Genome-wide mapping of copy number variation in humans: Comparative analysis of high resolution array platforms

Rajini R. Haraksingh, Alexej Abyzov, Mark Gerstein, Alexander E. Urban, Michael Snyder

Research output: Contribution to journalArticle

47 Citations (Scopus)

Abstract

Accurate and efficient genome-wide detection of copy number variants (CNVs) is essential for understanding human genomic variation, genome-wide CNV association type studies, cytogenetics research and diagnostics, and independent validation of CNVs identified from sequencing based technologies. Numerous, array-based platforms for CNV detection exist utilizing array Comparative Genome Hybridization (aCGH), Single Nucleotide Polymorphism (SNP) genotyping or both. We have quantitatively assessed the abilities of twelve leading genome-wide CNV detection platforms to accurately detect Gold Standard sets of CNVs in the genome of HapMap CEU sample NA12878, and found significant differences in performance. The technologies analyzed were the NimbleGen 4.2 M, 2.1 M and 3×720 K Whole Genome and CNV focused arrays, the Agilent 1×1 M CGH and High Resolution and 2×400 K CNV and SNP+CGH arrays, the Illumina Human Omni1Quad array and the Affymetrix SNP 6.0 array. The Gold Standards used were a 1000 Genomes Project sequencing-based set of 3997 validated CNVs and an ultra high-resolution aCGH-based set of 756 validated CNVs. We found that sensitivity, total number, size range and breakpoint resolution of CNV calls were highest for CNV focused arrays. Our results are important for cost effective CNV detection and validation for both basic and clinical applications.

Original languageEnglish (US)
Article numbere27859
JournalPLoS One
Volume6
Issue number11
DOIs
StatePublished - Nov 30 2011
Externally publishedYes

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Chromosome Mapping
Genes
Genome
genome
single nucleotide polymorphism
comparative genomic hybridization
Single Nucleotide Polymorphism
Comparative Genomic Hybridization
Polymorphism
gold
Nucleotides
HapMap Project
Technology
cytogenetics
Cytogenetics
genotyping
genomics
Costs and Cost Analysis
Research

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Genome-wide mapping of copy number variation in humans : Comparative analysis of high resolution array platforms. / Haraksingh, Rajini R.; Abyzov, Alexej; Gerstein, Mark; Urban, Alexander E.; Snyder, Michael.

In: PLoS One, Vol. 6, No. 11, e27859, 30.11.2011.

Research output: Contribution to journalArticle

Haraksingh, Rajini R. ; Abyzov, Alexej ; Gerstein, Mark ; Urban, Alexander E. ; Snyder, Michael. / Genome-wide mapping of copy number variation in humans : Comparative analysis of high resolution array platforms. In: PLoS One. 2011 ; Vol. 6, No. 11.
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