9 ms·
Whole Genome Sequencing
- superb-owl 4y agoI gave my DNA to 23 and Me at the age of 19 or so. They won't dispose of the data. They say it's due to California law, which I'm sure is not untrue, but it feels like they're taking advantage of it.
- nibbleshifter 4y agoIf you want to really fuck with them, travel, and have some money: briefly relocate to an European country with mandatory residence registration (Germany) for a month. Register as a resident. Apply GDPR. Leave.
- toomuchtodo 4y agoFeedback 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!
- gillesjacobs 4y agoA 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 4y agoDo 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 https://nanoporetech.com/products/minion [1]: https://www.youtube.com/watch?v=iS1pz3IhJvU https://www.youtube.com/watch?v=iS1pz3IhJvU
- aroch 4y agoNot 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 4y agoNot 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 4y agoThis 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
- mbreese 4y agoDoes it still require a pipettor, or could it work with just a transfer pipet? Their field kit should probably be as minimal as it could be. Last I looked into it, it was a minimal set of extra equipment -- votexer, centrifuge, etc... nothing unusual for a bio lab. And even most of that could be handled with a good snap of the wrist, if you weren't trying to be super precise.
- ejstronge 4y agoIf one is patient, the only tool needed in the wet lab is a transfer pipettor and a scale - I think this could be done without a micropipettor
- xipho 4y agoI 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.
- topynate 4y agoI 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_read_depth_and_reads/ 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.
- mbreese 4y agoIt's hard to tell what the 12Mb of sequence they are calling "other" is. It could be bacterial, or a decoy contig that is used to capture low-quality reads. Sometimes you'll see reference sequences also include things like EBV. Or it could be the ALT assemblies that represent different ways of putting together the reference (like HLA differences). The fact that you got 39X raw reads is pretty good. Also, it is usually called hg38, not hs38... I'm not sure where that came from. If you want to be super accurate, you could also use GRCh38, but there are sometimes subtle differences between the two. https://gatk.broadinstitute.org/hc/en-us/articles/360035890951-Human-genome-reference-builds-GRCh38-or-hg38-b37-hg19 https://gatk.broadinstitute.org/hc/en-us/articles/3600358909...
- aroch 4y agoEh, 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.
- seydor 4y agoI gotta be honest, considering how you still can't get 23andme health reports in europe because of regulations, i got my 30x DNA just in case this gets outlawed in the future as well.
- saxonww 4y agoChuckling 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 4y agoGoes 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.
- yawnxyz 4y agoIf this is truly WGS then I'm amazed at how it's only a few hundred dollars to run.
- peter303 4y agoVenters company was charging $25K. That included lots of other diagnostic tests too. (Venter was the first human sequenced. By his own company.)
- henearkr 4y agoImportant 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 introns (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! Edited: s/exon/intron/
- aroch 4y agoI 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?
- henearkr 4y agoThanks, I've fixed the mistake s/exon/intron/.
- brofallon 4y agoJust 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
- exact_string 4y agoI 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-sequencing-kit-terms-and-conditions 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 4y ago> 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 4y agoI 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 4y agoI believe allofus provides you with your WGS data if you opt into receiving it, and it's free. https://allofus.nih.gov/ https://allofus.nih.gov/ My mom did Nebula, which was kind of a pain, but she eventually got her results.
- riffic 4y agothis looks rad, thanks for sharing.
- elektor 4y agoI've done both Sequencing.com and All of US WGS so I can chime in here. Sequencing.com had a pretty quick turnaround whereas Im still waiting for the All of Us results, so far they've only given me very generic results like if I like cilantro. That said, Sequencing.com was $349 and All of Us was free, they even gave me a gift card for donating my DNA + urine sample.
- bobsmooth 4y agoThe sample report is quite a read.
- 2snakes 4y agoI bought this last year. Great apps, great integration, and they promise to protect and store your data. I learned some things about MTHFR and curcumin.
- geoffeg 4y agoI always thought it'd be cool to get my whole genome sequenced and keep a copy in my wallet. I don't know why but having a copy of my source code in my pocket seems cool.
- protocontrol 4y agoDo Sequencing.com provide financial compensation in the event of breach of the service contract?
- seventytwo 4y agoAnecdote, but I recently had to deal with WGS for medical reasons. We ended up doing a commercial provider yo expedite the process, and it cost about $2000, with results and interpretation in 1 month. I’m skeptical that Sequencing provides the same level of a) WGS fidelity, and b) the same level of interpretation and cross reference of alleles to known or suspected pathogenic variants.