Show me your genome, and I’ll show you mine!

Show me your genome, and I’ll show you mine! Only 10 years ago, the complete sequencing of all 6 billion+base pairs of the human genome was announced. Back then, it would have cost a cool $100 million to have your genome unraveled. Now, the price is expected to crash down to $1,000 per person, hitting that sweet spot to trigger mass sequencing of your genome and mine. About 30,000 people are expected to have their DNA sequenced by this year.

Will this help diagnose and predict disease better than ever? In the case of syndromic diseases, yes! Rare, genetic disorders caused by a single mutation could be detected and treated as in the heartwarming success story of a 6 yr old Wisconsin boy who became a candidate for an umbilical cord blood transplant after whole genome sequencing discovered the genetic cause of his mysterious and life threatening intestinal disorder. More common, complex illnesses (hypertension, autism) have susceptibility variations all over the genome. We will need an army of biostatisticians and geneticists to make sense of these.

Genetic exceptionalism? Companies that offer direct-to-consumer genetic tests, like 23andMe , have received warning letters that “the analytical or clinical validity of their tests have not been submitted to FDA for clearance or approval.. Consumers may make medical decisions in reliance on this [genetic] information”. But in the absence of other guidance from the FDA, these companies have been left in limbo, leaving open the possibility that the industry may simply move overseas. Alan Dow, vice president and legal counsel at Complete Genomics, suggests that the foot dragging may be due to old ideas of genetic exceptionalism, that is “genetic information is inherently unique and should be treated differently in law than other forms of personal or medical information”. Yet, legal and medical scholars do not seem to have a problem with this.

What will you or your doctor or your insurer do with this information? Two thoughtful articles in Slate’s Future Tense section:

Edit: Recommend this informative and entertaining 10 min TED talk :

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31 Responses to Show me your genome, and I’ll show you mine!

  1. Ahem. This is all good news. But I do take some offense, on behalf of my autistic wife, at having autism labeled an ‘illness’. It is nothing of the sort. Many people live perfectly good lives with autism, and indeed many of the greatest advances in science and art have come from the hands of people thought or known to be autistic. Simply labeling it an illness is disingenuous as well as discriminatory.

  2. I worry that as the price drops then the cost/benefit balance would benefit insurance companies a little too much.

    Lets say I apply for a mortgage and I have to provide such a test beforehand. And the cost of the test is added to the mortgage so I have to pay it. And it shows my cancer risk as a false positive…

  3. DaFreak says:

    As a transhumanist I agree 100% with Gert Sønderby.

    As long as people are happy being who they are, there can’t be any talk of illness. It is even suggested that many of our smartest minds had some form of autism. We should encourage people to be different and not try to make everyone the same or view our current state of mind and being as a model for all of mankind.

    PS: I totally get, that you didn’t mean it this way.

    On topic; I love the kind of progress that we are making but at the same time, as Mike McLoughlin has already indicated, I worry about our genomic information being freely available. Just recently I read a story on VISA submitting a patent application mentioning gathering of DNA data for marketing purposes;

    We have to be on the lookout for the drastic changes that this technology will bring and be mindful of its possibilities for abuse.

  4. Rajini Rao says:

    No offence meant Gert Sønderby . As you know, the autism spectrum ranges from high functioning intellects with Aspergers to severely impaired people with Retts/Timothy/Williams syndromes. Where our loved one falls on the scale may well influence our perspective on ASD. I was at an autism conference recently, listening to a number of clinicians and neuroscientists. It was clear that synapse function was compromised in ASD, together with a range of issues including epilepsy, immune, digestive and sleep disorders. This is the so-called co-morbidity for ASD…for example, 1/3 of autistic children have epilepsy. Two of the genes I study have mutations associated with ASD and at a cellular and molecular level, they are associated with loss of function..specifically, they interfere with release and reuptake of neurotransmitter at the synapse. So from my molecular and cellular perspective, it is as disorder. Overall, I didn’t get the sense from the autism conference that most cases were at the high functioning range but just “different”…which is sort of a benign view.

    On the more positive side, what I did take away was that understanding the basis for behavioral differences (autistic children develop expertise with the physical world as opposed to the social world) can inform us on different teaching/training so that language development is not impaired. I hope this makes sense.

  5. Rajini Rao says:

    Mike McLoughlin , there will have to be guidelines in place for ethical and legal uses of genomic information..perhaps an extension of current HIPAA rules (Health Insurance Portability and Accountability Act of 1996) to cover genomic information. Predisposition to cancer based on genetic information is in some ways not much different from predisposition to cardiac failure from family or personal history (information already in your doctor’s records).

