Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays

被引：155

作者：

Popova, Tatiana ^{[1
,2
]}

Manie, Elodie ^{[1
,2
]}

Stoppa-Lyonnet, Dominique ^{[1
,2
,3
,4
]}

Rigaill, Guillem ^{[5
,6
]}

Barillot, Emmanuel ^{[1
,7
,8
]}

Stern, Marc Henri ^{[1
,2
]}

机构：

[1] Inst Curie, Ctr Rech, F-75248 Paris, France

[2] Inst Curie, INSERM, U830, F-75248 Paris, France

[3] Inst Curie, Dept Tumor Biol, F-75248 Paris, France

[4] Univ Paris 05, F-75270 Paris, France

[5] Inst Curie, Translat Res Dept, F-75475 Paris, France

[6] AgroParisTech INRA, MIA 518, F-75231 Paris, France

[7] Inst Curie, INSERM, U900, F-75248 Paris, France

[8] Ecole Mines ParisTech, F-77305 Fontainebleau, France

来源：

GENOME BIOLOGY | 2009年 / 10卷 / 11期

关键词：

NUCLEOTIDE POLYMORPHISM ARRAY; BASAL-LIKE CARCINOMAS; HIDDEN MARKOV MODEL; BREAST-CANCER; CGH DATA; TUMOR SAMPLES; COPY-NUMBERS; BRCA1; ABERRATIONS; HETEROZYGOSITY;

D O I：

10.1186/gb-2009-10-11-r128

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：

We describe a method for automatic detection of absolute segmental copy numbers and genotype status in complex cancer genome profiles measured with single-nucleotide polymorphism (SNP) arrays. The method is based on pattern recognition of segmented and smoothed copy number and allelic imbalance profiles. Assignments were verified by DNA indexes of primary tumors and karyotypes of cell lines. The method performs well even for poor-quality data, low tumor content, and highly rearranged tumor genomes.

引用

页数：14

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