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from the how-do-you-know-how-much-you-don't-know? dept.
The feat made headlines around the world: "Scientists Say Human Genome is Complete," The New York Times announced in 2003. "The Human Genome," the journals Science and Nature said in identical ta-dah cover lines unveiling the historic achievement.
There was one little problem.
"As a matter of truth in advertising, the 'finished' sequence isn't finished," said Eric Lander, who led the lab at the Whitehead Institute that deciphered more of the genome for the government-funded Human Genome Project than any other. "I always say 'finished' is a term of art."
"It's very fair to say the human genome was never fully sequenced," Craig Venter, another genomics luminary, told STAT.
"The human genome has not been completely sequenced and neither has any other mammalian genome as far as I'm aware," said Harvard Medical School bioengineer George Church, who made key early advances in sequencing technology.
[...] FAQs from the National Institutes of Health refer to the sequence's "essential completion," and to the question, "Is the human genome completely sequenced?" they answer, "Yes," with the caveat — that it's "as complete as it can be" given available technology.
[...] Church estimates 4 percent to 9 percent of the human genome hasn't been sequenced. Miga thinks it's 8 percent.
https://www.statnews.com/2017/06/20/human-genome-not-fully-sequenced/
I'm glad this is finally getting some coverage. A few years ago I looked into the human genome to prove to myself it didn't contain a certain sequence, and found this was impossible since ~10% of it was missing. When they talk about "sequencing a genome" it is total false advertising.
(Score: 2, Insightful) by Anonymous Coward on Sunday July 30 2017, @05:56PM (5 children)
Any molecular biology student that gets its first classes in how sequencing is done, should know that 100% isn't feasible with current technology (highly repetitive regions are just difficult to sequence). Even if it would be possible, the question would arise what 100% human (or for almost any other organism) would mean due to variabilities between individuals that would be allowed. Then we would move the boundary for the same question to hybrids, sub-species and such.
(Score: 0) by Anonymous Coward on Sunday July 30 2017, @06:23PM (3 children)
It is like the "average man", such an entity does not exist and optimizing for him is a mistake. Likewise, it is extremely unlikely that anyone contains a cell with a sequence that matches what they call "the human genome" exactly.
(Score: 2) by HiThere on Sunday July 30 2017, @07:04PM (2 children)
I thought Craig Venter had loads of cells that matched the sequence he described. (Yeah, it's not 100%, but I'm not convinced the areas with lots of repeats are that important...certainly not the precise number of repeats.)
P.S.: Someone earlier said "the human genetic machinery can copy those regions", but they were a bit wrong. Copies of those regions tend to have lots of errors in the number of copies...but nobody's found any real link between that and any actual effect. Perhaps there's a link between the number of teleomers and aging, but that's not a long repeat. Neither its the one involved in Huntington's disease. Those are short repeats, and they frequently *are* significant.
Javascript is what you use to allow unknown third parties to run software you have no idea about on your computer.
(Score: 1, Insightful) by Anonymous Coward on Sunday July 30 2017, @08:22PM
If a non-repetitive region is flanked by regions which are repetitive, you'll have to go through quite some hoops to obtain the sequence of that region. It takes time and money. And, you might obtain let's say 99.5% of all the sequences, but connecting them into the full sequence is another problem.
As for the telomeres, they are not the only repetitive sequences. 10 times an 'A' in an intron can really mess up your sequencing progresses in a single gene (own experience).
The statement "the human genetic machinery can copy those regions" might be true, but many of the polymerases in an organism are not used in sequencing.
(Score: 0) by Anonymous Coward on Sunday July 30 2017, @08:23PM
If you have 6 billion basepairs with 1 in 100 million indel and 1 in 100 chromosomal missegregation rates it is extremely unlikely any two cells will have exactly the same sequence.
(Score: 2) by Immerman on Monday July 31 2017, @01:39PM
>the question would arise what 100% human (or for almost any other organism) would mean
Quite. If for example if w were to assume that 95% of DNA were shared identically by 100% of humans, then you might think you could perfectly sequence one person's DNA and get 95% of the human genome. But that's ignoring the fact that 95% shared DNA doesn't mean that you have 95% of the human genome - to know that percentage you need to already know how much variation there is within the remaining 5% - assume an average of only 10 variants per gene, and the variations account for a third of the total genome. And even that is assuming that all differences are variations of an existing gene, rather than entirely new genes that have arisen over the millenia.