  6. Rajini Rao says:

    All, a great ~10 min TED talk on the future of genome sequencing, dramatic falling costs and its implications:

  7. DaFreak says:

    This might sound strange but I would also recommend everyone to have a look at the film; Gattaca. >

    Besides being a genuine work of art, it is becoming ever more relevant. It deals with a society where everybody’s genetic code is freely available for everyone to scrutinize. At its core it has the issue of genetic based discrimination in both a social and work environment. Trust me, this is not Michael Bay BS, it’s art :p

  8. Rajini Rao says:

    Koen De Paus , very cool movie, agree! Starring the divine Uma Thurman and Nathan Hawke. Dystopian stories are awesome.

  9. I signed up to National Geographic’s Genographic project. I am not entirely sure what this involves in terms of the data generated but it does mean that “my”ness is going to be even more enmeshed in the “system” than I already am.

  10. Rajini Rao says:

    Suhail Manzoor , curious to know what you find out..a cousin had this done and sent me the results..I was amazed. Apparently, our ancestors trekked over to Siberia and one group turned back while the other went on to cross the Bering Sea into North America. Honestly, I just couldn’t believe it! 🙂

  11. DaFreak says:

    Suhail Manzoor I wouldn’t worry too much about it. NGEO gathers data from all over the world and normally they anonymize everything. You supported some serious scientific work that provides us with a much better understanding of mankind’s history!

    I only found heard about this quite recently and was totally blown away at the insane amount of information that genetics manages to preserve. I knew comparative genomics was crazy cool but this is just too much! :p

    *mind = blown

  12. Rajini Rao says:

    Journey of Mankind map (link above) is really very well done, Koen De Paus , and deserving of its own post!

  13. I will be sure to share whatever I find with you Rajini Rao . I expect some really weird stuff. For starters, my paternal grandmother had blue eyes (?) and men of that side have these deep set eyes and thick, squarish foreheads. I can speculate on what they mean. On my mother’s side, we have women who have African hair, light brown eyes and their ancestral home on Jew Street in Kochi. I do not know what it all means but I am fully expecting to be blown away by what ever NatGeo finds.

  14. Thanks for the link Koen De Paus and I think Rajini said it best. I am not really worried about this data being made public. It is what it is I am afraid. And if society or parts of our societies end up discriminating me on the basis of my genomic materials, I think it tells you more about our society than me 🙂

  15. DaFreak says:

    Thx for the final push! I had thought about it before but I wasn’t sure whether a simple link would garner enough attention in this day and age of hyperactive internet browsing. Totally nailed it though! I added a trailer as bait which should get them on the hook. 😉

  16. Tom Lee says:

    Great post and information, as usual… Rajini Rao

  17. Let’s hack god’s genome!

  18. Kapil Ranade says:

    I’ve always wondered, if the shroud of Turin is TRUE, do we have access to God’s Y chromosome?

  19. Rajini Rao says:

    Kapil Ranade , excellent idea. Why not extract the nucleic acids, perform a polymerase chain reaction and sequence it? You are very clever to refer to the Y chromosome, my friend, I caught that! Although, paternal genes should make up half the genome, so simply digging into the prevailing genotypes of the middle east should reveal the difference. 🙂

  20. Kapil Ranade says:

    Dr Rajini Rao, my highschool level biology, definitely rusty, would make me think that the Y chromosome in the veins of Jesus of Nazareth would need to derive from God the father; I’d presume the blessed Mary may have been unable to provide a suitable Y chromosome. That is all – no gender bias intended.

  21. Norman M. says:

    How can the sequence be validated? Can it be anonymous? Who is the owner of the sequence?

  22. Rajini Rao says:

    Kapil Ranade , I was referring to the Y chromosome being paternally inherited of course (nothing about gender bias at all)..not a whole lot of info residing on Y, unfortunately, but 50% of the rest should be paternal. Norman Ma , which sequence? If you mean Shroud of Turin, we were just kidding around (not serious at all!) 🙂

  23. Norman M. says:

    Where is this decoding taking place?

  24. DaFreak says:

    What do you mean? DNA is being sequenced in labs all over the world. They do this by running strands of DNA through a sequencer, a machine that reads out the letters in the genome. Understanding what these letters really mean or in other words what they do, is called decoding the genome and everyone from independent research scientists to biohackers and major companies are working on this.

  25. Norman M. says:

    Koen De Paus I meant the time-labor intensive steps of sequencing personal DNA… Is there some place in the world that specializes in sequence personal DNA for a fee?

  26. DaFreak says: does this but they have been criticized for not doing a proper job. I would sit it out for the time being. It’s still pretty expensive and although it can tell us quite a bit, it will not compare to what they will be able to tell you 5 years from now for a fraction of the cost.

