AHSG 2015 Roundup – Big Data, Heritability, Epigenetics, Enhancers, and Patients as Partners

The ASHG conference in Baltimore was accompanied by some broadly discussed highlights which are reflected in how the media and the social networks embraced it. It was nice to see that the coverage spanned not just commercial launches, but also included research highlights and other general announcements.

Before summarizing the different announcements, I want to state how exciting it was hearing Dr. Francis Collins (Director of NIH) talking about his vision of the new Precision Medicine Initiative (PMI) and the many opportunities it presents to advance its clinical application by creating a cohort of a million individuals. In his presentation, he was asking for a new rule of participants in health studies. In the same go he thanked the Henrietta Lacks family, which was present in the audience, for all they did to further science – the Henrietta Lacks’ descendants now serve as advisers to the NIH.

Another highlight of the conference was the first “Art and Science of Science Communication” session put in place by Chris Gunter, this year’s program Chair. The invited panel consisted of Ed Yong, staff scientist at The Atlantic and author of the blog “Not Exactly Rocket Science”, Liz Neeley, executive director of The Story Collider, and Andrea Downing, author of the blog Brave Bosom and creator of an online community around BRCA findings. It was exciting to see how well received this session was, in particular as it demonstrated that there is an important place for such non-hard core science events, usually not found at these types of conferences. It clearly demonstrated that science communication is a very important component not to be neglected and that it addresses the critical task of sharing our research findings and methods with the research community, and the general public. Andrea Drowning, a BRCA1 mutation carrier and patient advocate, quoted Rosalind Franklin who at one point said “Science and everyday life cannot and should not be separated.” As such, she made a very strong case that data is power and does not equal trade secrets. Data is a source of power for patients that we should envision to be accessible without barriers in the near future. For Andrea Drowning data represented empowerment, as it provided her with knowledge of what an individual can do with a specific finding (e.g. a BRCA1 mutation). This entire session demonstrated that research should be done with patients as partners. To conclude, it was also highlighted that science journalism is fundamentally different from science communication in that it is not merely advocating for science, but also critiquing science, which is paramount for its success.

Image credit: Yaniv Erlich lab – twitter feed analysis.

Let us now briefly review the different announcements that coincided with the conference. They spanned commercial product launches, new partnerships and collaborations, product integrations, and other interesting and relevant announcements.

Data management, analysis, and interpretation

• Artificially intelligent ‘Betsy’ will analyze 100,000 genomes for UK Government: The Boston “Berg Interrogative Biology” program, a form of artificial intelligence, was employed by the UK government to work its Genome project. The platform will use a combination of systems biology techniques to analyze up to 100,000 genomes sourced from England’sNational Health Service (NHS) for Genomics England (owned by the UK Department of Health) for disease research.

• Illumina expands genomics analysis platform and adds to Open Source Initiative with the launch of BaseSpace Professional and Enterprise Editions, fully integrated Laboratory Information Management System (LIMS) solutions and advanced infrastructure upgrades. Genomic researchers will be able to select from advanced services that are optimized to enhance the user experience and improve efficiency in sequencing labs. BaseSpace Professional will provide multi-user access and automated app launch. BaseSpace Enterprise adds greater security and convenience through individual domains, multiple-users and groups, and single sign-on. The Enterprise edition will also have optional integration with LIMS solutions from GenoLogics, which was acquired by Illumina in August 2015, leading to improved efficiency and productivity in laboratories with high throughput.

• Qiagen launches new bioinformatics solution for Hereditary Diseases. The offering includes QIAGEN’s Biomedical Genomics Workbench, Biomedical Genomics Server Solution, Ingenuity® Variant Analysis™, and HGMD® Human Gene Mutation Database.

• Maverix launches new gene expression analysis kit, made available via its Maverix Analytic Platform The Enhancements of the launched RNA-Seq 3.0 version includes optimization for high throughput large-scale analysis projects, additional differential expression analysis tools, methods for the exploration of patterns in data, and support for more organisms, which includes human, numerous animal models, plants, and fungi. The new Maverix analysis kit has a simple and easy to use interface, is designed for scientists, even without bioinformatics experience, to perform complex genomic analyses, and obtain meaningful results.

Cloud-based apps and software integrations

• New BaseSpace app – QIIME The new QIIME app (for “Quantitative Insights Into Microbial Ecology”) built by University of California, San Diego School of Medicine’s Rob Knight, PhD, and his team, is a highly utilized tool in metagenomics research and now made available via the Illumina ecosystem.

