Complete Genomics Inc., the whole human genome sequencing company that has developed and commercialized an innovative DNA sequencing service,  has sequenced the genomes of 600 individuals from 20 Mexican-American families from San Antonio in what is thought to be the largest whole genome sequencing family study conducted to date and the first such study of its kind in a Latino population.

“We are optimistic that this multigenerational, whole genome sequencing study will help us to identify some of the rare variants involved in type 2 diabetes that have eluded us to date,” said Dr. John Blangero, a geneticist at the Texas Biomedical Research Institute in San Antonio and one of the researchers. “Our aim is to identify genetic variants that play a role in type 2 diabetes risk or influence variability in diabetes-related traits, such as blood glucose levels and body mass index.”

The study, carried out as part of the T2D-GENES (Type 2 Diabetes Genetic Exploration by Next-generation sequencing in multi-Ethnic Samples) consortium, is funded by the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) of the National Institutes of Health.

Researchers at the Texas Biomedical Research Institute and their collaborators have been collecting healthcare data from approximately 2,500 members of 85 Mexican-American families since 1991. The 600 individuals selected for this whole genome sequencing study were previously genotyped in an earlier genome-wide association study and are members of several of the largest families with increased prevalence of diabetes. While the earlier study targeted common genetic variants associated with diabetes, the whole genome sequencing study will now facilitate the search for less common and rare variants associated with diabetes. This new study has the potential to reveal subtypes of type 2 diabetes and identify novel therapeutic targets.

“We have already begun analyzing the whole genome sequencing data that we received from Complete Genomics. The genomes were sequenced to an average of >50x coverage and we are very pleased with the high quality of the data,” said Dr. Blangero. “We will use the sequencing data to fill in the gaps in our genotyping data.”

Mexican-Americans are almost twice as likely as non-Hispanic whites to be diagnosed with diabetes, according to the US Department of Health and Human Services. This population also has higher rates of end-stage renal disease, which can be caused by diabetes, and is 50 per cent more likely to die from diabetes than are non-Hispanic whites. Type 2 diabetes, in which the body doesn’t make enough insulin, affects more than 25 million Americans.

By carefully selecting individuals from large pedigrees and choosing to have those individuals whole genome sequenced by Complete Genomics, the diabetes study offers researchers the unique ability to use their pre-existing genome-wide association data to impute the whole genome sequencing results from 600 individuals into other family members. This will provide complete whole genotype information for more than 1,000 individuals, nearly doubling the set of whole genome sequenced individuals.

“We are delighted to work with the T2D-GENES researchers to develop new ways to maximize genomics’ potential to further medical knowledge,” said Dr. Clifford Reid, chairman, president and CEO of Complete Genomics. “We hope that their smart, elegant and cost-effective approach will lead to the development of targeted therapies for type 2 diabetes.”

T2D-GENES is an international consortium that involves investigators from more than 20 academic centers worldwide.