I really like how this article was written. This is often hyped as the $100 genome sequence, but as the article frames it, its more of a genetic map for $100.
Very promising tech, but we still have a ways to go before the $100 full-genome sequence. Until then, genome-wide mapping for $100 will lead us to further breakthroughs.
This article is definitely about the potential to sequence people's genomes for $100. Part of the confusion may be that a process called mapping is a necessary step to figure out where each of the hundreds of millions of ~200 nucleotide reads for a genome came from - you "map" them back to the human reference genome for comparison.
I have registered for All of Us but have yet to be called in for an in-person visit. I live in central NJ but it seems the closest medical centers are in NYC.
tbf their website is marketing 0.4x genome coverage for $99 coverage, and the "possible free sequencing and other rewards" is all research-institute-interest dependent.
which makes me feel better about the (obviously also subsidised by potential research use) $199 full genome Black Friday deal I just ordered...
If I find the VCF insufficient I can always pay another $60 for a disk with the BAM file on which still works out as better value. Am more worried about their less than stellar customer service reputation tbh.
I joined the program a week ago. Did all surveys and I'm currently sitting on 550 credits.
To qualify for a their main genome sequencing, "Low-pass Whole Genome Sequencing (0.4x coverage)", you need 1000 credits or $99.
But if you want whole genome sequenced, you need to order their flagship product, "Clinical-grade Whole Genome Sequencing (30x coverage)". Which is greyed out on their website currently. And I'm not even going to guess how many credits is that going to cost.
As a point of reference, the rate for ~30X human whole-genome sequencing is about $1,300, though this number depends on a few factors like the sequencing machine one uses.
There are reasons to sequence an individual multiple times: tracking their microbiome, tracking the genetic evolution of their tumor, looking at gene expression, etc. There's not much value in sequencing someone's genome over and over again though.
Additionally, there's a lot more to sequence besides just human. Illumina does genotyping for agriculture, they supply 23andme and Ancestry with their SNP chips, sequencing for forensic applications, etc.
> There's not much value in sequencing someone's genome over and over again though.
There's plenty of value to each custodian that gets their own copy though, just like every cloud company wants their own copy of your name, email, and physical address.
a) we generally don't have access to the records of any other health systems in the area.
b) we generally assume the older data is stale. In the case of omics: did they keep the unaligned reads? What version of the genome was it aligned against? Was it a graph alignment? What depth? Did my geneticist approve of this methodology? The SNP evaluation? The variants? This goes all the way down. They'll question what generation of instrument produced the data, the duty cycles on the instrument, and on, and on, and on.
Agreed. The somatic genome changes a tiny amount every cell division (1 miscopy per 100 million bases) due to spontaneous mutations, gene expression and occasional recombination. These may be useful for diagnosing disease and determining effective drug treatments.
It'll be interesting to see if other things are sequenced as well. Histone mapping comes to mind. Histones are responsible for packing the DNA and exposing different segments. This is one major factor in why we have some many different types of cells with the same DNA.
You could also sequence bacteria, viruses, tumors, and many many more. It could also impact agriculture as well. Once sequencing becomes cheap enough, I think it'll extend far beyond a one and done test per person.
In India/China with population in Billions, these tests aren't available or affordable.
No company is building Genome Databank through user-friendly collection of saliva.
I don't know why 23andme doesn't have local offering in India.
Who will courier sample to an international lab? Specially, from a country like India where sending anything out or importing in is just too difficult.
23andme isn't expensive for me but they don't offer pickup service in India?
>>In India/China with population in Billions, these tests aren't available or affordable.
Probably the government will be offering them for free--and mandatory. In China, I'm almost certain that it's just a matter of years. Driving license, passport? Let's swab a bit the inside of your cheek.
Yes this is the biggest issue. If I can send off my DNA with a $100 bill and get a computer generated report encrypted and sent back to me with no trace left behind of my DNA or identity then, sure. Otherwise, I can wait.
This article written by a non-expert. The cost of genome sequencing has been relatively flat in the last couple of years; and Illumina, being the monopoly, has no incentives to reduce the cost of sequencing. Also; despite what some commenters seem to think, it doesn't get to keep the data people sequence on its devices, any more than your printer company owns the content of what you print.
One would likely get sequenced many times over a lifetime - a so-called "liquid biopsy", meaning sequencing circulating DNA & tumor cells in your blood, can catch aberrant cancer-related mutations earlier and help predict cancer / catch it earlier. Once this is mature, people will likely take this test every 5 years etc.
I think the BGI/MGI will probably provide an incentive. Recent reports suggest that their instruments are starting to produce reasonable data (80% > Q30).
Illumina have ~90% [1] markup on consumables. They can afford to reduce their price to $100 per genome (and have said they will). With the pressure applied by the BGI I can certainly see this happening.
Oxford Nanopore is the disruptive company putting pressure on Illumina. They're racing to the $100 genome and Nanopore is the newer, cheaper tech that Illumina is trying to mimic.
Illumina is a bloated monopoly that hasn't lowered its prices in years. They are anti-innovation.
Oxford Nanopore is currently far more expensive and lower quality than Illumina sequencing. A single minion run costs $500. It doesn’t even provide a single x1 complete human genome.
You can currently get a complete x30 human genome using Illumina or BGI sequencing for similar cost.
