longitudinal_sc_variants: Mutation data from Rambow, Florian, et al. "Toward minimal...

In gian-asco/test: Longitudinal Analysis of Cancer Evolution (LACE)

Mutation data from Rambow, Florian, et al. "Toward minimal residual disease-directed therapy in melanoma." Cell 174.4 (2018): 843-855.

Description

The dataset includes somatic single nucleotide variants at the single cell resolution. SNVs are called from SMARTseq2 fastq obtained from Gene Expression Omnibus database with the accession number: GSE116237. The dataset includes single cell data from a PDX melanoma model before and on treatment with BRAF and MEK inhibitors. The fastq files are processed to obtain the mutational profile following GATK best practice (https://gatkforums.broadinstitute.org/gatk/discussion/3891/calling-variants-in-rnaseq) usign the GRCh38 human genome as reference. Mutation data are stored in an N x M binary matrix with N single cells and M somatic single nucleotide variants. Row names report the ID of the fastq file related to a specific single cell; columns names report the SNV that are formatted as GeneName_chromosome_position_referenceAllele_alternateAllele. Each matrix entry can be 1 (mutation detected), 0 (mutation absent) or NA (too low coverage to determine the presence or absence of that mutation). For further details, please refer to the Methods Section and the section 3.1 of supplementary materials of Ramazzotti, Daniele, et al. "Longitudinal cancer evolution from single cells." bioRxiv (2020).

Usage

data(longitudinal_sc_variants)

Format

List of mutation data for four time points

Value

List of mutational data for a total of 475 single cells

Source

Rambow, Florian, et al. "Toward minimal residual disease-directed therapy in melanoma." Cell 174.4 (2018): 843-855.

gian-asco/test documentation built on April 11, 2022, 12:05 a.m.