What can a person do with whole genome sequencing data

As of 2019, I think 3 different companies are offering a whole genome sequencing for $600-700. Places like 23andme only checks <1% of your genome.

Is there anything you can do with your whole genome sequenced?

I’m assuming in the next few years the price will be down to $200 or so. But I don’t know if there are any useful bits of info you can gather as of 2019 with whole genome sequencing. I know there are various websites you can use your 23andme data on, not sure about whole genome.

Also yay the board is back up.

I don’t think there’s a whole lot you can do with it yet without a decent knowledge of bioinformatics. For genetic genealogy it probably doesn’t add much beyond what you get with genome-wide genotyping, except perhaps for the sex chromosomes.

For health, there should be a lot more information in WGS since you’ll pick up rare variants, de novo mutations, duplications and deletions. Genome-wide genotyping will mostly only pick up common single nucleotide variants (I think present at >1% in a population?)

I couldn’t find any easily accesible third party WGS analysis tools but I imagine they’ll become available as more people get sequenced. WGS data analysis is a lot more demanding that genotyping data. The format of genotyping data has the variant location in one column and the nucleotide in another so finding risk variants is a straightforward lookup. Raw WGS data is many small fragments sequences with no genomic position information so is essentially meaningless until the sequences are aligned with a human genome database. Then there are other steps like filtering for artefacts.

There also other issues regarding interpretation of the variants you find. If they are rare or de novo, there may be no empirical understanding of their effects.

For companies like MyHeritage and FTDNA and public sites like gedmatch that accept uploaded raw DNA files you can generate a file that lets you do all the genetic genealogy stuff.

There are lots of sites that offer a similar service for the health aspect offered by 23andMe and now also by MyHeritage. In my opinion this is not really advisable. There are really no genetic tests outside of those ordered by a physician for a specific purpose that are helpful to us as individuals, and a lot of unnecessary worry to be had by learning that you have a doubled risk of Sprungjoun’s Syndrome (absolute risk increase 0.004).

You could also look up any and all variants that pop up in the news, or that you search for in the SNP-databases for whatever reason.

When I got my 23andMe back (I didn’t pay for the health analysis) I was curious and did a quick check of a couple of things and discovered that a SNP linked to tritanomaly, which I probably have, was in the 23andMe data, and that I was heterozygous for the variant in question. It was just dumb luck though that what I was curious about was actually tested for there. With my whole genome available no luck would be required.

But since I haven’t thought “I wonder if I have that variant” ever since, I’m not shelling out for that test.

Most of the genome of humans is shared among most humans. So knowing more than the 1% which normally varies usually won’t tell you anything. However, in the rare cases where it does tell you something, it can tell you a lot.

It’s not very interesting to learn that you have a gene that 30% of the population has. It’s very interesting to learn that you have a gene that 0.0000001% of the population has.

I think the one case where it might be useful is if you know you have a syndrome that you suspect is of genetic origin but don’t have a clear idea of exactly what it is. Tests like 23 and me are generally looking at SNPs that occur naturally in the normal population. So it will pick up most of the common hereditary traits and diseases. What it won’t pick up is random mutations that aren’t found with great frequency in the population, but which may lead to genetic malfunction. The difficulty is once you get the set of mutations interpreting what they mean.

Which brings us to another suggestion. Only about 1.5% of our genome actually consists of genes that code protein. The rest is made up of so called Junk DNA. Now this is a misnomer as there have been multiple studies that show that this DNA has important regulatory feature. But how it does its regulatory things is still not well understood. Also it tends to be very highly variable across the population since there is no evolutionary pressure to keep it from changing. As a result doing a whole genome sequence is going to give you a whole bunch of “mutations” that may do absolutely nothing, and even if they did do something we don’t know what. Therefor in my opinion it makes more sense to do what is known as a whole exome sequencing which only looks at the DNA regions that are part of genes. Since it only has to look at about 1.5% of the genome, it can do a better job of identifying mutations for much cheaper. It won’t cover everything but it will cover pretty much everything that is actually interpretable.

“a syndrome that you suspect is of genetic origin but don’t have a clear idea of exactly what it is”

Unless there’s been studies that have shown possible candidate mutations for this syndrome and your doctor is recommending testing (which might be possible to do target for less than the whole genome), looking at just your own genome is unlikely to help you to even identify the mutation, much less give you any actionable information.

Medical DNA testing has a bright future, but today there are few worthwhile tests even for doctors, and for the general public it’s a whole lot of nonsense and unnecessary worries.