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DNA Profiling

Theory and Practice
  • Karen M. Sullivan
Protocol
  • 1k Downloads
Part of the Springer Protocols Handbooks book series (SPH)

Abstract

Of the vast range of techniques in use in modern molecular biology, DNA protiling is one of the more difficult to describe, primarily because the term “DNA Protiling” itself means very different things to different people. It is, in fact, a widely applied term that describes a number of technically diverse approaches to the study of hypervariable DNA This ambiguity is compounded by the fact that the term “hypervariable DNA” describes more than one fraction of genomic DNA The aim of this chapter is, therefore, to describe the common molecular basis of the varying forms of hypervariable-DNA analyses, and how this may be exploited for genetic identity and relationship testing, to examme the practical approaches available for such studies and their respective strengths and hmitations, and finally to look at the range of applications of each DNA-proliling technique

Keywords

Variable Number Tandem Repeat Paternity Testing Molar Pregnancy Relationship Testing Modern Molecular Biology 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

References

  1. 1.
    Jeffreys, A J, Wilson, V, and Them, S L (1985) Hypervarrable mm~satellrte’ regions in human DNA Nature 314,67–73PubMedCrossRefGoogle Scholar
  2. 2.
    Higgs, D R, Goodbourn, S K Y, Wamscoat, J S, Clegg, J B, and Weatherall, D J(1981) Highly variable regions flank the human alpha-globm genesNucleic ACS Res 9,4213,4214CrossRefGoogle Scholar
  3. 3.
    Goodbourn, S. K Y, Hrggs, D R, Clegg, J. B, and Weatherall, D J (1983) Molecularbasts of length polymorphrsm in the human zeta globm gene complex Proc Natl Acad Sci USA 80,5022–5026PubMedCrossRefGoogle Scholar
  4. 4.
    Goodbourn, S K Y, Htggs, D R, Clegg, J B, and Weatherall, D J (1984) Allehc vartatton and linkage properties of a hrghly polymorphtc restrrction fragment in humans Mol Biol Med 2,223–238PubMedGoogle Scholar
  5. 5.
    Jeffreys, A J, Wilson, V, Them, S L, Weatherall, D J, and Ponder, B A J (1986)DNA “fingerprmts” and segregatron analysts of multiple markers in human pedtgrees Am J Hum Genet 39, 11–34PubMedGoogle Scholar
  6. 6.
    Jeffreys, A J, Royle, N J, Wilson, V, and Wong, Z (1988) Spontaneous mutation rates to new length alleles at tandem-repetitive hypervartable loci in human DNA Nature 332,278–281.PubMedCrossRefGoogle Scholar
  7. 7.
    Fowler, S J, Gill, P, Werret, D J, and Htggs, D R (1988) Indtvrdual specific DNA fingerprints from a hypervartable region probe alpha-globm 3’HVRHum Genet 79,142–146.PubMedCrossRefGoogle Scholar
  8. 8.
    Chen, P, Hayward, N K., Ktdson, C, and Ellem, K A O (1990) Condtttons for generating well-resolved human DNA fingerprints using Ml3 phage DNA Nuclezc Aczds Res 18, 1065CrossRefGoogle Scholar
  9. 9.
    Nettzel, H, Digweed, M, Nurnberg, P, Popperl, A, Schmidt, C A, Tmschert, S, and Sperling, K (1991) Routine appllcatrons of DNA fingerprmting with the ollgonucleottde probe (CAC)S/(GTG) S Clan Genet, 39,97–103.CrossRefGoogle Scholar
  10. 10.
    Gtll, P, Jeffreys, A J, and Werrett, D J. (1985) Forensic applications of DNA Iingerprints Nature 318,577–579CrossRefGoogle Scholar
  11. 11.
