In stopsack/prostateredcap: Load and check the MSK Prostate REDCap Prostate clinical database
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
This data dictionary describes the full set of derived variables to use for analyses after running load_prostate_redcap() and check_prostate_redcap(recommended_only = TRUE). Additional variables may be available, especially if disabling recommended_only.
For definitions and underlying data collection, see the data dictionary of the REDCap database.
Patient-level data
Available in the datasets$pts dataset.
At diagnosis
Variable | Description | Levels | Reasons for missing values
---------+----------------------+-----------------------+------------------------
ptid | Patient ID. Will be sequential integer number in deidentified data. | -- | (No missing values)
age_dx | Age at prostate cancer diagnosis (in years) | Continuous | Date of birth or diagnosis unavailable (unusual^1^)
race4 | Self-reported race, 4 categories | Asian; Black or African American; White; Other (the latter category to avoid identifiability in uncommon categories) | Not reported
race3 | Self-reported race, 3 categories | Asian; White; Black | Another category or not reported
smoking | Self-reported smoking status around first contact | Current; Former; Never | Not reported
bx_gl34 | Gleason score at biopsy (diagnosis), grade-grouped | <7; 3+4; 4+3; 8; 9-10 | Not available or Gleason score sum 7 with unknown major/minor pattern
psa_dx | Prostate-specific antigen at cancer diagnosis (ng/ml) | Continuous | Unavailable
psa_dxcat | Prostate-specific antigen at cancer diagnosis (ng/ml) | <4; 4-10; 10-20; >20 | Unavailable
lnpsa_dx | Prostate-specific antigen at cancer diagnosis (ng/ml), log~e~-transformed | Continuous | Unavailable
stage | Clinical TNM stage at diagnosis | N0/NX M0; N1 M0; M1 | Metastasis (M) stage component unavailable (unusual^1^)
clin_tstage | Clinical T (tumor) stage at diagnosis | T1/T2; T3; T4 | Not available (many are M1)
clin_nstage | Clinical N (nodal) stage at diagnosis | N1 M0; N1 M0 | Not available (many are M1)
mstage | M (metastasis) stage at diagnosis | M0; M1 | Unavailable (unusual^1^)
^1^ A dataset processed through check_prostate_redcap() excludes records with missing values in the key characteristics, age at diagnosis and M stage. Missingness will only occur if QC filters in check_prostate_redcap() were manually disabled.
Primary treatment
Variable | Description | Levels | Reasons for missing values
---------+----------------------+-----------------------+------------------------
rxprim | Primary treatment | Many levels due to treatment combinations; also "No Primary Therapy" and "Other" | Unknown
rxprim_rp | Primary treatment included radical prostatectomy | TRUE; FALSE | None (FALSE if no report about prostatectomy)
rxprim_adt | Primary treatment included androgen deprivation therapy | TRUE; FALSE | None (FALSE if no report about primary ADT)
rxprim_chemo| Primary treatment included chemotherapy | TRUE; FALSE | None (FALSE if no report about primary chemotherapy)
rxprim_xrt | Primary treatment included radiation therapy | TRUE; FALSE | None (FALSE if no report about XRT)
rxprim_other| Primary treatment included free-text | TRUE; FALSE | None (FALSE if no free-text)
rxprim_oth | Primary treatment, other | Freetext | Predefined treatment combination used, or primary treatment unknown
rp_gl34 | Gleason score at radical prostatectomy, grade-grouped | <7; 3+4; 4+3; 8; 9-10 | Not available, no radical prostatectomy, or Gleason score sum 7 with unknown major/minor pattern
path_t | pT (tumor) stage at radical prostatectomy | 2; 2a; 2b; 2c;; 3; 3a; 3b; 4 | Unknown or no radical prostatectomy
path_n | pN (nodal) stage at radical prostatectomy | 0; 1 | Unknown or no radical prostatectomy
Sample-level data
Available in the datasets$smp dataset.
