For anyone wondering if there's any real benefit to having your genome sequence, here's my anecdote. Thanks to Promethease, I found out at a young age that I had hereditary hemochromatosis. This condition basically results in the slow over-accumulation of iron over a period of decades. The symptoms are so non-specific that without genetic testing, it's very rarely diagnosed until major damage has been done.
However if detected early, the treatment is dead simple. Regular phlebotomies to keep iron in line. One trip to the blood bank every few months means that the disease has literally zero impact on health or quality of life. Without genenome sequencing, I likely would have lost 10-20 years of life, and even more in terms of quality adjusted years. And this isn't some freak corner case. As many as 1 in 200 Northern Europeans have the genetic condition.
I've been wary about submitting my DNA to a company so this is very intriguing. Is there enough data and/or a community and open software to support things like ancestry and disease profiles locally?
I've been curious about what my DNA says, and went so far as to buy a 23andme kit years ago. I never sent it in, because I don't like the idea of some company retaining that kind of deeply personal data about me. It's useless to resist, though; my sister and some cousins submitted theirs, and that's enough to destroy any real sense of anonymity I might have. I don't have any particular concern; it's just one of the myriad ways that privacy no longer exists.
we don't have even the slightest idea of where it could go right now. look 30 years ago and DNA wasn't a thing that people were worried about and now it's catching sloppy criminals. the technology opens up new, unexpected opportunities
The first use of DNA in a criminal case only goes back to 1987. As such 30 years ago people generally weren’t really aware of generic testing or any of it’s implications outside of science fiction.
I am talking about DNA wrt crimes... it was first proposed as possible in 85 and in the early 90s used for it. I'd say my timeline was fairly ok give or take a few years for an off the cuff recollection of events.
You could (for example) submit the data you get to Promethease which will do the processing for you. Promethease is now owned by MyHeritage, so I'm not sure how their terms are looking - I'd be a little cautious about using that.
There is plenty of open software and data in genomics. The hard part is knowing what to do, using the software correctly, and interpreting the results. Bioinformatics is still mostly research-level work, so you'll need years of experience and lots of trial and error to get anything done.
Would be rather interesting to create sth like bloom filters from ones DNA to find relatives. In contrast to phone numbers the DNA space here might really be big enough for private "contact" discovery to work ...
Good question. I'm always afraid most of the useful medical data will be kept secret by these giant corporations, but let's hope this is not already the case.
0.1X coverage is nowhere near enough to get any useful information. The Nanopore error rate is huge (10-15%), with substitutions, insertions and deletions all common. The required coverage is more like 10X to 30X or more to get some accuracy in base calling and identifying variants.
Far far better idea to just pay someone to do short read resequencing. Long read sequencing is great for assembling genomes and finding structural variants.
Nanopore looks cheap in the first instance, but it's just not designed for this job. HiFi sequencing gives the best of both worlds - accuracy of short reads and decent length.
Weird because last time I sequenced with Nanopore, the accuracy was around 95%, and with the new Q20 chemistry it reaches to 98% :) I think you have 5 years outdated information
I might actually try this! I have a disabling genetic disorder (hypermobile Ehlers-Danlos syndrome) for which the genes responsible haven't yet been identified, but there are a few dozen genes of interest. Since the diagnosis is clinical, my geneticist didn't order testing for me, so I've stayed curious.
I'd probably approach it by ordering primers for my regions of interest, doing PCR to amplify them, then running it through the flongle in a single shot.
Of course anything this DIY would be useless for diagnosis or research - you want Sanger sequencing for accurate transcription of each gene, and whole-genome sequencing for identifying candidate mutations - but it's enough motivation to try such a fun little project. Also I can potentially play along at home with the results of the HEDGE study, which is trying to find the cause of hEDS.
As a middle ground between DIY and leaving it unknown you could also hire a contract lab to do this with you. As an experiment in this, I found a contract lab, ordered PCR primers, and sent in McDonalds burgers and McFish samples to do species identification. (Result: $300 all in, nothing too exciting, Bovine and iirc Alaskan Cod).
From [1], it seems like cooking doesn't completely destroy DNA, but does make it so you get smaller segments post-PCR. Maybe species identification is okay with small segments?
Have you looked into Nebula Genomics? They will do 30X coverage WGS for $299, and will give you the underlying data so you can analyze it on your own (in addition to their analyses).
I have this as well - I only found out a month ago after decades of searching and dozens of doctors, hundreds of tests, across 4 countries, all telling me there is nothing wrong. It should have been super obvious in retrospect. The vast majority of people who have hEDS will never know it. I highly recommend everyone check themselves for it. It could easily be 1% of the population. I only found out when my sister recently came down with CFS/ME in much the same way I did so I searched for genetic causes of CFS/ME. It can affect your whole life in a way you don’t even know isn’t normal, because everyone around you is telling you it is normal.
A lot of people seem to do well until their 20s and then come abruptly crashing down. That was the case for me. As a kid I had pain and could do all the crazy party tricks, but was more or less abled. Now at 30 I've fully dislocated my shoulder taking my jacket off, and need a walker.