    Jeffreys, A J, Brookfield, J F Y, and Semeonoff, R (1985) Postttve tdenttficatton of an mmugratron test case using human DNA fingerprmts Nature 317,818,819PubMedCrossRefGoogle Scholar
  12. 12.
    Wong, Z, Wilson, V, Jeffreys, A J, and Them, S L (1986) Cloning a selected fragment from a human DNA fingerprmt’ tsolatton of an extremely polymorphtc mmtsatelhte Nucleic Acids Res 14,4605–4616PubMedCrossRefGoogle Scholar
  13. 13.
    Wong, Z, Wilson, V, Patel, I, Povey, S, and Jeffreys, A J (1987) Charactertsatton of a panel of htghly variable mmtsatellues cloned from human DNA Ann Human Genet 51,269–288CrossRefGoogle Scholar
  14. 14.
    Allard, J E (1992) Murder in South London a novel use of DNA profiling J Forenszc Sci Sot 32,49–58CrossRefGoogle Scholar
  15. 15.
    Li, H, Gyllensten, U B, Cur, X, Satkt, R K, Erhch, H A, and Arnhetm, N (1988) Ampllficatton and analysts of DNA sequences in single human sperm and diplotd cells Nature 335,414–417PubMedCrossRefGoogle Scholar
  16. 16.
    Jeffreys, A J, Royle, N J, Patel, I, Armour, A L, MacLeod, A, Colhck, A, Gray, I C, Neumann, R, Gibbs, M, Crosser, M, Htll, M, Signer, E, and Monckton, D (1991)Principles and recent advances in human DNA fingerprinting, in DNA Flngerpnntvzg,Approaches and Applzcatzons (Burke, T, Dolf, G, Jeffreys, A. J, and Wolff, R, eds ),Btrkhauser Verlag, Basel, Switzerland, pp 1–19Google Scholar
  17. 17.
    Lttt, M., and Luty, J A (1989) A hypervartable mtcrosatehte revealed by in vitro amphficatton of a dmucleottde repeat wrthm the carrdatc muscle actm geneAm J Hum Genet 44,397–401Google Scholar
  18. 18.
    Tautz, D (1989) Hypervartabtlny of sample sequences as a general source for polymorphic DNA markers Nuclezc Aczds Res 17,6463–6471CrossRefGoogle Scholar
  19. 19.
    Royle, N J, Clarkson, R E, Wong, Z., and Jeffreys, A J (1988) Clustering of hypervartable mmtsatelhtes in the protermmal regions of human autosomes Genomlcs 3,352–360CrossRefGoogle Scholar
  20. 20.
    Mansfield, D C, Brown, A F, Green, D K, Carothers, A D, Mans, S W, Evans, H J,and Wright, A F (1994) Automation of genetic linkage analysts using fluorescent microsatellite markers Genomics 24,225–233PubMedCrossRefGoogle Scholar
  21. 21.
    Sander, A, Murray, J C, Cherpbler-Heddema, T, Buetow, K H, Welssenbach, J, Zingg, IM, Ludwig, K, and Schmelzle, R (1995) Mlcrosatelhte based fine mapping of the Van der Woude Syndrome locus to an mterval of 4 1 CM between DIS245 and DIS4 14 Am J Hum Genet Sci 310–318Google Scholar
  22. 22.
    Carmcl, F, Pezzettl, F, Scapoh, L, Padula, E, Baclhero, U, Cunom, C, and Tognon, M (1995) Non-symdromlc cleft lip and palate. evidence of linkage to a mlcrosatelhte marker on 6~23 Am J Hum Genet 56,337–339Google Scholar
  23. 23.
    Loudlanos, G, FIgus, A L, Lol, A, Anglus, A, Dessl, V, Delana, M, De Vlrgllns, S, Monm, G, Cao, A, and Plrastu, M (1994) Improvement of prenatal dlagnosls of Wilson Disease using mlcrosatelhte markers Prenatal Drag 14,999–1002CrossRefGoogle Scholar
  24. 24.
    Mao, L, Lee, D J, To&man, M S, Erozan, Y S, Askm, F, and Sldransky, D (1994) Mlcrosatelhte alterations as clonal markers for the detection of human cancer Proc Natl Acad Scz USA 91,9871–9875CrossRefGoogle Scholar
  25. 25.
    Huff, V, Jafe, N, Saunders, G F, Strong, L C, Vlllalba, F, and Routeshouser, E C (1995) WTl exon 1 deletlon/msertlon mutations in Wllms Tumour patients, associated with dl-and trmucleotlde repeats and deletion hotspot concensus sequences Am J Genet 56,84–90Google Scholar
