Evaluation of the Ion Torrent™ HID SNP 169-plex: A SNP typing assay developed for human identification by second generation sequencing

Forensic Science International: Genetics

Volumn 12, Issue , 2014, Pages 144-154

  Børsting, Claus ^a   Fordyce, Sarah L ^a   Olofsson, Jill ^a   Mogensen, Helle Smidt ^a   Morling, Niels ^a  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

Forensic genetics; Human identification; Ion PGM ; Second generation sequencing; SNP typing; SNPforID

Indexed keywords

ALLELE; ARTICLE; CONTROLLED STUDY; DIAGNOSTIC EQUIPMENT; EVALUATION STUDY; FEMALE; GENETIC SCREENING; GENOME; GENOTYPE; HETEROZYGOTE; HUMAN; MALE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; SENSITIVITY ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; Y CHROMOSOME; DNA SEQUENCE; PHYSICAL ANTHROPOLOGY; PROCEDURES;

CHROMOSOMES, HUMAN, Y; FORENSIC ANTHROPOLOGY; HUMANS; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA;

EID: 84903994768     PISSN: 18724973     EISSN: 18780326     Source Type: Journal    
DOI: 10.1016/j.fsigen.2014.06.004     Document Type: Article

References (25)

1. S.L. Fordyce, M.C. Avila-Arcos, E. Rockenbauer, C. Børsting, R. Frank-Hansen, F.T. Petersen, E. Willerslev, A.J. Hansen, N. Morling, and M.T. Gilbert High-throughput sequencing of core STR loci for forensic genetic investigations using the Roche Genome Sequencer FLX platform Biotechniques 51 2011 127 133
2. D.M. Bornman, M.E. Hester, J.M. Schuetter, M.D. Kasoji, A. Minard-Smith, C.A. Barden, S.C. Nelson, G.D. Godbold, C.H. Baker, B. Yang, J.E. Walther, I.E. Tornes, P.S. Yan, B. Rodriguez, R. Bundschuh, M.L. Dickens, B.A. Young, and S.A. Faith Short-read high-throughput sequencing technology for STR genotyping Biotechniques 2012 1 6 10.2144/000113857
3. D.H. Warshauer, D. Lin, K. Hari, R. Jain, C. Davis, B. LaRue, J.L. King, and B. Budowle STRait razor: a length-based forensic STR allele-calling tool for use with second generation sequencing data Forensic Sci. Int. Genet. 7 2013 409 417
4. C. Van Neste, M. Vandewoestyne, W. Van Criekinge, D. Deforce, and F. Van Nieuwerburgh My-Forensic-Loci-queries (MyFLq) framework for analysis of forensic STR data generated by massive parallel sequencing Forensic Sci. Int. Genet. 9 2014 1 8
5. E. Rockenbauer, S. Hansen, M. Mikkelsen, C. Børsting, and N. Morling Characterization of mutations and sequence variants in the D21S11 locus by next generation sequencing Forensic Sci. Int. Genet. 8 2014 68 72
6. S. Dalsgaard, E. Rockenbauer, A. Buchard, H.S. Mogensen, R. Frank-Hansen, C. Børsting, and N. Morling Non-uniform phenotyping of D12S391 resolved by second generation sequencing Forensic Sci. Int. Genet. 8 2014 195 199
7. M. Mikkelsen, E. Rockenbauer, A. Wächter, L. Fendt, B. Zimmermann, W. Parson, S.A. Nielsen, T. Gilbert, E. Willerslev, and N. Morling Application of full mitochondrial geneome sequencing using 454 GS FLX pyrosequencing Forensic Sci. Int. Genet. Suppl. 2 2009 518 519
8. W. Parson, C. Strobl, G. Huber, B. Zimmermann, S.M. Gomes, L. Souto, L. Fendt, R. Delport, R. Langit, S. Wootton, R. Lagacé, and J. Irwin Evaluation of next generation mtGenome sequencing using the ion Torrent Personal Genome Machine (PGM) Forensic Sci. Int. Genet. 7 2013 543 549
9. S.B. Seo, J.L. King, D.H. Warshauer, C.P. Davis, J. Ge, and B. Budowle Single nucleotide polymorphism typing with massively parallel sequencing for human identification Int. J. Legal Med. 127 2013 1079 1086
10. J.J. Sanchez, C. Phillips, C. Børsting, K. Balogh, M. Bogus, M. Fondevila, C.D. Harrison, E. Musgrave-Brown, A. Salas, D. Syndercombe-Court, P.M. Schneider, A. Carracedo, and N. Morling A multiplex assay with 52 single nucleotide polymorphisms for human identification Electrophoresis 27 2006 1713 1724
