Analysis of array CGH data:: from signal ratio to gain and loss of DNA regions

被引：401

作者：

Hupé, P

Stransky, N

Thiery, JP

Radvanyi, F

Barillot, E

机构：

[1] Inst Curie, Serv Bioinformat, F-75248 Paris 05, France

[2] Inst Curie, CNRS, UMR 144, F-75248 Paris 05, France

来源：

BIOINFORMATICS | 2004年 / 20卷 / 18期

关键词：

D O I：

10.1093/bioinformatics/bth418

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Motivation: Genomic DNA regions are frequently lost or gained during tumor progression. Array Comparative Genomic Hybridization (array CGH) technology makes it possible to assess these changes in DNA in cancers, by comparison with a normal reference. The identification of systematically deleted or amplified genomic regions in a set of tumors enables biologists to identify genes involved in cancer progression because tumor suppressor genes are thought to be located in lost genomic regions and oncogenes, in gained regions. Array CGH profiles should also improve the classification of tumors. The achievement of these goals requires a methodology for detecting the breakpoints delimiting altered regions in genomic patterns and assigning a status (normal, gained or lost) to each chromosomal region. Results: We have developed a methodology for the automatic detection of breakpoints from array CGH profile, and the assignment of a status to each chromosomal region. The breakpoint detection step is based on the Adaptive Weights Smoothing (AWS) procedure and provides highly convincing results: our algorithm detects 97, 100 and 94% of breakpoints in simulated data, karyotyping results and manually analyzed profiles, respectively. The percentage of correctly assigned statuses ranges from 98.9 to 99.8% for simulated data and is 100% for karyotyping results. Our algorithm also outperforms other solutions on a public reference dataset.

引用

页码：3413 / 3422

页数：10

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