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Biotech Science

Sequencing the Unborn 146

Posted by Soulskill
from the time-to-reboot-gattaca dept.
sciencehabit writes "What if you could read much of your child's medical future while it was still in the womb? Taking a major step toward that goal, one fraught with therapeutic potential and ethical questions, scientists have now accurately predicted almost the whole genome of an unborn child by sequencing DNA from the mother's blood and DNA from the father's saliva (abstract)."
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Sequencing the Unborn

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  • by taktoa (1995544)

    I don't see how this is possible, given that genetic recombination happens. Unless the parents are very genetically similar (ick), there should be billions of possibilities.

    • Re: (Score:2, Informative)

      by Anonymous Coward

      I think this is the relevant part of the article: "In most cases, for a particular genetic sequence on a specific chromosome, the variants from each pair should be represented equally in the woman's blood. But in an expectant woman, whose child has received only one variant as part of its genetic inheritance, her blood will contain a little more of that variant because of the free-floating fetal DNA. If the mother's patterns of genetic variants, or haplotypes, are known, statistics allow researchers to conc

      • Re:Odd (Score:5, Informative)

        by interkin3tic (1469267) on Wednesday June 06, 2012 @05:59PM (#40237777)
        To summarize: it's not yet possible to isolate only embryonic DNA from the mothers' blood, so using the father and mother's DNA sequences, they can tell which sequences are from the mother and which one are from the embryo.

        Without the father's sequence, the confidence in the sequencing probably goes down, but is still possible.
        • I'm thinking that it would be kind of nice if genetic therapies could be initiated for those of us that are "out" of the womb.
        • by Vornzog (409419)

          It is possible to get embryonic cells and DNA from the mother's blood, but isolating it so it is free from contamination for a clean sequence is difficult. The technology is already being used in an array-based assay to detect Down Syndrome and a few others. See here [sequenom.com].

          That page doesn't say much, but the confidence intervals are already on par with the risk factors for an amino, which means the amino is on the way out. Sequence data would be better, having the father's genome might help, but regardless of

    • Re: (Score:3, Informative)

      by Anonymous Coward

      I don't see how this is possible, given that genetic recombination happens. Unless the parents are very genetically similar (ick), there should be billions of possibilities.

      This problem is my area of research (didn't RTFA, just assuming this is how they did it). There is cell free fetal DNA circulating in mothers and the challenge is isolating enough of it for deep sequencing without contamination from mom. I'm assuming they are using dad's DNA to help 'choose' between competing reads to figure out which ones are mom and which ones are fetal in origin. A less sophisticated version of this approach has been used to test for TS21 (Down's syndrome).

      • by Anonymous Coward

        This problem is my area of research (didn't RTFA, just assuming this is how they did it).

        Am I the only one who thinks this is kind of amusing?

        • It could bring a whole new meaning to "Soccer Mom."
        • This problem is my area of research (didn't RTFA, just assuming this is how they did it).

          Am I the only one who thinks this is kind of amusing?

          Amusing and also kinda sad. At the least the poster deduced things correctly, I guess ...

          Wonder if this is the first time someone's discovered they've been scooped by reading /.??

    • I think, and it really is this sad, that they're referring to the "they're human, they have ears, they have arms" genes. Oh and the like 99% of useless, do-nothing genes or whatever. how pointless is that? "Well, it looks like you're going to have a.....human baby" lol.
  • "I don't think it would be ethical to use this to screen for late-onset diseases like Alzheimer's or cardiovascular diseases, for example."

    To which I have to say, "No shit, Sherlock".

    Let's hope those ethical concerns have some weight when this process rolls out as a voluntary, or perhaps even mandatory, screening process.

    • by CodeHxr (2471822) on Wednesday June 06, 2012 @05:35PM (#40237543)
      The caveat to this is that "ethical" is opinionated and everyone's is different. Even if the laws of your area are completely aligned with exactly how you feel about the ethical implications, there will be other areas that have vastly different laws. Even within any given area, there will be people who think the law doesn't apply to them and take things into their own hands.
      • by cayenne8 (626475)

        The caveat to this is that "ethical" is opinionated and everyone's is different.

