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Evaluation of the InnoTyper® 21 genotyping kit in multi-ethnic populations

      Highlights

      • Evaluation of the novel InnoTyper® 21 forensic genotyping kit for South African population groups.
      • The HID parameters for InnoTyper® 21 outperformed both Investigator DIPplex® and GlobalFiler® with fragment sizes ≤ 125 bp.
      • Its PD is higher than that obtained for the mtDNA control region, which is ideal for compromised biological material.
      • Low frequency off-ladder allele in two Bantu groups reveals a third allele for locus RG148.

      Abstract

      We report the findings of the evaluation of the InnoTyper® 21 genotyping kit for the use of human identification (HID) and paternity testing in South Africa. This novel forensic kit evaluates 20 retrotransposable elements (AC4027, MLS26, ALU79712, NBC216, NBC106, RG148, NBC13, AC2265, MLS09, AC1141, TARBP, AC2305, HS4.69, NBC51, ACA1766, NBC120, NBC10, NBC102, SB19.12 and NBC148) and the Amelogenin locus for sex determination. The evaluation of the genotyping performance showed no significant spectral pull-up for peak heights between 100 and 30,000 RFUs. All loci presented biallelic patterns except the triallelic RG148 locus resulting from a variant insertion allele, named RG148I-1, observed exclusively in the Bantu. The InnoTyper® 21 kit was found to be highly discriminatory between the 507 unrelated individuals of the Afrikaaner, Asian Indian, Coloured, amaXhosa and amaZulu groups. The HID parameters: the CPD ranged between 0.99999987 and 0.9999999845, and the CMP between 1.0335 × 10−7 and 1.5506 × 10−8. The paternity parameters: the CPI ranged between 0.0202 and 0.3177, and the CPE between 0.9161 and 0.9749. There were no significant signs of deviations from HWE or linkage disequilibrium (LD) after applying a Bonferroni correction. This kit also showed minor levels of population structure which could differentiate between the African and non-African population groups. Finally, in challenging casework with severely degraded biological material, the InnoTyper® 21 genotyping kit was compatible with GlobalFiler® and Investigator DIPplex® to increase the HID parameters.

      Abbreviations:

      BIC (Bayesian information criterion), CE (capillary electrophoresis), cM (centiMorgan), K (clusters), CPM (combined match probability), CPI (combined paternity index), CDP (combined power of discrimination), CPE (combined probability of exclusion), CGP (critical genotyping point), DAPC (discriminant analysis of principal components), EM (expectation-maximisation), He (expected heterozygosity), HID (human identification), INNULS (insertion/null alleles), InDel (insertion-deletion polymorphism), LD (linkage disequilibrium), LCN (low copy number), MCMC (Markov chain Monte Carlo), MP (match probability), Ho (observed heterozygosity), PI (paternity index), PHR (peak height ratios), PIC (polymorphic information content), PD (power of discrimination), PE (probability of exclusion), RFU (relative fluorescent unit), RE (retrotransposable element), SNP (single nucleotide polymorphism)