  26. 26.
    Gill, P, Lygo, J. E, Fowler, S J, and Werret, D J (1987) An evaluation of DNA fingerprmting for forensic purposes Electrophoreszs 8, 38–44CrossRefGoogle Scholar
  27. 27.
    Honma, M, Yoshn, T, Ishlyama, I, Mltam, K, Kommaml, R, and Muramatsu, M (1989) Indlvldual ldentlficatlon from semen by the deoxyrlbonuclelc acid (DNA) fingerprint techmque J Forenszc Scl 34,222–227Google Scholar
  28. 28.
    Bar, W and Hummel, K (1991) DNA Fingerprmting Its apphcatlons in forensic casework,m DNAFlngerprlntvzg Approaches and Appllcatlons, (Burke, T, Dolf, G, Jeffreys, A J, and Wolff, R, eds), Blrkhauser Verlag, Basel, Switzerland, pp 349–355Google Scholar
  29. 29.
    Gill, P and Werrett, D J (1987) Exclusion of a man charged with murder by DNA fingerprinting Forensic Sci Intl 35, 145–148CrossRefGoogle Scholar
  30. 30.
    Syndercombe Court, D, Fedor, T, Gouldstone, M, Lincoln, P J, Phillips, C P, Tate, V, Thomson, J A,and Watts, P W (1992) Investlgatlon of the between-gel and wlthm-gel variation in fragment size determmatlons found when using single locus DNA probes Forensic Sci Intl 53, 173–191CrossRefGoogle Scholar
  31. 31.
    Pascah, V L, Moscettl, A, Dobosz, M, Pescarmona, M, and d’AloJa, E (1992) Errors in slzing bands of hypervarlable DNA profiles on autoradlograms are they Gaussian? Electrophoresls 13,341–345CrossRefGoogle Scholar
  32. 32.
    Nichols, R A and Balding, D J (1993) Effects of population structure on DNA fingerprint analysis in forensic scienceHeredity 66, 297–302CrossRefGoogle Scholar
  33. 33.
    Chakraborty, R and Jm, L (1992) Heterozygote deficiency, poluatlon substructure and their lmphcatlons in DNA fingerprinting Hum Genet 88,267–272Google Scholar
  34. 34.
    Walsh, J J (1992) The population genetics of DNA typing “Could It have been someone else?” Cram Law Quar 34,469–497Google Scholar
  35. 35.
    Devlm, B, Rlsch, N, and Roeder, K (1990) No excess of homozygoslty at loci used for DNA fingerprmting Sczence 249, 1416–1419Google Scholar
  36. 36.
    Gill, P Klmpton, C, D’AloJa, E, Andersen, J F, Bar, W, Brmkman, B, Holgersson, S, Johnsson, V, Kloosterman, A D, Lareu, M V, Nelleman, L, Pfitzinger, H, Phillips, C P, Scmltter, H, Schneider, P in, and Stenersen, M (1994) Report of the European DNA profiling group (EDNAPj-towards standardlsatlon of short tandem repeat (STR) loci Forensic Sci Int 65,51–59PubMedCrossRefGoogle Scholar
  37. 37.
    van Helden, P D and Wnd, I J F (1987) Appllcatlon of DNA fingerprinting to the investigation of cell line genotype SA J Scz 83,244Google Scholar
  38. 38.
    van Helden, P D, Wnd, I J F, Albrecht, C F, Theron, E, Thornley, A L, and Hoal-van Helden, K G. (1988) Cross-contammation of human esophageal squamous carcimona cell lines detected by DNA fingerprint analysis Cancer Res 48, 5660–5662PubMedGoogle Scholar
  39. 39.
    Thacker, J, Webb, M B T, and Debenham, P G (1988) Fingerprmting cell lines use of human hypervariable DNA probes to charactertse mammalian cell cultures Somatzc Cell Mol. Genet 14,519–525CrossRefGoogle Scholar
  40. 40.
    Jones, L, Them, S L, Apperley, J F, Catovsky, D, and Goldman, J in (1987) Identical twm marrow transplantation for 5 patients with chronic myeloid leukaemia role of DNA fingerprmting to confirm monozygosity in 3 cases Eur J Haematol 39, 144–147PubMedCrossRefGoogle Scholar
  41. 41.