        For sure.

        I mean, I would nave absolutely NO problem with wanting to terminate the pregnancy if I found out the kid was going to be retarded, or crippled....anything that would keep it from starting out with a 'normal' childhood. In fact, I'd welcome it...I think many people might like this option, especially if you're a bit older having kids....which is happening more and more these days.

        Different strokes for different folks

        • What about the people that terminate because it's a girl?

          • by Azghoul (25786)

            Not you.
            Not me.
            Not government, ffs.
            Social pressure. If theirs is a culture that is completely retarded in that way, let them fall on their own.

    • by Anonymous Coward

      In my experience, any ethical concerns with regards to science will be met with "How dare you try to force your morals on me? This is {for the good of the species, in the name of science, perfectly reasonable and you're a moron for questioning it}". Then there will probably be something about the mother's right to choose whether she wants to raise an "imperfect" child and it will become a big social battle.

    • Re: (Score:3, Insightful)

      by Anonymous Coward

      Forget about traditional ethical concerns, the later in onset and more multi-factorial the disease, the less informative genetics and genomics is. Even if genetic loci can explain 10% of phenotypic variation in a given cardiovascular phenotype, who cares (aside from, perhaps, a poorly run insurance company)? Any number of biochemical markers of disease are MUCH more predictive than genotype for a host of such diseases. Your BMI, your random and fasting blood glucoses all predict your risk of T2DM MUCH mo

      • The informative-ness of genetics doesn't change as we age.

        Source code is source code, regardless of how long the app has been running or what crappy inputs it's been fed.

        • by spazdor (902907)

          no, but the informative-ness of your medical history grows monotonically as you age.

    • by interkin3tic (1469267) on Wednesday June 06, 2012 @05:50PM (#40237697)
      I disagree with you both. I find nothing ethically wrong with abortion or screening for diseases. How about we let parents decide whether it's ethical for them?
      • by readin (838620)

        I disagree with you both. I find nothing ethically wrong with abortion or screening for diseases. How about we let parents decide whether it's ethical for them?

        For how long?

      • by Anonymous Coward

        I'm sorry, but I'm afraid our screening process has determined your son is going to be a huge fag.

      • by LordLimecat (1103839) on Wednesday June 06, 2012 @06:31PM (#40238173)

        How about we let parents decide whether it's ethical for them?

        Thats begging the question: Its only OK to let the parents decide whats ethical, if your stance on abortion is correct. If it isnt, your argument would be akin to "why not let the parents decide if they want to abandon their newborn".

        Not trying to be flame/troll bait here (even tho I likely will be modded as such), but the entire argument from most prolifers is that the fetus is every bit as human as a newborn is. Unless you start off by assuming theyre wrong (again, begging the question), you cant just say "well, lets let the parents decide whether thats true"-- because we DONT take that stance with a baby post-birth.

        • Re: (Score:3, Insightful)

          by Anonymous Coward

          Well, I just don't care for turning women into baby-making machines and telling them they don't control their own bodies. Freedom of an already born, thinking individual > life of an unborn human leeching off of a women. For me, anyway.

          • Well, I just don't care for turning women into baby-making machines and telling them they don't control their own bodies.

            And that, friends, is what we call a false dichotomy.

            Im fairly certain that there are a plethora of choices that dont involve an abortion-- even if you dont count the "day-after" pill.

            • by jrroche (1937546)

              Im fairly certain that there are a plethora of choices that dont involve an abortion-- even if you dont count the "day-after" pill.

              What? There are two choices. The woman carries the child to term or she doesn't. If a woman is pregnant, the only choice other than abortion is to carry the child to term, unless you count an unintended miscarriage as a choice, which, if unintended, it could not be. ...wait, are you thinking of that DS9 episode where Bashir transplants Keiko's baby into Kira? You know that's not real, right?

              • Once she is pregnant, yes. I was talking about avoiding the pregnancy.

                "There are only two options once pregnant" is no more a valid defense of abortion than "once the baby is born you either kill it or you dont" is a defense of infanticide. The fact that that infant is with you for the long haul is kind of a consequence of events set in motion long ago @ conception-- just like the pregnancy itself.

