News and Notes from ASHG 2016
October 20, 2016 | The American Society of Human Genetics annual meeting is currently underway in Vancouver, Canada. Here are some of the product news and company announcements released so far this week.
UWash, Color Genomics Launch Free Breast Cancer Gene Candidate Database
A team of researchers from the University of Washington and Color Genomics introduced a publicly available database of variants in 27 known and candidate breast cancer genes from cancer-free women over 70 years old. The database, nicknamed FLOSSIES for the "Fabulous Ladies Over Seventy," whose DNA was sequenced as part of the project, is intended to provide the research community with a resource of control cases to aid in the evaluation of variants of unknown significance in breast cancer. GenomeWeb
Oxford Nanopore Sequences Human Genomes with MinION
Oxford Nanopore announced the first attempt to sequence a human genome using the MinION device. Analysis is still early, but the company did share that it sequenced HapMap sample NA12878 on the MinION Mk1B using the upgraded kits and flow cells announced last month. Five flow cells provided more than 11x coverage, the company reported, and the cost was $2,750; 30x coverage could be achieved with 14 flow cells. ONT News
Illumina Contributes to ClinVar Database
Illumina announced on Thursday that the company has contributed over 95,000 human genetic variants to ClinVar, a public database hosted by the National Center for Biotechnology Information (NCBI). Illumina’s contribution includes variants of all classifications, from pathogenic to benign, identified during interpretation of whole genome sequences generated in the CLIA-certified, CAP-accredited Illumina Clinical Services Laboratory. Press release
ExAC Gets Upgraded to Genome Aggregation Database (Beta)
Daniel MacArthur announced Genome Aggregation Database, containing more than 120,000 exomes and 15,000 genomes. The Genome Aggregation Database (gnomAD), is a coalition of investigators seeking to aggregate and harmonize exome and genome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. gnomAD is an update to the Exome Aggregation Consortium (ExAC), which contained exclusively exome data. Press release
Rady Children’s Hospital Selects Omicia for NICU/PICU Rapid Whole Genome Sequencing Project
San Diego-based Rady Children’s Institute for Genomic Medicine has chosen Omicia as its first line genome interpretation partner for the implementation of Rady Children’s rapid genome testing in their neonatal and pediatric intensive care units (NICU/ PICU). Rapid turnaround time is critical to improving outcomes for newborns and infants in intensive care units with urgent, life-threatening issues. To support this turnaround time requirement, Omicia has introduced a new STAT feature in its Opal Clinicalsoftware that delivers clinically interpretable information from next-generation sequencing (NGS) data within one hour. This rapid decision support service enables Rady Children’s clinical team to quickly and accurately diagnose patients and develop targeted treatment plans. Press release
Early BabySeq Results Are In
Early results from the BabySeq Project, a Boston-based study exploring the impact of whole-exome sequencing (WES) on newborn infants and their families, suggest some utility in genetically sequencing these infants and offer new insights into parental attitudes toward the procedure and results. So far, the researchers have identified potentially harmful variants in two healthy infants who were sequenced – variants that would not have been detected otherwise – suggesting some value in sequencing infants with no family history of genetic disease. It is not yet known how this knowledge will affect the families’ medical actions or the infants’ eventual health outcomes. But more surprisingly, the project has had unexpected difficulty recruiting participants. Only 7% of parents have agreed to the sequencing. Press release and coverage in Science
QIAGEN Launches New Products for Liquid Biopsies and Hereditary Diseases
QIAGEN has launched the QIAseq cfDNA All-in-One Kit, combining cell-free DNA extraction and library preparation in the first dedicated solution for liquid biopsy analysis on any next-generation sequencing (NGS) platform. The company also released a bioinformatics workflow for cfDNA and another for hereditary and rare diseases, offering unique capabilities for research using liquid biopsies in non-invasive prenatal testing (NIPT) as well as cancer biomarker discovery. The All-in-One kit integrates with QIAGEN’s recently launched PAXgene Blood ccfDNA Tube for collection and stabilization of blood samples with the bioinformatics workflow, creating a streamlined testing solution that allows faster, more convenient and reliable analysis of cell-free DNA from sample collection to interpreted result. Press release