    Fey, M F, Wells, R A, Wamscoat, J S, and Them, S L (1988) JAssesment of clonahty in gastrointestinal cancer by DNA fingerprmting Clrn Znvest 1532–1537Google Scholar
  42. 42.
    Boltz, E in, Harnett, P, Leary, J, Houghton, R, Kefford, R F, and Friedlander, M L (1990) Demonstration of somattc rearrangements and genomic heterogeneity in human ovarian cancer by DNA tingerprmting Br J Cancer 62,23–37CrossRefGoogle Scholar
  43. 43.
    Hayward, N, Chen, P, Nancarrow, D, Kearsley, J, Smith, P, Kidson, C, and Ellem, K (1990) Detection of somatic mutations in tumours of diverse types by DNA fingerprmting with Ml3 phage DNA Int J Cancer 45,687–690PubMedCrossRefGoogle Scholar
  44. 44.
    Lee, J H, Kavanagh, J J, Wildrick, D in, Wharton, J T, and Thick, M (1990) Frequent loss of heterozygosity on chromosomes 6q, 11 and 17 in human ovarian cancer Cancer Res Sci 2724–2728Google Scholar
  45. 45.
    Agurell, E, Li, R, Rannug, U, Norming, U, Trtbukait, B, and Ramel, C (1992) Detection of DNA alterations in human bladder tumours by DNA fingerprmt analysis Cancer Genet Cytogenet 60,53–60CrossRefGoogle Scholar
  46. 46.
    Pakkala, S, Knuutila, S, Helmmen, P, Ruutu, T, Saarmen, U in, and Peltonen, L (1990) DNA-fingerprint changes compared to karyotypes in acute leukemia Leukemza 4,866–870Google Scholar
  47. 47.
    Mao, L, Lee, D J, To&man, M S, Erozan, Y S, Askm, F, and Sidransky, D (1994)Microsatelhte alterations as clonal markers for the detection of human cancer Proc Natl Acad Scl USA 91,9871–9875CrossRefGoogle Scholar
  48. 48.
    Gmeburg, D, Antm, J H, Smith, B R, Orkm, S H, and Rappeport, J in (1985) Origin of cell populations after bone marrow transplantation J Chn Invest 75,596–603CrossRefGoogle Scholar
  49. 49.
    Pakkala, S, Helmmen, P, Saarmen, U, Ahtalo, R, and Peltonen, L (1988) Differences in DNA fingerprints between remission and relapse in childhood acute lymphoblastic leukaemia Leukemia Res 9,757–762CrossRefGoogle Scholar
  50. 50.
    Helmmen, P, Ehnholm, C, Lokki, M L, Jeffreys, A, and Peltonen, L (1988) Apphcanon of DNA “fingerprmts” to paternity determmattons Lancet 12, 574–576CrossRefGoogle Scholar
  51. 51.
    Rntner, C, Schaker, U, Rithner, G, and Schneider, P in (1988) Apphcation of DNA polymorphisms in paternity testing in Germany solution of an Incest case using bacteriophage in 13 hybridisation with hypervariable mnnsatellite DNA Adv Forenszc Haemogenet 2,388–391Google Scholar
  52. 52.
    Fisher, R A, Lawler, S D, Povey, S,and Bagshawe, K D (1988) Genetically homozygous choriocarcmoma following pregnancy with hydatidiform mole Br J Cancer 58,788–792CrossRefGoogle Scholar
  53. 53.
    Azuma, C, SaJi, F, Nobunaga, T, Kammra, S, Kimura, T, Tokugawa, Y, Koyama, M, and Tamzawa, O (1990) Studies on the pathogenests of choriocarcmoma by analysis of restrictton fragment length polymorphisms Cancer Res 50,488–491PubMedGoogle Scholar
  54. 54.
    Nobunaga, T, Azuma, C, Kimura, T, Tokugawa, Y, Takemura, M, Kammra, S, San, F,and Tamzawa, O (1990) Differential dtagnosts between complete mole and hydropic abortus by deoxyribonucleic acid fingerprmts Am J Obstet Gynecol 163, 634–638PubMedGoogle Scholar
  55. 55.
    Georges, M, Lequarre, A S, Castelh, M, Hanset, R, and Vassart, G (1988) DNA fingerprinting in domestic animals using four different mm~satelhte probes Cytogenet Cell Genet 47,127–131PubMedCrossRefGoogle Scholar
  56. 56.
