273P", "TP53 R273S", "TP53 R280*", "TP53 R280G", "TP53 R280I",
"TP53 R280K", "TP53 R280S", "TP53 R280T", "TP53 R282_R283del",
"TP53 R282=", "TP53 R282G", "TP53 R282L", "TP53 R282P", "TP53 R282Q",
"TP53 R282W", "TP53 R306*", "TP53 R306Q", "TP53 R337C", "TP53 R337G",
"TP53 R337H", "TP53 R337L", "TP53 R337P", "TP53 R337S", "TP53 R342*",
"TP53 R342P", "TP53 S127=", "TP53 S127C", "TP53 S127F", "TP53 S127P",
"TP53 S127T", "TP53 S127Y", "TP53 S183_G187delinsC", "TP53 S215C",
"TP53 S215G", "TP53 S215I", "TP53 S215N", "TP53 S215R", "TP53 S215T",
"TP53 S240_C242del", "TP53 S240_S241del", "TP53 S241=", "TP53 S241A",
"TP53 S241C", "TP53 S241dup", "TP53 S241F", "TP53 S241P", "TP53 S241T",
"TP53 S241Y", "TP53 S260_L264dup", "TP53 S269_E271del", "TP53 S269_E271delinsK",
"TP53 T125=", "TP53 T125A", "TP53 T125K", "TP53 T125M", "TP53 T125P",
"TP53 T125R", "TP53 T150_R158del", "TP53 T155_A161del", "TP53 T155_R156del",
"TP53 T155_R158del", "TP53 T155=", "TP53 T155I", "TP53 T155N",
"TP53 T155P", "TP53 T231_I232del", "TP53 T231_I232insTDCTT",
"TP53 T253_L257del", "TP53 T253dup", "TP53 T256_S260del", "TP53 T256del",
"TP53 V143_P153del", "TP53 V143A", "TP53 V143E", "TP53 V143G",
"TP53 V143M", "TP53 V147_D148dup", "TP53 V157_R158del", "TP53 V157_R158dup",
"TP53 V157=", "TP53 V157A", "TP53 V157D", "TP53 V157F", "TP53 V157G",
"TP53 V157L", "TP53 V172D", "TP53 V172F", "TP53 V172G", "TP53 V173_R175del",
"TP53 V173A", "TP53 V173dup", "TP53 V173E", "TP53 V173G", "TP53 V173L",
"TP53 V173M", "TP53 V197_N200del", "TP53 V197=", "TP53 V197E",
"TP53 V197G", "TP53 V197L", "TP53 V197M", "TP53 V216E", "TP53 V216G",
"TP53 V216L", "TP53 V216M", "TP53 V218=", "TP53 V218E", "TP53 V218G",
"TP53 V218L", "TP53 V218M", "TP53 V272_R273insL", "TP53 V272=",
"TP53 V272A", "TP53 V272E", "TP53 V272G", "TP53 V272K", "TP53 V272L",
"TP53 V272M", "TP53 V274_C275dup", "TP53 V274_G279del", "TP53 V274A",
"TP53 V274D", "TP53 V274dup", "TP53 V274F", "TP53 V274G", "TP53 V274L",
"TP53 W146*", "TP53 W146C", "TP53 W146G", "TP53 W146S", "TP53 W53*",
"TP53 W91*", "TP53 X125_splice", "TP53 X126_splice", "TP53 X187_splice",
"TP53 X224_splice", "TP53 X225_splice", "TP53 X261_splice", "TP53 X307_splice",
"TP53 X32_splice", "TP53 X33_splice", "TP53 X331_splice", "TP53 X332_splice",
"TP53 Y107*", "TP53 Y107=", "TP53 Y107D", "TP53 Y126*", "TP53 Y126C",
"TP53 Y126D", "TP53 Y126H", "TP53 Y126N", "TP53 Y126S", "TP53 Y163*",
"TP53 Y163C", "TP53 Y163D", "TP53 Y163H", "TP53 Y163N", "TP53 Y205*",
"TP53 Y205C", "TP53 Y205D", "TP53 Y205F", "TP53 Y205H", "TP53 Y205N",
"TP53 Y205S", "TP53 Y220*", "TP53 Y220C", "TP53 Y220D", "TP53 Y220H",
"TP53 Y220N", "TP53 Y220S", "TP53 Y234_M237del", "TP53 Y234*",
"TP53 Y234C", "TP53 Y234D", "TP53 Y234del", "TP53 Y234H", "TP53 Y234N",
"TP53 Y234S", "TP53 Y236_M237delinsL", "TP53 Y236*", "TP53 Y236C",
"TP53 Y236D", "TP53 Y236H", "TP53 Y236N", "TP53 Y236S", "TP63 E609K",
"TP63 R379C", "TP63 R379H", "TP63 R379S", "TP63 S365*", "TP63 S365=",
"TP63 S365L", "TP63 X194_splice", "TPTE2 M41V", "TRAF7 N520S",
"TRAF7 N520Y", "TRAF7 R189=", "TRAF7 R189L", "TRAF7 R189P", "TRAF7 R189W",
"TRIM65 H383L", "TRIM65 H383N", "TROAP S562I", "TSC1 X797_splice",
"TSC22D2 S735F", "TSC22D2 S735Y", "TUBGCP4 A8D", "TUBGCP4 A8T",
"TUBGCP6 S1192=", "U2AF1 G222_G223del", "U2AF1 G223del", "U2AF1 G223dup",
"U2AF1 I24T", "U2AF1 I24V", "U2AF1 Q157P", "U2AF1 Q157R", "U2AF1 S34F",
"U2AF1 S34Y", "UBE2D3 M32V", "UCHL1 H161Y", "VHL C162*", "VHL C162F",
"VHL C162R", "VHL C162W", "VHL C162Y", "VHL D121G", "VHL D121V",
"VHL D121Y", "VHL E70_R79dup", "VHL F76del", "VHL G114A", "VHL G114C",
"VHL G114R", "VHL H115N", "VHL H115Q", "VHL H115Y", "VHL I151F",
"VHL I151N", "VHL I151S", "VHL I151T", "VHL I75_C77del", "VHL L135*",
"VHL L135F", "VHL L158=", "VHL L158P", "VHL L158Q", "VHL L158V",
"VHL L169P", "VHL L89=", "VHL L89H", "VHL L89P", "VHL N78D",
"VHL N78K", "VHL N78S", "VHL N78Y", "VHL P86L", "VHL P86R", "VHL P86S",
"VHL P86T", "VHL R161*", "VHL R161L", "VHL R161Q", "VHL R79_S80del",
"VHL S111=", "VHL S111N", "VHL S111P", "VHL S111R", "VHL S65*",
"VHL S65L", "VHL S65P", "VHL S65T", "VHL S65W", "VHL S68*", "VHL S68P",
"VHL S80=", "VHL S80I", "VHL S80N", "VHL S80R", "VHL V74=", "VHL V74D",
"VHL V74G", "VHL W117*", "VHL W117C", "VHL W117L", "VHL W88*",
"VHL W88L", "VHL W88R", "VHL X114_splice", "VHL X155_splice",
"VHL Y112*", "VHL Y112=", "VHL Y112C", "VHL Y112D", "WDR73 G316R",
"WHSC1 T1150A", "XPO1 E571A", "XPO1 E571K", "XPO1 E571V", "XPO1 R749*",
"XPO1 R749Q", "XPO6 I274T", "XPO6 I274V", "ZBTB7A K424N", "ZBTB7A K424T",
"ZHX3 N249K", "ZNF516 A256D", "ZNF623 T500K", "ZNF649 R198I",
"ZNF649 R198K", "ZNF649 R198S")
#' @name hotspots
#' @title something
#' @description
#'
#' Hotspots - MSK-IMPACT 341
#'
#' @param maf
#'
#' @return binary table of hotpots in the 341 IMPACT gene panel
#' @export
hotspots <- function( maf = maf ){
if("Tumor_Sample_Barcode" %in% names(maf)){
setnames(maf, "Tumor_Sample_Barcode", "SAMPLE_ID")
}
setkey(maf, "SAMPLE_ID")
# maf[Protein_position == "",
# Protein_position := gsub("/.*$", "", CDS_position)]
#
# suppressWarnings(maf[Variant_Type == "SNP",
# Amino_Acid := as.integer(gsub("/.*$", "", Protein_position))])
#
# maf[paste(Hugo_Symbol, Amino_Acid) %in% MolecularDiagnosis::hotspot.v11.mutations.filtered,
# hotspot := ]
if("HGVSp_Short" %in% names(maf)) {
maf[, Hugo_Symbol_Allele := paste0(Hugo_Symbol, " ", gsub("^p.", "", HGVSp_Short))]
} else {
maf[, Hugo_Symbol_Allele := paste0(Hugo_Symbol, " ", gsub("^p.", "", Amino_Acid_Change))]
}
hotspot_genes <- unique(sort(gsub(" .*$", "", hotspot_list)))
# hotspot_allele_genes <- c("KRAS", "BRAF", "EGFR")
hotspot_allele_genes <- hotspot_genes
hotspot_allele_genes_regex <- paste0("^", paste(hotspot_allele_genes, collapse = "|^"))
hotspot_allele_list <- hotspot_list[hotspot_list %like% hotspot_allele_genes_regex]
maf_allele_hotspots <- maf[Hugo_Symbol %in% hotspot_allele_genes &
Hugo_Symbol_Allele %in% hotspot_allele_list]
maf_allele_hotspots[, Hugo_Symbol := factor(Hugo_Symbol, levels = hotspot_allele_genes)]
if(maf_allele_hotspots[, .N] > 0){
hotspots_allele_d <- dcast.data.table(
maf[Hugo_Symbol_Allele %in% hotspot_allele_list],
SAMPLE_ID ~ Hugo_Symbol_Allele,
value.var = "Hugo_Symbol_Allele",
fill = 0,
drop = FALSE,
fun.aggregate = function(x) {
ifelse(length(x) > 0, 1, 0)
}
)
absent_hotspots <- setdiff(hotspot_allele_list,
colnames(hotspots_allele_d))
suppressWarnings(hotspots_allele_d[, absent_hotspots := 0, with = FALSE])
}
maf_hotspots <- maf[Hugo_Symbol %in% hotspot_genes &
Hugo_Symbol_Allele %in% hotspot_list]
maf_hotspots[, Hugo_Symbol := factor(Hugo_Symbol, levels = hotspot_genes)]
if(maf_hotspots[, .N] > 0){
hotspots_d <- dcast.data.table(
maf[Hugo_Symbol %in% hotspot_genes &
Hugo_Symbol_Allele %in% hotspot_list],
SAMPLE_ID ~ Hugo_Symbol,
value.var = "Hugo_Symbol",
fill = 0,
drop = F,
fun.aggregate = function(x) {
ifelse(length(x) > 0, 1, 0)
}
)
absent_hotspots <- setdiff(hotspot_genes,
colnames(hotspots_d))
suppressWarnings(hotspots_d[, absent_hotspots := 0, with = F])
hotspot_names <-
setnames(hotspots_d, c(
names(hotspots_d)[1],
paste0(names(hotspots_d)[-1], "_hotspot")
))
} else {
hotspots_d <- as.data.table(data.matrix(matrix(0, nrow = maf[, uniqueN(SAMPLE_ID)], ncol = 1+length(hotspot_list))))
colnames(hotspots_d) <- c("SAMPLE_ID", hotspot_list)
hotspots_d[, SAMPLE_ID := maf[, unique(SAMPLE_ID)] ]
}
if("Tumor_Sample_Barcode" %in% names(maf)) setnames(maf, "Tumor_Sample_Barcode", "SAMPLE_ID")
setnames(hotspots_d, gsub(" ", "_", names(hotspots_d)))
hotspots_d <- merge(hotspots_d, hotspots_allele_d, by = "SAMPLE_ID", all = T)
hotspots_d[is.na(hotspots_d)] <- 0
setnames(hotspots_d, make.names(names(hotspots_d), unique = T))
copy(hotspots_d)
}
#' @name focal_cn_portal
#' @title something
#' @description
#'
#' Focal amplifications and homozygous deletions portal style - MSK-IMPACT 341
#'
#' This function creates a feature table of focal copy number alterations of type:
#' Amp (amplification, cn == 2)
#' HomDel (homozygous deletion, cn == -1)
#'
#' @param cna
#'
#' @return binary table of focal copy number alterations in the 341 IMPACT gene panel
#'
#' @export
focal_cn_portal = function( cna = cn ) {
setnames(cna, 1, "Hugo_Symbol")
# cna[ Hugo_Symbol == "FAM123B", Hugo_Symbol := "AMER1"]
# cna[Hugo_Symbol == "MLL", Hugo_Symbol := "KMT2A"]
# cna[Hugo_Symbol == "MLL2", Hugo_Symbol := "KMT2D"]
# cna[Hugo_Symbol == "MLL3", Hugo_Symbol := "KMT2C"]
cna[Hugo_Symbol == "MYCL1", Hugo_Symbol := "MYCL"]
cna[, Hugo_Symbol := gsub("-", ".", Hugo_Symbol)]
cna <- cna[Hugo_Symbol %in% MolecularDiagnosis::msk_impact_341]
setkey(cna, Hugo_Symbol)
sample_cols <- 2:ncol(cna)
### Amp table
cna_amp <- data.table(cna)
cna_amp[, (sample_cols) := lapply(.SD, function(x)
as.integer(x == 2)), .SDcols = sample_cols]
cna_amp[, Hugo_Symbol := paste0(Hugo_Symbol, "_Amp")]
### HomDel table
cna[, (sample_cols) := lapply(.SD, function(x)
as.integer(x == -2)), .SDcols = sample_cols]
cna[, Hugo_Symbol := paste0(Hugo_Symbol, "_HomDel")]
cna <- rbind(cna_amp, cna)
cna <- tdt(cna)
setnames(cna, 1, "SAMPLE_ID")
return(cna)
}
#' @name broad_cn
#' @title something
#' @description
#'
#' Broad copy number alterations
#'
#' @param seg
#' @param log_ratio_threshold
#'
#' @return binary table of broad copy number alterations in the 341 IMPACT gene panel
#'
#' @export
broad_cn = function(seg = seg, log_ratio_threshold = 0.2){
setnames(seg,
c(
"SAMPLE_ID",
"chr",
"start",
"end",
"num.mark",
"seg.mean"
))
seg <- seg[num.mark >= 10 & !chr == "Y"]
seg[, chr := as.character(chr)]
setkey(seg, chr, start, end)
Cytoband_Table <- MolecularDiagnosis::Cytoband_Table[!chr == "Y"]
Cytoband_Table[, Length := (end - start) + 1]
setkey(Cytoband_Table, chr, start, end)
seg_arm <- foverlaps(seg, Cytoband_Table,
nomatch = 0, type = "any")
### make sure that segments do not count towards more than one arm
setnames(seg_arm, "i.start", "segment_start")
setnames(seg_arm, "i.end", "segment_end")
seg_arm[, segment_start := pmax(segment_start, start)]
seg_arm[, segment_end := pmin(segment_end, end)]
seg_arm[, width := (segment_end - segment_start) + 1]
seg_arm[seg.mean <= -log_ratio_threshold,
cna := "Del"]
seg_arm[seg.mean >= log_ratio_threshold,
cna := "Amp"]
seg_arm_Fc <-
seg_arm[, .(TSB_alt_width = sum(as.numeric(width))), by = c("SAMPLE_ID", "arm", "cna")]
seg_arm_Fc <-
merge(seg_arm_Fc, Cytoband_Table, all.x = TRUE, by = "arm")
seg_arm_Fc[, fc_arm_cna := round(TSB_alt_width / Length, digits = 3)]
seg_arm_Fc[fc_arm_cna >= 0.5, arm_alt := "Y"]
seg_arm_Fc[cna == "Del" & arm_alt == "Y", cn := -1]
seg_arm_Fc[cna == "Amp" & arm_alt == "Y", cn := 1]
seg_arm_Fc[is.na(arm_alt) , cn := 0]
setkey(seg_arm_Fc, cn)
broad_cn_alterations <-
c(
paste0("Del_", Cytoband_Table$arm),
paste0("Amp_", Cytoband_Table$arm)
)
if(!sum(seg_arm_Fc$cn, na.rm = T)) {
mat <- matrix(
0,
nrow = uniqueN(seg_arm_Fc$SAMPLE_ID),
ncol = length(broad_cn_alterations)
)
colnames(mat) <- broad_cn_alterations
broadCNAs_d <- data.table(mat)
broadCNAs_d <-
cbind(SAMPLE_ID = unique(seg_arm_Fc$SAMPLE_ID),
broadCNAs_d)
} else {
broadCNAs_d <- merge(
data.table(
dcast.data.table(
seg_arm_Fc[cn == -1] ,
SAMPLE_ID ~ paste0("Del_", arm),
value.var = 'cn',
fun.aggregate = function(x) {
ifelse(length(x) > 0, 1, 0)
}
)
),
data.table(
dcast.data.table(
seg_arm_Fc[cn == 1] ,
SAMPLE_ID ~ paste0("Amp_", arm),
value.var = 'cn',
fun.aggregate = function(x) {
ifelse(length(x) > 0, 1, 0)
}
)
),
all = TRUE,
by = "SAMPLE_ID"
)
# replace NAs with 0s
for(i in seq_along(broadCNAs_d))
set(broadCNAs_d,
i = which(is.na(broadCNAs_d[[i]])),
j = i,
value = 0)
unaltered_arms <- setdiff(broad_cn_alterations,
colnames(broadCNAs_d))
suppressWarnings(broadCNAs_d[, unaltered_arms := 0, with = F])
TSB_noBroadcnas <-
unique(seg_arm_Fc[cn == 0 &
!SAMPLE_ID %in% broadCNAs_d$SAMPLE_ID,
list(SAMPLE_ID)])
TSB_noBroadcnas[, (broad_cn_alterations) := 0]
broadCNAs_d <- rbind(broadCNAs_d, TSB_noBroadcnas)
setcolorder(broadCNAs_d,
c("SAMPLE_ID", broad_cn_alterations))
}
return(broadCNAs_d)
}
#' @name fusions
#' @title something
#' @description
#'
#' Fusions
#'
#' @param SV
#'
#' @return binary table of structural variants involving genes in the 341 IMPACT gene panel
fusions = function(SV = SV){
if("Tumor_Sample_Barcode" %in% names(SV)) setnames(SV, "Tumor_Sample_Barcode", "SAMPLE_ID")
SV[, fusion_column_name :=
ifelse(Fusion %in% c("TMPRSS2-ERG fusion", "ETV1-TMPRSS2 fusion"), "ETS_TMPRSS2_fusion",
ifelse(Fusion %in% c("EML4-ALK fusion", "ALK-EML4 fusion"), "EML4_ALK_fusion",
ifelse(Fusion %in% c("CD74-ROS1 fusion", "EZR-ROS1 fusion", "ROS1-SDC4 fusion"), "ROS1_fusion",
ifelse(Fusion == "EGFR-intragenic", "EGFR_SV", NA))))]
SV_tab <- dcast.data.table(
SV[!is.na(fusion_column_name)],
SAMPLE_ID ~ fusion_column_name,
value.var = "fusion_column_name",
fun.aggregate = function(x) {
ifelse(length(x) > 0, 1, 0)
},
fill = 0
)
return(SV_tab)
}
#' #' @name mutational_signatures
#' #' @title something
#' #' @description
#' #'
#' #' Mutational signatures
#' #'
#' #' @param maf
#' #'
#' ## #' @import Biostrings
#' ## #' @import GenomeInfoDb
#' ## #' @import BSgenome.Hsapiens.UCSC.hg19
#' #' @return binary table of mutational signatures in the 341 IMPACT gene panel
#' ## #' @export
#' mutational_signatures <- function( maf = maf){
#'
#' maf <- as.data.table(maf)
#'
#' if("Tumor_Sample_Barcode" %in% names(maf)) setnames(maf, "Tumor_Sample_Barcode", "SAMPLE_ID")
#'
#' setkey(maf, "SAMPLE_ID")
#'
#' dt <- maf
#' flank <- 1
#' hg19 <- BSgenome.Hsapiens.UCSC.hg19::BSgenome.Hsapiens.UCSC.hg19
#' GenomeInfoDb::seqlevelsStyle(hg19) <- "NCBI"
#'
#' if(!"Mut_Tri" %in% colnames(maf)) {
#' ### annotate_maf_with_tri_nucleotide
#' ### data.table not working when in separate function (?)
