Whole genomic sequencing companies (who I use and who to avoid)¶
by u/Drwillpowers · 80 points · 42 comments · source
Over the past year while Nebula Genomics (who used to be great) basically imploded and screwed over everyone, I haven't had a good company to replace them.
Sequencing.com was decent, but every genome they did for me was missing the X-chromosomal data when browsed in gene.iobio.
They promised me this would be fixed by the end of august, and well, they kept their word. I just reviewed a genome a few days ago from them which worked. There was some sort of glitch in the way they produced data and gene.iobio processed it, and the two of them resolved the problem.
So as of now, sequencing.com is the fastest/cheapest/most reliable option available to me. So for now, I recommend them over any other company.
I am at times seeing bottom outs in a few random places on 30x genome sequences where the depth is near zero. There is benefit to a 100x if you can afford the increased price. But, overall, 30x does the job for most people's needs.
As is tradition with me, I will discard one pharmacy/service/whatever for another if someone can do something better/cheaper/both for my patients. I have no brand loyalties. But as of today, Sequencing.com appears to be the most reliable and swift option available that provides the data necessary to browse in gene.iobio my list of all known genes related to gender dysphoria:
Not everyone gets an answer as to why. But sometimes, when I browse, I find some catastrophic failure somewhere in the genes related to T or E production/signaling which makes it pretty clear something went very wrong.
Comments¶
u/stable-islander · 27 points
A trivial clinical note, and maybe one that's unwelcome or unhelpful, but it may be helpful to hedge against some of the ruminative fatalism that trans people can be prone to, particularly in terms of saying that something has gone very wrong. The great thing about knowing where something works different to wild type is being able to work out what parts of the solution space may be worth exploring. It's understandable that damn near everyone fears they're going to be the rare person for whom there is no pathway to feminization or virilization or whatever, but if anyone's work shows that it's worth persisting, it's yours. People may have some weird locks and some weird keys, but medical progress and certain hard-working humans (some of whom may just be family medicine docs in the US) can come up with all kinds of creative ways to pick locks. A catastrophic failure in a receptor or an enzyme need not be blackpill fodder.
u/Drwillpowers · 30 points
This is spot on. I have had people whom initially, based on their genetic result, I had no idea what to do about them. They were screwed. And yeah their transition was failing. But we tried and failed and tried and failed and tried and failed and then tried and then finally succeeded with something different. Sometimes it takes a little ingenuity, and a little luck. Certainly some trial and error is in there as well.
u/HiddenStill · 28 points
Unfortunately, the standard doctor's approach is, I’ve tried nothing and I’m all out of ideas.
u/The1Bun · 11 points
I wish I could upvote this twice because I agree, and because of the Simpsons ref. 👌🏼
u/Far-Scientist-641 · 6 points
Still waiting on my dnacomplete results…. Past that 12 week mark now in their time line estimate.
u/AndesCan · 4 points
Did you happen to take a picture of the original shipping label you sent your sample with? Willing to bet it took near a month to get there….. I was tracking mine and it was essentially lost and their customer support is 👎
u/umm-marisa · 3 points
I'm at about 9 weeks and waiting. It says they received it but the extraction step hasn't started yet.
u/The1Bun · 5 points
I did my genome through Sequencing over a year ago or so. I haven't been able to load it into gene.iobio yet because the files provided to me in my account aren't compatible. I would need to convert them. Haven't been able to do that. Any advice? Tips? Hints? Do I need to reach out to Sequencing and request the proper file types? I've been struggling on and off with trying to work this out since back when you very kindly replied to a comment I left over in one of the ftm subreddits. Any help would be appreciated from you, or anyone else reading this. I did already reach out to Kate, who was very kind. If I recall correctly, we pretty much landed on the conclusion that I needed to convert the files I have in order to plug them in on gene.iobo. We just didn't know how. If someone out there has done this before, I would be super-duper eternally grateful for some kind of short tutorial or something on this. Haha (The file conversion method(s), mostly.)
Anyway, thank you so much for all you and Kate (and I imagine others behind the scenes) have been doing to try and help us out. I truly appreciate it. My wonky hormone signaling is impacting my health in many ways. So, this will go a long way toward my being able to help my healthcare team help me.
u/Drwillpowers · 11 points
Ask support at sequencing for the tbi and vcf files. They will make them for you.
u/The1Bun · 3 points
Will do, Dr. Powers! Thanks, again! 🫱🏼🫲🏻✨️
u/WitchOfTheWesst · 1 points
I’m curious…it’s been about 3 months since your post and I’m wondering if asking them for those files worked everything out for you?
u/The1Bun · 1 points
It did, somewhat. I had numerous issues while analyzing the data. Gene.iobio kept glitching out. So, I'd have to re-upload my files frequently.
u/WitchOfTheWesst · 2 points
Ok thanks
u/The1Bun · 1 points
Sure thing
u/SkyVisionArt · 3 points
What is the benefit of 100x vs 30x?
u/Drwillpowers · 16 points
The amount of times one area of the genome has been sequenced on average.
30x means that on average, every codon has been sequenced 30 times.
The process is not perfect. There are errors. So if you get 20 A's and 10 t's for a particular codon, you can reasonably guess that the a is most likely correct. But you'd feel a lot more confident if it was 80 A's and 20 t's.
