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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) by gringer on Sunday July 30 2017, @11:37PM (6 children)
Highly repetitive sequences that are longer than the template length of Sanger sequencing and Illumina sequencing:
http://i.imgur.com/p5U1YCz.jpg [imgur.com]
https://twitter.com/gringene_bio/status/887822844280709120 [twitter.com]
https://twitter.com/gringene_bio/status/882006992268648449 [twitter.com]
Long non-tandem repeats also cause problems.
Ask me about Sequencing DNA in front of Linus Torvalds [youtube.com]
(Score: 2) by kaszz on Monday July 31 2017, @02:13PM (1 child)
The last tweet is intriguing .. "The missing bits of code in the human genome could be key for understanding cancer.".
(Score: 0) by Anonymous Coward on Monday July 31 2017, @03:13PM
The tweet links to an article that links back to the article in the OP.
(Score: 2) by kaszz on Monday July 31 2017, @02:17PM (3 children)
If repetitive sequences is the problem. Then the solution seems to be to stabilize long enough sequences and read them. The question is then, how long sequences do these need to be? and how long is the total?
Is it possible to read the DNA code in place using say laser interferometry etc?
Or other complete out-of-the-box methods.
(Score: 2) by gringer on Monday July 31 2017, @08:23PM (2 children)
To capture everything, about 3 million bases in length, according to Karen Miga at the London Calling conference this year.
There are a lot of "totals" that I can pull out of human genome statistics; you need to be more specific than that. Concentrating just on centromeric regions, she said that the average centromeric length is about 3 Mb, so that suggests there's a bit over 60Mb of highly-repetitive sequence in the human genome.
Lasers and/or SEM are not yet able to scan at the 0.33 nm resolution required to resolve single bases of DNA. There have been a couple of papers in the last month or so discussing methods of visually resolving the 3D structure of DNA, but nothing about an adapter-free resolution of the sequence.
Nanopore sequencing is pretty good; it's what I used to make those images. Nick Loman has managed to get a read of a bit over 750 kb, and I expect that if ONT can get their accuracy for most 100bp sub-sequences up to Q30, or quadruple the read length, reads that span (or unambiguously cover) centromeres will be possible.
Ask me about Sequencing DNA in front of Linus Torvalds [youtube.com]
(Score: 2) by kaszz on Tuesday August 01 2017, @12:52AM
Just a thought.. 8 kV would accelerate electrons with the energy for a x-ray photon at 0.1 nm wavelength. Possible solution?
I'm thinking if the x-ray photon is shoot at different angles and the output angle is measured. A problem can be if the sample is not still though.
(Score: 2) by gringer on Tuesday August 01 2017, @06:11AM
Karen Miga has just put a preprint paper onto BioRXiv about resolving the centromere of the Y chromosome using nanopore reads:
http://www.biorxiv.org/content/early/2017/07/31/170373 [biorxiv.org]
Ask me about Sequencing DNA in front of Linus Torvalds [youtube.com]