The output from a HiSeq instrument can reach up to 600 GB per run, with more than 80% of the reads with an average quality score higher than 30 (99.9% accurate). Bridging PCR amplification of fragmented genomic DNA in a flow cell and sequencing-by-synthesis chemical reactions truly realize massive parallel sequencing from both ends of a DNA fragment. The resequencing market is currently dominated by Illumina HiSeq sequencing platforms (hereafter referred to as HiSeq) that have been applied in large population studies. The application of human WGS to large-population genetics requires rapid, low cost, and accurate validation technologies. Whole-genome sequencing (WGS) of human genomic DNA with next-generation sequencers (NGSs) has opened a new avenue for personalized healthcare and personalized medicine based on the detection of genetic variations related to physical traits. Our results show the versatility and usefulness of the combination of exome sequencing with whole-genome sequencing in studies of human population genetics and demonstrate that combining data from multiple sequencing platforms is an efficient approach to validate and supplement SNP calls. We compared the variant calls for the 12 samples, and found that the concordance between the two next-generation sequencing platforms varied between 83% and 97%. Single nucleotide polymorphism (SNP) calls based on the Illumina Human Omni 2.5-8 SNP chip data were used as the reference. Here, we analyzed 12 independent Japanese genomes using two next-generation sequencing platforms: the Illumina HiSeq 2500 platform for whole-genome sequencing (average depth 32.4×), and the Ion Proton semiconductor sequencer for whole exome sequencing (average depth 109×). A combination of different types of next-generation sequencers for analyzing individual genomes may be an efficient means of validating multiple single nucleotide variations calls simultaneously. Validation of single nucleotide variations in whole-genome sequencing is critical for studying disease-related variations in large populations.
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