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Evaluation of a SNP-STR haplotype panel for forensic genotype imputation

Published:October 17, 2022DOI:https://doi.org/10.1016/j.fsigen.2022.102801

      Highlights

      • A novel study of performing genotype imputation across disjoint genetic marker sets based on a 1000 Genomes SNP-STR haplotype panel.
      • Genotype imputation has great application potential for extracting genetic information associated with STRs.
      • Match score analysis after genotype imputation may help for individual identification.

      Abstract

      Short tandem repeat polymorphism (STR)-based individual identification is a popular and reliable method in many forensic applications. However, STRs still frequently fail to find any matched records. In such cases, if known STRs could provide more information, it would be very helpful to solve specific problems. Genotype imputation has long been used in the study of single nucleotide polymorphisms (SNPs) and has recently been introduced into forensic fields. The idea is that, through a reference haplotype panel containing SNPs and STRs, we can obtain unknown genetic information through genotype imputation based on known STR or SNP genotypes. Several recent studies have already demonstrated this exciting idea, and a 1000 Genomes SNP-STR haplotype panel has also been released. To further study the performance of genotype imputation in forensic fields, we collected STR, microhaplotype (MH) and SNP array genotypes from Chinese Han population individuals and then performed genotype imputation analysis based on the released reference panel. As a result, the average locus imputation accuracy was ∼83 % (or ∼70 %) when SNPs in the SNP array (or MH SNPs) were imputed from STRs, and was ∼30 % when highly polymorphic markers (STRs and MHs) were imputed from each other. When STRs were imputed from SNP array, the average locus imputation accuracy increased to ∼48 %. After analyzing the match scores between real STRs and the STRs imputed from SNPs, ∼80 % of studied STR records can be connected to corresponding SNP records, which may help for individual identification. Our results indicate that genotype imputation has great potential for forensic applications.

