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Massively parallel sequence data of 31 autosomal STR loci from 496 Spanish individuals revealed concordance with CE-STR technology and enhanced discrimination power.
Forensic Sci Int Genet. 2019 09; 42:49-55.FS

Abstract

This study reports Short Tandem Repeat (STR) sequence-based allele data from 496 Spanish individuals across 31 autosomal STR (auSTR) loci included in the Precision ID GlobalFiler™ NGS STR Panel v2: D12S391, D13S317, D8S1179, D21S11, D3S1358, D5S818, D1S1656, D2S1338, vWA, D2S441, D5S2800, D7S820, D16S539, D6S474, D12ATA63, D4S2408, D6S1043, D19S433, D14S1434, CSF1PO, D10S1248, D18S51, D1S1677, D22S1045, D2S1776, D3S4529, FGA, Penta D, Penta E, TH01 and TPOX. The sequence of each allele was aligned to the reference sequence GRCh37 (hg19) and formatted according to the guidance of the International Society for Forensic Genetics. A subset of 221 samples was evaluated for testing concordance with allele calls derived from CE-based analysis using PowerPlex Fusion 6C, and there was 99.95% allele concordance. Twenty-five out of 31 auSTR loci showed an increased number of alleles due to repeat region sequence variation and/or single nucleotide polymorphisms (SNP) residing in the flanking regions. A total of 18 loci showed increased observed heterozygosity due to sequence variation; the loci exhibiting the greatest increase were: D13S317 (12% points), D5S818 (10% points), D8S1179 (7% points), D3S1358 (7% points), and D21S11 (6% points). The combined match probability decreased from 2.022E-24 (length-based data) to 1.042E-27 (sequence-based data) for the 20 CODIS core STR loci. The combined match probability (sequence-based data) for the 31 STR loci studied was 4.777E-40. The combined typical paternity index increased from 1.118E + 12 to 8.179E + 13 using length and sequence-based data, respectively. This Spanish population study performed in the framework of the EU-funded DNASEQEX project is expected to provide STR sequence-based allele frequencies for forensic casework and support implementation of massively parallel sequencing (MPS) technology in forensic laboratories.

Authors+Show Affiliations

National Institute of Toxicology and Forensic Sciences, Madrid Department, Spain. Electronic address: pedro.barrio@justicia.es.National Institute of Toxicology and Forensic Sciences, Madrid Department, Spain.National Institute of Toxicology and Forensic Sciences, Madrid Department, Spain.Institute of Legal Medicine, Medical University of Innsbruck, Austria.Institute of Legal Medicine, Medical University of Innsbruck, Austria.Institute of Legal Medicine, Medical University of Innsbruck, Austria.Institute of Legal Medicine, Medical University of Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, PA, USA.Center for Human Identification, University of North Texas Health Science Center, USA.No affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

31252251

Citation

Barrio, Pedro A., et al. "Massively Parallel Sequence Data of 31 Autosomal STR Loci From 496 Spanish Individuals Revealed Concordance With CE-STR Technology and Enhanced Discrimination Power." Forensic Science International. Genetics, vol. 42, 2019, pp. 49-55.
Barrio PA, Martín P, Alonso A, et al. Massively parallel sequence data of 31 autosomal STR loci from 496 Spanish individuals revealed concordance with CE-STR technology and enhanced discrimination power. Forensic Sci Int Genet. 2019;42:49-55.
Barrio, P. A., Martín, P., Alonso, A., Müller, P., Bodner, M., Berger, B., Parson, W., & Budowle, B. (2019). Massively parallel sequence data of 31 autosomal STR loci from 496 Spanish individuals revealed concordance with CE-STR technology and enhanced discrimination power. Forensic Science International. Genetics, 42, 49-55. https://doi.org/10.1016/j.fsigen.2019.06.009
Barrio PA, et al. Massively Parallel Sequence Data of 31 Autosomal STR Loci From 496 Spanish Individuals Revealed Concordance With CE-STR Technology and Enhanced Discrimination Power. Forensic Sci Int Genet. 2019;42:49-55. PubMed PMID: 31252251.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Massively parallel sequence data of 31 autosomal STR loci from 496 Spanish individuals revealed concordance with CE-STR technology and enhanced discrimination power. AU - Barrio,Pedro A, AU - Martín,Pablo, AU - Alonso,Antonio, AU - Müller,Petra, AU - Bodner,Martin, AU - Berger,Burkhard, AU - Parson,Walther, AU - Budowle,Bruce, AU - ,, Y1 - 2019/06/14/ PY - 2019/03/14/received PY - 2019/06/13/revised PY - 2019/06/13/accepted PY - 2019/6/30/pubmed PY - 2019/12/20/medline PY - 2019/6/29/entrez KW - Allele frequency KW - Bioinformatics KW - Massively parallel sequencing (MPS) KW - Population study KW - Sequence variants KW - Short tandem repeat (STR) KW - Spain SP - 49 EP - 55 JF - Forensic science international. Genetics JO - Forensic Sci Int Genet VL - 42 N2 - This study reports Short Tandem Repeat (STR) sequence-based allele data from 496 Spanish individuals across 31 autosomal STR (auSTR) loci included in the Precision ID GlobalFiler™ NGS STR Panel v2: D12S391, D13S317, D8S1179, D21S11, D3S1358, D5S818, D1S1656, D2S1338, vWA, D2S441, D5S2800, D7S820, D16S539, D6S474, D12ATA63, D4S2408, D6S1043, D19S433, D14S1434, CSF1PO, D10S1248, D18S51, D1S1677, D22S1045, D2S1776, D3S4529, FGA, Penta D, Penta E, TH01 and TPOX. The sequence of each allele was aligned to the reference sequence GRCh37 (hg19) and formatted according to the guidance of the International Society for Forensic Genetics. A subset of 221 samples was evaluated for testing concordance with allele calls derived from CE-based analysis using PowerPlex Fusion 6C, and there was 99.95% allele concordance. Twenty-five out of 31 auSTR loci showed an increased number of alleles due to repeat region sequence variation and/or single nucleotide polymorphisms (SNP) residing in the flanking regions. A total of 18 loci showed increased observed heterozygosity due to sequence variation; the loci exhibiting the greatest increase were: D13S317 (12% points), D5S818 (10% points), D8S1179 (7% points), D3S1358 (7% points), and D21S11 (6% points). The combined match probability decreased from 2.022E-24 (length-based data) to 1.042E-27 (sequence-based data) for the 20 CODIS core STR loci. The combined match probability (sequence-based data) for the 31 STR loci studied was 4.777E-40. The combined typical paternity index increased from 1.118E + 12 to 8.179E + 13 using length and sequence-based data, respectively. This Spanish population study performed in the framework of the EU-funded DNASEQEX project is expected to provide STR sequence-based allele frequencies for forensic casework and support implementation of massively parallel sequencing (MPS) technology in forensic laboratories. SN - 1878-0326 UR - https://www.unboundmedicine.com/medline/citation/31252251/Massively_parallel_sequence_data_of_31_autosomal_STR_loci_from_496_Spanish_individuals_revealed_concordance_with_CE_STR_technology_and_enhanced_discrimination_power_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S1872-4973(19)30113-9 DB - PRIME DP - Unbound Medicine ER -