Performance assessment of copy number microarray platforms using a spike-in experiment

被引：15

作者：

Halper-Stromberg, Eitan ^{[1
,2
]}

Frelin, Laurence ^{[3
]}

Ruczinski, Ingo ^{[1
]}

Scharpf, Robert ^{[1
]}

Jie, Chunfa ^{[4
]}

Carvalho, Benilton ^{[5
]}

Hao, Haiping ^{[4
]}

Hetrick, Kurt ^{[6
]}

Jedlicka, Anne ^{[7
]}

Dziedzic, Amanda ^{[7
]}

Doheny, Kim ^{[6
]}

Scott, Alan F. ^{[6
]}

Baylin, Steve ^{[8
]}

Pevsner, Jonathan ^{[3
,9
]}

Spencer, Forrest ^{[10
]}

Irizarry, Rafael A. ^{[1
]}

机构：

[1] Bloomberg Sch Publ Hlth, Dept Biostat, Baltimore, MD USA

[2] Johns Hopkins Univ, Sch Med, Program Human Genet & Mol Biol, Baltimore, MD USA

[3] Hugo W Moser Res Inst Kennedy Krieger, Dept Neurol, Baltimore, MD USA

[4] Johns Hopkins Univ, Sch Med, High Throughput Biol Ctr, JHMI Microarray Core, Baltimore, MD USA

[5] Univ Cambridge, CRUK Cambridge Res Inst, Li Ka Shing Ctr, Dept Oncol, Cambridge CB2 0RE, England

[6] Johns Hopkins Univ, Ctr Inherited Dis Res, Baltimore, MD USA

[7] Johns Hopkins Univ, Dept Mol Microbiol & Immunol, Johns Hopkins Malaria Res Inst, Johns Hopkins Bloomberg Sch Publ Hlth, Baltimore, MD USA

[8] Johns Hopkins Univ, Sch Med, Dept Oncol, Baltimore, MD 21205 USA

[9] Johns Hopkins Univ, Sch Med, Dept Neurosci, Baltimore, MD 21205 USA

[10] Johns Hopkins Univ, Sch Med, McKusick Nathans Inst Genet Med, Baltimore, MD 21205 USA

来源：

BIOINFORMATICS | 2011年 / 27卷 / 08期

基金：

美国国家卫生研究院;

关键词：

HIDDEN-MARKOV MODEL; NORMALIZATION; ALGORITHMS; DETECT;

D O I：

10.1093/bioinformatics/btr106

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Motivation: Changes in the copy number of chromosomal DNA segments [copy number variants (CNVs)] have been implicated in human variation, heritable diseases and cancers. Microarray-based platforms are the current established technology of choice for studies reporting these discoveries and constitute the benchmark against which emergent sequence-based approaches will be evaluated. Research that depends on CNV analysis is rapidly increasing, and systematic platform assessments that distinguish strengths and weaknesses are needed to guide informed choice. Results: We evaluated the sensitivity and specificity of six platforms, provided by four leading vendors, using a spike-in experiment. NimbleGen and Agilent platforms outperformed Illumina and Affymetrix in accuracy and precision of copy number dosage estimates. However, Illumina and Affymetrix algorithms that leverage single nucleotide polymorphism (SNP) information make up for this disadvantage and perform well at variant detection. Overall, the NimbleGen 2.1M platform outperformed others, but only with the use of an alternative data analysis pipeline to the one offered by the manufacturer.

引用

页码：1052 / 1060

页数：9

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