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

Published: December 01, 2015

Author(s)

Katherine B. Gettings, Kevin M. Kiesler, Seth A. Faith, Elizabeth Montano, Christine H. Baker, Brian A. Young, Richard A. Guerreri, Peter M. Vallone

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 results from the library preparation of 183 DNA samples, including African American, Caucasian, and Hispanic individuals, in 96-well format and subsequent sequencing of 22 autosomal forensic STR loci on the Illumina MiSeq instrument. The resulting dataset has been used to perform population genetic analyses of allelic diversity by length compared to sequence, and the results exemplify 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.
Citation: Forensic Science International: Genetics
Volume: 21
Pub Type: Journals

Keywords

Short Tandem Repeat (STR), Next generation sequencing (NGS)
Created December 01, 2015, Updated November 10, 2018