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Medicine Science

Scientists Say They Can Read Nearly the Whole Genome of an IVF-Created Embryo (science.org) 44

Posted by BeauHD from the exploratory-research dept.
sciencehabit shares a report from Science.org: A California company says it can decipher almost all the DNA code of a days-old embryo created through in vitro fertilization (IVF) -- a challenging feat because of the tiny volume of genetic material available for analysis. The advance depends on fully sequencing both parents' DNA and "reconstructing" an embryo's genome with the help of those data. And the company suggests it could make it possible to forecast risk for common diseases that develop decades down the line. Currently, such genetic risk prediction is being tested in adults, and sometimes offered clinically. The idea of applying it to IVF embryos has generated intense scientific and ethical controversy. But that hasn't stopped the technology from galloping ahead.

Predicting a person's chance of a specific illness by blending this genetic variability into what's called a "polygenic risk score" remains under study in adults, in part because our understanding of how gene variants come together to drive or protect against disease remains a work in progress. In embryos it's even harder to prove a risk score's accuracy, researchers say. The new work on polygenic risk scores for IVF embryos is "exploratory research," says Premal Shah, CEO of MyOme, the company reporting the results. Today in Nature Medicine, the MyOme team, led by company co-founders and scientists Matthew Rabinowitz and Akash Kumar, along with colleagues elsewhere, describe creating such scores by first sequencing the genomes of 10 pairs of parents who had already undergone IVF and had babies. The researchers then used data collected during the IVF process: The couples' embryos, 110 in all, had undergone limited genetic testing at that time, a sort of spot sequencing of cells, called microarray measurements. Such analysis can test for an abnormal number of chromosomes, certain genetic diseases, and rearrangements of large chunks of DNA, and it has become an increasingly common part of IVF treatment in the United States. By combining these patchy embryo data with the more complete parental genome sequences, and applying statistical and population genomics techniques, the researchers could account for the gene shuffling that occurs during reproduction and calculate which chromosomes each parent had passed down to each embryo. In this way, they could predict much of that embryo's DNA.

The researchers had a handy way to see whether their reconstruction was accurate: Check the couples' babies. They collected cheek swab samples from the babies and sequenced their full genome, just as they'd done with the parents. They then compared that "true sequence" with the reconstructed genome for the embryo from which the child originated. The comparison revealed, essentially, a match: For a 3-day-old embryo, at least 96% of the reconstructed genome aligned with the inherited gene variants in the corresponding baby; for a 5-day-old embryo, it was at least 98%. (Because much of the human genome is the same across all people, the researchers focused on the DNA variability that made the parents, and their babies, unique.) Once they had reconstructed embryo genomes in hand, the researchers turned to published data from large genomic studies of adults with or without common chronic diseases and the polygenic risk score models that were derived from that information. Then, MyOme applied those models to the embryos, crunching polygenic risk scores for 12 diseases, including breast cancer, coronary artery disease, and type 2 diabetes. The team also experimented with combining the reconstructed embryo sequence of single genes, such as BRCA1 and BRCA2, that are known to dramatically raise risk of certain diseases, with an embryo's polygenic risk scores for that condition -- in this case, breast cancer.
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Scientists Say They Can Read Nearly the Whole Genome of an IVF-Created Embryo More

Scientists Say They Can Read Nearly the Whole Genome of an IVF-Created Embryo

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  • Imagine if his parents had had his DNA read and saw he was going to have severe health problems later in life. Where would the scientific world be if they decided it was for the best if he didn't see the light of day?

    • Presumably supporting the parents decision to have a termination?

      Not sure I'm understanding what you think the problem is here?

      • Not supporting termination. Just that some people decide that the value of an unborn child to both itself and the wider world is predominately weighted by its state of health, without knowing what its future life in other aspects will actually turn out to be. In any case, its a terrible situation for any parent to be in, and I don't wish it upon anybody.

        • Itâ(TM)s gene editing, parents have the option of fixing mutations in DNA.

        • An embryo is not a child (other than in Texas or Iran etc).

          Yes S Hawking's parents might have decided to terminate the pregnancy... but by the same token, some bright young Texan girl who got knocked up might have become the next scientific genius but oh she had to quit school and become a teenage mom. These what-ifs lead nowhere.

          • Absolutely, this shit of treating embryos as legally a human child/ person needs to stop. It's still borderline fine if someone believes it in a religion but not legally. That's fully taliban territory

            There are people who consider sperms as having rights too ! It's not a slippery slope but a huge cliff.