• New BaseSpace app  – to streamline NGS analysis for sequence data generated with NuGEN target enrichment technology. The new app is for scientists and clinicians using NuGEN’s Ovation Target Enrichment System to prepare biologic samples for genomic analysis. The new app marks duplicates and performs quality trimming.
• New DNAnexus app – BioNano Genomics’ genome analysis algorithm and pipeline (IrysSolve®). With this collaboration BioNano’s genome analysis algorithms and pipeline (IrysSolve®) are now made available on the DNAnexus Platform. IrysSolve® is designed to provide researchers with the capability of performing comprehensive analysis of the whole genome, with the computational power and scalability of the DNAnexus Cloud Genomics Platform.

• Seamless integration between DNAnexus and Ingenuity Variant Analysis Researchers have now the ability to choose a sequencer independent, cloud-based solution for analyzing and interpreting their NGS data by uploading raw sequencing data into the scalable DNAnexus cloud platform and seamlessly generating uniquely actionable biological insights through QIAGEN’s Ingenuity Variant Analysis.

Strategic partnerships and collaborations

• Amoy Diagnostics and Illumina enter strategic collaboration for next-generation sequencing cancer diagnostics in China Under the collaboration, Amoy will develop and commercialize a series of oncology-related tests based on Illumina’s next-generation sequencing (NGS) platforms, including the recently released research use only TruSight Tumor 15 as transferred from Illumina to Amoy. The collaboration reflects the commitment of both companies to provide integrated solutions to meet clinical needs in China.

• WuXi NextCODE and Sidra Medical and Research Center announced a broad, long-term agreement to provide and co-develop comprehensive research and bioinformatics programs. Within a flexible multi-year framework, the partnership will enable Sidra to leverage Wuxi NextCODE’s clinical, research and bioinformatics teams to deliver genomic medicine for its own patients as well as enhance its expertise to develop national, regional and global genomics research initiatives. The implementation will also allow Sidra to develop customized applications to support the genetic research needs of several health and research programs currently underway in Qatar, such as the Qatar Genome Project (QGP).

Product launches

• Veritas Genomics announced it would offer full genome sequencing to Personal Genome Project (PGP) participants for under $1,000. For now, the mapping is only available to the early adopters of PGP participants, a big leap for a company that only launched its first product, a BRCA screening test, in June of 2015.

• Pacific Biosciences launches new sequencing platform Sequel™ System based on its SMRT technology which offers significantly higher throughput at reduced project cost and at less time. The core of the Sequel System is the capacity of its redesigned SMRT Cells, which contain one million zero-mode waveguides (ZMWs) at launch, compared to 150,000 ZMWs in the PacBio RS II. The Sequel System is designed for whole-genome de novo assemblies and the characterization of a wide variety of genomic variation types. The system can also be used to generate data for full-length transcriptomes and targeted transcripts using the company’s Iso-SeqTM protocol.

• Interestingly, the system was developed as part of a collaboration with F. Hoffman-La Roche Ltd (Roche) to provide a nucleic acid sequencing system for use in human in vitro diagnostics. Under that agreement, Roche agreed to pay Pacific Biosciences a total of $40 million in milestone payments related to the development of the Sequel System.

• Bioo Scientific launched a number of new kits designed to improve exome capture. These complete solutions offer optimized library prep, blocking and barcoding, interfacing with Agilent SureSelect XT and XT2 systems and Roche’s Nimblegen SeqCap systems.

• HTG Molecular Diagnostics Launches Next-Generation Sequencing-Based HTG edgeSeq Immuno-Oncology Assay for digitally measuring the mRNA expression of 549 genes implicated in the host immune response to tumors. Automated on the HTG EdgeSeq system, HTG EdgeSeq Immuno-Oncology Assay (for research use only) couples HTG’s proprietary nuclease protection chemistry with next-generation sequencing (NGS).

• Personalis launches ACE ImmunoID NGS services for Immuno-Oncology based on the Personalis ACE (Accuracy and Content Enhanced) sequencing, informatics and content technology platform. The ACE ImmunoID assays, optimized and validated for cancer, are ideal for immuno-oncology studies that require broad neoantigen detection and gene expression analysis to complement DNA variant analysis.

• Ambry Genetics launched a new educational website for patients and families affected by  hereditary breast and ovarian cancer. The new website www.hereditarycancer.com was launched in honor of the Breast Cancer Awareness Month, and provides individuals with a number of resources to learn more about genetics, hereditary cancer, and genetic testing, as well as tools to assess their own risk, construct their family’s medical health history, and kick-start a conversation with their healthcare provider.

• Claritas Genomics launched a novel diagnostic test, its Clinical Exome, to exploit the strengths of multiple DNA sequencing platforms simultaneously to deliver confirmed results for a patient’s clinical whole exome within 4 weeks, compared to the industry standard of 12 weeks or more. Patients with rare disease typically seek a diagnosis for 8-12 years, receiving 3-5 separate tests at a high cost.

