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Study Description

We present a database of copy number variations (CNVs) detected in 2,026 disease-free individuals, using high-density, SNP-based oligonucleotide microarrays. This large cohort analyzed for CNVs in a single study using a uniform array platform and computational tools, comprises mainly of Caucasians (65.2%) and African-Americans (34.2%), We have catalogued and characterized 54,462 individual CNVs, 77.8% of which were identified in multiple unrelated individuals. These non-unique CNVs mapped to 3,272 distinct regions of genomic variation spanning 5.9% of the genome; 51.5% of these were previously unreported, and >85% are rare. Our annotation and analysis confirmed and extended previously reported correlations between CNVs and several genomic features such as repetitive DNA elements, segmental duplications and genes. We demonstrate the utility of this data set in distinguishing CNVs with pathologic significance from normal variants. Together, this analysis and annotation provides a useful resource to assist with the assessment of CNVs in the contexts of human variation, disease susceptibility, and clinical molecular diagnostics. The CNV resource is available at: Reprinted from Shaikh T., et al., High-Resolution Mapping and Analysis of Copy Number Variations in the Human Genome: A Data Resource for Clinical and Research Applications Genome Research. 2009, with permission from Genome Research.

CHOP CNVs from 2,026 disease-free individuals are available through dbVar at

  • Study Weblink: Copy Number Variation
  • Study Type: Control Set
  • Number of study subjects that have individual level data available through Authorized Access: 2026

Authorized Access
Publicly Available Data (Public ftp)

Connect to the public download site. The site contains release notes and manifests. If available, the site also contains data dictionaries, variable summaries, documents, and truncated analyses.

Study Inclusion/Exclusion Criteria

Control Inclusions:

Healthy controls

Molecular Data
TypeSourcePlatformNumber of Oligos/SNPsSNP Batch IdComment
Whole Genome Genotyping Illumina HumanHap550v1.1 555352 38431
Study History
Samples were collected and typed by the Center for Applied Genomics at Children's Hospital of Philadelphia.
Selected publications
Diseases/Traits Related to Study (MESH terms)
Links to Related Resources
Authorized Data Access Requests
Study Attribution
  • Principal Investigator
    • Hakon Hakonarson, MD, PhD. Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
  • Co-Investigators
    • Tamim H. Shaikh, PhD. Department of Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
    • Peter S. White, PhD. Center for Biomedical Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
  • Funding Source
    • Developmental Research Award from the Cotswold Foundation. Cotswold Foundation, Broomall, PA, USA
    • Institutional Award. Children's Hospital of Philadelphia, Philadelphia, PA, USA
    • GM081519. National Institutes of Health, Bethesda, MD, USA
    • SAP 4100037707. Pennsylvania Department of Health, Harrisburg, PA, USA
    • David Lawrence Altschuler Chair in Genomics and Computational Biology. Children's Hospital of Philadelphia, Philadelphia, PA, USA