Somatic mutations and Loss of Heterozygosity (LOH) of a Glioblastoma tumor (TCGA-06-0152-01)

datasets

Expanding Ploidy and Allele Frequency on Nested Subpopulations (ExPANdS) characterizes coexisting subpopulations (SPs) in a tumor using copy number and allele frequencies derived from exome- or whole genome sequencing input data. The model amplifies the statistical power to detect coexisting genotypes, by fully exploiting run-specific tradeoffs between depth of coverage and breadth of coverage. ExPANdS predicts the number of clonal expansions, the size of the resulting SPs in the tumor bulk, the mutations specific to each SP and tumor purity. The main function runExPANdS provides the complete functionality needed to predict coexisting SPs from single nucleotide variations (SNVs) and associated copy numbers.  The robustness of the subpopulation predictions by ExPANdS increases with the number of mutations provided. It is recommended that at least 200 mutations are used as an input to obtain stable results.

Noemi Andor

expands

ExPANdS

snv function

Numeric matrix with 773 rows (one per mutation) and 7 columns:chr - the chromosome startpos - genomic position endpos - same as above REF - ASCII code of the reference nucleotide (in hg18/hg19) ALT - ASCII code of the B-allele nucleotide AF_Tumor - allele frequeny of B-allele PN_B - ploidy of B-allele in normal cells (1 if B-allele is a germline variant, 0 if the B-allele is a consequence of a somatic mutation)

format

Data derived from The Cancer Genome Atlas (TCGA)

snv: Single Nucleotide Variations

Description

Usage

Arguments

format

source