• N-of-One launches PrecisionInsights™ for cost effective, quality clinical interpretation of small 15-20 gene NGS solid tumor panels, a new clinical interpretation solution. This new solutions, a clinical interpretation report, is meant for organizations with targeted 15-20 gene NGS panels for molecular profiling in oncology. N-of-One PrecisionInsights™ is a concise, two-page report for each case providing the most recent clinical and scientific evidence specific to the identified genes and variants in the context of the specific cancer sub type.

• BD Launches the BD FACSseq™ Cell Sorter with BD™ Precise Assays for High Precision Single Cell Genomics. The BD FACSseq cell sorter combined with BD Precise Assays offers a high-throughput research method for single cell gene expression analysis to enable thousands of cells to be analyzed accurately, quickly, easily and affordably. BD Precise Assays, a product line developed at Cellular Research, Inc. which was recently acquired by BD, allows for a high throughput single cell genetic analysis based on their proprietary Molecular Indexing technology to enable gene expression profiles from single cells. This technology, combined with BD’s cell sorting capabilities, provides for a simple and integrated workflow for single cell analysis.

• Molecular Health to Offer Early Access Program for SafetyMAP(TM).  Molecular Health, provider of a cloud-based healthcare decision support technology to optimize the selection of therapies for improved patient outcomes announced that it will initiate an early access program (EAP) offering its SafetyMAP^TM software to pharmaceutical companies and clinical professionals involved in drug safety starting in November 2015.

• WaferGen Bio-systems announced the commercial launch of the ICELL8™ Single-Cell System for the isolation of thousands of single-cells and the ability to identify rare cells from a cell population at a high sensitivity.

• Illumina introduces new TruSeq® library preparation kits and Infinium® arrays to enable researchers to explore genetic variation on a more comprehensive scale. The new additions to the application-driven portfolio address a broad range of genetic studies from whole exome to population and disease specific genotyping, leveraging the Illumina industry-leading portfolio of genomic analysis systems.

• Invitae announces expansion of genetic testing menu to 600 genes and will begin releasing the new content between now and the end of the year. Invitae is immediately expanding its menu with dozens of new test panels for hereditary cancer, cardiovascular, neuromuscular, and pediatric and other rare disorders.

Other

• Illumina intends to start generating revenue from its cloud-based app platform BaseSpace via a three tier model for different organizations. The plan includes the creation of two paid-for packages that bundle together assorted features, some of which are targeted specifically at larger organizations. Starting in 2016, users will choose one of three subscription packages, the most basic of which is free but limited. The top-tier gives BaseSpace users the option to integrate laboratory information management systems (LIMS) from Illumina’s recent acquisition GenoLogics, plus a domain for up to 25 users and the ability to keep tabs on multiple instruments and sequencing runs. Subscribers to the basic package will have access to the BaseMount command line interface and the ability to share data, but will need to pay to make full use of BaseSpace and its app ecosystem.

Illumina is making 1TB of storage available to everyone for free, but above this users must buy extra space at the retail price charged by Amazon Web Services (AWS). Currently, an additional terabyte will cost users $360 a year. Illumina is also tying the cost of computation to AWS rates. The free computation provided by Illumina to date will end in March 2016, although all new and existing users will start out with a $200 in credit. Illumina has not yet revealed its pricing structure for the two paid-for subscription tiers.

• Epilepsy Society becomes third customer of Complete Genomics’ newly introduced Revolocity system.  The Revolocity system, is a supersequencer for large-scale, high-quality whole genome and whole exome sequencing.

• The BabySeq Project – Genome Sequence-Based Screening for Childhood Risk and Newborn Illness a randomized clinical trial designed to examine how best to use genomics in clinical pediatric medicine by creating and safely testing methods for integrating sequencing into the care of newborns. As such the National Institute of Child Health and Human Development (NICHD) and the National Human Genome Research Institute (NHGRI) have committed $25 million over five years to four projects that will investigate the use of genomic sequencing in newborns. In Boston, the BabySeq Project is being led by Dr. Robert C. Green of Brigham and Women’s Hospital (BWH) and Dr. Alan H. Beggs of Boston Children’s Hospital (BCH).

• UN panel warns against ‘designer babies’ and eugenics in ‘editing’ of human DNA and called for a moratorium on “editing” the human genome, pending wider public debate lest changes in DNA be transmitted to future generations or foster eugenics. While acknowledging the therapeutic value of genetic interventions, the panel stressed that the process raises serious concerns, especially if the editing of the human genome should be applied to the germline, thereby introducing hereditary modifications.

