Human Longevity, Inc. Researchers Develop New Algorithm to Rapidly and Accurately Predict HLA Types Using Illumina Next Generation Sequencing Technology
(SAN DIEGO, CA)—July 3, 2017—Researchers from Human Longevity, Inc. (HLI) have developed a new algorithm called xHLA to rapidly and accurately determine the sequence of the human leukocyte antigen (HLA) gene region from 30x whole genome sequencing using Illumina HiSeq X10 and NovaSeq sequencing technology. This work was published by lead author Chao Xie, Ph.D. and senior author J. Craig Venter, Ph.D., in the journal Proceedings from the National Academy of Sciences (PNAS) early online edition.
The HLA region, located on chromosome 6, is one of the most diverse regions in the human genome with thousands of alleles present in the human population. The HLA complex is responsible for regulation of the human immune system and thus plays an important role in diseases of autoimmunity (such as rheumatoid arthritis), cancer, organ transplant compatibility, allergic reactions and response to vaccines.
Since HLA gene regions have a high degree of DNA sequence similarities it has been difficult to accurately predict HLA type using whole genome sequencing technologies. Instead, HLA typing has been done through more cumbersome serotyping and targeted sequencing, costing hundreds of dollars per test. Given HLI’s expertise in complete and accurate whole genome sequencing, machine learning and other informatic areas, the HLI-led team set out to develop a new tool, xHLA, to see if it could indeed be used with current generation sequencing technology for more precise and rapid HLA typing. They also wanted to compare xHLA to current HLA typing methods on the market.
The team tested xHLA against seven other HLA typing methods using three whole genome and three whole exome public datasets and showed that in all cases xHLA outperformed the other tests. The xHLA’s runtime was approximately 3 minutes for each 30x whole genome sample compared to 15 minutes to 5 hours for the other algorithms. One of the differentiators of xHLA is that it uses protein level sequence alignment which results in a more comprehensive alignment matrix giving higher accuracy than other methods.
The team concluded that this new tool should enable rapid and accurate HLA typing for any individual who has their genome sequenced by HLI. HLI currently offers physician ordered whole genome sequencing as a product, HLIQ Whole Genome and through the suite of Health Nucleus products which are: Health Nucleus Platinum, Health NucleusX Gold (HNX Gold) and Health NucleusX (HNX). In one whole genome sequence test HLI can offer screening for genes and variants proposed by the American College of Medical Genetics and Genomics (ACMG), pharmacogenetic testing, inherited cancer testing, carrier screening and now, rapid and accurate HLA testing.
Venter, who is HLI’s co-founder, executive chairman and head of scientific strategy, commented, “This paper is proof of the power of informatics and the need for complete and accurate clinical grade genomic sequencing to solve important scientific and clinical issues. The xHLA algorithm should enable seamless, accurate and rapid HLA typing for all genomic sequencing done today. HLI clients can get their HLA type as a part of their genome report, something that no other center can currently offer.”
In addition to researchers from HLI, scientists from Center for International Blood and Marrow Transplant Research, Minneapolis, MN, the J. Craig Venter Institute, La Jolla, CA; and the Department of Pathology, University of California, San Diego, La Jolla, CA all participated in this work.
About Human Longevity, Inc.™
Human Longevity, Inc. (HLI) is the genomic-based, health intelligence company empowering proactive healthcare and enabling a life better lived. HLI combines the largest database of genomic and phenotypic data with machine learning to drive discoveries and revolutionize the practice of medicine. HLI’s business areas include 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; HLIQ™ Whole Genome and HLIQ Oncology. For more information, please visit http://www.humanlongevity.com or http://www.healthnucleus.com.
Heather Kowalski, firstname.lastname@example.org, 858-361-0466