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It has been proposed that a globally useful resource need only be based on high frequency variants, identified from a few modest samples.
The potential DNA copy number variants identified from aCGH were further validated using TaqMan probe-based CNV real-time PCR in a data set containing 91 XFG cases and 52 controls.
Mendelian randomization analyses were conducted using summary statistics obtained for 423 genetic variants identified from a recent GWAS of adult height and from a cancer genetics consortium study of multiple cancers that included 47,800 cases and 81,353 controls.
A total of 23 independent cDNA clones were identified and aligned with the eight major variants identified from Japan.
Note that all of the variants identified from the GWAS findings are in non-coding regions and the functional consequences of these variants remain largely unknown, thus follow-up sequencing studies and functional experiments will be required.
Increased understanding of these elements will be crucial to obtain a coherent functional assessment of the large number of non-coding DNA variants identified from contemporary whole genome sequencing case-control studies, and to delineate their developmental and tissue-specific features and constraints.
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This represents one of the first examples of a rare, large effect variant identified from whole-genome sequencing at a population scale.
Affinities of several enhanced point-variants identified from the point-variant screen were determined by SPR using equilibrium binding responses across a series of peptide concentrations on an SPR chip containing varying levels of immobilized TNF-α with a predicted Rmax range of 40-120 RU.
Candidate variant identified from whole exome sequencing was confirmed using conventional Sanger sequencing to exclude the possibility of false positive.
HLAminer parses these alignment files and generates a score and probability for each putative HLA coding variant identified from sequence contigs.
The variant identified from the East Asian study, rs6467136, appears to be independent of our signal, with r = 0.044 in our Chinese samples (ESM Fig. 8).
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