Saturday Links

Due to a communication breakdown, no-one wrote a Friday Links post yesterday, so today we have a Saturday Links to make up for it.

Steve Hsu has a very appropriately named post, News from the future, about the Beijing Genomics Institute. The BGI is the largest genome sequencing center in China, and one of the largest in the world, and is growing faster than any other, and loading up on a shedload of high-tech HiSeq machines.

Steve reports that the BGI are claiming that their sequencing rate will soon be at 1000 genomes per day, with a cost of about $5k (£3.2k) each. To put a slight downer on these amazing numbers, he clarifies that this might be referring to 10X genomes, which would realistically mean ~300 high quality genomes a day, at $15k (£9.6). Either way, if you want to keep an eye on how fast whole-genome sequencing is progressing, perhaps with an eye to when you’re ready to shell out to get your own done.

A question for the comments: how cheap would a whole-genome sequence have to get before you’d order one?

On the subject of whole-genome sequencing, Dan Kobolt has written about annotating a mutation as functional. This is a pretty common problem with whole-genome sequencing; you identify a variant that is present in a tumour sample, or in a few patients with a Mendelian disease, or perhaps in a personal genome. However, we are packed full of mutations, most of which have no little or effect on our biology. So, how can we find out if this mutation is functional, if it is contributing to the disease, or any other phenotype? Most of the techniques are computational, and thus can be rolled into your variant calling stage, though good experimental validation is also very valuable.

Finally, an interesting little video profile of Jill Steinberg, who had a double mastectomy after discovering that she was carried a BRCA mutation that put her at high risk of developing breast cancer. This is common, and women with a family history of breast cancer will often get BRCA tested, and many have (pretty drastic) preventative surgery. However, the notable thing about Jill’s case was that she had no family history of cancer, and learned of the mutation via a DTC genetic test.

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9 Responses to “Saturday Links”

  • A question for the comments: how cheap would a whole-genome sequence have to get before you’d order one?

    i asked armand leroi this in the fall of 2005:

    10) If in 10 years you could purchase your own full genome sequence for a month of your salary, would you do it? (assume privacy concerns are obviated)

    i don’t know what armand’s salary is, but it looks like was a probably on the conservative since, as it will be cheapish by 2015.

  • I still don’t get it.

    What would having my sequenced genome tell me?

    My grand parents died of heart disease or stroke at an advanced age. All died with their “marbles”, more or less.

    I’m not looking for any lost Vikings in my family. (I’m of Scots-English descent, but no, I don’t care if Hagar is in my blood.)

    There’s little cancer in my family, so I’m probably not at increased risk in that category.

    I fail to see what having my genome sequence would tell me.

    On the other hand, our family has recently had several battles with our health insurance company, the notorious Anthem Blue Cross, which included a letter war to get them to insure an urgent care visit when our daughter put her tooth through her lip.

    So, in an answer to your question, I will get my genome sequenced when our health insurance company pays me to cover the potential inconvenience cost of legally having to defend my genome. Half a million should do it.

  • @Marnie

    Most of the GNZ authors (including me) were in a similar position to you, not expecting to find anything of unusual or notable in their genotype data. Watch this space to see what they we did learn!

    I can see your point about insurance discrimination based on your genome data (its not always something that occurs to me, given that I living in a civilised country country with a national health service). In America, such discrimination seems to be pretty clearly illegal under GINA, and I’d hope that no companies would try it. However, you’re right that a company could (it seems at least possible that this will happen a few times, before companies learn their lesson), and it’d be a pain to defend in court. I’ll ask Dan V to comment on what the likelihood of this would be, and how likely such discrimination would be to go on beyond a simple cease-and-desist.

  • Regarding China:

    Their government and their investors continue to invest directly toward long term fundamental research.

    The US, on the other hand, refuses to do so. Private equity and venture capital in the US in the past ten years continue to seek out the biggest bang for the quickest buck. We continue to try to morph research efforts so that they will attract these impatient investors. Gone is Bell Labs, NASA and stalwarts who looked out a generation ahead, and did not continuously try to invest ill fated, short term business models.

    Genomic research, and many other fields, would do better if they had access to funders that were in it for the long haul.

  • @Luke

    It may be illegal under GINA to discriminate against someone based on their genomic data.

    However, you would have to prove that you are being discriminated against.

    Consider a common situation in the US:

    Person A works for a Small Company, small enough that if they have a major illness, the cost of insuring Small Company increases. So the cost of insurance for Small Company goes up if they have a sick employee with expensive medical costs. Now Small Company starts to look more carefully at their potential employees. Woman likely to have children soon: resume to the bottom of the pile. Scientist at risk for expensive, long term, but treatable illness: resume to the bottom of the pile.

    Just think how gleeful the health insurance companies would be if they could estimate health cost risk for potential employees based on genomic data. The public would never know and hence would not even have the opportunity to defend their genome. So I doubt that GINA can protect the public and their genomic information.

    Don’t fool yourself that it is just Mom and Pop operations that have to worry about this. Many startup companies (California) have difficulty containing their health care costs. In addition to health care costs, companies are extremely fearful of disability and life insurance costs.

    For this reason, I believe that publicly insured countries such as France or Canada are probably far more likely to use genomic data effectively in the public interest. For example, it could be used to examine more closely the risk across the population for various illnesses and set public health policy accordingly.

    But again, in the US, I would be extremely hesitant to believe that genomic data won’t be used by health insurance companies and employers to limit their health risks and costs.

  • The answer to the question above is less than 1.000 USA Dolars for my personal genome. I have set this limit in 1995 and I will not change my mind about it.

    Next question is: is it worth that much? My answer is: Yes. Knowing my own genome sequence will satisfy my long desire to know what I am made of.

    Hope to see that the price of sequencing goes down faster than as it is so that I could get my genes spread out in front of my eyes.
    My thanks go to the people working towards to that end.

  • @Marnie: You make an important point: simply because a behavior is proscribed, does not mean that it will not occur. Detection and enforcement are equally important.

    For just this reason, here is what the Genomes Unzipped participant information document has to say on the matter:

    Although some countries have laws that prohibit certain forms of genetic discrimination, these laws may not apply to you, may not protect against all forms of discrimination or may not stop a third party from discriminating against you even where it is prohibited by law.

    Similarly, here is how the Personal Genome Project’s consent form deals with the issue:

    Although the United States has a law that bars certain forms of genetic discrimination (the Genetic Information Nondiscrimination Act, also known as GINA), this law does not apply to the use of genetic information in all circumstances and, even where it does apply, it does not guarantee that your genetic information will not be used against you in a way that you feel is discriminatory or otherwise harmful to you and/or your family.

    I happen to disagree that GINA’s prohibitions are likely to be widely and successfully ignored, particularly because discriminating based on genetic information seems unlikely to result in significant enough savings to most employers or insurers to justify the consequences of being found in violation. At least for now. Still, the fact remains that (1) due to its ongoing implementation we still know very little about how GINA will operate in practice, (2) because it requires proving a negative it will be difficult to demonstrate that GINA is effective in preventing genetic discrimination and, (3) as you point out, GINA does not prohibit all possibly detrimental uses of genetic information.

    With respect to acquiring (and publishing) my genetic data, I came to a different conclusion than you did. That was based on my own personal, family and employer situation. Obviously others, including you, will have a different set of circumstances, and could reasonably reach the conclusion that genetic data is not a good value at any price, at least at this point in time.

  • Thanks, Dan, for your considered reply. Appreciated.

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