      Keywords

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      References

        • Phillips C.
        • Prieto L.
        • Fondevila M.
        • Salas A.
        • Gómez-Tato A.
        • Álvarez-Dios J.
        • Alonso A.
        • Blanco-Verea A.
        • Brión M.
        • Montesino M.
        • Á Carracedo
        • Lareu M.V.
        Ancestry analysis in the 11-M madrid bomb attack investigation.
        PLoS One. 2009; 4: e6583https://doi.org/10.1371/journal.pone.0006583
        • Sanchez J.J.
        • Phillips C.
        • Børsting C.
        • Balogh K.
        • Bogus M.
        • Fondevila M.
        • Harrison C.D.
        • Musgrave-Brown E.
        • Salas A.
        • Syndercombe-Court D.
        • Schneider P.M.
        • Carracedo A.
        • Morling N.
        A multiplex assay with 52 single nucleotide polymorphisms for human identification.
        Electrophoresis. 2006; 27: 1713-1724https://doi.org/10.1002/elps.200500671
        • LaRue B.L.
        • Ge J.
        • King J.L.
        • Budowle B.
        A validation study of the Qiagen Investigator DIPplex® kit; an INDEL-based assay for human identification.
        Int. J. Legal Med. 2012; 126: 533-540https://doi.org/10.1007/s00414-012-0667-9
        • Fondevila M.
        • Phillips C.
        • Santos C.
        • Pereira R.
        • Gusmão L.
        • Carracedo A.
        • Butler J.M.
        • Lareu M.V.
        • Vallone P.M.
        Forensic performance of two insertion–deletion marker assays.
        Int. J. Legal Med. 2012; 126: 725-737https://doi.org/10.1007/s00414-012-0721-7
        • Pereira R.
        • Phillips C.
        • Pinto N.
        • Santos C.
        • dos Santos S.E.B.
        • Amorim A.
        • Carracedo Á.
        • Gusmão L.
        Straightforward inference of ancestry and admixture proportions through ancestry-Informative insertion deletion multiplexing.
        PLoS One. 2012; 7: e29684https://doi.org/10.1371/journal.pone.0029684
        • Sinha S.
        • Murphy G.
        • Brown H.
        • Green A.
        • Montgomery A.
        • Carrol M.
        • Tabak J.
        Retrotransposable elements: novel and sensitive DNA markers and their application in human identity.
        Forensic Sci. Int. Genet. Suppl. Ser. 2015; 5: e627-e629https://doi.org/10.1016/j.fsigss.2015.10.005
        • Larue B.L.
        • Sinha S.K.
        • Montgomery A.H.
        • Thompson R.
        • Klaskala L.
        • Ge J.
        • King J.
        • Turnbough M.
        • Budowle B.
        INNULs A novel design amplification strategy for retrotransposable elements for studying population variation.
        Hum. Hered. 2012; 74: 27-35https://doi.org/10.1159/000343050
        • Finnegan D.J.
        Retrotransposons.
        Curr. Biol. 2012; 22: 432-437https://doi.org/10.1016/j.cub.2012.04.025
        • Cordaux R.
        • Srikanta D.
        • Lee J.
        • Stoneking M.
        • Batzer M.A.
        In search of polymorphic Alu insertions with restricted geographic distributions.
        Genomics. 2007; 90: 154-158https://doi.org/10.1016/j.ygeno.2007.03.010
        • Terreros M.C.
        • Alfonso-Sánchez M.A.
        • Novick G.E.
        • Luis J.R.
        • Lacau H.
        • Lowery R.K.
        • Regueiro M.
        • Herrera R.J.
        Insights on human evolution: an analysis of Alu insertion polymorphisms.
        J. Hum. Genet. 2009; 54: 603-611https://doi.org/10.1038/jhg.2009.86
        • Brown H.
        • Thompson R.
        • Murphy G.
        • Peters D.
        • La Rue B.
        • King J.
        • Montgomery A.H.
        • Carroll M.
        • Baus J.
        • Sinha S.
        • Wendt F.R.
        • Song B.
        • Chakraborty R.
        • Budowle B.
        • Sinha S.K.
        Development and validation of a novel multiplexed DNA analysis system, InnoTyper ® 21.
        Forensic Sci Int. Genet. 2017; 29: 80-99https://doi.org/10.1016/j.fsigen.2017.03.017
        • van den Berge M.
        • Wiskerke D.
        • Gerretsen R.R.R.
        • Tabak J.
        • Sijen T.
        DNA and RNA profiling of excavated human remains with varying postmortem intervals.
        Int. J. Legal Med. 2016; 130: 1471-1480https://doi.org/10.1007/s00414-016-1438-9
        • Villeme A.
        • Bartizal G.
        • Steffen C.R.
        • Coble M.D.
        Examination of 20 Retrotransposable Polymorphic Insertion/Null (INNUL) Markers for Their Utility in Kinship Testing Using a Commercial Software Program (LSAM).
        2016
        • Morris A.G.
        • Heinze A.
        • Chan E.K.F.
        • Smith A.B.
        • Hayes V.M.
        First ancient mitochondrial human genome from a prepastoralist southern african.
        Genome Biol. Evol. 2014; 6: 2647-2653https://doi.org/10.1093/gbe/evu202
        • Sealy J.
        • Pfeiffer S.
        Diet, body size, and landscape use among holocene people in the southern cape, South Africa.
        Curr. Anthropol. 2000; 41: 642-655https://doi.org/10.1086/317392
        • Pfeiffer S.
        • Sealy J.
        Body size among Holocene foragers of the Cape Ecozone, southern Africa.
        Am. J. Phys. Anthropol. 2006; 129: 1-11https://doi.org/10.1002/ajpa.20231
      1. Statistics South Africa, Community Survey 2016 Statistical Release, Stats SA Stat. South Africa. 2016 Community Survey 2016 Results. http://cs2016. statssa.gov.za/.

