Homo sapiens strain:NA12248 Targeted Locus (Loci)

Background: The ability to accurately and cost-effectively capture and sequence large, contiguous DNA segments is a major factor that will significantly impact the comprehensive characterization of complex genomic regions. Such large pieces are more reliable to assemble because they provide much greater sequence context; enough to span confounding sequence elements, such as homologous regions, repeats, transposons and rearrangements or insertions of unknown sequences even in the absence of a feasible reference sequence.Results: This report presents a long-range capture technology, region-specific extraction (RSE), which enables sequencing for variant detection across the continuum of megabase-sized genomic regions. RSE uses short and highly specific sequence elements as target points to capture genomic segments that can be as large as the fragments generated after the initial DNA extraction from variable tissues - which means that if the length of the extracted DNA material is as large as hundreds of thousands of bases, RSE's principle of operation allows the direct capture of these large fragments. RSE capture is achieved by a single primer extension step during which a newly synthesized strand labeled with biotinylated nucleotides firmly locks the genomic DNA target segments onto streptavidin-coated magnetic beads for capture. These segments, which extend far into both directions from any single capture point, are then whole genome amplified for use in NGS.Conclusions: We demonstrate the accuracy, simplicity and utility of RSE across the region with the highest genetic variability of the human genome: the 4Mbp major histocompatibility complex (MHC). RSE provides long DNA fragments, which upon sequencing provides high quality data that simplifies and improves the detection of both genic and intergenic variations that might otherwise be missed by current commercial targeted sequencing methodologies utilizing shorter DNA fragments.