Whole Genome Sequencing

As Whole Genome Sequencing (WGS) gets cheaper, faster and more accurate, I thought it would be helpful to start a new thread to discuss how to analyze our genomes. What Single Nucleotide Polymorphisms (SNPs) do you find most relevant to your healthspan?

Which paid or free software are you using to analyze your genome both now and in the future as relevant new research becomes available? What strategies are you using to share what you learn with your doctor in order to enable healthcare more personalized to your genome?

My research has just begun and the amount of data to review seems overwhelming. I am personally interested in both Promethease to analyze my genome now and Verkko in the future to reduce/eliminate genome gaps.


In theory, the cost right now is about $1,000 to get a Human WGS done - but what companies provide this service other than Human Longevity, Inc.? HLI is about $7,500 with a 5 year commitment right now (yearly scans, I think), but that seems very high. Have you found any other services that do WGS for individuals?

Harvard/George Church connected Nebula does it for $249 + lifetime membership of $295 for a total all in of $544 - at 30X sequencing depth. I got this one for my wife.

(you can go less depth and get whole genome for $299 all in).


In addition to Nebula that you just mentioned there is also Sequencing and Dante the later of which now offers HiFi reads as well.

Hardware competition is increasing and I expect companies like Oxford Nanopore and PacBio to continue to drive down WGS prices while capturing market share from Illumina. Of course the market itself if growing so there should be room for multiple firms to find a niche and thrive.

From a consumer perspective the biggest frustration currently may be the long wait times for sequencing (varies by company).


Just out

Grounds Truths summary piece
Polygenic Risk Scores: Ready for Prime Time??

Paper: Selection, optimization and validation of ten chronic disease polygenic risk scores for clinical implementation in diverse US populations


Interesting paper! I think the value of WGS is already quite attractive and will continue to become even more so as our ability to analyze it improves.

The type of risk scores in this paper can be quite valuable to people. When I ordered my WGS I was looking forward to learning more about my genetic risks that relate to cardiovascular disease, neurodegenerative disease, and insulin resistance. I was already aware of my APOE status and family history so much of what I have found was not shocking.

However I did find some SNPs that I was not expecting. Analyzing that surprise data felt empowering to me as I know that early screening and interventions can greatly reduce some of my newly discovered genetic risk factors.

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I am not sure if you have children or not but I think that price is an absolute bargain compared the cost of raising a healthy child. Outcomes for many childhood diseases can be improved drastically with early intervention and analyzing the genome of both parents can help prepare families to know some of the things to look for and do exactly that!


I wholeheartedly agree. I got my Sequencing dot com 30x results back a few days ago and some of the information has confirmed issues that I’ve only been able to uncover and diagnose in the past year. Had I known about some of these things a few decades ago, I think I would have been a happier and healthier person with a great deal more energy. I fully intend on purchasing sequencing for my children.

Regarding options, I initially was favoring Nebula, but went with Sequencing after investigating user satisfaction. The bundle I purchased was $399 (a Black Friday deal with some reports included), but they try to get you onto a subscription plan. Instead, I’ve requested the raw files and intend on converting the BAM to RAW using https://wgsextract.github.io/

If that doesn’t work, I may use a service like https://www.dnagenics.com/article/bam-to-raw .

Once it is in RAW format, I’ll start off using https://www.geneticlifehacks.com/ to get some quick, decent reports, but I’m also having fun on https://snpedia.com/ and will probably use https://promethease.com/

Other services, like https://selfdecode.com are tempting, but expensive and probably redundant. The core Sequencing reports are rather extensive and I’m skeptical that there would be much more to learn as I think these sites are all looking for the same mutations.


What kind of DNA files are you talking about. I’ve done DNA test with myheritage and downloaded the DNA file. I’ve used to to see what kind of illness and deficiencies I might have. Is that the same?

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What I am wondering about is how easy it is to get the Mitochondrial DNA sequenced. I know that has been possible recently and it will give an idea then as to the level of heteroplasmy (where different mitochondrial dna exists for different mitochondria or in the same mitochondrion).

This raises an inherent problem that is we are then looking at white blood cells and not other tissues. The level of heteroplasmy is likely to vary between tissues as well as between cells.


I was not familiar with that site. It appears useful. Thanks!

I also used WGS Extract and was happy with it. I like the idea of controlling my genetic data locally. While I think both Promethease and SNPedia are very useful I was disappointed when I learned they were acquired by MyHeritage. Privacy and security of genetic data is extremely important but unfortunately many companies do not pay enough attention to it.

While end to end encryption cannot be easily achieved unless we are willing to download our own genetic data and encrypt it ourselves at least most of the major service providers are beginning to offer two factor authentication (although it is often optional rather than mandatory with more the more secure U2F standard still being far less common than the weaker TOTP and the joke level SMS standard).

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Here is an article that explains the difference. You can learn a lot with the DNA test that you performed. However WGS looks at your entire genome rather than a tiny fraction of it, providing multiple orders of magnitude more data to analyze.


That is an exciting area indeed. In addition I am also excited about future microbiome sequencing improvements

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Dante includes mtdna in their wgs


Does anyone know the differences between the 30x and 100x nebula package? What do they actually do?

Do you have a link to that?

I presume this is only WBCs though.


I see that they have a sale now e199, not their lowest price, sometimes they’ll go as low as 169 but still a very good price for 30x wgs

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Greater accuracy. If you know you have cancer (for example) more accuracy may be helpful (somatic genetic testing). Absent knowledge of rare mutations I am guessing most people will choose 30x for germline purposes (based on price).

Looking at the website it appears to be Nuclear Mitochondrial DNA not Mitochondrial DNA itself.

I will rethink Promethease then. I have just been using SNPedia as a reference.

I did 23andme at one point, but used a fake name, VPN, throwaway email address, and did not buy the kit through their site.

On the privacy theme, I was warned by the hospital’s genetic counselor prior to getting a doctor-ordered cancer mutation screening that I should get my life insurance in order prior to the test. I paused the process and bought more life insurance, and sure enough, during underwriting they wanted to know if I had followed through and had any genetic results. They seemed satisfied with my answer “no, they said my risk was so low that I decided it was a waste of money.” I then got the test and it came back null anyway.