DNA Based Identification

  • Mohamed AbouelhodaEmail author
  • Amine Nait-ali
Part of the Series in BioEngineering book series (SERBIOENG)


In this first chapter of the book, DNA will be investigated as a deepest Hidden Biometrics modality. After presenting some basic ideas, techniques, and some major applications, a special interest will be addressed to recent research topics related to prediction of visible physical traits.


  1. 1.
    International Human Genome Sequencing Consortium: Initial sequencing and analysis of the human genome. Nature 409, 860–921 (2001)CrossRefGoogle Scholar
  2. 2.
    Venter J.C., et al.: The sequence of the human genome. Science (80-.) 291(5507), 1304–1351 (2001)Google Scholar
  3. 3.
    Debrauwere, H., Gendrel, C.G., Lechat, S., Dutreix, M.: Differences and similarities between various tandem repeat sequences: minisatellites and microsatellites. Biochimie 79(9–10), 577–586 (1997)CrossRefGoogle Scholar
  4. 4.
    Ramel, C.: Mini- and microsatellites. Environ. Health Perspect. 105(Suppl 4), 781–9 (1997)CrossRefGoogle Scholar
  5. 5.
    Mirkin, S.M.: Expandable DNA repeats and human disease. Nature 447(7147), 932–940 (2007)CrossRefGoogle Scholar
  6. 6.
    Doi, K., et al.: Rapid detection of expanded short tandem repeats in personal genomics using hybrid sequencing. Bioinformatics 30(6), 815–22 (2014)CrossRefGoogle Scholar
  7. 7.
    Fan, H., Chu, J.-Y.: A brief review of short tandem repeat mutation. Genomics. Proteomics Bioinform. 5(1), 7–14 (2007)CrossRefGoogle Scholar
  8. 8.
    Sanger, F., Coulson, A.R.: A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. J. Mol. Biol. 94(3), 441–448 (1975)CrossRefGoogle Scholar
  9. 9.
    Bentley, D.R., et al.: Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456(7218), 53–59 (2008)CrossRefGoogle Scholar
  10. 10.
    Merriman, B., I.T. R&D Team, Rothberg, J.M.: Progress in Ion Torrent semiconductor chip based sequencing. Electrophoresis 33(23), 3397–3417 (2012)Google Scholar
  11. 11.
    Rothberg, J.M., et al.: An integrated semiconductor device enabling non-optical genome sequencing. Nature 475(7356), 348–352 (2011)CrossRefGoogle Scholar
  12. 12.
    Armour, J.A.L., et al.: Minisatellite diversity supports a recent African origin for modern humans. Nat. Genet. 13(2), 154–160 (1996)CrossRefGoogle Scholar
  13. 13.
    Jobling, M.A., Bouzekri, N., Taylor, P.G.: Hypervariable digital DNA codes for human paternal lineages: MVR-PCR at the Y-specific minisatellite, MSY1 (DYF155S1). Hum. Mol. Genet. 7(4), 643–653 (1998)CrossRefGoogle Scholar
  14. 14.
    Gibbs, R.A., et al.: A global reference for human genetic variation. Nature 526(7571), 68–74 (2015)CrossRefGoogle Scholar
  15. 15.
    Durbin, R.M., et al.: A map of human genome variation from population-scale sequencing. Nature 467(7319), 1061–1073 (2010)CrossRefGoogle Scholar
  16. 16.
    Gettings, K.B., et al.: A 50-SNP assay for biogeographic ancestry and phenotype prediction in the U.S. population. Forensic Sci. Int. Genet. 8(1), 101–108 (2014)CrossRefGoogle Scholar
  17. 17.
    Gudbjartsson, D.F., et al.: Large-scale whole-genome sequencing of the Icelandic population. Nat. Genet. 47(5), 435–444 (2015)CrossRefGoogle Scholar
  18. 18.
    Chen, H.: Population genetic studies in the genomic sequencing era. Dong wu xue yan jiu = Zool. Res. 36(4), 223–32 (2015)Google Scholar
  19. 19.
    Carrasco-Ramiro, F., Peiró-Pastor, R., Aguado, B.: Human genomics projects and precision medicine. Gene Ther. 24(9), 551–561 (2017)CrossRefGoogle Scholar
  20. 20.
    Roewer, L.: DNA fingerprinting in forensics: past, present, future. Investig. Genet. 4(1), 22 (2013)CrossRefGoogle Scholar
  21. 21.
    Saad, R.: Discovery, development, and current applications of DNA identity testing. Bayl. Univ. Med. Cent. Proc. 18(2), 130–3 (2005)CrossRefGoogle Scholar
  22. 22.
    Jeffreys, A.J., Brookfield, J.F.Y., Semeonoff, R.: Positive identification of an immigration test-case using human DNA fingerprints. Nature 317(6040), 818–819 (1985)CrossRefGoogle Scholar
  23. 23.
    Alonso, S., Armour, J.A.: MS205 minisatellite diversity in Basques: evidence for a pre-Neolithic component. Genome Res. 8(12), 1289–1298 (1998)CrossRefGoogle Scholar
  24. 24.
    Rogers, E.J., Shone, A.C., Alonso, S., May, C.A., Armour, J.A.: Integrated analysis of sequence evolution and population history using hypervariable compound haplotypes. Hum. Mol. Genet. 9(18), 2675–2681 (2000)CrossRefGoogle Scholar
