At Bio-IT World, All Eyes Were on the Cloud and Big Data!

As expected, the 10th annual Bio-IT World Conference & Expo was both exhausting and invigorating. With three jam-packed days of great talks, demos, and networking opportunities, we came away from the meeting eager for a long nap. A huge thank you to all the people who stopped by our booth and engaged us in really interesting conversations! Talking with current and potential users has sent us back to Mountain View with the reinforced knowledge that our product really is making a difference in people’s lives — and making next-gen sequence data easier to manage and analyze for labs that don’t have production-scale compute resources, as well as for IT groups that find themselves juggling a lot of different computing needs. This gives us an even greater sense of urgency in launching our new platform this summer.

One of the most interesting facts about this year’s Bio-IT World conference was a shift in focus in the exhibit hall. In years past, there have always been a lot of vendors showing off servers, cluster improvement tools, chip accelerators, and other hardware offerings. This year, hardware was unusually hard to come by. It seems that the field has tacitly acknowledged that cloud-based data storage is indeed the way to go for the vast majority of genomic labs.

Scientists who spoke at the conference or visited our booth offered further validation of that trend. After years spent trying to figure out how to write scripts that work best on a cluster or with an FPGA, the biologists were relieved to be back where they wanted: focused on the data, not on the compute infrastructure. When talking to attendees in our booth, it was clear that the most pressing thing for this community is getting the right scientific answer, a sentiment that resonates with us.

In a keynote talk, Jill Mesirov from the Broad Institute spoke about the critical need to integrate tools and workflows for analysis and management of large data sets. She introduced GenomeSpace, the Broad’s new platform that combines various tools, including the UCSC genome browser, Cytoscape, GenePattern, Galaxy, and more.

On the commercial side, the emphasis on putting compute infrastructure behind the scenes so that scientists can focus on answers was reinforced by a number of news announcements tied to new cloud-based services from organizations including Illumina, BGI, and others. While the commercial services haven’t officially launched yet, we look forward to trying them out later in the year as they’re released.

Finally, we’re delighted to see that people are already flocking to our new Landing page at dnanexusX.com, which has information on the new DNAnexus platform to be launched this summer. If you haven’t signed up already, we encourage you to do so. This way you will be the first to learn about the capabilities the new platform will support and exact timing of the roll out. It’s simple: just enter your e-mail address and we will keep you posted with ongoing information about our best-in-class security, unified environment for instant collaborations, custom workflows, and more. You’ll also be automatically entered in a monthly drawing for a free iPad in May and June. Sign up early for the best chance of winning! Stay tuned — the winner for the April drawing has been pulled and will be announced shortly on our blog.

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!

 

Scientific Collaborators in New York and Jerusalem Uncover New Mutation Underlying Rare Sensory Disease

The study described below was published in the April 2012 edition of the Annals of Neurology, the journal for the American Neurological Association and the Child Neurological Society.

At a time when many people are asking when DNA sequence information will have a real application in healthcare, a nonprofit organization based in Brooklyn, New York, is proving that linkage mapping and exome sequencing are already making a major difference in people’s lives.

Bonei Olam is charged with helping families with genetic or undiagnosed diseases, many of them dealing with infertility challenges, to conceive healthy babies using tools such as pre-implantation genetic diagnosis. In 2008, Bonei Olam opened its Center for Rare Jewish Genetic Disorders to find the underlying molecular causes of some of these conditions. They responded to hundreds of families who had been unable to find a diagnosis through traditional medical routes, and established key collaborations with universities, including Hadassah Medical Center in Israel, to help perform the studies. Over the years, the center has funded SNP arrays, Sanger sequencing, variant validation, and the sequencing of more than 100 exomes for family after family.

It was through one of those studies that collaborators from Hadassah Medical Center, New York University, and Bonei Olam discovered a novel mutation that leads to a previously uncharacterized disease linked to hereditary sensory autonomic neuropathy, a group of disorders with the common theme of loss of function in peripheral sensory nerves. This new version is far more severe than its familial dysautonomia cousin and is caused by a mutation in the DST gene, which destabilizes the Dystonin protein. The study, called “Hereditary sensory autonomic neuropathy caused by a mutation in dystonin” was published by Dr. Simon Edvardson, Prof. Orly Elpeleg, and the rest of their team in the Department of Genetic and Metabolic Diseases at Hadassah in the April 2012 issue of Annals of Neurology.

Chaim Jalas, Director of Genetic Resources and Services at the Center for Rare Jewish Genetic Disorders and a co-author on the paper, says that this particular project began when two related families approached Bonei Olam, each having lost at least one child to this uncharacterized disease. The disorder was lethal: all of the affected children, three in total, died by the age of 2.

The team started off with SNP arrays to perform linkage analysis in both families, and later performed exome sequencing on one of the affected children to find the causative mutation. Much of the clinical and functional work in the eight-month project — including identifying the mutated gene and studying its effect in cell lines — was led by Prof. Orly Elpeleg at Hadassah Medical Center in Jerusalem.

Since Bonei Olam doesn’t have an in-house bioinformatics team, Jalas relies for interpretation on various software tools as well as the cloud-based storage and analysis platform from DNAnexus. For this project, he uploaded the raw sequence reads to DNAnexus and ran the Exome analysis tool followed by the Variant analysis tool, which located the mutation — the DST variant that results in an unstable transcript in Dystonin, a protein used in the cytoskeleton. “What DNAnexus does for us is all the bioinformatics, starting from uploading raw reads to performing the alignment, the variant calling, the annotation, and graphical display of the reads on the reference genome,” Jalas says. In the past, the DNAnexus Variant analysis tool has been able to find a variant that other software packages have missed, he says — but he’s most confident when two different software packages call the same variant so it’s more likely to be real.

Once DNAnexus returned the answer, Jalas shared the data with his collaborators, who could log in with their own accounts to review the information. Finally, the research team confirmed the mutation by Sanger sequencing.

Since Bonei Olam isn’t your typical research institute, the real triumph was not the research finding or the publication of this mutation; it’s that “one of the two families is currently pregnant with a healthy baby,” Jalas says.

Ultimately, the success of these studies may prompt Bonei Olam to move toward whole genome sequencing. “I think at some point we will do whole genomes,” Jalas says. “We’re looking into a pilot study of families for whom exome sequencing did not find a causative genetic mutation where we know for sure it’s a genetic condition.”

Paper information:
Hereditary sensory autonomic neuropathy caused by a mutation in dystonin
Simon Edvardson, MD; Yuval Cinnamon, PhD; Avraham Shaag, PhD; Orly Elpeleg, MD, from Monique and Jacques Roboh Department of Genetic Research, Hadassah, Hebrew University Medical Center
Chaim Jalas, from Bonei Olam, Center for Rare Jewish Genetic Disorders
Channa Maayan, MD, from Department of Pediatrics, Hadassah, Hebrew University Medical Center
Felicia B. Axelrod, MD, from Department of Pediatrics, New York University School of Medicine
DOI: 10.1002/ana.23524
http://onlinelibrary.wiley.com/doi/10.1002/ana.23524/abstract