#' Ref_Tri <- dt[, Biostrings::getSeq(hg19,
#' name = Chromosome,
#' start = Start_Position - flank,
#' end = End_Position + flank)]
#' # with(dt, ifelse()
#' Ref_Tri_CT <- Ref_Tri
#' Ref_Tri_CT[substr(Ref_Tri, 2, 2) %in% c("A", "G")] <-
#' Biostrings::reverseComplement(Ref_Tri_CT[substr(Ref_Tri, 2, 2) %in% c("A", "G")])
#' Ref_Tri <- as.character(Ref_Tri)
#' Ref_Tri_CT <- as.character(Ref_Tri_CT)
#' Ref_Tri_CT[dt$Variant_Type != "SNP"] <- NA
#'
#' Tumor_Seq_Allele2_CT <- dt$Tumor_Seq_Allele2
#' Tumor_Seq_Allele2_CT[substr(Ref_Tri, 2, 2) %in% c("A", "G")] <-
#' as.character(Biostrings::reverseComplement(
#' Biostrings::DNAStringSet(Tumor_Seq_Allele2_CT[substr(Ref_Tri, 2, 2) %in% c("A", "G")])))
#'
#' ### remove synonymous mutations
#' Ref_Tri_CT[substr(Ref_Tri_CT, 2, 2) == Tumor_Seq_Allele2_CT] <-
#' NA
#' ### remove positions with no identified reference (ie MT)
#' Ref_Tri_CT[substr(Ref_Tri_CT, 2, 2) == "N"] <- NA
#'
#' Mut_Tri <- with(dt,
#' ifelse(
#' Variant_Type != "SNP" | is.na(Ref_Tri_CT) ,
#' NA,
#' paste0(
#' substr(Ref_Tri_CT, 1, 1),
#' "[",
#' substr(Ref_Tri_CT, 2, 2),
#' "/",
#' Tumor_Seq_Allele2_CT,
#' "]",
#' substr(Ref_Tri_CT, 3, 3)
#' )
#' ))
#'
#' dt[, Ref_Tri := Ref_Tri] # dt specific, add column
#' dt[, Mut_Tri := Mut_Tri] # dt specific, add column
#' ###
#' maf <- dt
#' }
#' maf <- maf[!Mut_Tri %like% "^N"]
#'
#' trinuc_counts <- dcast.data.table(maf[!is.na(Mut_Tri),
#' .N,
#' by = list(name = Tumor_Sample_Barcode,
#' Mut_Tri)],
#' name ~ Mut_Tri,
#' value.var = "N",
#' fill = 0)
#'
#' trinuc_counts_norm_to_one <- with(trinuc_counts,
#' data.table(
#' name = name,
#' number = rowSums(trinuc_counts[, -1, with = FALSE]),
#' trinuc_counts[, -1, with = FALSE] / rowSums(trinuc_counts[, -1, with =
#' FALSE])
#' ))
#' setnames(trinuc_counts_norm_to_one, gsub("[^[:alnum:] ]", "", names(trinuc_counts_norm_to_one)))
#'
#' adam_trinuc_colnames = c(
#' "name",
#' "number",
#' "ACAA",
#' "ACAC",
#' "ACAG",
#' "ACAT",
#' "CCAA",
#' "CCAC",
#' "CCAG",
#' "CCAT",
#' "GCAA",
#' "GCAC",
#' "GCAG",
#' "GCAT",
#' "TCAA",
#' "TCAC",
#' "TCAG",
#' "TCAT",
#' "ACGA",
#' "ACGC",
#' "ACGG",
#' "ACGT",
#' "CCGA",
#' "CCGC",
#' "CCGG",
#' "CCGT",
#' "GCGA",
#' "GCGC",
#' "GCGG",
#' "GCGT",
#' "TCGA",
#' "TCGC",
#' "TCGG",
#' "TCGT",
#' "ACTA",
#' "ACTC",
#' "ACTG",
#' "ACTT",
#' "CCTA",
#' "CCTC",
#' "CCTG",
#' "CCTT",
#' "GCTA",
#' "GCTC",
#' "GCTG",
#' "GCTT",
#' "TCTA",
#' "TCTC",
#' "TCTG",
#' "TCTT",
#' "ATAA",
#' "ATAC",
#' "ATAG",
#' "ATAT",
#' "CTAA",
#' "CTAC",
#' "CTAG",
#' "CTAT",
#' "GTAA",
#' "GTAC",
#' "GTAG",
#' "GTAT",
#' "TTAA",
#' "TTAC",
#' "TTAG",
#' "TTAT",
#' "ATCA",
#' "ATCC",
#' "ATCG",
#' "ATCT",
#' "CTCA",
#' "CTCC",
#' "CTCG",
#' "CTCT",
#' "GTCA",
#' "GTCC",
#' "GTCG",
#' "GTCT",
#' "TTCA",
#' "TTCC",
#' "TTCG",
#' "TTCT",
#' "ATGA",
#' "ATGC",
#' "ATGG",
#' "ATGT",
#' "CTGA",
#' "CTGC",
#' "CTGG",
#' "CTGT",
#' "GTGA",
#' "GTGC",
#' "GTGG",
#' "GTGT",
#' "TTGA",
#' "TTGC",
#' "TTGG",
#' "TTGT"
#' )
#'
#' new_names = setdiff(adam_trinuc_colnames, names(trinuc_counts_norm_to_one))
#' suppressWarnings(trinuc_counts_norm_to_one[, new_names := 0, with = F])
#' trinuc_counts_norm_to_one <- trinuc_counts_norm_to_one[, adam_trinuc_colnames, with = F]
#' setcolorder(trinuc_counts_norm_to_one, adam_trinuc_colnames)
#'
#' signature_fractions = stratton_signatures_summ(trinuc_counts_norm_to_one)
#'
#' col_names = c(
#' "Signature.1 (age)",
#' "Signature.2 (APOBEC)",
#' "Signature.3 (BRCA1/2)",
#' "Signature.4 (smoking)",
#' "Signature.5",
#' "Signature.6 (DNA mismatch repair)",
#' "Signature.7 (ultraviolet light)",
#' "Signature.8",
#' "Signature.9 (POLH)",
#' "Signature.10 (POLE)",
#' "Signature.11 (temozolomide)",
#' "Signature.12",
#' "Signature.13 (APOBEC)",
#' "Signature.14",
#' "Signature.15 (DNA mismatch repair)",
#' "Signature.16",
#' "Signature.17",
#' "Signature.18",
#' "Signature.19",
#' "Signature.20 (DNA mismatch repair?)",
#' "Signature.21",
#' "Signature.22 (aristolochic acid)",
#' "Signature.23",
#' "Signature.24 (aflatoxin)",
#' "Signature.25",
#' "Signature.26",
#' "Signature.27",
#' "Signature.28",
#' "Signature.29 (tobacco chewing)",
#' "Signature.30"
#' )
#'
#' if(!nrow(signature_fractions)) {
#' signature_fractions <- trinuc_counts_norm_to_one[, list(name)]
#' signature_fractions[, (col_names) := 0]
#' }
#'
#' setnames(signature_fractions, "name", "SAMPLE_ID")
#'
#' nMut <- maf[, .N, by = "SAMPLE_ID"]
#' nMut <- nMut[order(N)]
#' # nMut[N < 10, signature_fraction_threshold := 1]
#' # nMut[N >= 10 & N < 50, signature_fraction_threshold := 0.3]
#' # nMut[N >= 50 & N < 100, signature_fraction_threshold := 0.2]
#' # nMut[N >= 100 & N < 200, signature_fraction_threshold := 0.15]
#' # nMut[N >= 200, signature_fraction_threshold := 0.1]
#' nMut[, signature_fraction_threshold := 0.4]
#' signature_fractions <- merge(signature_fractions, nMut,
#' by = "SAMPLE_ID")
#'
#' ### create boolean for signatures based on threshold
#' for(i in 1:nrow(signature_fractions)) {
#' for(j in 2:(ncol(signature_fractions) - 2)) {
#' set(
#' signature_fractions,
#' i,
#' j,
#' as.integer(
#' signature_fractions[i, j, with = F] > signature_fractions[i]$signature_fraction_threshold
#' )
#' )
#' }
#' }
#'
#' signature_fractions <-
#' signature_fractions[,!c("N", "signature_fraction_threshold"), with = F]
#'
#' setkey(signature_fractions, SAMPLE_ID)
#'
#' setnames(signature_fractions,
#' names(signature_fractions),
#' gsub("\\(|\\)|\\?", "", names(signature_fractions)))
#' setnames(signature_fractions,
#' names(signature_fractions),
#' gsub("\\/|\\ ", ".", names(signature_fractions)))
#'
#' col_names <- names(signature_fractions)
#' col_names <- col_names[-1]
#'
#' setcolorder(signature_fractions, c("SAMPLE_ID", col_names))
#'
#' signatures = c(
#' "Signature.1.age",
#' "Signature.2.APOBEC",
#' "Signature.3.BRCA1.2",
#' "Signature.4.smoking",
#' "Signature.5",
#' "Signature.6.DNA.mismatch.repair",
#' "Signature.7.ultraviolet.light",
#' "Signature.8",
#' "Signature.9.POLH",
#' "Signature.10.POLE",
#' "Signature.11.temozolomide",
#' "Signature.12",
#' "Signature.13.APOBEC",
#' "Signature.14",
#' "Signature.15.DNA.mismatch.repair",
#' "Signature.16",
#' "Signature.17",
#' "Signature.18",
#' "Signature.19",
#' "Signature.20.DNA.mismatch.repair",
#' "Signature.21",
#' "Signature.22.aristolochic.acid",
#' "Signature.23",
#' "Signature.24.aflatoxin",
#' "Signature.25",
#' "Signature.26",
#' "Signature.27",
#' "Signature.28",
#' "Signature.29.tobacco.chewing",
#' "Signature.30"
#' )
#'
#' absent_signatures <- setdiff(signatures,
#' colnames(signature_fractions))
#'
#' suppressWarnings(signature_fractions[, absent_signatures := 0, with =
#' F])
#'
#' setcolorder(signature_fractions, c("SAMPLE_ID", signatures))
#'
#' return(signature_fractions)
#'
#' }
#' @name mutation_count
#' @title something
#' @description
#'
#' Mutation count
#'
#' @param maf
#'
#' @return table of mutation counts in the 341 IMPACT gene panel
#'
#' @export
mutation_count = function( maf = maf ) {
maf <- as.data.table(maf)
if("Tumor_Sample_Barcode" %in% names(maf)){
setnames(maf, "Tumor_Sample_Barcode", "SAMPLE_ID")
}
setkey(maf, "SAMPLE_ID")
mutations <- maf[ (Consequence %in% MolecularDiagnosis::Nonsyn_Consequence |
(Consequence=="upstream_gene_variant" &
Hugo_Symbol=="TERT")) &
Hugo_Symbol %in% MolecularDiagnosis::msk_impact_341 ]
mutations_c <- mutations[, .(length(Hugo_Symbol)), by = "SAMPLE_ID" ]
setnames(mutations_c, 2, "Mutation_Count")
return(mutations_c)
}
#' @name cn_burden
#' @title something
#' @description
#'
#' Copy number burden
#'
#' @param seg
#' @param log_ratio_threshold
#'
#' @return copy number burden of samples from selected cancer types
#'
#' @export
cn_burden = function(seg = seg, log_ratio_threshold = 0.2){
seg <- as.data.table(seg)
setnames(seg, c("SAMPLE_ID", "Chromosome", "Start_Position", "End_Position", "Num_Mark", "Seg_Mean"))
# seg <- seg[ is.na(Num_Mark) | Num_Mark>10 ]
setkey( seg, Seg_Mean )
seg[ Seg_Mean <= -log_ratio_threshold,
CNA := "Del"]
seg[ Seg_Mean >= log_ratio_threshold,
CNA := "Amp"]
seg[, Width := (End_Position - Start_Position) + 1 ]
cn_burden <- merge(seg[, .(gen_cov = sum(Width)), by= "SAMPLE_ID" ],
seg[ !is.na(CNA), .(gen_alt = sum(Width)), by= "SAMPLE_ID" ],
by= "SAMPLE_ID" )
cn_burden[, CN_Burden := round( gen_alt / gen_cov , digits=3 )*100 ]
cn_burden <- cn_burden[, list(SAMPLE_ID, CN_Burden)]
return(cn_burden)
}
bergerm1/GenomeDerivedDiagnosis documentation built on Nov. 4, 2019, 7:15 a.m.
R Package Documentation
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Defines functions mutations truncating_mutations hotspots focal_cn_portal broad_cn fun.aggregate
Documented in broad_cn focal_cn_portal hotspots mutations truncating_mutations
tdt <- function (inpdt){
transposed <- t(inpdt[, -1, with = F])
colnames(transposed) <- inpdt[[1]]
transposed <- data.table(transposed, keep.rownames = T)
setnames(transposed, 1, names(inpdt)[1])
return(transposed)
}
#' @name mutations
#' @title something
#' @description
#'
#' Mutations - MSK-IMPACT 341
#'
#' @param maf
#'
#' @return binary table of mutations in the 341 IMPACT gene panel
mutations = function(maf = maf){
Nonsyn_Consequences = c("missense_variant", "stop_gained", "frameshift_variant", "splice_donor_variant",
"splice_acceptor_variant", "inframe_insertion", "inframe_deletion",
"stop_lost", "exon_loss_variant", "disruptive_inframe_deletion",
"disruptive_inframe_insertion", "start_lost")
maf = as.data.table(maf)
if("Tumor_Sample_Barcode" %in% names(maf)){
setnames(maf, "Tumor_Sample_Barcode", "SAMPLE_ID")
}
setkey(maf, "SAMPLE_ID")
mutations_d = dcast.data.table(
maf[ Consequence %like% paste(collapse = "|", Nonsyn_Consequences) & Hugo_Symbol %in% MolecularDiagnosis::msk_impact_341],
SAMPLE_ID ~ Hugo_Symbol,
value.var = 'SAMPLE_ID',
fun.aggregate = function(x) {
ifelse(length(x) > 0, 1, 0)
}
)
mutations_d = as.data.table(mutations_d)
unmutated_impact_genes = setdiff(MolecularDiagnosis::msk_impact_341, colnames(mutations_d))
suppressWarnings(mutations_d[, unmutated_impact_genes := 0, with = F])
# add TERT promoter as an additional feature
mutations_d[SAMPLE_ID %in% maf[Consequence == "upstream_gene_variant" &
Hugo_Symbol == "TERT"]$SAMPLE_ID, TERTp := 1]
mutations_d[!SAMPLE_ID %in% maf[Consequence == "upstream_gene_variant" &
Hugo_Symbol == "TERT"]$SAMPLE_ID, TERTp := 0]
setcolorder(mutations_d, c("SAMPLE_ID", sort(MolecularDiagnosis::msk_impact_341), "TERTp"))
if("Tumor_Sample_Barcode" %in% names(maf)){
setnames(maf, "Tumor_Sample_Barcode", "SAMPLE_ID")
}
copy(mutations_d)
}
#' @name truncating_mutations
#' @title something
#' @description
#'
#' Truncating mutations - MSK-IMPACT341
#'
#' @param maf
#'
#' @return binary table of truncating mutations in the 341 IMPACT gene panel
truncating_mutations = function(maf = maf) {
if("Tumor_Sample_Barcode" %in% names(maf)){
setnames(maf, "Tumor_Sample_Barcode", "SAMPLE_ID")
}
setkey(maf, "SAMPLE_ID")
if("Consequence" %in% names(maf)) {
trunc <- c("stop_gained", "frameshift_variant", "splice_donor_variant",
"splice_acceptor_variant", "stop_lost", "exon_loss_variant")
mutations_d <- dcast.data.table(
maf[Consequence %like% paste(collapse = "|", trunc) &
Hugo_Symbol %in% MolecularDiagnosis::msk_impact_341],
SAMPLE_ID ~ paste0(Hugo_Symbol, "_", "TRUNC"),
value.var = 'SAMPLE_ID',
fun.aggregate = function(x) {
ifelse(length(x) > 0, 1, 0)
}
)
} else {
trunc <- c("Frame_Shift_Del", "Splice_Site", "Frame_Shift_Ins",
"Nonsense_Mutation", "Nonstop_Mutation")
mutations_d <- dcast.data.table(
maf[ Variant_Classification %like% paste(collapse = "|", trunc) & Hugo_Symbol %in% MolecularDiagnosis::msk_impact_341],
SAMPLE_ID ~ paste0(Hugo_Symbol, "_", "TRUNC"),
value.var = 'SAMPLE_ID',
fun.aggregate = function(x) {
ifelse(length(x) > 0, 1, 0)
}
)
}
mutations_d <- as.data.table(mutations_d)
unmutated_impact_genes <- setdiff(paste0(MolecularDiagnosis::msk_impact_341, "_", "TRUNC"), colnames(mutations_d))
suppressWarnings(mutations_d[, unmutated_impact_genes := 0, with = F])
setcolorder(mutations_d, c("SAMPLE_ID", paste0(
sort(MolecularDiagnosis::msk_impact_341), "_", "TRUNC"
)))
if("Tumor_Sample_Barcode" %in% names(maf)) setnames(maf, "Tumor_Sample_Barcode", "SAMPLE_ID")
copy(mutations_d)
}
#' Hotspots - MSK-IMPACT 341
#'
#' @param maf
#'
#' @return binary table of hotpots in the 341 IMPACT gene panel
#'
#' @export hotspots
hotspot_list <- c("ABCC10 R570L", "ABCC10 R570Q", "ABCC10 R570W", "ACADS R330C",
"ACADS R330H", "ACP6 V29G", "ACSBG2 I250M", "ACVR1 G328E", "ACVR1 G328V",
"ACVR1 R206H", "ACVR1 R258G", "ACVR1 R258M", "ACVR1B R485*",
"AHI1 Q294R", "AKT1 D323G", "AKT1 D323N", "AKT1 D323Y", "AKT1 E17*",