It’s not clear that Oxford Nanopore can reduce costs. It’s not even clear to me that the Minion runs are currently sold at a profit. The chips are quite big, and not easily reused. Fabrication costs are likely significant.
Not there are several vastly different genetic identity tests. You would game each kind differently.
The oldest was blood types. This can in sone, but not all situations exclude paternity. Next more detailed is antigen matching for transplants. These have a hereditical character.
Police forensics use about 30 markers in the non-coding DNA. Good enough for identity matching, but not for disease or ancestry.
The ancestry companies look at seceral thousand markers via custom silicon-biochemical chips.
Then there is exome full sequencing. This is just 2% the codes for protein.
Finally full sequencing of 90%+ plus of all bases in the genome. Depending on the techniques some have difficulty with repeated DNA sequences, usually in the junk areas.
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[ 2.8 ms ] story [ 102 ms ] threadVery promising tech, but we still have a ways to go before the $100 full-genome sequence. Until then, genome-wide mapping for $100 will lead us to further breakthroughs.
This article is definitely about the potential to sequence people's genomes for $100. Part of the confusion may be that a process called mapping is a necessary step to figure out where each of the hundreds of millions of ~200 nucleotide reads for a genome came from - you "map" them back to the human reference genome for comparison.
Source: https://www.biospace.com/article/releases/nebula-genomics-la...
Have you had a chance to do so?
which makes me feel better about the (obviously also subsidised by potential research use) $199 full genome Black Friday deal I just ordered...
That's an amazing sequence of words.
I joined the program a week ago. Did all surveys and I'm currently sitting on 550 credits. To qualify for a their main genome sequencing, "Low-pass Whole Genome Sequencing (0.4x coverage)", you need 1000 credits or $99. But if you want whole genome sequenced, you need to order their flagship product, "Clinical-grade Whole Genome Sequencing (30x coverage)". Which is greyed out on their website currently. And I'm not even going to guess how many credits is that going to cost.
https://us.dantelabs.com/blogs/news/dante-labs-black-friday-...
In addition to the variant containing VCF file, on request they offer the raw read data on hard disk in FASTQ and BAM format (mapped I presume).
Doesn't a 100$ test put a cap of 100$ per person?
Once sequenced, you don't need to sequence your DNA again, right?
Additionally, there's a lot more to sequence besides just human. Illumina does genotyping for agriculture, they supply 23andme and Ancestry with their SNP chips, sequencing for forensic applications, etc.
There's plenty of value to each custodian that gets their own copy though, just like every cloud company wants their own copy of your name, email, and physical address.
b) we generally assume the older data is stale. In the case of omics: did they keep the unaligned reads? What version of the genome was it aligned against? Was it a graph alignment? What depth? Did my geneticist approve of this methodology? The SNP evaluation? The variants? This goes all the way down. They'll question what generation of instrument produced the data, the duty cycles on the instrument, and on, and on, and on.
You could also sequence bacteria, viruses, tumors, and many many more. It could also impact agriculture as well. Once sequencing becomes cheap enough, I think it'll extend far beyond a one and done test per person.
https://www.genomicsengland.co.uk/about-genomics-england/the...
and there are many other similar efforts underway.
No company is building Genome Databank through user-friendly collection of saliva.
I don't know why 23andme doesn't have local offering in India.
Who will courier sample to an international lab? Specially, from a country like India where sending anything out or importing in is just too difficult.
23andme isn't expensive for me but they don't offer pickup service in India?
Probably the government will be offering them for free--and mandatory. In China, I'm almost certain that it's just a matter of years. Driving license, passport? Let's swab a bit the inside of your cheek.
India also has https://www.latimes.com/world/la-fg-india-database-2017-stor... ...DNA is the next logical step
https://www.wired.com/2016/02/gene-sequencing-goliath-wants-...
https://www.forbes.com/sites/matthewherper/2014/08/20/flatle...
So this prediction is based on business principles, not new technology? I'm skeptical.
At least I'm in the EU, thank god for the GDPR.
One would likely get sequenced many times over a lifetime - a so-called "liquid biopsy", meaning sequencing circulating DNA & tumor cells in your blood, can catch aberrant cancer-related mutations earlier and help predict cancer / catch it earlier. Once this is mature, people will likely take this test every 5 years etc.
Illumina have ~90% [1] markup on consumables. They can afford to reduce their price to $100 per genome (and have said they will). With the pressure applied by the BGI I can certainly see this happening.
[1] http://41j.com/blog/2018/11/illumina-consumables-are-90-prof...
Illumina is a bloated monopoly that hasn't lowered its prices in years. They are anti-innovation.
You can currently get a complete x30 human genome using Illumina or BGI sequencing for similar cost.
It’s not clear that Oxford Nanopore can reduce costs. It’s not even clear to me that the Minion runs are currently sold at a profit. The chips are quite big, and not easily reused. Fabrication costs are likely significant.
I really doubt that you want to do the latter.
The oldest was blood types. This can in sone, but not all situations exclude paternity. Next more detailed is antigen matching for transplants. These have a hereditical character.
Police forensics use about 30 markers in the non-coding DNA. Good enough for identity matching, but not for disease or ancestry.
The ancestry companies look at seceral thousand markers via custom silicon-biochemical chips.
Then there is exome full sequencing. This is just 2% the codes for protein.
Finally full sequencing of 90%+ plus of all bases in the genome. Depending on the techniques some have difficulty with repeated DNA sequences, usually in the junk areas.