TY - JOUR
T1 - Assessing sequence variation and genetic diversity of currently untapped Y-STR loci
AU - King, Jonathan L.
AU - Woerner, August E.
AU - Muenzler, Melissa K.
AU - Kapema, Kapema Bupe
AU - Bus, Magdalena M.
AU - Smuts, Amy
AU - Ge, Jianye
AU - Budowle, Bruce
N1 - Funding Information:
This work was supported in part by award 2015-DN-BX-K067, awarded by the National Institute of Justice, Office of Justice Programs, U.S. Department of Justice. The opinions, findings, and conclusions or recommendations expressed are those of the authors and do not necessarily reflect those of the U.S. Department of Justice. The authors would like to thank Maiko Takahashi for her technical assistance and Dr. Michael Coble for thoughtful discussion regarding the forensic parameters and data analysis. Additionally, the authors would like to extend special thanks to Illumina Technical Support for their assistance with multiplex design. Lastly, the authors would like to thank Lisa Borsuk from NIST Applied Genetics for initial help with identification of Y-STR locus names. All authors provided considerable contributions to the study and approved the final manuscript. BB obtained funding for the study. JLK, AEW, and BB, Conceptualization; MKM, KBK, and AS, Methodology; JLK, AEW, KBK, MMB, and JG, Formal analysis; JLK and AEW, Writing – original draft. All authors, Writing – review & editing. This work was supported in part by award 2015-DN-BX-K067, awarded by the National Institute of Justice, Office of Justice Programs, U.S. Department of Justice.
Funding Information:
This work was supported in part by award 2015-DN-BX-K067, awarded by the National Institute of Justice, Office of Justice Programs, U.S. Department of Justice.
Funding Information:
This work was supported in part by award 2015-DN-BX-K067 , awarded by the National Institute of Justice, Office of Justice Programs, U.S. Department of Justice . The opinions, findings, and conclusions or recommendations expressed are those of the authors and do not necessarily reflect those of the U.S. Department of Justice. The authors would like to thank Maiko Takahashi for her technical assistance and Dr. Michael Coble for thoughtful discussion regarding the forensic parameters and data analysis. Additionally, the authors would like to extend special thanks to Illumina Technical Support for their assistance with multiplex design. Lastly, the authors would like to thank Lisa Borsuk from NIST Applied Genetics for initial help with identification of Y-STR locus names.
Publisher Copyright:
© 2022 The Authors
PY - 2022/12
Y1 - 2022/12
N2 - With the advent of massively parallel sequencing (MPS) the full genetic variation of short tandem repeat (STR) markers can be assessed. Most MPS efforts of forensic interest to date have focused on autosomal STRs, with far less attention to the potential genetic variation contained within Y-STR loci. Many of the non-commercialized Y-STR loci described previously have not been reassessed with MPS to determine the full level of genetic diversity of these markers at the sequence level. In this study, genomic data were mined from the Phase 3 1000 Genomes Project to identify forensically relevant STRs using lobSTR, HipSTR, and an in-house pipeline. These loci then were typed in a dual-phase approach with an Illumina Custom Amplicon (281 markers; ≤ 425 bp) panel followed by an AmpliSeq Custom Amplicon (83 markers; ≤ 275 bp) panel using four populations (African American, US Caucasian, US East Asian, and US Southwest Hispanic). STRs also were assayed with the ForenSeq Signature Prep Kit. The genetic diversity of the loci was assessed and ranked for a final set of 81 loci. When ranking all loci with respect to genetic diversity highest-to-lowest, seven of the top ten loci are not utilized in a current commercial assay.
AB - With the advent of massively parallel sequencing (MPS) the full genetic variation of short tandem repeat (STR) markers can be assessed. Most MPS efforts of forensic interest to date have focused on autosomal STRs, with far less attention to the potential genetic variation contained within Y-STR loci. Many of the non-commercialized Y-STR loci described previously have not been reassessed with MPS to determine the full level of genetic diversity of these markers at the sequence level. In this study, genomic data were mined from the Phase 3 1000 Genomes Project to identify forensically relevant STRs using lobSTR, HipSTR, and an in-house pipeline. These loci then were typed in a dual-phase approach with an Illumina Custom Amplicon (281 markers; ≤ 425 bp) panel followed by an AmpliSeq Custom Amplicon (83 markers; ≤ 275 bp) panel using four populations (African American, US Caucasian, US East Asian, and US Southwest Hispanic). STRs also were assayed with the ForenSeq Signature Prep Kit. The genetic diversity of the loci was assessed and ranked for a final set of 81 loci. When ranking all loci with respect to genetic diversity highest-to-lowest, seven of the top ten loci are not utilized in a current commercial assay.
KW - DNA mixtures
KW - Massively parallel sequencing
KW - Mixture deconvolution
KW - Next-generation sequencing
KW - Y-STR
UR - http://www.scopus.com/inward/record.url?scp=85141396675&partnerID=8YFLogxK
U2 - 10.1016/j.fsir.2022.100298
DO - 10.1016/j.fsir.2022.100298
M3 - Article
AN - SCOPUS:85141396675
SN - 2665-9107
VL - 6
JO - Forensic Science International: Reports
JF - Forensic Science International: Reports
M1 - 100298
ER -