                In case you want to continue to be super dense about this, I was talking about condoms, IUDs, hormone therapy

              • by mug funky (910186)

                never heard of adoption?

                you'd better have a long and serious talk with your parents. you may want to be sitting down.

                really, adoption is always left out of these arguments. back in the day it was the only option - the girl "goes on holiday", or "goes to boarding school" and returns a few months later.

        • by mcl630 (1839996)

          How about we let parents decide whether it's ethical for them?

          Thats begging the question: Its only OK to let the parents decide whats ethical, if your stance on abortion is correct. If it isnt, your argument would be akin to "why not let the parents decide if they want to abandon their newborn".

          Not trying to be flame/troll bait here (even tho I likely will be modded as such), but the entire argument from most prolifers is that the fetus is every bit as human as a newborn is. Unless you start off by assuming theyre wrong (again, begging the question), you cant just say "well, lets let the parents decide whether thats true"-- because we DONT take that stance with a baby post-birth.

          Actually we do let parents give up the baby post-birth... it's called adoption. Granted, that's not "abandoning their newborn" in the leave it on a doorstep or in a dumpster sense, but they do have a legal option to get rid of the kid post-birth.

          • Actually we do let parents give up the baby post-birth... it's called adoption.

            Which has nothing to do with my post, the discussion, or anything else. The point isnt whether adoption is viable, but whether "let people decide for themselves morality regarding killing an infant" is a viable argument.

            • by mcl630 (1839996)

              You didn't say kill, you said abandon.

              • by d3ac0n (715594)

                In the sense he meant it, "Abandon" means; To leave exposed and uncared for alone. In such a situation, a newborn would almost certainly die, given enough time without being discovered by someone willing to care for the child. There is a reason child abandonment laws exist, and why they are held to the same punishment level (in some cases) as manslaughter or murder. [uslegal.com]

                Personally, I find it abhorrent that we will blithely slaughter a human just because they haven't yet fully exited the birth canal.

                That said,

                • If you want to find something fascinating, find it fascinating the way the community responds to these discussions. The very fallacies I pointed out continue to be trotted out in this very discussion, and thats not uncommon. People will continue to focus on "woman's rights" in a discussion primarily about whether or not the thing being killed has a right to live-- as if we would EVER talk about Jack the Ripper's right to choose to kill, but somehow its DIFFERENT when the human in question is inside anothe

                  • People will continue to focus on "woman's rights" in a discussion primarily about whether or not the thing being killed has a right to live

                    Some people feel a women should have a right to control her own body more than the infant should have a right to stick around in her womb. It's mere preference.

                    If you could somehow remove the baby and keep it alive, I wouldn't have a problem with that. Just as long as the mother can remove it.

                    as if we would EVER talk about Jack the Ripper's right to choose to kill, but somehow its DIFFERENT when the human in question is inside another's womb.

                    And to them, it may very well be different. In fact, it is different, because it is a different situation. It's just your own opinion that the differences are irrelevant (assuming that's your opinion). If you're lookin

                    • I mean that if you look at the posts in the thread, I bemoaned begging the question; one of my respondants promptly begged the question, and was modded +5 insightful. I then pointed out how he utterly missed my point and was modded, of all things, Offtopic (certainly if I was off topic, then so was he?)

                      You will see similar things with DRM discussions, or anything else that slashdot has an allergy to. Get too pointed in your criticisms, and all the wierdest moderation begins to happen-- only so long as the

        • by interkin3tic (1469267) on Wednesday June 06, 2012 @07:31PM (#40238711)

          Thats begging the question

          Stop right there. No it's not. I'll let you ask your question anyway, but it's going to be a strawman argument.

          your argument would be akin to "why not let the parents decide if they want to abandon their newborn".

          Called it! That's a strawman. We're not talking about a newborn, we're talking about an embryo. Everyone agrees that a newborn has rights, there is no consensus as to whether an embryo does. Furthermore, a newborn is not an obligate dependent on one specific person, newborns can be dropped off at any safe baby haven or given up for adoption. There's no similar alternative for pregnant women.

          My point here is that this is a totally separate issue from abandoning a newborn.