            Next you know we have to file a petition in supreme court before jerking off else go to jail ?
            What if both the partners' umm.. 'juices' get mixed up on the bed sheet ? Rush it to an incubator ??

            Next some sa

            • consider sperms as having rights too ! It's not a slippery slope ...

              pun opportunity missed, inexcusable!

            • So, at what point does that embryo become a person? Without a clearly defined and damn-well justified line between person and ball of cells, you're just making meaningless and angry noise. As it stands, all you have done is make absurd analogies and ridiculous slippery-slope arguments.

              How about you prove beyond even an iota of doubt that an embryo is not a human being before you let yourself pretend there is anything justified about the idea of abortion? Given that the context is ending human life, th

              • Exactly. At this point in history, laws of several jurisdictions consider an embryo or fetus is not human until it draws its first breath. Until then, it's all just a 'bundle of cells'.

                That is the rationale for late term abortions, or even partial birth abortions, in some jurisdictions. Baby still 'breathing' through its umbilical? Its fair game!

                I see shades of the Dred Scott decision here. This must change.

    • Re: (Score:1)

      by vivian ( 156520 )

      How about the alternative approach - if you could get to the point of being able to choose the blend of genes from each parent to avoid genetic problems, ie.
      The child would still only use DNA that came from one parent or another - would that be ethical?

      • It is easier to just fix the mutation with gene editing technology. As long it the mutation is not a chromosomal aberration, it is well within even current technology (if it was not from a politics-based ban on gene editing of embryos.)

        • It's even even easier to just let nature do the gene editing (through the existing sperm/egg mutation process) and simply choose the correct embryo from a few dozen that were allowed to grow to 8 cell big (so that one cell can be plucked off for sequencing) and then choose the correct embryo to put back into the woman to become a full baby.

          You know, the way it's done now...

    • Who says they have to destroy the embryo, they can fix the DNA. You never heard of gene editing?

      • Gene editing is done on a single instance of a genome before it's copied (typically into a bunch of "child" bacteria to produce some drug etc) if you've got a multi-cell embryo it's too late!

        • "Gene editing is done on a single instance of a genome before it's copied (typically into a bunch of "child" bacteria to produce some drug etc) if you've got a multi-cell embryo it's too late!"

          This in-vitro stuff start with single cells.

      • IVF results in excess embryos.

        You can't implant them all, so most of them need to be flushed.

        You might as well screen them and pick the healthiest to keep.

        It is the same as thining vegetable seedlings. You keep the strong, discard the weak.

    • Re: (Score:2)

      by AmiMoJo ( 196126 )

      This already happens with stuff like Down Syndrome. We have fairly effective tests for it and many countries routinely offer them. I suppose it's a bit different because Hawking had a fairly normal childhood, i.e. his parents were not exceptionally burdened.

    • Re: (Score:1)

      by bokske ( 1429119 )

      We have a daughter with a rare genetic disease, which causes her muscle tissue to dissolve. It turns out that both parents were carriers of a recessive gene defect, without ever noticing anything, so we had 1/4 chance of a disabled child. This has absolutely devastated our lives. For me, the obvious decision "if we had known" would have been to terminate that pregnancy.
      She is now 18 years old and an absolute sweetheart, always cheerful and charming - bumbling through her freshman year at college right now.

    • "Imagine if his parents had had his DNA read and saw he was going to have severe health problems later in life. Where would the scientific world be if they decided it was for the best if he didn't see the light of day?"

      Lots of doomsday stories would be lost, that's for sure.

    • I jerk off millions of Steven Hawkings per day that never see the light of day. Please don't tell me that 8 or so cells of an embryo is a baby. *eye roll* They pick the correct 8 or so clump of cells, and yes, discard the other ones.

    • It is possible to do gene editing of embryos.

  • If they could scan the fetus genome and come up with a reliable determination of whether the baby would grow up to be a liberal douchebag, so that the parents could take the appropriate action - that would be great.

    • They have. But no people that use those words are smart enough to do it. Not surprisingly, consider how people like you do everything they can to undermine schools.

    • Or, they could find the gene that makes people afraid of their own shadows, and empty out the GOP.

    • "If they could scan the fetus genome and come up with a reliable determination of whether the baby would grow up to be a liberal douchebag, "

      If not, they could just level the IQ of the conservative fetus to above 100 and he would be born a Democrat.

  • It was inevitable (Score:1)

    by Anonymous Coward
    Because... Gattaca.

  • I heard the movie will be better. :-)

  • They're talking about reading the genome of something that is comprised of only a few dozen cells at that point. How do they extract DNA without destroying what can be plausibly called a human life?

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