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Adding CNV’s to the Mix

Augusts 8, 2007 | “CNV analysis is reaching a fever pitch,” says Christophe Lambert of Golden Helix, noting the additional challenges whole genome CNV studies present (see “The One Percent Difference,” Bio•IT World, Jan. 2007).

“Copy number data is much less easy to compress in memory space [compared to SNP data],” Lambert explains, with even modestly sized CNV studies generating 10’s to 100’s of gigabytes of data. Golden Helix will shortly release a software application that will enable WGA studies based on CNV data. To date, researchers have identified about 1,700 CNV regions in the human genome. The challenge now is to figure out which insertions, deletions, and amplifications can be correlated to disease types.

“Software must be flexible to handle differing experimental designs, large scale studies, and integration of related information (copy number, annotation, etc.),” says Tom Downey of Partek. “I expect analysis strategies to change over time as more investigators begin incorporating CNVs into studies and provide the community with feedback on techniques they found useful while analyzing their data.”

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