Submitted via IRC for SoyCow1984
Widely Used Reference for the Human Genome is Missing 300 Million Bits of DNA
Known as the GRCh38 reference genome, it is periodically updated with DNA sequences from other individuals, but in a new analysis, Johns Hopkins scientists now say that the collective genomes of 910 people of African descent have a large chunk — about 300 million bits — of genetic material that is missing from the basic reference genome.
“There’s so much more human DNA than we originally thought,” says Steven Salzberg, Ph.D., the Bloomberg Distinguished Professor of Biomedical Engineering, Computer Science, and Biostatistics at The Johns Hopkins University.
Knowing the variations in genomes across populations is essential to research design to reveal why certain people or groups of people may be more or less susceptible to common health conditions, such as heart disease, cancer and diabetes, and Salzberg says that scientists need to build more reference genomes that more closely reflect different populations.
“The whole world is relying on what is essentially a single reference genome, and when a particular DNA analysis doesn’t match the reference and you throw away those non-matching sequences, those discarded bits may in fact hold the answers and clues you are seeking,” says Salzberg.
(Score: 2) by MichaelDavidCrawford on Wednesday November 21 2018, @07:04AM
Veritas Genetics will sequence my genome for a reasonable price [veritasgenetics.com].
But if not them, there is a company that will do it for free in the near future, with the expectation researchers will pay to obtain one's sequence. Despite that they will sell one's sequence, the person whose genome it is retains the rights to it and may feel free to license it independently. Which company I'll go with depends on how my contracting work goes for me the next few months. (I have what is likely to soon be a client, but we're still negotiating.)
I'm going to post my entire sequence on my website in hopes of contributing to a cure for, or at least better treatments for Bipolar-Type Schizoaffective Disorder and Attention Deficit Hyperactivity Disorder.
(I was diagnosed with ADHD in the Summer of 2008 but don't mention it much as I don't want to be taken as a hypochondriac. I'm decidedly _not_ hyperactive now but I was during elementary school. I had a frequent flyer card for the Principal's Office. :-( )
Yes I Have No Bananas. [gofundme.com]
(Score: 1, Insightful) by Anonymous Coward on Wednesday November 21 2018, @07:31AM (2 children)
It's only skin deep. I don't see what the issue is. If you disagree, you're a racist bigot Nazi.
(Score: 2) by MichaelDavidCrawford on Wednesday November 21 2018, @07:54AM
- my diseases out of proportion to their population.
Sickle cell anemia and high blood pressure, perhaps there are others
Ashkenazi jews are more prone to Tay-Sachs Disease
Yes I Have No Bananas. [gofundme.com]
(Score: 0) by Anonymous Coward on Wednesday November 21 2018, @12:29PM
And perhaps also includes a 20-40 IQ deficiency as compared to the Asian racist Nazi bigots. How do you explain that if not due to genetic make up?
(Score: 0) by Anonymous Coward on Wednesday November 21 2018, @09:01AM (9 children)
The HIV sequence is actually human but is "hidden" within one of the high repeat regions with a bunch of other transposons and former transposons? No one knows for sure but that would make a whole lot of oddities about HIV make sense.
(Score: 0) by Anonymous Coward on Wednesday November 21 2018, @09:08AM (8 children)
So how come it's endemic in monkeys? Maybe HIV is actually monkey buy "hidden" within one of the high repeat regions.... who knows? Or maybe monkeys are human.
(Score: 0) by Anonymous Coward on Wednesday November 21 2018, @09:32AM (7 children)
There is no hiv in monkeys, there is "siv" found in chimps but it doesnt cause illness:
https://www.nationalgeographic.com/science/2003/06/news-hiv-aids-monkeys-chimps-origin/ [nationalgeographic.com]
Also, this "jumping" from ape to human seems to have happened at least a dozen times in the last 30 years but no one ever noticed aids before that... that part of the story doesnt make sense either:
https://evolution.berkeley.edu/evolibrary/news/081101_hivorigins [berkeley.edu]
(Score: 0) by Anonymous Coward on Wednesday November 21 2018, @03:53PM (2 children)
Of course it doesn't make sense. Humans are apes. "Jumping from apes to humans" is a nonsense statement. You are an ape. I am an ape. Everybody on here is an ape (with the possible exception of Bot).
Until researchers get over this christian bullshit that 'humans' are not animals they will continue to fuck it up.
You are an ape. Get over it.
(Score: 0) by Anonymous Coward on Wednesday November 21 2018, @08:46PM (1 child)
Ape = Non-human primates.
(Score: 0) by Anonymous Coward on Thursday November 22 2018, @01:11AM
human = religiously deluded ape.
(Score: 0) by Anonymous Coward on Thursday November 22 2018, @04:08AM (3 children)
"the story doesnt make sense either"
Just because you lack the knowledge to understand something, it doesn't mean that others share that deficiency.
IIRC SIV does cause disease it's just not very obvious due to survivor bias. The fact that immunodeficiency causes death due to opportunistic infections also clouds the issue.
(Score: 0) by Anonymous Coward on Thursday November 22 2018, @09:39AM (2 children)
How much will you bet the hiv sequence is not in there?
(Score: 0) by Anonymous Coward on Thursday November 22 2018, @03:13PM (1 child)
In the genome of an uninfected person?
All I have and as much money that I could borrow.
I've personally done PCRs to identify integration sites of HIV. Much is known about the region preferences of HIV integration and the mechanisms of which it targets them.
How much would you bet?
(Score: 0) by Anonymous Coward on Friday November 23 2018, @03:54AM
I would bet 1-3 btc it is.
(Score: 1) by shrewdsheep on Wednesday November 21 2018, @03:27PM (1 child)
This article goes to show that huge chunks of science hinge on some critical assumptions that go unchecked/unquestioned for long periods of time. Apart from the reference genome in genetics all fields have their version of a "reference genome". The standard model in physics or the frequentist/Bayesian paradigms in statistics come to mind.
I do not believe that this is a problem as these "axioms" are there for a reason, it just makes us aware of how little we know and how naive we are.
(Score: 2, Insightful) by Anonymous Coward on Wednesday November 21 2018, @08:42PM
Meh, I tried to use the reference genome to check for a sequence once and immediately came across that huge swaths were missing. Then I wanted to compare a difference sequence between human and cows and found the human genome had been used to "scaffold" the cow genome so they were not independent. If you don't figure this stuff out really quickly when working with it there is something wrong with you.
(Score: 3, Touché) by tangomargarine on Wednesday November 21 2018, @03:47PM (1 child)
For a scientific publication, I really expected to be able to find the number of total genes not buried so fricking deep in the article. Is 300 million shocking because the genome is only 305 million, or is this clickbait because the genome is actually 5 billion?
So, the latter then.
"Is that really true?" "I just spent the last hour telling you to think for yourself! Didn't you hear anything I said?"
(Score: 2) by HiThere on Wednesday November 21 2018, @06:14PM
10% is a bit more than "a minor fluff". How serious it is, though, depends on what's in the missing chunks. Based on technical problems, I'd be willing to bet that a lot of it is in high repetition areas.
Javascript is what you use to allow unknown third parties to run software you have no idea about on your computer.