March 07, 2008

Using pedigree information to infer ancestral proportions

This is a nice paper, which would be potentially very useful to genetic genealogists. Roughly speaking, existing methods for inferring ancestry rely either on pedigrees (one's ancestry is inferred from the ancestry of one's known ancestors), or on comparisons between the genotype of the unknown individual and those of reference populations. The novelty is this work is that it shows how genotypes and pedigree data can be combined to provide a better estimate of a person's ancestral proportions.

Am J Hum Genet. 2008 Mar;82(3):748-55.

Estimating ethnic admixture from pedigree data.

Sinsheimer JS, Plaisier CL, Huertas-Vazquez A, Aguilar-Salinas C, Tusie-Luna T, Pajukanta P, Lange K.

This paper introduces a likelihood method of estimating ethnic admixture that uses individuals, pedigrees, or a combination of individuals and pedigrees. For each founder of a pedigree, admixture proportions are calculated by conditioning on the pedigree-wide genotypes at all ancestry-informative markers. These estimates are then propagated down the pedigree to the nonfounders by a simple averaging process. The large-sample standard errors of the founders' proportions can be similarly transformed into standard errors for the admixture proportions of the descendants. These standard errors are smaller than the corresponding standard errors when each individual is treated independently. Both hard and soft information on a founder's ancestry can be accommodated in this scheme, which has been implemented in the genetic software package Mendel. The utility of the method is demonstrated on simulated data and a real data example involving Mexican families of mixed Amerindian and Spanish ancestry.


1 comment:

n/a said...

The idea is hardly novel. DNAprint marks/customers glommed onto this tack years ago.

And that's the thing--as relates to individual admixture estimates, you only really need to do this if you're typing an insufficient number of markers per individual and need to increase your your sample size. If you want to tighten an individual admixture estimate, just increase the number of markers examined.

Many genetic genealogists will want to sample forebears, siblings, and cousins, but not, on the whole, to tighten individual continent-level admixture estimates. (Individual admixture being the proportion of genes the individual inherits from each ethnic group, as opposed to ancestry, the fraction of ones ancestors who belonged to each ethnic group.)

I found this paper more interesting.