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ISB Identifies Candidate Disease Genes with Complete Genomics Data

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Scientists from the Institute for Systems Biology analyzed the genomes of a four-member family sequenced by Complete Genomics and pinpointed three candidate disease genes for the children, who suffer from rare Mendelian disorders.

Lee Rowen, a senior research scientist at ISB, presented the results earlier this fall at the Personal Genomes conference at Cold Spring Harbor Laboratory. For Complete Genomics, the study provided the first independent validation of the company's sequencing service by an early-access customer.

At the conference, Rowen discussed early results from the institute's unpublished pilot project. Based on those, ISB plans to send Complete Genomics another 100 samples from multi-generational families, she said.

For the study, Complete Genomics sequenced the genomes of two healthy parents and their two children, who both suffer from a rare craniofacial malformation syndrome as well as from severe lung disease.

The project had three main aims, Rowen said: to evaluate Complete's sequencing technology; to study how genes are passed on from one generation to another — including recombination and new variations; and to find candidate genes for the children's diseases.

At a cost of $20,000 per genome, Complete Genomics generated about 120 gigabases of data per sample, which it provided to ISB researchers in May, including reads mapped to the hg18 reference genome, coverage tables, and variation tables.

The researchers also assessed the technology's error rate, which they currently estimate to be about 10 to 20 bases per megabase, depending on the portion of the genome analyzed. Overall, they found the data quality to be "extremely high," she added.

In order to pinpoint candidate disease genes, the researchers — assuming that the children suffer from rare Mendelian diseases — searched the data for novel non-synonymous SNPs in the children's exons and ended up with a short list of three genes.

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