Genetic Future

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Zoe McDougall from Oxford Nanopore points me to a press release from Illumina announcing a new era of celebrity genomics:

Illumina, Inc. (NASDAQ:ILMN) today announced that it has sequenced the DNA of American actress Glenn Close, the first publicly named female to have her DNA sequenced to full coverage. The service was completed in Illumina’s CLIA certified and CAP accredited laboratory utilizing Illumina’s Genome Analyzer technology and following the established process shown at http://www.everygenome.com/. Ms. Close’s DNA was sequenced to an average depth greater than 30 fold, providing information on SNP variation and allowing for the analysis of other structural characteristics of the genome such as insertions, deletions and rearrangements. Specifically, over 95% of the known genome was reported, including over 12 million genotype calls on previously documented SNPs. In addition, 379,000 SNPs previously not reported in any public database were found.

While there’s nothing new about celebrity genomics, previous examples have largely been “scientific celebrities” (such as Jim Watson and Craig Venter) – so Close is the first genome with broader celebrity status, and also the first named individual without a Y chromosome to rack up her 6 billion base pairs. That’s of negligible interest scientifically, but there’s no doubt this will dramatically increase the public profile of whole genome sequencing.
(Added in edit: I’ve just been reminded by Misha Angrist that technically Close isn’t the first named female to be sequenced – a press release back in May 2008 announced the sequencing of Dutch geneticist Marjolein Kriek, although we’re yet to see an actual publication of those data and the quality of the sequence is unclear.)
Illumina launched its retail genome sequencing service (which requires a doctor’s permission) back in June. It’s not cheap – currently a whole genome will set you back a hefty $48,000 – but it’s likely that prices will tumble this year as competition heats up from emerging sequencing provider Complete Genomics
Complete doesn’t offer sequencing direct to customers, but it will partner with personal genomics companies such as Knome to offer its product to high-end consumers. I have a longer article about Complete in the works, but it’s worth noting that based on its recent analysis of four complete genomes it seems to have an error profile comparable with – or even better than – Illumina’s technology.
Meanwhile, it looks like Illumina has bigger plans ahead for its own sequencing service:

Illumina intends to create a social community for the education and exchange of information among those who have had their genomes sequenced. As more information becomes available, participants will be in a position to mine their personal genome sequence data to understand their identity in ways that never have been possible.

In addition to the sequencing service, Illumina is establishing a protocol, infrastructure, and community to enable large-scale adoption of personal genome sequencing. This includes the creation of a network of partners to offer a variety of services. Data analysis partners, physicians and genetic counselors will play an important role in Illumina’s Personal Genome Sequencing Service. A physician’s network is being created since physicians will be critical to the service – to discuss the process with the consumer, order the sequencing service, collect DNA samples and deliver final sequencing data to the consumer.

It sounds as though Illumina is serious about investing in its sequencing service; that’s going to make things tricky for the company, since it will then be in indirect competition with its own technology-selling arm. Exactly how it will resolve that internal conflict remains to be seen.
But either way, this is good news for those of us looking forward to getting our own genomes sequenced: the hotter the competition, the sooner the price drops to the point where even academics like me can afford it.
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Comments

  1. #1 Misha
    March 11, 2010

    “Close is the first named individual without a Y chromosome to rack up her 6 billion base pairs.”

    Not quite:
    http://www.eurekalert.org/pub_releases/2008-05/nofs-lss052708.php

    Admittedly, we’ve not yet seen Dr. Kriek’s genome.

  2. #2 Daniel MacArthur
    March 11, 2010

    Fair point, and corrected above.

    The fact that Kriek’s genome has not yet reached publication almost two years after the press release suggests that the sequence quality was fairly poor – not unexpected for a short-read genome using mid-2008 technology.

  3. #3 Michael T.
    March 11, 2010

    Maybe less blogging and more reading the literature in order?
    Nature. 2008 Nov 6;456(7218):66-72.
    Admittedly, we didn’t consider the sex of the patient to be newsworthy.

  4. #4 Daniel MacArthur
    March 11, 2010

    Hi Michael,

    Note “the first named female”. I don’t think “patient 933124″ qualifies.

