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DNA Based Identification

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

Abstract

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.

References

  1. 1.
    International Human Genome Sequencing Consortium: Initial sequencing and analysis of the human genome. Nature 409, 860–921 (2001)Google 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)Google Scholar
  4. 4.
    Ramel, C.: Mini- and microsatellites. Environ. Health Perspect. 105(Suppl 4), 781–9 (1997)Google Scholar
  5. 5.
    Mirkin, S.M.: Expandable DNA repeats and human disease. Nature 447(7147), 932–940 (2007)Google 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)Google Scholar
  7. 7.
    Fan, H., Chu, J.-Y.: A brief review of short tandem repeat mutation. Genomics. Proteomics Bioinform. 5(1), 7–14 (2007)Google 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)Google Scholar
  9. 9.
    Bentley, D.R., et al.: Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456(7218), 53–59 (2008)Google 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)Google 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)Google 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)Google Scholar
  14. 14.
    Gibbs, R.A., et al.: A global reference for human genetic variation. Nature 526(7571), 68–74 (2015)Google Scholar
  15. 15.
    Durbin, R.M., et al.: A map of human genome variation from population-scale sequencing. Nature 467(7319), 1061–1073 (2010)Google 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)Google Scholar
  17. 17.
    Gudbjartsson, D.F., et al.: Large-scale whole-genome sequencing of the Icelandic population. Nat. Genet. 47(5), 435–444 (2015)Google 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)Google Scholar
  20. 20.
    Roewer, L.: DNA fingerprinting in forensics: past, present, future. Investig. Genet. 4(1), 22 (2013)Google Scholar
  21. 21.
    Saad, R.: Discovery, development, and current applications of DNA identity testing. Bayl. Univ. Med. Cent. Proc. 18(2), 130–3 (2005)Google 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)Google 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)Google 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)Google 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)Google 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)Google Scholar
  27. 27.
    Foster, E.A., et al.: Jefferson fathered slave’s last child. Nature 396(6706), 27–28 (1998)Google 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)Google 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)Google 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)Google 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)Google 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)Google 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)Google 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)Google 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)Google 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)Google 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)Google 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)Google Scholar
  43. 43.
    Claes, P., et al.: Modeling 3D facial shape from DNA. PLoS Genet. 10(3), e1004224 (2014)Google 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)Google 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)Google 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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