In the year 2015….

By Razib Khan | October 23, 2011 2:58 pm

Recently I was having a discussion with some friends about getting the full genomes of everyone in my immediate family when the price point comes down to $1,000, just as I have had my immediately family genotyped. You can find some interesting stuff just from the genotype alone, which for current affordable platforms aims for ~1 million variant markers out of ~3 billion base pairs. For example, I inferred that two of my siblings have a coefficient of relatedness of ~0.41, 3 standard deviations below the expectation of 0.50. Another way to put it might be that they’re 1/3rd of the way to being half-siblings! With whole genomes the opportunities are even greater. You could for example ascertain the distribution of novel mutations by comparing parental genomes to offspring. I also began to consider the fact that we might start developing intuitions about the expected number of new mutations a child should have based on how old their parents are.

This led me to reread Armand Leroi’s 2006 piece, The future of neo-eugenics. Now that many people approve the elimination of certain genetically defective fetuses, is society closer to screening all fetuses for all known mutations? One particular section jumped out at me because it is surprisingly dated for a five-year-old essay:

One impediment to a universal, total prenatal screen for all known mutations is the invasive nature of the procedure—it requires amniocentesis…or chorionic sampling to retrieve cells from the amniotic sac—and the traumatic nature of the treatment, which is therapeutic abortion. Perhaps, then, a total mutation screen will not be used in prenatal diagnosis, but rather in preimplantation genetic diagnosis (PGD). This procedure tests embryos produced by in vitro fertilization (IVF) for chromosomal abnormalities and specific mutations before implantation, by removing a single cell from the embryo at the eight-cell stage. Healthy embryos are then implanted; poor embryos—showing one or several abnormalities—are frozen or discarded. As in prenatal diagnosis, PGD is generally carried out only when a family medical history suggests that the embryo is at risk of a specific disease….

Within the next few years we’ll be able to ascertain a fetus’ genotype from a simple blood test. I think this is going to make a huge difference. Amniocentesis and CVS are both stressful for expectant parents, because you’re told repeatedly about the miscarriage risks. With a blood test the barrier to entry is reduced considerably.

Another aspect of the essay is that in 2006 I recall many people feeling that Leroi had not addressed ethical objections to this sort of procedure robustly enough. But at this point it seems as if a lot of the developments which he foresaw are near fruition, and people aren’t making a big fuss about it. Why? Because it’s one of those things that happens gradually, and the potentially ethically dubious becomes normalized.

  • DK

    In the year 2015 we will probably have $1000 exome sequencing but the whole genome? Doubt it very much. In the world where something as trivial as blood lipid profile costs $50, how can a whole genome sequencing cost $1000?

  • Neuro-conservative

    @DK — We already have $1000 exome sequencing at both the research and DTC levels. It is virtually certain that we will have $1000 genomes by the end of 2015, even with currently available technologies.

    @Razib — I think you might be a bit optimistic on the prenatal blood screening. Current technology for sequencing cell-free fetal DNA is only able to detect chromosomal aneuploidy. In particular, maternally transmitted mutations will be difficult to genotype in the fetus for the foreseeable future. Nevertheless, it is probably merely a technical challenge, and not an absolute obstacle to noninvasive prenatal diagnosis.

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    In the world where something as trivial as blood lipid profile costs $50, how can a whole genome sequencing cost $1000?

    my understanding is that a lot of the price points for lab work are due to the structural issues having to do with modern insurance payments. i know that 1,000 SNP tests using amnio/cvs tissue costs $2,000 dollars, when 23andMe charges $200 for 1 million SNPs (i believe they’re losing money on the initial purchase, and hope to make it up on their personal genome service, but i doubt it really is $2,000 for a million markers).

  • DK

    Neuro-conservative: We already have $1000 exome sequencing at both the research and DTC levels.

    Right. My bad. 23andMe and Otogenetics offer it. Now let see if it is commercially viable offering. I suspect that for now it is heavily subsidized.

  • Neuro-conservative

    @DK — It is not heavily subsidized. $1000 is greater than cost for well-equipped sequencing cores.

  • Daniel MacArthur

    As Neuro-conservative says, a $1000 exome is already commercially viable (and with a growing margin, of course).

    I’d expect the first retail $1000 genome some time in late 2012 or early 2013. In this case it will probably be a loss leader, but the PR advantage of being the first to have reached this arbimagical number (NYT headline: “The $1,000 Genome Is Here”) will be substantial and very attractive.

  • http://blog.jim.com James A Donald

    To noninvasively examine embryo genome, need some way of separating millions of maternal cells in the bloodstream from two or three embryo cells. Embryo cells will express paternal antigens. Have chip with hundreds of common antibodies on it, to which cells stick. The parts of the chip that are completely covered in cells are the parts of the chip with maternal antigens. The parts with just a few cells – have embryo cells on them. Genotype those cells.

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Gene Expression

This blog is about evolution, genetics, genomics and their interstices. Please beware that comments are aggressively moderated. Uncivil or churlish comments will likely get you banned immediately, so make any contribution count!

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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