Confirmation of <i>HOXB13</i> G84E mutation status from classification and regression tree.

<p>The top of the figure shows three CART trees produced for the computationally phased haplotypes of the enriched reference panel of 93 individuals (22 carriers) plus 1000 Genomes data (2 carriers). Listed in the trees are the splits that classify the G84E mutation. The leaves in the tree contain the best guess classification of G84E on the top, and the number of reference alleles on the left and the number of G84E mutations on the right. The first tree, in black, is formed from selecting amongst all 57 SNPs +/− 3 crossovers. The second tree, in green, is formed from selecting from the same set of SNPs except excluding the 3 found in the first tree. The third tree, in blue, is formed from selecting amongst the same set of SNPs except excluding the 7 found in the first and second trees. Below the trees is a local chromosome plot of the region in reference to the surrounding genes and recombination rate of the region, with the color of the rs# for each SNP indicating the tree from which it was derived. KGW, 1000 Genomes white race/ethnicity individuals; frq, frequency.</p

Pleiotropic effect of G84E mutation on risk of cancer.

<p>Pleiotropic effect of G84E mutation on risk of cancer.</p

Ancestry of the HOXB13 G84E variant.

<p>Using the first two principal components (PCs) we created a smoothed estimate of the carrier frequency of each individual’s expected additive coding by using the 2,000 closest individuals (Euclidean distance) to calculate a G84E carrier frequency at that location, excluding individuals with >25% Ashkenazi ancestry. Text for the center of each Human Genome Diversity Project (HGDP) population is given to enhance interpretation; the mutation is most prevalent in northwestern Europe and Russian groups. To further adjust for incomplete LD, we multiplied the imputation carrier frequency by the r² estimate of 0.57.</p