[HN Gopher] Whole Genome Sequencing
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Whole Genome Sequencing
Author : faebi
Score : 29 points
Date : 2022-07-25 20:57 UTC (2 hours ago)
(HTM) web link (sequencing.com)
(TXT) w3m dump (sequencing.com)
| henearkr wrote:
| Important note: whole genome does not mean whole DNA.
|
| Their claim to sequence 100% of the genome could not be true if
| it was 100% DNA, as some locations like near the centromere or
| the telomeres are notoriousy difficult to sequence (and just
| impossible with the technique of alignment that they use).
|
| It's not that bad, you can already know a lot of interesting
| things with a whole genome, but it won't be enough information to
| e.g. synthesize a copy of your DNA or be able to repair all of
| your adult cell's genetic damages (supposing this kind of tech
| exists in some future).
|
| There are also more and more research on how the exons (DNA _not_
| in some gene) participate in the regulation of genes and are
| involved in many diseases.
|
| I'd like to see some real (and affordable) 100% DNA sequencing in
| a near future!
| aroch wrote:
| 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?
| brofallon wrote:
| Just to clarify, exons are the portions of genes that code for
| protein sequence (they are expressed). Introns span the
| distance between exons and may contain regulatory or splicing
| information. Areas between genes are referred to as intergenic,
| and also may contain regulatory sequences that affect how genes
| are expressed.
|
| Part of the issue with centromeric or telomeric sequence is
| that not only is it hard to sequence (being super repetitive),
| little is known about what a sequence variant in such an area
| might mean. It's kind of a chicken-and-egg issue: it doesn't
| get much attention because no one knows how to interpret
| variants there, and since no one knows how to interpret
| variants there it doesn't get much attention
| mbreese wrote:
| Just to pile on to the existing comments... if you're getting
| the raw FASTQ files, you will have telomeric and centromeric
| DNA sequences. You just won't necessarily be able to accurately
| align the data. Sequencing those regions is easy... you just
| can't assemble the data into larger contiguous regions because
| of the lack of variation.
|
| And given the consistency of those regions, you will have
| 99(.999)% of all of the information you would need to make a
| copy of your DNA.
|
| There are some regions that are difficult to sequence, but the
| major problem isn't getting the raw sequence, but the alignment
| process.
| gillesjacobs wrote:
| A note on these WGS services: The industry is nacent, DNA
| extraction and the sequencing fail often. You'll be shipping
| samples across the globe and waiting on your data for about 12
| weeks to a few months at best. My advice: If you're not looking
| for a hobby you can follow up on every few weeks, don't buy these
| budget direct-to-consumer services yet.
|
| I heard good things about Sequencing.com, but then again also
| Nebula Genomics when I bought their service end of 2021. I ended
| up asking a refund due to the painfully slow processes and
| communication last week. Dante Labs is a previous pioneer but has
| also fallen from grace with long delays and undelivered data.
| Caveat Emptor.
| torquemodwanted wrote:
| Do you think something like the Oxford Nanopore MinION [0] is a
| viable alternative, assuming you'd want to do just the
| sequencing yourself? I suspect most people wouldn't be able to
| do the prep without proper wet lab training and equipment [1],
| but the starter kit is $1000 for the device, a single flow
| cell, and one rapid sequencing kit (SQK-RAD004).
|
| [0]: https://nanoporetech.com/products/minion
|
| [1]: https://www.youtube.com/watch?v=iS1pz3IhJvU
| aroch wrote:
| 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.
| mbreese wrote:
| Not to mention there is a good chunk of required "extra"
| equipment that is expected (centrifuges, etc) that bring
| the initial cost to well over $1000. You could buy most
| thing used, but some of the reagents could be difficult to
| acquire outside of a traditional lab.
| ejstronge wrote:
| This is not strictly true - there is a transposase based
| prep that does not require special equipment.
|
| Still, ONT users would need to understand how to convert
| raw reads into useable basecalls at loci of clinical
| interest
| xipho wrote:
| I suspect many people that frequent HN could use the MinION
| to generate the raw data, but generating gigabytes of DNA
| reads != assembling a genome. Remember, only this year the
| very _first_ genome for any human was "completed". You're
| going to get thousands of overlapping reads, of varying
| lengths. Then you'll need serious processing power to combine
| these overlaps, then overlap the overlaps, so to speak, and
| on and on. What software to pick, how to parameterize/use it,
| this is the job of post-docs and others who like to tear
| their hair out. I haven't looked lately, but many one-off
| scientific machines have their own propitiatory binary
| versions of the data, for vendor lock in, so that you must
| also buy their crappy software to process it, double check
| that this isn't the case.
|
| When your first run fails, are you willing to pay again as
| much for the kits to run it again (these machines are very
| much following the cheap printer/expensive ink model IMO)?
|
| Once you have some data, do you know how you will BLAST it
| against annotated genomes to figure out if you have mutation
| X? How do you interpret e-scores, etc?
|
| For the OP company, when they say "download the data" do they
| mean the raw reads, or assemblies? Make sure this is spelled
| out (it likely is, I haven't looked lately). Do the
| downloads/service provide adequate metadata on the data
| generation process so that you can tease out errors in reads
| from reality (real single-nucleotide mutations), etc.?
|
| All fun stuff, but only for a _very_ serious hobbyist, so to
| speak.
| aroch wrote:
| 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.
| jefftk wrote:
| I think your typical programmer could automate the
| assembly, even without reading about existing algorithms.
