Doing a Whole Genome Sequencing (WGS)

[Snow Leopard]

The genotyping data you get from Ancestry.com or 23andme is a tiny fraction of the data (0.03%) you will get from WGS (Whole genome sequencing).

There are ethical issues eg: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4796706/
But these issues also exist with genotyping, only there is less data generated.

WGS is a bit of a misnomer however as due to genetic variation it is only really about 97% of the genome that is covered and accurate - but the exome (known genes) should be close to 100% give decent "coverage". Keeping in mind the "30x" coverage is a statistical phenomena.

If you want to compare the merits of exome vs whole genome sequencing:

http://allseq.com/knowledge-bank/1000-genome/wgs-vs-wes/

 

[Research 1st]

The genotyping data you get from Ancestry.com or 23andme is a tiny fraction of the data (0.03%) you will get from WGS (Whole genome sequencing).

There are ethical issues eg: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4796706/
But these issues also exist with genotyping, only there is less data generated.

WGS is a bit of a misnomer however as due to genetic variation it is only really about 97% of the genome that is covered and accurate - but the exome (known genes) should be close to 100% give decent "coverage". Keeping in mind the "30x" coverage is a statistical phenomena.

If you want to compare the merits of exome vs whole genome sequencing:

http://allseq.com/knowledge-bank/1000-genome/wgs-vs-wes/

Thanks for educating us Snow Leopard, as I'm rather confused about all this.

On some websites (PROMETHEASE.COM) they charge you $12 per go, but you can add 'other sources', if you pay more. E.g. you can chose to upload additional files.

So I was tempted to do just this, to 'add' an old 23andME test I have (the data) just in case it 'catches' something a whole Genome WGS misses.

But.... it sounds like from what you're saying, it's largely pointless doing this - pay some dollars more if you have a higher quality 120X WGS already uploaded, to then add a lesser comprehensive test like the 23andME assay?

I hope I have that correct!

 

[alicec]

Could someone clarify the value in doing a WGS through one of these companies versus getting the raw data from Ancestry.com? Do you just get more data through a WGS?

WGS or WES (whole genome or whole exome screening) provide far more information than services like ancestry or 23andme. The latter test only selected SNPs (single nucleotide polymorphisms) across the genome. WGS sequences the entire genome, WES sequences all the protein coding regions.

I'm working with a geneticist in Australia who will interpret the data for me (Denise Furness). She has recommended Ancestry as the most cost-effective option, but there are some specific genes I'm interested in (listed below) that I'm not sure they'll cover.

If she is recommending Ancestry then she should be able to justify her recommendation and answer your question about whether those genes are covered.

If she can't then I suggest you reconsider using her services.

Ancestry is only a few dollars cheaper the 23andme and it is my understanding that if you are interested in health-related aspects rather than ancestry, then 23andme is superior.

WES or WGS would ensure that you get full coverage of the genes you are interested in - along with all others of course.

Interpreting the results of course is the difficulty. You have to work at this. Enlis and Promethease can be useful in helping to search your results.

You should also ask Dr Furness what assistance she can give with interpreting WES or WGS. This would be a good test of her flexibility. Often people who set up such services have a limited selection of SNPs they are interested in and their advice centres on those SNPs only.

Frankly I am suspicious that she is such a person if she is recommending Ancestry.

Ask her more questions.

 

[shoponl]

WGS or WES (whole genome or whole exome screening) provide far more information than services like ancestry or 23andme.

23andme/Ancestry also have a higher miscall (error) rate than a 30X WGS or 120x WES. And the 30X and 120X assays have higher error rates than clinical diagnostic tests.

 

[Carl]

I wished that I had not missed the Dante labs offer on Amazon prime day €399/£35x is a bit too much ATM. €299/£28x would of been more tolerable.

 

[BeautifulDay]

If she is recommending Ancestry then she should be able to justify her recommendation and answer your question about whether those genes are covered.

If she can't then I suggest you reconsider using her services.
.....
Frankly I am suspicious that she is such a person if she is recommending Ancestry.

@alicec I agree, anybody doing this for health research should veer away from Ancestry. Ancestry DNA is great for matching a person with relatives and unraveling family tree mysteries. But Ancestry is very thin for covering the health related snp's. I am also surprised someone in the field would recommend Ancestry DNA for trying to figure out health related issues.

 

[Research 1st]

A question please to our resident geniuses.

If we did a WGS, can we look up genes using special software programs to search for genes that shouldn't be there but are, e.g like genes for Borrelia, Viruses etc?

It just struck me that if pathogens alter gene expression in disease, surely all we need to do is spend hours researching genes associated to these infections in published research, and see if anything shows up on our result personally?

Or is that wishful thinking as if it was that simple, everyone would simply go out and do a WGS and then have some vague evidence they may harbour chronic variants of various infections, like Borrelia, retroviruses etc?

Thank you.

 

[Lalia]

If we did a WGS, can we look up genes using special software programs to search for genes that shouldn't be there but are, e.g like genes for Borrelia, Viruses etc?.

Someone else will answer this far more comprehensively than I will - but viruses and pathogens are different to genes. So for example, if you have Borrelia - that’s a pathogen - not a gene. It won’t show up in your genetic testing.

The best you could try to do is use your genes to determine the ‘weak spots’ in your genetic make up. I’d be asking what genes may be expressing themselves due to pathogens or viruses, and contributing to your symptoms.

For example, I know I have polymorphisms in a range of Phase 1/ Phase 2 detox genes, so I need to be careful about toxins going in and support my body to remove toxins. That’s a really simplistic example though, it’s more complex than that, there’s a lot we don’t understand and I don’t think there are any decent research papers that show specific genes being implicated in CFS/ ME (although again I might be wrong here).

The genetics really need to be looked at by a professional, as one part of your health puzzle. I hope that helps somewhat.

 

[Paralee]

Sooooo......... I got pretty bad for a while but somehow a sinus infection can make you feel like death is knocking on your door, I honestly feel like there's more to it than that but.....now that I'm really ready (and capable) of sending off for a complete genetic test I've lost track of which one could tell me the most for maybe around $500 or less?
Does anyone have any ideas? I've found a heart problem on the 10% or under genes plus a lot of other ones and if I don't get things started I might not finish. Anyway, I need to quit "living" from day to day and do something.
Thanks if you can help. Paralee