At ASHG 2014 genomics was everywhere, with big data and variant analysis/interpretation

AHSG Last week the annual gathering of human geneticists happened at the convention center in sunny San Diego. This year this engaging conference was dominated by genomics, and in particular the topics of big data, variant analysis and interpretation. This emphasis was clearly reflected in the scientific talks, but also in the commercial sector with many companies focusing on providing new solutions on variant analysis, reaching even into the clinical space.

Besides the scientific and commercial aspect of ASHG, which I will summarize later in this blog post, this year the conferences had a strong human side associated with it. For the first time two movies were presented – Genetics in Motion Movies – that were engaging and spot on considering recent news and announcements about the benefits and/or conflicts of knowing and understanding genetic diseases. The first movie [Twitch with Kristen Powers] explored the impact of genetic testing on a young person whose mother had Huntington’s disease. While the movie follows Kristen Powers as she undergoes testing for the disease, it also examines the basic science of the disease itself. The second movie [On Beauty with Rick Guidotti] nicely addresses the need of first recognizing the person before the disease. Rick Guidotti achieves this phenomenally by capturing the beauty of an individual person and not focusing primarily on the disease – his pictures are indeed amazing. Of special interest in this context is

Positive Exposure, a non-profit organization, that Rick started and that is definitely worth exploring.

In addition to these movies, The Genetic Portrait Project took place upstairs as an interactive art initiative. The task was simple yet demanding at the same time: any contributor was asked, “How do you think genetic research will affect the future?”.  As a result, a series of pictures now tell a compelling and powerful story of our inner fears, desires, and obligations when thinking about genetic testing, genetic research, and/or genetic diseases.

GeneticPortrait

Now turning our attention to the commercial side of the conference: The amount of sequencing and clinical applications was far-reaching and as a result, the number of companies focusing on sequencing software solutions seems to be never ending with many trying to address the clinical need of actionable and summarized reports. As such, the number of announcements associated with this conference is clearly in concordance with this. Here some of the major announcements from the conference:

Of general importance

  • The official release of the 63,000 exome project with allele frequency data now fully accessible as an open source database to the community via the Exome Aggregation Consortium (ExAC) – presented by Daniel MacArthur (MGH Boston and the Broad Institute). Coinciding with this release was the plenary talk by Konrad Karczewski (post-doc in Daniel MacArthur’s lab at MGH Boston and the Broad Institute), who presented an impressive Human Knockout Project and the systematic discovery of loss-of-function variants in humans which was based on this exome project.
  • Global Alliance for Genomics and Health Members Meet to Advance Genomic Data Sharing – bringing together more than 250 international leaders to collaborate on the development of innovative solutions to accelerate sharing of genomic and clinical data. At their plenary meeting, Alliance members shared progress to date and discussed next steps for the effort. The Global Alliance is an international coalition of over 140 member organizations dedicated to improving human health by maximizing the potential of genomic medicine. The group’s diverse membership includes world-leading institutions in healthcare, research, patient and disease advocacy, life science, and information technology who are working together on open interfaces and catalytic projects to enable effective and responsible data sharing and guide this quickly evolving field.

Data management, analysis, and interpretation

  • Genomics England publishes results of its annotation assessment. Genomics England, the company leading the UK’s 100,000 Genomes Project, has released details of those companies that distinguished themselves in its annotation assessment exercise. Genomics England is committed to kick-starting the development of a UK genomics industry and this assessment exercise is part of that aim, as well as to evaluate and select potential service providers for the 100,000 Genomes Project. As a result, the following companies have been selected to move to the next stage of evaluation as potential service providers for the variant annotation and clinical interpretation element of the program: Congenica, Diploid, Nantomics, Genomics Ltd, Illumina, Qiagen, Lockheed Martin, Nextcode, Omicia, and Personalis.
  • QIAGEN Demonstrates Expanded Bioinformatics Workflows which includes a number of new capabilities for its Ingenuity® Variant Analysis™ and CLC Cancer Research Workbench solutions for next-generation sequencing (NGS). With this extension, the Ingenuity Variant Analysis now integrates BIOBASE HGMD Professional which provides researchers access to HGMD without the requirement of a separate license. Furthermore, CLC Cancer Research Workbench adds CNV detection and integration with Ingenuity Variant Analysis.
  • Maverix Biomics adds DNA sequencing Analysis Kits to its HIPAA compliant Maverix Analytic Platform. The new end-to-end Analysis Kits allows the analysis of variants in whole genome, exome, and targeted re-sequencing data and enables researcher to identify and annotate genetic variants that are part of the gene pathways related to a specific disease or condition, or can be used as unique signatures for diagnostic and testing applications. The new DNA sequencing Analysis Kits are based on popular peer-reviewed open source tools, such as FastQC for sequencing quality checking, BWA for read mapping, and SnpEff for variant effect prediction.
  • NextCODE Health launched a new genomic data sharing environment called the NextCODE Exchange. Data shared on the Exchange can be accessed over the web, letting users share their top-level findings including their raw sequencing data. The NextCODE Exchange is an extension of genomic discovery tools. The Exchange’s online interface, and associated genome browser, comes equipped with analytics tools for finding variants in a patient’s genome that may explain unusual symptoms and phenotypes. These tools can filter variants by inheritance patterns and their predicted impact on protein expression, as well as draw on the massive database of variants from the Icelandic population assembled by deCODE genetics over more than a decade of population-scale sequencing.

Partnerships and collaborations

  • DNAnexus Powers Novel Genomic Collaborations between Regeneron Genetics Center and Leading Healthcare Institutions. DNAnexus provides the technology backbone that enables various RGC research partnerships through the sharing and management of data and tools around large volumes of sequencing data. In one major collaboration, the RGC plans to sequence over 100,000 DNA samples obtained from Geisinger Health System and provide the data to Geisinger. Via the cloud-based genome center, the RGC will integrate the resulting genomic data with corresponding de-identified clinical information, also provided by Geisinger, to guide drug discovery.

Other

  • Personalis introduces new services for cancer research and clinical trials based on its ACE (Accuracy and Content Enhanced) sequencing, informatics, and content technology platform. At the center of Personalis’ cancer research products is a core set of more than 1,300 protein-coding genes and more than 200 miRNA genes related to cancer. Personalis supports this common gene set in both panel and exome configurations. Both combine DNA and RNA assays, which can be performed from a single common sample. Both configurations also include key content outside the coding regions. The ACE Exome for Cancer provides data from the common gene set in the broader context of more than 8,000 medically related genes with augmented coverage, and 20,000 genes overall.
  • Edico Genome launches its flagship DRAGEN processor. The DRAGEN is a chip that users can integrate into their servers or sequencing instruments, providing compute hardware specifically to map sequencing reads to a reference genome. Its aim is to piece short reads together into a complete genome, much faster than can be accomplished using a general-purpose server, relieving one of the most time-intensive steps in working with genomic data.

Funding

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