Variable | Description | Levels | Reasons for missing values
---------+----------------------+-----------------------+------------------------
ptid | Patient ID. Will be sequential integer number in deidentified data. Matches ptid in the pts dataset. | -- | (No missing values)
dmpid | Sample ID | -- | (No missing values)
hist_smp | Histology of the sample | Adenocarcinoma / poorly differentiated carcinoma; Adenocarcinoma/poorly differentiated carcinoma with ductal or intraductal features; Adenocarcinoma/poorly differentiated carcinoma with Neuroendocrine features; Other (Text box); Pure Small Cell / Neuroendocrine Carcinoma | Unknown
dzextent_smp | Disease extent at sample (biopsy) | Localized; Regional nodes; Metastatic hormone-sensitive; Non-metastatic castration-resistant; Metastatic castration-resistant; Metastatic, variant histology | Unavailable (unusual, see footnote above)
dzextent_seq | Disease extent at sequencing | Localized; Regional nodes; Metastatic hormone-sensitive; Non-metastatic castration-resistant; Metastatic castration-resistant; Metastatic, variant histology | Unavailable (unusual, see footnote above)
ext_pros | Disease extent at sampling includes prostate | TRUE; FALSE | None (FALSE if no known prostate disease)
ext_lndis | Disease extent at sampling includes distant lymph nodes | TRUE; FALSE | None (FALSE if no known distant lymph node)
ext_bone | Disease extent at sampling includes bone | TRUE; FALSE | None (FALSE if no known bone disease)
ext_vis | Disease extent at sampling includes visceral disease (liver, lung, other soft tissue) | TRUE; FALSE | None (FALSE if no known visceral disease)
ext_liver | Disease extent at sampling includes liver | TRUE; FALSE | None (FALSE if no known liver disease)
ext_lung | Disease extent at sampling includes lung | TRUE; FALSE | None (FALSE if no known lung disease)
ext_other | Disease extent at sampling includes other soft tissue | TRUE; FALSE | None (FALSE if no known other soft tissue)
bonevol | Volume of bone disease at sample (biopsy) | High-Volume Bone Metastases; Low-Volume Bone Metastases | Unknown or none bone metastases
cntadt | Sample on continuous androgen deprivation therapy | Yes; No | Unknown
tissue | Sample tissue | Bone; Liver; Lung; Lymph Node; Other soft tissue; Prostate | None
smp_pros | Sample tissue is prostate | Prostate; Non-prostate | None
smp_tissue | Sample tissue (collapse) | Prostate; Lymph node; Bone; Visceral; Other soft tissue | None
primmet_smp | Disease extent at sample: primary or regional nodes ("Primary") vs. all others ("Metastatic") | Primary; Metastatic | Unknown
age_smp | Age at sample (biopsy, in years) | Continuous | Unavailable (unusual, see footnote above)
age_seq | Age at sequencing (in years) | Continuous | Unavailable (unusual, see footnote above)
dx_smp_mos | Time from diagnosis to sample (biopsy, in months) | Continuous | Unavailable (unusual, see footnote above)
adt_smp_mos | Time from ADT initiation to sample (biopsy, in months) | Continuous | Unavailable
dx_seq_mos | Time from diagnosis to sequencing (in months) | Continuous | Unavailable (unusual, see footnote above)
dzvol | Disease volume at sample (biopsy): composite of disease extent (high if visceral) and bone volume (high if >=4 bone metastases) | Low-volume disease; high-volume disease | Non-metastatic disease at sample
denovom_smp | De-novo metastatic disease: metastases since diagnosis (M1) vs. M0 at diagnosis and metastases detected after diagnosis but before sample | Metastatic recurrence; de-novo metastatic | Non-metastatic disease at sample
denovom_seq | De-novo metastatic disease: metastases since diagnosis (M1) vs. M0 at diagnosis and metastases detected after diagnosis but before sequencing | Metastatic recurrence; de-novo metastatic | Non-metastatic disease at sequencing
Outcomes
Setup:
- Indicator (event) variables are in
datasets$pts, because events can only occur once per person.
- Time variables are in
datasets$smp, because time intervals between start of follow-up and event depend on when start of follow-up is set and thus differ for different samples from the same person. For analyses, select samples and then merge patient data by ptid.
Time variables will be missing:
- If the patient is not at risk of the event at the start of follow up because the event already occurred, e.g., metastasis when starting follow-up in metastatic castration-resistant disease.
- If the patient is not at risk because the event cannot occur, e.g., a variant histology indicates castration resistance and the patient will by definition not be followed for this outcome.
