Advertisement

Future of DNA Fingerprinting: Application of NGS in Forensic Science

  • Jahangir Imam
  • Pankaj Shrivastava
  • Shivani Dixit
  • Amita Shrivastava
Chapter

Abstract

In the relatively short time frame since 2005, NGS has fundamentally altered genomics research and allowed investigators to conduct experiments that were previously not technically feasible or affordable. The various technologies that constitute this new paradigm continue to evolve, and further improvements in technology robustness and process streamlining will pave the path for translation into clinical diagnostics. NGS is no doubt one of most important and noteworthy technological advances in the biological sciences in the last two decades. NGS has also made its mark in the application in forensic sciences. It has overcome the limitations of capillary electrophoresis and also have the potential to provide multi-information like sequence variation detections, differentiating monozygotic twins, STR typing of degraded samples, etc. The best part of NGS is that we can parallel do the typing of CODIS STRs loci and sequencing study to detect the allelic variations simultaneously. Currently many NGS kits are being developed and available which have huge application in forensic field. This chapter reviews the discovery, advancement, applications, and development of new NGS-based forensic kits and highlighted the applications of NGS in the field of forensic science and criminal justice system.

Keywords

NGS CODIS Genomics Forensic science Multi-informative Monozygotic twins 

References

  1. 1.
    Abdelkrim J, Robertson B, Stanton JA, Gemmell N (2009) Fast, cost-effective development of species-specific microsatellite markers by genomic sequencing. BioTechniques 46:185–192CrossRefGoogle Scholar
  2. 2.
    Allentoft M, Schuster SC, Holdaway R, Hale M, McLay E, Oskam C et al (2009) Identification of microsatellites from an extinct moa species using high-throughput (454) sequence data. BioTechniques 46:195–200CrossRefGoogle Scholar
  3. 3.
    Allentoft ME, Oskam C, Houston J, Hale ML, Gilbert MT, Rasmussen M et al (2011) Profiling the dead: generating microsatellite data from fossil bones of extinct megafauna – protocols, problems, and prospects. PLoS One 6:e16670CrossRefGoogle Scholar
  4. 4.
    Ayres KL, Chaseling J, Balding DJ (2002) Implications for DNA identification arising from an analysis of Australian forensic databases. Forensic Sci Int 129:90–98CrossRefGoogle Scholar
  5. 5.
    Berglund EC, Kiialainen A, Syvänen AC (2011) Next-generation sequencing technologies and applications for human genetic history and forensics. Investig Genet 2:23–37CrossRefGoogle Scholar
  6. 6.
    Bocklandt S, Lin W, Sehl ME, Sanchez FJ, Sinsheimer JS, Horvath S et al (2011) Epigenetic predictor of age. PLoS One 6:e14821CrossRefGoogle Scholar
  7. 7.
    Bornman DM, Hester ME, Schuetter JM, Kasoji MD, Minard-Smith A, Barden CA, Nelson SC, Godbold GD, Baker CH, Yang B, Walther JE, Tornes IE, Yan PS, Rodriguez B, Bundschuh R, Dickens ML, Young BA, Faith SA (2012) Short-read, high-throughput sequencing technology for STR genotyping. Biotech Rapid Dispatches:1–6Google Scholar
  8. 8.
    Børsting C, Morling N (2015) Next generation sequencing and its applications in forensic genetics. Forensic Sci Int Genet 18:78–89CrossRefGoogle Scholar
  9. 9.
