[HN Gopher] The era of fast, cheap genome sequencing is here
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The era of fast, cheap genome sequencing is here
Author : ColinWright
Score : 75 points
Date : 2022-10-01 12:24 UTC (10 hours ago)
(HTM) web link (www.wired.com)
(TXT) w3m dump (www.wired.com)
| mattnewport wrote:
| And yet the era of being able to do anything really useful with
| the information has yet to arrive.
| Der_Einzige wrote:
| Clustering, dimensionality reduction, frequent pattern matching
| can get you a lot of the way there.
| FollowingTheDao wrote:
| This is the biggest misconception. I have literally reverse my
| hyperlipidemia, hypertension, and been able to get off all of
| my meds for my schizoaffective Bipolar Disorder because of what
| I have learned from my genetics and changing my diet/lifestyle
| to suit what my body needs.
|
| Just because doctors do not know what to do with it (they are
| decades behind most research) it does not mean you cannot learn
| about this and take action on your own.
|
| Just knowing my FADS1, FADS2 genetics was enough to change my
| diet to seafood only and raise my HDL from a consistent 35 to
| over 55 in three weeks. Doctors put me on a statin which
| lowered my HDL to 25.
| dominotw wrote:
| > seafood only and raise my HDL
|
| Seafood helps everyone with HDL. Is 35 -> 55 not possible
| with those genes that you mentioned ?
| mbreese wrote:
| Rare disease diagnosis, newborn screening, molecularly targeted
| cancer therapies...
|
| We're starting to get some good utility from sequencing.
| Currently whole exome is more informative than whole genome.
| But, there are definitely some good clinical uses!
| sacul wrote:
| My daughter has a rare genetic disorder, cardiofaciocutaneous
| syndrome (CFC), and it was not until 2 years in that we were
| able to get a diagnosis after a whole gene sequence. It was
| game-changing to get the diagnosis, because it connected a to
| a community and to doctors who could help.
|
| https://rarediseases.info.nih.gov/diseases/9146/cardiofacioc.
| ..
| cjbgkagh wrote:
| That future is just not evenly distributed yet.
| pfdietz wrote:
| Sequencing cancer cell genes is quite common now, to determine
| just what kind of cancer is there and which treatments are
| appropriate.
| dominotw wrote:
| GP probably meant for completely healthy people who are the
| target audience for doing these .
|
| Also the cancer drugs like PARP inhibitors seem to be helping
| everyone regardless of mutation status in clinical trials. So
| the connection is much less clear.
| pfdietz wrote:
| There are many cancer drugs that target mutations in
| specific proteins. Just what treatment will be given for a
| cancer often depends on what's been mutated.
| derekja wrote:
| sequencing continue to drop in price far faster than moore's law.
| https://www.genome.gov/about-genomics/fact-sheets/DNA-Sequen...
|
| Here is the archive of the wired article, btw:
| https://web.archive.org/web/20221001173347/https://www.wired...
| giuliomagnifico wrote:
| This should be a good news, because with DNA test you can find
| some hereditary diseases, but I'm a bit skeptical about the
| privacy, in particular when I read things like this: "Mass DNA
| Collection in the Tibet Autonomous Region from 2016-2022"
| https://citizenlab.ca/2022/09/mass-dna-collection-in-the-tib...
|
| The law will absolutely have to adapt to these changes.
| bpodgursky wrote:
| I have an honest question: what are the specific negative
| consequences you, personally, are worried about if your genome,
| today, was made completely public?
| colinsane wrote:
| during extreme wartime or societal setback, we often see
| society look for scapegoats. the outgroups created in living
| memory have been based on social standing but also ancestry
| and things tightly related to the genome.
|
| if/when the time comes of a meaningful societal regression
| like this, i want it to not be so easy to drag me into it.
| it's precautionary.
| giuliomagnifico wrote:
| For example an insurance company can rise the price of your
| contract if they know that you are genetically predisposed
| for some diseases.
| lotsofpulp wrote:
| In the US, a health insurance company cannot price premiums
| based on health or any pre existing conditions.
|
| https://www.healthcare.gov/how-plans-set-your-premiums
|
| > FYI Your health, medical history, or gender can't affect
| your premium.
|
| However, life insurance, long term disability insurance,
| and I presume other types of insurance are free to use
| health data for pricing. Of course, if genetic data was
| known to be worth it for predicting probability of death or
| disability by a certain age, those insurance companies
| would already be requiring applicants to provide genetic
| data.
| bpodgursky wrote:
| I'm asking at a personal level, because in the US this
| genetic discrimination is against federal law, and I
| (personally) have 0 fear that an insurance company will
| seek out and use this information to illegally discriminate
| against me.