- If the event time is unknown.
Outcome: Transition | Population of Interest | Event variable (Descriptive) | Event variable (modeling) | Time variable (from sequencing) | Time variables (late-entry models)^1^
--------------+-----------------+---------------+------------+----------------+----------------
Metastasis: Sequencing to metastasis | Disease extent "Localized" or "Regional nodes" at sequencing | is_met: No; Yes | met_event: 0; 1 | seq_met_mos: Months from sequencing to metastasis or last clinic visit | dx_met_mos: Months from diagnosis to metastasis or last clinic visit
Metastasis-free survival: Sequencing to metastasis or death from any cause (composite endpoint) | Disease extent "Localized" or "Regional nodes" at sequencing | is_mfs: Event-free; Metastasis/death | mfs_event: 0; 1 | seq_mfs_mos: Months from sequencing to metastasis, death, or last clinic visit (if neither) | dx_mfs_mos: Months from diagnosis to metastasis, death, or last clinic visit (if neither)
CRPC: Sequencing to castration resistance | Disease extent "Localized", "Regional nodes", or "Metastatic hormone-sensitive" at sequencing | is_crpc: No; Yes; N/A-Pure Other Histology at Diagnosis; N/A-Pure small cell/neuroendocrine at diagnosis | crpc_event: 0; 1; missing (if variant histology) | seq_crpc_mos: Months from sequencing to castration resistance or last clinic visit | dx_crpc_mos: Months from diagnosis to castration resistance or last clinic visit
Overall survival: Sequencing to death | All | is_dead: Alive; Dead | death_event: 0; 1 | seq_os_mos: Months from sequencing to death or last contact | dx_os_mos: Months from diagnosis to death or last contact; adt_os_mos: Months from ADT initiation to death or last contact; met_os_mos: Months from metastasis to death or last contact
^1^ In late entry models, participants should enter risk sets at the time of sequencing using appropriate variables, i.e., dx_seq_mos (diagnosis to sequencing), adt_seq_mos (ADT initiation to sequencing), or met_seq_mos (metastasis to sequencing).
stopsack/prostateredcap documentation built on June 3, 2023, 12:51 a.m.
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knitr::opts_chunk$set( collapse = TRUE, comment = "#>" )
This data dictionary describes the full set of derived variables to use for analyses after running load_prostate_redcap() and check_prostate_redcap(recommended_only = TRUE). Additional variables may be available, especially if disabling recommended_only.
For definitions and underlying data collection, see the data dictionary of the REDCap database.
Patient-level data
Available in the datasets$pts dataset.
At diagnosis
Variable | Description | Levels | Reasons for missing values
---------+----------------------+-----------------------+------------------------
ptid | Patient ID. Will be sequential integer number in deidentified data. | -- | (No missing values)
age_dx | Age at prostate cancer diagnosis (in years) | Continuous | Date of birth or diagnosis unavailable (unusual^1^)
race4 | Self-reported race, 4 categories | Asian; Black or African American; White; Other (the latter category to avoid identifiability in uncommon categories) | Not reported
race3 | Self-reported race, 3 categories | Asian; White; Black | Another category or not reported
smoking | Self-reported smoking status around first contact | Current; Former; Never | Not reported
bx_gl34 | Gleason score at biopsy (diagnosis), grade-grouped | <7; 3+4; 4+3; 8; 9-10 | Not available or Gleason score sum 7 with unknown major/minor pattern
psa_dx | Prostate-specific antigen at cancer diagnosis (ng/ml) | Continuous | Unavailable
psa_dxcat | Prostate-specific antigen at cancer diagnosis (ng/ml) | <4; 4-10; 10-20; >20 | Unavailable
lnpsa_dx | Prostate-specific antigen at cancer diagnosis (ng/ml), log~e~-transformed | Continuous | Unavailable
stage | Clinical TNM stage at diagnosis | N0/NX M0; N1 M0; M1 | Metastasis (M) stage component unavailable (unusual^1^)
clin_tstage | Clinical T (tumor) stage at diagnosis | T1/T2; T3; T4 | Not available (many are M1)
clin_nstage | Clinical N (nodal) stage at diagnosis | N1 M0; N1 M0 | Not available (many are M1)
mstage | M (metastasis) stage at diagnosis | M0; M1 | Unavailable (unusual^1^)
^1^ A dataset processed through check_prostate_redcap() excludes records with missing values in the key characteristics, age at diagnosis and M stage. Missingness will only occur if QC filters in check_prostate_redcap() were manually disabled.