    Børsting C, Fordyce SL, Olofsson J, Mogensen HS, Morling N (2013) Evaluation of the ion torrent HID SNP 169-plex: a SNP typing assay developed for human identification by second generation sequencing. Forensic Sci Int Genet 12:144–154CrossRefGoogle Scholar
  10. 10.
    Brenig B, Beck J, Schütz E (2010) Shotgun metagenomics of biological stains using ultra-deep DNA sequencing. Forensic Sci Int Genet 4:228–231CrossRefGoogle Scholar
  11. 11.
    Bruder CE, Piotrowski A, Gijsbers AA, Andersson R, Erickson S, Diaz de Ståhl T, Menzel U et al (2008) Phenotypically concordant and discordant monozygotic twins display different DNA copy number-variation profile. Amer J Hum Genet 82:763–771CrossRefGoogle Scholar
  12. 12.
    Budowle B (2014) Editors pick: Molecular genetic investigative leads to differentiate monozygotic twins. Invest Genet 5:11CrossRefGoogle Scholar
  13. 13.
    Butler JM (2012) Advanced topics in forensic DNA typing: methodology. Elsevier, Inc, WalthamGoogle Scholar
  14. 14.
    Caratti S, Turrina S, Ferrian M, Cosentino E, Leo DD (2015) MiSeqFGx sequencing system: a new platform for forensic genetics. Forensic Sci Int 5:e98.  https://doi.org/10.1016/j.fsigss.2015.09.040 CrossRefGoogle Scholar
  15. 15.
    Castoe TA, Hall KT, Guibotsy Mboulas ML, Gu W, de Koning AP, Fox SE et al (2011) Discovery of highly divergent repeat landscapes in snake genomes using high throughput sequencing. Genome Biol Evol 3:641–653CrossRefGoogle Scholar
  16. 16.
    Churchill JD, Schmedes SE, King JL, Budowle B (2016) Evaluation of the Illumina (®) beta version ForenSeq™ DNA signature prep kit for use in genetic profiling. Forensic Sci Int Genet 20:20–29CrossRefGoogle Scholar
  17. 17.
    Dalsgaard S, Rockenbauer E, Gelardi C, Børsting C, Fordyce SL, Morling N (2013) Characterization of mutations and sequence variations in complex STR loci by second generation sequencing. Forensic Sci Int Genet Suppl Ser 4:e218–e219CrossRefGoogle Scholar
  18. 18.
    Dalsgaard S, Rockenbauer E, Buchard A, Mogensen HS, Frank-Hansen R, Børsting C, Morling N (2014) Non-uniform phenotyping of D12S391 resolved by second generation sequencing. Forensic Sci Int Genet 8:195–199CrossRefGoogle Scholar
  19. 19.
    Eduardoff M, Santos C, de la Puente M, Gross TE, Fondevila M, Strobl C et al (2015) Inter-laboratory evaluation of SNP-based forensic identification by massively parallel sequencing using the ion PGM™. Forensic Sci Int Genet 17:110–121CrossRefGoogle Scholar
  20. 20.
    Eduardoff M, Gross TE, Santos C, de la Puente M, Ballard D, Strobl C et al (2016) Inter-laboratory evaluation of the EUROFORGEN global ancestry-informative SNP panel by massively parallel sequencing using the ion PGM™. Forensic Sci Int Genet 23:178–189CrossRefGoogle Scholar
  21. 21.
    Fordyce SL, Avila-Arcos MC, Rockenbauer E, Børsting C, Frank-Hansen R, Petersen FT, Willerslev E, Hansen AJ, Morling N, Gilbert MT (2011) High-throughput sequencing of core STR loci for forensic genetic investigations using the Roche genome sequencer FLX platform. BioTechniques 51:127–133PubMedGoogle Scholar
  22. 22.
    Fordyce SL, Mogensen HS, Børsting C, Lagac’e RE, Chang CW, Rajagopalan N, Morling N (2015) Second-generation sequencing of forensic STRs using the ion TorrentTM HID STR 10-plex and the ion PGMTM. Forensic Sci Int Genet 14:132–140CrossRefGoogle Scholar
  23. 23.
    Frumkin D, Wasserstrom A, Budowle B, Davidson A (2011) DNA methylation-based forensic tissue identification. Forensic Sci Int Genet 5:517–524CrossRefGoogle Scholar
  24. 24.