          Answering your point, no, I don't think letting the parents decide whether abortion is right or not for them is only ethical if we assume life does not begin at conception. In most countries, most ethical decisions are left up to the individual. There's no law that says I can't cheat on my wife, it's up to me to decide if I think that's ethical or want to do that. Lacking a law against adultery is not an unethical situation, it simply leaves the responsibility up to the individual.

          Legalizing abortion doesn't endorse abortion, it only leaves the ethical question up to the people who deserve to make the choice: the parents.

          • Re: (Score:1, Offtopic)

            by LordLimecat (1103839)

            Called it! That's a strawman. We're not talking about a newborn, we're talking about an embryo.

            And you just demonstrated, again, begging the question.

            What is begging the question? Why, its the fallacy of beginning your argument by assuming the thing to be argued. And what did you just do, in an argument that is basically about whether or not an embryo is a human? Why, you started with the assumption that it isnt.

            If you were to take anything from this, its that in future discussions you should to argue your point, not assume it.

          • by Anonymous Coward

            Legalizing abortion doesn't endorse abortion, it only leaves the ethical question up to the people who deserve to make the choice: the parents.

            Exactly. I'm not so sure why an eager parent, on finding out their "unborn child" has no chance of any cognition but 100% chance of multiple gruesome surgeries, can't decide to abort as a parenting decision. Christ, we let parents opt out from leukemia treatment for their walking, talking kids. Anybody that's willing to say a prospective parent can't be trus

          • Glad you've got the final say on what is and isn't human enough to kill and not some misogynist Bedouin or sheet wearing redneck. That could get morally messy, since every other time in history someone decided to use any sort of qualitative factor to determine humanity has worked out so well..

            • by Anonymous Coward

              Glad you've got the final say on what is and isn't human enough to kill and not some misogynist Bedouin or sheet wearing redneck.

              I'd say it's better than someone declaring that women don't control their own bodies, quite possibly forcing them to risk getting abortions from shady characters utilizing coat hangers. Like it or not, that's what happened often in the past. Then you lose both the woman and the baby all because someone decided that free-thinking, independent human beings don't actually own their own bodies.

              since every other time in history someone decided to use any sort of qualitative factor to determine humanity has worked out so well..

              Society certainly doesn't seem to be breaking down because of abortions. I really don't see how that'd happen.

      • People are flawed. Left to their own passions, they will murder, rape, kidnap and steal.

        People need laws to stop them from descending into savagery.

        • You think the government is ever less savage or flawed than its citizens? That's... interesting... Don't hear too many people around here espousing authoritarian views...
      • by chispito (1870390)

        I disagree with you both. I find nothing ethically wrong with abortion or screening for diseases. How about we let parents decide whether it's ethical for them?

        Then how about your insurance company gives you breaks on your premiums if you ONLY bring the most genetically suitable offspring to full term (or your government gives you tax breaks if the government is the insurer)?

    • by Loughla (2531696)

      With as many folks as we have in the US that are very, very, very against abortion, I am interested as to what you believe a screening process would accomplish. The only things that I can see are (a) higher insurance premiums - in which case, this is going to be a hard sell to even the lowest common denominator, (b) to abort the fetus before the issues arise - but GOD made my child be born without arms, so let it be born, or (c) for shits and giggles - and that's just confusing.

      So, what would the uses of a

    • Wouldn't using Genetic Therapies bypass the Gattaca issue? Like getting a phyisical agmentation.
    • by mug funky (910186)

      when this sort of thing comes up, it's good to remember that practically every kind of screening is voluntary.

      hell, people still opt out of finding out the sex of the baby (though in my case it was a surprise anyway - expected a daughter, got a son).

      when things like this start becoming mandatory, we'll have already been too far gone as a society for a long time.

  • And it was called Gattaca.
    • by Jeng (926980)

      Yes in Gattaca you could tell the genetics of your unborn child, but you could also do genetic engineering on the unborn child in Gattaca and it was that portion that had more to do with the plot.

      • Re: (Score:2, Informative)

        by blind biker (1066130)

        Yes in Gattaca you could tell the genetics of your unborn child, but you could also do genetic engineering on the unborn child in Gattaca and it was that portion that had more to do with the plot.

