Whole Genome Sequencing(sequencing.com)
sequencing.com
Whole Genome Sequencing
https://sequencing.com/
68 comments
> 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.
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.
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.
(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.
...and seems that Nebula Genomics also outsources their sequencing:
> At its discretion, Nebula may use third-party laboratories to perform DNA extraction, sequencing, and data analysis.
(https://nebulagenomics.zendesk.com/hc/en-us/articles/3600243...)
I would guess the samples are eventually sequenced by BGI although Nebula FAQ (https://nebula.org/faqs/) says they sequence in EU.
> At its discretion, Nebula may use third-party laboratories to perform DNA extraction, sequencing, and data analysis.
(https://nebulagenomics.zendesk.com/hc/en-us/articles/3600243...)
I would guess the samples are eventually sequenced by BGI although Nebula FAQ (https://nebula.org/faqs/) says they sequence in EU.
Oh my...RUN FOR THE HILLS! Seriously, search for the complaints about them on Twitter.
Thank you so much for revealing this to everyone.
Thank you so much for revealing this to everyone.
What happened with Nebula? I have been genuinely considering trying out that service and this is the first negative thing I've seen about it.
It is hard, but if you search you will find countless stories like this:
https://twitter.com/TrentBrown/status/1434246929035055105
https://twitter.com/TrentBrown/status/1434246929035055105
I was scared off from using Nebula when they claimed to secure my data privacy by using a blockchain.
Note FDA rules require them to retain the data for a few years.
Any idea what the reasoning behind these FDA rules is?
European here: I can't wait to use my gdpr superpowers to cause an expectation violation there.
Doesn't the GDPR have an exception for data required for legal reasons?
Anyway, an US lab won't care about it.
Anyway, an US lab won't care about it.
It has some cut outs, but not as many as you would think.
The US lab is marketing to EU customers. They will care about GDPR (heck, they even claim to be compliant on their website).
The US lab is marketing to EU customers. They will care about GDPR (heck, they even claim to be compliant on their website).
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.
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.
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.
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.
It'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/3600358909...
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/3600358909...
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.
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
[0]: https://nanoporetech.com/products/minion
[1]: https://www.youtube.com/watch?v=iS1pz3IhJvU
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.
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.
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
Still, ONT users would need to understand how to convert raw reads into useable basecalls at loci of clinical interest
Does 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.
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.
If 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
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.
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.
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.
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.
I think your typical programmer could automate the alignment, 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?)
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?)
> your typical programmer could automate the assembly
Alignment. You could easily automate alignment of raw sequencing reads to their position in the reference genome. From there, even variant calling (finding your individual changes from the reference) is pretty easy as well.
Assembly is a bigger challenge that takes the raw reads and puts them together into a larger (graph) structure. This is usually de-novo, but could be able to be done with a reference as well. But this is not really something that is routine or possible with 30X sequence coverage to the degree one would expect.
The wet-lab portion isn't terrible and anyone with skills making anything (soldering, for example), should be able to do it -- once you figured out some of the jargon.
The bigger challenge someone not trained in this would have is interpreting the variations that you'd find. This can be quite difficult to figure out if an A>C at a particular position is meaningful or not. Again, much of these can be filtered using existing tools, but even then, it can be quite difficult to interpret results.
Alignment. You could easily automate alignment of raw sequencing reads to their position in the reference genome. From there, even variant calling (finding your individual changes from the reference) is pretty easy as well.
Assembly is a bigger challenge that takes the raw reads and puts them together into a larger (graph) structure. This is usually de-novo, but could be able to be done with a reference as well. But this is not really something that is routine or possible with 30X sequence coverage to the degree one would expect.
The wet-lab portion isn't terrible and anyone with skills making anything (soldering, for example), should be able to do it -- once you figured out some of the jargon.
The bigger challenge someone not trained in this would have is interpreting the variations that you'd find. This can be quite difficult to figure out if an A>C at a particular position is meaningful or not. Again, much of these can be filtered using existing tools, but even then, it can be quite difficult to interpret results.
> Alignment
Whoops; fixed!
> This can be quite difficult to figure out if an A>C at a particular position is meaningful or not.
What about https://promethease.com ?
Whoops; fixed!
> This can be quite difficult to figure out if an A>C at a particular position is meaningful or not.
What about https://promethease.com ?
Promethease isn’t a bad place to start. I don’t know how it works with uncharacterized variants, but it would be a good place to start.
Note: I do this work for cancer genomes (WGS, tumor and germline). Promethease is not something that I use for annotations, but my workflows are significantly more complex.
