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Jun 23, 2011

Ash, smoke provide grim reminders at genetics conference

I’m writing this blog entry as I’m on the plane, on my way back from San Diego after the ASHG conference (American Society of Human Genetics for you non-genetics types). Despite the fires burning around the area and the losses faced by so many people in the region, the meetings proceeded as planned. It seemed a bit surreal to us all that in the downtown near the convention center, so little was affected, with the exception of the air, which was unpleasant to breathe due to smoke and ash. As the plane approached San Diego, we got quite a look at the smoke covering the region and some glimpses of fires still burning.

We were constantly reminded that we were near a disaster zone as local ASHG attendees spoke of mandatory and voluntary evacuations and homes lost or nearly lost. One person reported to us that his mailbox was singed but his house was spared! Unfortunately, many were not so lucky. We met other San Diego residents who were staying in our hotel after leaving their homes. Many had small children and pets with them. Our hearts go out to everyone who is dealing with the ongoing effects of this natural disaster.

For Philadelphia’s sake, I hope next year’s ASHG meeting will lack any reminder of natural disaster. Last year’s ASHG meetings (held in New Orleans a year after Katrina) took place in the partially renovated convention center where so many gathered during the aftermath of the flooding from Katrina. Although the French Quarter and the area near the convention center in New Orleans were not heavily affected, we saw plenty of other neighborhoods that had been devastated by flooding.

Despite the surrounding tragedy, the meetings were really fantastic. Doug Robinson and I were glad to be joined by three other members of the JMP Genomics team, giving us all time to talk to customers and potential users, attend talks, and network with partners. We were so happy to have so many SAS/Genetics and JMP Genomics users stop by the booth! It was so cool to hear from them about what they were doing and how our software is helping them with their analyses.

There was a lot of interest in the new copy number functionality we have added for JMP Genomics 3.1. Copy number functionality, and the whole-genome association capabilities we added for version 3.0 were hot topics of conversation with ASHG attendees. Potential customers were most impressed with the fact that we can handle data set sizes that many other programs can’t. Particularly for copy number, we heard the words “choke” and “crash” a lot when referring to other products. The fact that we run SAS to process the large genomics data sets was really intriguing to a number of SAS-coding data analysts who stopped at the booth. They liked the fact that SAS drives most of the JMP Genomics processes and that SAS and JMP analytic methods are so well-documented compared to programs which take a black-box approach (even with their own customers).

Clearly, groups who are anticipating Voluntary Genomic Data Submissions (VGDS) find it appealing to be able to archive SAS code used to run a JMP Genomics analytic process. SAS has long been trusted for FDA submissions, and medical reviewers regularly use JMP in the review process. The JMP Genomics team has already been heavily involved in the FDA-led Microarray Quality Control (MAQC) consortium aimed at evaluating the sources of variance in microarray data and validating the technology. We expect that JMP Genomics will be likely used in the VGDS review process at FDA. We will certainly put our tools to use shortly on the data sets to be used for analysis by the Genome-Wide Association Study subgroup of Phase II of the MAQC.

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