Primary treatment
Variable | Description | Levels | Reasons for missing values
---------+----------------------+-----------------------+------------------------
rxprim | Primary treatment | Many levels due to treatment combinations; also "No Primary Therapy" and "Other" | Unknown
rxprim_rp | Primary treatment included radical prostatectomy | TRUE; FALSE | None (FALSE if no report about prostatectomy)
rxprim_adt | Primary treatment included androgen deprivation therapy | TRUE; FALSE | None (FALSE if no report about primary ADT)
rxprim_chemo| Primary treatment included chemotherapy | TRUE; FALSE | None (FALSE if no report about primary chemotherapy)
rxprim_xrt | Primary treatment included radiation therapy | TRUE; FALSE | None (FALSE if no report about XRT)
rxprim_other| Primary treatment included free-text | TRUE; FALSE | None (FALSE if no free-text)
rxprim_oth | Primary treatment, other | Freetext | Predefined treatment combination used, or primary treatment unknown
rp_gl34 | Gleason score at radical prostatectomy, grade-grouped | <7; 3+4; 4+3; 8; 9-10 | Not available, no radical prostatectomy, or Gleason score sum 7 with unknown major/minor pattern
path_t | pT (tumor) stage at radical prostatectomy | 2; 2a; 2b; 2c;; 3; 3a; 3b; 4 | Unknown or no radical prostatectomy
path_n | pN (nodal) stage at radical prostatectomy | 0; 1 | Unknown or no radical prostatectomy
Sample-level data
Available in the datasets$smp dataset.
Variable | Description | Levels | Reasons for missing values
---------+----------------------+-----------------------+------------------------
ptid | Patient ID. Will be sequential integer number in deidentified data. Matches ptid in the pts dataset. | -- | (No missing values)
dmpid | Sample ID | -- | (No missing values)
hist_smp | Histology of the sample | Adenocarcinoma / poorly differentiated carcinoma; Adenocarcinoma/poorly differentiated carcinoma with ductal or intraductal features; Adenocarcinoma/poorly differentiated carcinoma with Neuroendocrine features; Other (Text box); Pure Small Cell / Neuroendocrine Carcinoma | Unknown
dzextent_smp | Disease extent at sample (biopsy) | Localized; Regional nodes; Metastatic hormone-sensitive; Non-metastatic castration-resistant; Metastatic castration-resistant; Metastatic, variant histology | Unavailable (unusual, see footnote above)
dzextent_seq | Disease extent at sequencing | Localized; Regional nodes; Metastatic hormone-sensitive; Non-metastatic castration-resistant; Metastatic castration-resistant; Metastatic, variant histology | Unavailable (unusual, see footnote above)
ext_pros | Disease extent at sampling includes prostate | TRUE; FALSE | None (FALSE if no known prostate disease)
ext_lndis | Disease extent at sampling includes distant lymph nodes | TRUE; FALSE | None (FALSE if no known distant lymph node)
ext_bone | Disease extent at sampling includes bone | TRUE; FALSE | None (FALSE if no known bone disease)
ext_vis | Disease extent at sampling includes visceral disease (liver, lung, other soft tissue) | TRUE; FALSE | None (FALSE if no known visceral disease)
ext_liver | Disease extent at sampling includes liver | TRUE; FALSE | None (FALSE if no known liver disease)
ext_lung | Disease extent at sampling includes lung | TRUE; FALSE | None (FALSE if no known lung disease)
ext_other | Disease extent at sampling includes other soft tissue | TRUE; FALSE | None (FALSE if no known other soft tissue)
bonevol | Volume of bone disease at sample (biopsy) | High-Volume Bone Metastases; Low-Volume Bone Metastases | Unknown or none bone metastases
cntadt | Sample on continuous androgen deprivation therapy | Yes; No | Unknown
tissue | Sample tissue | Bone; Liver; Lung; Lymph Node; Other soft tissue; Prostate | None
smp_pros | Sample tissue is prostate | Prostate; Non-prostate | None
smp_tissue | Sample tissue (collapse) | Prostate; Lymph node; Bone; Visceral; Other soft tissue | None
primmet_smp | Disease extent at sample: primary or regional nodes ("Primary") vs. all others ("Metastatic") | Primary; Metastatic | Unknown
