Next-generation sequencing methods: impact of sequencing accuracy on SNP discovery

The advent of next-generation sequencing technologies has spurred remarkable progress in the field of genomics. Whereas traditional Sanger sequencing has yielded the first complete human genome sequence, next-generation methods have been able to resequence several human genomes. In this manner, next-generation approaches have powerful capabilities for understanding human variation. The throughput for these approaches is often measured in billions of base pairs per run, astounding numbers when compared with the millions of base pairs per day generated by automated capillary DNA sequencers. However, unlike traditional Sanger dideoxy sequencing, these methods have lower accuracy and shorter read lengths than the dideoxy gold standard. Are these limitations offset by the higher throughputs? An in-depth look at the single read and composite accuracy of these methods is presented. The stringent requirements for single nucleotide polymorphism (SNP) discovery utilizing these approaches is discussed along with a review of studies that have successfully employed next-generation sequencing methods for large-scale SNP discovery. Ultimately, the application of these ultra-high-throughput sequencing methods for SNP discovery will open up new horizons for understanding human genomic variation.