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Next generation sequencing: Improved resolution for paternal/maternal duos analysis

      Highlights

      • The NGS results were compared with CE-based STR results in duo cases.
      • MiSeq FGx system could offer comprehensive information of different types of markers.
      • The information from NGS can provide a higher amount of resolution for some samples if there is ambiguity based on CE data.

      Abstract

      In the case of two mismatches observed in alleged parent-offspring pairs, there is doubt as to whether there is an exclusion of the putative parent or the existence of two mutations. Here, we report on four cases with two mismatches in paternal/maternal duos based on capillary electrophoresis (CE) results. The analyzed next generation sequencing (NGS) results were compared with 20 autosomal STRs derived from previous CE-based analysis. In summary, the NGS samples used offered comprehensive information of different types of markers that can improve resolutions for paternal/maternal duos analysis.

      Keywords

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      References

        • Zhu W.Q.
        • Jin B.
        • Su Q.
        • Luo H.B.
        • Li Y.B.
        • Wu J.
        • Yan J.
        • Hou Y.P.
        • Liang W.B.
        • Zhang L.
        Mutation study of 28 autosomal STR loci in Southwest Chinese Han population.
        Forensic Sci. Int. 2015; https://doi.org/10.1016/j.fsigss.2015.09.118
        • Drabek J.
        Validation of software for calculating the likelihood ratio for parentage and kinship.
        Forensic Sci. Int. 2009; 3: 112-118
        • Gomes C.
        • Magalhaes M.
        • Alves C.
        • Amorim A.
        • Pinto N.
        • Gusmao L.
        Comparative evaluation of alternative battery of genetic markers to complement autosomal STRs in kinship investigations: autosomal indels vs. X-chromosome STRs.
        Int. J. Legal Med. 2012; 126: 917-921
        • Caratti S.
        • Turrina S.
        • Ferrian M.
        • Cosentino E.
        • Leo D.D.
        MiSeqFGx sequencing system: a new platform for forensic genetics.
        Forensic Sci. Int. 2015; https://doi.org/10.1016/j.fsigss.2015.09.040
        • Gettings K.B.
        • Aponte R.A.
        • Vallone P.M.
        • Butler J.M.
        STR allele sequence variation: current knowledge and future issues.
        Forensic Sci. Int. 2015; 18: 118-130
        • Gelardi C.
        • Rockenbauer E.
        • Dalsgaard S.
        • Borsting C.
        • Morling N.
        Second generation sequencing of three STRs D3S1358, D12S391 and D21S11 in Danes and a new nomenclature for sequenced STR alleles.
        Forensic Sci. Int. 2014; 12: 38-41
        • Zeng X.
        • King J.L.
        • Stoljarova M.
        • Warshauer D.H.
        • LaRue B.L.
        • Sajantila A.
        • Patel J.
        • Storts D.R.
        • Budowle B.
        High sensitivity multiplex short tandem repeat loci analyses with massively parallel sequencing.
        Forensic Sci. Int. 2015; 16: 38-47
        • Borsting C.
        • Morling N.
        Next generation sequencing and its applications in forensic genetics.
        Forensic Sci. Int. 2015; 18: 78-89
        • Thys K.
        • Verhasselt P.
        • Reumers J.
        • Verbist B.M.P.
        • Maes B.
        Performance assessment of the Illumina massively parallel sequencing platform for deep sequencing analysis of viral minority variants.
        J. Virol. Methods. 2015; 221: 29-38
        • Gettings K.B.
        • Aponte R.A.
        • Kiesler K.M.
        • Vallone P.M.
        The next dimension in STR sequencing: polymorphisms in flanking regions and their allelic associations.
        Forensic Sci. Int. 2015; https://doi.org/10.1016/j.fsigss.2015.09.049
        • Rockenbauer E.
        • Hansen S.
        • Mikkelsen M.
        • Borsting C.
        • Morling N.
        Characterization of mutations and sequence variants in the D21S11 locus by next generation sequencing.
        Forensic Sci. Int. 2014; 8: 68-72
        • Rockenbauer E.
        • Hansen S.
        • Andersen M.R.
        • Heerup E.F.
        • Borsting C.
        • Fordyce S.L.
        • Morling N.
        Forensic Sci. Int. 2013; 4: e302-e303
        • Dalsgaard S.
        • Rockenbauer E.
        • Gelardi C.
        • Borsting C.
        • Fordyce S.L.
        • Morling N.
        Characterization of mutations and sequence variations in complex STR loci by second generation sequencing.
        Forensic Sci. Int. 2013; 4: e218-e219
        • Fordyce S.L.
        • Mogensen H.S.
        • Borsting C.
        • Lagace R.E.
        • Chang C.W.
        • Rajagopalan N.
        • Morling N.
        Second generation sequencing of forensic STRs using the ion torrent™ HID STR 10-plex and the ion PGM™.
        Forensic Sci. Int. 2015; 14: 132-140
        • Dalsgaard S.
        • Rockenbauer E.
        • Buchard A.
        • Mogensen H.S.
        • Hansen R.F.
        • Borsting C.
        • Morling N.
        Non-uniform phenotyping of D12S391 resolved by second generation sequencing.
        Forensic Sci. Int. 2014; 8: 195-199
        • Keersbergen P.
        • van Eede P.H.
        • Kraaijenbrink T.
        • Lardy N.M.
        • Sijen T.
        • Bakker E.
        • de Knijff P.
        False positive or true paternity: investigating one or two STR mismatches by detailed SNP analyses.
        Forensic Sci. Int. 2008; 1: 518-519
      1. Illumina, Inc. System Specification Sheet: Forensic Genomics.

      2. Illumina, Inc. ForenSeq™ DNA Signature Prep Guide, February 2015(Part #15049528 Rev. D).

      3. Illumina, Inc. ForenSeq™ Universal Analysis Software Guide, February 2015(Part #5053876 Rev. B).

      4. Illumina, Inc. MiSeqFGx Instrument Reference Guide, February 2015(Part #15050524 Rev. C).

        • Li L.
        • Ge J.
        • Zhang S.
        • Guo J.
        • Zhao S.
        • Li C.
        • Tang H.
        • Davis C.
        • Budowle B.
        • Hou Y.
        • Liu Y.
        Maternity exclusion with a very high autosomal STRs kinship index.
        Int. J. Legal Med. 2012;
        • Ibarra A.
        • Martinez M.
        • Freire-Aradas A.
        • Fondevila M.
        • Carracedo A.
        • Porras L.
        • Gusmao L.
        Using STR, miniSTR and SNP markers to solve complex cases of kinship analysis.
        Forensic Sci. Int. 2013; 4: e91-e92
        • Gao T.Z.
        • Yun L.B.
        • He W.
        • Gu Y.
        • Hou Y.P.
        The application of multi-InDel as supplementary in paternity cases with STR mutation.
        Forensic Sci. Int. 2015; https://doi.org/10.1016/j.fsigss.2015.09.087