San Diego Biotechs at #ASHG14: Apps, Analysis, Panels, and Detection

ASHG Day 3
The Pathway Genomics booth at #ASHG14

In many ways, San Diego is the perfect location for the ASHG 2014 annual meeting, and not just for the perfect weather and the beautiful convention center. The area is home to the two top genomic technology leaders, Illumina, and Life Technologies (now Thermo Fisher). Apart from these powerhouses, a large number of smaller biotechs in the area also deal with genomics. Yesterday, I listed several of them represented at the meeting as exhibitors: Cypher Genomics, which provides specialized bioinformatics services, Edico Genome, which recently launched the first microprocessor dedicated for genome sequencing, Genection, which is developing a NGS panel for testing mutations in AML, and Pathway Genomics, which provides a host of genetic tests related to personalized health. I forgot to add to the list, BioNano Genomics, which has a platform for detecting structural variations in human genomes. With such a variety of exciting technologies, it seems appropriate to devote a blog post focusing on these upcoming genomic businesses. Here goes:

Pathway Genomics:  Pathway is probably the first to provide a person’s genomic information in the palm of their hands, literally (well, almost). During ASHG, they announced the launch of their patient app that allows existing Pathway customers to view their genetic data on mobile devices. Ardy Arianpour, the Chief Strategy Officer at Pathway provided a demo of this sleek app. Customers who have, or will order any of the several physician-prescribed genomic tests offered by Pathway will be able to see the data under two main tabs: ‘Report’ and ‘Lifestyle’. Each tab has comprehensive details of the genes tested, risk factors, and other important information. Perhaps the coolest feature of the app is that for each sections related to either specific genes, or certain lifestyle aspects, there is a link at the bottom that will connect the patient to a genetic counselor on a click. This is in line with Pathway’s commitment to provide “accessibility of customer data, and great customer service” according to Arianpour. He also added that Pathway was very focused on providing good genetic counseling (Very prominent ‘Recruiting Genetic Counselor’ signs were hanging at the Pathway booth for those looking for jobs in the area). The app is available for download both through iTunes and Google Play stores.

Cypher Genomics: Cypher has developed a software for improved annotation and interpretation of genomic data. According to Co-Fouder and CEO Ashley Van Zeeland, “Cypher Genomics is thrilled to be a part of the vibrant San Diego genomics and life science community that was on display at this year’s ASHG meeting.  Our genome interpretation technology was highlighted in two platform presentations that illustrated the value and importance of accurate genome interpretation as the technology moves out of the research lab and into the clinic”. The details on one of the talks, identifying a new cause of a debilitating rare disease, was covered in a press release. The second talk by Lauren Ariniello of Scripps Translational Science Institute looked at 56 specific known and expected pathogenic (the ‘ACMG-56’, which – according to the ACMG – is implicated in various diseases for the elderly population. Arinello and colleagues wanted to find the likelihood of these pathogenic variants in a healthy population. They recruited and sequenced patients aged between 85-107 years old, recruited through Scripp’s Wellderly group (with a mean age of 95, this was easily the oldest cohort study being reported at ASHG!). Using the Cypher’s bioinformatics pipeline, they reported that 6% of Wellderly individuals have pathogenic variants deemed reportable by ACMG.

Genection: A number of academic and commercial entities at the meeting spoke about next-generation sequencing (NGS)-based cancel panels, including customizable ones. Genection, a subsidiary of Invivoscribe, is focused on Acute Myeloid Leukemia (AML), and has developed MyAML, a NGS panel that targets 194 genes for the prognosis and stratification of AML patients. Genection presented a scientific poster at ASHG with data demonstrating the comprehensiveness of myAML in characterizing clinical AML samples. According to Suzanne Graham, Senior Manager for Marketing and Business Development at Genection:  “By identifying all contributing mutations, MyAML can assist in identifying the drug cocktail that would eliminate all relevant clones.  We have the ability to identify critical gene fusions at the gDNA level, thus identifying biomarkers that can be used to follow patient through their drug treatments.”

Edico Genomes: Edico, which was in the news recently for raising $10million in series A financing, has developed the first ever processor optimized and dedicated for rapid analysis of NGS data. The processor called DRAGEN (Dynamic Read Analysis of GENomeware) was formally launched at ASHG at an event titled ‘Enter the DRAGEN’ (but of course!). However, the company already had an early launch customer in Sequenom, another San Diego based firm that is the leading provider of non-invasive prenatal testing. A joint poster presented by the two at ASGH demonstrated that data analyzed by the DRAGEN process was in excellent concordance with previous analysis, but also ~30x faster!

BioNano Genomics: Though originally founded in Philadelphia, PA, the company moved its headquarters to San Diego several years ago. Its platform Irys, along with associated reagents and chips, enables high-resolution, single-molecule imaging of non-amplified DNA by channeling and confining molecules through proprietary nanoarrays. This enables direct observation of structural variants including replications, deletions, translocations and inversions. BioNano had couple of major announcements at ASH, including a simplified workflow by reducing the number of chips required to analyze a full human genome (thereby reducing cost), as well as the adoption of the Irys system by four major genomic centers. A number of posters were also presented by scientists from Baylor College of Medicine, UCSF etc. demonstrating successful use of the Irys platform.

Among the two heavyweights, I already covered Illumina’s session on expanding into the clinics on Monday, October 20th. Ion Torrent held a similar session Tuesday. That will be covered in the next, and concluding blog post about ASHG14.