"AKT1 E17K", "AKT1 L52H", "AKT1 L52R", "AKT1 P68_C77dup", "AKT1 Q79K",
"AKT1 T65_I75dup", "AKT2 C60_I75dup", "AKT2 L78_Q79insHANTFVIRCL",
"AKT2 R67_L78dup", "AKT2 R76_I84dup", "AKT3 E17*", "AKT3 E17K",
"ALK F1174C", "ALK F1174L", "ALK F1174V", "ALK F1245I", "ALK F1245V",
"ALK R1275*", "ALK R1275L", "ALK R1275Q", "ALK R395=", "ALK R395H",
"ALK R401*", "ALK R401L", "ALK R401Q", "AMPD1 L631F", "AMPD1 L631V",
"ANKRD11 E1008_P1015del", "ANKRD11 K1012del", "ANKRD11 K1461del",
"ANKRD11 K369R", "ANKZF1 A650=", "ANKZF1 A650V", "APC E1353*",
"APC E1379*", "APC E1397*", "APC E1408*", "APC Q1294*", "APC Q1303*",
"APC Q1328*", "APC Q1338*", "APC Q1367*", "APC Q1367E", "APC Q1378*",
"APC Q1406*", "APC Q1406H", "APC Q1429*", "APC Q1429R", "APC R1114*",
"APC R1450*", "APC R213*", "APC R216*", "APC R232*", "APC R499*",
"APC R564*", "APC R876*", "APC R876Q", "APC S1315*", "APC Y935*",
"AR H875Y", "AR L702=", "AR L702H", "AR T878A", "AR T878S", "AR W742C",
"AR W742L", "ARAF P216L", "ARAF P216R", "ARAF S214=", "ARAF S214A",
"ARAF S214C", "ARAF S214F", "ARAF S214P", "ARAF S214Y", "ARHGAP28 L277P",
"ARHGAP28 L277R", "ARID1A G2087E", "ARID1A G2087R", "ARID1A Q1142*",
"ARID1A R1276*", "ARID1A R1276Q", "ARID1A R1335*", "ARID1A R1461*",
"ARID1A R1461Q", "ARID1A R1721*", "ARID1A R1722*", "ARID1A R1989*",
"ARID1A R1989Q", "ARID1A R2158*", "ARID1A R2158=", "ARID1A R2158Q",
"ARID1A R693*", "ARID1A X911_splice", "ARID1B G966D", "ARID1B Q1179*",
"ARID1B Q1179P", "ARID1B T1652=", "ARID1B T1652A", "ARID1B T1652M",
"ARID2 R314C", "ARID2 R314S", "ARID2 S297=", "ARID2 S297F", "ARID3A S557G",
"ARIH1 A409E", "ARL16 G6R", "ASF1B P21=", "ASF1B P21L", "ASXL2 E330D",
"ASXL2 E330K", "ASXL2 E330Q", "ASXL2 M1?", "ASXL2 R357*", "ATM I2888L",
"ATM I2888T", "ATM L2890P", "ATM L2890R", "ATM L2890V", "ATM N2875K",
"ATM N2875S", "ATM N2875T", "ATM R1466*", "ATM R1466P", "ATM R1466Q",
"ATM R250*", "ATM R250P", "ATM R2832C", "ATM R2832S", "ATM R3008C",
"ATM R3008H", "ATM R3008L", "ATM R337C", "ATM R337H", "ATP6V1B2 P352=",
"ATP6V1B2 P352S", "ATRX R1426*", "ATRX R1426=", "ATRX R907*",
"ATRX X199_splice", "AXIN1 X652_splice", "AXL A273P", "AXL A273V",
"AXL T443=", "B2M L12=", "B2M L12P", "B2M L12Q", "B2M L7*", "B2M L7S",
"B2M M1?", "B2M X23_splice", "BAP1 E31del", "BAP1 K25_D34delinsN",
"BAP1 K25_Q28del", "BAP1 Y33del", "BCL10 E178=", "BCL10 E178D",
"BCL10 L174*", "BCL10 N173H", "BCL2 A131D", "BCL2 A131T", "BCL2 A131V",
"BCL2 G33=", "BCL2 G33R", "BCL2 K22*", "BCL2 K22=", "BCL2 K22R",
"BCL2 N172=", "BCL2 N172Q", "BCL2 N172S", "BCL2L11 G156*", "BCL2L11 G156E",
"BCL2L11 G156R", "BCL2L12 F17=", "BCL2L12 F8=", "BCL2L12 R18W",
"BCL6 R594G", "BCL6 R594Q", "BCL6 R618C", "BCL6 R618H", "BCOR N1459S",
"BNC2 S575I", "BNC2 S575R", "BRAF D594E", "BRAF D594G", "BRAF D594H",
"BRAF D594N", "BRAF D594V", "BRAF D594Y", "BRAF G466A", "BRAF G466E",
"BRAF G466V", "BRAF G469*", "BRAF G469=", "BRAF G469A", "BRAF G469E",
"BRAF G469R", "BRAF G469S", "BRAF G469V", "BRAF G596C", "BRAF G596D",
"BRAF G596R", "BRAF G596S", "BRAF G596V", "BRAF I592_A598dup",
"BRAF K601_W604del", "BRAF K601E", "BRAF K601N", "BRAF K601T",
"BRAF L485*", "BRAF L485F", "BRAF L485S", "BRAF L485W", "BRAF L597=",
"BRAF L597Q", "BRAF L597R", "BRAF L597S", "BRAF L597V", "BRAF N486_A489delinsK",
"BRAF N486_P490del", "BRAF N581D", "BRAF N581H", "BRAF N581I",
"BRAF N581S", "BRAF N581T", "BRAF N581Y", "BRAF P490_Q494del",
"BRAF T488_P492del", "BRAF T488_Q493delinsK", "BRAF T599dup",
"BRAF V600_K601delinsE", "BRAF V600_R603del", "BRAF V600=", "BRAF V600E",
"BRAF V600G", "BRAF V600K", "BRAF V600M", "BRAF V600R", "BRAF X327_splice",
"BRCA2 S2303=", "BRCA2 S2303F", "BRD4 P1065=", "BRD4 P1065R",
"BRD7 Y455*", "BRINP1 G713=", "BTBD11 K1003M", "BTBD11 K1003R",
"BTBD11 K1003T", "C16orf80 R100C", "C16orf80 R100H", "C3orf70 S6*",
"C3orf70 S6L", "C3orf70 S6W", "C5orf49 K130T", "C6 K817R", "C6 K817T",
"CANT1 K131R", "CARD11 D357N", "CARD11 D357V", "CARD11 D401N",
"CARD11 E626*", "CARD11 E626K", "CARD11 E626Q", "CARD11 E93D",
"CARD11 E93K", "CARD11 E93Q", "CARD11 K215M", "CARD11 K215N",
"CARD11 K215T", "CARD11 L251P", "CARD11 R337*", "CARD11 R337Q",
"CARD11 R423=", "CARD11 R423Q", "CARD11 R423W", "CASP8 R127*",
"CASP8 R127Q", "CASP8 R292Q", "CASP8 R292W", "CASP8 R491*", "CASP8 R491Q",
"CASP8 R494*", "CASP8 X243_splice", "CBFB W73*", "CBL C384R",
"CBL C384W", "CCND1 C47S", "CCND1 E9=", "CCND1 E9D", "CCND1 E9K",
"CCND1 P287A", "CCND1 P287L", "CCND1 P287R", "CCND1 P287S", "CCND1 P287T",
"CCND1 T286A", "CCND1 T286I", "CCND1 Y44*", "CCND1 Y44C", "CCND1 Y44D",
"CCND1 Y44F", "CCND1 Y44H", "CCND1 Y44S", "CCND3 I290K", "CCND3 I290R",
"CCND3 Q276*", "CCT8 I86T", "CD79B X185_splice", "CD79B Y197C",
"CD79B Y197D", "CD79B Y197F", "CD79B Y197H", "CD79B Y197N", "CD79B Y197R",
"CD79B Y197S", "CDH1 D254E", "CDH1 D254N", "CDH1 D254Y", "CDH1 D288N",
"CDH1 D288V", "CDH1 Q23*", "CDH1 R335*", "CDH1 R335Q", "CDH1 R63*",
"CDH1 R63G", "CDH1 R63P", "CDH1 X177_splice", "CDH1 X278_splice",
"CDH1 X440_splice", "CDH1 X722_splice", "CDH1 Y190C", "CDK12 R890H",
"CDK4 K22M", "CDK4 K22Q", "CDK4 R24C", "CDK4 R24H", "CDK4 R24L",
"CDK4 R24S", "CDK6 L65=", "CDKN1B G72=", "CDKN1B G72A", "CDKN1B G72D",
"CDKN1B X159_splice", "CDKN2A A36_N39delinsD", "CDKN2A D108G",
"CDKN2A D108H", "CDKN2A D108N", "CDKN2A D108V", "CDKN2A D108Y",
"CDKN2A D74G", "CDKN2A D74N", "CDKN2A D74V", "CDKN2A D74Y", "CDKN2A D84A",
"CDKN2A D84G", "CDKN2A D84N", "CDKN2A D84V", "CDKN2A D84Y", "CDKN2A E120*",
"CDKN2A E120D", "CDKN2A E120K", "CDKN2A E27del", "CDKN2A E88*",
"CDKN2A E88K", "CDKN2A G35_A36del", "CDKN2A H83D", "CDKN2A H83N",
"CDKN2A H83Q", "CDKN2A H83R", "CDKN2A H83Y", "CDKN2A L130Q",
"CDKN2A L130R", "CDKN2A L130V", "CDKN2A L32_L37del", "CDKN2A N39_N42del",
"CDKN2A N42H", "CDKN2A N42I", "CDKN2A N42K", "CDKN2A N42Y", "CDKN2A P114F",
"CDKN2A P114H", "CDKN2A P114L", "CDKN2A P114S", "CDKN2A P114T",
"CDKN2A P48L", "CDKN2A P48R", "CDKN2A Q50*", "CDKN2A Q50=", "CDKN2A Q50H",
"CDKN2A Q50R", "CDKN2A R140C", "CDKN2A R170C", "CDKN2A R29_A34del",
"CDKN2A R58*", "CDKN2A R80*", "CDKN2A R80Q", "CDKN2A S114R",
"CDKN2A S12*", "CDKN2A S12L", "CDKN2A V28_E33del", "CDKN2A W110*",
"CDKN2A X153_splice", "CDKN2A X51_splice", "CDKN2A Y129*", "CDKN2A Y129C",
"CEBPA N307_E309delinsK", "CEBPA T310_Q311insKQNP", "CEBPA T310_Q311insW",
"CEBPA V308dup", "CELSR1 W1958C", "CEP63 S153=", "CEP63 S153L",
"CEP89 S153I", "CHEK2 R346C", "CHEK2 R346G", "CHEK2 R346H", "CHEK2 R346S",
"CHIT1 W358*", "CIC N205S", "CIC P203A", "CIC P203L", "CIC P203S",
"CIC R1512C", "CIC R1512H", "CIC R1512L", "CIC R1512S", "CIC R1515C",
"CIC R1515H", "CIC R201=", "CIC R201W", "CIC R202Q", "CIC R202W",
"CIC R215=", "CIC R215Q", "CIC R215W", "CIC S231G", "CIC S231I",
"CIC S231N", "CIC W238*", "CIC W238R", "CIC X151_splice", "CIZ1 L59P",
"CLEC14A R193=", "CLEC14A R193C", "CLEC14A R193H", "COBL E480D",
"CR1 R1842C", "CR1 R1842H", "CRB1 F630S", "CRB1 F630V", "CREBBP D1435G",
"CREBBP D1435H", "CREBBP D1435N", "CREBBP D1435Y", "CREBBP I1431=",
"CREBBP I1431N", "CREBBP I1431S", "CREBBP I1431V", "CREBBP L1499P",
"CREBBP L1499Q", "CREBBP L1499R", "CREBBP R1446C", "CREBBP R1446G",
"CREBBP R1446H", "CREBBP R1446L", "CREBBP R1446P", "CREBBP R1446S",
"CREBBP S1680del", "CREBBP W1472C", "CREBBP W1472G", "CREBBP W1472R",
"CREBBP W1472S", "CREBBP W1502*", "CREBBP W1502C", "CREBBP W1502L",
"CREBBP W1502R", "CREBBP Y1450C", "CREBBP Y1450D", "CREBBP Y1450N",
"CREBBP Y1482C", "CREBBP Y1482D", "CREBBP Y1482H", "CREBBP Y1482N",
"CREBBP Y1503C", "CREBBP Y1503D", "CREBBP Y1503H", "CREBBP Y1503N",
"CREBBP Y1503S", "CRLF2 S128=", "CRLF2 S128L", "CRNKL1 S128=",
"CRNKL1 S128F", "CSPG5 R365=", "CSPG5 R365Q", "CSPG5 R365W",
"CTCF H284N", "CTCF H284P", "CTCF H284Y", "CTCF H288D", "CTCF H288R",
"CTCF H288Y", "CTCF R377C", "CTCF R377H", "CTCF R448*", "CTCF S354F",
"CTCF S354Y", "CTCF Y226C", "CTNNB1 A43_P44dup", "CTNNB1 D32_I35delinsV",
"CTNNB1 D32_S33del", "CTNNB1 D32_S37delinsA", "CTNNB1 D32A",
"CTNNB1 D32G", "CTNNB1 D32H", "CTNNB1 D32N", "CTNNB1 D32V", "CTNNB1 D32Y",
"CTNNB1 G34_S71del", "CTNNB1 G34*", "CTNNB1 G34A", "CTNNB1 G34E",
"CTNNB1 G34L", "CTNNB1 G34R", "CTNNB1 G34V", "CTNNB1 G38_P44del",
"CTNNB1 H36P", "CTNNB1 H36Y", "CTNNB1 I35=", "CTNNB1 I35S", "CTNNB1 K292E",
"CTNNB1 K292T", "CTNNB1 K335I", "CTNNB1 K335T", "CTNNB1 L31_I35del",
"CTNNB1 L31_S33del", "CTNNB1 N387I", "CTNNB1 N387K", "CTNNB1 N387Y",
"CTNNB1 P44_S60del", "CTNNB1 Q26_D32delinsH", "CTNNB1 Q28_D32delinsH",
"CTNNB1 R535*", "CTNNB1 R535Q", "CTNNB1 S23_S33del", "CTNNB1 S33_A39del",
"CTNNB1 S33A", "CTNNB1 S33C", "CTNNB1 S33F", "CTNNB1 S33P", "CTNNB1 S33T",
"CTNNB1 S33Y", "CTNNB1 S37A", "CTNNB1 S37C", "CTNNB1 S37F", "CTNNB1 S37P",
"CTNNB1 S37Y", "CTNNB1 S45_P52del", "CTNNB1 S45=", "CTNNB1 S45A",
"CTNNB1 S45C", "CTNNB1 S45del", "CTNNB1 S45F", "CTNNB1 S45P",
"CTNNB1 S45Y", "CTNNB1 T41_S45del", "CTNNB1 T41_S47del", "CTNNB1 T41A",
"CTNNB1 T41I", "CTNNB1 T41N", "CTNNB1 T42_K49del", "CTNNB1 W25_D32del",
"CTNNB1 W25_H36del", "CTNNB1 W383C", "CTNNB1 W383G", "CTNNB1 W383R",
"CTNNB1 W383S", "CTNNB1 Y30_S33del", "CUL3 A20=", "CUL3 M299R",
"CUL3 M299V", "CYP2C8 P402L", "CYP2C8 P402S", "CYP4A11 I491T",
"CYP7B1 K332T", "CYSLTR2 L129Q", "DCAF13 T118=", "DDX28 S442=",
"DDX28 S442F", "DHRS4 T102M", "DICER1 D1709N", "DICER1 D1810A",
"DICER1 D1810H", "DICER1 D1810N", "DICER1 D1810V", "DICER1 D1810Y",
"DICER1 E1813A", "DICER1 E1813G", "DICER1 E1813K", "DICER1 E1813Q",
"DICER1 S1344I", "DICER1 S1344L", "DIS3 D479G", "DIS3 D479H",
"DIS3 D479V", "DIS3 D479Y", "DIS3 D488A", "DIS3 D488G", "DIS3 D488H",
"DIS3 D488N", "DIS3 D488Y", "DIS3 L767F", "DIS3 R382G", "DIS3 R382Q",
"DIS3 R689G", "DIS3 R689Q", "DIS3 R780G", "DIS3 R780K", "DIS3 R780S",
"DIS3 R780T", "DNAH9 E2368D", "DNAH9 E2368K", "DNAJB1 L190=",
"DNMT1 E432K", "DNMT1 E51K", "DNMT3A R882C", "DNMT3A R882H",
"DNMT3A R882P", "DNMT3B V229=", "DNMT3B V229L", "DNMT3B V229M",
"DUSP16 R483*", "EBF2 G444E", "EBF2 G444V", "EGFR A289D", "EGFR A289I",
"EGFR A289N", "EGFR A289T", "EGFR A289V", "EGFR A750=", "EGFR A750P",
"EGFR A767_V769dup", "EGFR D770_N771insG", "EGFR D770_N771insGF",
"EGFR D770_N771insGL", "EGFR D770_N771insY", "EGFR D770_P772dup",
"EGFR E709_T710delinsD", "EGFR E709A", "EGFR E709K", "EGFR E709Q",
"EGFR E746_A750del", "EGFR E746_T751delinsA", "EGFR G598A", "EGFR G598E",
"EGFR G598V", "EGFR G719A", "EGFR G719C", "EGFR G719D", "EGFR G719S",
"EGFR H304Y", "EGFR H773_V774dup", "EGFR H773dup", "EGFR K745_E746insVPVAIK",
"EGFR K754_I759del", "EGFR K754=", "EGFR K754E", "EGFR K754I",
"EGFR L62R", "EGFR L747_E749del", "EGFR L747_P753delinsS", "EGFR L747_S752del",
"EGFR L747_T751del", "EGFR L747=", "EGFR L747F", "EGFR L747P",
"EGFR L747S", "EGFR L833F", "EGFR L833M", "EGFR L833V", "EGFR L838M",
"EGFR L838P", "EGFR L858R", "EGFR L861Q", "EGFR N771_H773dup",
"EGFR N771_P772insH", "EGFR N771_P772insHH", "EGFR N771_P772insV",
"EGFR P596=", "EGFR P596L", "EGFR P596R", "EGFR P596S", "EGFR P772_H773dup",
"EGFR P772_H773insTPNP", "EGFR R108G", "EGFR R108K", "EGFR R222C",
"EGFR R222H", "EGFR R252C", "EGFR R252H", "EGFR R252P", "EGFR S752_I759del",
"EGFR S768_D770dup", "EGFR S768I", "EGFR S768T", "EGFR T263I",
"EGFR T263P", "EGFR T363A", "EGFR T363I", "EGFR T363N", "EGFR T751_A755del",
"EGFR T751_E758del", "EGFR T790=", "EGFR T790M", "EGFR Y764_D770dup",
"EIF1AX G15=", "EIF1AX G15D", "EIF1AX G15V", "EIF1AX G6C", "EIF1AX G6D",
"EIF1AX G6R", "EIF1AX G6S", "EIF1AX G8E", "EIF1AX G8R", "EIF1AX G9D",
"EIF1AX G9R", "EIF1AX G9V", "EIF1AX K10E", "EIF1AX K10T", "EIF1AX N4I",
"EIF1AX N4S", "EIF1AX N4Y", "EIF1AX P2=", "EIF1AX P2L", "EIF1AX P2S",
"EIF1AX R13C", "EIF1AX R13G", "EIF1AX R13H", "EIF1AX R13L", "EIF1AX R13P",
"EIF1AX X113_splice", "EIF1AX X6_splice", "ELTD1 S11=", "ELTD1 S11F",
"ELTD1 S11P", "EP300 C1164S", "EP300 C1164Y", "EP300 D1399E",
"EP300 D1399N", "EP300 D1399Y", "EP300 H1451=", "EP300 H1451L",
"EP300 H1451P", "EP300 H1451Q", "EP300 H1451R", "EP300 L415P",
"EP300 Q1455=", "EP300 Q1455H", "EP300 Q1455R", "EP300 W1466*",
"EP300 W1466C", "EP300 W1466G", "EP300 W1466L", "EP300 W1466R",
"EP300 X1429_splice", "EP300 X1539_splice", "EP300 Y1414C", "EP300 Y1414D",
"EP300 Y1467C", "EP300 Y1467D", "EP300 Y1467H", "EP300 Y1467K",
"EP300 Y1467N", "EP300 Y1467S", "EPAS1 P531A", "EPAS1 P531L",
"EPAS1 P531S", "EPAS1 Y532C", "EPHA3 R136*", "EPHA7 G656=", "EPHA7 G656E",
"EPHA7 G656R", "EPHA7 G656W", "EPHB1 R743=", "EPHB1 R743Q", "EPHB1 R743W",
"ERBB2 A293P", "ERBB2 A293T", "ERBB2 A293V", "ERBB2 D277G", "ERBB2 D277H",
"ERBB2 D277V", "ERBB2 D277Y", "ERBB2 D769H", "ERBB2 D769N", "ERBB2 D769Y",
"ERBB2 G660=", "ERBB2 G660D", "ERBB2 G660R", "ERBB2 G776S", "ERBB2 G776V",
"ERBB2 G778_P780dup", "ERBB2 I767M", "ERBB2 L755=", "ERBB2 L755A",
"ERBB2 L755M", "ERBB2 L755P", "ERBB2 L755S", "ERBB2 L755W", "ERBB2 L869R",
