Real Time Genomics, J. Craig Venter Institute announce collaborations

Organizations to partner on stem cell, genomic variant research

Kelsey Kaustinen
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SAN FRANCISCO BAY AREA, Calif.—Real Time Genomics, Inc.(RTG) and the J. Craig Venter Institute (JCVI), a not-for-profit genomicresearch institute that focuses on research in structural, functional andcomparative analysis of genomes and gene products, have established a long-termstrategic collaboration. Under the terms of their agreement, the twoorganizations will seek to understand and analyze the genetic changes thatinduced pluripotent stem cells might undergo in the process of differentiating.No financial details for the collaboration were disclosed.
RTG and the JCVI also announced a collaboration for thediscovery and validation of highly accurate human variant information throughthe use of the Venter human reference diploid genome and associated orthogonalinformation. The resulting information will be made available to thelife-sciences community through public databases. It is the partners' hope thatthey will be able to define best practices and create standardized referencedatasets for genome sequencers.
"The stem cell collaboration with JCVI is an excitingopportunity to move our technology into new areas, as cell lineage progressionstudies are becoming important in a wide range of [next-generation sequencing]applications," Francisco De La Vega, vice president of Genome Sciences at RealTime Genomics, commented in a statement. "At the same time, a problem inclinical applications of sequencing is the difficulty knowing whethersequencing data and results meet a specific accuracy criteria. RTG and thebroader community are working to collectively settle on a set of validateddatasets to improve research. Because JCVI has considerable orthogonalinformation related to the Venter reference genome, including Sanger long-readsequence data, data from multiple next-generation sequencing platforms and evenRNAseq data and full phasing information, there is an opportunity to contributea standard back to the community to improve the sensitivity and specificity ofhuman disease applications using NGS."
JCVI will utilize RTG's platform and work directly with RTGscientists for the identification of SNPs, indels, structural variants and denovo mutations in data from bothcollaborations.
RTG's platform offers variant accuracy in family studies forboth germline and de novo variants, andworks with most platforms. Their platform, the company notes, combines a"Bayesian calling framework that delivers variants from [high-throughputsequencing] data by simultaneously considering all samples in a pedigree,incorporating a Mendelian segregation model and leveraging shared haplotypes inthe family members." RTG calls Bayesian statistics "the modern approach forvariant calling of [high-throughput sequencing] data, integrating sequencingerror models with prior knowledge about allele frequencies and populationstatistics."  
"There is considerable interest in understanding the natureof de novo mutations that are acquiredduring reprogramming and differentiation of iPSCs. These mutations might affecthow iPSCs behave as disease models and could limit the therapeutic use of thesecells, but there are many pitfalls in analyzing sequence data to locate andinterpret these rare mutations," Mark Adams, scientific director for the J.Craig Venter Institute, said in a press release. "Since sequencing andpublishing the Venter reference human genome in 2007, we have built asignificant dataset around this genome and want to help others leverage theinformation to improve their own research. RTG is an ideal partner for theseprojects because of their ability to rapidly analyze data from multiplesequencing platforms with improved accuracy of the resulting variant catalog.We are excited to be working with them on these two important collaborations."

Kelsey Kaustinen

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