|
| Are you worried that companies will not respect this law?
| Or are you not US based.
| rnk wrote:
| It's illegal but companies will figure out a way to work
| around it. Why can't they just require your authorization
| as part of getting insurance? You might notice lots of
| services require you to give up certain privacy rights. I
| don't want the phone company to sell my location data, I
| don't want apps on my phone to sell my location data.
| There are all these tenuous yet successful ways where
| your right to opt out is overcome. I'm happy to click in
| boxes in apps, I've done it lots of times, I turn off
| location history when possible. But because I carry a
| phone I believe it's certain that some apps somewhere are
| storing my location. Same for having a recent car with a
| data modem in it. And then there are license plate
| readers. I want to disallow all of these things, but the
| battle is basically lots as far as I can tell.
| novok wrote:
| That just means the laws don't have teeth. Often if they
| do, they straight out say it's illegal to even get
| 'authorization' or anything approaching it. It would be a
| straight out ban vs. an "ok with consent" which is what
| authorization is about.
|
| You can't sign a contract to sign yourself into slavery,
| it's just straight out illegal. And thus you don't see
| anybody being signed into slavery via contract in the
| USA, and there many other things that act this way in
| law.
| lotsofpulp wrote:
| > It's illegal but companies will figure out a way to
| work around it. Why can't they just require your
| authorization as part of getting insurance?
|
| Because it is highly regulated, with no known examples of
| insurance companies and regulators colluding to
| incorporate health data for pricing purposes.
|
| https://www.healthcare.gov/how-plans-set-your-premiums
|
| For example, you can even figure out your health
| insurance premium in the state of NJ just based on this
| pdf:
|
| https://www.state.nj.us/dobi/division_insurance/ihcseh/ih
| cra...
| JZL003 wrote:
| The thing is it's not much data in absolute terms, but it's
| not going to change for over human timescales and tells you
| something about your entire family, going back generations in
| the past and many in the future. On the other hand, look at
| GWAS studies, if you have many people and know if they get a
| disease or not, you can narrow down exactly what parts of the
| genome are implicated in the disease, and start designing
| drugs for it. It's hard work and doesn't always work, but it
| allows us to go from high level disease phenotype -> exact
| mechanistic problems
| bpodgursky wrote:
| Yeah and I'm digging into this because I personally would
| _much_ prefer that these GWAS studies have access to my
| genome and medical data, so they can design drugs for
| whatever my specific genotype is. I think it 's far more
| likely that this will benefit me and my children, than hurt
| me.
|
| I'm not telling other people they are wrong to be afraid,
| but I want to understand the exact mechanism of those
| fears.
| JZL003 wrote:
| If you're interested and a US citizen, look into the All
| of Us program by NIH. They're going to sequence a million
| people's genome (!!) and allow researchers to use it. And
| they're doing it in a very careful safe way. It will mean
| many researchers will have your deanonymized genome (and
| it's up for debate if it's possible to truly future-proof
| deanonymize a genome) but it's not sketchy at all and
| will be a huge help for future generations IMO.
|
| And if you're in another country, especially european
| ones, look into other research programs, there are lots
| round
| FollowingTheDao wrote:
| Why drugs? These GWAS studies should be looking at
| nutrition.
| JZL003 wrote:
| I guess I agree on principle and diet is understated. But
| let's say, as has happened recently, you're looking at
| Alzheimer's or lewey body syndrome and you find the gwas
| returns a lot of results for a certain cellular pathway
| (like a stress response or where a cell breaks down
| misfolded proteins, leading to plaques). You can look for
| small molecule drug which targets that, or try a fancier
| treatment to target that exact protein. But how would
| that insight extend to diet?
|
| Beyond just eating more health (in whatever way) and
| exercising more, which does go a long way. Thse drugs are
| trying to be extremely targeted and intricate in now they
| work
| sometimeshuman wrote:
| Would you want a dating App telling your potential match all
| of your negative genetic predispositions ? How about your
| employer ? Or your parents, would they have raised you
| differently if they had unnecessary paranoia about a
| predisposition that you would never manifest.
|
| Human nature values first impressions and you can expose your
| flaws after you have established your reputation a bit. This
| data has the potential to short-circuit that and could lead
| to yet another technology that is maladapted to human nature.
| [deleted]
| Dracophoenix wrote:
| This will certainly put a damper on the sperm donation market.
| quesera wrote:
| An individual sperm cell does not contain a full genome.
|
| You cannot even reliably determine a donor's hair color, from
| a single sperm cell.
|
| I imagine it's much more difficult to reconstruct a full
| genome from a sperm donation than from, say, saliva on a
| discarded cup.
| chromatin wrote:
| This comment is misleading, and possibly wrong depending on
| what you mean by "full genome" (not an accepted technical
| term).
