RTG Software used for independent analysis of whole human genome data from Complete Genomics
October 01, 2010
SAN FRANCISCO, California, September 30, 2010 -- Real Time Genomics, Inc., today announced that it has licensed its RTG v2 Software to VIB, a non-profit life sciences research institute based in Vlanders, Belgium, for variant detection with Complete Genomics data. With this announcement, RTG becomes the only independent provider of short read alignment and variant calling software for use in analysis that includes Complete Genomics, Illumina and 454 sequence reads.
"Through their Early Access Program (EAP), Real Time Genomics enabled VIB to independently assess and validate the results from Complete Genomics," said Diether Lambrechts, Group leader of Complex Genetics at VIB. "Looking forward, RTG software gives us the flexibility to perform novel bioinformatics analysis with existing and new Complete Genomics read data.”
During the EAP, VIB collaborated with Real Time Genomics to evaluate the use of Complete Genomics for whole human genome sequence production, which would enable organization-wide human health and disease investigation without the overhead of a sequencing core facility. VIB wanted an independent assessment of the Complete Genomics data, but no bioinformatics algorithms and software existed that could align the uniquely gapped reads.
RTG gapped alignment functions for read mapping, based on sensitive and accurate sequence search technology, were adapted to the Complete Genomics reads. When sequence variant calls from Complete Genomics were filtered with the RTG variant calls, the complementary nature of the two algorithms enabled superior results to be obtained, increasing reported true positives and reducing reported false negatives. This approach was applied to both a cancer and a twins study, and the results for both are currently pending publication.
RTG software creates new alignment files in the SAM format, and allows mapping against any reference genome. This makes a number of sequence analysis approaches possible. Sequence variant and structural variation detection can be performed with RTG or other open source tools, allowing comparison that accelerates validation. Novel types of sequence analysis are made possible, such as mixed sequence technology read mapping, mapping of reads from 1 family member to another, or matching of a tumor sample to a normal.
Complete Genomics provides a service-based approach to the delivery of whole human genome sequences, delivering high quality sequence production results to biological investigators without sequencing facilities. Lower per genome sequencing costs allow investigators to run more experiments with more genomes. The unique gapped structure of Complete Genomics short reads makes sequence alignment challenging. Real Time Genomics successfully responded to this challenge and now offers an independent option for short read alignment and variant calling that enables deep downstream analysis.
VIB is a non-profit research institute specialized in the life sciences. Approximately 1,200 scientists conduct strategic fundamental research on the molecular mechanisms that are responsible for the functioning of the human body, plants, and micro-organisms. Through a close partnership with four Flemish universities − UGent, K.U.Leuven, University of Antwerp and Vrije Universiteit Brussel − and a solid funding programme, VIB unites the forces of 72 research groups in a single institute. The goal of the research is to extend the boundaries of our knowledge of life profoundly. Through its technology transfer activities, VIB strives to convert research results into products for the benefit of consumers and patients. VIB develops and disseminates a wide range of scientifically substantiated information about all aspects of biotechnology. More information: www.vib.be.
Real Time Genomics, Inc.
Real Time Genomics offers solutions for deep genomic analysis to researchers who use next generation sequencing technologies. These solutions include RTG sequence analysis software for read mapping, variant detection, protein search and metagenomics applications. Patented pattern search technology from the company enables accurate gapped alignment with a unique combination of speed and sensitivity. Real Time Genomics is a private, San Francisco based company backed by investment from Catamount Ventures and Lightspeed Venture Partners.