  25. 25.
    Brión, M., Cao, R., Salas, A., Lareu, M.V., Carracedo, A.: New method to measure minisatellite variant repeat variation in population genetic studies. Am. J. Hum. Biol. 14(4), 421–428 (2002)CrossRefGoogle Scholar
  26. 26.
    Yuan, Q.-H., et al.: Minisatellite MS32 alleles show population specificity among Thai, Chinese, and Japanese. J. Mol. Evol. 68(2), 126–133 (2009)CrossRefGoogle Scholar
  27. 27.
    Foster, E.A., et al.: Jefferson fathered slave’s last child. Nature 396(6706), 27–28 (1998)CrossRefGoogle Scholar
  28. 28.
    Brace, S., et al.: Population replacement in early Neolithic Britain. bioRxiv, 267443 (2018)Google Scholar
  29. 29.
    Hoole, M., et al.: ‘Ava’: a Beaker-associated woman from a cist at Achavanich. Proc. Soc. Antiq. Scotl. 147, 73–118 (2018)Google Scholar
  30. 30.
    Abouelhoda, M., Giegerich, R., Behzadi, B., Steyaert, J.M.: Alignment of minisatellite maps based on run length encoding scheme. J. Bioinforma. Comput. Biol. 7(2), 287–308 (2009)CrossRefGoogle Scholar
  31. 31.
    Abouelhoda, M., El-Kalioby, M., Giegerich, R.: WAMI: a web server for the analysis of minisatellite maps. BMC Evol. Biol. 10, 167 (2010)CrossRefGoogle Scholar
  32. 32.
    Edwards, A., Civitello, A., Hammond, H.A., Caskey, C.T.: DNA typing and genetic mapping with trimeric and tetrameric tandem repeats. Am. J. Hum. Genet. 49(4), 746–756 (1991)Google Scholar
  33. 33.
    Coble, M.D., Butler, J.M.: Characterization of new miniSTR loci to aid analysis of degraded DNA. J. Forensic Sci. 50(1), 43–53 (2005)CrossRefGoogle Scholar
  34. 34.
    Butler, J.M.: Forensic DNA Typing : Biology, Technology, and Genetics of STR Markers. Elsevier Academic Press (2005)Google Scholar
  35. 35.
    Butler, J.M.: Genetics and genomics of core short tandem repeat loci used in human identity testing. J. Forensic Sci. 51(2), 253–265 (2006)CrossRefGoogle Scholar
  36. 36.
    Hares, D.R.: Selection and implementation of expanded CODIS core loci in the United States. Forensic Sci. Int. Genet. 17, 33–34 (2015)CrossRefGoogle Scholar
  37. 37.
    Moretti, T.R., et al.: Population data on the expanded CODIS core STR loci for eleven populations of significance for forensic DNA analyses in the United States. Forensic Sci. Int. Genet. 25, 175–181 (2016)CrossRefGoogle Scholar
  38. 38.
    Chaitanya, L., et al.: The HIrisPlex-S system for eye, hair and skin colour prediction from DNA: Introduction and forensic developmental validation. Forensic Sci. Int. Genet. 35, 123–135 (2018)CrossRefGoogle Scholar
  39. 39.
    Walsh, S., et al.: Developmental validation of the IrisPlex system: determination of blue and brown iris colour for forensic intelligence. Forensic Sci. Int. Genet. 5(5), 464–471 (2011)CrossRefGoogle Scholar
  40. 40.
    Pneuman, A. Budimlija, Z.M., Caragine, T., Prinz M., et al.: Verification of eye and skin color predictors in various populations. Leg. Med 14(2), 78–83 (2012)CrossRefGoogle Scholar
  41. 41.
    Walsh, S., et al.: The HIrisPlex system for simultaneous prediction of hair and eye colour from DNA. Forensic Sci. Int. Genet. 7(1), 98–115 (2013)CrossRefGoogle Scholar
  42. 42.
    Shaffer, J.R., et al.: Genome-wide association study reveals multiple loci influencing normal human facial morphology. PLoS Genet. 12(8), e1006149 (2016)CrossRefGoogle Scholar
  43. 43.
    Claes, P., et al.: Modeling 3D facial shape from DNA. PLoS Genet. 10(3), e1004224 (2014)CrossRefGoogle Scholar
  44. 44.
    Claes, P., et al.: Genome-wide mapping of global-to-local genetic effects on human facial shape. Nat. Genet. 50(3), 414–423 (2018)CrossRefGoogle Scholar
  45. 45.
    Lippert, C., et al.: Identification of individuals by trait prediction using whole-genome sequencing data. Proc. Natl. Acad. Sci. U. S. A. 114(38), 10166–10171 (2017)CrossRefGoogle Scholar
  46. 46.
    Erlich, Y.: Major flaws in “Identification of individuals by trait prediction using whole-genome”. bioRxiv, 185330 (2017)Google Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2020

Authors and Affiliations

  1. 1.Systems and Biomedical Engineering DepartmentCairo UniversityGizaEgypt
  2. 2.Saudi Human Genome ProgramKing Abdulaziz City for Science and TechnologyRiyadh, KSASaudi Arabia
  3. 3.King Faisal Specialist Hospital and Research CenterRiyadh, KSASaudi Arabia
  4. 4.Université Paris-Est, LISSI, UPECVitry sur SeineFrance

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