New Products and Announcements at the American Society of Human Genetics Meeting

By Bio-IT World Staff

October 9, 2015 | The annual meeting of the American Society of Human Genetics (ASHG) is ongoing in Baltimore, Md., and almost every major player in the genomics industry is there demonstrating the wealth of hardware, software, and services that are expanding the field’s scope at an exponential pace. Here are a few of the biggest announcements to emerge this week from the ASHG floor: 

The sequencing companies continue to dominate the news in genomics, as providers of the foundational technology that sets the pace for research and clinical discovery. Market leader Illumina has a near monopoly on population-scale sequencing, and its most recent announcements suggest it’s working hard on ease of use and the front and back ends of its sequencing pipeline, to shore up its natural lead in throughput. “Sequencing has gotten so affordable and easy,” Kirk Malloy, Senior Vice President of Life Sciences, told Bio-IT World, that customers are paying “way more attention to library preparation and analytics.”

For sample prep, Illumina released a new set of TruSeq kits, which prepare DNA libraries for whole exome sequencing. The new kits are reportedly more robust to damaged DNA samples, including the small volumes of DNA derived from formalin-fixed, paraffin-embedded tissue samples common in oncology.

Shortly before the ASHG meeting, Illumina also announced major changes to BaseSpace, its cloud-based analytics environment where users can store data and analyze it using tools selected from an app store. BaseSpace will now be converting to a more commercial model, introducing Professional and Enterprise Editions for regular users, which will include new bioinformatics support services and integration with the GenoLogics Laboratory Information Management System. BaseSpace will begin charging users to store data over one terabyte, according to Senior Director of Strategy and Market Development for Enterprise Informatics Brady Davis, at the same rate charged by Amazon Web Services.

Finally, Illumina for the first time is allowing users of its top-end HiSeq X instruments to use them for whole genome sequencing of species other than humans. “The whole intent of the platform was to drive human whole genome sequencing,” says Kirk Malloy, a mission that now appears accomplished with massive commercial efforts like Human Longevity, Inc., and a growing number of public projects like Genomics England. Malloy says that Illumina is already in discussions with model animal labs and agricultural institutions to apply the massive throughput of the HiSeq X to non-human animal sequencing.

Meanwhile, Illumina’s only competitor for sequencing on the scale of tens of thousands of whole genomes a year, Complete Genomics, shared new details of its recently released Revolocity system. Complete Genomics, a subsidiary of Shenzhen-based BGI, reported a direct comparison sequencing the benchmark NA12878 human genome on the Revolocity and the HiSeq X systems, claiming its system provided equivalent accuracy on single-nucleotide variants, but higher fidelity in capturing small structural events and copy number variants. Complete Genomics also announced its third customer for Revolocity, the UK Epilepsy Society.

Probably the sequencer causing the most buzz at the ASHG meeting was Pacific Biosciences’ Sequel System, announced last week. (See our coverage, “A Worthy Sequel.”) Chief Scientific Officer Jonas Korlach credited “the realization that quality matters” for interest in the Sequel, which should provide a clearer look at structural variation in the genome than any other system, at a fraction the cost of the company’s previous RS II sequencer. More details on how the sequencer performs will probably have to wait until the first instruments reach users, but ASHG did provide the first customer announcement for the Sequel: the Icahn School of Medicine at Mount Sinai, already an RS II customer, has purchased two.

Jonas Korlach, Chief Scientific Officer of Pacific Biosciences, shows off a display version of the Sequel System at the ASHG meeting in Baltimore.

Meanwhile, service companies supporting the genomics community also made big announcements at the meeting. Invitae, one of the largest commercial providers of genetic testing, revealed that it has doubled the overall size of its gene panels to cover over 600 genes, with expanded panels in cancer risk, cardiovascular risk, rare pediatric disease, and neuromuscular disease. Invitae was founded with ambitions to sell a single test covering the full spectrum of well-understood genetic risk, and while it has since split its service into more focused panels, it is inching closer to a comprehensive product.

QIAGEN launched an integrated informatics solution for solving rare disease cases. QIAGEN has been buying up some of the industry’s leading analytics companies and combining their products for an end-to-end genomic analysis solution — its new product includes the Biomedical Genomics Workbench and Biomedical Genomics Server Solution from the former CLC bio, Ingenuity Variant Analysis from the former Ingenuity, and the HGMD Human Gene Mutation Database. Together, these elements will allow clinical labs to go from raw genomic data to strong leads on pathogenic variants in trying to diagnose rare hereditary disorders.

QIAGEN also unveiled a partnership with DNAnexus, whose cloud-based genomic informatics service in recent years has helped expand the scale and speed of whole-genome analysis. DNAnexus has made many widely used informatics tools available to its customers, and now that menu includes Ingenuity Variant Analysis.

A direct competitor with QIAGEN in this field is WuXi NextCODE, which also has an end-to-end solution for clinical exploration of genome data. NextCODE announced a major partnership at ASHG: the company will work with Sidra Medical and Research Center in Qatar on a program to link its bioinformatics solutions with the national electronic health record system of Qatar, for both clinical care and national-scale genomic research. (See our coverage, “Sidra Medical Center Deploys NextCODE for Qatar Genome Project.”)

There is much more going on at the ASHG meeting, and Bio-IT World will continue to cover the event.