|
| A sperm cell contains one complete haploid genome.
| quesera wrote:
| You're right, it's not as simple as I described.
|
| But (my bio is rusty) a haploid genome (gamete) cannot
| fully represent the genome of a diploid human.
|
| If you're looking for genetic disorders, these will often
| be the result of recessive traits, right? So having only
| half of the chromosome sets is not indicative.
|
| That's my example of hair color. With a full genome
| sequence, you could determine the person's hair color,
| but with a haploid genome, you could not.
|
| If OP's joke is about the privacy implications of sperm
| donation, then saliva seems more risky.
| omgwtfbyobbq wrote:
| From what I've read, recessive genetic disorders tend to
| be worse, but there are plenty of dominant and polygenic
| disorders with _varying degrees of penetrance.
|
| _ This I think indicates some other genetic and/or
| environmental factors we don't have a good grasp of.
| d110af5ccf wrote:
| A _single_ sperm cell can 't. But you presumably have an
| awful lot of them in a single sample. So this seems
| irrelevant to the privacy concerns being discussed here.
| quesera wrote:
| ...and that's what I said. It would be _more difficult_
| than from saliva.
| etiam wrote:
| As you're probably aware, most people who donate sperm opt
| for more than a single cell...
| quesera wrote:
| Right. Hence "more difficult" than from saliva.
|
| Think about it. Each sperm cell gets a random mix of your
| chromosome sets. There are 2^23 possibilities.
|
| But of course you only need to find the matched pair for
| each chromosome. So you'd only need a few hundred cells.
|
| I'm not a geneticist, but that sounds like a much harder
| genome sequencing/assembly problem than the fully matched
| set you'd get from saliva etc.
| nanomonkey wrote:
| My father died of pancreatic cancer this week after getting a
| diagnosis 36 days prior. Since then I've been on a minor crusade
| to find methods of making sure I have a better diagnosis of
| anything similar.
|
| Full body MRI can be had for ~$2k. I can imagine going in and
| getting a genome sequencing and an MRI scan done, and then over
| the years having a much better idea of the changes going on in
| your body as you age, along with an evolving map of what to look
| out for.
|
| It's exiting, and yet I'm worried about handing over information
| that could be used against me by corporations, the government or
| insurance companies.
| FollowingTheDao wrote:
| Sorry man, my father died of pancreatic cancer as well. I have
| found two homozygous SNPs in my ABO gene (rs505922, rs657152)
| that are linked to Pancreatic Cancer. ABO needs manganese as a
| cofactor so I eat a lot of mussels.
|
| They gave my father one year if he went on Chemo and the chemo
| killed him in there weeks.
|
| Check out these links about the ABO gene and Manganese in
| pancreatic cancer.
|
| https://pubmed.ncbi.nlm.nih.gov/12649190/
|
| https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2657095/
|
| https://pubmed.ncbi.nlm.nih.gov/12700280/
|
| I suffer from a lot of genetic stuff that I have fixed
| understanding my genetics. That is more valuable than any harm
| that could be done with my genetics.
| walnutclosefarm wrote:
| My condolences. My wife has lost both her mother and brother in
| similar "bolt from the blue" fashion. It's hard.
|
| But, before you conclude that you want to try whole body MRI as
| your response, I recommend you read this: https://cancerimaging
| journal.biomedcentral.com/articles/10.1.... It's heavy going if
| your're not au fait with statistics, but important. The
| potential for more harm than good is quite real.
| dominotw wrote:
| i am sorry for your loss. That must be such a shock to everyone
| in your family.
|
| We are getting HRR genome testing done for my father this week
| for his prostate cancer. Some of the PARP inhibitors seem to
| have decent success in prostate cancer.
| divbzero wrote:
| I am very sorry for your loss.
|
| I know there are efforts like Galleri [1] to detect cancer
| early using liquid biopsy [2] but I don't know how effective
| they are at the moment.
|
| [1]: https://www.galleri.com/
|
| [2]: https://en.wikipedia.org/wiki/Liquid_biopsy
| pavlov wrote:
| Maybe get your MRI and genome done in Europe which has very
| strong protections for this kind of data?
| etrautmann wrote:
| My wife is a physician and this is a contentious issue.
| Virtually any full scan will turn up things that seem like a
| cause for concern when you're fine. The risk of false positives
| is fairly high when testing is nonspecific/un-targeted. This
| results in real stress, difficult decisions, and often times
| worse care.
| m463 wrote:
| I was wondering when I would see this answer, since that's
| what they would always say on House.
|
| I still think there are probably big obvious things that need
| to be caught early.
