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. 2016 Mar:21:15-21.
doi: 10.1016/j.fsigen.2015.11.005. Epub 2015 Dec 1.

Sequence variation of 22 autosomal STR loci detected by next generation sequencing

Katherine Butler Gettings  1 , Kevin M Kiesler  2 , Seth A Faith  3 , Elizabeth Montano  4 , Christine H Baker  5 , Brian A Young  6 , Richard A Guerrieri  7 , Peter M Vallone  8
Affiliations

Sequence variation of 22 autosomal STR loci detected by next generation sequencing

Katherine Butler Gettings et al. Forensic Sci Int Genet. 2016 Mar.

Abstract

Sequencing short tandem repeat (STR) loci allows for determination of repeat motif variations within the STR (or entire PCR amplicon) which cannot be ascertained by size-based PCR fragment analysis. Sanger sequencing has been used in research laboratories to further characterize STR loci, but is impractical for routine forensic use due to the laborious nature of the procedure in general and additional steps required to separate heterozygous alleles. Recent advances in library preparation methods enable high-throughput next generation sequencing (NGS) and technological improvements in sequencing chemistries now offer sufficient read lengths to encompass STR alleles. Herein, we present sequencing results from 183 DNA samples, including African American, Caucasian, and Hispanic individuals, at 22 autosomal forensic STR loci using an assay designed for NGS. The resulting dataset has been used to perform population genetic analyses of allelic diversity by length compared to sequence, and exemplifies which loci are likely to achieve the greatest gains in discrimination via sequencing. Within this data set, six loci demonstrate greater than double the number of alleles obtained by sequence compared to the number of alleles obtained by length: D12S391, D2S1338, D21S11, D8S1179, vWA, and D3S1358. As expected, repeat region sequences which had not previously been reported in forensic literature were identified.

Keywords: Next generation sequencing; Population genetics; STR.

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Figures

Figure 1
Figure 1
Within-locus distribution of increase in alleles via sequencing. Numbers not in parentheses reflect the length-based alleles obtained in N=183; whereas numbers in parentheses (when present) represent how many sequence variants were observed in N=183. Loci are arranged by simple repeats ordered by increasing numbers of length-based alleles followed by compound/complex repeats ordered by increasing number of length-based alleles. Color coding ranges from dark green = least sequence variation to red = greatest sequence variation.
See this image and copyright information in PMC

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