        • Petersen D.C.
        • Libiger O.
        • Tindall E.A.
        • Hardie R.A.
        • Hannick L.I.
        • Glashoff R.H.
        • Mukerji M.
        • Fernandez P.
        • Haacke W.
        • Schork N.J.
        • Hayes V.M.
        Complex patterns of genomic admixture within southern africa.
        PLoS Genet. 2013; 9: 10-13https://doi.org/10.1371/journal.pgen.1003309
        • Miller S.A.
        • Dykes D.D.
        • Polesky H.F.
        A simple salting out procedure for extracting DNA from human nucleated cells.
        Nucleic Acids Res. 1988; 16: 1215https://doi.org/10.1093/nar/16.3.1215
        • Cloete K.W.
        • Ristow P.G.
        • Kasu M.
        • D’Amato M.E.
        Design, installation and performance evaluation of a custom dye matrix standard for automated capillary electrophoresis.
        Electrophoresis. 2016; : 1-16https://doi.org/10.1002/elps.201600257
        • Schneider P.M.
        Scientific standards for studies in forensic genetics.
        Forensic Sci. Int. 2007; 165: 238-243https://doi.org/10.1016/j.forsciint.2006.06.067
        • Dyer R.J.
        Analyses and Functions Related to the Spatial Analysis of Genetic Marker Data.
        2014
        • Jombart T.
        Adegenet: a R package for the multivariate analysis of genetic markers.
        Bioinformatics. 2008; 24: 1403-1405https://doi.org/10.1093/bioinformatics/btn129
        • Wickham H.
        • Francois R.
        Dplyr: A Grammar of Data Manipulation, R Packag Version 0.4 1.
        2015: 20
        • Wickham H.
        Plyr: Tools for Splitting, Applying and Combining Data, R Packag Version 0.1 9.
        2009: 651
        • Wickham H.
        Ggplot2: Elegant Graphics for Data Analysis.
        Springer, 2016
        • Wickham H.
        Reshape2: Flexibly Reshape Data: a Reboot of the Reshape Package, R Packag Version. 1.
        2012
        • R Development Core Team
        R: A Language and Environment for Statistical Computing.
        R Found. Stat. Comput., Vienna Austria2016 (0 {ISBN} 3-900051-07-0)
      2. 10.1038/sj.hdy.6800737.

