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Researchers Create Database of CNVs in Healthy Individuals

NEW YORK (GenomeWeb News) – Researchers from the Children's Hospital of Philadelphia and the University of Pennsylvania have developed a database of copy number variations present in thousands of healthy individuals. The resource is based on the team's recent Genome Research study, which catalogued CNVs in thousands of healthy individuals.

"Some CNVs contribute to a disorder, but most of them do not, and it is often challenging to determine which are important," co-senior author Peter White, a molecular genetic researcher and director of CHOP's Center for Biomedical Informatics, said in a statement. "Our map provides a large and uniform baseline standard to indicate which CNVs represent normal variation."

The team used Illumina microarrays to look for structural variants in more than 2,000 individuals. On average, they found that healthy individuals carried dozens of CNVs. And altogether their search revealed nearly 55,000 variants — about half of which had not been detected before. By making their findings available to other researchers, the team hopes to provide a resource for those working to understand the role of structural variation in human disease.

"In order to pinpoint the one CNV that is the cause of a disease, it is critical to quickly eliminate those that are part of the spectrum of normal variation that exists in the human genome," lead author Tamim Shaikh, a CHOP molecular genetic researcher, said in a statement. "That's what this CNV data and other similar resources allow us to do."

In an effort to collect CNV data for distinguishing between harmless and potentially deleterious variants down the road, the researchers catalogued CNVs in 2,026 healthy individuals — including both children and parents — using the Illumina HumanHap 550 BeadChip, a high-density, SNP-based, oligonucleotide microarray. The subjects included both children and parents. About 65 percent of participants were Caucasian and 34 percent were African-American.

Using this approach, the researchers detected 54,462 different CNVs. Of these, 77.8 percent of the CNVs were found in more than one unrelated individual.

More than half of the CNVs — 51.5 percent — had not been detected in previous studies. And most (73 percent) of those that were non-unique overlapped with CNVs found in the Database of Genomic Variants, a genomic structural variation resource hosted by the Hospital for Sick Children's Centre for Applied Genomics.

While the researchers expect that many of these copy number polymorphisms are benign, co-senior author Hakon Hakonarson, director of the Center for Applied Genomics at CHOP, said that some may turn out to be disease-related in the future. "Although these CNVs were detected in healthy children, they may have significant disease implications that may not manifest until later in life," he said in a statement.

The team is making their new CNV database freely available online. "Our analysis and annotation provides a useful resource to assist with the assessment of structural variants in the contexts of human variation, disease susceptibility, and clinical molecular diagnostics," the authors wrote.

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