Hope to See You at Bio-IT World!

Here at DNAnexus, we’ve been gearing up for the 10th annual Bio-IT World Conference & Expo, which starts today in Boston at the World Trade Center. It’s one of the biggest bio-IT events on the calendar, with more than 2,000 attendees last year and even more people expected this year. It’s also a special event for us, since it marks the two-year anniversary of the launch of our current product.

We’re looking forward to keynote talks from Martin Leach and Jill Mesirov, who are in charge of informatics and IT at the Broad Institute. They will surely have much to say about their experience in managing a slew of next-gen sequence data.

We are particularly excited as we are getting ready to launch the new DNAnexus platform this summer. Stop by our booth in the exhibit hall (#413, not far from the registration area) and learn more about the new product. Say hi and get to know the exciting DNAnexus team.

If you don’t catch up with us at Bio-IT World, please check out our new Landing page (dnanexusX.com) to learn about the new DNAnexus. If you sign up with your e-mail address, we’ll send you updates about the product and its functionality as we get closer to the launch. As a bonus for signing up, you’ll automatically be entered in a contest to win an iPad at the end of each month from April through June. The earlier you sign up, the more chances you have to win!

 

On the Scene at AMIA: Clinical Promise and Informatics Opportunities for Whole-Genome Sequencing

I recently got to attend the American Medical Informatics Association’s (AMIA) Joint Summits on Translational Science, held in nearby San Francisco. The event had tracks for both translational bioinformatics as well as clinical research informatics and served as a unique opportunity to hear about the informatics challenges that are being faced in the clinical realm right now.

Here are a few highlights from the talks I found particularly interesting:

Howard Jacob, director of the Human and Molecular Genetics Center at the Medical College of Wisconsin, gave a very charismatic talk on genome sequencing in the clinic. He told attendees the most compelling reason to use genome sequence with patients is that it’s family history with data. Jacob described an ongoing pilot whole-genome sequencing program at the college, noting that for a patient to be considered for the program, two physicians must nominate him or her and show that the sequencing would be actionable and “end a diagnostic odyssey.” Accepted patients must determine at the outset how much information they want to receive when returning results; some choose to know just the minimum, while others want to know about genetic variations for which we don’t yet understand the disease implications. Enrolled patients receive six to 10 hours of genetic counseling as part of the process.

Jacob said that with an 20% patient acceptance rate (16 out of 80) for the pilot program, clinicians are now eager to eliminate the approval process altogether to get their patients sequenced. To my surprise, four of the 10 cases submitted for insurance approval have gone through. Jacob added that as the cost continues to drop, it will be hard for clinicians not to use this approach for patients, especially for rare diseases and for pharmacogenomics decisions. (He noted that one lesson learned already is that clinical sequencing is not ready for common diseases, with the exception of cancer.) Jacob said the challenges in scaling up sequencing operations in the clinic will be: delivering adequate genetic counseling; selecting the most appropriate analytical tools for clinical sequencing; and determining who can order whole genome sequencing tests.

In another talk, Peter Tonalleto, a professor at the Center for Biomedical Informatics at Harvard Medical School, highlighted the medical opportunities associated with a patient’s genomic variation landscape. His research group is working on analysis pipelines for DNA sequencing, RNA-seq, microRNAs, and methylation. Those pipelines, coupled with preclinical and clinical variant annotation, yield application in areas such as risk prediction, tumor classification, and pathway analysis for alternative treatment approaches. He also noted a cost comparison his team did for a breast cancer project, in which standard practice cost about $19K and next-gen sequencing practice cost about $25K. With these costs finally being on par, Tonalleto told the audience that more clinicians at Harvard Medical School are eager to adopt whole genome sequencing for breast cancer patients.

In all, the conference offered valuable insight into how next-gen sequencing is being adopted in the clinic. It was clear from the talks I saw that clinicians are eager to embrace this new technology, despite the number of hurdles — including insurance reimbursement, approval processes, and technology learning curve — standing in the way. While there are a number of challenges to consider, I walked away from this conference feeling optimistic about the uptake of whole-genome sequencing in healthcare already.

ABRF: A Quick Meeting Recap

Here at DNAnexus, we’re lucky to have a terrific team supporting our goals. In this blog post, we wanted to share highlights from the recent ABRF meeting from the perspective of our marketing manager, Cristin Smith. Here’s her recap.

Just when we thought the Marco Island resort couldn’t be beaten for location, here comes the annual Association for Biomolecular Resource Facilities (ABRF) conference, held at the lakeside Disney Contemporary Resort right in the heart of Disney World, complete with a view of Space Mountain. I’m pretty sure the team back home in Mountain View was a little concerned that we weren’t going to come back.

The meeting’s opening keynote came from Trisha Davis, who runs the Yeast Resource Center at the University of Washington. Her work has focused on using yeast as a proving ground for various technologies, noting that as her center has evolved, so too has her team’s ability to really drill down into targeted interrogations of the organism. During her talk, entitled “Technology Development in a Multidisciplinary Center,” she noted how important it is to integrate multiple complex analyses in an attempt to relate genotype to phenotype.

On the final day of the meeting, “Omics Technologies to Transform Research, Health & Daily Life” also resonated with me. This was Harvard professor George Church’s vision of a future where genome sequence information is widely used and readily available. He spoke about some current logistical limitations, such as the fact that a $100 blood draw is cost-prohibitive, and that the field will have to move toward buccal swabs and other technologies that may cost only $1 to process in order for ’omic testing to become affordable. Citing some 37 next-gen sequencing technologies as the driver for the rapid drop in sequence costs, he said that his own estimate of the current genome price — from sample to interpretation — is $4,000. In order for genome sequencing to become medically useful, Church noted a few factors that will have to be addressed: a focus on completeness and standards to give FDA confidence in these technologies; the need for significantly more genetic counselors than we have right now; and better interpretation software that makes genome analysis truly straightforward.

Overall, we were excited to see how eager the core lab community is to receive technology improvements that generate a higher quantity and quality of sequence data for their customers in support of their research. This enthusiasm was a great setting to unveil our newly redesigned booth at the exhibit hall. It’s hard to find a more tech-loving crowd than the people who run core facilities, and we were glad to meet so many of them last week.