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A comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variants (Human1Mv1_C)

ABSTRACT: Systematic evaluation of eleven array platforms commonly used for CNV detection to address parameters of quality and CNV calling. 36 Samples

ORGANISM(S): Homo sapiens

SUBMITTER: Dalila Pinto

PROVIDER: E-GEOD-28092 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variants.

Pinto Dalila D Darvishi Katayoon K Shi Xinghua X Rajan Diana D Rigler Diane D Fitzgerald Tom T Lionel Anath C AC Thiruvahindrapuram Bhooma B Macdonald Jeffrey R JR Mills Ryan R Prasad Aparna A Noonan Kristin K Gribble Susan S Prigmore Elena E Donahoe Patricia K PK Smith Richard S RS Park Ji Hyeon JH Hurles Matthew E ME Carter Nigel P NP Lee Charles C Scherer Stephen W SW Feuk Lars L

Nature biotechnology 20110508 6

We have systematically compared copy number variant (CNV) detection on eleven microarrays to evaluate data quality and CNV calling, reproducibility, concordance across array platforms and laboratory sites, breakpoint accuracy and analysis tool variability. Different analytic tools applied to the same raw data typically yield CNV calls with <50% concordance. Moreover, reproducibility in replicate experiments is <70% for most platforms. Nevertheless, these findings should not preclude detection of ...[more]

PMID: 21552272

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