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In simple Mendelian genetics, a single change in one gene can produce a large change in mortality. The National Human Genome Research Institute (NHGRI) will be funding genomics studies on Mendelian traits using a similar strategy.

NHGRI will fund a small number of centers, dominant centers you might say, and look for large changes. The sequencing centers that will benefit are the Broad Institute, Washington University, and Baylor College of Medicine. For the next four years, the big three will be dividing $86 million a year according to a press release from NHGRI. I’m not sure what algorithms predict a larger return from funding a smaller number of researchers, but the future looks like fun for those on a small budgets who can figure out how to slurp up the data and quickly spit out results.

Studies on Mendelian disorders will benefit from the proposed funding plan as well. According to the NIH press release, only half of the estimated 6,000 rare diseases, inherited in a Mendelian pattern, have been linked to a genetic cause. Although each disease is rare, in combination, these diseases affect approximately 25 million Americans. Today’s DNA sequencing technologies offer an unprecedented ability to find the basis for these diseases, particularly when the genomes of entire families are compared.

Which brings us to clinical sequencing and new interesting issues.

Earlier genetic tests raised all kinds of ethical controversies. Does everyone have a right to be tested? Should test results be shared with one’s family? Should parents be allowed to test children? Should someone have a right to know, to not know, etc. Identifying all the stakeholders and their issues can make your head spin.

And those tests typically looked at single genes.

Today, when we sequence a genome, we will find much more information about many thousands more genes whether we want it or not. Genome sequencing is like remodeling. A simple quest to check out a foundation always goes along with the chance of finding water leaks or ant colonies.

We could sequence a genome from a cancer patient for example, to determine the best drug for treatment, and uncover an undiagnosed predisposition to some other bad news of kind of trait. What doctor wants to share the news that they can cure someone’s cancer but that early Alzheimer’s gene they found, uh sorry, maybe you want to look into assisted living?

Many of us see enormous potential in genomic sequencing. But, in the end successfully using genomics will require us to go well beyond the work of developing the technology to prepare genome sequencing for the clinic. We’re going to have to prepare the clinic for genome sequencing.

Comments

  1. #1 Mike the Mad Biologist
    December 7, 2011

    “NHGRI will fund a small number of centers, dominant centers you might say, and look for large changes. The sequencing centers that will benefit are the Broad Institute, Washington University, and Baylor College of Medicine. For the next four years, the big three will be dividing $86 million a year according to a press release from NHGRI. I’m not sure what algorithms predict a larger return from funding a smaller number of researchers”

    There seems to be some confusion about this. This represents, in absolute dollar terms, more than a 20% cut for the large scale centers. All of these centers have had to lay people off (Wash U alone let 54 people go). So I guess, from a certain perspective, a smaller number of researchers are being funded. In addition, NHGRI has shifted money to (relatively) smaller clinical genomic centers, although that’s not highlighted in the release–the total funding and number of recipients has increased.

  2. #2 Sandra Porter
    December 7, 2011

    You’re right, the overall funding levels are down. The press release didn’t contain information about the past levels, just the new levels.

    In the past, weren’t a larger number of genome centers funded overall?

  3. #3 Mike the Mad Biologist
    December 7, 2011

    In the previous award, Baylor, Wash U, and Broad were the only three recipients.

  4. #4 Sandra Porter
    December 8, 2011

    The NCBI trace archive lists about 140 DNA sequencing centers (http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=stat&f=xml_list_centers&m=obtain&s=center).

    Many of the groups on this list are not in the US. Other groups are companies, and others like “Direct submission from individual investigator” are not really sequencing centers at all.

    Still, there are lots of groups beyond Broad, WashU, and Baylor, that are sequencing large amounts of DNA. Some of these groups were NIH-funded genome centers in the past, like Cold Spring Harbor Labs, University of Oklahoma, Standford Genome Center, TIGR, University of Utah, University of Washington, and JGI.

    I don’t know whether it’s better to concentrate funding on a few centers or to spread it around. I I just noted that a large amount of funding is concentrated on a few centers.

  5. Hi Sandra,
    I’m glad to see you will be at @scio12 this year. We met last year on the bus!

    I’m stopping by each blog for the attendees of #scio12 and saying hi and giving a shoutout on twitter!

    Look forward to seeing you again!