    Bmns, M in, Holmes, N G, Holhman, A, and Scott, A in (1995) The mdentlficatlon of polymorphic mlcrosatelhte loci in the hoere and their use in thoroughbred parentage testing Br Vet J 151,9–15CrossRefGoogle Scholar
  57. 57.
    Burke, T and Bruford, W (1987) DNA fingerprinting in buds Nature 327, 149–152PubMedCrossRefGoogle Scholar
  58. 58.
    Jones, C S, Lessells, C in, and Krebs, J R (1991) Helpers-at-the-nest in european bee-eaters (Merops aplaster) a genetic analysis, in DNAFingerpnnting Approaches and Applzcatlons (Burke, T, Dolf, G, Jeffreys, A J,and Wolff, R,eds ), Blrkhauser Verlag,Basel, Switzerland, pp 169–192Google Scholar
  59. 59.
    Graves, J, Hay, R T, Scallan, M, and Rowe, S (1992) Extra-pair patermty in the shag, Phalacrocorax arlstotehs as determined by DNA fingerprinting J ZoolLondon 226,399–408CrossRefGoogle Scholar
  60. 60.
    Wolfes, R., Mathe, J, and Seltz, A (1991) Forensics of birds of prey by DNA fingerprmting with 32P-labelled ohgonucleotlde probes Electrophoreszs 12, 175–180CrossRefGoogle Scholar
  61. 61.
    Blackett, R S and Kelm, P (1992) Big game species ldentlficatton by deoxyrlbonuclelc acid (DNA) probes J Forenszc Scz 37,590–596Google Scholar
  62. 62.
    Meng, A, Carter, R E, and Parkm, D T (1990) The varlablhty of DNA fingerprints in three species of swan Heredzty 64,73–80CrossRefGoogle Scholar
  63. 63.
    Scnbner, K T, Arntzen, J W, and Burke, T (1994) Comparative analysis of mtra-and mterpopulatlon genetic dlverslty in Bufo bufo, using allozyme, single-locus mlcrosatelhte, mmlsatelhte and multllocus mmlsatelhte data A4oZ Bzol Evol 11,737–748Google Scholar
  64. 64.
    Wetton, J H, Carter, R E, Parkm, D T, and Walters, D (1987) Demographic study of a wild house sparrow population by DNA fingerprinting Nature 327, 147–149PubMedCrossRefGoogle Scholar
  65. 65.
    Gilbert, D A, Lehman, N, O’Brien, S J, and Wayne, R K (1990) Genetic fingerprmting reflects population dlfferentlatlon in the Cahforma Channel Island fox Nature 344,764–766PubMedCrossRefGoogle Scholar
  66. 66.
    Georges, M, Lathrop, M, Hllbert, P, Marcotte, A, Sewers, A, Swillens, S, Vassart, G,and Hanset, R (1990) On the use of DNA fingerprinting for linkage studies in cattle Genomlcs 6,461–474CrossRefGoogle Scholar
  67. 67.
    Kuhnlem, U, Zadworny, D, Gavora, J S, and FaIrfull, R W (1991) Identlficatlon of markers associated with quantltatlve trait loci in chickens by DNA fingerprinting, in DNA Flngerpnnting Approaches and Applzcattons(Burke, T, Dolf, G, Jeffreys, A J, and Wolff, R, eds), Blrkhauser Verlag, Base& Switzerland, pp 274–282Google Scholar
  68. 68.
    Trapman, J, Sleddens, H F B in, van der Welden, M in, DmJems, W in N, Koing, J J, Schroder, F H, Faber, P W, and Bosman, F T (1994) Loss of heterozygoslty of chomosome 8 microsatellite loci lmphcates a candidate tumour suppressor gene between the loci D8S87 and D8S133 in human prostate cancer Cancer Res 54,6061–6064PubMedGoogle Scholar
  69. 69.
    Pykett, M J, Murphy, M, Harmsch, P R, and George, D L (1994) Identlficatlon of a microsatellite mstabuty phenotype in meninglomas Cancer Res 54, 6340–6343PubMedGoogle Scholar

Copyright information

© Humana Press Inc , Totowa, NJ. 1998

Authors and Affiliations

  • Karen M. Sullivan
    • 1
  1. 1.Department of Molecular and Life SciencesUniversity of AbertayUK

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