Baylor HGSC and Roche have worked together for three years to optimize methods.
The Baylor College of Medicine Human Genome Sequencing Center (HGSC) reports that it plans to sequence over 5,000 exomes in the next two years to identify genetic variants underlying multiple human diseases. The project will use the NimbleGen SeqCap EZ Exome technology and customized NimbleGen exome designs.
Baylor HGSC says that it has already standardized its target-enrichment human disease research studies on this Roche NimbleGen sequence capture exome technology. The Baylor HGSC researchers will investigate more than 15 different diseases including brain, liver, pancreatic, colon, ovarian, and bladder cancers, heart disease, diabetes, autism, and other inherited diseases. The goal is to better understand causative mutations and their impact on these diseases.
The studies are supported by multiple funds from the NIH and other research consortia. Through a collaboration with Roche NimbleGen, Baylor HGSC has established and optimized its pipeline for high-throughput exome capture and sequencing with multiple next-generation sequencing platforms. Baylor has already captured and sequenced over 2,000 samples, with roughly 1,000 of these using exome sequencing.
“We have now been working with scientists from Roche NimbleGen for more than three years developing these optimized capture methods,” says Richard Gibbs, Ph.D., director of HGSC and Wofford Cain professor from the department of molecular and human genetics at Baylor. “The different configurations of the SeqCap EZ Exome technology have superb performance in our hands and will have profound influence on human disease studies.”
Because the majority of known disease-causing mutations occur in the coding regions of the human genome, sequencing the exome allows researchers to focus on this highly important 1% of the genome and efficiently identify genetic variants that are important for genetic diseases. The cost savings gained by exome sequencing in comparison to whole-genome sequencing allows researchers to investigate more biological samples and to do so more rapidly, Roche points out. It is also important for cancer studies, as heterogeneous tumor tissues often require very deep sequencing, which is made economically possible by targeted enrichment, the company adds.
In a study published in Genome Biology, scientists from Baylor HGSC and Roche NimbleGen used SeqCap EZ Exome to demonstrate that as little as 3 Gb of raw sequence data is needed to discover >95% of expected heterozygous single base variants. In this study, SeqCap EZ Exome technology was coupled with multiple high-throughput sequencing platforms for resequencing of protein coding regions within the human genome.