11. A.J. Pakstis, W.C. Speed, R. Fang, F.C. Hyland, M.R. Furtado, J.R. Kidd, and K.K. Kidd SNPs for a universal individual identification panel Hum. Genet. 127 2010 315 324
12. T.M. Karafet, F.L. Mendez, M.B. Meilerman, P.A. Underhill, S.L. Zegura, and M.F. Hammer New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree Genome Res. 18 2008 830 838 (Pubitemid 351645073)
13. C. Børsting, E. Rockenbauer, and N. Morling Validation of a single nucleotide polymorphism (SNP) typing assay with 49 SNPs for forensic genetic testing in a laboratory accredited according to the ISO 17025 standard Forensic Sci. Int. Genet. 4 2009 34 42
14. S. Walsh, A. Lindenbergh, S.B. Zuniga, T. Sijen, P. de Knijff, M. Kayser, and K.N. Ballantyne Developmental validation of the IrisPlex system: determination of blue and brown iris colour for forensic intelligence Forensic Sci. Int. Genet. 5 2011 464 471
15. C. Børsting, M. Mikkelsen, and N. Morling Kinship analysis with diallelic SNPs - experiences with the SNPforID multiplex in an ISO17025 accreditated laboratory Transfus. Med. Hemother. 39 2012 195 201
16. T. Schwark, P. Meyer, M. Harder, J.H. Modrow, and N. von Wurmb-Schwark The SNPforID assay as a supplementary method in kinship and trace analysis Transfus. Med. Hemother. 39 2012 187 193
17. C. Børsting, C. Tomas, and N. Morling Typing of 49 autosomal SNPs by single base extension and capillary electrophoresis for forensic genetic testing Methods Mol. Biol. 830 2012 87 107
18. E. Musgrave-Brown, D. Ballard, K. Balogh, K. Bender, B. Berger, M. Bogus, C. Børsting, M. Brion, M. Fondevila, C. Harrison, C. Oguzturun, W. Parson, C. Phillips, C. Proff, E. Ramos-Luis, J.J. Sanchez, D.P. Sanchez, R.B. Sobrino, B. Stradmann-Bellinghausen, C. Thacker, A. Carracedo, N. Morling, R. Scheithauer, P.M. Schneider, and D. Syndercombe Court Forensic validation of the SNPforID 52-plex assay Forensic Sci. Int. Genet. 1 2007 186 190 (Pubitemid 46778189)
19. J.J. Sanchez, C. Børsting, K. Balogh, B. Berger, M. Bogus, J.M. Butler, A. Carracedo, D.S. Court, L.A. Dixon, B. Filipovic, M. Fondevila, P. Gill, C.D. Harrison, C. Hohoff, R. Huel, B. Ludes, W. Parson, T.J. Parsons, E. Petkovski, C. Phillips, H. Schmitter, P.M. Schneider, P.M. Vallone, and N. Morling Forensic typing of autosomal SNPs with a 29 SNP-multiplex - results of a collaborative EDNAP exercise Forensic Sci. Int. Genet. 2 2008 176 183
20. J. Bright, J. Turlington, and J. Buckleton Examination of the variability in mixed DNA profile parameters for the Identifiler™ multiplex Forensic Sci. Int. Genet. 4 2010 111 114
21. C. Tomas, I.E. Diez, E. Moncada, C. Børsting, and N. Morling Analysis of 49 autosomal SNPs in an Iraqi population Forensic Sci. Int. Genet. 1 2013 198 199
22. J.J. Sanchez, C. Hallenberg, C. Børsting, A. Hernandez, and N. Morling High frequencies of Y chromosome lineages characterized by E3b1, DYS19-11, DYS392-12 in Somali males Eur. J. Hum. Genet. 13 2005 856 866 (Pubitemid 40946085)
23. W. Bao, S. Zhu, A. Pandya, T. Zerjal, J. Xu, Q. Shu, R. Du, H. Yang, and C. Tyler-Smith MSY2: a slowly evolving minisatellite on the human Y chromosome which provides a useful polymorphic marker in Chinese populations Gene 244 2000 29 33 (Pubitemid 30109557)
24. C. Børsting, H.S. Mogensen, and N. Morling Forensic genetic SNP typing of low-template DNA and highly degraded DNA from crime case samples Forensic Sci. Int. Genet. 7 2013 345 352
25. ® NGM SElect™ PCR Amplification Kit: a next-generation STR multiplex with the SE33 locus Forensic Sci. Int. Genet. 7 2013 41 51