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Whole genome sequencing vs SNP genotyping
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.
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Since risk from individual SNP's 'should' not be aggregated to indicate an individual's risk based on multiple sources of evidence, how are the magnitudes for genosets determined?. Can bayes or another method be used to interpret a promethease report?
Even genetic epidemiology textbooks seem pessimistic: about the usefulness of the genetic research underpinning precision medicine:
The references in question are about the impact of population stratification on genetic association studies. That doesn’t seem to substantiate such a broad stroke about the non-replicability of genetic epidemiology. I don't know what to make of these findings.
Here is a link to a screenshot of those references
It suprises me that entrepreneurial machine learning analysts don’t beg for genetic research to identify how combinatorial patterns of genes to be able to characterise individual risk. It seems like if/once they can get hold of that information, the sequence from genetic science to consumer actionable health information is bridged. So where are the 'lean gene learning machine' startups? I certainly don’t have the lean gene to do it myself. I don’t know machine learning.
Regulatory issues seems like the biggest hurdle. To the best of my google-fu, 23andme doesn't even disclose what it's 'Established Research' genes are. So, once regulatory hurdles are surmounted, lots of useful research will flood out.