First-generation sequencing and genome-wide association technologies. (A) Stylized schematic of fluorescence-based (Sanger) sequencing chromatogram result showing heterozygosity for T/C at position Y. (B) Cartoon of genome-wide SNP marker genotyping array (SNP array) showing detection of differential hybridization (green or red if homozygous, yellow if heterozygous) of fluorescently labeled DNA representing common SNPs to the chip. (C) Cartoons of results from genetic array data. In GWAS, a “Manhattan plot” is typically used to summarize the large number of P values obtained, as represented by genomic coordinates displayed along the x-axis, with the negative logarithm of the association P value for each SNP displayed on the y-axis. A −log P value, such as indicated by the dashed line, is generated which is considered to meet the threshold for statistical significance. SNPs with significant values would appear above the line (shown in red). (D) For array CGH, gains and losses of DNA are given as a ratio and plotted against genomic position. This example shows loss of a region compared with the reference.