Additionally, it's 30x on average. This means that there will be areas with more than 30x and then areas that are less than 30x. Some areas of the genome are notoriously hard to sequence. You might only get 5x depth with a 30. Sure some area is going to be 60x, but some 5x. It averages out to 30.
u/[deleted] · 2 points
[deleted]
u/Drwillpowers · 4 points
Being technically correct is the best kind of correct, but there's always a more complex and deeper understanding of a thing and sometimes I limit what I put here.
The idea that even Chimerism or mosaicism are rare is kind of funny. But like it's rare when it's hugely obvious. Lots of people are walking around with it totally oblivious.
u/Shoddy_Corner3618 · 3 points
To get the fixed data do I need to reach out to them? I’m looking at the files dashboard and none of the dates are updated. If I redownload these will the files be updated with the fixed X chromosome data?
u/Drwillpowers · 2 points
Yes. Reach out to support
u/Shoddy_Corner3618 · 2 points
For information purposes, I reached out to support and they said that there's no need to reprocess or update the files, since whatever issue was fixed completely on the gene.iobio side of things.
I haven't confirmed this with my downloaded data yet.
u/Drwillpowers · 3 points
Yes but you're still going to need a TBI file
u/ithacabored · 2 points
How do you order 100x and what is the price? All 3 bundles I see are 30x.
u/Drwillpowers · 2 points
They apparently no longer offer it. So with sequencing it's going to be the far left option that's the cheapest with 30X.
u/ithacabored · 2 points
ok, ty. Would it be possible to pay a fee to you to have you review the results even if I can't visit you in person? Or I can maybe get one in-person visit. I split my time between the west coast and portugal. If not, is there another reputable person who could review the genome for me to look for anomalies that might affect my transition?
u/Drwillpowers · 1 points
That is something that I only do for my actual DPC patients and it's because it takes me many hours to do it. Honestly it consumes the vast majority of my free time right now.
u/stable-islander · 3 points
I know you're surrounded with trans women eager to help, but this really seems like something it would be worth making a tiny expert system or something around, or even just some tooling to speed things up and make your workflow more efficient.
u/Drwillpowers · 2 points
We have one for snp arrays. But a WGS is 250gb of data. It has to be explored by hand.
u/stable-islander · 2 points
I know how big a WGS is, and that's not a lot of data, and the patterns you're looking for aren't that complicated, especially given that you've already done this enough that you know which genes you want to look at, even if you widened that scope considerably over what's currently in the other post. Giving you a summary of things you're likely looking for should take on the order of seconds, maybe a minute if you want it to be pretty.
u/cookieloverrrrr · 2 points
I had a really disappointing experience with Sequencing.com and want to share in case it helps someone else.
They make it sound like you’ll get a complete set of DNA results, but what really happens is they only give you little pieces at a time. To unlock more, they want $679 for the test and then $129 every single month. Even then, the information doesn’t feel very clear or useful.
I decided to go with them because I have hypermobile Ehlers-Danlos Syndrome (hEDS) and kept hearing they were the only ones who tested for every type of EDS. That was the main reason I spent the money. But after my results came back, they told me they don’t test for hEDS at all.
To me, that’s misleading and it felt like a waste. If you’re looking for real genetic answers, I’d recommend trying a different company.
u/Drwillpowers · 4 points
I don't think you understand what the purpose of that test was for.
You don't need sequencing to do anything or unlock anything.
All you have to do is take your raw data from sequencing, download it, and load it into a gene browser like gene.iobio
You can even lazily use the phenolizer instead of actually searching for genes and just put in hypermobility. Set the advanced preferences to show you the top 100 genes for hypermobility.
If you have mutations in those genes they will show up under the variant report and then you can look at it and see has this shown up in other people, is it common, what does this mean. What is the Revel score?
hEDS is just the garbage band where we throw people when we don't know exactly what genetically caused them to be hypermobile. There's never going to be a test for it. But you can do the work yourself with what you already have. Just download your raw data and do this. That's what I do for my patients.
u/cookieloverrrrr · 2 points
Thank you very much Dr.
u/Drwillpowers · 3 points
I specifically went and spoke to the creators of Gene Io bio about the situation.
They recently made an edit and fixed the phenolizer app for me. It's a little sub thing inside of gene.iobio.
Load up your genome into it, and use the phenolizer to search for hypermobile or Ehlers-Danlos and see what comes up. That should work for you now. Where it wouldn't have worked when I made the comment.
u/cookieloverrrrr · 2 points
Damn Doctor, you’re the best. I really appreciate your help.
u/Far-Scientist-641 · 1 points
Well that is really bad news
u/rvauofrsol · 1 points
The more expensive options for sequencing.com aren't worth it, right?
I'm asking because it looks like the sequencing process is the same, and the only thing different is the number of "reports" that come with it (which is info that can be obtained elsewhere for cheaper, right?).
u/Drwillpowers · 3 points
That's my opinion
u/rvauofrsol · 1 points
Thank you so much!
u/SkyVisionArt · 1 points
Is sequencing.com ($399) a good option for figuring out how to navigate HRT? HRT has been complicated and difficult for me and I’ve went thru many doctors trying to figure out what’s going on with me. So I’m resorting to genetic testing
u/KyaDash · 1 points
sequencing.com doesn't report to health insurances, do they? Interested in examining stuff, but would really like to anything private and to myself.
u/Drwillpowers · 2 points
All the information you give these companies is what you give them. So if you give them fake information, that's what they have
Archived 2026-04-20 from https://www.reddit.com/r/DrWillPowers/comments/1n7pu2y/whole_genomic_sequencing_companies_who_i_use_and/ via scrape-tools/social.