The biggest thing I’d look out for is mindset. Biology is very different from comp sci. CS is very deterministic. You change something here, you get a result there. Biology, on the other hand, is very messy. There are compensation mechanisms on top of compensation mechanisms, and everything favors life. If you see a deleterious variant, that still doesn’t mean you’ll see a phenotype (effect on you). It’s quite a different world and can be very scary if you are looking at your own data.
Note: I do this work for cancer genomes (WGS, tumor and germline). Promethease is not something that I use for annotations, but my workflows are significantly more complex.
The biggest thing I’d look out for is mindset. Biology is very different from comp sci. CS is very deterministic. You change something here, you get a result there. Biology, on the other hand, is very messy. There are compensation mechanisms on top of compensation mechanisms, and everything favors life. If you see a deleterious variant, that still doesn’t mean you’ll see a phenotype (effect on you). It’s quite a different world and can be very scary if you are looking at your own data.
I think the biggest reason it's scary is a statistics literacy problem: everyone has lots of mutations, and a mutation is much more likely to be bad than good. This means that when people look at a Prometheus report and see a long list of deleterious mutations they tend to take it, overall, as bad news: so much red! But since that's what you would expect to see even before looking at the report it shouldn't move your opinion either way.
My prior is that any random variant would likely do nothing. It’s all about location, location, location. First off, a variant would need to be in a gene to do something (not entirely true, but a good enough approximation). Then, the variant would need to be in a coding region/exon. Finally, the variant would need to change the amino acid (there is a Twitter/biorxiv war going on about this specifically now). You have approximately 0.1% unique DNA sequence compared to someone else. But there are 3 billion bp in the human genome. So that’s an expected 3 million variants. And that’s just to start. And just to add to the prior probabilities — you’re probably living, right? So, whatever variants you might find haven’t been lethal yet! (Even better if you’ve made it to adulthood!)
And to complicate things further, one variant in a gene could do nothing if the other copy is still good. Even if you have two bad variants in a single gene, they might be on the same allele (from the same parent). In which case, you still have one good copy! It’s like how Iceman got hit twice in the same engine at the end of the original Top Gun. He still had one good engine to get home. For many genes, that’s all you need. For others, you might not even need one good copy as other genes could take over the same job.
Yes, there are some variants that you don’t want to see. Things that might indicate high likelihood of disease down the road. But even that is bound by statistical probabilities. Good news — some of those can’t be seen by this type of sequencing.
You’re absolutely right though — it can be scary. After looking at many genomes, it can be amazing that we all work as well as we do.
And to complicate things further, one variant in a gene could do nothing if the other copy is still good. Even if you have two bad variants in a single gene, they might be on the same allele (from the same parent). In which case, you still have one good copy! It’s like how Iceman got hit twice in the same engine at the end of the original Top Gun. He still had one good engine to get home. For many genes, that’s all you need. For others, you might not even need one good copy as other genes could take over the same job.
Yes, there are some variants that you don’t want to see. Things that might indicate high likelihood of disease down the road. But even that is bound by statistical probabilities. Good news — some of those can’t be seen by this type of sequencing.
You’re absolutely right though — it can be scary. After looking at many genomes, it can be amazing that we all work as well as we do.
I used https://genvue.geneticgenie.org/ – it's free and I've found it to be the best starting point for further investigation. I also have access to Nebula Genomics' tools as part of the package I paid for. Yes, there is a fear factor when you're looking at your own genome. On the other hand, seeing you have an increased risk of something can be quite motivating to make some compensating lifestyle changes.
This is patronizing to say a programmer could write algorithms that are complex enough there is a major dedicated to it at most universities. You have to realize that you're probably thinking of using a naive solution that produces an extra another order of runtime complexity for datasets that reach 100GB easily.
The complexity comes from trying to do it efficiently, both in using the hardware well and in squeezing as much data as possible out of the sequencing reads you have. But if you relax both of those it's a manageable problem for an amateur.
Efficiency is crucial though. Running cutting edge published alignment tools running on the best AWS server will take hours to process a 30x human genome. An amateur approach for NGS on anything but a model organism would take years or decades to finish alignment on current hardware.
Part of why the best tools take so long is that they are trying really hard, but an amateur approach can do a decent job in far less time by trying less hard. (No fuzzy matching, only exact matching on shortish chunks)
Additionally, we're talking about nanopore data, which is much longer reads, and so is going to be computationally a bit easier.
Additionally, we're talking about nanopore data, which is much longer reads, and so is going to be computationally a bit easier.
I 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.
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.
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.
