I have datasets and upgraded conversions from a 2015 23andme sample. I have submitted these datasets to Promethease a few times and understand the benefits and risks of various interpretations but have decided to obtain a whole or mostly whole, health-focused analysis based on a new sample.
When I review vendors, I see marketing hype, upsell, and vagary, Can anyone recommend a good company that produces a decent dataset (it doesn’t need to be based on as many iterations as is common for research samples – 30 or 100 is typical) and gives me full access to a standardized dataset (VCF preferred) that i can download at any time? A standardized datafile that I own is most important because I want to submit it to Promethease.
I’m in the same boat as Rob.
Genome via 23&Me and Promethase gone so far.
What I’d like is to get some polygenic risk scores.
Don’t really want to put my genome data via any open AI.
Advice?
As a Medical Geneticist, I’d go with Nebula Genomics. They have several tiers of whole genome sequencing for reasonable prices and then full evaluation. This company was essentially started by George Church. Click around their website and see if it is what you are looking for. These days it is most cost effective to do a whole genome (rather than just SNP’s or exome) and then reanalyze the data periodically as new scientific papers come out describing new disease associations. Nebula’s website has these options. https://nebula.org/
Thank you. I looked at their website as well as their other company (DNA Complete) that apparently sells the whole genome sequencing. The only thing I was less than clear on was whether you could pay for the sequencing and then download your compressed files with or without availing yourself of their subscription reporting services. These services might be fine but I want to ability to analyze my data on several platforms over time without it being tied to the company that dis the sequencing.
Yes Nebula provides the raw sequence, (FASTQ), aligned files (CRAM/BAM), and VCF formats. You can clarify how to access all this when you sign up. I believe the files are automatically archived (because they are huge) so you have to go through a few steps on their website to de-archive and download them.
I’m not affiliated with Nebula, nor have I had my genome done by them. I did my genome as a control in my lab. It’s worth considering not just going with their lowest coverage offer but getting something closer to 5-10x coverage for reliability. I wouldn’t necessarily subscribe to a subscription service for periodic reanalysis but I would welcome their initial analysis, probably one of the more thorough analysis tools available.
Also, re polygenic disease, this is still a nut being cracked. Genome sequencing is more about risk factors, and dominant and recessive disease risk at the moment but polygenic diseases should be coming online and you can usually identify components of polygenic disease that put you at higher risk of having the disease you are querying (like APOE4 for example). AI will likely help with these more complex genetic interactions so again having your sequence and being able to reanalyze it at will should be useful to you or your relatives.
Thank you for all of this very good information. The 30x seems like a reasonable choice for one-off personal use. Opening a conversational strand on this could be very helpful to many in our group. Even with the limited sequencing of 23andme, I have learned things that I believe have led to optimizing my diet and supplement stack. I have also learned what kinds of information should be ignored or pushed to the margin. Also, given the possibility of errors in the 23andme data, I would like to confirm the sequencing on some of the high magnitude health-related SNPs. I need to study Verkko and other open source tools. Perhaps that could become a thread as well.