Second, SNP-based eQTL mapping is particularly suited for identifying ancestry-predictive eQTL that carry population-specific alleles for distant ethnic groups such as YRI and CEU.
I would appreciate further details about the following statement from the article entitled "A 1920's Estate Garden Is Carefully Restored" (June 18): "In other notes she left, Caroline Ferriday identified ancestry of a weeping willow in the orchard.
The project is using more than 250 genetic markers to identify ancestry.
Self identified ancestry was shown in previous studies to be a reliable measure of ancestry [ 21].
The authors identified ancestry indicators, controlled these as confounders but did not stratify their analysis by these markers.
However, having completed a GWAS it is straightforward to identify ancestry and compensate for any stratification (Devlin and Roeder, 1999; Bacanu et al., 2000; Devlin et al., 2004).
Here, it was used to detect single-nucleotide polymorphisms in the FUT2 locus, genotype the ABO locus, and identify ancestry based on 1723 ancestral informative markers.
This decision was based on the fact that most of the AIM panels available were designed to identify ancestry from main population groups.
To identify ancestry outliers, we used principal component analysis (PCA) of similarly genotyped data from 16 global populations sourced from HapMap Phase 3 (HM3; 11 populations) and a previously published study of Northern European genetic diversity (GEUT; 5 populations) (36).
We use this capability for exploratory data analysis, where we experiment with various thresholds on minimal spacing between SNVs (to increase independence), minimal FST between the source populations (to identify "ancestry informative markers"), and switch penalty, to reach conclusions that are robust to changes in analysis parameters.
In the first step, we identified ancestry-informative transcripts.
