SAN DIEGO, Oct. 4, 2016 /PRNewswire/ -- Researchers from Human Longevity, Inc. (HLI), the genomics-based, technology-driven company revolutionizing health, have published results today of their high quality, in-depth sequencing (30 to 40X coverage) of 10,545 human genomes. The paper, which represents the most genomes sequenced to date at high coverage, was led by first author Amalio Telenti, M.D., Ph.D., and senior author, J. Craig Venter, Ph.D., and is published today in the journal Proceedings of the National Academy of Sciences (PNAS).
The team found that 84% of an individual human genome can be sequenced with high confidence using the Illumina HiSeq X Ten. This coverage includes 90% of exons and more than 95% of known pathogenic variant sites. In contrast, some of the other human genome sequencing efforts are only doing an average of 7x coverage of the genome which severely limits the precision on the high confidence regions of the genome. The HLI team concludes that the level of coverage and accuracy of genome sequencing at HLI is very high quality and can be used for discovery and clinical applications.
To the surprise of the researchers, common variants in the human population (variants that nearly all people share) saturated in the HLI database after sequencing only about 8,500 genomes. The team uncovered 150 million new single nucleotide genetic variants (SNVs), 82 million of which were novel. Most of the variations occurred with less than 1% frequency and each sequenced genome contributed more than 8,500 novel variants. They also identified hundreds of thousands of novel human DNA sequences.
Using more than one billion data points, the team mapped the invariant sites in the genome. The invariant genome included, for example, intron-exon splice sites, which were particularly intolerant of variation. These variation-intolerant sites were associated with high frequencies of known pathogenic variants, suggesting that these sites are essential for life or health.
"The paper published today is a demonstration of our critically high sequencing and analysis standards in genomics and shows that having thousands of high quality genome sequences will lead to dramatic new scientific and clinical findings," said Dr. Venter, Co-founder and CEO, HLI.
Dr. Telenti, HLI's Chief Data Scientist, added, "Understanding the performance and quality metrics of genome sequencing will allow us to finally realize the potential for genomics in changing healthcare and impacting individuals' lives. This is the face of a new genomics — where traits and diseases may result from a unique genetic change shared with few other human beings."
The company is also unveiling a new tool, HLI Open Search, for beta testing in conjunction with the publication of this research. HLI Open Search is an efficient, rapid, interactive way to explore genomic data and subsequent variant knowledge, created by HLI via a web-based search engine. For the beta test, users will be able to log on and search on the variants and other data from this research paper. The lead architect of HLI Open Search is Victor Lavrenko, Ph.D., who is the technical lead for HLI Open Search and a key member of HLI's Mountain View team of software engineers and machine learning experts. Dr. Telenti and Istvan Bartha, Ph.D., were also key contributors to this dynamic new tool.
"We believe accessing genomic information should be as fast and easy as anything we search for online," said Dr. Lavrenko. "HLI Open Search puts the world's largest trove of genomic data at the fingertips of every researcher and physician who are seeking deeper knowledge and new clinical insights."
The 10,545 human genomes are part of the HLI's database, which currently contains more than 30,000 high-quality genomic and phenotypic integrated health records. HLI's goal is to have one million integrated health records in the database by 2020.
Other authors on the paper are: Levi Pierce, Ph.D., William Biggs, Ph.D., Julia di Iulio, Ph.D., Emily Wong, Ph.D., Martin Fabani, Ph.D., Ewen Kirkness, Ph.D., Ahmed Moustafa, Ph.D., Naisha Shah, Ph.D., Chao Xie, Ph.D., Suzanne Brewerton, Ph.D., Nadeem Bulsara, Ph.D., Chad Garner, D.Phil., Gary Metzker, B.A., Efren Sandoval, B.A., Brad Perkins, M.D., Franz Och, Ph.D., and Yaron Turpaz, Ph.D.
About Human Longevity, Inc™ Human Longevity, Inc. (HLI) is the genomics-based, technology-driven company creating the world's largest and most comprehensive database of whole genome, phenotype and clinical data. HLI is developing and applying large scale computing and machine learning to make novel discoveries to revolutionize the practice of medicine. HLI's business also includes the HLI Health Nucleus, a genomic powered clinical research center which uses whole genome sequence analysis, advanced clinical imaging and innovative machine learning, along with curated personal health information, to deliver the most complete picture of individual health. For more information, please visit http://www.humanlongevity.com or http://www.healthnucleus.com.