age_smp | Age at sample (biopsy, in years) | Continuous | Unavailable (unusual, see footnote above)
age_seq | Age at sequencing (in years) | Continuous | Unavailable (unusual, see footnote above)
dx_smp_mos | Time from diagnosis to sample (biopsy, in months) | Continuous | Unavailable (unusual, see footnote above)
adt_smp_mos | Time from ADT initiation to sample (biopsy, in months) | Continuous | Unavailable
dx_seq_mos | Time from diagnosis to sequencing (in months) | Continuous | Unavailable (unusual, see footnote above)
dzvol | Disease volume at sample (biopsy): composite of disease extent (high if visceral) and bone volume (high if >=4 bone metastases) | Low-volume disease; high-volume disease | Non-metastatic disease at sample
denovom_smp | De-novo metastatic disease: metastases since diagnosis (M1) vs. M0 at diagnosis and metastases detected after diagnosis but before sample | Metastatic recurrence; de-novo metastatic | Non-metastatic disease at sample
denovom_seq | De-novo metastatic disease: metastases since diagnosis (M1) vs. M0 at diagnosis and metastases detected after diagnosis but before sequencing | Metastatic recurrence; de-novo metastatic | Non-metastatic disease at sequencing
Outcomes
Setup:
- Indicator (event) variables are in
datasets$pts, because events can only occur once per person. - Time variables are in
datasets$smp, because time intervals between start of follow-up and event depend on when start of follow-up is set and thus differ for different samples from the same person. For analyses, select samples and then merge patient data byptid.
Time variables will be missing:
- If the patient is not at risk of the event at the start of follow up because the event already occurred, e.g., metastasis when starting follow-up in metastatic castration-resistant disease.
- If the patient is not at risk because the event cannot occur, e.g., a variant histology indicates castration resistance and the patient will by definition not be followed for this outcome.
- If the event time is unknown.
Outcome: Transition | Population of Interest | Event variable (Descriptive) | Event variable (modeling) | Time variable (from sequencing) | Time variables (late-entry models)^1^
--------------+-----------------+---------------+------------+----------------+----------------
Metastasis: Sequencing to metastasis | Disease extent "Localized" or "Regional nodes" at sequencing | is_met: No; Yes | met_event: 0; 1 | seq_met_mos: Months from sequencing to metastasis or last clinic visit | dx_met_mos: Months from diagnosis to metastasis or last clinic visit
Metastasis-free survival: Sequencing to metastasis or death from any cause (composite endpoint) | Disease extent "Localized" or "Regional nodes" at sequencing | is_mfs: Event-free; Metastasis/death | mfs_event: 0; 1 | seq_mfs_mos: Months from sequencing to metastasis, death, or last clinic visit (if neither) | dx_mfs_mos: Months from diagnosis to metastasis, death, or last clinic visit (if neither)
CRPC: Sequencing to castration resistance | Disease extent "Localized", "Regional nodes", or "Metastatic hormone-sensitive" at sequencing | is_crpc: No; Yes; N/A-Pure Other Histology at Diagnosis; N/A-Pure small cell/neuroendocrine at diagnosis | crpc_event: 0; 1; missing (if variant histology) | seq_crpc_mos: Months from sequencing to castration resistance or last clinic visit | dx_crpc_mos: Months from diagnosis to castration resistance or last clinic visit
Overall survival: Sequencing to death | All | is_dead: Alive; Dead | death_event: 0; 1 | seq_os_mos: Months from sequencing to death or last contact | dx_os_mos: Months from diagnosis to death or last contact; adt_os_mos: Months from ADT initiation to death or last contact; met_os_mos: Months from metastasis to death or last contact
^1^ In late entry models, participants should enter risk sets at the time of sequencing using appropriate variables, i.e., dx_seq_mos (diagnosis to sequencing), adt_seq_mos (ADT initiation to sequencing), or met_seq_mos (metastasis to sequencing).
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