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 in a single tumor sample using copy number and allele frequencies derived from exome- or whole genome sequencing input data (http://www.ncbi.nlm.nih.gov/pubmed/24177718). The model detects coexisting genotypes by leveraging run-specific tradeoffs between depth of coverage and breadth of coverage. This package predicts the number of clonal expansions, the size of the resulting subpopulations in the tumor bulk, the mutations specific to each subpopulation, tumor purity and phylogeny. The main function runExPANdS() provides the complete functionality needed to predict coexisting subpopulations from single nucleotide variations (SNVs) and associated copy numbers.  The robustness of subpopulation predictions increases with the number of mutations provided. It is recommended that at least 200 mutations are used as input to obtain stable results. Updates in version 1.7 include: (1) Higher subpopulation detection specificity, in particular for small subpopulations. (2) Higher accuracy for mutation assignment to subpopulations. (3) Whenever possible, SNVs are assigned not only to the subpopulation in which they first occurred, but also to descending subpopulations. (4) Two additional output files are created: subpopulation specific ploidy matrix and a summary file of all detected subpopulations, including information on the inferred ancestor and the closest descendant of each subpopulation. (5) New subpopulation plotting options (function plotSPs). (6) New phylogeny plotting option: user can choose between consensus and germline population to be included as control. (7) 50 simulated samples of various genetic complexities and measurement precision included for user testing. Special thanks to Dr. Ryan Morin for his contributions that have led to higher accuracy measures during simulations for mutation assignment to subpopulations, as well as advanced visualization features of assigned mutations. Further documentation and FAQ available at http://dna-discovery.stanford.edu/software/expands.

Noemi Andor

expands

Expanding Ploidy and Allele-Frequency on Nested Subpopulations

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. A value of 0 indicates that the mutation has only been detected in the tumor sample (i.e. somatic mutations). A value of 1 indicates that the mutation is also present in the normal (control) sample, albeit at reduced allele frequency (i.e. mutation is consequence of LOH). Other mutations should not be included.

format

Data derived from The Cancer Genome Atlas (TCGA).

snv: Single Nucleotide Variations

Description

Usage

Arguments

format

source