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Exome sequencing and analysis of 450k UK Biobank participants

nature.com

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Re: Exome sequencing and analysis of 450k UK Biobank participants

#41

Post by pfisherman »

hybrid_cluster wrote: post #19

Not too related, but I got my genome sequenced for fun the other day ( Ok, so I have a high genetic predisposition for thinness, walking fast [0], and bipolar disorder? So now what? I never noticed except for the thinness. They even scared me with 'you're genetically in the 99th percentile for critical covid disease progression,' but reading the results of the paper in question, it turned out the heritability of the…

In most cases, your sequence info will be useless to you, but in some situations it can have a huge impact, such as predicting how you might respond to epidural anesthesia if you are a woman in labor.

Also, things like personalized immunity therapies for cancers and such are not far off. Unless they completely fail - which is always a possibility in therapeutic development.

Re: Exome sequencing and analysis of 450k UK Biobank participants

#42

Post by tweedledee »

This is absolutely world changing. I've known that this was coming and was only a matter of time, it did get here sooner than I expected. I have hypermobile Ehelers Danlos Syndrome (hEDS) from a TNXB mutation. I was incorrectly told by doctors for decades that I was perfectly healthy and my issues were psychosomatic. It wasn't until I did a careful large scale behavioral analysis that I was able to identify similar people and from there the root cause. A $500 (30x) DNA test confirmed it. hEDS is massively under diagnosed, the vast majority never get a diagnosis.

I strongly suspect that most mental problems are physical in nature and most physical problems are DNA related. And even when they're not DNA related, treatment ideas could be gleaned from 'natures large scale experiment'. The number of issues that can be identified from a $100 (1x) test and then subsequently treated is mind boggling. For me, that cost is less than a single doctors visit. This side steps the medical establishment which is slow and in many ways archaic. This will lead to a massive leap forward in medicine.

In other news; I'm also of the opinion that IQ is largely determined by DNA, nature as opposed to nurture, and once that is properly figured out I'm sure designer babies are next. I don't think that is a door that can be kept closed. There is already a black market for it. I'll be watching from the sidelines, I think this is going to get interesting.

Re: Exome sequencing and analysis of 450k UK Biobank participants

#43

Post by yellowcake0 »

scrollaway wrote: post #31
adolph wrote: post #17

Earlier quoted context omitted.

the marbled lungfish has the largest recorded genome of any eukaryote. One haploid copy of this fish's genome is composed of a whopping 132.8 billion base pairs, while one copy of a human haploid genome has only 3.5 billion http://www.nature.com/scitable/topicpage/eukaryotic-genome-c...

DNA developers these days just use electron and don’t care about efficiency. That lungfish is ripe for a refactoring. Bet I could implement a new lungfish with only a few million base pairs in a weekend.

Is electron some sort of synthetic genome compiler?

Re: Exome sequencing and analysis of 450k UK Biobank participants

#44

Post by ComputerGuru »

yellowcake0 wrote: post #43
scrollaway wrote: post #31

Earlier quoted context omitted.

DNA developers these days just use electron and don’t care about efficiency. That lungfish is ripe for a refactoring. Bet I could implement a new lungfish with only a few million base pairs in a weekend.

Is electron some sort of synthetic genome compiler?

It’s a (not well executed) joke about electron’s memory consumption and how developers refuse to use anything better.

Re: Exome sequencing and analysis of 450k UK Biobank participants

#45

Post by hyperbovine »

msandford wrote: post #3

Does anyone remember the days when some geneticists were saying that 98% of DNA is "junk" DNA? When I heard it I knew it couldn't be true but it's probably going to take another 50 years to figure out how much really does get used. I can't help but suspect that a lot of the genome is a part of the boot sequence that helps you go from one cell up to all the differentiated organs and tissues and systems.

That hypothesis is a little dated, but it should be noted that the exome (the thing being discussed in this article) is 1% of the overall human genome.

