Whole exome-sequencing of pooled genomic DNA samples to detect quantitative trait loci in esotropia and exotropia of strabismus in Japanese. Homo sapiens

Background: Esotropia and exotropia are two major phenotypes of comitant strabismus. It remains controversial whether esotropia and exotropia would share common genetic background. In this study, we used quantitative trait locus (QTL)-sequencing pipeline for diploid plants to screen for susceptibility loci of strabismus in whole exome suquencing of pooled genomic DNAs of individuals. Methods:Pooled genomic DNA (2.5 ng each) of 20 individuals in three groups, patients with esotropia and exotropia, and normal members in the families, was sequenced after exome capture. The sequencing of the same pooled libraries was repeated, and the first and second sets of data in each group were combined to increase the read depth. The SNP index, as the ratio of variant genotype reads to all reads, and delta (SNP index) values, as the difference of SNP index between two groups, were calculated by sliding window analysis with the 4Mb window size and 10 kb slide size. The rows of 200 Ns were inserted as a putative 200-b spacer between every adjoining loci to depict delta (SNP index) plots on each chromosome. SNP positions with depth <20 as well as SNP positions with SNP index of <0.3 were excluded.