Innovator in Dairy Cattle Genetics Uses RTG Pedigree Solution in Landmark Use of Whole Genome Sequencing in Agricultural Genomics
October 04, 2012
SAN FRANCISCO, California, October 4, 2012--Real Time Genomics, Inc., a leading developer of genome analysis tools and applications, today announced that the Livestock Improvement Corporation (LIC) has chosen the RTG platform as its analytical framework for a mammoth study of the genetics of dairy cattle in order to improve the milk production of the five (5) million cows in the New Zealand dairy industry. The study will sequence 500+ animals using whole genome sequencing methods to identify important genetic variants relevant to milk production. This genetic information will be used to improve the herd’s overall productivity, which is fundamental to LIC’s mission. RTG was selected based on the ability of its genome analysis platform to accurately and cost-effectively identify the DNA variants found in each individual in the study.
LIC, with headquarters in Hamilton, New Zealand, is a world leader in dairy genetics and provides the genetics for a large component of the country’s dairy stock. It created a new bovine breed designed for the New Zealand dairy farmer, the Kiwi Cross, 10 years ago. LIC just completed a year-long pilot program to study the use of whole genome sequencing (WGS) methods in its genetics research framework. The pilot proved to LIC that WGS, when combined with advanced analytics from RTG, can significantly improve their understanding of the genetics of the new breed across its prized bull and breeding cow population. RTG collaborated in the pilot study with LIC computational biologists to develop an extension of its whole genome variant ID application to analyze the genomes associated with complex pedigree structures – trios of father (sire), mother (dam) and offspring; and half-sibs – offspring that share a sire or a dam.
In the LIC analytical workflow, the core RTG technology provides ultra fast mapping and alignment to the bovine reference genome of billions of sequence reads for each individual genome. Once reads are aligned, the RTG Pedigree Caller jointly analyzes the data from the three genomes within a single Bayesian algorithmic framework that uses the rules of genetics (Mendel’s laws) to accurately identify the variants among all three individuals. In the pilot program, the RTG Pedigree Caller delivered the best analytical results as compared to the commonly available academic solutions.
“RTG Pedigree provides a 7x improvement in accuracy, as measured by the Mendelian error rate, when compared to the next best pipeline, and over 40X improvement to the other pipelines we investigated”, stated Richard Spelman, general manager of research and development at LIC. “RTG delivers this accuracy while maintaining ~6x as many potential variants per error. And it performs the analysis at rates that are ~7X faster than the other pipelines.”
“When sequencing the genomes of related individuals, in essence we are redundantly analyzing the DNA segments shared between each pedigree member,” said Francisco De La Vega, VP of Genome Science of Real Time Genomics. “The RTG Pedigree Caller is aware of how Mendelian inheritance works and thus leverages the redundancy inherent in pedigree sequencing, improving variant calling across all related individuals and resulting in an amazingly low Mendelian error rate in the resulting variants. This is a significant improvement on how variants are identified by NGS.”
The Version 1.0 RTG Pedigree Caller is available now for customers to analyze trios from any species. Future versions will allow for the analysis of complex and multi-generational pedigrees.
RTG has also verified the performance of the Pedigree Caller with human samples and is currently forming collaborations with leading human genetics labs to assess its performance in human research.
Real Time Genomics (www.realtimegenomics.com) has a passion for genomics. The company offers software tools and applications for the extraction of unique value from genomes. Its competency lies in applying the combination of its patented core technology and deep computational expertise in algorithms to solve problems in next generation genomic analysis. Real Time Genomics is a private San Francisco based company backed by investment from Catamount Ventures, Lightspeed Venture Partners, and GeneValue Ltd.