I think transitioning hormonally accelerated it.. estrogen and progesterone loosen ligaments, and I lost my muscle mass from T.
NGS (Illumina style) is high enough quality to identify mutations. You can get a whole human genome for as little as 150 Euros (Dante labs has an offer at this price in 2020). Much cheaper per genome than suggested in the post, and you just send in the sample.
To get a comparable genome using the method suggested in the blog post will be much much expensive, in part because you have to buy all the equipment. But also because it’s Nanopore sequencing which has a much higher baseline error rate.
For markers, I don't recall off the top of my head, but I'd go with one of the connective tissue disorder gene baskets, and add other genes that are metabolically connected to those. The collagen genes COL3A1, etc. and TNXB definitely. 23andme is not likely to tell you much since it's just the 50k "greatest hits" of the human genome.
As for how I'm disabled: I have to use a rollator full-time now, and I've just been prescribed a neck brace, despite doing PT religiously for most of a year. I'm just too loose.. my knees give out, I sprain ankles all the time, my neck is too wobbly to hold my head up etc. I also have neurological issues that make me really clumsy, and dysautonomia that leaves me fatigued and woozy. Brain fog is the worst of it, since my mind is my livelihood.
No French background, Scots-Irish. Weirdly I don't know anyone else in the family with it, but I'm extremely hypermobile so it may have been a new mutation.
That's rough. Women have a much harder time with hEDS. I use Low Dose Naltrexone for the brain fog. It is not without its side effects but it works for me. I've been on it for 5 years for CFS before I knew it was for hEDS and would have considered myself normal if I wasn't getting injured all the time.
My theory, and this isn't standard, is that for hEDS the hormones drive the collagen deposition. Other EDS have a more direct link for mutation in collagen. I subscribe to the metabolic trap theory of CFS (see Dr Ron Davis) work, in my view this trap could upset the hormones which affects collagen.
In the past month I've been taking collagen peptides and other joint supplements and have noticed my fingernails have become substantially harder. I think the common refrain in the hEDS community that those don't help is wrong.
Trans men report a substantial improvement with TRT. There is an actual trial going on now treating women with testosterone.
There is anecdotal evidence that healing peptides and hGH is very effective. Especially for neck instability, or in my case degenerative disk disease. My gray market supply should arrive in a few days. I didn't want to wait for modern medicine to catch up. The pipeline for hEDS treatments is pretty sparse.
Long Covid seems to have a ton of similarities to heads so hopefully treatments will cross over.
thanks for the tips! I think long covid has more similarities to POTS than to hEDS, but most of us have POTS or OI too, so I agree it will help.
on the subject of sketchy gray-market meds, have you heard of BPC-157? I know an hEDSer who seemed to really bounce back after using it, but I can't quite work up the nerve to inject myself with internet peptides.
What do you read to stay informed about this stuff?
Yup; I’m starting out with BPC-157 and TB-4 in an oral form, before adding hGH injections later so I can tell which does what. Maybe a supplemental amount of testosterone after that. The hGH will help tethered cord syndrome which I don’t have but you might. It is a potential very painful temporary complication you might want to be mindful of. Anecdotally it is a better fix for that than surgery which hEDS people have a hard time healing from.
Even if someone seeks a hEDS diagnosis they are given a false negative 85% of the time. The vast majority don’t know to even seek it. It’s surprisingly prevalent, but also a spectrum. Many will present as just anxiety and burnout.
I read preprint research on ResearchGate and the NIH website - including mouse studies, as well as research done in Eastern Europe. I chat to friends who work in computational biology and longevity. I read a ton of comments across Facebook, Reddit, YouTube, and Twitter looking for anecdotal data. Bodybuilders and athletes are another good source of anecdotal information.
I used to be an applied researcher in machine learning; so I’m used to finding mistakes in others work. There is a lot of false confidence in medicine due to p-hacking and selection biases. I worked with behavioral data so I’m also used to cleaning anecdotal data and making it useful.
I got lucky; I was told young that weightlifting will help straighten my back and keep my shoulders from subluxating so I’ve worked out most of my life. Also why I knew more PT wasn’t going to help. At my high school gifted program I was warned that people at my level pretty much always burn out young; so I’ve always kept that in mind and readily slow
down when burning out. It has been hell but it could easily have been worse.
I think the weightlifting helps a ton with the testosterone and hGH and maybe other hormones. So does sunlight, it’s more than just vitamin D. But I can’t maintain the intensity and invariably get injured and relapse. This has been a cycle for me for many years.
There is also the mitochondrial repair approaches which I’ve yet to experiment with.
I think it could easily be 5-10-15 years for a proper cure. It’s a very neglected field.
Not OP; but have hEDS. CFS with brain fog is the most disabling part. Chronic back pain is the second. Post exertion malease means if I accidentally overexert myself I can be stuck in bed for days recovering. Bad posture due to loose ligaments.
