1 out of 100 benefit from whole genome sequencing

By Razib Khan | February 18, 2013 5:10 pm

Perhaps. The New York Times has a piece out reviewing the vogue for sequencing the genomes of children who have mysterious diseases. The numbers are what matters here I think:

A few years ago, this sort of test was so difficult and expensive that it was generally only available to participants in research projects like those sponsored by the National Institutes of Health. But the price has plunged in just a few years from tens of thousands of dollars to around $7,000 to $9,000 for a family. Baylor College of Medicine and a handful of companies are now offering it. Insurers usually pay.

Demand has soared — at Baylor, for example, scientists analyzed 5 to 10 DNA sequences a month when the program started in November 2011. Now they are doing more than 130 analyses a month. At the National Institutes of Health, which handles about 300 cases a year as part of its research program, demand is so great that the program is expected to ultimately take on 800 to 900 a year.

Experts caution that gene sequencing is no panacea. It finds a genetic aberration in only about 25 to 30 percent of cases. About 3 percent of patients end up with better management of their disorder. About 1 percent get a treatment and a major benefit.

It seems this is a floor in terms of the results outcome for these children, as some of them may receive better or more effective treatments in the future, because the specific nature of their disease is already known. Since most medical treatments today are marginal in effect these outcomes don’t surprise or depress me, and the price point is sure to come down. In the near future I imagine that everyone will have a whole genome sequence, and relevant information about your specific genetic profile in relation to the sea of biomedical literature constantly coming out may be sent to you in a drip, drip, fashion by a phone or web app.

CATEGORIZED UNDER: Personal Genomics
  • https://delicious.com/robertford Robert Ford

    Don’t these tests include testing of the fetus to see if there are genetic defects? That seems like an added benefit to that 1% number as you could then terminate and start over. In the case of those parents I’d prefer they’d call it a day. I was just reading that article and I feel it’s outrageous that a couple who is obviously prone to genetic defects can have multiple kids that now need lifelong care at the expense of society. Unbelievably selfish…

  • Dmitry Pruss

    These tests are currently ordered only after the existing metabolic tests, and simpler gene panel tests, have already failed. The 1% success rate are unqualified successes, typically when a missing nutrient or a toxic nutrient are discovered, and a straightforward dietary adjustment fixes it all. Alas, sometimes the damage is already done for what would have been an eminently preventable condition, had it been differentially dx’d sooner.

    Most of the identified, but incurable, problems involve fatal breakdowns of the genes of nervous system function. One may argue that these families are also helped by making it clear that the child’s condition is no fault of theirs, and that nothing can help. Or one may argue otherwise. Looking for these answers is very expensive with or without sequencing, and it must be done one way or another.

    • http://www.gwern.net/ gwern

      > These tests are currently ordered only after the existing metabolic tests, and simpler gene panel tests, have already failed.

      Maybe that’s how they *used* to be done, in which case you would be correct: when they’re “used as a court of last resort” any success is an unqualified success and a large marginal gain. But Razib’s link describes them as moving earlier in the pipeline where the raw estimates of success are not the marginal successes: ‘…Dr. Chung said. “Now we can think of it as a first-line test.”’

      • razibkhan

        the numbers in the article don’t seem to suggest it is a first line test yet. unfortunately there are way more congenital metabolic problems from what i know than the counts for whole genome sequencing. but shit moves fast in this area….


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About Razib Khan

I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. In relation to nationality I'm a American Northwesterner, in politics I'm a reactionary, and as for religion I have none (I'm an atheist). If you want to know more, see the links at http://www.razib.com


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