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Thread: Concepts – Imputation

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    Concepts – Imputation

    Until recently, the word imputation wasn’t a part of the vocabulary of genetic genealogy, but earlier this year, it became a factor and will become even more important in coming months.

    Illumina, the company that provides chips to companies that test autosomal DNA for genetic genealogy has obsoleted their OmniExpress chip previously in use, forcing companies to utilize their new Global Screening Array (GSA) chip when their current chip supply runs out.

    https://dna-explained.com/2017/09/05...tion/#comments

    I don't really understand whether imputation is a good or bad thing in terms of producing results. I am interested in the thoughts of those who are more knowledgeable than I am.
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    I was reading that article myself this morning trying to learn more which is how I came upon your posting.

    Only about 20% of the DNA locations previously tested by genetic genealogy companies are tested on this new platform.
    That 20% really concerns me. I've paid for a lot of family members tests to build up a large bank of reference material. Hoping that investment isn't about to be rendered useless in the coming years. Guess I don't understand why they wouldn't make new chips backward compatible to allow accurate comparisons with all of the previous testing. Lot of concerns here, hopefully those in the know can alleviate those concerns.

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    Quote Originally Posted by firemonkey View Post
    Until recently, the word imputation wasn’t a part of the vocabulary of genetic genealogy, but earlier this year, it became a factor and will become even more important in coming months.

    Illumina, the company that provides chips to companies that test autosomal DNA for genetic genealogy has obsoleted their OmniExpress chip previously in use, forcing companies to utilize their new Global Screening Array (GSA) chip when their current chip supply runs out.

    https://dna-explained.com/2017/09/05...tion/#comments

    I don't really understand whether imputation is a good or bad thing in terms of producing results. I am interested in the thoughts of those who are more knowledgeable than I am.
    It's all about increasing the profit margin. At $100 the companies are hardly making any profit with the current micro-arrays. So the idea is genotype less markers, and make up for it by imputing(guessing) the gaps.

    Imputation accuracy depends on among other things how close the references are to the test subject. If they are close then accuracy is higher, if the concordance reference-test subject is lower, your imputed SNPs will be less accurate.

    Also, the more SNPs you have to impute the lower the accuracy. I definitely don't buy the idea of 97% accuracy if they have to impute 39 out 40 million markers, no matter what quality control measures you have.

    Ex, if you have to impute the missing letters in " I see a _ellow _at " vs "I _ee a _e____ _a_"

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    Thanks Kurd, your explanation makes a lot of sense

    should have known it was the marketing weasels behind this one...they must have dug deep into some old thesaurus to come up with a word that makes 'guess' sound good

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    A question. If the company (FTDNA) has the sample. Can they retest then to the new chip? How is it going to influence matching between two close relatives? Ethnicity estimates? Gedmatch?

    Anybody knows when FTDNA switches to GSA?
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    Quote Originally Posted by MikeWhalen View Post
    Thanks Kurd, your explanation makes a lot of sense

    should have known it was the marketing weasels behind this one...they must have dug deep into some old thesaurus to come up with a word that makes 'guess' sound good

    Mike
    All I can think is "Thank God I already bought three tests pre-imputation"

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    Quote Originally Posted by Aha View Post
    A question. If the company (FTDNA) has the sample. Can they retest then to the new chip? How is it going to influence matching between two close relatives? Ethnicity estimates? Gedmatch?

    Anybody knows when FTDNA switches to GSA?
    You would have to give them another DNA sample. If they use the same references as before then you can compare your results with and without imputation

    An easy way to check imputation accuracy is to prune out a random 200 or 300,000 markers from your 23 Or Ancestry or FTDNA and upload the file to DNAland, My Heritage or GenePlaza, and see how much your results change

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    Quote Originally Posted by Kurd View Post
    You would have to give them another DNA sample.
    Well that sucks. Many of my kits can no longer be resampled.

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    Quote Originally Posted by Kurd View Post
    You would have to give them another DNA sample.
    But why? I have heard they keep the sample for 25 years. They have two vials with samples. For example, I can order mtDNA or bigY tests 5 years from now. Why couldn't they retest Autosomal?
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    Quote Originally Posted by Aha View Post
    But why? I have heard they keep the sample for 25 years. They have two vials with samples. For example, I can order mtDNA or bigY tests 5 years from now. Why couldn't they retest Autosomal?
    Because sequencing is not free. They would have to charge to cover that cost

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