    Nice paper, though.

  5. #5 Larry Helseth
    March 11, 2010

    Ms. Close’s father was a physician working in Africa during the first documented Ebola outbreak in 1976. His book (http://www.amazon.com/Ebola-Dr-William-Close/dp/0804114323) provides a chilling account of the spread of that disease. Wikipedia states that blood samples Dr. Close collected in the 1970s were used to study the origins of the AIDS virus. Clearly Ms. Close has a special connection to biomedical research and should be commended for her role in publicizing this emerging approach to medical research.

  6. #6 Nancy
    March 11, 2010

    Only a man could so wrong as to think and to say that a new sequence that represents more than half of the human genomes on earth would be “…of negligible interest scientifically”.

  7. #7 Keith Grimaldi
    March 12, 2010

    When I read this i first thought of the PGP 10 (2 XX genomes http://www.personalgenomes.org/pgp10.html) but going back to check on the project it’s turned out to be exomes only (partial genome project?)

    Illumina has a history of competing with its customers

  8. #8 Daniel MacArthur
    March 12, 2010

    Nancy,

    What exactly is it you think is present in a female’s genome sequence that isn’t present in a male’s?

    A female genome contains less unique DNA than a male one (because it has no Y chromosome). It’s not misogynist to point this out, even on ScienceBlogs.

  9. #9 Michael T.
    March 12, 2010

    Named individual? Really? I see I missed the PR focus of your post. But still…you know that names and medical research are mutually exclusive due to HIPAA, right? If your cause is to have sequencing technology for the masses, then we should focus on biological relevance before the PR. I realize that is a minority view in this field, but it’s my little dream.

    And just to help Nancy out a bit–what is present in the female will be epigenetic differences, right? Yes, yes, you did say genome sequence, but please don’t parse us to death.

  10. #10 Daniel MacArthur
    March 12, 2010

    Hi Michael,

    Your paper was a genuine advance in medical genomics. This press release is not; its value is purely in its effect on the public awareness of genomics, and in what it tells us about the commercial strategy of Illumina. Hence the focus of my post.

    Should we abandon cancer genomics for sequencing Hollywood celebrities? Of course not. I’m right there with you on the need for sequencing phenotyped (and anonymised) individuals to further medical genomics, and I write about those papers. But if Illumina wants to pump out some celebrity genomes and give some PR to whole-genome sequencing I’ll write about that too.

    And seriously, noting that epigenetic differences aren’t revealed by genome sequencing is “parsing to death”? Come on, that’s pretty unfair. You know that Nancy’s criticism is misplaced; just say it.

  11. #11 Dan Vorhaus
    March 13, 2010

    Michael -

    Names and medical research are not mutually exclusive, whether due to HIPAA or otherwise. HIPAA applies to covered entities (i.e., healthcare providers) and their business associates. And, of course, HIPAA is United States (and not global) legislation. There are plenty of circumstances, including within HIPAA provided that appropriate waivers are obtained, where medical research might include names (or other personally identifiable information).

    One example: the Personal Genome Project that Keith refers to (Keith: whole genomes are coming but, for now, yes, only exomes are published for Rosalynn and Esther). Although names are not specifically disclosed, the presence of other identifying information (birth date, medical history data, facial photographs, etc.) has led to the ready identification of the first 10 participants in the PGP.

    I also agree with Daniel that scientific advancement requires not only solid science but also adequate funding. And funding, in turn, requires public awareness. To the extent that sequencing Close’s genome improves the latter, over the long run I suspect it will be quite helpful to the field even if, in isolation, it is just an eye-catching piece of PR.

  12. #12 Keith Grimaldi
    March 14, 2010

    Thanks for the PGP update Dan (V). As you say, the personal info is easy to find e.g. on SNPedia and the GET conference page (for most of them).

  13. #13 Stephen Downes
    March 15, 2010

    Now if only somebody could find her shirt…

  14. #14 Steven Murphy MD
    March 15, 2010

    You want PR? Genomicize Lady Gaga! Please……
    -Steve

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