| jghn wrote:
| It's tricky. At a population scale it looks more and more
| like early detection for many things causes more harm than
| good. On the other hand, if you're the person who could
| have had a better outcome with early detection it's hard to
| argue that point.
| [deleted]
| zemvpferreira wrote:
| My condolences for your loss.
|
| My own father is a physican and very against any elective exams
| himself. His reasoning is that his colleagues are excessively
| interventive so the less medicine, the better. I wish your own
| father had been diagnosed in time but I can see the downside in
| doing too many exams as well. Doctors won't be able to keep
| their hands off treating any little lump they find, even if
| it's to your detriment.
|
| Case in point, surgery for back pain causes said pains to
| worsen at about the same rate as it improves them.
| hawk_ wrote:
| What you do when you find something out is still a choice. If
| that backpain isn't getting in the way of most of your
| lifestyle then the risks of a surgery aren't justified. A
| lump in the pancreas well I think most of us would be better
| served by finding that out earlier than later.
| novok wrote:
| That partly comes from the liability / malpractice system of
| the USA. They are induced to jump on everything so they don't
| get sued by malpractice lawsuits. The amount of detrimental
| behavior in medical system driven by this stuff is extremely
| saddening and if you know doctors, how much they think /
| worry about this stuff is so fucking annoying and sad.
| _tom_ wrote:
| While I totally understand his point about excessive
| intervention, ignorance is not the answer. You absolutely can
| say "no" to doctors.
|
| Of course, with tests that are of themselves dangerous,
| that's another issue. Skip those if the risk/reward is too
| high.
|
| Getting diagnosed too late is much worse than having to say
| no.
| godmode2019 wrote:
| I agree, often having more information is worse because you
| notice things and over react to things that would otherwise
| go unnoticed and fix them self.
|
| I noticed this first when tracking sleep data, but it can
| also be applied to many other areas were humans try fix small
| problems but tend to make things worse.
| gavinray wrote:
| It's not common knowledge, but there's an algorithm called
| "genomic imputation"
|
| It can take incomplete data, like the kind you get from 23andMe,
| etc, and magically "fill in the gaps" to compute the majority of
| the rest of your genome
|
| There used to be a free service https://impute.me that would do
| this for you
|
| https://twitter.com/lassefolkersen/status/154763708634953728...
|
| Search Google Scholar for "Lasse Folkersen", he is active in the
| field and has a lot of great papers about this
| bilsbie wrote:
| I recall this being predicted something like 10 years ago. I
| wonder why a slowdown happened.
| peter303 wrote:
| The second identifiable person to have his genome sequenced-
| James Watson- had around 30 known genome defects at the time.
| However most of them did not manifest as disease. That is a
| mystery.
| FollowingTheDao wrote:
| SNP changes in genes are not usually mutations that cause
| "defects". Most usually they increase or decrease risk for a
| disorder based on more of a polygenic profile.
| tejtm wrote:
| For small enough values of defect, it is par for the course.
| sometimeshuman wrote:
| Can someone recommend where one can order a full genetic sequence
| currently in the US and get the raw data ? It seemed highly-
| regulated when I last checked and required it be order through
| your doctor. The article touches on this a bit how the price gets
| into the thousands due to markups and counseling.
|
| Also how many full sequences would I have to get before the data
| is statistically sound. Since there is likely a base pair or two
| that will be different between the cells (maybe) and the
| sequencer hardware and process will likely have errors too. My
| gut tells me 10 to 20 but perhaps that seems like overkill since
| many base-pairs might be junk/repeats/irrelevant anyway and the
| raw data will have some confidence indication as well IIRC.
| jghn wrote:
| You should be looking for 30x coverage.
|
| There are a number of companies that will do 30x WGS and give
| you the BAM file. I believe Nebula is one of them, but know
| there are other names out there.
| aroch wrote:
| Nebula most likely ship your samples to China for processing
| and sequencing because it's so much cheaper. While that might
| not be a deal breaker for some, I would personally prefer my
| sample not be shipped elsewhere.
| FollowingTheDao wrote:
| Stay away from Nebula. I had such a hassle with them and
| after six months of complaining with mostly no response I had
| to threaten then with a civil suit and they finally replied
| "your sample was no good, here is your money back."
| chrisrohlf wrote:
| I asked this same question not long ago and the CEO of a well
| known company in this same research area reached out and
| recommended Veritas Genomics
| https://veritasgenetics.com/mygenome/
|
| I've yet to finish the order process but I share this here
| because in my research of companies providing full sequencing
| services I never came across them and yet they seem far more
| reputable than others. Current SEO for these services turns up
| a lot of sketchy companies.
| theNJR wrote:
| Any idea how much this costs? The order buttons on their
| website are greyed out for some reason
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