"ERBB2 M774dup", "ERBB2 R103Q", "ERBB2 R138Q", "ERBB2 R138W",
"ERBB2 R678Q", "ERBB2 R678W", "ERBB2 S310=", "ERBB2 S310F", "ERBB2 S310Y",
"ERBB2 T733I", "ERBB2 T862A", "ERBB2 V659=", "ERBB2 V659D", "ERBB2 V659E",
"ERBB2 V697L", "ERBB2 V777L", "ERBB2 V777M", "ERBB2 V842I", "ERBB2 Y772_A775dup",
"ERBB3 A232T", "ERBB3 A232V", "ERBB3 D297A", "ERBB3 D297H", "ERBB3 D297N",
"ERBB3 D297V", "ERBB3 D297Y", "ERBB3 E332K", "ERBB3 E332Q", "ERBB3 E928G",
"ERBB3 E928K", "ERBB3 F219C", "ERBB3 F219L", "ERBB3 G284R", "ERBB3 H228Q",
"ERBB3 H228R", "ERBB3 K329E", "ERBB3 K329R", "ERBB3 K329T", "ERBB3 M60K",
"ERBB3 M60R", "ERBB3 M91I", "ERBB3 N126I", "ERBB3 N126K", "ERBB3 R103=",
"ERBB3 R103G", "ERBB3 R103H", "ERBB3 R475W", "ERBB3 S846I", "ERBB3 T355A",
"ERBB3 T355I", "ERBB3 T355P", "ERBB3 V104L", "ERBB3 V104M", "ERBB4 F1102=",
"ERBB4 F1102C", "ERBB4 K1002R", "ERBB4 K1002T", "ERBB4 K1223M",
"ERBB4 K1223R", "ERBB4 K1223T", "ERBB4 L798=", "ERBB4 L798H",
"ERBB4 L798P", "ERBB4 L798R", "ERBB4 Q707=", "ERBB4 Q707E", "ERBB4 S1289A",
"ERBB4 S774G", "ERBB4 S774N", "ERBB4 S774R", "ERCC2 D609E", "ERCC2 D609G",
"ERCC2 E606G", "ERCC2 E606Q", "ERCC2 N238S", "ERCC2 P463L", "ERCC2 P463Q",
"ERCC2 P463S", "ERCC2 S246=", "ERCC2 S246F", "ERCC2 S246Y", "ERCC2 T484A",
"ERCC2 T484M", "ERCC2 Y14C", "ERCC2 Y24C", "ERCC2 Y72C", "ERCC3 L713=",
"ERG R354=", "ERRFI1 K116*", "ERRFI1 K409N", "ERRFI1 K409Q",
"ESR1 D538G", "ESR1 E380Q", "ESR1 L536=", "ESR1 L536H", "ESR1 L536P",
"ESR1 L536Q", "ESR1 L536R", "ESR1 V422del", "ESR1 Y537C", "ESR1 Y537D",
"ESR1 Y537N", "ESR1 Y537S", "ETV6 R369=", "ETV6 R369L", "ETV6 R369Q",
"ETV6 R369W", "ETV6 S284=", "ETV6 S284F", "ETV6 X11_splice",
"EYA4 L152H", "EYA4 L152I", "EYA4 L152P", "EYA4 L152R", "EYA4 L152V",
"EZH2 K515R", "EZH2 K665E", "EZH2 K665R", "EZH2 Y646=", "EZH2 Y646C",
"EZH2 Y646F", "EZH2 Y646H", "EZH2 Y646N", "EZH2 Y646S", "FAM46D S69G",
"FAM46D S69R", "FAM58A X141_splice", "FAT1 R1627*", "FAT1 R1627Q",
"FBXW7 D520G", "FBXW7 D520H", "FBXW7 D520N", "FBXW7 D520V", "FBXW7 D520Y",
"FBXW7 E287D", "FBXW7 E287K", "FBXW7 E287Q", "FBXW7 E287V", "FBXW7 G423*",
"FBXW7 G423A", "FBXW7 G423V", "FBXW7 G437*", "FBXW7 G437=", "FBXW7 G437E",
"FBXW7 G437V", "FBXW7 R14*", "FBXW7 R14Q", "FBXW7 R224*", "FBXW7 R224Q",
"FBXW7 R278*", "FBXW7 R367*", "FBXW7 R367P", "FBXW7 R393*", "FBXW7 R393Q",
"FBXW7 R441G", "FBXW7 R441L", "FBXW7 R441Q", "FBXW7 R441W", "FBXW7 R465C",
"FBXW7 R465G", "FBXW7 R465H", "FBXW7 R465L", "FBXW7 R465P", "FBXW7 R465S",
"FBXW7 R479*", "FBXW7 R479=", "FBXW7 R479G", "FBXW7 R479L", "FBXW7 R479P",
"FBXW7 R479Q", "FBXW7 R505C", "FBXW7 R505G", "FBXW7 R505H", "FBXW7 R505L",
"FBXW7 R505P", "FBXW7 R505S", "FBXW7 R658*", "FBXW7 R658=", "FBXW7 R658Q",
"FBXW7 R689Q", "FBXW7 R689W", "FBXW7 S546*", "FBXW7 S546L", "FBXW7 S546P",
"FBXW7 S582=", "FBXW7 S582L", "FBXW7 S582P", "FBXW7 T385I", "FBXW7 T385K",
"FBXW7 T385P", "FBXW7 T532I", "FBXW7 T532P", "FBXW7 X195_splice",
"FBXW7 Y545*", "FBXW7 Y545C", "FGFR1 K687*", "FGFR1 K687=", "FGFR1 K687E",
"FGFR1 K687N", "FGFR1 N577D", "FGFR1 N577K", "FGFR2 C382R", "FGFR2 C382Y",
"FGFR2 F276C", "FGFR2 F276I", "FGFR2 N549H", "FGFR2 N549K", "FGFR2 N549S",
"FGFR2 N549T", "FGFR2 P253L", "FGFR2 P253R", "FGFR2 R203C", "FGFR2 R203H",
"FGFR2 S252=", "FGFR2 S252L", "FGFR2 S252W", "FGFR2 Y375C", "FGFR3 G370C",
"FGFR3 G380R", "FGFR3 K650E", "FGFR3 K650M", "FGFR3 K650N", "FGFR3 K650T",
"FGFR3 L8=", "FGFR3 R248C", "FGFR3 S249C", "FGFR3 S371C", "FGFR3 Y373C",
"FGFR4 N535K", "FGFR4 V550L", "FGFR4 V550M", "FH M336I", "FH M336L",
"FLT3 D586_E596dup", "FLT3 D593_F594insSPEDNEYFYVD", "FLT3 D835E",
"FLT3 D835H", "FLT3 D835V", "FLT3 D835Y", "FLT3 E598_F612dup",
"FLT3 E598_Y599insSGSSDNEYFYVDFREYE", "FLT3 E598_Y599insVAYVDFREYE",
"FLT3 E604_F605insSPRGGNEYFYVDFREYEYDLKWE", "FLT3 F594_D600dup",
"FLT3 F594_R595insGTGSSDNEYFYVDF", "FLT3 F612_G613insQGFYVDFREYEYDLKWEFPRENLEF",
"FLT3 L601_K602insNVDFREYEYDL", "FLT3 M578_E598dup", "FLT3 N587_D600dup",
"FLT3 R595_E596insDYVDFR", "FLT3 R595_L601dup", "FLT3 S584_D600dup",
"FLT3 S584_F605dup", "FLT3 S585_F594dup", "FLT3 Y597_E598insAGSSDNEYFYVDFREY",
"FLT3 Y597_E598insDEYFYVDFREY", "FLT3 Y597_K602dup", "FLT3 Y599_D600insEYEYEYEY",
"FLT3 Y599_D600insPAPQIMSTSTLISENMNIA", "FLT3 Y599_E604dup",
"FOXA1 A323_P326del", "FOXA1 C258_R261del", "FOXA1 D226G", "FOXA1 D226N",
"FOXA1 D249_F254del", "FOXA1 D249_N252del", "FOXA1 E255_N256del",
"FOXA1 F254_E255del", "FOXA1 F254_G257delinsC", "FOXA1 F254_L260del",
"FOXA1 F254_N256delinsY", "FOXA1 F266=", "FOXA1 F266C", "FOXA1 F266I",
"FOXA1 F266L", "FOXA1 F266S", "FOXA1 F266V", "FOXA1 G251_F254del",
"FOXA1 G251_G257del", "FOXA1 G284_G290del", "FOXA1 H247L", "FOXA1 H247Q",
"FOXA1 H247R", "FOXA1 H247Y", "FOXA1 I176M", "FOXA1 I176V", "FOXA1 K264_K267del",
"FOXA1 K264dup", "FOXA1 K267dup", "FOXA1 M253_N256del", "FOXA1 M253_Y259del",
"FOXA1 M253K", "FOXA1 M253R", "FOXA1 M253T", "FOXA1 N252_C258del",
"FOXA1 N252_G257del", "FOXA1 N252_S408del", "FOXA1 N397_F400del",
"FOXA1 Q263_C268del", "FOXA1 Q263_D296delinsH", "FOXA1 Q263_G281del",
"FOXA1 Q263del", "FOXA1 R219=", "FOXA1 R219C", "FOXA1 R219G",
"FOXA1 R219S", "FOXA1 R261C", "FOXA1 R261G", "FOXA1 R261H", "FOXA1 R261S",
"FOXA1 R265_K270del", "FOXA1 S242F", "FOXA1 S242Y", "FOXA1 S250_F254del",
"FOXA1 S250_N252del", "FOXA1 S250_Y259del", "FOXA1 S250F", "FOXA1 S250Y",
"FOXA1 S282_G283dup", "FOXA1 S409del", "FOXA1 Y259C", "FOXA1 Y259F",
"FOXA1 Y259S", "FOXL2 C134W", "FOXL2 E118K", "FOXL2 E118Q", "FOXO1 S205=",
"FOXO1 S205N", "FOXO1 S22=", "FOXO1 S22P", "FOXO1 S22W", "FOXO1 T24I",
"FOXO1 T24M", "FOXP1 R514C", "FOXP1 R514H", "FOXP1 S448=", "FOXP1 S448L",
"FOXP1 X511_splice", "FRMD4B P368F", "FRMD4B P368L", "FRMD4B P368S",
"FRMD6 S17=", "FRMD6 S17C", "FRMD6 S17I", "FUBP1 R430C", "FUBP1 R430H",
"FZD10 S22R", "GATA2 C352*", "GATA2 C352=", "GATA2 C352F", "GATA2 C352R",
"GATA3 M293K", "GATA3 M293R", "GATA3 R364G", "GATA3 R364S", "GATA3 R364T",
"GATA3 R366*", "GATA3 R366Q", "GLI1 R380*", "GLI1 R380=", "GLI1 R380Q",
"GNA11 Q209H", "GNA11 Q209L", "GNA11 Q209P", "GNA11 R183=", "GNA11 R183C",
"GNA11 R183H", "GNAQ G48*", "GNAQ G48L", "GNAQ G48V", "GNAQ Q209H",
"GNAQ Q209L", "GNAQ Q209P", "GNAQ R183*", "GNAQ R183Q", "GNAS Q227H",
"GNAS Q227K", "GNAS Q227L", "GNAS R160C", "GNAS R160H", "GNAS R160P",
"GNAS R201C", "GNAS R201H", "GNAS R201L", "GNAS R201S", "GPS2 X242_splice",
"GSK3B X239_splice", "GTF2I F641C", "GTF2I L424H", "GTF2I N440S",
"H3F3A G35R", "H3F3A G35V", "H3F3A G35W", "H3F3A K28M", "H3F3A K28R",
"HGF G229A", "HGF G229D", "HIST1H1C A180=", "HIST1H1C A180P",
"HIST1H1C E115K", "HIST1H1C K23del", "HIST1H3B E106=", "HIST1H3B E106K",
"HIST1H3B E106Q", "HIST1H3B E51=", "HIST1H3B E51D", "HIST1H3B E51K",
"HIST1H3B E51Q", "HIST1H3B K28E", "HIST1H3B K28M", "HIST1H3C K37=",
"HIST1H3C K37M", "HIST1H3H K37E", "HIST1H3H K37M", "HNF1A G338=",
"HNF1A G338A", "HNF1A R114C", "HNF1A R114H", "HNF1A R114L", "HNF1A S591=",
"HNF1A S591Y", "HNMT L145=", "HOOK2 S630=", "HOOK2 S630A", "HOOK2 S630F",
"HOXB2 P335=", "HRAS G12A", "HRAS G12C", "HRAS G12D", "HRAS G12N",
"HRAS G12S", "HRAS G12V", "HRAS G13C", "HRAS G13D", "HRAS G13I",
"HRAS G13N", "HRAS G13R", "HRAS G13S", "HRAS G13V", "HRAS K117N",
"HRAS K117R", "HRAS Q61H", "HRAS Q61K", "HRAS Q61L", "HRAS Q61R",
"HSD11B1 G45=", "HSD11B1 G45E", "HSD11B1 G45R", "HSD11B1 G45V",
"HSD11B1 G45W", "IDH1 R132C", "IDH1 R132G", "IDH1 R132H", "IDH1 R132I",
"IDH1 R132L", "IDH1 R132S", "IDH2 R140L", "IDH2 R140Q", "IDH2 R140W",
"IDH2 R172=", "IDH2 R172G", "IDH2 R172K", "IDH2 R172M", "IDH2 R172S",
"IDH2 R172T", "IDH2 R172W", "IGF1R G129=", "IGF1R G129A", "IGF1R G129R",
"IKZF1 E304K", "IKZF1 E304Q", "IL7R I241F", "IL7R I241L", "IL7R I241M",
"IL7R I241V", "IL7R K395=", "IL7R K395M", "IL7R K395N", "IL7R K395R",
"IL7R K395T", "IL7R R206*", "IL7R R206Q", "ING1 R339*", "INMT S212=",
"INMT S212F", "INPPL1 R70H", "INTS12 M1?", "IRF4 C99=", "IRF4 C99R",
"IRF4 C99Y", "IRF4 K123R", "IRF4 Y428*", "IRF4 Y428H", "JAK1 L910=",
"JAK1 L910P", "JAK1 L910S", "JUN E112K", "JUN E112Q", "KAT8 R98Q",
"KAT8 R98W", "KCNH5 T147=", "KCNJ12 E430*", "KCNJ8 G417D", "KCNJ8 G417E",
"KCNJ8 G417R", "KCNQ5 G273E", "KCNQ5 G273R", "KDM6A G526*", "KDM6A G526=",
"KDM6A G526E", "KDM6A G526V", "KDM6A Q1003*", "KDM6A Q1003P",
"KDM6A Q555*", "KDM6A X1246_splice", "KDM6A X129_splice", "KDM6A X1293_splice",
"KDM6A X1336_splice", "KDM6A X76_splice", "KDR C482*", "KDR R1032*",
"KDR R1032Q", "KDR S1037=", "KDR S1037L", "KDR S1037T", "KEAP1 G333C",
"KEAP1 G333F", "KEAP1 G333S", "KEAP1 G417E", "KEAP1 G417R", "KEAP1 G417V",
"KEAP1 G417W", "KEAP1 G480=", "KEAP1 G480V", "KEAP1 G480W", "KEAP1 M110I",
"KEAP1 M110V", "KEAP1 R260*", "KEAP1 R260L", "KEAP1 R260Q", "KEAP1 R272C",
"KEAP1 R272H", "KEAP1 R272L", "KEAP1 R272P", "KEAP1 R320L", "KEAP1 R320M",
"KEAP1 R320P", "KEAP1 R320Q", "KEAP1 R320W", "KEAP1 R470C", "KEAP1 R470H",
"KEAP1 R470S", "KEAP1 R601L", "KEAP1 R601W", "KEAP1 V155A", "KEAP1 V155F",
"KIAA0020 K63R", "KIF26B R2024C", "KIF26B R2024H", "KIF26B R2024S",
"KIT A502_Y503dup", "KIT D579del", "KIT D816A", "KIT D816H",
"KIT D816V", "KIT D816Y", "KIT D820A", "KIT D820E", "KIT D820G",
"KIT D820V", "KIT D820Y", "KIT G565_T574delinsA", "KIT K550_P551del",
"KIT K558_V560del", "KIT K558_V560delinsN", "KIT K642E", "KIT K642N",
"KIT K642Q", "KIT L576_H580dup", "KIT L576del", "KIT L576P",
"KIT M552_E554delinsI", "KIT M552_V555del", "KIT M552_V555delinsI",
"KIT M552_W557del", "KIT M552_Y570del", "KIT N566_P573del", "KIT N822I",
"KIT N822K", "KIT N822Y", "KIT P551_M552delinsL", "KIT P551_V555del",
"KIT P551_Y553delinsH", "KIT Q556_D572del", "KIT Q556_V560delinsH",
"KIT Q575del", "KIT R888=", "KIT R888Q", "KIT R888W", "KIT T574_H580dup",
"KIT V559_E561del", "KIT V559_G565del", "KIT V559_N566delinsD",
"KIT V559_P573del", "KIT V559A", "KIT V559D", "KIT V559G", "KIT V560=",
"KIT V560A", "KIT V560D", "KIT V560del", "KIT V560G", "KIT V654A",
"KIT W557_E561del", "KIT W557_K558del", "KIT W557_V559delinsF",
"KIT W557C", "KIT W557G", "KIT W557R", "KIT W557S", "KIT Y553_E554del",
"KIT Y570_L576del", "KIT Y578_D579insEQQLPY", "KIT Y823C", "KIT Y823D",
"KLF4 K409N", "KLF4 K409Q", "KLF5 E419K", "KLF5 E419Q", "KMT2A R1264*",
"KMT2C R4549C", "KMT2C R4549H", "KMT2C R4549S", "KMT2C R56*",
"KMT2C R56Q", "KMT2D L1375=", "KMT2D L1375I", "KMT2D R1903*",
"KMT2D R1903=", "KMT2D R2685*", "KMT2D R2685=", "KMT2D R5179C",
"KMT2D R5179H", "KMT2D R5179L", "KMT2D R5179P", "KMT2D R5432=",
"KMT2D R5432Q", "KMT2D R5432W", "KNSTRN C22S", "KNSTRN C22Y",
"KNSTRN P28L", "KNSTRN P28S", "KNSTRN S24F", "KNSTRN V12=", "KNSTRN V12G",
"KRAS A11=", "KRAS A11T", "KRAS A146P", "KRAS A146T", "KRAS A146V",
"KRAS A59=", "KRAS A59E", "KRAS A59G", "KRAS A59T", "KRAS D33E",
"KRAS G12=", "KRAS G12A", "KRAS G12C", "KRAS G12D", "KRAS G12F",
"KRAS G12I", "KRAS G12L", "KRAS G12R", "KRAS G12S", "KRAS G12V",
"KRAS G13=", "KRAS G13A", "KRAS G13C", "KRAS G13D", "KRAS G13E",
"KRAS G13R", "KRAS G13V", "KRAS G60=", "KRAS G60D", "KRAS G60S",
"KRAS G60V", "KRAS K117N", "KRAS K117R", "KRAS K5E", "KRAS L19F",
"KRAS Q22H", "KRAS Q22K", "KRAS Q61A", "KRAS Q61E", "KRAS Q61H",
"KRAS Q61K", "KRAS Q61L", "KRAS Q61P", "KRAS Q61R", "LAMC1 P641=",
"LAMC1 P641L", "LATS2 P479_A480insPP", "LCE1A K28M", "LCE1A K28R",
"LCE1A K28T", "LCE1F P27=", "LCE1F P27L", "LCE1F P27Q", "LRP1 P1058L",
"LRP1 P1058T", "LRP5 S1609=", "LRP5 S1609P", "LRRC71 K324=",
"LSM14A R272C", "LSM14A R272H", "LST3 R709=", "LST3 R709K", "LST3 R709T",
"LTN1 S19F", "LTN1 S19Y", "LYN I364L", "LYN I364N", "MAGEC1 K1046N",
"MAGI2 L603P", "MAGI2 L603R", "MAGOH I137T", "MAP2K1 C121=",
"MAP2K1 C121S", "MAP2K1 E102_I103del", "MAP2K1 E203K", "MAP2K1 E203V",
"MAP2K1 F53C", "MAP2K1 F53I", "MAP2K1 F53L", "MAP2K1 F53V", "MAP2K1 G128D",
"MAP2K1 G128R", "MAP2K1 G128V", "MAP2K1 I103_K104del", "MAP2K1 I99_K104del",
"MAP2K1 K57E", "MAP2K1 K57N", "MAP2K1 K57T", "MAP2K1 N122D",
"MAP2K1 P105_A106del", "MAP2K1 P105_I107delinsL", "MAP2K1 P124=",
"MAP2K1 P124L", "MAP2K1 P124M", "MAP2K1 P124Q", "MAP2K1 P124R",
"MAP2K1 P124S", "MAP2K1 Q56P", "MAP2K1 T386=", "MAP2K1 Y130C",
"MAP2K1 Y130H", "MAP2K1 Y130N", "MAP2K2 F57L", "MAP2K2 F57V",
"MAP2K4 R110*", "MAP2K4 R110L", "MAP2K4 R110P", "MAP2K4 R110Q",
"MAP2K4 R134L", "MAP2K4 R134Q", "MAP2K4 R134W", "MAP2K4 S184=",
"MAP2K4 S184L", "MAP2K4 S184W", "MAP2K4 X297_splice", "MAP2K4 X347_splice",
"MAP3K1 L380S", "MAP3K1 S1330L", "MAP3K1 S1330W", "MAP3K13 X502_splice",
"MAPK1 E322*", "MAPK1 E322A", "MAPK1 E322K", "MAPK7 A501D", "MARCH10 G241=",
"MARCH10 G241E", "MARCH10 G241R", "MAX H28R", "MAX R36W", "MAX R60=",
"MAX R60Q", "MAX R60W", "MDC1 I1020_R1028del", "MDC1 K1025del",
"MED12 G44_F45del", "MED12 G44A", "MED12 G44C", "MED12 G44D",
"MED12 G44S", "MED12 G44V", "MED12 K42_N46del", "MED12 L1224F",
"MED12 L1224V", "MED12 N46_S52del", "MED12 P49_E55del", "MED12 V1223L",
