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STRinNGS v2.0: Improved tool for analysis and reporting of STR sequencing data.
Forensic Sci Int Genet. 2020 09; 48:102331.FS

Abstract

High throughput sequencing of multiplexed PCR amplicons with Short Tandem Repeats (STRs) requires software solutions that sort the information and allow a comprehensive overview of the results without overwhelming the data analyst with details. Here, we present an updated version (2.0) of the STR analysis tool STRinNGS. It is freely available as a Docker image or zip file ready for downloading. STRinNGS predicts genotypes using criteria for read depth, noise, flanking region lengths, mismatches in the flanking regions, locus balance, and heterozygote balance. Warning flags highlight suspicious genotypes as well as suspicious sequences that are not identified as either noise or alleles in the result table used for the manual analysis. STRinNGS analyses both the STR and the flanking regions, and names the alleles according to the STRidER guidelines as well as an in-house nomenclature that also include variants in the flanking regions. Furthermore, STRinNGS generates files with analysed data in a format that may be uploaded directly to the STRidER database. We re-analysed 627 sample files from eight different MiSeq FGx runs with STRinNGS v2.0. The samples were previously typed with the ForenSeq™ Signature Prep Kit and analysed with STRinNGS v1.0 and the Universal Analysis Software. Apart from three poorly performing loci with large heterozygote imbalances (Penta E and D22S1045) or frequent single nucleotide errors (DYS461), only 58 genotype calls (0.2 %) had to be manually corrected and only 14 genotype calls were discordant with the previous analyses. The discordant calls were primarily caused by manual oversights and in every case, the STRinNGS v2.0 analysis was correct.

Authors+Show Affiliations

Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Institute of Forensic Medicine, West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu, China.Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. Electronic address: claus.boersting@sund.ku.dk.

Pub Type(s)

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

Language

eng

PubMed ID

32623352

Citation

Jønck, Carina Grøntved, et al. "STRinNGS V2.0: Improved Tool for Analysis and Reporting of STR Sequencing Data." Forensic Science International. Genetics, vol. 48, 2020, p. 102331.
Jønck CG, Qian X, Simayijiang H, et al. STRinNGS v2.0: Improved tool for analysis and reporting of STR sequencing data. Forensic Sci Int Genet. 2020;48:102331.
Jønck, C. G., Qian, X., Simayijiang, H., & Børsting, C. (2020). STRinNGS v2.0: Improved tool for analysis and reporting of STR sequencing data. Forensic Science International. Genetics, 48, 102331. https://doi.org/10.1016/j.fsigen.2020.102331
Jønck CG, et al. STRinNGS V2.0: Improved Tool for Analysis and Reporting of STR Sequencing Data. Forensic Sci Int Genet. 2020;48:102331. PubMed PMID: 32623352.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - STRinNGS v2.0: Improved tool for analysis and reporting of STR sequencing data. AU - Jønck,Carina Grøntved, AU - Qian,Xiaoqin, AU - Simayijiang,Halimureti, AU - Børsting,Claus, Y1 - 2020/06/20/ PY - 2019/12/30/received PY - 2020/04/23/revised PY - 2020/06/04/accepted PY - 2020/7/6/pubmed PY - 2021/7/13/medline PY - 2020/7/6/entrez KW - Forensic genetics KW - Massively parallel sequencing KW - Next generation sequencing KW - STR analysis KW - STRidER KW - STRinNGS python script SP - 102331 EP - 102331 JF - Forensic science international. Genetics JO - Forensic Sci Int Genet VL - 48 N2 - High throughput sequencing of multiplexed PCR amplicons with Short Tandem Repeats (STRs) requires software solutions that sort the information and allow a comprehensive overview of the results without overwhelming the data analyst with details. Here, we present an updated version (2.0) of the STR analysis tool STRinNGS. It is freely available as a Docker image or zip file ready for downloading. STRinNGS predicts genotypes using criteria for read depth, noise, flanking region lengths, mismatches in the flanking regions, locus balance, and heterozygote balance. Warning flags highlight suspicious genotypes as well as suspicious sequences that are not identified as either noise or alleles in the result table used for the manual analysis. STRinNGS analyses both the STR and the flanking regions, and names the alleles according to the STRidER guidelines as well as an in-house nomenclature that also include variants in the flanking regions. Furthermore, STRinNGS generates files with analysed data in a format that may be uploaded directly to the STRidER database. We re-analysed 627 sample files from eight different MiSeq FGx runs with STRinNGS v2.0. The samples were previously typed with the ForenSeq™ Signature Prep Kit and analysed with STRinNGS v1.0 and the Universal Analysis Software. Apart from three poorly performing loci with large heterozygote imbalances (Penta E and D22S1045) or frequent single nucleotide errors (DYS461), only 58 genotype calls (0.2 %) had to be manually corrected and only 14 genotype calls were discordant with the previous analyses. The discordant calls were primarily caused by manual oversights and in every case, the STRinNGS v2.0 analysis was correct. SN - 1878-0326 UR - https://www.unboundmedicine.com/medline/citation/32623352/STRinNGS_v2_0:_Improved_tool_for_analysis_and_reporting_of_STR_sequencing_data_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S1872-4973(20)30104-6 DB - PRIME DP - Unbound Medicine ER -