        What fucking genetic engineering on the unborn child did you see? They clearly showed that children were selected from a number of fertlized eggs while the rest of the embryos were discarded.

        I'm assuming you didn't actually see Gattaca but another movie, and are confusing the two.

        • I guess that depends on how you view the 'engineering'.

          No modifications were made to fertilized eggs, iirc.

          But let's say you have 8 fertilized eggs, but only the desire for 1 child - then isn't picking one of those 8 that meets your 'demands' tantamount to engineering?
          What if you don't pick any of the 8, and instead fertilize 8 more, and again, and again, until you hit the result you were hoping for?

          This is at the core of much of the debate on genetic engineering, in that some genetic modifications are simp

        • by zill (1690130) on Wednesday June 06, 2012 @06:19PM (#40238025)
          Straight from the script: [imsdb.com]

          Now you appreciate I can only work with the raw material I have at my disposal but for a little extra...I could also attempt to insert sequences associated with enhanced mathematical or musical ability.

          Emphasis mine.

        • I believe the phyisican's son was a great fan of what the character Vincent Freeman was doing. The phyisican paid for a smarter child, and was short changed. That scene is toward the end of the movie.
    • Actually no, in the movie, they were only able to sequence your genome after you were born.

      Also, call me a technophile, but I don't think the problem with Gattaca's dystopia was that sequencing was possible. I think the problem was how people used the technology. Much like, oh, every technology ever invented.
      • The problem with Gattaca's dystopia was that it applied statistical probabilities to individuals. Someone is more likely to have heart problems? Employers know, and will reject that applicant from phsically stressful jobs. Even though it's just a probability. In the real world, this would be like companies observing the statistical truth (politically incorrect as it is) that black Americans are significently more likely to commit a crime than white Americans, and thus refusing to hire any blacks on the grou
    • by Loughla (2531696)
      And a book, it was called A Brave New World.
    • 'KHAAAAAAAAAAAAAAAAAAN!'

      They're also a few steps away from this.

  • Of course genetics are not everything. The environment, even within the womb, affects development. But, after enough genome wide association studies are performed, gattaca does not seem too far away.
    • James Watson was the 3rd human fully sequenced about 8 years ago. The Nature article tsaid hat he had 20 defects matching the then defect database (about 5000 entries), none which were expressed. It said he should have had retinitis pigmentosa, which he did have. Our knowledge of genetic density is still primitive. Definitely too shaky for insurance filtring.
      • by TWX (665546)

        Our knowledge of genetic density is still primitive. Definitely too shaky for insurance filtring[sic].

        Don't be too sure about that latter part. Once insurance companies feel that they have a method to screen for a demographic subgroup that doesn't violate civil rights they'll be happy to define it and use it, especially if investigation of that group yields viable statistics. That doesn't mean that every member of that group, especially a genetically-defined group, will manifest the traits associated wit

        • With the standardization of Medical Research, and organizing of medical data procedures, and records. I'm thinking a team of Network Admin's could maintain the information on a cloud based system. I'm not seeing a future need for something as procedural as medical therapies and record keeping being maintained by large businesses. As for research, Educators and Students can easily search the Internet for any topic for things like Cures, Diseases, Therapies, and previous work compiled on the subject in questi
  • Reading this, since they took the dna from blood and saliva, not from the fetus, it raised the question for me, why wait until conception?

    In the future, will couples get genetically screened during pre-marital counseling, to see if they have good compatibility (in terms of not having high risk of genetic problems in offspring)? Sounds terribly un-romantic, doesn't it?

    • by zlives (2009072)

      the future is now? if you have the money to get tested.

    • The ultimate in totalitarianism. State sponsored fertility engineering where a sperm is pre-selected from a bank and matched with the right women to become impregnated -by law- when she turns 18. There is no choice about it. The government decides who your offspring will be. Both the mother and father have no say so. Marriage is just a social aspect to raise government engineered children. The ultimate form of God. How could they not resist such power and control?

      • by Jeng (926980)

        I imagine that artificial wombs will be invented long before the government gets into the child making business.

      • by eugene6 (2627513)

        How could they not resist such power and control?