| It isn't much harder than a standard interview question,
| especially if you're willing to use your hardware
| inefficiently?
|
| You aren't trying to sequence the human genome from
| nothing, but instead have a reference genome to work with.
| You take each of the reads you get from the sequencer and
| find where it best matches up with the reference genome.
|
| I think the wet portion is a far bigger challenge for the
| typical computer programmer hobbyist.
|
| (Also I don't think $1,000 will get you, in addition to the
| sequencer, a flow cell sufficient to gather enough reads to
| tell the difference between sequencing errors and
| mutations?)
| topynate wrote:
| I bought the Nebula 30x product and got my results quite
| quickly, in under three months. It's hard to tell if my
| experience is better than average or not, given that people
| tend not to speak up about services when they're delivered on
| time. There may be some issues with the data quality. I
| happened to post about it a couple of hours ago:
| https://www.reddit.com/r/Nebulagenomics/comments/w8013t/rate...
|
| My current best guess is that more data than usual were of
| bacterial origin, but I'll have to learn a bit more
| bioinformatics to test that.
| saxonww wrote:
| Chuckling a little at the prominent "Security Grade: A+" display
| on their privacy page. It's the Qualys score for their site,
| which they are kind of implying is an overall security metric for
| their business. Not very inspiring.
| walnutclosefarm wrote:
| Goes along with a big badge saying they are HIPAA compliant. I
| mean, if they are a covered entity (which is to say, if they
| are providing healthcare services), they have to be HIPAA
| compliant, or be prepared to be fined heavily by the Feds for
| breaking the law. If they are not a covered entity, they don't
| really have any meaningful obligations under HIPAA, so being
| compliant is meaningless.
| exact_string wrote:
| I assume this is yet another sequencing company outsourcing the
| actual sequencing?
|
| >> Do you sell or share my data with anyone?
|
| > No, we do not sell or share your data, including your DNA data,
| with anyone.
|
| However, in their privacy policy:
|
| > Your Personal Information may be shared in the following ways:
|
| > With our service providers, allowing them to provide their
| services to us.
|
| edit:
|
| More clearly stated here:
|
| https://sequencing.com/ordering-dna-test-kit-and-genome-sequ...
|
| > When you purchase the Ultimate DNA Test or Ultimate Genome
| Sequencing test, your test will be processed by our Laboratory
| Partners. We will provide our Laboratory Partner with only your
| basic contact information so that it can send you a DNA
| collection kit; we will not share your billing information with
| our Laboratory Partner but will pass on your payments to them.
| FollowingTheDao wrote:
| > However, in their privacy policy:
|
| That does not mean they are sharing your genetic data, maybe
| just address phone number etc.
|
| I had the WORST experience with Nebula Genomics which ended up
| with them refunding my money after waiting 6 months.
|
| I hope this is not another one of those companies. I still have
| some blank spots I am trying to understand from my 23andMe
| results and this would be great.
| adora wrote:
| I emailed Sequencing.com asking what the difference was
| between them and Nebula Genomics and this is what they wrote
| back:
|
| _(1) Nebula is our laboratory partner, and they sequence
| with high-throughput MGI DNBSEQ-T7 DNA sequencing machines.
|
| (2) They are our laboratory provider, but the product is not
| the same! The whole genome sequencing product sold by Nebula
| on their site is different from the Ultimate Genome
| Sequencing service we offer in some key ways. One big one is
| that our service includes more than $200 in DNA analysis apps
| and reports (such as the Healthcare Pro report designed for
| healthcare providers and the Rare Disease Screen that
| analyzes thousands of rare diseases).
|
| The biggest difference, however, is in the processing of the
| raw genetic data into data files that you can then use to get
| health insights. We have enhanced processing for these kits
| that is able to create insights not available from Nebula
| directly, including enhanced raw data processing through two
| special bioinformatics pipelines that provide comprehensive
| data and analysis of structural variations, copy number
| variations, and mitochondrial heteroplasmy. Both Telomere
| Length and HLA Typing are coming soon and will be
| retroactively added to all past purchases of our Ultimate
| Genome Sequencing service.
|
| This is all fed into our One Genome technology, which allows
| you to do analysis in ways that you can't do anywhere else.
| This technology takes all of your genetic data and turns it
| into an enhanced virtual genome. This advantage of this is
| that you can run analysis on everything all at once, where in
| some other cases you might have separate files that can't be
| analyzed simultaneously.
|
| The long and short of it is that it takes a lot of processing
| to turn raw genetic data into usable data, and then to
| analyze that data. That piece is where we come in, and are at
| the forefront of the field._
| omgwtfbyobbq wrote:
| I believe allofus provides you with your WGS data if you opt into
| receiving it, and it's free.
|
| https://allofus.nih.gov/
|
| My mom did Nebula, which was kind of a pain, but she eventually
| got her results.
| yawnxyz wrote:
| If this is truly WGS then I'm amazed at how it's only a few
| hundred dollars to run.
| adora wrote:
| Potentially sending to China.
| toomuchtodo wrote:
| Feedback if someone from sequencing.com sees this: import from
| 23andme.com doesn't appear to work if you use Sign In with Apple
| for 23andme. Regardless, I love the broker functionality to pull
| data from other sequencing providers. Kudos!
| peter303 wrote:
| Venters company was charging $25K. That included lots of other
| diagnostic tests too. (Venter was the first human sequenced. By
| his own company.)
| bobsmooth wrote:
| The sample report is quite a read.
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