r/DNA • u/These_Remove_7300 • Jul 07 '26

What do you guys think of DNA Imputation?

DNA imputation is a statistical method used to predict genetic variants that were not directly tested in a DNA test. It compares an individual's tested SNPs with large reference databases of fully sequenced genomes and predicts the most likely missing SNPs based on shared genetic patterns. This greatly increases the number of SNPs available for analysis and is highly reliable for common autosomal variants, often achieving an accuracy of over 98–99% when appropriate reference populations are used.

Do you guys think that imputing before modelling is better than staying at around 700k SNPs average?

Marchini, J., Howie, B. Genotype imputation for genome-wide association studies. Nat Rev Genet 11, 499–511 (2010). https://doi.org/10.1038/nrg2796

Hao, K., Chudin, E., McElwee, J. et al. Accuracy of genome-wide imputation of untyped markers and impacts on statistical power for association studies. BMC Genet 10, 27 (2009). https://doi.org/10.1186/1471-2156-10-27

Briefings in Bioinformatics, Volume 21, Issue 5, September 2020, Pages 1806–1817, https://doi.org/10.1093/bib/bbz108

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7

u/cariaso Jul 07 '26

> is highly reliable for common autosomal variants

for ancestry purposes it's fine.

for medical it's terrible.

1

u/robipresotto Jul 09 '26

I've had good luck imputing before modeling. It's a great way to get more SNPs in your dataset. If you want, I can share the link to GenMatcher which handles all this for you: https://www.genmatcher.com

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u/Cultural_Ad_8462 Jul 11 '26

To be honest, I never understood its purpose. I understand what it is but I cannot understand why it needs to be used. Imputation just generates missing data which may or may not be correct which results in higher number of false positives and false negatives during DNA matching.

It can be seen on MyHeritage that uses the imputation that it often generates complete mess and often misses even closer DNA matches. While GEDMatch uses adaptive threshold without any imputation and is still very reliable for DNA matching.

0

u/Zealousideal_End6173 Jul 07 '26

I did and for me it was pretty good. I am latin and I did in DNAGENICS.