        • Excoffier L.
        • Laval G.
        • Schneider S.
        Arlequin (version 3.0): an integrated software package for population genetics data analysis.
        Evol. Bioinform. 2005; (Online. 1): 47-50https://doi.org/10.1111/j. 1755-0998.2010.02847. x
        • Ristow P.G.
        • Cloete K.W.
        • D’Amato M.E.
        GlobalFiler® Express DNA amplification kit in South Africa: extracting the past from the present.
        Forensic Sci. Int. Genet. 2016; 24: 194-201https://doi.org/10.1016/j.fsigen.2016.07.007
        • Hefke G.
        • Davison S.
        • D’Amato M.E.
        Forensic performance of Investigator DIPplex indels genotyping kit in native, immigrant and admixed populations in South Africa.
        Electrophoresis. 2015; 36: 3018-3025
        • Pritchard J.K.
        • Stephens M.
        • Donnelly P.
        Inference of population structure using multilocus genotype data.
        Genetics. 2000; 155: 945-959
        • Evanno G.
        • Regnaut S.
        • Goudet J.
        Detecting the number of clusters of individuals using the software STRUCTURE: A simulation study.
        Mol. Ecol. 2005; 14: 2611-2620https://doi.org/10.1111/j.1365-294X.2005.02553. x
        • Jakobsson M.
        • Rosenberg N.A.
        CLUMPP. A cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure.
        Bioinformatics. 2007; 23: 1801-1806https://doi.org/10.1093/bioinformatics/btm233
        • Rosenberg N.A.
        Distruct A program for the graphical display of population structure.
        Mol. Ecol. Notes. 2004; 4: 137-138
        • Kopelman N.M.
        • Mayzel J.
        • Jakobsson M.
        • Rosenberg N.A.
        • Mayrose I.
        Clumpak: a program for identifying clustering modes and packaging population structure inferences across K.
        Mol. Ecol. Resour. 2015; 15: 1179-1191https://doi.org/10.1111/1755-0998.12387
        • Carvalho A.
        • Cainé L.
        • Carvalho R.
        • Pinheiro M.F.
        Application of indels (investigator DIPplex) in mixture samples.
        Forensic Sci. Int. Genet. Suppl. Ser. 2011; 3: e351-e352https://doi.org/10.1016/j.fsigss.2011.09.038
        • LaRue B.L.
        • Lagacé R.
        • Chang C.-W.
        • Holt A.
        • Hennessy L.
        • Ge J.
        • King J.L.
        • Chakraborty R.
        • Budowle B.
        Characterization of 114 insertion/deletion (INDEL) polymorphisms, and selection for a global INDEL panel for human identification.
        Leg. Med. 2014; 16: 26-32https://doi.org/10.1016/j.legalmed.2013.10.006
        • Nei M.
        Molecular Evolutionary Genetics.
        Columbia University Press, 1987
        • Quintana-Murci L.
        • Harmant C.
        • Quach H.
        • Balanovsky O.
        • Zaporozhchenko V.
        • Bormans C.
        • van Helden P.D.
        • Hoal E.G.
        • Behar D.M.
        Strong maternal khoisan contribution to the south african coloured population: a case of gender-Biased admixture.
        Am. J. Hum. Genet. 2010; 86: 611-620https://doi.org/10.1016/j.ajhg.2010.02.014
        • Phillips C.
        • Ballard D.
        • Gill P.
        • Court D.S.
        • Carracedo Á.
        • Lareu M.V.
        The recombination landscape around forensic STRs: accurate measurement of genetic distances between syntenic STR pairs using HapMap high density SNP data.
        Forensic Sci. Int. Genet. 2012; 6: 354-365https://doi.org/10.1016/j.fsigen.2011.07.012
        • Kosambi D.D.
        The estimation of map distances from recombination values.
        Ann. Eugen. 1943; 12: 172-175https://doi.org/10.1111/j. 1469-1809.1943. tb02321. x
        • Lane A.B.
        • Soodyall H.
        • Arndt S.
        • Ratshikhopha M.E.
        • Jonker E.
        • Freeman C.
        • Young L.
        • Morar B.
        • Toffie L.
        Genetic substructure in south african bantu-speakers: evidence from autosomal DNA and Y-chromosome studies.
        Am. J. Phys. Anthropol. 2002; 119: 175-185https://doi.org/10.1002/ajpa.10097
        • Kaeuffer R.
        • Réale D.
        • Coltman D.W.
        • Pontier D.
        Detecting population structure using STRUCTURE software: effect of background linkage disequilibrium.
