Hi, I was considering possibility of undergoing some kind of genetic testing for a while now. But I hesitated because I have a quite limited financial resources available right now. Eventually I've figured that in the future I'd do it anyway, so why don't just do it right away. Especially taking into account that knowing some data available via such tests in an earlier stage of life and acting on it could be quite beneficial in a long run.
So after that realization I've thought about going with 23andme and performing SNP genotyping. But in the process of browsing related information I've encountered article about rapid decreasing in price for Whole genome sequencing. After that I've found this listing: https://www.scienceexchange.com/services/whole-genome-seq?page=2 and the lowest price tag there is $795 (but it's not clear whether that particular option is applicable to human genomes).
And as a result the whole WGS thing seems quite appealing, but I have some concerns here. I still have quite limited finance and WGS seems to have at least 10x prize in relation to SNP. And the other concern is data applicability (more on this one further).
Information about what and how you can do with WGS data is somewhat scarce on the Internet. So I have some questions here:
- What can I actually do with data from WGS?
I know that for SNP tests there are tools like Promethease (http://www.snpedia.com/index.php/Promethease) that allow you to analyze your data. But I was not able to find anything about tools for analyzing your WGS data.
So are there any good tools available for you to analyze your WGS data? And: Is it computationally feasible to get results in an adequate time, using a general pc for this purposes?
- Do you know any end-customer oriented company that provides WGS for a good price?
And finally with all above said: should I go for whole genome sequencing/SNP/or my whole line of reasoning is invalid and I should wait for now and get WGS in a few years for a smaller price?
(My main concern here is positive influence on health in a long run.)
Thanks.
The main idea of WGS is having >all< the SNPs whereas you only get the most common SNPs with the SNP tests.
I'm not really sure how you would use the data from WGS (let's say the genome is assembled too - or maybe that would cost more ?). You would probably use BLAT on your local machine to search for genes with known SNPs. I don't think you could do anything more (finding novel SNPs is out of reach here).
I would guess the main idea would be to be able to check for new SNPs as more and more are found in the literature. However, the literature is not that easy to skim through except for the most common SNPs that are already included in the SNP tests.
Going back on the literature: for most multi-factorial diseases, you will see data coming from GWAS and linkage disequilibrium studies that will be really hard to interpret. A SNP popping up like that does not necessarily mean that you've got the trait associated with it.
My comment was probably not really well oriented, but I should still conclude. In my opinion, do a WGS only if you've got enough knowledge of bioinformatics (and I mean an engineer's level). SNP tests are cheap and will provide you with almost everything you could get from a WGS.
I agree with your general point, but here is a technical comment: 23andMe is the million most common SNPs, but that is not the same as the million most common variants, because not all variation is in the form of a SNP. SNP stands for "single nucleotide polymorphism" -- it means that one letter is changed while the context is unchanged. They are easy to detect because of that context, and that ease of detection is why they are used.
Another kind of variation is an insertion or a deletion. They are harder to detect, which is why 23andMe only detect... (read more)