"MED12 V41_S52del", "MED28 G7C", "MEF2A P99S", "MEF2B K4E", "MET D1010H",
"MET D1010N", "MET D1010Y", "MET F1200I", "MET F1200V", "MET H1094R",
"MET H1094Y", "MET M1250T", "MET T222=", "MET V1070A", "MET V1070E",
"MET V1070R", "MET X1010_splice", "MET Y1003*", "MET Y1003C",
"MET Y1003F", "MET Y1230C", "MET Y1230H", "MET Y1230S", "METTL14 R298H",
"METTL14 R298P", "MGA R1242*", "MSH2 E580*", "MTOR A1459_D1468del",
"MTOR A1459D", "MTOR A1459P", "MTOR A1459V", "MTOR A1971P", "MTOR A1971S",
"MTOR A1971T", "MTOR C1483F", "MTOR C1483R", "MTOR C1483W", "MTOR C1483Y",
"MTOR E1455_D1458dup", "MTOR E1455_E1457dup", "MTOR E1799K",
"MTOR F1888I", "MTOR F1888L", "MTOR F1888V", "MTOR I2500F", "MTOR I2500M",
"MTOR I2500N", "MTOR L1460P", "MTOR L2427Q", "MTOR L2427R", "MTOR M2327I",
"MTOR M2327V", "MTOR S2215F", "MTOR S2215T", "MTOR S2215Y", "MTOR T1977I",
"MTOR T1977K", "MTOR T1977R", "MTOR T1977S", "MTOR V2006=", "MTOR V2006F",
"MTOR V2006I", "MTOR V2006L", "MTOR W1456_L1460delinsC", "MTOR Y1450_W1456del",
"MXRA5 G792=", "MYC P74L", "MYC P74Q", "MYC P74R", "MYC P74S",
"MYC P74T", "MYC S161L", "MYC S298del", "MYC T73I", "MYC V7M",
"MYCN P44F", "MYCN P44L", "MYD88 L265P", "MYD88 M232T", "MYD88 P166=",
"MYD88 P166L", "MYD88 S243N", "MYO18A G979=", "MYO18A G979A",
"MYO18B P1018=", "MYO18B P1018L", "MYO18B P1018S", "MYO18B P1018T",
"MYO9A P1300=", "MYO9A P1300L", "MYO9A P1300S", "MYOD1 L122=",
"MYOD1 L122M", "MYOD1 L122R", "MYT1L K203R", "MYT1L K203T", "NAP1L3 K502=",
"NAP1L3 K502M", "NAP1L3 K502N", "NAP1L3 K502R", "NAP1L3 K502T",
"NCOA3 R80C", "NCOA3 R80H", "NCR1 E42=", "NCR1 E42G", "NCR1 E42K",
"NF1 R1241*", "NF1 R1870Q", "NF1 R1870W", "NF1 R2450*", "NF1 R2450Q",
"NF1 R440*", "NF1 R440Q", "NF1 R461*", "NF1 R461Q", "NFE2L2 D21_I22delinsE",
"NFE2L2 D27del", "NFE2L2 D29G", "NFE2L2 D29H", "NFE2L2 D29N",
"NFE2L2 D29Y", "NFE2L2 D77G", "NFE2L2 D77H", "NFE2L2 D77V", "NFE2L2 D77Y",
"NFE2L2 E35_R42del", "NFE2L2 E79*", "NFE2L2 E79D", "NFE2L2 E79del",
"NFE2L2 E79G", "NFE2L2 E79K", "NFE2L2 E79Q", "NFE2L2 E79V", "NFE2L2 E82A",
"NFE2L2 E82D", "NFE2L2 E82G", "NFE2L2 E82Q", "NFE2L2 F37del",
"NFE2L2 G31A", "NFE2L2 G31del", "NFE2L2 G31E", "NFE2L2 G31R",
"NFE2L2 G31V", "NFE2L2 G81A", "NFE2L2 G81C", "NFE2L2 G81D", "NFE2L2 G81R",
"NFE2L2 G81S", "NFE2L2 G81V", "NFE2L2 I22_D29del", "NFE2L2 I28dup",
"NFE2L2 I28T", "NFE2L2 L30_S33del", "NFE2L2 L30F", "NFE2L2 L30H",
"NFE2L2 L30P", "NFE2L2 L30R", "NFE2L2 L74_Q87del", "NFE2L2 L76_E82del",
"NFE2L2 Q26H", "NFE2L2 Q26K", "NFE2L2 Q26L", "NFE2L2 Q26P", "NFE2L2 Q26R",
"NFE2L2 Q73_T80del", "NFE2L2 R34_F37delinsL", "NFE2L2 R34_S40del",
"NFE2L2 R34*", "NFE2L2 R34G", "NFE2L2 R34L", "NFE2L2 R34P", "NFE2L2 R34Q",
"NFE2L2 S33_R34del", "NFE2L2 T80A", "NFE2L2 T80I", "NFE2L2 T80K",
"NFE2L2 T80P", "NFE2L2 T80R", "NFE2L2 W24_D29delinsY", "NFE2L2 W24C",
"NFE2L2 W24R", "NFE2L2 W24S", "NFIC S339P", "NOL4 L423=", "NOL4 L423M",
"NOL4 L423V", "NOTCH1 C359del", "NOTCH1 C440F", "NOTCH1 C440R",
"NOTCH1 C440S", "NOTCH1 C440W", "NOTCH1 D338del", "NOTCH1 E455=",
"NOTCH1 E455K", "NOTCH1 F357del", "NOTCH1 F853C", "NOTCH1 F853I",
"NOTCH1 G310E", "NOTCH1 G310R", "NOTCH1 I471T", "NOTCH1 R365C",
"NOTCH1 R365S", "NOTCH1 S356del", "NOTCH1 Y358del", "NOTCH2 R2400*",
"NOTCH2 T235S", "NPAS1 F159=", "NPAS1 F159L", "NRAS G12A", "NRAS G12C",
"NRAS G12D", "NRAS G12R", "NRAS G12S", "NRAS G12V", "NRAS G13C",
"NRAS G13D", "NRAS G13F", "NRAS G13R", "NRAS G13S", "NRAS G13V",
"NRAS G60=", "NRAS G60E", "NRAS G60V", "NRAS Q61*", "NRAS Q61H",
"NRAS Q61K", "NRAS Q61L", "NRAS Q61P", "NRAS Q61R", "NSD1 C1710*",
"NSD1 C1710S", "NSD1 C1710Y", "NSD1 F392=", "NUP93 E14G", "NUP93 E14K",
"NUP93 Q15*", "NUP93 Q15K", "OBP2B S133P", "OXA1L L57F", "PACS2 Q87=",
"PACS2 Q87H", "PAK7 M173I", "PARP1 G500=", "PASD1 M338I", "PAX5 V26G",
"PBRM1 R1160*", "PBRM1 R1160P", "PBRM1 R1160Q", "PBRM1 R710*",
"PBRM1 R710G", "PBRM1 R921*", "PBRM1 X856_splice", "PCBP1 L102P",
"PCBP1 L102Q", "PCBP1 L102R", "PCED1B S343F", "PCED1B S343P",
"PCED1B S343Y", "PCMTD1 P342L", "PCSK5 W924*", "PCSK5 W924L",
"PDGFRA C235R", "PDGFRA C235S", "PDGFRA C235Y", "PDGFRA D842=",
"PDGFRA D842H", "PDGFRA D842I", "PDGFRA D842V", "PDGFRA E229*",
"PDGFRA E229K", "PDGFRA E229V", "PDGFRA N659K", "PDGFRA N659S",
"PDGFRA N659Y", "PDHA1 G145D", "PDPK1 P499L", "PDPK1 P499S",
"PGR R836*", "PGR R836Q", "PIK3CA C378F", "PIK3CA C378R", "PIK3CA C378Y",
"PIK3CA C420G", "PIK3CA C420R", "PIK3CA C604R", "PIK3CA C901F",
"PIK3CA C90G", "PIK3CA C90R", "PIK3CA C90S", "PIK3CA C90Y", "PIK3CA D350G",
"PIK3CA D350N", "PIK3CA D350V", "PIK3CA D939G", "PIK3CA E110_K111dup",
"PIK3CA E110del", "PIK3CA E365K", "PIK3CA E365V", "PIK3CA E39G",
"PIK3CA E39K", "PIK3CA E453_D454del", "PIK3CA E453_P466del",
"PIK3CA E453_T462del", "PIK3CA E453D", "PIK3CA E453del", "PIK3CA E453K",
"PIK3CA E453Q", "PIK3CA E542A", "PIK3CA E542G", "PIK3CA E542K",
"PIK3CA E542Q", "PIK3CA E542V", "PIK3CA E545A", "PIK3CA E545D",
"PIK3CA E545G", "PIK3CA E545K", "PIK3CA E545Q", "PIK3CA E726A",
"PIK3CA E726K", "PIK3CA E81*", "PIK3CA E81K", "PIK3CA E970K",
"PIK3CA G1007D", "PIK3CA G1007R", "PIK3CA G1049A", "PIK3CA G1049R",
"PIK3CA G106_N107del", "PIK3CA G106_R108del", "PIK3CA G106C",
"PIK3CA G106R", "PIK3CA G106S", "PIK3CA G106V", "PIK3CA G118D",
"PIK3CA G364A", "PIK3CA G364R", "PIK3CA G451_D454del", "PIK3CA G463_N465delinsD",
"PIK3CA H1047L", "PIK3CA H1047Q", "PIK3CA H1047R", "PIK3CA H1047Y",
"PIK3CA H1065L", "PIK3CA H1065Y", "PIK3CA H419_C420del", "PIK3CA H419_L422del",
"PIK3CA H450_L455del", "PIK3CA I102_E103delinsK", "PIK3CA I102del",
"PIK3CA I112_L113del", "PIK3CA K111_I112del", "PIK3CA K111del",
"PIK3CA K111E", "PIK3CA K111N", "PIK3CA K111Q", "PIK3CA K111R",
"PIK3CA L10_M16del", "PIK3CA L113del", "PIK3CA L436_P449dup",
"PIK3CA L452_G460del", "PIK3CA L452_P458del", "PIK3CA L455_G460delinsF",
"PIK3CA M1004I", "PIK3CA M1004V", "PIK3CA M1043I", "PIK3CA M1043L",
"PIK3CA M1043T", "PIK3CA M1043V", "PIK3CA N1044K", "PIK3CA N1044Y",
"PIK3CA N107=", "PIK3CA N107I", "PIK3CA N107S", "PIK3CA N114del",
"PIK3CA N345=", "PIK3CA N345D", "PIK3CA N345H", "PIK3CA N345I",
"PIK3CA N345K", "PIK3CA N345T", "PIK3CA N345Y", "PIK3CA P104_V105del",
"PIK3CA P104L", "PIK3CA P104R", "PIK3CA P447_L455del", "PIK3CA P449_L452del",
"PIK3CA P449_L456del", "PIK3CA P471A", "PIK3CA P471L", "PIK3CA P539R",
"PIK3CA Q546E", "PIK3CA Q546H", "PIK3CA Q546K", "PIK3CA Q546L",
"PIK3CA Q546P", "PIK3CA Q546R", "PIK3CA R108del", "PIK3CA R108H",
"PIK3CA R108L", "PIK3CA R108S", "PIK3CA R115L", "PIK3CA R115P",
"PIK3CA R115Q", "PIK3CA R357*", "PIK3CA R357G", "PIK3CA R357L",
"PIK3CA R357Q", "PIK3CA R38C", "PIK3CA R38G", "PIK3CA R38H",
"PIK3CA R38L", "PIK3CA R38S", "PIK3CA R88Q", "PIK3CA R93L", "PIK3CA R93Q",
"PIK3CA R93W", "PIK3CA T1025A", "PIK3CA T1025S", "PIK3CA T1052K",
"PIK3CA V344A", "PIK3CA V344G", "PIK3CA V344M", "PIK3CA W11_H14delinsY",
"PIK3CA W11_P18del", "PIK3CA Y1021C", "PIK3CA Y1021H", "PIK3CB D1067A",
"PIK3CB D1067H", "PIK3CB D1067V", "PIK3CB D1067Y", "PIK3CB E1051G",
"PIK3CB E1051K", "PIK3CB R321Q", "PIK3CD C416R", "PIK3CD E1021K",
"PIK3CD R894=", "PIK3CD R894Q", "PIK3R1 D440_E451del", "PIK3R1 D440_K448del",
"PIK3R1 D440del", "PIK3R1 D464_E468dup", "PIK3R1 D464_Y467del",
"PIK3R1 D464_Y470dup", "PIK3R1 D560G", "PIK3R1 D560H", "PIK3R1 D560N",
"PIK3R1 D560Y", "PIK3R1 D569_L570delinsV", "PIK3R1 D569_L581delinsE",
"PIK3R1 D569dup", "PIK3R1 D578_M582delinsE", "PIK3R1 E403_L404del",
"PIK3R1 E403_L404delinsV", "PIK3R1 E439del", "PIK3R1 E451_Y452del",
"PIK3R1 E451del", "PIK3R1 E458_K459del", "PIK3R1 E458_Y463dup",
"PIK3R1 E458del", "PIK3R1 E462_R465del", "PIK3R1 E462_Y463delinsD",
"PIK3R1 E462dup", "PIK3R1 E468_E469insGEYDRLYE", "PIK3R1 E468_E469insGLYE",
"PIK3R1 E468_Y470dup", "PIK3R1 E558_K561del", "PIK3R1 E558_R562del",
"PIK3R1 F456_K459del", "PIK3R1 F456_Q457del", "PIK3R1 G376R",
"PIK3R1 G446_E451del", "PIK3R1 G446_L449delinsV", "PIK3R1 H450_E451del",
"PIK3R1 H450_E451dup", "PIK3R1 H450_E451insD", "PIK3R1 H450_E451insVH",
"PIK3R1 H450_K459del", "PIK3R1 H450_Q455dup", "PIK3R1 H450_T454del",
"PIK3R1 H450del", "PIK3R1 I405_L420del", "PIK3R1 I405del", "PIK3R1 I442_E443delinsK",
"PIK3R1 I442_N453del", "PIK3R1 I566_P568delinsT", "PIK3R1 I571_K575del",
"PIK3R1 I571_L581del", "PIK3R1 I571_Q572insR", "PIK3R1 I571_R574del",
"PIK3R1 K379del", "PIK3R1 K379E", "PIK3R1 K379N", "PIK3R1 K448_N453del",
"PIK3R1 K448_Y452del", "PIK3R1 K459del", "PIK3R1 K567_I571del",
"PIK3R1 K567_L570del", "PIK3R1 K567del", "PIK3R1 K567E", "PIK3R1 K575_L581delinsM",
"PIK3R1 K575_R577del", "PIK3R1 K575_R577dup", "PIK3R1 K575_T576del",
"PIK3R1 L380del", "PIK3R1 L449_H450insQ", "PIK3R1 L449_K459del",
"PIK3R1 L449_Q455del", "PIK3R1 L449del", "PIK3R1 L466_E469del",
"PIK3R1 L466_Y470delinsF", "PIK3R1 L466del", "PIK3R1 L570_D578del",
"PIK3R1 L570_I571insY", "PIK3R1 L573_K575del", "PIK3R1 L573_R574del",
"PIK3R1 L573del", "PIK3R1 M563_L570delinsI", "PIK3R1 M563_N564delinsI",
"PIK3R1 N378del", "PIK3R1 N441_T454del", "PIK3R1 N453_D464dup",
"PIK3R1 N453_Q455delinsK", "PIK3R1 N453_Q457del", "PIK3R1 N453_Y463del",
"PIK3R1 N453del", "PIK3R1 N564_P568delinsT", "PIK3R1 N564D",
"PIK3R1 P568_L573del", "PIK3R1 Q455_F456insL", "PIK3R1 Q455_K459del",
"PIK3R1 Q455_S460dup", "PIK3R1 Q457_E462del", "PIK3R1 Q457_S460del",
"PIK3R1 Q579_Y580delinsH", "PIK3R1 R348*", "PIK3R1 R461_E462delinsQ",
"PIK3R1 R465_Y467del", "PIK3R1 R465dup", "PIK3R1 R574del", "PIK3R1 R577_D578del",
"PIK3R1 R577_L581del", "PIK3R1 R577del", "PIK3R1 S399_L404del",
"PIK3R1 S460_D464del", "PIK3R1 T397_V401del", "PIK3R1 T576del",
"PIK3R1 V401_H407del", "PIK3R1 V401_N406del", "PIK3R1 V402_L413del",
"PIK3R1 X434_splice", "PIK3R1 X475_splice", "PIK3R1 X582_splice",
"PIK3R1 Y452_N453insF", "PIK3R1 Y452_Q457del", "PIK3R1 Y452C",
"PIK3R1 Y452dup", "PIK3R1 Y452H", "PIK3R1 Y452N", "PIK3R1 Y463_E468dup",
"PIK3R1 Y467_Y470del", "PIK3R1 Y580_L581insF", "PIK3R2 D557G",
"PIK3R2 D557H", "PIK3R2 D557N", "PIK3R2 D557Y", "PIK3R2 G373R",
"PIM1 E79=", "PIM1 E79D", "PIM1 G28A", "PIM1 G28D", "PIM1 G28V",
"PIM1 K24=", "PIM1 K24N", "PIM1 L2F", "PIM1 L2V", "PIM1 N7=",
"PIM1 Q37=", "PIM1 S97=", "PIM1 S97N", "PIM1 S97R", "PIM1 S97T",
"PLCB3 T909P", "PLK2 L208P", "PLK2 L208V", "PNLIPRP3 K431R",
"PNLIPRP3 K431T", "PODXL S22P", "POLE E18K", "POLE P286H", "POLE P286L",
"POLE P286R", "POLE P286S", "POLE P286T", "POLE V411L", "POM121 N94S",
"PPM1D E525*", "PPP2R1A P179L", "PPP2R1A P179R", "PPP2R1A R182=",
"PPP2R1A R182W", "PPP2R1A R183G", "PPP2R1A R183Q", "PPP2R1A R183W",
"PPP2R1A S256F", "PPP2R1A S256Y", "PPP6C R264C", "PPP6C S270L",
"PRDM14 F204=", "PRDM14 F204V", "PRDM14 R505C", "PRDM14 R505H",
"PREX2 L50=", "PREX2 L50V", "PRKCI R480C", "PRKCI R480H", "PRKCI R480S",
"PSG4 E263K", "PTEN A126D", "PTEN A126G", "PTEN A126S", "PTEN A126V",
"PTEN C105*", "PTEN C105G", "PTEN C105R", "PTEN C105S", "PTEN C105W",
"PTEN C105Y", "PTEN C124G", "PTEN C124R", "PTEN C124S", "PTEN C124Y",
"PTEN C136*", "PTEN C136F", "PTEN C136R", "PTEN C136Y", "PTEN C71*",
"PTEN C71F", "PTEN C71Y", "PTEN D24E", "PTEN D24G", "PTEN D24H",
"PTEN D24N", "PTEN D24V", "PTEN D92E", "PTEN D92G", "PTEN D92H",
"PTEN D92N", "PTEN D92V", "PTEN D92Y", "PTEN G127*", "PTEN G127E",
"PTEN G127R", "PTEN G127V", "PTEN G129*", "PTEN G129=", "PTEN G129E",
"PTEN G129R", "PTEN G129V", "PTEN G132A", "PTEN G132D", "PTEN G132S",
"PTEN G132V", "PTEN G165*", "PTEN G165E", "PTEN G165R", "PTEN G251A",
"PTEN G251D", "PTEN G251V", "PTEN H61N", "PTEN H61R", "PTEN H61Y",
"PTEN H93L", "PTEN H93P", "PTEN H93R", "PTEN H93Y", "PTEN I101T",
"PTEN I67K", "PTEN I67T", "PTEN I67V", "PTEN L140*", "PTEN L140F",
"PTEN L146*", "PTEN L247*", "PTEN L247F", "PTEN L320*", "PTEN L320S",
"PTEN L320V", "PTEN M35I", "PTEN M35L", "PTEN M35V", "PTEN P38F",
"PTEN P38L", "PTEN P38S", "PTEN Q171*", "PTEN Q171K", "PTEN Q171R",
"PTEN R130*", "PTEN R130=", "PTEN R130G", "PTEN R130L", "PTEN R130P",
"PTEN R130Q", "PTEN R130S", "PTEN R173C", "PTEN R173H", "PTEN R173P",
"PTEN R233*", "PTEN R233Q", "PTEN R335*", "PTEN R335G", "PTEN R335P",
"PTEN S170G", "PTEN S170I", "PTEN S170N", "PTEN T277*", "PTEN T277A",
"PTEN T277I", "PTEN T277N", "PTEN W111*", "PTEN W111G", "PTEN W111R",
"PTEN W111S", "PTEN W274*", "PTEN W274S", "PTEN X212_splice",
"PTEN X267_splice", "PTEN X268_splice", "PTEN X342_splice", "PTEN X343_splice",
"PTEN X70_splice", "PTEN X85_splice", "PTEN Y155C", "PTEN Y155H",
"PTEN Y16*", "PTEN Y16=", "PTEN Y16D", "PTEN Y174*", "PTEN Y174D",
"PTEN Y174H", "PTEN Y177*", "PTEN Y177C", "PTEN Y177D", "PTEN Y177F",
"PTEN Y178*", "PTEN Y178C", "PTEN Y178H", "PTEN Y27*", "PTEN Y27C",
"PTEN Y27D", "PTEN Y27H", "PTEN Y27N", "PTEN Y336*", "PTEN Y346*",
"PTEN Y346C", "PTEN Y346D", "PTEN Y346H", "PTEN Y65*", "PTEN Y68*",
"PTEN Y68C", "PTEN Y68H", "PTEN Y68N", "PTN K44M", "PTN K44T",
"PTPN11 A461G", "PTPN11 A461T", "PTPN11 A72D", "PTPN11 A72G",