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.
https://allofus.nih.gov/
My mom did Nebula, which was kind of a pain, but she eventually got her results.
I'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.
this looks rad, thanks for sharing.
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!
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 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/
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/
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?
Thanks, I've fixed the mistake s/exon/intron/.
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
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
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.
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.
Then that's an annoying ambiguity in the word sequencing.
If sequencing is the technique, then it's true that you can sequence anywhere in the DNA, but the technique will not always be able to give you the actual DNA sequence, in particular for centromeres or telomeres.
If sequencing meant "find out the DNA sequence", which is what people are actually buying, then it is just false that you can "sequence" anywhere in the chromosomes.
If sequencing is the technique, then it's true that you can sequence anywhere in the DNA, but the technique will not always be able to give you the actual DNA sequence, in particular for centromeres or telomeres.
If sequencing meant "find out the DNA sequence", which is what people are actually buying, then it is just false that you can "sequence" anywhere in the chromosomes.
No, it does give you the sequence… what it doesn’t give you is the context. The WGS data we’re talking about here only give you two 150bp fragments. You know these fragments are 100-300bp away from each other, but that’s it.
There are other techniques for getting more of the context, but that’s not the WGS we are talking about here.
It’s like copying pages from a book, but without page numbers. And some pages might be copied more than once. Or not at all (Poisson statistics FTW!). You can get fragments of stories, and can probably get the gist of the plot. But this might not give you an exact copy of the full book, in the right order.
To keep going with the analogy — what you’re asking for (telomeres and centromeres) would be the equivalent of placing every “this page left intentionally blank” page in the right place. Even though, they are all quite similar. You will be able to “copy” (sequence) each of these pages, but putting them in the right order is still difficult.
There are other techniques for getting more of the context, but that’s not the WGS we are talking about here.
It’s like copying pages from a book, but without page numbers. And some pages might be copied more than once. Or not at all (Poisson statistics FTW!). You can get fragments of stories, and can probably get the gist of the plot. But this might not give you an exact copy of the full book, in the right order.
To keep going with the analogy — what you’re asking for (telomeres and centromeres) would be the equivalent of placing every “this page left intentionally blank” page in the right place. Even though, they are all quite similar. You will be able to “copy” (sequence) each of these pages, but putting them in the right order is still difficult.
You sum up exactly the problem: the WSG technique does not give the whole global sequence of bases, from telomere to telomere through all of the centromere and for each chromosome branch.
This is what I would like to see as an affordable product: get the whole sequence, so that ultimately one could theoretically re-synthesize their own chromosomes in the future. And get it now that we are still young and there is not too much damage in the DNA, information to be stored for later.
One point in what you wrote: the blank pages (introns) can be really important (like for gene expression regulation, through chromatine folding, or promoters of transcription), we just can't be sure, and that's why it is paramount (when thinking of chromosomes synthesis applications) to have it all.
About the specifics of our discussion: Again, ambiguity! Because we're saying the same thing.
When I say it does not give the sequence, I mean the whole sequence (not only local subsequences), which means including the context.
(Although the notion of context is actually meaningful only if we are talking about local subsequences, as the global sequence is the context (or includes the context, if we reduce "context" to mean the reference global sequence against which the subseqs are aligned)).
Of course with your meaning you are right.
This is what I would like to see as an affordable product: get the whole sequence, so that ultimately one could theoretically re-synthesize their own chromosomes in the future. And get it now that we are still young and there is not too much damage in the DNA, information to be stored for later.
One point in what you wrote: the blank pages (introns) can be really important (like for gene expression regulation, through chromatine folding, or promoters of transcription), we just can't be sure, and that's why it is paramount (when thinking of chromosomes synthesis applications) to have it all.
About the specifics of our discussion: Again, ambiguity! Because we're saying the same thing.
When I say it does not give the sequence, I mean the whole sequence (not only local subsequences), which means including the context.
(Although the notion of context is actually meaningful only if we are talking about local subsequences, as the global sequence is the context (or includes the context, if we reduce "context" to mean the reference global sequence against which the subseqs are aligned)).
Of course with your meaning you are right.
> One point in what you wrote: the blank pages (introns) can be really important
Yes it is -- which is why you get that data with WGS. Seriously, the only sequence that is really difficult to get is around centromeres and telomeres (and some smaller repetitive regions). The other issues that we have with germline sequence is when there are novel structural rearrangements, but with enough depth (or a slightly different technology), we can see those too.
> Because we're saying the same thing
I don't think we are... you keep misusing some of the key terms here. Those "blank pages" weren't introns, they were the ends of the chromosomes (telomere) and the middle (centromere). Those are hard and repetitive. The rest -- the parts you'd really care about if you wanted to do some late life genetic replacement -- are largely covered.
