High-Definition Reconstruction of Clonal Composition in Cancer

被引：120

作者：

Fischer, Andrej ^{[1
]}

Vazquez-Garcia, Ignacio ^{[1
,2
]}

Illingworth, Christopher J. R. ^{[3
]}

Mustonen, Ville ^{[1
]}

机构：

[1] Wellcome Trust Sanger Inst, Cambridge CB10 1SA, England

[2] Univ Cambridge, Ctr Math Sci, Dept Appl Math & Theoret Phys, Cambridge CB3 0WA, England

[3] Univ Cambridge, Dept Genet, Cambridge CB2 3EH, England

来源：

CELL REPORTS | 2014年 / 7卷 / 05期

基金：

英国惠康基金;

关键词：

TERT PROMOTER MUTATIONS; COPY NUMBER ANALYSIS; TUMOR SAMPLES; EVOLUTION; GENOME; HETEROGENEITY; HETEROZYGOSITY; CONSEQUENCES; TECHNOLOGIES; SIGNATURES;

D O I：

10.1016/j.celrep.2014.04.055

中图分类号：

Q2 [细胞生物学];

学科分类号：

071009 ; 090102 ;

摘要：

The extensive genetic heterogeneity of cancers can greatly affect therapy success due to the existence of subclonal mutations conferring resistance. However, the characterization of subclones in mixed-cell populations is computationally challenging due to the short length of sequence reads that are generated by current sequencing technologies. Here, we report cloneHD, a probabilistic algorithm for the performance of subclone reconstruction from data generated by high-throughput DNA sequencing: read depth, B-allele counts at germline heterozygous loci, and somatic mutation counts. The algorithm can exploit the added information present in correlated longitudinal or multiregion samples and takes into account correlations along genomes caused by events such as copy-number changes. We apply cloneHD to two case studies: a breast cancer sample and time-resolved samples of chronic lymphocytic leukemia, where we demonstrate that monitoring the response of a patient to therapy regimens is feasible. Our work provides new opportunities for tracking cancer development.

引用

页码：1740 / 1752

页数：13

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