DNAnexus Collaboration Yields New Genetic Variant Data Set for 1000 Genomes Project

05 Dec 2013
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DNAnexus, a pioneer in cloud-based solutions for large-scale DNA data management and analysis, has announced a collaboration with Stanford University that has resulted in a new 1000 Genomes Project data set of genetic variation. Through this collaboration, scientists have analyzed and identified genetic variants in more than 80 terabytes (TB) of raw BAM files – a binary format for storing DNA sequence data – using the DNAnexus Platform-as-a-Service (PaaS) and have made these data publicly available for follow-on biomedical research.

Launched in January 2008, the 1000 Genomes Project was the first international effort to sequence a large number of individual genomes with the goal of developing a comprehensive and freely accessible resource on human genetic variation. The project has grown to include genomic data from more than 2,500 individuals across 26 separate ethnic populations and is expected to conclude in the spring of 2014.

One of many international teams contributing to the 1000 Genomes Project is the lab of Carlos D. Bustamante, PhD, professor of genetics at Stanford University School of Medicine. The data generated by the project is expected to support a deeper understanding of genetic variation patterns in underserved populations, including African-Americans and Hispanic-Latinos. These data will also enable the development of rich catalogs of DNA variants that could help researchers develop new medical tools such as tests for evaluating disease susceptibility in different populations.

“We believe that many genetic variants exist in present-day admixed populations that have never been seen in typical European-centric biomedical studies. By looking at these groups more closely, we hope not only to increase the overall understanding of haplotype, nucleotide, and structural variation diversity, but also to bring these underserved communities into the fold of medical genetics research,” said Andrew Carroll, PhD, lead DNAnexus scientist on this collaboration.

In this project, Stanford scientists performed variant calling on low-coverage (4-5x) whole-genome sequencing data from 2,535 individuals across 26 different global populations. The variant-calling pipeline was developed by Real Time Genomics and ported to the DNAnexus platform, which is built on top of Amazon Web Services. After computational filtering, some 56 million single-nucleotide polymorphisms (SNPs) and 5.6 million inserts or deletions (indels) were identified across the samples. The call set shows high sensitivity for standard variant sets and considerable variation was observed in the number of polymorphisms across populations. Principal component analysis shows that these variants capture genetic variation at continental and sub-continental levels.

“The size and scope of DNA sequencing projects is rapidly moving toward an era where the analysis of data from thousands of human genomes is the norm. To realize the promise of these projects will necessitate IT infrastructures that exceed the in-house capabilities of most research labs and require bursts of computational resources that would be prohibitively expensive and time-consuming to deploy,” said Richard Daly, CEO of DNAnexus. “DNAnexus pioneered the cloud-based genomics platform and has successfully demonstrated its capacity to cost effectively perform in a number of very large, high-value projects.”

DNAnexus provides an enterprise-focused API-based PaaS that enables clinical and research enterprises to efficiently move their analysis pipelines into the cloud, using their own algorithms alongside industry-recognized tools and reference resources to create customized workflows in a secure, cost-effective and compliant environment. With DNAnexus, labs of any size can build and run their data analysis applications and workflows from anywhere in the world, and work securely with research and clinical collaborators.

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