NEW YORK (GenomeWeb News) – Real Time Genomics and the J. Craig Venter Institute have forged a long-term research pact focused on analyzing the genetic mutations that induced pluripotent stem cells acquire during differentiation, RTG said today.
The partners also will work on identifying and validating human variant information using the Venter human reference diploid genome and associated orthogonal information. They plan to deposit this information in public databases where it can be accessed and used by the life sciences community.
Researchers from both organizations will use RTG's platform and JCVI's infrastructure to identify single nucleotide polymorphisms, insertions and deletions, structural variants, and de novo mutations in data collected from both projects.
"The stem cell collaboration with JCVI is an exciting opportunity to move our technology into new areas as cell lineage progression studies are becoming important in a wide range of" next-generation sequencing applications, Francisco De La Vega, RTG's VP of genome sciences, said in a statement.
He also said that the collaboration affords an opportunity to create standard datasets that can serve as yardstick for measuring the accuracy of other sequencing data and results.
"Because JCVI has considerable orthogonal information related to the Venter reference genome, including Sanger long-read sequence data, data from multiple next-generation sequencing platforms, and even RNAseq data and full phasing information, there is an opportunity to contribute a standard back to the community to improve the sensitivity and specificity of human disease applications using NGS," he said.
Mark Adams, JCVI's scientific director, noted that a better understanding of iPSC mutations would have implications for their use in developing new therapies.
"These mutations might affect how iPSCs behave as disease models and could limit the therapeutic use of these cells, but there are many pitfalls in analyzing sequence data to locate and interpret these rare mutations," he said.
At JCVI, "we have built a significant dataset around this genome and want to help others leverage the information to improve their own research," he added.