Is @NebulaGenomics using @MGI_BGI for their 30x 2x150bp #WGS genome sequencing? Image
I received an email from @NebulaGenomics today, with a discount code for a $299 genome sequencing offer. Which made me wonder: are they using the already cheaper @MGI_BGI #DNBSEQTx sequencing for this? It would mean they can run it at cost or make a small profit from it.
Then you realise there is "analysis" charge on top of the $299 which you can't untick, so the $299 #WGS 30x genome goes up to $499. Still, at $499, you would find it difficult to make money if you were @NebulaGenomics and you were using something like an @illumina #NovaSeq
as the list price for a genome on each #NovaSeq #S4 kit is around $600. So the only option to be able to run this and not make a loss is to go for @MGI_BGI #DNBSEQTx: send 10E5-10E6 samples to MGI Shenzhen, and have them sequenced on their factory-like Tx system: ImageImage
Would @NebulaGenomics have to disclose that their samples are being sent to MGI Shenzhen for sequencing? They are the company that pioneered Homomorphic Encryption for genomic data, so in terms of data privacy, there shouldn't be a *technical* reason to complain,
but maybe there is a compliance requirement for biological/DNA samples being sent, say, from the US to China regardless of how they are used or profiled. Happy to learn more on this, if someone knows the details.
The other option, and this wouldn't be a surprise having heard the way George Church describes the @NebulaGenomics model in interviews, is that they are making a small loss for every genome, but the homomorphic encryption method (#crypto #genomics) that they are using is building
a large #WGS database that can be mined for new drug targets, low-frequency variant identification or similar purposes. This large database, which is inherently encrypted at source, would allow @NebulaGenomics to follow the #23andMe model of reselling the data to large parties.
The difference here is that @23andMe only (or mostly) has profiles for around 1M common SNPs, and can't give any information on low-frequency variants or private SNPs, as one can do with 30x #WGS approaches.

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More from @AlbertVilella

3 Mar
As we approach Q30+ on now 4 competing platforms, 2 short read and 2 long read platforms, it's a useful reminder that only PCR-free preps benefit from high quality base-calling, as any PCR-based method incorporates errors wrt the original material.
More importantly, any PCR-based method devised so far also erases #epigenetic marks, which can only be read in conjunction with the 4-base alphabet if it's from a PCR-free method.
So if your application where to benefit from, say, a Q33 better than a Q31 modal base-calling, first ask yourself: have I got enough DNA for a PCR-free prep?
Read 4 tweets
2 Mar
My highlights of the @10xGenomics #Xperience2021 event. The list of products keeps growing, I would highlight Chromium Connect as an underappreciated tool to bring the products up another level of throughput. Important as with #NGS, it won't take long to go from n=1 to n=96+. Image
#CellPlex species-agnostic multiplexing up to 12 samples: not dissimilar to products such as TotalSeq, but baked-in so that it's been tested to work with the rest of the workflow. Image
Going close to 1M cells, the #ChromiumX brings about 100x fold throughput increase, all marked with 'HT' in the Kits. I'd be interesting to know how the different #BodyAtlas projects embrace this and for what. ImageImage
Read 31 tweets
28 Feb
There are a bunch of Twitter accounts, real or fake to some extend, doing the rounds every time someone tweets about #NGS #genomics or #LiquidBiopsy. They seem clearly wanting to hype a certain listed company
in a pump-and-dump fashion, which is not new, and existed before the GameStop/Robin Hood saga. I chose to mute the accounts, so my threads are not polluted from these accounts. I may start blocking them if it gets worse.
I am not muting the ticker for the company itself, as I am genuinely interested in following their developments, and they are not responsible for the behaviour of the pump-and-dump accounts.
Read 5 tweets
18 Feb
A more polished thread on #epigenomic #biomarkers for #LiquidBiopsy and #CancerScreening:
Epigenomic biomarkers are becoming more established for #LiquidBiopsy and #CancerScreening, and we have seen the big players positioning themselves in this #epigenomics race recently.
Catching signs of #cancer early is crucially important to the disease management and survival rates, so the question is: how can we find out if there is something wrong going on early enough, ideally in a low-cost assay that can be performed regularly on healthy individuals?
Read 39 tweets
17 Feb
@sbarnettARK Epigenomic biomarkers are becoming more established for #LiquidBiopsy and #CancerScreening, and we have seen the big players positioning themselves in this #epigenomics race recently.
@sbarnettARK Catching signs of #cancer early is crucially important to the disease management and survival rates, so the question is: how can we find out if there is something wrong going on early enough?
@sbarnettARK The first generation of high-throughput technologies was predicated on finding mutated (tumor) DNA in the individual's body (somatic), different from their (normal) DNA. Tumor/Normal (T/N) comparisons of the individual's samples, biopsies or ctDNA will indicate if there
Read 38 tweets
25 Jan
We are not far away from routinely #genome sequencing every newborn suspected of having a rare/hereditary disorder.
In fact, there will be a point, especially in single-payer health care systems, where it'll be logistically preferable to routinely #genome sequence every newborn.
What will it take? Management, machines, and money (3M), in that order:
1/ A management system that handles sample collection, carries on the sequencing effectively, and makes the result available: we are not far away from this in, e.g. the UK's (@NHS+Wales/Scotland/NI).
We are much better at this now than, say, 1-2 years ago. See a successful system of coordinating this for lower throughput sequencing but high numbers of samples in #COVID19
Read 12 tweets

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