August News and Product Briefs

News Briefs

Invitae Corporation published new data describing the clinical actionability of multi-gene testing for hereditary breast and ovarian cancer risk in JAMA Oncology. The study was a collaboration among Massachusetts General Hospital, Harvard Medical School, Stanford University, Beth Israel Deaconess Medical Center and Invitae. More than 1,000 patients were tested with multi-gene panels, and the clinical actions that would be considered were reviewed for all 63 patients testing positive for cancer genes other than BRCA1 or BRCA2. For more than half of these patients, the genetic test suggested a change in care, based on the most recent recommendations from the National Comprehensive Cancer Network. Invitae recently made tests like these available for direct patient orders, as reported in Bio-IT World. Press release

10X Genomics released linked-read data generated by the GemCode Platform using several National Institute of Standards and Technologies (NIST) reference samples. The 10X Genomics data will contributed to NIST’s Genome in a Bottle Consortium, to produce well-characterized whole human genomes as reference materials. Visualizations of 10X data for two samples, NA12878 and NA24385, are publicly available through a web-based instance of 10X Genomics’ haplotype-aware Loupe genome browser. (For more on NIST’s reference materials, see “Genome in a Bottle Uncapped.” For more on the GemCode Platform, see “10X Genomics at AGBT.”) Press release

Inova Translational Medicine Institute (ITMI) has implemented SGI’s UV 2000 advanced symmetric multiprocessing system in its 512-core data center. The system will power analyses in ITMI’s genomic database, which is one of the largest in the world and is connected directly to a community health system. ITMI has conducted three core studies using this system, including a study of 1,000 families to predict and prevent pre-term births; a longitudinal genomic study that will enroll over 5,000 families to track infants’ health outcomes over the course of 18 years; and a translational study that focuses on babies in the neonatal intensive-care unit who are sick and not yet diagnosed. Press release

Cypher Genomics, in partnership with the Rare Genomics Institute, announced winners in the 2015 BeHEARD Challenge. BeHEARD is a global competition that funds projects submitted by researchers studying rare diseases or individuals affected by them. The prize winners will work with Cypher to investigate the genetic causes of two diseases: Dr. W. Martin Kast of the University of Southern California will work to identify the genetic basis of the skin disorder epidermodysplasia verruciformis, while Dr. Michail S. Lionakis of the National Institute of Allergy and Infectious Diseases will analyze the genetic underpinnings of the complex immune disease autoimmune polyglandular syndrome-1. (For more on the Rare Genomics Institute’s recent activities, see “Rare Genomics Institute Quantifies Crowdsourcing, Weighs in on Patient Engagement.”) Press release

Gen9, Inc. and iGEM, the International Genetically Engineered Machine Competition, announced a collaboration to provide the synthetic biology community with freely available DNA parts. The iGEM Registry of Standard Biological Parts is the world’s largest collection of more than 20,000 DNA parts, known as BioBricks. Through this collaboration, Gen9 will use its BioFab platform to manufacture new, synthetic versions of the most well-documented and highly used DNA parts. These sequence-verified, clonal constructs will allow scientists to design and engineer new biological systems. Press release

CareDx, a company focused on diagnostic surveillance solutions for organ transplant recipients, has selected DNAnexus’ cloud genomics platform to support its ongoing R&D activities as well as clinical trials and registries. The platform will also host the release of CareDx’s analytically validated cell-free DNA assay later this year. Press release

MIT Press announced that its collection will be made available on the ReadCube platform. Through the ReadCube Discover service, over 29,000 articles from 30 scholarly journals have been indexed for discoverability through ReadCube’s search engines, feeds and personalized recommendation engine. MIT Press is the 60th publishing partner to sign onto the service, joining Springer, Nature, Wiley, deGruyter, the Royal Society of Chemistry, Allen Press, SciELO, and many more. The agreement also makes the MIT press collection available as Enhanced PDFs, with hyperlinked in-line citations, annotation tools, instant access to supplemental materials and figures, clickable author names, social sharing, and Altmetrics. (For more on ReadCube, see “Kickstarter Launched for Social Reader.”) Press release

Ginkgo Bioworks, a synthetic biology company, partnered with Ajinomoto Co., a manufacturer of food and amino acid-based products. Ginkgo will use its automated foundry, Bioworks1, to deliver an improved strain to Ajinomoto. (For more on Ginkgo’s manufacturing process, see “Ginkgo Bioworks Opens Its Genetic Engineering Foundry.”) Press release

Nuclea Biotechnologies is partnering with the Institut de Recherches Cliniques de Montréal (IRCM) to validate quantitative mass spectrometry-based assays for insulin, proinsulin, and c-peptide with the goal of developing new assays to determine risk and progression of type 2 diabetes. The partnership will include running studies on clinical samples in both locations, testing the assays for precision, sensitivity, and reproducibility. Nuclea plans to incorporate these new assays into its CLIA lab in Cambridge. Press release (PDF)

New Products

PierianDx released a new version of its bioinformatics software platform to address exome sequencing workflow. The PierianDx Clinical Genomicist Workstation (CGW) version 3.0 provides clinical insights for somatic cancer as well as constitutional assays, based on the American College of Medical Genetics and Genomics’ most up-to-date guidance on variant classification. Press release

Optibrium and Integrated Chemistry Design, providers of software solutions and services for drug discovery, released Asteris 1.1, an updated version of the iPad app that delivers chemistry drawing tools with predictive modelling. The latest version of Asteris features improved gesture recognition, and a new chemistry “groups” panel of commonly used chemistry templates. Asteris’ predictive models, guided by the Glowing Molecule visualisation, has also been extended with the introduction of new predictive models for properties, including drug volume of distribution in human. Press release (PDF)

Liaison Technologies and ClearDATA have partnered to launch a secure, HIPAA-compliant solution for data integration and management. Healthcare and life sciences organizations can now use Liaison’s ALLOY Health platform inside ClearDATA’s cloud environment. The solution will have the data storage and application hosting capacity to accommodate intermittent surges in demand from researchers and healthcare providers for data analytics. Press release

Insight Genetics announced the launch of its Insight RET Screen, a CLIA-validated assay to detect oncogenic RET expression in non-small cell lung cancer patients. The Insight RET Screen is a qPCR assay that detects RET expression driven by chromosomal fusions regardless of the fusion partner. The new assay provides results within 48 hours and with minimal tissue requirement. In a head-to-head comparison to a RET FISH assay, the Insight RET Screen identified 67% more patients who were RET fusion-positive. Press release

Corning Incorporated announced the launch of Corning HepatoCells, an alternative to primary human hepatocytes for ADME/Tox research. HepatoCells are single-use, cryopreserved cells derived from primary human hepatocytes, which exhibit the distinct morphology of mature primary hepatocytes. The HepatoCells are qualified for applications including Cytochrome P450 induction and cytotoxicity. Press release

Pall ForteBio LLC launched the Octet K2 system, for kinetic characterization of antibody, protein and small-molecule binding interactions. Octet systems offer a fluidics-free alternative to surface plasmon resonance for assay development and optimization. The Octet K2 system increases accessibility to BLI as a two-channel instrument, providing binding affinity data for molecules down to 150 daltons in size. Press release