For the context, we use a reference genome. We then look to see where the smaller subsequences align to the the reference genome. This isn't a wet-lab technique, but a dry-lab technique. With enough copies of the smaller sequences (coverage), we can establish what the underlying "full" sequence is. Given sufficient depth, this is a solved problem at this point. The only issues are depth and cost (of sequencing and processing/storage). I left this part out earlier because it wasn't what you were asking about.
We don't have a technique that you can spit in a tube and get the entire sequence of a chromosome all at once. They are simply too long for that to be practical. We do have technology to get a lot (millions) of shorter reads that we can align back to a reference (the company we are talking about in the post does this). We also have technology to get very long sequences (up to 2Mb), but they aren't as accurate as shorter reads. But, if you merge the two together, it can get you all the data you're really after here, even without a reference genome.
Yes it is -- which is why you get that data with WGS. Seriously, the only sequence that is really difficult to get is around centromeres and telomeres (and some smaller repetitive regions). The other issues that we have with germline sequence is when there are novel structural rearrangements, but with enough depth (or a slightly different technology), we can see those too.
> Because we're saying the same thing
I don't think we are... you keep misusing some of the key terms here. Those "blank pages" weren't introns, they were the ends of the chromosomes (telomere) and the middle (centromere). Those are hard and repetitive. The rest -- the parts you'd really care about if you wanted to do some late life genetic replacement -- are largely covered.
For the context, we use a reference genome. We then look to see where the smaller subsequences align to the the reference genome. This isn't a wet-lab technique, but a dry-lab technique. With enough copies of the smaller sequences (coverage), we can establish what the underlying "full" sequence is. Given sufficient depth, this is a solved problem at this point. The only issues are depth and cost (of sequencing and processing/storage). I left this part out earlier because it wasn't what you were asking about.
We don't have a technique that you can spit in a tube and get the entire sequence of a chromosome all at once. They are simply too long for that to be practical. We do have technology to get a lot (millions) of shorter reads that we can align back to a reference (the company we are talking about in the post does this). We also have technology to get very long sequences (up to 2Mb), but they aren't as accurate as shorter reads. But, if you merge the two together, it can get you all the data you're really after here, even without a reference genome.
Ok, thank you!
So, this means there is hope for getting the data required for a full DNA restoration:
- bases near the telomeres, difficult to get (i.e. difficult to locate) with standard sequencing, can be sequenced (and located) with long-sequence sequencing (but this kind of GWS cheap service doesn't use long-sequencing right?)
- for bases around centromeres, do we assume that they are surrounded by a sea of nothingness, and that relying on a unique reference genome's centromere is enough? Isn't that risky, are we really sure that individual variations do not matter for centromeres?
My aim is to imagine a future where any defects, including centromeres, could be fixed, if necessary by regenerating whole chromosomes. Using data gathered now and safely stored.
So, this means there is hope for getting the data required for a full DNA restoration:
- bases near the telomeres, difficult to get (i.e. difficult to locate) with standard sequencing, can be sequenced (and located) with long-sequence sequencing (but this kind of GWS cheap service doesn't use long-sequencing right?)
- for bases around centromeres, do we assume that they are surrounded by a sea of nothingness, and that relying on a unique reference genome's centromere is enough? Isn't that risky, are we really sure that individual variations do not matter for centromeres?
My aim is to imagine a future where any defects, including centromeres, could be fixed, if necessary by regenerating whole chromosomes. Using data gathered now and safely stored.
This really is putting the cart before the horse though, we will have whole genome assembly technology long before we understand functional genomics well enough to do the type of restorative genetic engineering that you propose.
Well you're right but the idea of getting all of the DNA information is precisely to be sure to not rely on what we think we know, so that if in the future we discover that previously thought useless parts are meaningful we would already have them in store (gathered long before the DNA gets damaged by age).
Once we have everything, we can apply additional knowledge to this data as soon as it is discovered and without needing to do more sequencing.
Once we have everything, we can apply additional knowledge to this data as soon as it is discovered and without needing to do more sequencing.
I 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.
Anecdote, 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.
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.
If this is truly WGS then I'm amazed at how it's only a few hundred dollars to run.
I 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.
If 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.
I 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.
Do Sequencing.com provide financial compensation in the event of breach of the service contract?
The sample report is quite a read.
Venters company was charging $25K. That included lots of other diagnostic tests too. (Venter was the first human sequenced. By his own company.)
>> 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.