        Heredity (Edinb). 2007; 99: 374-380https://doi.org/10.1038/sj.hdy.6801010
        • Weir B.S.
        Genetic Data Analysis II: Methods for Discrete Population Genetic Data.
        Sinauer Assoc., Sunderland, MA1996: 376https://doi.org/10.1136/jmg.29.3.216
        • Rapley R.
        • Whitehouse D.
        Molecular Forensics.
        John Wiley & Sons, 2007
        • Shewale J.G.
        • Liu R.H.
        Forensic DNA Analysis: Current Practices and Emerging Technologies.
        CRC Press, 2013
        • Strachan T.
        • Read A.
        Human Molecular Genetics.
        4th ed. Garland Science, 2010
        • Wu W.
        • Hao H.
        • Liu Q.
        • Han X.
        • Wu Y.
        • Cheng J.
        • Lu D.
        Analysis of linkage and linkage disequilibrium for syntenic STRs on 12 chromosomes.
        Int. J. Legal Med. 2014; 128: 735-739https://doi.org/10.1007/s00414-014-1032-y
        • Tillmar A.O.
        • Phillips C.
        Evaluation of the impact of genetic linkage in forensic identity and relationship testing for expanded DNA marker sets.
        Forensic Sci. Int. Genet. 2017; 26: 58-65https://doi.org/10.1016/j.fsigen.2016.10.007
        • Gill P.
        • Phillips C.
        • McGovern C.
        • Bright J.
        • Buckleton J.
        An evaluation of potential allelic association between the STRs vWA and D12S391: Implications in criminal casework and applications to short pedigrees.
        Forensic Sci. Int. Genet. 2012; 6: 477-486https://doi.org/10.1016/j.fsigen.2011.11.001
        • Westen A.A.
        • Haned H.
        • Grol L.J.W.
        • Harteveld J.
        • van der Gaag K.J.
        • de Knijff P.
        • Sijen T.
        Combining results of forensic STR kits: hDplex validation including allelic association and linkage testing with NGM and Identifiler loci.
        Int. J. Legal Med. 2012; 126: 781-789https://doi.org/10.1007/s00414-012-0724-4
        • Burri H.
        • Sulzer A.
        • Voegeli P.
        • Kratzer A.
        Accounting for linkage between the STR loci D5S818/CSF1PO and vWA/D12S391 in kinship analyses: impact on likelihood ratio values.
        Forensic Sci. Int. Genet. Suppl. Ser. 2015; 5: e387-e389https://doi.org/10.1016/j.fsigss.2015.09.153
        • Dørum G.
        • Kling D.
        • Tillmar A.
        • Vigeland M.D.
        • Egeland T.
        Mixtures with relatives and linked markers.
        Int. J. Legal Med. 2016; 130: 621-634https://doi.org/10.1007/s00414-015-1288-x
        • Tillmar A.O.
        • Kling D.
        • Butler J.M.
        • Parson W.
        • Prinz M.
        • Schneider P.M.
        • Egeland T.
        • Gusmão L.
        DNA Commission of the International Society for Forensic Genetics (ISFG): Guidelines on the use of X-STRs in kinship analysis.
        Forensic Sci. Int. Genet. 2017; 29: 269-275https://doi.org/10.1016/j.fsigen.2017.05.005
        • Fondevila M.
        • Santos C.
        • Phillips C.
        • Carracedo Á.
        • Butler J.M.
        • Lareu M.V.
        • Vallone P.M.
        an Assessment of Linkage Between Forensic Markers: Core Strs, Mini-strs and Indels.
        Natl. Inst. Stand. Technol. Chem. Sci. Technol. Lab. (CSTL), 2011
        • Budowle B.
        • Ge J.
        • Chakraborty R.
        • Eisenberg A.J.
        • Green R.
        • Mulero J.
        • Lagace R.
        • Hennessy L.
        Population genetic analyses of the NGM STR loci.
        Int. J. Legal Med. 2011; 125: 101-109https://doi.org/10.1007/s00414-010-0516-7
        • Ge J.
        • Budowle B.
        • Planz J.V.
        • Chakraborty R.
        Haplotype block: a new type of forensic DNA markers.
        Int. J. Legal Med. 2010; 124: 353-361https://doi.org/10.1007/s00414-009-0400-5
        • Kidd K.K.
        • Pakstis A.J.
        • Speed W.C.
        • Lagacé R.
        • Chang J.
        • Wootton S.
        • Haigh E.
        • Kidd J.R.
        Current sequencing technology makes microhaplotypes a powerful new type of genetic marker for forensics.
        Forensic Sci. Int. Genet. 2014; 12: 215-224https://doi.org/10.1016/j.fsigen.2014.06.014