"PTPN11 A72S", "PTPN11 A72T", "PTPN11 A72V", "PTPN11 D61N", "PTPN11 D61Y",
"PTPN11 E69D", "PTPN11 E69K", "PTPN11 E76A", "PTPN11 E76G", "PTPN11 E76K",
"PTPN11 E76Q", "PTPN11 F285S", "PTPN11 F285V", "PTPN11 G503=",
"PTPN11 G503V", "PTPN11 N308D", "PTPN11 N308S", "PTPN11 Q510E",
"PTPN11 Q510H", "PTPN11 Q510L", "PTPN11 T468=", "PTPN11 T468M",
"PTPN11 T507K", "PTPRD S431*", "PTPRD S431=", "PTPRD S431L",
"PTPRS R1492=", "PTPRS R1492Q", "PTPRS R1492W", "PTPRS Y398=",
"PTPRT E548G", "PTPRT E548K", "PTPRT L668=", "PTPRT L668V", "PTPRT L695=",
"PTPRT L695F", "PTPRT L695R", "PTPRT R364*", "PTPRT R364=", "PTPRT R364Q",
"RAC1 A178V", "RAC1 C18F", "RAC1 C18S", "RAC1 C18Y", "RAC1 G12R",
"RAC1 G12V", "RAC1 K135N", "RAC1 K135R", "RAC1 N111I", "RAC1 N111K",
"RAC1 N111S", "RAC1 P29F", "RAC1 P29L", "RAC1 P29S", "RAC1 P29T",
"RAC1 P34H", "RAC1 P34R", "RAC1 P34S", "RAC1 Q61K", "RAC1 Q61R",
"RAD50 D69N", "RAD50 D69Y", "RAD51C P21A", "RAD51C P21S", "RAD51C P21T",
"RAD51C Y224H", "RAD52 R396=", "RAD52 R396H", "RAF1 S257L", "RAF1 S257W",
"RAF1 S259=", "RAF1 S259C", "RAF1 S259F", "RAF1 S259P", "RARA F286C",
"RARA F286I", "RARA F286S", "RB1 R251*", "RB1 R251Q", "RB1 R320*",
"RB1 R445*", "RB1 R455*", "RB1 R467*", "RB1 R552*", "RB1 R579*",
"RB1 R787*", "RB1 R787Q", "RB1 X127_splice", "RB1 X203_splice",
"RB1 X405_splice", "RB1 X406_splice", "RB1 X445_splice", "RB1 X46_splice",
"RB1 X463_splice", "RB1 X474_splice", "RB1 X500_splice", "RB1 X605_splice",
"RB1 X654_splice", "RB1 X702_splice", "RB1 X776_splice", "RB1 X830_splice",
"RB1 X89_splice", "RB1 Y606*", "RB1 Y606C", "RBM10 R153*", "RBM10 R153G",
"RBM10 X91_splice", "RBM39 T353=", "RBM39 T353I", "RECQL4 X766_splice",
"RET M918T", "RHEB Y35*", "RHEB Y35C", "RHEB Y35H", "RHEB Y35N",
"RHEB Y35S", "RHOA A161T", "RHOA A161V", "RHOA E40*", "RHOA E40D",
"RHOA E40K", "RHOA E40Q", "RHOA E40V", "RHOA E47K", "RHOA G17A",
"RHOA G17E", "RHOA G17V", "RHOA G62E", "RHOA G62R", "RHOA G62V",
"RHOA L22=", "RHOA L22P", "RHOA L22R", "RHOA L57V", "RHOA L69M",
"RHOA L69P", "RHOA L69R", "RHOA R5L", "RHOA R5Q", "RHOA R5W",
"RHOA T37A", "RHOA T37I", "RHOA T37S", "RHOA Y34C", "RHOA Y34F",
"RHOA Y42C", "RHOA Y42F", "RHOA Y42I", "RHOA Y42S", "RICTOR S1101=",
"RICTOR S1101L", "RIMS1 R71=", "RIMS1 R71G", "RIMS2 S423=", "RINT1 K85N",
"RINT1 K85T", "RIPPLY2 S110*", "RIPPLY2 S110L", "RIT1 A77P",
"RIT1 A77S", "RIT1 A77T", "RIT1 F82C", "RIT1 F82L", "RIT1 M90I",
"RNF43 H86R", "RNF43 H86Y", "RNF43 R132*", "RNF43 R145*", "RNF43 R371*",
"RPL10L K156M", "RPL10L K156R", "RPL10L K156T", "RPS6KA4 R629=",
"RPS6KA4 R629C", "RPS6KA4 R629H", "RPS6KA4 S236=", "RPS6KA4 S236L",
"RPTOR R139H", "RQCD1 P131L", "RQCD1 P131S", "RQCD1 S87C", "RQCD1 S87P",
"RRAS2 Q72H", "RRAS2 Q72L", "RTKN2 R33*", "RTKN2 R33Q", "RUNX1 R162G",
"RUNX1 R162K", "RUNX1 R162S", "RUNX1 R201*", "RUNX1 R201G", "RUNX1 R201Q",
"RXRA S427F", "RXRA S427Y", "S100A3 P97=", "S100A3 P97S", "S100A8 K49R",
"SDHA L639V", "SDHA S445=", "SDHA S445L", "SDHA V644L", "SDHA V644M",
"SDHAF2 S10*", "SDHAF2 S10A", "SDHAF2 S10L", "SDHAF2 X87_splice",
"SEMA4B S231=", "SEMA4B S231F", "SESN2 I425V", "SETD2 H1603R",
"SETD2 H1603Y", "SETD2 R1625C", "SETD2 R1625H", "SETD2 R1625L",
"SETD2 R1625S", "SETD2 X1572_splice", "SETD2 Y1666*", "SETD2 Y1666C",
"SETD2 Y1666H", "SF3B1 D894A", "SF3B1 D894G", "SF3B1 D894N",
"SF3B1 D894Y", "SF3B1 E902G", "SF3B1 E902K", "SF3B1 E902Q", "SF3B1 G740E",
"SF3B1 G740V", "SF3B1 G742D", "SF3B1 K666E", "SF3B1 K666M", "SF3B1 K666N",
"SF3B1 K666Q", "SF3B1 K666T", "SF3B1 K700=", "SF3B1 K700E", "SF3B1 K700R",
"SF3B1 K741*", "SF3B1 K741E", "SF3B1 K741N", "SF3B1 K741Q", "SF3B1 K741T",
"SF3B1 N626D", "SF3B1 N626H", "SF3B1 N626Y", "SF3B1 R625C", "SF3B1 R625G",
"SF3B1 R625H", "SF3B1 R625L", "SF3B1 V701A", "SF3B1 V701F", "SF3B1 V701I",
"SF3B1 Y623C", "SF3B1 Y623H", "SF3B1 Y623S", "SHB A460T", "SHROOM1 P300T",
"SLC16A13 F158L", "SLC27A5 T554=", "SLC27A5 T554I", "SLCO1B7 E27K",
"SMAD2 C463*", "SMAD2 C463F", "SMAD2 P305L", "SMAD2 P305Q", "SMAD2 P305T",
"SMAD2 R182*", "SMAD2 R182=", "SMAD2 R321*", "SMAD2 R321Q", "SMAD2 S464*",
"SMAD2 T303I", "SMAD2 T303R", "SMAD3 R268C", "SMAD3 R268H", "SMAD3 R287Q",
"SMAD3 R287W", "SMAD4 A118V", "SMAD4 C363del", "SMAD4 C363F",
"SMAD4 C363R", "SMAD4 C363S", "SMAD4 C363Y", "SMAD4 D351A", "SMAD4 D351G",
"SMAD4 D351H", "SMAD4 D351N", "SMAD4 D351V", "SMAD4 D351Y", "SMAD4 D355G",
"SMAD4 D355V", "SMAD4 D355Y", "SMAD4 D493A", "SMAD4 D493G", "SMAD4 D493H",
"SMAD4 D493N", "SMAD4 D537_E538dup", "SMAD4 D537A", "SMAD4 D537E",
"SMAD4 D537G", "SMAD4 D537H", "SMAD4 D537V", "SMAD4 D537Y", "SMAD4 E330*",
"SMAD4 E330G", "SMAD4 E330K", "SMAD4 E330Q", "SMAD4 E526*", "SMAD4 E526A",
"SMAD4 E526D", "SMAD4 E526K", "SMAD4 E526Q", "SMAD4 E526V", "SMAD4 F362_H371del",
"SMAD4 G352*", "SMAD4 G352A", "SMAD4 G352E", "SMAD4 G352L", "SMAD4 G352R",
"SMAD4 G352V", "SMAD4 G358_D360del", "SMAD4 G365_E377del", "SMAD4 G386A",
"SMAD4 G386C", "SMAD4 G386D", "SMAD4 G386R", "SMAD4 G386S", "SMAD4 G386V",
"SMAD4 G419R", "SMAD4 G419V", "SMAD4 G419W", "SMAD4 G510*", "SMAD4 G510A",
"SMAD4 G510E", "SMAD4 G510R", "SMAD4 L536_E538delinsQ", "SMAD4 L536P",
"SMAD4 L536Q", "SMAD4 L536R", "SMAD4 L540del", "SMAD4 P356H",
"SMAD4 P356L", "SMAD4 P356R", "SMAD4 P356S", "SMAD4 Q534*", "SMAD4 Q534P",
"SMAD4 R361_G365del", "SMAD4 R361_L364del", "SMAD4 R361C", "SMAD4 R361G",
"SMAD4 R361H", "SMAD4 R361L", "SMAD4 R361P", "SMAD4 R361S", "SMAD4 R445*",
"SMAD4 R445Q", "SMAD4 S178*", "SMAD4 S357_G365del", "SMAD4 V539_A546del",
"SMAD4 W524C", "SMAD4 W524L", "SMAD4 W524R", "SMAD4 W524S", "SMAD4 Y353C",
"SMAD4 Y353D", "SMAD4 Y353N", "SMAD4 Y95*", "SMAD4 Y95C", "SMAD4 Y95H",
"SMARCA4 E821D", "SMARCA4 E821K", "SMARCA4 G1232C", "SMARCA4 G1232D",
"SMARCA4 G1232S", "SMARCA4 G1232V", "SMARCA4 K546del", "SMARCA4 M781I",
"SMARCA4 M781L", "SMARCA4 M781V", "SMARCA4 R1135Q", "SMARCA4 R1135W",
"SMARCA4 R1157Q", "SMARCA4 R1157W", "SMARCA4 R1189*", "SMARCA4 R1189G",
"SMARCA4 R1189L", "SMARCA4 R1189Q", "SMARCA4 R1192C", "SMARCA4 R1192H",
"SMARCA4 R1192P", "SMARCA4 R1243G", "SMARCA4 R1243L", "SMARCA4 R1243P",
"SMARCA4 R1243W", "SMARCA4 R973Q", "SMARCA4 R973W", "SMARCA4 T910=",
"SMARCA4 T910A", "SMARCA4 T910M", "SMARCA4 T910R", "SMARCB1 K364del",
"SMARCB1 R374Q", "SMARCB1 R374W", "SMARCB1 R377C", "SMARCB1 R377H",
"SMARCB1 R377L", "SMARCD1 R183*", "SMARCD1 R183L", "SMARCD1 R183Q",
"SMO L412=", "SMO L412F", "SMO V414=", "SMO V414A", "SMO V414G",
"SMO W535L", "SMTNL2 X244_splice", "SNRPD3 G96C", "SNRPD3 G96R",
"SNRPD3 G96S", "SNRPD3 G96V", "SOCS1 A3E", "SOCS1 A3P", "SOCS1 A3R",
"SOCS1 A3T", "SOS1 A90=", "SOS1 A90T", "SOS1 A90V", "SOS1 N233Y",
"SOX17 A96G", "SOX17 S403I", "SOX9 K167del", "SOX9 R152_K167del",
"SOX9 R152del", "SPOP F102C", "SPOP F102I", "SPOP F102L", "SPOP F102S",
"SPOP F102V", "SPOP F125C", "SPOP F125I", "SPOP F125L", "SPOP F125V",
"SPOP F133C", "SPOP F133I", "SPOP F133L", "SPOP F133S", "SPOP F133V",
"SPOP K129E", "SPOP M117V", "SPOP W131C", "SPOP W131G", "SPOP W131L",
"SPOP W131R", "SPOP W131S", "SPOP Y87C", "SPOP Y87D", "SPOP Y87N",
"SPOP Y87S", "SPRED1 R349S", "SPRED1 R349W", "SPTA1 K1732T",
"SRSF2 P95_H99del", "SRSF2 P95_R102del", "SRSF2 P95_R117del",
"SRSF2 P95H", "SRSF2 P95L", "SRSF2 P95R", "SRSF2 Y92_H100del",
"SRSF2 Y92_H99del", "SSBP3 K6R", "STAG2 R216*", "STAG2 R216=",
"STAG2 R216Q", "STAT3 D661V", "STAT3 D661Y", "STAT3 E616del",
"STAT3 F384L", "STAT3 F384V", "STAT3 F384Y", "STAT3 H410P", "STAT3 H410R",
"STAT3 S614R", "STK11 D194G", "STK11 D194H", "STK11 D194N", "STK11 D194V",
"STK11 D194Y", "STK11 E165*", "STK11 E165K", "STK11 E165Q", "STK11 E223*",
"STK11 E223K", "STK11 E223V", "STK11 G196=", "STK11 G196R", "STK11 G196V",
"STK11 G242=", "STK11 G242R", "STK11 G242V", "STK11 G242W", "STK11 G251C",
"STK11 G251R", "STK11 G251V", "STK11 H174=", "STK11 H174D", "STK11 H174L",
"STK11 H174R", "STK11 H174Y", "STK11 K84*", "STK11 N181I", "STK11 N181S",
"STK11 N181T", "STK11 N181Y", "STK11 P179L", "STK11 P179Q", "STK11 P179R",
"STK11 P221=", "STK11 P221L", "STK11 P221S", "STK11 Q220*", "STK11 Q220P",
"STK11 S216=", "STK11 S216F", "STK11 W239*", "STK11 W239C", "STK11 W239S",
"STK11 W308*", "STK11 W308C", "STK11 W308L", "STK11 X125_splice",
"STK11 X155_splice", "STK11 X199_splice", "STK11 X200_splice",
"STK11 X245_splice", "STK11 X288_splice", "STK11 X307_splice",
"STK11 X97_splice", "STK19 D89=", "STK19 D89N", "SUZ12 R101*",
"SUZ12 R101Q", "SWI5 P34S", "SYT13 P228S", "SYT13 P228T", "TACC3 P417=",
"TACC3 P417S", "TARBP2 E191*", "TARBP2 E191=", "TBX2 S192I",
"TBX3 W113*", "TBX3 W113R", "TCEB1 Y79*", "TCEB1 Y79C", "TCEB1 Y79F",
"TCEB1 Y79N", "TCEB1 Y79S", "TCF20 P815L", "TCF20 P815S", "TCF3 N551K",
"TCF7L2 R471C", "TCF7L2 R471H", "TCF7L2 R471S", "TET1 P1752=",
"TET1 P1752S", "TET2 R550*", "TGFBR1 I259=", "TGFBR1 I259N",
"TGFBR1 R487Q", "TGFBR1 R487W", "TGFBR1 S241*", "TGFBR1 S241=",
"TGFBR1 S241L", "TGFBR1 T375I", "TGFBR1 T375K", "TGFBR1 T375R",
"TGFBR2 D471N", "TGFBR2 D471V", "TGFBR2 D471Y", "TGFBR2 E544K",
"TGFBR2 R520*", "TGFBR2 R520=", "TGFBR2 R553C", "TGFBR2 R553G",
"TGFBR2 R553H", "TGFBR2 R553L", "TGFBRAP1 P824=", "TGFBRAP1 P824F",
"TGFBRAP1 P824L", "TGFBRAP1 P824S", "THBD C554=", "THRA R79H",
"THSD7B E1181K", "THSD7B G557E", "THSD7B G557R", "THSD7B G557V",
"TMEM131 E1319*", "TMEM131 E1319K", "TMEM131 E1319Q", "TMEM147 A92=",
"TMEM147 A92V", "TMEM200C R19C", "TMEM200C R19H", "TMEM200C R19S",
"TNFRSF14 C111W", "TNFRSF14 C111Y", "TOP2B R651H", "TP53 A138_L145del",
"TP53 A138_P142del", "TP53 A159=", "TP53 A159D", "TP53 A159del",
"TP53 A159P", "TP53 A159V", "TP53 A161_I162del", "TP53 A161D",
"TP53 A161S", "TP53 A161T", "TP53 A161V", "TP53 A276_C277dup",
"TP53 A276_E285del", "TP53 C135_L137delinsW", "TP53 C135*", "TP53 C135F",
"TP53 C135G", "TP53 C135R", "TP53 C135S", "TP53 C135W", "TP53 C135Y",
"TP53 C141_P142del", "TP53 C141*", "TP53 C141F", "TP53 C141G",
"TP53 C141R", "TP53 C141S", "TP53 C141W", "TP53 C141Y", "TP53 C176_H179del",
"TP53 C176*", "TP53 C176=", "TP53 C176dup", "TP53 C176F", "TP53 C176G",
"TP53 C176R", "TP53 C176S", "TP53 C176W", "TP53 C176Y", "TP53 C229_H233del",
"TP53 C229_T230del", "TP53 C238_M243del", "TP53 C238_N239delinsY",
"TP53 C238_S240del", "TP53 C238F", "TP53 C238G", "TP53 C238R",
"TP53 C238S", "TP53 C238W", "TP53 C238Y", "TP53 C242*", "TP53 C242=",
"TP53 C242F", "TP53 C242G", "TP53 C242R", "TP53 C242S", "TP53 C242W",
"TP53 C242Y", "TP53 C275_R282delinsW", "TP53 C275*", "TP53 C275F",
"TP53 C275G", "TP53 C275R", "TP53 C275S", "TP53 C275W", "TP53 C275Y",
"TP53 C277*", "TP53 C277dup", "TP53 C277F", "TP53 C277G", "TP53 C277W",
"TP53 C277Y", "TP53 D148_T150del", "TP53 D148_T155dup", "TP53 D148del",
"TP53 D208E", "TP53 D208G", "TP53 D208N", "TP53 D208V", "TP53 D259=",
"TP53 D259H", "TP53 D259N", "TP53 D259V", "TP53 D259Y", "TP53 D281_R282insP",
"TP53 D281=", "TP53 D281A", "TP53 D281E", "TP53 D281G", "TP53 D281H",
"TP53 D281N", "TP53 D281P", "TP53 D281V", "TP53 D281Y", "TP53 E180_D184del",
"TP53 E198*", "TP53 E204_L206del", "TP53 E258*", "TP53 E258=",
"TP53 E258A", "TP53 E258D", "TP53 E258G", "TP53 E258K", "TP53 E258Q",
"TP53 E258V", "TP53 E271*", "TP53 E271K", "TP53 E271Q", "TP53 E271V",
"TP53 E285_K292del", "TP53 E285*", "TP53 E285=", "TP53 E285K",
"TP53 E285Q", "TP53 E285V", "TP53 E286_E287del", "TP53 E286*",
"TP53 E286A", "TP53 E286G", "TP53 E286K", "TP53 E286Q", "TP53 E286V",
"TP53 E294*", "TP53 E298*", "TP53 E298Q", "TP53 F109C", "TP53 F109I",
"TP53 F109S", "TP53 F109V", "TP53 F113=", "TP53 F113C", "TP53 F113L",
"TP53 F113P", "TP53 F113S", "TP53 F113V", "TP53 F134C", "TP53 F134I",
"TP53 F134L", "TP53 F134S", "TP53 F134V", "TP53 F270C", "TP53 F270del",
"TP53 F270I", "TP53 F270L", "TP53 F270S", "TP53 F270V", "TP53 G105=",
"TP53 G105C", "TP53 G105D", "TP53 G105R", "TP53 G105S", "TP53 G105V",
"TP53 G154_T155del", "TP53 G154C", "TP53 G154D", "TP53 G154V",
"TP53 G199_E204del", "TP53 G244_M246delinsV", "TP53 G244=", "TP53 G244A",
"TP53 G244C", "TP53 G244D", "TP53 G244F", "TP53 G244R", "TP53 G244S",
"TP53 G244V", "TP53 G245_P250delinsA", "TP53 G245A", "TP53 G245C",
"TP53 G245D", "TP53 G245N", "TP53 G245R", "TP53 G245S", "TP53 G245V",
"TP53 G262del", "TP53 G262V", "TP53 G266*", "TP53 G266E", "TP53 G266K",
"TP53 G266R", "TP53 G266T", "TP53 G266V", "TP53 H168L", "TP53 H168P",
"TP53 H168R", "TP53 H178_S183del", "TP53 H178D", "TP53 H178N",
"TP53 H178P", "TP53 H178Q", "TP53 H179_D184del", "TP53 H179D",
"TP53 H179del", "TP53 H179L", "TP53 H179N", "TP53 H179P", "TP53 H179Q",
"TP53 H179R", "TP53 H179Y", "TP53 H193D", "TP53 H193L", "TP53 H193N",
"TP53 H193P", "TP53 H193Q", "TP53 H193R", "TP53 H193Y", "TP53 H214L",
"TP53 H214P", "TP53 H214Q", "TP53 H214R", "TP53 I162_Y163delinsN",
"TP53 I162dup", "TP53 I195_G199del", "TP53 I195=", "TP53 I195F",
"TP53 I195K", "TP53 I195M", "TP53 I195N", "TP53 I195S", "TP53 I195T",