    Gelardi C, Rockenbauer E, Dalsgaard S, Børsting C, Morling N (2014) Second generation sequencing of three complex STRs D3S1358, D21S11 and D12S391 in Danes and a proposal for nomenclature of sequenced STR alleles. Forensic Sci Int Genet 12:38–41CrossRefGoogle Scholar
  25. 25.
    Gettings KB, Aponte RA, Vallone PM, Butler JM (2015) STR allele sequence variation: current knowledge and future issues. Forensic Sci Int 18:118–130CrossRefGoogle Scholar
  26. 26.
    Gettings KB, Kiesler KM, Faith SA, Montano E, Baker CH, Young BA et al (2016) Sequence variation of 22 autosomal STR loci detected by next generation sequencing. Forensic Sci Int Genet 21:15–21CrossRefGoogle Scholar
  27. 27.
    Grunau C, Clark SJ, Rosenthal A (2001) Bisulfite genomic sequencing: systematic investigation of critical experimental parameters. Nucleic Acids Res 29:E65–E65CrossRefGoogle Scholar
  28. 28.
    Guo F, Zhou Y, Liu F, Yu J, Song H, Shen H et al (2016) Evaluation of the early access STR kit v1 on the ion torrent PGM™ platform. Forensic Sci Int Genet 23:111–120CrossRefGoogle Scholar
  29. 29.
    Gymrek M, Golan D, Rosset S, Erlich Y (2012) lobSTR: a short tandem repeat profiler for personal genomes. Genome Res 22:1154–1162CrossRefGoogle Scholar
  30. 30.
    Hares DR (2012) Expanding the CODIS Core Loci in the United States. Forensic Sci Int Genet 6:e52–e54CrossRefGoogle Scholar
  31. 31.
    Hares DR (2015) Selection and implementation of expanded CODIS core loci in the United States. Forensic Sci Int Genet 17:33–34CrossRefGoogle Scholar
  32. 32.
    Holland MM, McQuillan MR, O’Hanlon KA (2011) Second generation sequencing allows for mtDNA mixture deconvolution and high resolution detection of heteroplasmy. Croat Med J 52:299–313CrossRefGoogle Scholar
  33. 33.
    Jeffreys AJ, Brookfield JF, Semeonoff R (1985a) Positive identification of an immigration test-case using human DNA fingerprints. Nature 317:818–819CrossRefGoogle Scholar
  34. 34.
    Jeffreys AJ, Wilson V, Thein SL (1985b) Individual-specific ‘fingerprints’ of human DNA. Nature 314:67–74CrossRefGoogle Scholar
  35. 35.
    Jobbing MA, Gill P (2004) Encoded evidence: DNA in forensic analysis. Nat Rev Genet 5:739–751CrossRefGoogle Scholar
  36. 36.
    Kayser M, de Knijff P (2011) Improving human forensics through advances in genetics, genomics and molecular biology. Nat Rev Genet 12:179–192CrossRefGoogle Scholar
  37. 37.
    Kim EH, Lee HY, Yang IS, Jung SE, Yang WI, Shin KJ (2016) Massively parallel sequencing of 17 commonly used forensic autosomal STRs and amelogenin with small amplicons. Forensic Sci Int Genet 22:1–7CrossRefGoogle Scholar
  38. 38.
    King JL, LaRue BL, Novroski NM, Stoljarova M, Seo SB, Zeng X et al (2014) Highquality and high-throughput massively parallel sequencing of the human mitochondrial genome using the Illumina MiSeq. Forensic Sci Int Genet 12:128–135CrossRefGoogle Scholar
  39. 39.
    Kondo S, Schutte BC, Richardson RJ, Bjork BC, Knight AS, Watanabe Y, Howard E, de Lima RL et al (2002) Mutations in IRF6 cause van der woude and popliteal pterygium syndromes. Nat Genet 32:285–289CrossRefGoogle Scholar
  40. 40.
    Li C, Zhao S, Zhang N, Zhang S, Hou Y (2013) Differences of DNA methylation profiles between monozygotic twins’ blood samples. Mol Biol Rep 40:5275–5280CrossRefGoogle Scholar
  41. 41.
    Li R, Montpetit A, Rousseau M, Wu SY, Greenwood CM, Spector TD, Pollak M, Polychronakos C, Richards JB (2014) Somatic point mutations occurring early in development: a monozygotic twin study. J Med Genet 51:28–34CrossRefGoogle Scholar
