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I will obtain array genotype data from approximately 60 related individuals who all share a rare pathogenic variant, which is at such a high frequency in the enlarged family due to a founder effect.
Is there any software that I can use to estimate the "age" of this founder effect i.e. how long ago there was a "most recent common ancestor", basing on the haplotypes observed from genotype data?

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  • $\begingroup$ Welcome to Biology.SE. Coalescent theory is what you need. Take a look at this list of available software. $\endgroup$ – AlexDeLarge Sep 8 '16 at 15:09
  • $\begingroup$ You will need genome-wide data to make a good estimate of the time to founder effect. If you only genotyped individuals for the single locus explaining variance for the disease, you won't be able to estimate much. What kind of data do you have exactly? $\endgroup$ – Remi.b Sep 8 '16 at 16:37
  • $\begingroup$ ABC to the Jensen style might be useful but it won't be as easy as feeding your raw data to a software. $\endgroup$ – Remi.b Sep 8 '16 at 16:52
  • $\begingroup$ I am not sure on the exact array version on which samples have been genotyped, but it will be genome-wide (I guess it'll be Illumina Omni Express, approx 700k SNPs). Thanks for the suggestions, please let me know if you happen to find some other software....I am also looking in the literature but there seems not to be anything particularly user-friendly to do this... $\endgroup$ – Franz Sep 9 '16 at 9:21

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