"TP53 I232=", "TP53 I232F", "TP53 I232N", "TP53 I232S", "TP53 I232T",
"TP53 I251=", "TP53 I251F", "TP53 I251M", "TP53 I251N", "TP53 I251S",
"TP53 I254_T256del", "TP53 I254F", "TP53 I254L", "TP53 I254M",
"TP53 I254N", "TP53 I254S", "TP53 I254V", "TP53 I255=", "TP53 I255del",
"TP53 I255dup", "TP53 I255F", "TP53 I255N", "TP53 I255S", "TP53 I255T",
"TP53 K120*", "TP53 K120E", "TP53 K120M", "TP53 K120N", "TP53 K132*",
"TP53 K132E", "TP53 K132M", "TP53 K132N", "TP53 K132Q", "TP53 K132R",
"TP53 K132T", "TP53 K139_P142delinsT", "TP53 K164*", "TP53 K164E",
"TP53 L111M", "TP53 L111P", "TP53 L111Q", "TP53 L111R", "TP53 L130_A138dup",
"TP53 L130del", "TP53 L130F", "TP53 L130H", "TP53 L130P", "TP53 L130R",
"TP53 L130V", "TP53 L194F", "TP53 L194H", "TP53 L194P", "TP53 L194R",
"TP53 L252_I254del", "TP53 L252del", "TP53 L252dup", "TP53 L257=",
"TP53 L257P", "TP53 L257Q", "TP53 L257R", "TP53 L257V", "TP53 L264_N268del",
"TP53 L265=", "TP53 L265del", "TP53 L265M", "TP53 L265P", "TP53 L265R",
"TP53 M133I", "TP53 M133K", "TP53 M133R", "TP53 M133T", "TP53 M237_N239del",
"TP53 M237I", "TP53 M237K", "TP53 M237V", "TP53 M243_I255del",
"TP53 M246I", "TP53 M246K", "TP53 M246L", "TP53 M246R", "TP53 M246T",
"TP53 M246V", "TP53 N131=", "TP53 N131del", "TP53 N131I", "TP53 N131K",
"TP53 N131S", "TP53 N235_Y236dup", "TP53 N235del", "TP53 N239_S240del",
"TP53 N239_S241del", "TP53 N239D", "TP53 N239dup", "TP53 N239H",
"TP53 N239K", "TP53 N239S", "TP53 N239T", "TP53 N247=", "TP53 N247I",
"TP53 N263_N268del", "TP53 N268_R273del", "TP53 P128_L130del",
"TP53 P128del", "TP53 P142dup", "TP53 P151A", "TP53 P151F", "TP53 P151H",
"TP53 P151L", "TP53 P151R", "TP53 P151S", "TP53 P151T", "TP53 P152=",
"TP53 P152K", "TP53 P152L", "TP53 P152Q", "TP53 P152R", "TP53 P152S",
"TP53 P152T", "TP53 P153_G154del", "TP53 P153del", "TP53 P177_C182del",
"TP53 P177_H178del", "TP53 P190L", "TP53 P190R", "TP53 P190S",
"TP53 P190T", "TP53 P191_L201del", "TP53 P191del", "TP53 P250_I251delinsL",
"TP53 P250_L252del", "TP53 P250=", "TP53 P250L", "TP53 P250R",
"TP53 P278A", "TP53 P278F", "TP53 P278H", "TP53 P278L", "TP53 P278R",
"TP53 P278S", "TP53 P278T", "TP53 Q104*", "TP53 Q104H", "TP53 Q136_C141del",
"TP53 Q136*", "TP53 Q136del", "TP53 Q136E", "TP53 Q136H", "TP53 Q136L",
"TP53 Q136P", "TP53 Q144*", "TP53 Q144H", "TP53 Q144L", "TP53 Q144P",
"TP53 Q165*", "TP53 Q165H", "TP53 Q167*", "TP53 Q192*", "TP53 Q192del",
"TP53 Q192L", "TP53 Q317*", "TP53 Q331*", "TP53 Q331H", "TP53 R110C",
"TP53 R110H", "TP53 R110L", "TP53 R110P", "TP53 R156del", "TP53 R158_A159del",
"TP53 R158_A159dup", "TP53 R158C", "TP53 R158F", "TP53 R158G",
"TP53 R158H", "TP53 R158L", "TP53 R158P", "TP53 R158S", "TP53 R175C",
"TP53 R175G", "TP53 R175H", "TP53 R175L", "TP53 R181C", "TP53 R181H",
"TP53 R181P", "TP53 R196*", "TP53 R196L", "TP53 R196P", "TP53 R196Q",
"TP53 R202_L206del", "TP53 R213*", "TP53 R213G", "TP53 R213L",
"TP53 R213P", "TP53 R213Q", "TP53 R248=", "TP53 R248G", "TP53 R248L",
"TP53 R248P", "TP53 R248Q", "TP53 R248W", "TP53 R249G", "TP53 R249I",
"TP53 R249K", "TP53 R249M", "TP53 R249S", "TP53 R249T", "TP53 R249W",
"TP53 R267=", "TP53 R267G", "TP53 R267L", "TP53 R267P", "TP53 R267Q",
"TP53 R267W", "TP53 R273C", "TP53 R273G", "TP53 R273H", "TP53 R273L",
"TP53 R273P", "TP53 R273S", "TP53 R280*", "TP53 R280G", "TP53 R280I",
"TP53 R280K", "TP53 R280S", "TP53 R280T", "TP53 R282_R283del",
"TP53 R282=", "TP53 R282G", "TP53 R282L", "TP53 R282P", "TP53 R282Q",
"TP53 R282W", "TP53 R306*", "TP53 R306Q", "TP53 R337C", "TP53 R337G",
"TP53 R337H", "TP53 R337L", "TP53 R337P", "TP53 R337S", "TP53 R342*",
"TP53 R342P", "TP53 S127=", "TP53 S127C", "TP53 S127F", "TP53 S127P",
"TP53 S127T", "TP53 S127Y", "TP53 S183_G187delinsC", "TP53 S215C",
"TP53 S215G", "TP53 S215I", "TP53 S215N", "TP53 S215R", "TP53 S215T",
"TP53 S240_C242del", "TP53 S240_S241del", "TP53 S241=", "TP53 S241A",
"TP53 S241C", "TP53 S241dup", "TP53 S241F", "TP53 S241P", "TP53 S241T",
"TP53 S241Y", "TP53 S260_L264dup", "TP53 S269_E271del", "TP53 S269_E271delinsK",
"TP53 T125=", "TP53 T125A", "TP53 T125K", "TP53 T125M", "TP53 T125P",
"TP53 T125R", "TP53 T150_R158del", "TP53 T155_A161del", "TP53 T155_R156del",
"TP53 T155_R158del", "TP53 T155=", "TP53 T155I", "TP53 T155N",
"TP53 T155P", "TP53 T231_I232del", "TP53 T231_I232insTDCTT",
"TP53 T253_L257del", "TP53 T253dup", "TP53 T256_S260del", "TP53 T256del",
"TP53 V143_P153del", "TP53 V143A", "TP53 V143E", "TP53 V143G",
"TP53 V143M", "TP53 V147_D148dup", "TP53 V157_R158del", "TP53 V157_R158dup",
"TP53 V157=", "TP53 V157A", "TP53 V157D", "TP53 V157F", "TP53 V157G",
"TP53 V157L", "TP53 V172D", "TP53 V172F", "TP53 V172G", "TP53 V173_R175del",
"TP53 V173A", "TP53 V173dup", "TP53 V173E", "TP53 V173G", "TP53 V173L",
"TP53 V173M", "TP53 V197_N200del", "TP53 V197=", "TP53 V197E",
"TP53 V197G", "TP53 V197L", "TP53 V197M", "TP53 V216E", "TP53 V216G",
"TP53 V216L", "TP53 V216M", "TP53 V218=", "TP53 V218E", "TP53 V218G",
"TP53 V218L", "TP53 V218M", "TP53 V272_R273insL", "TP53 V272=",
"TP53 V272A", "TP53 V272E", "TP53 V272G", "TP53 V272K", "TP53 V272L",
"TP53 V272M", "TP53 V274_C275dup", "TP53 V274_G279del", "TP53 V274A",
"TP53 V274D", "TP53 V274dup", "TP53 V274F", "TP53 V274G", "TP53 V274L",
"TP53 W146*", "TP53 W146C", "TP53 W146G", "TP53 W146S", "TP53 W53*",
"TP53 W91*", "TP53 X125_splice", "TP53 X126_splice", "TP53 X187_splice",
"TP53 X224_splice", "TP53 X225_splice", "TP53 X261_splice", "TP53 X307_splice",
"TP53 X32_splice", "TP53 X33_splice", "TP53 X331_splice", "TP53 X332_splice",
"TP53 Y107*", "TP53 Y107=", "TP53 Y107D", "TP53 Y126*", "TP53 Y126C",
"TP53 Y126D", "TP53 Y126H", "TP53 Y126N", "TP53 Y126S", "TP53 Y163*",
"TP53 Y163C", "TP53 Y163D", "TP53 Y163H", "TP53 Y163N", "TP53 Y205*",
"TP53 Y205C", "TP53 Y205D", "TP53 Y205F", "TP53 Y205H", "TP53 Y205N",
"TP53 Y205S", "TP53 Y220*", "TP53 Y220C", "TP53 Y220D", "TP53 Y220H",
"TP53 Y220N", "TP53 Y220S", "TP53 Y234_M237del", "TP53 Y234*",
"TP53 Y234C", "TP53 Y234D", "TP53 Y234del", "TP53 Y234H", "TP53 Y234N",
"TP53 Y234S", "TP53 Y236_M237delinsL", "TP53 Y236*", "TP53 Y236C",
"TP53 Y236D", "TP53 Y236H", "TP53 Y236N", "TP53 Y236S", "TP63 E609K",
"TP63 R379C", "TP63 R379H", "TP63 R379S", "TP63 S365*", "TP63 S365=",
"TP63 S365L", "TP63 X194_splice", "TPTE2 M41V", "TRAF7 N520S",
"TRAF7 N520Y", "TRAF7 R189=", "TRAF7 R189L", "TRAF7 R189P", "TRAF7 R189W",
"TRIM65 H383L", "TRIM65 H383N", "TROAP S562I", "TSC1 X797_splice",
"TSC22D2 S735F", "TSC22D2 S735Y", "TUBGCP4 A8D", "TUBGCP4 A8T",
"TUBGCP6 S1192=", "U2AF1 G222_G223del", "U2AF1 G223del", "U2AF1 G223dup",
"U2AF1 I24T", "U2AF1 I24V", "U2AF1 Q157P", "U2AF1 Q157R", "U2AF1 S34F",
"U2AF1 S34Y", "UBE2D3 M32V", "UCHL1 H161Y", "VHL C162*", "VHL C162F",
"VHL C162R", "VHL C162W", "VHL C162Y", "VHL D121G", "VHL D121V",
"VHL D121Y", "VHL E70_R79dup", "VHL F76del", "VHL G114A", "VHL G114C",
"VHL G114R", "VHL H115N", "VHL H115Q", "VHL H115Y", "VHL I151F",
"VHL I151N", "VHL I151S", "VHL I151T", "VHL I75_C77del", "VHL L135*",
"VHL L135F", "VHL L158=", "VHL L158P", "VHL L158Q", "VHL L158V",
"VHL L169P", "VHL L89=", "VHL L89H", "VHL L89P", "VHL N78D",
"VHL N78K", "VHL N78S", "VHL N78Y", "VHL P86L", "VHL P86R", "VHL P86S",
"VHL P86T", "VHL R161*", "VHL R161L", "VHL R161Q", "VHL R79_S80del",
"VHL S111=", "VHL S111N", "VHL S111P", "VHL S111R", "VHL S65*",
"VHL S65L", "VHL S65P", "VHL S65T", "VHL S65W", "VHL S68*", "VHL S68P",
"VHL S80=", "VHL S80I", "VHL S80N", "VHL S80R", "VHL V74=", "VHL V74D",
"VHL V74G", "VHL W117*", "VHL W117C", "VHL W117L", "VHL W88*",
"VHL W88L", "VHL W88R", "VHL X114_splice", "VHL X155_splice",
"VHL Y112*", "VHL Y112=", "VHL Y112C", "VHL Y112D", "WDR73 G316R",
"WHSC1 T1150A", "XPO1 E571A", "XPO1 E571K", "XPO1 E571V", "XPO1 R749*",
"XPO1 R749Q", "XPO6 I274T", "XPO6 I274V", "ZBTB7A K424N", "ZBTB7A K424T",
"ZHX3 N249K", "ZNF516 A256D", "ZNF623 T500K", "ZNF649 R198I",
"ZNF649 R198K", "ZNF649 R198S")
#' @name hotspots
#' @title something
#' @description
#'
#' Hotspots - MSK-IMPACT 341
#'
#' @param maf
#'
#' @return binary table of hotpots in the 341 IMPACT gene panel
#' @export
hotspots <- function( maf = maf ){
if("Tumor_Sample_Barcode" %in% names(maf)){
setnames(maf, "Tumor_Sample_Barcode", "SAMPLE_ID")
}
setkey(maf, "SAMPLE_ID")
# maf[Protein_position == "",
# Protein_position := gsub("/.*$", "", CDS_position)]
#
# suppressWarnings(maf[Variant_Type == "SNP",
# Amino_Acid := as.integer(gsub("/.*$", "", Protein_position))])
#
# maf[paste(Hugo_Symbol, Amino_Acid) %in% MolecularDiagnosis::hotspot.v11.mutations.filtered,
# hotspot := ]
if("HGVSp_Short" %in% names(maf)) {
maf[, Hugo_Symbol_Allele := paste0(Hugo_Symbol, " ", gsub("^p.", "", HGVSp_Short))]
} else {
maf[, Hugo_Symbol_Allele := paste0(Hugo_Symbol, " ", gsub("^p.", "", Amino_Acid_Change))]
}
hotspot_genes <- unique(sort(gsub(" .*$", "", hotspot_list)))
# hotspot_allele_genes <- c("KRAS", "BRAF", "EGFR")
hotspot_allele_genes <- hotspot_genes
hotspot_allele_genes_regex <- paste0("^", paste(hotspot_allele_genes, collapse = "|^"))
hotspot_allele_list <- hotspot_list[hotspot_list %like% hotspot_allele_genes_regex]
maf_allele_hotspots <- maf[Hugo_Symbol %in% hotspot_allele_genes &
Hugo_Symbol_Allele %in% hotspot_allele_list]
maf_allele_hotspots[, Hugo_Symbol := factor(Hugo_Symbol, levels = hotspot_allele_genes)]
if(maf_allele_hotspots[, .N] > 0){
hotspots_allele_d <- dcast.data.table(
maf[Hugo_Symbol_Allele %in% hotspot_allele_list],
SAMPLE_ID ~ Hugo_Symbol_Allele,
value.var = "Hugo_Symbol_Allele",
fill = 0,
drop = FALSE,
fun.aggregate = function(x) {
ifelse(length(x) > 0, 1, 0)
}
)
absent_hotspots <- setdiff(hotspot_allele_list,
colnames(hotspots_allele_d))
suppressWarnings(hotspots_allele_d[, absent_hotspots := 0, with = FALSE])
}
maf_hotspots <- maf[Hugo_Symbol %in% hotspot_genes &
Hugo_Symbol_Allele %in% hotspot_list]
maf_hotspots[, Hugo_Symbol := factor(Hugo_Symbol, levels = hotspot_genes)]
if(maf_hotspots[, .N] > 0){
hotspots_d <- dcast.data.table(
maf[Hugo_Symbol %in% hotspot_genes &
Hugo_Symbol_Allele %in% hotspot_list],
SAMPLE_ID ~ Hugo_Symbol,
value.var = "Hugo_Symbol",
fill = 0,
drop = F,
fun.aggregate = function(x) {
ifelse(length(x) > 0, 1, 0)
}
)
absent_hotspots <- setdiff(hotspot_genes,
colnames(hotspots_d))
suppressWarnings(hotspots_d[, absent_hotspots := 0, with = F])
hotspot_names <-
setnames(hotspots_d, c(
names(hotspots_d)[1],
paste0(names(hotspots_d)[-1], "_hotspot")
))
} else {
hotspots_d <- as.data.table(data.matrix(matrix(0, nrow = maf[, uniqueN(SAMPLE_ID)], ncol = 1+length(hotspot_list))))
colnames(hotspots_d) <- c("SAMPLE_ID", hotspot_list)
hotspots_d[, SAMPLE_ID := maf[, unique(SAMPLE_ID)] ]
}
if("Tumor_Sample_Barcode" %in% names(maf)) setnames(maf, "Tumor_Sample_Barcode", "SAMPLE_ID")
setnames(hotspots_d, gsub(" ", "_", names(hotspots_d)))
hotspots_d <- merge(hotspots_d, hotspots_allele_d, by = "SAMPLE_ID", all = T)
hotspots_d[is.na(hotspots_d)] <- 0
setnames(hotspots_d, make.names(names(hotspots_d), unique = T))
copy(hotspots_d)
}
#' @name focal_cn_portal
#' @title something
#' @description
#'
#' Focal amplifications and homozygous deletions portal style - MSK-IMPACT 341
#'
#' This function creates a feature table of focal copy number alterations of type:
#' Amp (amplification, cn == 2)
#' HomDel (homozygous deletion, cn == -1)
#'
#' @param cna
#'
#' @return binary table of focal copy number alterations in the 341 IMPACT gene panel
#'
#' @export
focal_cn_portal = function( cna = cn ) {
setnames(cna, 1, "Hugo_Symbol")
# cna[ Hugo_Symbol == "FAM123B", Hugo_Symbol := "AMER1"]
# cna[Hugo_Symbol == "MLL", Hugo_Symbol := "KMT2A"]
# cna[Hugo_Symbol == "MLL2", Hugo_Symbol := "KMT2D"]
# cna[Hugo_Symbol == "MLL3", Hugo_Symbol := "KMT2C"]
cna[Hugo_Symbol == "MYCL1", Hugo_Symbol := "MYCL"]
cna[, Hugo_Symbol := gsub("-", ".", Hugo_Symbol)]
cna <- cna[Hugo_Symbol %in% MolecularDiagnosis::msk_impact_341]
setkey(cna, Hugo_Symbol)
sample_cols <- 2:ncol(cna)
### Amp table
cna_amp <- data.table(cna)
cna_amp[, (sample_cols) := lapply(.SD, function(x)
as.integer(x == 2)), .SDcols = sample_cols]
cna_amp[, Hugo_Symbol := paste0(Hugo_Symbol, "_Amp")]
### HomDel table
cna[, (sample_cols) := lapply(.SD, function(x)
as.integer(x == -2)), .SDcols = sample_cols]
cna[, Hugo_Symbol := paste0(Hugo_Symbol, "_HomDel")]
cna <- rbind(cna_amp, cna)
cna <- tdt(cna)
setnames(cna, 1, "SAMPLE_ID")
return(cna)
}
#' @name broad_cn
#' @title something
#' @description
#'
#' Broad copy number alterations
#'
#' @param seg
#' @param log_ratio_threshold
#'
#' @return binary table of broad copy number alterations in the 341 IMPACT gene panel
#'
#' @export
broad_cn = function(seg = seg, log_ratio_threshold = 0.2){
setnames(seg,
c(
"SAMPLE_ID",
"chr",
"start",
"end",
"num.mark",
"seg.mean"
))
seg <- seg[num.mark >= 10 & !chr == "Y"]
