ancestry help please?

[Mollyfan]

I have had a full genetic test done by ancestry and would be very grateful for any tips on how to search for information about relevant SNPs.

I have downloaded the ( very large!) file onto my iPad but have no idea how to find the bits that I want. For example, where are the SNPs for DIO1 and 2?

Or, has anyone used a program to find these things and if so, what is your experience/ recommendation?

jimh111 I think you said it was easy to search?

Thank you to all you wonderful people, you are an amazing group!

[helvella Administrator Thyroid UK]

There are several sites which make it (relatively) easy to check for SNPs.

For one example (it's the one I always remember!):

snpedia.com/

Within that, just search for, say, DIO2. (Search field at top right of their pages.)

For example, DIO2 is here:

snpedia.com/index.php/DIO2

However, I think you'll find that Ancestry, just like 23andme, only identifies a selection of SNPs. It is only a modest percentage of your whole genome. Therefore you might well find SNPs identified which you cannot look up on your results.

On 23andme it is easier to search on their site than in the download.

This link takes you to a page about the downloadable files and their formats, etc.

sequencing.com/blog/post/ho...

(The information on that site appears to be good quality but they really do want us all to buy their sequencing services. Hence lots of pushing towards their products. That is not why I have posted the link!)

[Mollyfan in reply to helvella]

Thank you so much, that is really helpful x

[WitchingHour2point0 in reply to helvella]

Hi Helvella,

I got my ancestry data today and I've been poking about in snpedia.

Some of the SNP's I've been looking at i.e. rs2305764 suggests a response should be 'C:C, C:T, or T:T... my result is A:G!

So I'm wondering where I've gone wrong and wondered if you might be able to explain? Or point me in the right direction... I am well out of my wheelhouse!

Thank you!

[WitchingHour2point0 in reply to WitchingHour2point0]

I found this: eu.customercare.23andme.com...

Why Don’t my Raw Data Results Match Another Source?

Each chromosome consists of two strands of DNA that are complementary to each other. The DNA nucleotide base adenine (A) always pairs with thymine (T) and the base guanine (G) always pairs with cytosine (C) across these two strands. One strand is called the positive (+) strand and the other is called the negative (-) strand.

By default, the Browse Raw Data tool reports genotypes based on the positive (+) strand of the GRCh37 assembly (“Build 37”), and you can optionally view your raw data based on the positive (+) strand of the NCBI GRCh38 assembly (“Build 38”). Other websites or publications might refer to the negative (-) strand and/or a different genome assembly instead. This would cause a mismatch between the genotypes reported by 23andMe and that source.

You need to know if the other source is referring to the positive (+) or negative (-) strand to find out if your genotype at 23andMe is the same as your genotype at the other source. If the other source is referring to the negative (-) strand, then your genotype from the other source and your genotype from 23andMe should be complementary. For example, if your 23andMe genotype at a given SNP is GG, that is the same as a CC genotype at that SNP from the other source.

[Jaydee1507 Administrator]

I used an upload service costing £15 (now £17.99) to analyse my ancestry results. mthfr-genetics.co.uk/DNA/ab...

It didn't include analysis of DIO1 & 2 so I had to search manually in my results for those. Just use a search tool which helps a lot and you need the SNP numbers. selfdecode.com/app/article/...

Also DIO1 selfdecode.com/app/article/...

There are some free analysis sites but their results are not always easy to understand.

[Mollyfan in reply to Jaydee1507]

Thank you!! Very helpful

[Wua13262348 in reply to Jaydee1507]

You are an absolute star, Jaydee, for mentioning this! Another piece of the puzzle . Unfortunately I don't understand the full implications . Hopefully the Endo might.

Your reference for DIO1 selfdecode.com/app/article/... states that Selenium and CYSTEINE are crucial for DIO1 activity. This is the first time I've seen particular mention of cysteine, as regards to DIO1. I have a double mutation for Cystathionine Beta Synthase enzyme, which Izabella Wentz states will cause hypothyroidism, without really explaining why, and exactly how it is caused. It is an enzyme which converts homocysteine to cysteine and glutathionine.

It is an upregulation defect. My selenium is upregulated. No idea what my cysteine level is. I am deficient in glutamine, a precursor to glutathionine. No idea what my glutathionine level is.

I have one rapid converter and one poor converter at DIO1.

Appreciate your input.

[Dandelade]

I have never thought to use ancestry DNA this way - genius idea! If you do get somewhere please let us know if you were successful…

[Feuerfrei]

I stumbled upon a site that gives the different builds of the genes. For example, you could have the DIO1 gene, but there's 2 versions, one maybe ending GG and the other AA. One would be more likely to make little difference to T4 conversion and the other more likely. It's a faff going through each condition but I found it useful geneticlifehacks.com/

You don't have to be a member to search through articles. As helvella said, you may not have all the sequences with your test. I found I have 2 different DIO1 genes of the poor conversion type, but my 23 &me test showed only that I have a DIO2 gene but not the genotype, sadly!

[Mollyfan in reply to Feuerfrei]

Thank you, I will have a look.