  42. 42.
    Loreille O, Koshinsky H, Fofanov VY, Irwin JA (2011) Application of next generation sequencing technologies to the identification of highly degraded unknown soldiers’ remains. Forensic Sci Int Genet Suppl Ser 3:e540–e541CrossRefGoogle Scholar
  43. 43.
    McElhoe JA, Holland MM, Makova KD, Su MS, Paul IM, Baker CH et al (2014) Development and assessment of an optimized next-generation DNA sequencing approach for the mtgenome using the Illumina MiSeq. Forensic Sci Int Genet 13:20–29CrossRefGoogle Scholar
  44. 44.
    Meissner A, Gnirke A, Bell GW, Ramsahoye B, Lander ES, Jaenisch R (2005) Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res 33:5868–5877CrossRefGoogle Scholar
  45. 45.
    Meldrum C, Doyle MA, Tothill RW (2011) Next-generation sequencing for cancer diagnostics: a practical perspective. Clin Biochem Rev 32:177–195PubMedPubMedCentralGoogle Scholar
  46. 46.
    Mikkelsen M, Rockenbauer E, Wächter A, Fendt L, Zimmermann B, Parson W, Abel Nielsen S, Gilbert T, Willerslev E, Morling N (2009) Application of full mitochondrial genome sequencing using 454 GS FLX pyrosequencing. Forensic Sci Int Genet Suppl Ser 2:518–519CrossRefGoogle Scholar
  47. 47.
    Paliwal A, Vaissiere T, Herceg Z (2010) Quantitative detection of DNA methylation states in minute amounts of DNA from body fluids. Methods 52:242–247CrossRefGoogle Scholar
  48. 48.
    Parson W, Strobl C, Huber G, Zimmermann B, Gomes SM, Souto L et al (2013a) Reprint of: evaluation of next generation mtGenome sequencing using the ion torrent personal genome machine (PGM). Forensic Sci Int Genet 7:632–639CrossRefGoogle Scholar
  49. 49.
    W. Parson, C. Strobl, G. Huber, B. Zimmermann, S.M. Gomes, L. Souto, L. Fendt, R. Delport, R. Langit, S. Wootton, R. Lagace´, J. Irwin, Evaluation of next generation mtGenome sequencing using the ion torrent personal genome machine (PGM), Forensic Sci Int Genet 7 (2013b) 543–549CrossRefGoogle Scholar
  50. 50.
    Phillips C, Gelabert-Besada M, Fernandez-Formoso L, García-Magariños M, Santos C, Fondevila M, Ballard D, Syndercombe Court D, Carracedo A, Lareu MV (2014) New turns from old STaRs: enhancing the capabilities of forensic short tandem repeat analysis. Electrophoresis 35:3173–3187CrossRefGoogle Scholar
  51. 51.
    Pitterl F, Schmidt K, Huber G, Zimmermann B, Delport R, Amory S, Ludes B, Oberacher H, Parson W (2010) Increasing the discrimination power of forensic STR testing by employing high-performance mass spectrometry, as illustrated in indigenous south African and central Asian populations. Int J Legal Med 124:551–558CrossRefGoogle Scholar
  52. 52.
    Planz JV, Sannes-Lowery KA, Duncan DD, Manalili S, Budowle B, Chakraborty R, Hofstadler SA, Hall TA (2012) Automated analysis of sequence polymorphism in STR alleles by PCR and direct electrospray ionization mass spectrometry. Forensic Sci Int Genet 6:594–606CrossRefGoogle Scholar
  53. 53.
    Rockenbauer E, Hansen S, Mikkelsen M, Børsting C, Morling N (2014) Characterization of mutations and sequence variants in the D21S11 locus by next generation sequencing. Forensic Sci Int Genet 8:68–72CrossRefGoogle Scholar
  54. 54.
    Santana Q, Coetzee M, Steenkamp E, Mlonyeni O, Hammond G, Wingfield M et al (2009) Microsatellite discovery by deep sequencing of enriched genomic libraries. BioTechniques 46:217–223CrossRefGoogle Scholar
  55. 55.
    Schadt EE, Turner S, Kasarskis A (2010) A window into third-generation sequencing. Human Mol Genet 19:2CrossRefGoogle Scholar