        What you wrote here does not make sense.

    • by ae1294 (1547521)

      yes.... There is a 100% chance that it will be law in the US in the next 30 years. Go ahead and add in the predictors for aggression and aversion to authority and you have the perfect country of slaves for our 400 masters. It will look something like this only slightly updated... http://www.youtube.com/watch?v=1i6ozLpNr3Q [youtube.com]

    • by OSU ChemE (974181)
      They took the blood from the mother after she was pregnant, when there was fetal DNA in her bloodstream and are essentially doing a 'process of elimination' among the fetus, mother, and father. So while you could do a pre-conception screen, and it may indicate probabilities for genetic disorders or diseases with a genetic component, it wouldn't be the same thing as in TFA.
    • by Kergan (780543)

      Per TFA, the fetus' DNA is in its mom's blood. So you cannot get any (non-random) information prior to conception.

    • by dwye (1127395)

      In the future, will couples get genetically screened during pre-marital counseling, to see if they have good compatibility (in terms of not having high risk of genetic problems in offspring)?

      Commonly done now, for Ashkenazi Jews to check for certain endemic problems (Cystic Fibrosa, I think), and it was certainly discussed for Sickle Cell Anemia.

      Sounds terribly un-romantic, doesn't it?

      No more unromantic than making up a pre-nup. Marriage contracts used to be common for guildsmen, let alone nobility. And, at 40+% divorce rate, maybe "romantic" is a tad over-rated.

  • by blind biker (1066130) on Wednesday June 06, 2012 @05:37PM (#40237563) Journal

    "Gattaca" wasn't fiction - it was an accurate prediction of a dystopian, fast-approaching and very real future.

    • by Hentes (2461350)

      The only thing from Gattaca that seems close is the technology, society is still very far from that.

    • by mcmonkey (96054)

      "Gattaca" wasn't fiction - it was an accurate prediction of a dystopian, fast-approaching and very real future.

      You misspelled "Idiocracy"

    • by PPH (736903)
      A world in which a genetic misfit like me has a chance at nailing Uma Thurman? I'm fine with it!
    • by couchslug (175151)

      Fapping to visions of dystopia is delectable, but humans have been breeding selectively by preference as long as we've existed.

      BTW if undesirables never make it to term by parental choice than no ones rights are violated or infringed. If you are choosing to produce offspring, why not have more granular control of outcomes?

      The world has enough window-lickers as it is.

      • by d3ac0n (715594)

        BTW if undesirables never make it to term by parental choice than no ones rights are violated or infringed. If you are choosing to produce offspring, why not have more granular control of outcomes?

        Emphasis mine.

        And just who determines who is undesirable? The parents? Why? Why do they get to determine the relative worth of a human being they haven't even met yet? And what traits make someone undesirable? Physical disability? Does having a less than perfect body make you worth less? Hellen Keller would

  • Eugenics (Score:5, Interesting)

    by Ironchew (1069966) on Wednesday June 06, 2012 @05:46PM (#40237651)

    What if you could read much of your child's medical future while it was still in the womb?

    The more worrying question here in the U.S. is, "What if your insurance company could decide your child's medical access while it was still in the womb, based on poorly-understood genetic risk factors and eugenics pseudoscience?"

    • Well since genetics is hereditary we do not really have to sequence the babies genes to know its medical future.

  • My WTF, explained (Score:5, Informative)

    by jfengel (409917) on Wednesday June 06, 2012 @05:58PM (#40237769) Homepage Journal

    What's decidedly unclear from the summary: they're sequencing fetal cells found in the mother's blood. It was separated from the mother's own blood cells with a nify trick using the father's DNA.

    So it allows them to sequence the baby's type without having to touch the infant itself. They're not making any "mother+father=baby" predictions before the baby is conceived, which would be impossible just from their ordinary (somatic) cells.

    • by ion++ (134665)

      What's decidedly unclear from the summary: they're sequencing fetal cells found in the mother's blood. It was separated from the mother's own blood cells with a nify trick using the father's DNA.

      What if the man the woman says is the father is not the father?

  • I accurately predicted almost all the numbers in the lotto draw last Saturday.

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