Genome sequencing for the people is near

When I first began writing on the internet genomics was an exciting field of science. Somewhat abstruse, but newly relevant and well known due to the completion of the draft of the human genome. Today it’s totally different. Genomics is ubiquitous. Instead of a novel field of science, it is transitioning into a personal technology.

But life comes at you fast. For all practical purposes the $1,000 genome is here.

And yet we haven’t seen a wholesale change in medicine. What happened? Obviously a major part of it is polygenicity of disease. Not to mention that a lot of illness will always have a random aspect. People who get back a “clean” genome and live a “healthy” life will still get cancer.

Another issue is a chicken & egg problem. When a large proportion of the population is sequenced and phenotyped we’ll probably discover actionable patterns. But until that moment the yield is going to not be too impressive.

Consider this piece in MIT Tech, DNA Testing Reveals the Chance of Bad News in Your Genes:

Out of 50 healthy adults [selected from a random 100] who had their genomes sequenced, 11—or 22 percent—discovered they had genetic variants in one of nearly 5,000 genes associated with rare inherited diseases. One surprise is that most of them had no symptoms at all. Two volunteers had genetic variants known to cause heart rhythm abnormalities, but their cardiology tests were normal.

There’s another possible consequence of people having their genome sequenced. For participants enrolled in the study, health-care costs rose an average of $350 per person compared with a control group in the six months after they received their test results. The authors don’t know whether those costs were directly related to the sequencing, but Vassy says it’s reasonable to think people might schedule follow-up appointments or get more testing on the basis of their results.

Researchers worry about this problem of increased costs. It’s not a trivial problem, and one that medicine doesn’t have a response to, as patients often find a way to follow up on likely false positives. But it seems that this is a phase we’ll have to go through. I see no chance that a substantial proportion of the American population in the 2020s will not be sequenced.

2 thoughts on “Genome sequencing for the people is near

  1. “Researchers worry about this problem of increased costs. It’s not a trivial problem, and one that medicine doesn’t have a response to, as patients often find a way to follow up on likely false positives. But it seems that this is a phase we’ll have to go through.”

    One key point is the genetic testing, once you get it to a medically useful level of detail and accuracy, is a once in a lifetime expense that is relevant not just to one condition, but to many, some of which result in reduced diagnostic cost and some of which result in increased diagnostic cost. (The initial testing costs also get spread over non-medical uses like determinations of paternity, screening people for genetic issues related to job performance (e.g. altitude sickness for a mountain division soldier), identification of lost children and missing persons and unidentified bodies, and forensic law enforcement uses.) And, in many cases there is no point is doing diagnostic tests for a condition that there is a genetic risk indicator for until there is some symptom of that condition.

    For example, every time a patient with a genome already in place has symptoms consistent with a genetically inherited disorder that you know from direct genome comparison that the patient does not have, the cost of doing testing to rule out that genetically inherited disorder as the source of the symptoms can be eliminated. And, the cost of interpreting the genome in that way would be little more than the cost of a cheap cell phone app for each disease in question – the doctor’s office would buy a complete or nearly complete set for a very reasonable price that could be used for all patients for all potential genetic conditions.

    In a lot of cases, “watchful waiting” is all one can do.

    Second generation, after genomes have been widespread for a generation or so, I suspect you will get to the point where you can compare the genomes of the symptomatic people with the identified risk gene to asymptomatic people with the identified risk gene and determine that Gene X is only a risk factor when also in the presence of Genes Y and Z, and only when protective Genes A and B are absent, or only in the presence of Environmental Triggers gamma and tau, in a large share of cases, further reducing the false positive rate that leads to unnecessary diagnostic testing. This will work better in systems like Iceland and Sweden with comprehensive national health databases than it will in the U.S., however.

    Ideally, you’d want to create a system where, for example, insurance companies that do diagnostic tests based upon genetic information only get a research and development tax credit for that expenditure much as one would in an ordinary clinical test, so long as the data is shared in some sort of anonymized joint databased for all of the insurance companies getting the tax credit.

  2. When my daughter was born, I had the three of us tested with 23andMe. After running the raw data through Promethease, I discovered that my S.O. has two copies of C282Y, which implies haemochromatosis.
    She made an appointment with her doctor and, after a number of appointments, it was confirmed by the French healthcare system(by supplementary genetic testing) and she began treatment for iron overload by phlebotomy (bloodletting).
    What we found incredible was that, at every step, the people involved reacted in the same way: “Personal genetic testing, what possible use could there be for that?!?” Well, let’s see, maybe in order to catch something exactly like this!

    Edit to add: When I got the testing done, 3.5 years ago, nobody I spoke to in France had even heard of personal genetics testing. Now, it’s somewhat better known but there are still no companies offering it here afaik.

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