seg[, chr := as.character(chr)]
setkey(seg, chr, start, end)
Cytoband_Table <- MolecularDiagnosis::Cytoband_Table[!chr == "Y"]
Cytoband_Table[, Length := (end - start) + 1]
setkey(Cytoband_Table, chr, start, end)
seg_arm <- foverlaps(seg, Cytoband_Table,
nomatch = 0, type = "any")
### make sure that segments do not count towards more than one arm
setnames(seg_arm, "i.start", "segment_start")
setnames(seg_arm, "i.end", "segment_end")
seg_arm[, segment_start := pmax(segment_start, start)]
seg_arm[, segment_end := pmin(segment_end, end)]
seg_arm[, width := (segment_end - segment_start) + 1]
seg_arm[seg.mean <= -log_ratio_threshold,
cna := "Del"]
seg_arm[seg.mean >= log_ratio_threshold,
cna := "Amp"]
seg_arm_Fc <-
seg_arm[, .(TSB_alt_width = sum(as.numeric(width))), by = c("SAMPLE_ID", "arm", "cna")]
seg_arm_Fc <-
merge(seg_arm_Fc, Cytoband_Table, all.x = TRUE, by = "arm")
seg_arm_Fc[, fc_arm_cna := round(TSB_alt_width / Length, digits = 3)]
seg_arm_Fc[fc_arm_cna >= 0.5, arm_alt := "Y"]
seg_arm_Fc[cna == "Del" & arm_alt == "Y", cn := -1]
seg_arm_Fc[cna == "Amp" & arm_alt == "Y", cn := 1]
seg_arm_Fc[is.na(arm_alt) , cn := 0]
setkey(seg_arm_Fc, cn)
broad_cn_alterations <-
c(
paste0("Del_", Cytoband_Table$arm),
paste0("Amp_", Cytoband_Table$arm)
)
if(!sum(seg_arm_Fc$cn, na.rm = T)) {
mat <- matrix(
0,
nrow = uniqueN(seg_arm_Fc$SAMPLE_ID),
ncol = length(broad_cn_alterations)
)
colnames(mat) <- broad_cn_alterations
broadCNAs_d <- data.table(mat)
broadCNAs_d <-
cbind(SAMPLE_ID = unique(seg_arm_Fc$SAMPLE_ID),
broadCNAs_d)
} else {
broadCNAs_d <- merge(
data.table(
dcast.data.table(
seg_arm_Fc[cn == -1] ,
SAMPLE_ID ~ paste0("Del_", arm),
value.var = 'cn',
fun.aggregate = function(x) {
ifelse(length(x) > 0, 1, 0)
}
)
),
data.table(
dcast.data.table(
seg_arm_Fc[cn == 1] ,
SAMPLE_ID ~ paste0("Amp_", arm),
value.var = 'cn',
fun.aggregate = function(x) {
ifelse(length(x) > 0, 1, 0)
}
)
),
all = TRUE,
by = "SAMPLE_ID"
)
# replace NAs with 0s
for(i in seq_along(broadCNAs_d))
set(broadCNAs_d,
i = which(is.na(broadCNAs_d[[i]])),
j = i,
value = 0)
unaltered_arms <- setdiff(broad_cn_alterations,
colnames(broadCNAs_d))
suppressWarnings(broadCNAs_d[, unaltered_arms := 0, with = F])
TSB_noBroadcnas <-
unique(seg_arm_Fc[cn == 0 &
!SAMPLE_ID %in% broadCNAs_d$SAMPLE_ID,
list(SAMPLE_ID)])
TSB_noBroadcnas[, (broad_cn_alterations) := 0]
broadCNAs_d <- rbind(broadCNAs_d, TSB_noBroadcnas)
setcolorder(broadCNAs_d,
c("SAMPLE_ID", broad_cn_alterations))
}
return(broadCNAs_d)
}
#' @name fusions
#' @title something
#' @description
#'
#' Fusions
#'
#' @param SV
#'
#' @return binary table of structural variants involving genes in the 341 IMPACT gene panel
fusions = function(SV = SV){
if("Tumor_Sample_Barcode" %in% names(SV)) setnames(SV, "Tumor_Sample_Barcode", "SAMPLE_ID")
SV[, fusion_column_name :=
ifelse(Fusion %in% c("TMPRSS2-ERG fusion", "ETV1-TMPRSS2 fusion"), "ETS_TMPRSS2_fusion",
ifelse(Fusion %in% c("EML4-ALK fusion", "ALK-EML4 fusion"), "EML4_ALK_fusion",
ifelse(Fusion %in% c("CD74-ROS1 fusion", "EZR-ROS1 fusion", "ROS1-SDC4 fusion"), "ROS1_fusion",
ifelse(Fusion == "EGFR-intragenic", "EGFR_SV", NA))))]
SV_tab <- dcast.data.table(
SV[!is.na(fusion_column_name)],
SAMPLE_ID ~ fusion_column_name,
value.var = "fusion_column_name",
fun.aggregate = function(x) {
ifelse(length(x) > 0, 1, 0)
},
fill = 0
)
return(SV_tab)
}
#' #' @name mutational_signatures
#' #' @title something
#' #' @description
#' #'
#' #' Mutational signatures
#' #'
#' #' @param maf
#' #'
#' ## #' @import Biostrings
#' ## #' @import GenomeInfoDb
#' ## #' @import BSgenome.Hsapiens.UCSC.hg19
#' #' @return binary table of mutational signatures in the 341 IMPACT gene panel
#' ## #' @export
#' mutational_signatures <- function( maf = maf){
#'
#' maf <- as.data.table(maf)
#'
#' if("Tumor_Sample_Barcode" %in% names(maf)) setnames(maf, "Tumor_Sample_Barcode", "SAMPLE_ID")
#'
#' setkey(maf, "SAMPLE_ID")
#'
#' dt <- maf
#' flank <- 1
#' hg19 <- BSgenome.Hsapiens.UCSC.hg19::BSgenome.Hsapiens.UCSC.hg19
#' GenomeInfoDb::seqlevelsStyle(hg19) <- "NCBI"
#'
#' if(!"Mut_Tri" %in% colnames(maf)) {
#' ### annotate_maf_with_tri_nucleotide
#' ### data.table not working when in separate function (?)
#' Ref_Tri <- dt[, Biostrings::getSeq(hg19,
#' name = Chromosome,
#' start = Start_Position - flank,
#' end = End_Position + flank)]
#' # with(dt, ifelse()
#' Ref_Tri_CT <- Ref_Tri
#' Ref_Tri_CT[substr(Ref_Tri, 2, 2) %in% c("A", "G")] <-
#' Biostrings::reverseComplement(Ref_Tri_CT[substr(Ref_Tri, 2, 2) %in% c("A", "G")])
#' Ref_Tri <- as.character(Ref_Tri)
#' Ref_Tri_CT <- as.character(Ref_Tri_CT)
#' Ref_Tri_CT[dt$Variant_Type != "SNP"] <- NA
#'
#' Tumor_Seq_Allele2_CT <- dt$Tumor_Seq_Allele2
#' Tumor_Seq_Allele2_CT[substr(Ref_Tri, 2, 2) %in% c("A", "G")] <-
#' as.character(Biostrings::reverseComplement(
#' Biostrings::DNAStringSet(Tumor_Seq_Allele2_CT[substr(Ref_Tri, 2, 2) %in% c("A", "G")])))
#'
#' ### remove synonymous mutations
#' Ref_Tri_CT[substr(Ref_Tri_CT, 2, 2) == Tumor_Seq_Allele2_CT] <-
#' NA
#' ### remove positions with no identified reference (ie MT)
#' Ref_Tri_CT[substr(Ref_Tri_CT, 2, 2) == "N"] <- NA
#'
#' Mut_Tri <- with(dt,
#' ifelse(
#' Variant_Type != "SNP" | is.na(Ref_Tri_CT) ,
#' NA,
#' paste0(
#' substr(Ref_Tri_CT, 1, 1),
#' "[",
#' substr(Ref_Tri_CT, 2, 2),
#' "/",
#' Tumor_Seq_Allele2_CT,
#' "]",
#' substr(Ref_Tri_CT, 3, 3)
#' )
#' ))
#'
#' dt[, Ref_Tri := Ref_Tri] # dt specific, add column
#' dt[, Mut_Tri := Mut_Tri] # dt specific, add column
#' ###
#' maf <- dt
#' }
#' maf <- maf[!Mut_Tri %like% "^N"]
#'
#' trinuc_counts <- dcast.data.table(maf[!is.na(Mut_Tri),
#' .N,
#' by = list(name = Tumor_Sample_Barcode,
#' Mut_Tri)],
#' name ~ Mut_Tri,
#' value.var = "N",
#' fill = 0)
#'
#' trinuc_counts_norm_to_one <- with(trinuc_counts,
#' data.table(
#' name = name,
#' number = rowSums(trinuc_counts[, -1, with = FALSE]),
#' trinuc_counts[, -1, with = FALSE] / rowSums(trinuc_counts[, -1, with =
#' FALSE])
#' ))
#' setnames(trinuc_counts_norm_to_one, gsub("[^[:alnum:] ]", "", names(trinuc_counts_norm_to_one)))
#'
#' adam_trinuc_colnames = c(
#' "name",
#' "number",
#' "ACAA",
#' "ACAC",
#' "ACAG",
#' "ACAT",
#' "CCAA",
#' "CCAC",
#' "CCAG",
#' "CCAT",
#' "GCAA",
#' "GCAC",
#' "GCAG",
#' "GCAT",
#' "TCAA",
#' "TCAC",
#' "TCAG",
#' "TCAT",
#' "ACGA",
#' "ACGC",
#' "ACGG",
#' "ACGT",
#' "CCGA",
#' "CCGC",
#' "CCGG",
#' "CCGT",
#' "GCGA",
#' "GCGC",
#' "GCGG",
#' "GCGT",
#' "TCGA",
#' "TCGC",
#' "TCGG",
#' "TCGT",
#' "ACTA",
#' "ACTC",
#' "ACTG",
#' "ACTT",
#' "CCTA",
#' "CCTC",
#' "CCTG",
#' "CCTT",
#' "GCTA",
#' "GCTC",
#' "GCTG",
#' "GCTT",
#' "TCTA",
#' "TCTC",
#' "TCTG",
#' "TCTT",
#' "ATAA",
#' "ATAC",
#' "ATAG",
#' "ATAT",
#' "CTAA",
#' "CTAC",
#' "CTAG",
#' "CTAT",
#' "GTAA",
#' "GTAC",
#' "GTAG",
#' "GTAT",
#' "TTAA",
#' "TTAC",
#' "TTAG",
#' "TTAT",
#' "ATCA",
#' "ATCC",
#' "ATCG",
#' "ATCT",
#' "CTCA",
#' "CTCC",
#' "CTCG",
#' "CTCT",
#' "GTCA",
#' "GTCC",
#' "GTCG",
#' "GTCT",
#' "TTCA",
#' "TTCC",
#' "TTCG",
#' "TTCT",
#' "ATGA",
#' "ATGC",
#' "ATGG",
#' "ATGT",
#' "CTGA",
#' "CTGC",
#' "CTGG",
#' "CTGT",
#' "GTGA",
#' "GTGC",
#' "GTGG",
#' "GTGT",
#' "TTGA",
#' "TTGC",
#' "TTGG",
#' "TTGT"
#' )
#'
#' new_names = setdiff(adam_trinuc_colnames, names(trinuc_counts_norm_to_one))
#' suppressWarnings(trinuc_counts_norm_to_one[, new_names := 0, with = F])
#' trinuc_counts_norm_to_one <- trinuc_counts_norm_to_one[, adam_trinuc_colnames, with = F]
#' setcolorder(trinuc_counts_norm_to_one, adam_trinuc_colnames)
#'
#' signature_fractions = stratton_signatures_summ(trinuc_counts_norm_to_one)
#'
#' col_names = c(
#' "Signature.1 (age)",
#' "Signature.2 (APOBEC)",
#' "Signature.3 (BRCA1/2)",
#' "Signature.4 (smoking)",
#' "Signature.5",
#' "Signature.6 (DNA mismatch repair)",
#' "Signature.7 (ultraviolet light)",
#' "Signature.8",
#' "Signature.9 (POLH)",
#' "Signature.10 (POLE)",
#' "Signature.11 (temozolomide)",
#' "Signature.12",
#' "Signature.13 (APOBEC)",
#' "Signature.14",
#' "Signature.15 (DNA mismatch repair)",
#' "Signature.16",
#' "Signature.17",
#' "Signature.18",
#' "Signature.19",
#' "Signature.20 (DNA mismatch repair?)",
#' "Signature.21",
#' "Signature.22 (aristolochic acid)",
#' "Signature.23",
#' "Signature.24 (aflatoxin)",
#' "Signature.25",
#' "Signature.26",
#' "Signature.27",
#' "Signature.28",
#' "Signature.29 (tobacco chewing)",
#' "Signature.30"
#' )
#'
#' if(!nrow(signature_fractions)) {
#' signature_fractions <- trinuc_counts_norm_to_one[, list(name)]
#' signature_fractions[, (col_names) := 0]
#' }
#'
#' setnames(signature_fractions, "name", "SAMPLE_ID")
#'
#' nMut <- maf[, .N, by = "SAMPLE_ID"]
#' nMut <- nMut[order(N)]
#' # nMut[N < 10, signature_fraction_threshold := 1]
#' # nMut[N >= 10 & N < 50, signature_fraction_threshold := 0.3]
#' # nMut[N >= 50 & N < 100, signature_fraction_threshold := 0.2]
#' # nMut[N >= 100 & N < 200, signature_fraction_threshold := 0.15]
#' # nMut[N >= 200, signature_fraction_threshold := 0.1]
#' nMut[, signature_fraction_threshold := 0.4]
#' signature_fractions <- merge(signature_fractions, nMut,
#' by = "SAMPLE_ID")
#'
#' ### create boolean for signatures based on threshold
#' for(i in 1:nrow(signature_fractions)) {
#' for(j in 2:(ncol(signature_fractions) - 2)) {
#' set(
#' signature_fractions,
#' i,
#' j,
#' as.integer(
#' signature_fractions[i, j, with = F] > signature_fractions[i]$signature_fraction_threshold
#' )
#' )
#' }
#' }
#'
#' signature_fractions <-
#' signature_fractions[,!c("N", "signature_fraction_threshold"), with = F]
#'
#' setkey(signature_fractions, SAMPLE_ID)
#'
#' setnames(signature_fractions,
#' names(signature_fractions),
#' gsub("\\(|\\)|\\?", "", names(signature_fractions)))
#' setnames(signature_fractions,
#' names(signature_fractions),
#' gsub("\\/|\\ ", ".", names(signature_fractions)))
#'
#' col_names <- names(signature_fractions)
#' col_names <- col_names[-1]
#'
#' setcolorder(signature_fractions, c("SAMPLE_ID", col_names))
#'
#' signatures = c(
#' "Signature.1.age",
#' "Signature.2.APOBEC",
#' "Signature.3.BRCA1.2",
#' "Signature.4.smoking",
#' "Signature.5",
#' "Signature.6.DNA.mismatch.repair",
#' "Signature.7.ultraviolet.light",
#' "Signature.8",
#' "Signature.9.POLH",
#' "Signature.10.POLE",
#' "Signature.11.temozolomide",
#' "Signature.12",
#' "Signature.13.APOBEC",
#' "Signature.14",
#' "Signature.15.DNA.mismatch.repair",
#' "Signature.16",
#' "Signature.17",
#' "Signature.18",
#' "Signature.19",
#' "Signature.20.DNA.mismatch.repair",
#' "Signature.21",
#' "Signature.22.aristolochic.acid",
#' "Signature.23",
#' "Signature.24.aflatoxin",
#' "Signature.25",
#' "Signature.26",
#' "Signature.27",
#' "Signature.28",
#' "Signature.29.tobacco.chewing",
#' "Signature.30"
#' )
#'
#' absent_signatures <- setdiff(signatures,
#' colnames(signature_fractions))
#'
#' suppressWarnings(signature_fractions[, absent_signatures := 0, with =
#' F])
#'
#' setcolorder(signature_fractions, c("SAMPLE_ID", signatures))
#'
#' return(signature_fractions)
#'
#' }
#' @name mutation_count
#' @title something
#' @description
#'
#' Mutation count
#'
#' @param maf
#'
#' @return table of mutation counts in the 341 IMPACT gene panel
#'
#' @export
mutation_count = function( maf = maf ) {
maf <- as.data.table(maf)
if("Tumor_Sample_Barcode" %in% names(maf)){
setnames(maf, "Tumor_Sample_Barcode", "SAMPLE_ID")
}
setkey(maf, "SAMPLE_ID")
mutations <- maf[ (Consequence %in% MolecularDiagnosis::Nonsyn_Consequence |
(Consequence=="upstream_gene_variant" &
Hugo_Symbol=="TERT")) &
Hugo_Symbol %in% MolecularDiagnosis::msk_impact_341 ]
mutations_c <- mutations[, .(length(Hugo_Symbol)), by = "SAMPLE_ID" ]
setnames(mutations_c, 2, "Mutation_Count")
return(mutations_c)
}
#' @name cn_burden
#' @title something
#' @description
#'
#' Copy number burden
#'
#' @param seg
#' @param log_ratio_threshold
#'
#' @return copy number burden of samples from selected cancer types
#'
#' @export
cn_burden = function(seg = seg, log_ratio_threshold = 0.2){
seg <- as.data.table(seg)
setnames(seg, c("SAMPLE_ID", "Chromosome", "Start_Position", "End_Position", "Num_Mark", "Seg_Mean"))
# seg <- seg[ is.na(Num_Mark) | Num_Mark>10 ]
setkey( seg, Seg_Mean )
seg[ Seg_Mean <= -log_ratio_threshold,
CNA := "Del"]
seg[ Seg_Mean >= log_ratio_threshold,
CNA := "Amp"]
seg[, Width := (End_Position - Start_Position) + 1 ]
cn_burden <- merge(seg[, .(gen_cov = sum(Width)), by= "SAMPLE_ID" ],
seg[ !is.na(CNA), .(gen_alt = sum(Width)), by= "SAMPLE_ID" ],
by= "SAMPLE_ID" )
cn_burden[, CN_Burden := round( gen_alt / gen_cov , digits=3 )*100 ]
cn_burden <- cn_burden[, list(SAMPLE_ID, CN_Burden)]
return(cn_burden)
}
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