The 82nd Annual Meeting of the American Association of Physical Anthropologists (2013)

Y-chromosome library construction for next-generation sequencing


1College of Agricultural and Life Sciences, University of Florida, Gainesville, 2Department of Anthropology, University of Florida, Gainesville, 3Genetics and Genomics Graduate Program, University of Florida, Gainesville

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The Y-chromosome is particularly useful for population history inferences through the investigation of haplogroup diversity among males. These haplogroups are defined by single nucleotide polymorphisms (SNPs). The cost of high-throughput sequencing of the entire Y-chromosome of multiple individuals for population analyses renders it prohibitive for SNP investigation. Selectively enriching for those areas of the Y-chromosome that provide the most useful information, via library construction, can make next-generation sequencing cost-effective. To this end, we are creating a protocol in which we enrich for Y-chromosome fragments containing lineage-defining SNPs through hybridization with PCR products of selected haplogroups. Two thousand base pair fragments were generated from these PCRs to serve as probes to capture complementary sequences on the Y-chromosome. The resulting PCR products were sheared to create a tiling effect that increased sequence diversity and coverage during hybridization. Individual samples were tagged with unique identifying sequences, allowing multiple samples to be pooled and sequenced on a single lane of the Illumina GAIIx after capture on custom probes. Sixty-three primer pairs were designed to produce probes containing over 150 Y-chromosome SNPs. SNPs were chosen that define major haplogroups, as well as more divergent subgroups of E and J haplogroups, which are of particular interest in our samples. Ninety-five samples were uniquely tagged and pooled for library construction. Approximately 1.824 billion bases mapped to the Y-chromosome, allowing for haplogroup determinations of all 95 samples. This method provides an unprecedented amount of Y-chromosome sequence data in order to address questions that have been intractable thus far.

Samples sequenced in the study were collected with support of NSF grant BCS-0518530

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