There is also an increased anxiety with high functioning autistic behavior. It causes insomnia and noise intolerance. It seems to reduce the sex hormones. There also seems to be a link to higher IQ.
I have a distant West German background on the affected side.
Yup! The chronic fatigue and brain fog are definitely the worst for me. My mobility is pretty limited now, and I'm getting much worse at being able to type, but brain fog could end my career.
I do also have high IQ, ASD, horrid anxiety and insomnia, and I wonder if the sex hormone thing is what made me trans.
I've considered getting my stool tested for microbiome. Another curiosity is Virscan (1) with perhaps the intent on getting the virome tested as well. A lot of my interest comes from the perspective that I have ulcerative colitis. I have read everything about the disease since diagnosis. I don't want to go into everything, but it got to the point where the gastro wanted to prescribe humira and if that failed to move onto pouch surgery. Always being prone to a gamble, I tried drinking raw bovine milk and making enemas from it. To my surprise things began to clear up within a few weeks. This was 6 years ago. I'm symptom free and my most recent colonoscopy was clear. I have attempted to talk to doctors at the local teaching hospital that have a microbiome research initiative but got turned away. The interest was to let them study me, however I get it in that they have other priorities. Either or.. I have the op article printed out as perhaps genome will aide in some home research. No idea. One of the things I suspect is that I've had uc for longer than when it became an issue. Have read it can be present in childhood without much symptoms. So the curiosity is just trying to figure out if it is genetics, environment.. what not.
Sequencing a genome is the easy part -- the difficulty is making sense of all of the data in a clinical/medical sense. I got my DNA sequenced/analyzed by https://www.nagenomics.com and found some interesting things that matched personal/family medical history.
This is definitely true. Even looking at risk SNP databases for a particular disease is fraught with caveats. You really need someone with experience in the field, like a medical geneticist, to interpret the data you get. 23andMe and Ancestry can at least provide that for people, but I don't necessarily like giving up that data to a company to hold for me. But that's cool you were able to find some known markers of your personal medical history
Oxford nanopore isn't that great for resequencing a human genome. Human DNA is too big and the minIon or flongle is too small and error prone. MinIons are best used for long reads for niche experiments like assembly or for field work, in my experience.
It is much cheaper, easier, and more accurate to use a service like Nebula Genomics. 300 dollars for an exome is an incredible deal. When looking for deleterious mutations, it is actually really important to have a highly accurate methodology, otherwise you may find errors you think are true deleterious mutations.
Coverage isn't directly relevant to whether a mutation is deleterious or not. Coverage is about getting accurate reads in the face of short-read sequencing. Modern sequencing will chop up DNA into 200-nucleotide-long fragments and then align those fragments against the reference genome. Because of the variation between individuals, sequencing errors, and the fact that there are only 4 nucleotides, one sequencing read may not be enough to unambiguously determine which DNA is present at what position in the genome. Coverage at a particular genomic coordinate or locus is the number of reads which have been aligned to that position.
Depending on the circumstances, clinical use of genomes requires 100x-500x coverage. Depending on your purposes, you may accept less sequencing depth/coverage. If I was just a hobbyist wanting some idea about my genome, 30x would be sufficient for me.
I've not heard of Promethease before this discussion. It appears it will collect literature based on Single Nucleotide Polymorphisms (SNPs) in the DNA you send it.
Variant callers are a family of algorithms that look at the DNA in your sample and determine the SNPs. When thinking about coverage, quality scores assigned to sequence reads, and other pieces of information that may affect the variant caller, I would think about these inputs through their effect on detecting/classifying a variant. In other words, through metrics like accuracy, false positive rate, or false negative rate. State of the art variant callers are a little more complicated now, but simpler variant calling pipelines filter out variants that are of insufficient quality or read depth. This will primarily improve the false positive rate. If you are okay with casting a wide net in your search for a diagnosis and acknowledge that you may be seeing more false positives, then it's okay to go with a lower coverage assay.
As other commenters have pointed out, 30x coverage is widely accepted for germline sequencing. This is in contrast to somatic sequencing, which is more often done in the clinic for conditions like cancer where we expect much more variation among the DNA in the sample. Since that is not a concern in this case, you are probably fine to go for lower coverage options.
30X is considered standard for germline whole genome sequencing and higher coverage is typically used for detecting somatic variation. That being said, all detection is statistical and there are regions of the genome that are inherently hard to sequence.
30x gets you in the ballpark. there are always regions that can't be sequenced well and types of mutations that cant be reconstructed from the data. But from a clinical utility point of view a good 30x genome gets you up into the 95% range for finding the subset of variation that is clinically interpretable at the moment.
However if detected early, the treatment is dead simple. Regular phlebotomies to keep iron in line. One trip to the blood bank every few months means that the disease has literally zero impact on health or quality of life. Without genenome sequencing, I likely would have lost 10-20 years of life, and even more in terms of quality adjusted years. And this isn't some freak corner case. As many as 1 in 200 Northern Europeans have the genetic condition.