  27. Rajini Rao says:

    Norman Ma , whole genome sequencing (WGS) is almost ready for prime time..but not quite, as Koen says, sit it out for now. I heard that Steve Jobs had it done, presumably to get some molecular insight into his particular form of cancer. It is pretty much automated, so not a technical challenge. The genomic (data) analysis is still at early stages. Koen De Paus , 23andMe does genotyping, which is almost as good as whole genome sequencing. I took the lazy way out and pulled out the description from their web site..for anyone who is interested:

    “Though you may hear both terms in reference to obtaining information about DNA, genotyping and sequencing refer to slightly different things. Genotyping is the process of determining which genetic variants an individual possesses. Genotyping can be performed through a variety of different methods, depending on the variants of interest and resources available. At 23andMe, we look at SNPs, and a good way of looking at many SNPs in a single individual is a recently developed technology called a “DNA chip.”

    Sequencing is a method used to determine the exact sequence of a certain length of DNA. Depending on the location, a given stretch may include some DNA that varies between individuals, like SNPs, in addition to regions that are constant. So sequencing is one way to genotype someone, but not the only way. You might wonder, then, why we don’t just sequence everyone’s entire genome, and find every single genetic variant they possess. Unfortunately, sequencing technology has not yet progressed to the point where it is feasible to sequence an entire genome quickly and cheaply. It took the Human Genome Project over 10 years’ work by multiple labs to sequence the three billion base pair genomes of just a few individuals. For now, genotyping technologies such as those used by 23andMe provide an efficient and cost-effective way of obtaining more than enough genetic information for scientists—and you—to study.”

  28. Matt Kuenzel says:

    The talk by Richard Resnick is awesome … it made me start wondering about the “cheating gene” that he mentioned, the Arginine vasopressin receptor 1A (officially called AVPR1A). From Wikipedia: “Homozygosity in allele 334 of AVPR1A repeat polymorphism RS3 is associated in men (but not women) with problems with pair-bonding behavior, measured by traits such as partner bonding, perceived marital problems, marital status, as well as spousal perception of marital quality.” Hmmm … (I’ve been married for 27 years but it would still be interesting to find out which alleles I carry.)

    I’m very upset that the FDA has taken such a paternalistic attitude towards 23andMe and the other genome scan companies and the full-genome labs. The idea that people benefit when they are kept ignorant of their genetic risks seems absurd.

    I can understand the problems facing doctors who may be asked by patients to assess their genetic health based on the patient’s genome or are expected to diagnose and treat using the latest genetic data. But it seems to me that this would generate demand for a new type of specialist to fill the need. I can’t imagine that currently doctors are expected to be aware of all the latest results across the whole field of medicine. It seems that this would be like any other lab test that returns a list of unusual findings along with some explanatory information.

    As to the data deluge, this will be another business opportunity for Google: a massive data warehouse for everyone’s genomes. My gmail account has about 5 GB available so I could store my genome there.

    Finally, thanks to the commenter who posted the Journey of Man link. That is very cool – I had no idea that there had been so many crossings from Asia into North America.

    Edit: The AMA recommends the prohibition of direct-to-consumer genetic testing. Very dispappointing.

  29. Rajini Rao says:

    Matt Kuenzel , Re. your allele 334 status of AVPR1, I would leave well alone!!! That must have been one remarkable, controversial study..we should hunt it down and take another look. Bizarre correlations for a receptor of the antidiuretic hormone (which regulates urine concentration!).That’s not all. On Wiki it says, “The activity / genetic variants of the AVPR1A gene might be related to generosity and altruistic behavior. NatureNews has referred to AVPR1A as the “ruthlessness gene”. ” Since it is also expressed in brain and amygdala, perhaps the key to this strange link lies there (amygdala holds the fear perhaps people carrying these variants unlink fear of being caught with cheating??

    I’m in agreement with you regarding the efforts to stall WGS efforts…it’s going to happen eventually, and information is never we use it is the issue. Thanks for the update on the AMA’s stance, had not known that. Thanks for your thoughtful comments, as always.

  30. DaFreak says:

    That pretty much hits the nail on the head. It would be convenient to have your genetic data in the cloud so that you can grant specific people, like your doctor, access to it when necessary. Afterwards you simply revoke their access and wipe device memory so that the data won’t linger on the device they used. What’s holding us back is a decent eSystem for hospitals and decent security. If we backup our data in the cloud, we are trusting that provider to have secure systems but there is never a 100% guarantee.

    Perhaps a better system would be to have this data coded into a piece of jewelry or a smartcard. You are at risk of not having it on you when you get in an accident but at least the data would be relatively safe.

    Then again, perhaps gene sequencers will one day literally sequence the entire genome in a second which makes all this irrelevant because then doctors could just get your code on the spot in realtime.

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