PhyloWGS: Reconstructing subclonal composition and evolution from whole-genome sequencing of tumors

被引：274

作者：

Deshwar, Amit G. ^{[1
]}

Vembu, Shankar ^{[2
]}

Yung, Christina K. ^{[3
]}

Jang, Gun Ho ^{[3
]}

Stein, Lincoln ^{[3
,5
]}

Morris, Quaid ^{[1
,2
,4
,5
]}

机构：

[1] Univ Toronto, Edward S Rogers Sr Dept Elect & Comp Engn, Toronto, ON, Canada

[2] Univ Toronto, Donnelly Ctr, Toronto, ON, Canada

[3] Ontario Inst Canc Res, Informat & Biocomp Program, Toronto, ON, Canada

[4] Univ Toronto, Dept Comp Sci, Toronto, ON, Canada

[5] Univ Toronto, Dept Mol Genet, Toronto, ON, Canada

来源：

GENOME BIOLOGY | 2015年 / 16卷

基金：

加拿大自然科学与工程研究理事会;

关键词：

CLONAL EVOLUTION; CANCER; HETEROGENEITY; NUMBER; POPULATION; MUTATIONS; HALLMARKS; INFERENCE;

D O I：

10.1186/s13059-015-0602-8

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

Tumors often contain multiple subpopulations of cancerous cells defined by distinct somatic mutations. We describe a new method, PhyloWGS, which can be applied to whole-genome sequencing data from one or more tumor samples to reconstruct complete genotypes of these subpopulations based on variant allele frequencies (VAFs) of point mutations and population frequencies of structural variations. We introduce a principled phylogenic correction for VAFs in loci affected by copy number alterations and we show that this correction greatly improves subclonal reconstruction compared to existing methods.

引用

页数：20

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