High sensitivity multiplex short tandem repeat loci analyses with massively parallel sequencing

Xiangpei Zeng, Jonathan L. King, Monika Stoljarova, David H. Warshauer, Bobby L. LaRue, Antti Sajantila, Jaynish Patel, Douglas R. Storts, Bruce Budowle

Research output: Contribution to journalArticle

53 Citations (Scopus)

Abstract

STR typing in forensic genetics has been performed traditionally using capillary electrophoresis (CE). However, CE-based method has some limitations: a small number of STR loci can be used; stutter products, dye artifacts and low level alleles. Massively parallel sequencing (MPS) has been considered a viable technology in recent years allowing high-throughput coverage at a relatively affordable price. Some of the CE-based limitations may be overcome with the application of MPS. In this study, a prototype multiplex STR System (Promega) was amplified and prepared using the TruSeq DNA LT Sample Preparation Kit (Illumina) in 24 samples. Results showed that the MinElute PCR Purification Kit (Qiagen) was a better size selection method compared with recommended diluted bead mixtures. The library input sensitivity study showed that a wide range of amplicon product (6-200 ng) could be used for library preparation without apparent differences in the STR profile. PCR sensitivity study indicated that 62 pg may be minimum input amount for generating complete profiles. Reliability study results on 24 different individuals showed that high depth of coverage (DoC) and balanced heterozygote allele coverage ratios (ACRs) could be obtained with 250 pg of input DNA, and 62 pg could generate complete or nearly complete profiles. These studies indicate that this STR multiplex system and the Illumina MiSeq can generate reliable STR profiles at a sensitivity level that competes with current widely used CE-based method.

Original languageEnglish
Pages (from-to)38-47
Number of pages10
JournalForensic Science International: Genetics
Volume16
DOIs
StatePublished - 1 Jan 2015

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High-Throughput Nucleotide Sequencing
Capillary Electrophoresis
Microsatellite Repeats
Libraries
Forensic Genetics
Alleles
Polymerase Chain Reaction
DNA
Heterozygote
Reproducibility of Results
Artifacts
Coloring Agents
Technology

Keywords

  • Illumina MiSeq
  • Massively parallel sequencing (MPS)
  • Short tandem repeat (STR)

Cite this

Zeng, Xiangpei ; King, Jonathan L. ; Stoljarova, Monika ; Warshauer, David H. ; LaRue, Bobby L. ; Sajantila, Antti ; Patel, Jaynish ; Storts, Douglas R. ; Budowle, Bruce. / High sensitivity multiplex short tandem repeat loci analyses with massively parallel sequencing. In: Forensic Science International: Genetics. 2015 ; Vol. 16. pp. 38-47.
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High sensitivity multiplex short tandem repeat loci analyses with massively parallel sequencing. / Zeng, Xiangpei; King, Jonathan L.; Stoljarova, Monika; Warshauer, David H.; LaRue, Bobby L.; Sajantila, Antti; Patel, Jaynish; Storts, Douglas R.; Budowle, Bruce.

In: Forensic Science International: Genetics, Vol. 16, 01.01.2015, p. 38-47.

Research output: Contribution to journalArticle

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