      Keywords

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      References

        • Taylor D.
        • Buckleton J.
        Can a reference 'match' an evidence profile if these have no loci in common?.
        Forensic Sci. Int. Genet. 2021; 53102520https://doi.org/10.1016/j.fsigen.2021.102520
        • Edge M.D.
        • Algee-Hewitt B.F.B.
        • Pemberton T.J.
        • et al.
        Linkage disequilibrium matches forensic genetic records to disjoint genomic marker sets.
        Proc. Natl. Acad. Sci. U. S. A. 2017; 114: 5671-5676https://doi.org/10.1073/pnas.1619944114
        • Kim J.
        • Edge M.D.
        • Algee-Hewitt B.F.B.
        • et al.
        Statistical detection of relatives typed with disjoint forensic and biomedical loci.
        Cell. 2018; 175 (.e6): 848-858https://doi.org/10.1016/j.cell.2018.09.008
        • Timpson N.J.
        • Greenwood C.M.T.
        • Soranzo N.
        • et al.
        Genetic architecture: the shape of the genetic contribution to human traits and disease.
        Nat. Rev. Genet. 2018; 19: 110-124https://doi.org/10.1038/nrg.2017.101
        • Saini S.
        • Mitra I.
        • Mousavi N.
        • et al.
        A reference haplotype panel for genome-wide imputation of short tandem repeats.
        Nat. Commun. 2018; 9: 4397https://doi.org/10.1038/s41467-018-06694-0
        • Sun S.
        • Liu Y.
        • Li J.
        • et al.
        Development and application of a nonbinary SNP-based microhaplotype panel for paternity testing involving close relatives.
        Forensic Sci. Int. Genet. 2020; 46102255https://doi.org/10.1016/j.fsigen.2020.102255
        • Chen P.
        • Yin C.
        • Li Z.
        • et al.
        Evaluation of the microhaplotypes panel for DNA mixture analyses.
        Forensic Sci. Int. Genet. 2018; 35: 149-155https://doi.org/10.1016/j.fsigen.2018.05.003
        • de la Puente M.
        • Phillips C.
        • Xavier C.
        • et al.
        Building a custom large-scale panel of novel microhaplotypes for forensic identification using MiSeq and Ion S5 massively parallel sequencing systems.
        Forensic Sci. Int. Genet. 2020; 45102213https://doi.org/10.1016/j.fsigen.2019.102213
        • Kidd K.K.
        • Speed W.C.
        • Pakstis A.J.
        • et al.
        Evaluating 130 microhaplotypes across a global set of 83 populations.
        Forensic Sci. Int. Genet. 2017; 29: 29-37https://doi.org/10.1016/j.fsigen.2017.03.014
        • Kureshi A.
        • Li J.
        • Wen D.
        • et al.
        Construction and forensic application of 20 highly polymorphic microhaplotypes.
        R. Soc. Open Sci. 2020; 7191937https://doi.org/10.1098/rsos.191937
        • Jin X.Y.
        • Cui W.
        • Chen C.
        • et al.
        Developing and population analysis of a new multiplex panel of 18 microhaplotypes and compound markers using next generation sequencing and its application in the Shaanxi Han population.
        Electrophoresis. 2020; 41: 1230-1237https://doi.org/10.1002/elps.201900451
        • Yang J.
        • Chen J.
        • Ji Q.
        • et al.
        A highly polymorphic panel of 40-plex microhaplotypes for the Chinese Han population and its application in estimating the number of contributors in DNA mixtures.
        Forensic Sci. Int. Genet. 2022; 56102600https://doi.org/10.1016/j.fsigen.2021.102600
        • Zhu J.
        • Zhou N.
        • Jiang Y.
        • et al.
        FLfinder: a novel software for the microhaplotype marker.
        Forensic Sci. Int.: Genet. Suppl. Ser. 2015; 5: e622-e624https://doi.org/10.1016/j.fsigss.2015.10.002
        • Li Z.
        • Yang J.
        • Liang W.
        • et al.
        Application of MHanalyser software in the study of microhaplotypes in forensics.
        Forensic Sci. Int.: Genet. Suppl. Ser. 2019; 7: 271-273https://doi.org/10.1016/j.fsigss.2019.09.104
        • B S.R.B.A.
        • B B.L.B.
        Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering.
        Am. J. Hum. Genet. 2007; 81: 1084-1097https://doi.org/10.1086/521987
        • Browning B.L.
        • Zhou Y.
        • Browning S.R.
        A one-penny imputed genome from next-generation reference panels.
        Am. J. Hum. Genet. 2018; 103: 338-348https://doi.org/10.1016/j.ajhg.2018.07.015
        • Kidd K.K.
        • Speed W.C.J.Ig
        Criteria for selecting microhaplotypes: mixture detection and deconvolution.
        Invest. Genet. 2015; 6: 1-10https://doi.org/10.1186/s13323-014-0018-3
        • Huang L.
        • Li Y.
        • Singleton A.B.
        • et al.
        Genotype-imputation accuracy across worldwide human populations.
        Am. J. Hum. Genet. 2009; 84: 235-250https://doi.org/10.1016/j.ajhg.2009.01.013
        • Zhang J.
        • Zhang J.
        • Tao R.
        • et al.
        A newly devised multiplex assay of novel polymorphic non-CODIS STRs as a valuable tool for forensic application.
        Forensic Sci. Int. Genet. 2020; 48102341https://doi.org/10.1016/j.fsigen.2020.102341
        • Zhao G.
        • Ma G.
        • Zhang C.
        • et al.
        BGISEQ-500RS sequencing of a 448-plex SNP panel for forensic individual identification and kinship analysis.
        Forensic Sci. Int. Genet. 2021; 55102580https://doi.org/10.1016/j.fsigen.2021.102580
        • Truelsen D.
        • Pereira V.
        • Phillips C.
        • et al.
        Evaluation of a custom GeneRead™ massively parallel sequencing assay with 210 ancestry informative SNPs using the Ion S5™ and MiSeq platforms.
        Forensic Sci. Int. Genet. 2021; 50102411https://doi.org/10.1016/j.fsigen.2020.102411
        • He G.
        • Liu J.
        • Wang M.
        • et al.
        Massively parallel sequencing of 165 ancestry-informative SNPs and forensic biogeographical ancestry inference in three southern Chinese Sinitic/Tai-Kadai populations.
        Forensic Sci. Int. Genet. 2021; 52102475https://doi.org/10.1016/j.fsigen.2021.102475
        • Tao R.
        • Wang S.
        • Chen A.
        • et al.
        Parallel sequencing of 87 STR and 294 SNP markers using the prototype of the SifaMPS panel on the MiSeq FGx™ system.
        Forensic Sci. Int. Genet. 2021; 52102490https://doi.org/10.1016/j.fsigen.2021.102490
        • Oldoni F.
        • Bader D.
        • Fantinato C.
        • et al.
        A sequence-based 74plex microhaplotype assay for analysis of forensic DNA mixtures.
        Forensic Sci. Int. Genet. 2020; 49102367https://doi.org/10.1016/j.fsigen.2020.102367
        • Sun S.
        • Liu Y.
        • Li J.
        • et al.
        Development and application of a nonbinary SNP-based microhaplotype panel for paternity testing involving close relatives.
        Forensic Sci. Int. Genet. 2020; 46102255https://doi.org/10.1016/j.fsigen.2020.102255
        • Gandotra N.
        • Speed W.
        • Qin W.
        • et al.
        Validation of novel forensic DNA markers using multiplex microhaplotype sequencing.
        Forensic Sci. Int. Genet. 2020; 47102275https://doi.org/10.1016/j.fsigen.2020.102275
        • Kidd K.
        • Pakstis A.
        • Gandotra N.
        • et al.
        A multipurpose panel of microhaplotypes for use with STR markers in casework.
        Forensic Sci. Int. Genet. 2022; 60102729https://doi.org/10.1016/j.fsigen.2022.102729
        • Zhang Q.
        • Zhou Z.
        • Wang L.
        • et al.
        Pairwise kinship testing with a combination of STR and SNP loci.
        Forensic Sci. Int. Genet. 2020; 46102265https://doi.org/10.1016/j.fsigen.2020.102265
        • Petrovick M.
        • Boettcher T.
        • Fremont-Smith P.
        • et al.
        Analysis of complex DNA mixtures using massively parallel sequencing of SNPs with low minor allele frequencies.
        Forensic Sci. Int. Genet. 2020; 46102234https://doi.org/10.1016/j.fsigen.2020.102234
        • Tillmar A.
        • Sjölund P.
        • Lundqvist B.
        • et al.
        Whole-genome sequencing of human remains to enable genealogy DNA database searches – a case report.
        Forensic Sci. Int. Genet. 2020; 46102233https://doi.org/10.1016/j.fsigen.2020.102233
        • Cho S.
        • Kim M.
        • Lee J.
        • et al.
        Large-scale identification of human bone remains via SNP microarray analysis with reference SNP database.
        Forensic Sci. Int. Genet. 2020; 47102293https://doi.org/10.1016/j.fsigen.2020.102293