> However–and here’s the rub–some 25 years after the human genome was sequenced, and despite huge efforts to link genes and disease, there are almost no SNPs that tell you anything consequential about your health. If you have a genetic disease, you almost certainly already know about it, and if you don’t know, then the 23andMe data just isn’t going to reveal anything.
For someone who “knows genomes”, this is a brain dead take on microarrays. Lots of the content on arrays _is_ directly tied to a phenotype because there’s limited space so we directly test variants that are known to cause problems!
Is he really claiming that BRCA1/2 variants don’t increase risk of breast cancer in a meaningful way? Or that there aren’t tons of people who are XXY who don’t know even though it’s the hidden cause of many infertility problems?
This is just such a bad take it is hard to take anything said here seriously
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.
Eh, your results look perfectly fine, especially for a budget sequencing run. Keep in mind there are a lot of repetitive DNA sequences that don't map well (search "mappability track" for more info). Depending on the reference they used, these may even be masked out and thus no alignment can even be attempted.
No one should be BLASTing individual reads... And pretty much no one is going to be assembling with OLC, even for ONT data.
On the products page it says they provide FASTQs, aligned BAM and VCF. Which is exactly what one would expect. They're almost certainly just running the DRAGEN pipeline (or something similar) and giving you the output it creates.
Not for home gamers, no. ONT is fairly low throughput and the prep is surprisingly difficult to do well without experience. You would need to run tens of flow cells to get enough sequencing data.
I have no skin in this particular game (Though I work in the sequencing industry), but...
I don't think anyone is fooled/trying to trick anyone when they say "whole genome sequencing" or that they sequence 100% of the genome. That is the term of art for non-targeted/unenriched sequencing of DNA (nb: it may be RNA/ribosome depleted, so fine it's technically enriched but not in a meaningful way).
Also exons are genic region, are you thinking introns (arguably genic or at least adjacent), or promoters/enhancers and chromatin state?
Lifetime license does not mean lifetime support. I get that that might be annoying, but why or how could they warranty third party software, that they don't control or version themselves, indefinitely?
Yes, but if your child is school age -- schools which are now increasingly going to in person instruction -- and you are immunocompromised, what are you going to do? Same question if you live in a multi-generational household, but now there are grandkids going to school and kids going to work.
I see elsewhere you're claiming that long Covid isn't a thing. It is, full stop. Unless you're suggesting that living with lung and heart damage caused by Covid isn't a complication of Covid?
1. They still get sick, even if asymptomatic, and can bring it home to the house where older people live
2. I don't know if there are published case report / data yet, but anecdotally the new strains are much more likely to cause complications and require hospitalizations for younger children.
3. Even asymptomatic infectious seem to cause "long covid" (Something like a third of long covid cases were asymptomatic). Potentially life-long alterations to lung or heart function doesn't sound like fun
The answer to "Why are they investigating?" is simple and, in fact, driven in part by the pharmaceutical industry itself.
First: The rate of thrombosis in AZ recipients is the less than it is in the general population -- Gen pop, ~.1% [1], AZ ~ 0.001% [2]. There is no evidence that the vaccine causes substantially higher risk. Also, the populations being prioritized for vaccination are a higher risk population for DVT to begin with.[1]
AZ, along with effectively every pharma company out there of note, takes the reporting of adverse drug responses (ADRs) very, very seriously. Both FDA and EMA require ALL companies that produce a labeled product (aka a drug you can "buy" and isn't only available in a trial setting) to investigate and report on every instance of a reported potential ADR. Companies want to investigate because they want to be able to keep selling their drugs. Regulators want to investigate because they want to limit ADRs as much as possible.
From the therapeutic point of view, it is bad if the treatment causes ADRs but also some may be unavoidable because of how the treatment works -- think chemo and cancer. The safety window for a drug is determined by balancing the therapeutic gain of treatment (usually, shorter time to recovery, increased QOL, or, in the case of cancers, increased life span/PFS) with the number and severity of known adverse effects. You might hear about cancer patients "cycling" their treatments, this is to allow time for the body to recover from known/expected ADRs.
Any way, this was a long winded way of saying every entity involved -- drug manufacturer, regulators, doctors, patients -- wants reports of ADRs investigated.
Thanks to them we now have a nearly completed genome, only missing the deconvoluted rDNA array segments (~12mb or so, we know the sequences since they’re basically identical but no one has accurately placed the individual array variants yet).
Sample prep, particularly if you want truly long reads, is 100% the hardest part.
Funnily, there are people out there who want to teach army/marine grunts on the front line to run minIONs. Most of the work is on making the sample prep automated and idiot proof.
This isn’t the case anymore. Pathogen surveillance labs use Nanopore for single-base resolution variant calls to determine antibiotic susceptibility and to “fingerprint” against known and previously sequences isolates.
I think you're stuck in the biotech == people mindset.
On the bacterial side, it is fantastic for quickly sequcinging and closing genomes. Personally, I think the killer use case is field portable and real time sequencing of pathogens. I've worked with groups (.gov and private, defense and health related) that want to put minION + flongles to use in applications like early detection for bio terrorism and pathogen surveillance.
Over the last few years there have been several (4-5) instances of British subs nearly striking surface ships in their home waters. Also running aground right outside their home port in 2010. Not exactly reassuring.
The US Navy is much bigger and has global operations. They're just as guilty of being careless but they also have proven war fighting capabilities. No one is asking the British to sail by as a show of power and solidarity.
For someone who “knows genomes”, this is a brain dead take on microarrays. Lots of the content on arrays _is_ directly tied to a phenotype because there’s limited space so we directly test variants that are known to cause problems!
Is he really claiming that BRCA1/2 variants don’t increase risk of breast cancer in a meaningful way? Or that there aren’t tons of people who are XXY who don’t know even though it’s the hidden cause of many infertility problems?
This is just such a bad take it is hard to take anything said here seriously