How to sequence your genome at home

For anyone wondering if there&#x27;s any real benefit to having your genome sequence, here&#x27;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&#x27;s very rarely diagnosed until major damage has been done.<p>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&#x27;t some freak corner case. As many as 1 in 200 Northern Europeans have the genetic condition.

I&#x27;ve been wary about submitting my DNA to a company so this is very intriguing. Is there enough data and&#x2F;or a community and open software to support things like ancestry and disease profiles locally?

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.<p>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.<p>Nanopore looks cheap in the first instance, but it&#x27;s just not designed for this job. HiFi sequencing gives the best of both worlds - accuracy of short reads and decent length.<p><a href="https:&#x2F;&#x2F;www.pacb.com&#x2F;smrt-science&#x2F;smrt-sequencing&#x2F;hifi-reads-for-highly-accurate-long-read-sequencing&#x2F;" rel="nofollow">https:&#x2F;&#x2F;www.pacb.com&#x2F;smrt-science&#x2F;smrt-sequencing&#x2F;hifi-reads...</a><p>Not accessible to the home user though.

I might actually try this! I have a disabling genetic disorder (hypermobile Ehlers-Danlos syndrome) for which the genes responsible haven&#x27;t yet been identified, but there are a few dozen genes of interest. Since the diagnosis is clinical, my geneticist didn&#x27;t order testing for me, so I&#x27;ve stayed curious.<p>I&#x27;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.<p>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&#x27;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.

I&#x27;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&#x27;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&#x27;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&#x27;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.<p>(1) <a href="https:&#x2F;&#x2F;science.sciencemag.org&#x2F;content&#x2F;348&#x2F;6239&#x2F;aaa0698" rel="nofollow">https:&#x2F;&#x2F;science.sciencemag.org&#x2F;content&#x2F;348&#x2F;6239&#x2F;aaa0698</a>

Sequencing a genome is the easy part -- the difficulty is making sense of all of the data in a clinical&#x2F;medical sense. I got my DNA sequenced&#x2F;analyzed by <a href="https:&#x2F;&#x2F;www.nagenomics.com" rel="nofollow">https:&#x2F;&#x2F;www.nagenomics.com</a> and found some interesting things that matched personal&#x2F;family medical history.

Oxford nanopore isn&#x27;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.<p>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.