High-resolution mapping of copy-number alterations with massively parallel sequencing

被引：244

作者：

Chiang, Derek Y. ^{[1
,2
,3
]}

Getz, Gad ^{[1
]}

Jaffe, David B. ^{[1
]}

O'Kelly, Michael J. T. ^{[1
]}

Zhao, Xiaojun ^{[4
]}

Carter, Scott L. ^{[1
,5
]}

Russ, Carsten ^{[1
]}

Nusbaum, Chad ^{[1
]}

Meyerson, Matthew ^{[1
,2
,3
]}

Lander, Eric S.

机构：

[1] Broad Inst MIT & Harvard, Cambridge, MA 02142 USA

[2] Dana Farber Canc Inst, Dept Med Oncol, Boston, MA 02115 USA

[3] Dana Farber Canc Inst, Ctr Canc Genome Discovery, Boston, MA 02115 USA

[4] Novartis Inst Biomed Res, Cambridge, MA 02139 USA

[5] Harvard Mit Div Hlth Sci & Technol, Cambridge, MA 02139 USA

来源：

NATURE METHODS | 2009年 / 6卷 / 01期

基金：

美国国家卫生研究院;

关键词：

ARRAY CGH DATA; STRUCTURAL VARIATION; HUMAN GENOME; CANCER; AMPLIFICATIONS; REARRANGEMENTS; DELETIONS; CELLS;

D O I：

10.1038/NMETH.1276

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Cancer results from somatic alterations in key genes, including point mutations, copy-number alterations and structural rearrangements. A powerful way to discover cancer-causing genes is to identify genomic regions that show recurrent copy-number alterations (gains and losses) in tumor genomes. Recent advances in sequencing technologies suggest that massively parallel sequencing may provide a feasible alternative to DNA microarrays for detecting copy-number alterations. Here we present: (i) a statistical analysis of the power to detect copy-number alterations of a given size; (ii) SegSeq, an algorithm to segment equal copy numbers from massively parallel sequence data; and (iii) analysis of experimental data from three matched pairs of tumor and normal cell lines. We show that a collection of similar to 14 million aligned sequence reads from human cell lines has comparable power to detect events as the current generation of DNA microarrays and has over twofold better precision for localizing breakpoints (typically, to within similar to 1 kilobase).

引用

页码：99 / 103

页数：5

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