SNP Genotyping of Native DNA using Oxford Nanopore MinION Sequencing
Ludwick, Whitney N.
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Short tandem repeats (STRs) are the primary system of genetic variation used for human identity testing in forensics; however, STR typing relies on the use of time- consuming polymerase chain reaction and expensive laboratory equipment. The use of single nucleotide polymorphisms (SNPs) in forensics have several advantages over STRs. In this study, a panel of Identity SNPs were interrogated and typed from native genomic DNA sequencing libraries using the Oxford Nanopore Technologies (ONT) MinION sequencer. We determined that SNPs could be effectively captured using existing software. Four different methods of alignment were investigated, and we found that aligning sequence data to the human genomic sequence (hg19) provided partial profiles, while aligning data to a merged reference profile resulted in more complete profiles. As ONT?s platform continues to improve, SNP genotyping using the MinION may be used to generate complete SNP profiles with the sufficient depth of coverage for reliable genotype determination.