• Australia’s highest court found unanimously that your genes are no longer patentable. The judges unanimously agreed on the outcome, but had different reasons. The majority of judges ruled that the key part of a gene is not its physical structure, but rather the information stored in it, which is not an invention. They wrote: “[Its] substance is information embodied in arrangements of nucleotides. The information is not ‘made’ by human action. It is discerned.” This decision rules against Myriad Genetics, yet another setback for Myriad in its efforts to patent the gene.

• Estonia wants to collect the DNA of all its citizens and hopes to one day have enough donors to totally overhaul its healthcare system. The program began in 2000 to collect DNA samples from a quarter of its country’s population. Currently filled with DNA, white blood cells, and plasma of more than 52,000 Estonians. Already, the Estonian government has begun developing a system to making this genetic data available to citizens (and their doctors), free of charge, with plans to launch by the end of 2015.

Available via GenomeWeb

• Genomics England taps Congenica and Omicia to handle UK 100K genomes interpretation. The two firms were selected from a pool of four informatics companies and one reserve that were tapped to participate in a test phase that launched this past summer. Genomics England plans to continue working with Nanthealth and WuXiNextcode — the two other companies that participated in this phase — and also with the reserve bidder Lockheed Martin, who has partnered with Cypher Genomics for the project.

• Strand Life Sciences is aiming to position its 152-gene cancer sequencing test for solid tumors as a tool that can be used early on in a patient’s disease in order to inform first-line therapy. The company launched a 48-gene version of the StrandAdvantage test in the US in April, but has since expanded it to 152 genes in order to boost the clinical utility to about 83 percent, from around 65 percent. The company plans to publish a validation study of its test in a peer-reviewed journal in the near future. The StrandAdvantage test has a list price of $4,000. On a self-pay basis, the test costs $2,800. Strand also has a financial assistance program.

• Broad was awarded $40M by the NHLBI for large-scale whole-genome sequencing project The project is part of NHLBI’s Trans-Omic for Precision Medicine (TOPMed) program and will be the first step towards a larger initiative to use whole-genome sequencing for discoveries in complex disease. Such discoveries, the Broad said, will serve as a resource to investigate factors that influence disease risk, identify disease subtypes, and develop more targeted and personalized treatments.

Cancer under the lens

• Virginia Tech researcher developed a new toolkit to visualize and structurally analyze BRCA1 protein and its associated parts in a near-native environment. The scientists collected the protein and the protein assemblies from the nuclear material of human breast cancer cells to visualize macromolecular regulatory complexes in human patient–derived cancer cells.

• WUSTL discusses the value of deep tumor, relapse sample sequencing. Li Ding touched on the somatic mutation and clonal evolution patterns that can be gleaned from sequencing tumor, matched normal, and relapse tumor samples at far greater depths than is the current standard. As part of a broader discussion on sequencing breadth, depth, analyses, and big data challenges associated with cancer genomics, Ding pointed to an acute myeloid leukemia case that she and her colleagues sequenced to coverage depths exceeding 300-fold, on average, followed by a validation sequencing and targeting sequencing done at depths of between 1,000-fold and 250,000-fold coverage.

• Ambry Genetics announced new data affirming the effectiveness of multi-gene panel testing in identifying TP53 gene mutations in people who might otherwise not have been tested. The findings presented includes data collected from more than 25,000 individuals having TP53 testing, of which 187 were positive. The tested cohort is the largest to date from a single testing laboratory.

Research highlights

• The 1,000 Genomes Project Consortium releases world’s largest catalog of human genomic variation: The resource was released with two published online studies on Sept. 30, 2015 in the journal Nature. Investigating the genomes of 2,504 people from 26 populations across Africa, East and South Asia, Europe and the Americas identified about 88 million sites in the human genome that vary among people, with ~12 million most likely shared by many of the populations. This large database was made available to researchers as a standard reference for how the genomic make-up of people varies in populations and around the world. This catalog more than doubles the number of known variant sites in the human genome. The study also showed that the greatest genomic diversity is in African populations, consistent with evidence that humans originated in Africa and that migrations from Africa established other populations around the world.

These reports mark the culmination of the 1000 Genomes Project, which found more than 99 percent of variants in the human genome that occur at a frequency of at least 1 percent in the populations studied.

• Scientists find DNA differences between gay men and their straight twin brothers. This controversial presentation by Tuck Ngun suggested that there are genetic markers that clues to sexual orientation. The study, which was based on a very small sample set with no statistical power, was further discussed in an article by Ed Yong in The Atlantic explaining why scientists did not find the “Gay Gene”.