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Three and a half decades later, in 1915, his correct ancestry was published, but not before the misinformation had been printed in an important source for Rhode Island genealogy.
We measure the accuracy of a method as the fraction of all the genotypes in the dataset for which the correct ancestry was inferred.
We observe that local ancestry prediction accuracy (i.e., the proportion of alleles assigned to the correct ancestry, see the section Materials and Methods) increases with the distance between ancestral locations from 55% of loci assigned accurately for very closely related ancestries (less than 500 km apart) to more than 70% for ancestries 2500 km apart.
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To account for population outliers and correct for differential ancestry between cases and controls that may exist in the dataset after familial outlier removal, a principal component (PC) analysis was conducted using the EIGENSTRAT software (Broad Institute, Boston, MA, USA) [ 38].
The presence of population stratification can inflate false positive rates or cause reduced power and it has become standard practice to evaluate and correct for genetic ancestry in GWASs [for a review see [ 7]].
In Figure 4 we showed that although on average the correct number of ancestries will be inferred, in a high proportion of cases the inferred number of ancestries will be mistaken.
However, the inflation of p-values for the differences was adequately controlled by correcting for genetic ancestry estimates derived from a reduced number of AIMs.
Also, we always use the correct number of ancestries M or N as input.
Associations for 40 of the 79 SNPs ranged from 1.3 × 10−5 ≥ P ≥ 4.4 × 10−27, recessive model, before correcting for African ancestry, and were found across the gene.
We corrected for local ancestry for HIVAN, FSGS and H-ESKD using 35 diallelic ancestry informative markers (AIMs) (mean delta difference between CEU and YRI 49.6%, range 22 76%) across chromosome 22.
The African ancestry is correct, but his family has been American for many, many generations.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com