News And Notes From ASHG 2017

October 20, 2017 | The American Society of Human Genetics (ASHG) hosted their annual meeting, the largest gathering of human genetics professionals in the world, this week in Orlando, Florida. Several companies took advantage of the ASHG audience to make new product and business announcements. Here are a few of the exciting announcements made during the meeting.

The Children’s Hospital of Philadelphia (CHOP) and Edico Genome set a new scientific world standard in rapidly processing whole human genomes into data files useable for researchers aiming to bring precision medicine into mainstream clinical practice. Utilizing Edico Genome’s DRAGEN Genome Pipeline deployed on 1,000 Amazon EC2 F1 instances on the Amazon Web Services (AWS) Cloud, 1,000 pediatric genomes were processed in two hours and twenty-five minutes. The team analyzed a pediatric cohort of 1,000 whole genomes from the Center for Applied Genomics (CAG), a specialized Center of Emphasis at CHOP with the primary goal of translating basic research findings to medical innovations. These samples were carefully curated to reflect the composition of the entire biobank and represent the most common complex disorders and rare single-gene diseases. Each patient’s data had previously been de-identified to protect personal privacy. Making use of the AWS Cloud allowed the team to simultaneously draw on the combined computing power of 1,000 field programmable gate array (FPGA) enabled Amazon EC2 F1 instances. Press release

LifeOmic has signed an agreement with Genomenon to use the Mastermind Genomic Search Engine to streamline clinical interpretation of LifeOmic’s genome sequencing data. Through this partnership, LifeOmic will automate prioritization of their genome sequencing data for clinical patients by annotating disease-causing variants with citations from relevant biomedical literature. By providing immediate insight into published scientific literature, Mastermind speeds the variant interpretation process by helping scientists at LifeOmic decide which variants are likely associated with disease and important for clinical care and which are likely benign and can be safely ignored. Press release

Genome Gateway, a web-based software portal created by HudsonAlpha Institute for Biotechnology, was highlighted in a presentation at the ASHG annual meeting. Genome Gateway manages interactions between genomic medicine patients and clinicians at the Smith Family Clinic for Genomic Medicine in Huntsville. Patients can use the software, which is hosted on a HIPAA-compliant server, to complete their initial paperwork, fill in family history to create a pedigree, and engage in educational activities prior to their initial visit, or throughout their care. Press release

Genomenon has announced that it will begin offering a free edition of the Mastermind Genomic Search Engine to clinical, research and academic institutions to advance genomic analysis and DNA data interpretation. Genomenon is making Mastermind freely available to promote more rapid advances in genome analysis and DNA sequencing interpretation.

Mastermind is the first-in-kind genomic search engine that connects clinicians and researchers directly to the most impactful scientific literature in their field. It provides a web-based search on a full complement of medical literature comprising over 5.5 million full text genomic articles cataloguing the genetic relationships to human diseases including cancer. With a simple query, Mastermind returns a list of prioritized, clinically relevant genomic articles including insight into gene, mutation and keyword matches for each article. Press release

Bionano presented Saphyr, its most advanced system for genome mapping. Saphyr has roughly 10 times the throughput of its predecessor, allowing the system to generate sufficient data in one day to map up to two human genomes. This increase in throughput enables larger scale studies like the ones presented at this conference. Press release

Duplications of large segments of noncoding DNA in the human genome may have contributed to the emergence of differences between humans and nonhuman primates, according to findings reported. Identifying these duplications, which include regulatory sequences, and their effect on traits and behavior may help scientists explain genetic contributions to human disease. Researchers at the University of California, Davis studied the history of human-specific duplications (HSDs), segments of DNA longer than 1,000 base pairs that are repeated in humans but not in primates or other animals. In this study, they focused on HSD regions that do not code for genes, but instead regulate the expression of other genes. Press release

GENEWIZ launches CLIA Sanger sequencing and new NGS amplicon sequencing. GENEWIZ's new Amplicon-EZ service builds on the advantages of NGS-based screening and provides a cost-effective, fast, and interactive solution for researchers to sequence mixed PCR products. Amplicon-EZ is designed to allow every researcher to utilize next generation sequencing, regardless of sample number or expertise. Starting at $50/sample, GENEWIZ provides easy-to-interpret results in as fast as three business days. GENEWIZ also expands into clinical genomics testing with the launch of its CLIA Sanger Sequencing service which is CLIA-certified and CAP Accredited. Contributing to the advancements in clinical development, personalized medicine and molecular diagnostics, GENEWIZ now provides clinical Sanger sequencing to complement the work being done by its clients in both research and clinical environments. Press release

Multi-omics profiling, the measurement and analysis of a person’s genome along with other biomolecular traits, is an important step toward personal health management that provides valuable, actionable information, according to findings presented by researchers at Stanford and The Jackson Laboratory, who focused their research on prediabetic individuals to study the potential for effective early intervention to prevent diabetes. Over four years, they sequenced the genomes of and collected longitudinal data on the RNA transcripts (transcriptomes), protein production (proteomes), metabolic products (metabolomes), and body microorganisms (microbiomes) of 98 participants with prediabetes, two with diabetes, and seven healthy controls. They also used wearable devices to track each participant’s activity level and skin temperature. ASHG release

MyGene2 presented results during the annual meeting that claims to help patients with rare genetic conditions, clinicians, and researchers share information, connect with one another, and enable faster gene discovery. The website helps patients enter their genetic data so it is searchable and useful to researchers and clinicians, along with detailed information about their phenotypes and experiences to help define symptoms and describe the course of disease. ASHG release

Several qualified researchers qualitatively and quantitatively analyzed essays submitted to ASHG’s 2016 DNA Day Essay Contest. The contest focused on whether adolescents should be encouraged to defer such testing for such conditions until adulthood, as recommended by a recent ASHG position statement. The researchers analyzed the views and reasoning expressed in 1,241 essays written by 9th-12th grade students from 44 U.S. states and 23 other countries. Approximately half of the essays agreed with the ASHG statement that testing should be deferred, and the other half refuted that argument. Press release

Low levels of physical activity and inefficient sleep patterns intensify the effects of genetic risk factors for obesity, according to results of a large-scale study. These results confirm and strengthen previous findings based on self-reported activity. Researchers at the University of Exeter Medical School study the genetics of body mass index (BMI) and Type 2 Diabetes. In the past it has been difficult to measure interactions between genetic risk factors and aspects of environment and lifestyle in a systematic way. In contrast, the new study made use of wrist accelerometer data, which is more objective and quantifiable, and a large genetic dataset from about 85,000 UK Biobank participants aged 40 to 70. ASHG release