  56. 56.
    Scheible M, Loreille O, Just R, Irwin J (2011) Short tandem repeat sequencing on the 454 platform. Forensic Sci Int Genet Suppl Ser 3:e357–e358CrossRefGoogle Scholar
  57. 57.
    Scheible M, Loreille O, Just R, Loreille O, Just R, Irwin J (2014) Short tandem repeat typing on the 454 platform: strategies and considerations for targeted sequencing of common forensic markers. Forensic Sci Int Genet 12:107–109CrossRefGoogle Scholar
  58. 58.
    Seo SB, King JL, Warshauer DH, Davis CP, Ge J, Budowle B (2013) Single nucleotide polymorphism typing with massively parallel sequencing. Int J Legal Med 127:1079–1086CrossRefGoogle Scholar
  59. 59.
    Shewale JG, Qi L, Calandro LM (2012) Principles, practice, and evolution of capillary electrophoresis as a tool for forensic DNA analysis. Forensic Sci Rev 24:79–100PubMedGoogle Scholar
  60. 60.
    Van Neste C, Van Nieuwerburgh F, Van Hoofstat D, Deforce D (2012) Forensic STR analysis using massive parallel sequencing. Forensic Sci Int Genet 6:810–818CrossRefGoogle Scholar
  61. 61.
    Voelkerding KV, Dames SA, Durtschi JD (2009) Next-generation sequencing: from basic research to diagnostics. Clin Chem 55:641–658CrossRefGoogle Scholar
  62. 62.
    Wang Z, Zhang S, Bian Y, Li C (2015) Differentiating between monozygotic twins in forensics through next generation mtGenome sequencing. Forensic Sci Int Genet Supp Ser 5:e58–e59CrossRefGoogle Scholar
  63. 63.
    Wang Z, Zhou D, Cao Y, Hu Z, Zhang S, Bian Y et al (2016) Characterization of microRNA expression profiles in blood and saliva using the ion personal genome machine® system (ion PGM™ system). Forensic Sci Int Genet 20:140–146CrossRefGoogle Scholar
  64. 64.
    Weber M, Davies JJ, Wittig D, Oakeley EJ, Haase M, Lam WL et al (2005) Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat Genet 37:853–862CrossRefGoogle Scholar
  65. 65.
    Weber-Lehmann J, Schilling E, Gradl G, Richter DC, Wiehler J, Rolf B (2014) Finding the needle in the haystack: differentiating identical twins in paternity testing and forensics by ultra-deep next generation sequencing. Forensic Sci Int Genet 9:42–46CrossRefGoogle Scholar
  66. 66.
    Zeng X, King J, Hermanson S, Patel J, Storts DR, Budowle B (2015a) An evaluation of the PowerSeq™ auto system: a multiplex short tandem repeat marker kit compatible with massively parallel sequencing. Forensic Sci Int Genet 19:172–179CrossRefGoogle Scholar
  67. 67.
    Zeng X, King JL, Stoljarova M, Warshauer DH, LaRue BL, Sajantila A et al (2015b) High sensitivity multiplex short tandem repeat loci analyses with massively parallel sequencing. Forensic Sci Int Genet 16:38–47CrossRefGoogle Scholar
  68. 68.
    Zhao X, Li H, Wang Z, Ma K, Cao Y, Liu W (2016) Massively parallel sequencing of 10 autosomal STRs in Chinese using the ion torrent personal genome machine (PGM). Forensic Sci Int Genet 25:34–38CrossRefGoogle Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2018

Authors and Affiliations

  • Jahangir Imam
    • 1
  • Pankaj Shrivastava
    • 2
  • Shivani Dixit
    • 2
  • Amita Shrivastava
    • 3
  1. 1.DNA Fingerprinting Unit, State Forensic Science Laboratory, Department of Home, Jail and Disaster ManagementGovernment of JharkhandRanchiIndia
  2. 2.DNA Fingerprinting Unit, State Forensic Science LaboratorySagarIndia
  3. 3.Department of P. G. Studies and Research in Biological SciencesRani Durgavati UniversityJabalpurIndia

Personalised recommendations