Journal
BIOINFORMATICS
Volume 27, Issue 8, Pages 1052-1060Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btr106
Keywords
-
Categories
Funding
- Johns Hopkins Fund for Medical Discovery
- National Institutes of Health [R01GM077456, R01GM083084, R01RR021967, T32GM974906, HD24061, UL1 RR 025005]
- Cancer Research UK [19556] Funding Source: researchfish
Ask authors/readers for more resources
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.
Authors
I am an author on this paper
Click your name to claim this paper and add it to your profile.
Reviews
Recommended
No Data Available