Whole genome sequencing slowly finds its way into the clinicSan Diego, CA – March 7th, 2013 - This year again, the Future of Genomic Medicine VI displayed an impressive list of speakers, including Michael Snyder*, Stephen Kingsmore, Stephen Quake, Elaine Mardis, Elias Zerhouni and George Church, among others. The two-day program, held in collaboration with AAAS/Science Translational Medicine provides a comprehensive overview of opportunities in genomic medicine.This year’s conference was summed up as whole genome sequencing (WGS) and whole exome sequencing (WES) move deeper into the clinic”. Thursday’s session started with the story of patient #1 of the IDIOM (Idiopathic Disease of Man) project, a 16 year old girl who had endured years of missed diagnosis at the hands of conventional medicine. Only when she was finally seen at Scripts Institute as part of their newly established IDIOM project, did they identify two rare genetic variants that were responsible for her condition. She responded to a change in medication, in yet another demonstration that WGS has a valuable future in the clinic.We noticed a number of interesting differences when compared to last year’s conference.

• Increased sequencing speed: In his talk, Stephen Kingsmore – who received this years’ Scripps Genomic Medicine Award for his pioneering work in neonatal care– highlighted his use of STAT-Seq, enabling the sequencing the genome of neonates in the ICU in 50 hours (including 25.5 hr sequencing and 17 hours secondary analysis), with plans to have this time go down to 18 hours in the next few months. He mentioned that up to 5% of babies are accepted in the NICU and maybe one third of those need some form of genome analysis.
• Increased sequencing depth and frequency: Mike Snyder outlined his team’s effort to conduct a longitudinal study repeatedly sequencing his whole genome over the last 38 months. He argued that comparing his health status vs. a healthy “self” made more sense than comparing it to the average population.
• Increased sequencing depth and read length: Multiple talks mentioned sequencing depth for WGS of 100x or more, or the importance of long reads in clinical settings in order to obtain haplotypic information. As a result, a number of participants expressed excitement about Illumina’s recent Moleculo acquisition.
• Continued interest in multiple platforms: Results presented in the conference continue to outline the need to sequence genomes with multiple platforms such as Complete Genomics and Illumina for optimal variant calling. In Mike Snyder’s case, both technologies identified 3.3M common variants (~89%), Illumina identified another ~345K (~9%) and Complete Genomics an additional ~100K (~2%).
• Shift away from microarrays: in 2012, a number of talked incorporated the use of microarrays in clinical settings. This year, only a couple of talks mentioned microarrays, and mostly for studied that were started a few years ago. NGS took center stage.
• Continued reimbursement issues: Reimbursement issues continue to be critical, especially in light of already fast-increasing insurance premiums (up from $5,791 to $13,375 from 1999-2009). Howard Jacob highlighted that complex genetic tests are not only not often reimbursed, but often excluded from reimbursement. He therefore emphasized the need for these results to be medically actionable. Dr. Jacob mentioned it was only a matter of time before NGS is deployed more broadly in clinical setting; the outstanding question is around timing of disease progression: at birth or in late disease stages.
• Continued controversy around giving the data back: The controversy surrounding what type of data should be given back to consumers / patients continue. Currently, IDIOM is not reporting secondary findings (i.e., findings not related to the primary medical condition). As expected, interest I secondary findings across patients, parents and doctors increase with the patient age (higher for adult onset disease) and availability of clinical treatment. A number of stakeholders, including companies such as 23andMe are expected to play a role in the development of tools to report data back to clients.

Additional feedback and conclusions from the conference (e.g., challenges around consolidation of data currently in different silos, feedback from Aetna) will be incorporated in the upcoming update of our NGS report (estimated release date: April 2013).* Michael Snyder (Professor of Molecular, Cellular and Developmental Biology at Yale University and Director of the Yale Center for Genomics and Proteomics), Stephen Kingsmore (President of the National Center For Genome Resources in Santa Fe, New Mexico), Stephen Quake (Professor of Bioengineering and of Applied Physics at Stanford University; co-founder of Helicos and Fluidigm), Elaine Mardis (Director of Technology Development, Genome Institute at Washington University), Elias Zerhouni (President of R&D, Sanofi-Aventis; 15th director of NIH) and George Church (Professor of Genetics at Harvard Medical School)

Authors: Stephane Budel, Partner at DeciBio, LLCConnect with Stephane Budel on Google+https://plus.google.com/+StephaneBudel