Re: Exome sequencing and analysis of 450k UK Biobank participants

#46

Post by cblconfederate »

I think DNA data should be considered public data. 99% of our DNA is shared, and the DNA degrees of separation between you and me is ~3. Practically we are all already identifiable from the small sample that exists in genealogy companies and it s been repeatedly done by law enforcement. I think it's bonkers that , after 10 years, companies like 23andme are not allowed to give us health reports because ... what reasons really? Especially in Europe it makes no sense to have such draconian laws about something that's important to everyone's health. Full sequencing costs like $200 today and i m sure millions would be willing to give their data to a public database that would take the field meaningfully forward. Instead what we get is we allow these companies to sell data which should be public domain. The US has its problems with their broken social security - here's a suggestion: fix it. Europe could use its public healthcare advantage to get ahead in genomic research while simultaneously improving the quality of its health systems. Instead we are stuck with outdated privacy laws (yet somehow making tax information public is OK). China could be using their own advantage and databases to get ahead in genomics while we 're still playing hide and seek.

Re: Exome sequencing and analysis of 450k UK Biobank participants

#47

Post by sbierwagen »

xyzelement wrote: post #6
msandford wrote: post #3

Does anyone remember the days when some geneticists were saying that 98% of DNA is "junk" DNA? When I heard it I knew it couldn't be true but it's probably going to take another 50 years to figure out how much really does get used. I can't help but suspect that a lot of the genome is a part of the boot sequence that helps you go from one cell up to all the differentiated organs and tissues and systems.

Had the exact thought when I read the headline. What arrogance. "I don't understand what these genes do. Must be junk"

Well, it was the 70s. The "start" and "stop" codons were known. They could work out that transcription proteins would seek out those codons, produce a strip of mRNA of the DNA bases between those codons, zip it on over to the ribosome, and crank out a protein.

Then there's the rest of the genome. Vast stretches of DNA that don't have the signals needed to transcribe proteins. Why?

They didn't know. They had no idea. It would be decades before they even had a complete copy of the genome. It was years of grinding effort, of trying to work out the big picture by staring through a straw. DNA methylation, gene expression, histone stuff, the entire field of epigeneics-- non-coding DNA playing an active role in cellular operation without directly producing proteins-- was still in the future.

Re: Exome sequencing and analysis of 450k UK Biobank participants

#48

Post by hoseja »

sbierwagen wrote: post #47
xyzelement wrote: post #6

Earlier quoted context omitted.

Had the exact thought when I read the headline. What arrogance. "I don't understand what these genes do. Must be junk"

Well, it was the 70s. The "start" and "stop" codons were known. They could work out that transcription proteins would seek out those codons, produce a strip of mRNA of the DNA bases between those codons, zip it on over to the ribosome, and crank out a protein. Then there's the rest of the genome. Vast stretches of DNA that don't have the signals needed to transcribe proteins. Why? They didn't know. They had no idea.…

Hah, they would kill for a straw.

Re: Exome sequencing and analysis of 450k UK Biobank participants

#49

Post by Zababa »

ComputerGuru wrote: post #44
yellowcake0 wrote: post #43

Earlier quoted context omitted.

Is electron some sort of synthetic genome compiler?

It’s a (not well executed) joke about electron’s memory consumption and how developers refuse to use anything better.

I think the joke may be about binary size and not memory, which would make sense when talking about DNA.

Re: Exome sequencing and analysis of 450k UK Biobank participants

#50

Post by richeyryan »

yellowcake0 wrote: post #43
scrollaway wrote: post #31

Earlier quoted context omitted.

DNA developers these days just use electron and don’t care about efficiency. That lungfish is ripe for a refactoring. Bet I could implement a new lungfish with only a few million base pairs in a weekend.

Is electron some sort of synthetic genome compiler?

To be specific, it is Javascript based desktop application platform. Each finished app ships its own version of Chrome which affects the size and arguably adds quite a lot of overhead. It also makes developing cross-platform desktop applications much more accessible, thus making it easier for more developers to make slow, unoptimized applications. Overall it has become a meme for bulky, slow desktop apps with Visual Studio Code being the notable exception.
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