Multiplex padlock targeted sequencing reveals human hypermutable CpG variations

摘要: Utilizing the full power of next-generation sequencing often requires ability to perform large-scale multiplex enrichment many specific genomic loci in multiple samples. Several technologies have been recently developed but await substantial improvements. We report 10,000-fold improvement a previously padlock-based approach, and apply assay identifying genetic variations hypermutable CpG regions across human chromosome 21. From approximately 3 million reads derived from single Illumina Genome Analyzer lane, 94% (approximately 50,500) target sites can be observed with at least one read. The uniformity coverage was also greatly improved; up 93% 57% all targets fell within 100- 10-fold range, respectively. Alleles >400,000 base positions were determined six subjects examined for nucleotide polymorphisms (SNPs), concordance independently obtained genotypes 98.4%-100%. detected >500 SNPs not currently dbSNP, 362 which targeted locations. Transitions 13.7 times more abundant than non-CpG transitions. Fractions polymorphic are lower CpG-rich show higher correlation human-chimpanzee divergence versus sites. This is consistent hypothesis that methylation rate heterogeneity along chromosomes contributes mutation variation humans. Our success suggests resequencing an efficient way identify common rare variations. In addition, significantly improved padlock capture technology readily applied other projects require sample preparation.