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. 1990 May;87(9):3415–3419. doi: 10.1073/pnas.87.9.3415

Construction of the physical map for three loci in chromosome band 13q14: comparison to the genetic map.

M J Higgins 1, C Turmel 1, J Noolandi 1, P E Neumann 1, M Lalande 1
PMCID: PMC53911  PMID: 1970636

Abstract

Pulsed-field gel electrophoresis (PFGE) and deletion mapping are being used to construct a physical map of the long arm of human chromosome 13. The present study reports a 2700-kilobase (kb) Not I long-range restriction map encompassing the 13q14-specific loci D13S10, D13S21, and D13S22, which are detected by the cloned DNA markers p7D2, pG24E2.4, and pG14E1.9, respectively. Analysis of a panel of seven cell lines that showed differential methylation at a Not I site between D13S10 and D13S21 proved physical linkage of the two loci to the same 875-kb Not I fragment. D13S22 mapped to a different Not I fragment, precluding the possibility that D13S22 is located between D13S10 and D13S21. PFGE analysis of Not I partial digests placed the 1850-kb Not I fragment containing D13S22 immediately adjacent to the 875-kb fragment containing the other two loci. The proximal rearrangement breakpoint in a cell line carrying a del13(q14.1q21.2) was detected by D13S21 but not by D13S10, demonstrating that D13S21 lies proximal to D13S10. Quantitative analysis of hybridization signals of the three DNA probes to DNA from the same cell line indicated that only D13S10 was deleted, establishing the order of these loci to be cen-D13S22-D13S21-D13S10-tel. Surprisingly, this order was estimated to be 35,000 times less likely than that favored by genetic linkage analysis.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Arveiler B., Vincent A., Mandel J. L. Toward a physical map of the Xq28 region in man: linking color vision, G6PD, and coagulation factor VIII genes to an X-Y homology region. Genomics. 1989 May;4(4):460–471. doi: 10.1016/0888-7543(89)90269-3. [DOI] [PubMed] [Google Scholar]
  2. Beaudet A., Bowcock A., Buchwald M., Cavalli-Sforza L., Farrall M., King M. C., Klinger K., Lalouel J. M., Lathrop G., Naylor S. Linkage of cystic fibrosis to two tightly linked DNA markers: joint report from a collaborative study. Am J Hum Genet. 1986 Dec;39(6):681–693. [PMC free article] [PubMed] [Google Scholar]
  3. Bowcock A. M., Farrer L. A., Hebert J. M., Agger M., Sternlieb I., Scheinberg I. H., Buys C. H., Scheffer H., Frydman M., Chajek-Saul T. Eight closely linked loci place the Wilson disease locus within 13q14-q21. Am J Hum Genet. 1988 Nov;43(5):664–674. [PMC free article] [PubMed] [Google Scholar]
  4. Burmeister M., Monaco A. P., Gillard E. F., van Ommen G. J., Affara N. A., Ferguson-Smith M. A., Kunkel L. M., Lehrach H. A 10-megabase physical map of human Xp21, including the Duchenne muscular dystrophy gene. Genomics. 1988 Apr;2(3):189–202. doi: 10.1016/0888-7543(88)90002-x. [DOI] [PubMed] [Google Scholar]
  5. Cavenee W., Leach R., Mohandas T., Pearson P., White R. Isolation and regional localization of DNA segments revealing polymorphic loci from human chromosome 13. Am J Hum Genet. 1984 Jan;36(1):10–24. [PMC free article] [PubMed] [Google Scholar]
  6. Cutting G. R., Kazazian H. H., Jr, Antonarakis S. E., Killen P. D., Yamada Y., Francomano C. A. Macrorestriction mapping of COL4A1 and COL4A2 collagen genes on human chromosome 13q34. Genomics. 1988 Oct;3(3):256–263. doi: 10.1016/0888-7543(88)90086-9. [DOI] [PubMed] [Google Scholar]
  7. Donis-Keller H., Green P., Helms C., Cartinhour S., Weiffenbach B., Stephens K., Keith T. P., Bowden D. W., Smith D. R., Lander E. S. A genetic linkage map of the human genome. Cell. 1987 Oct 23;51(2):319–337. doi: 10.1016/0092-8674(87)90158-9. [DOI] [PubMed] [Google Scholar]
  8. Douglass E. C., Valentine M., Etcubanas E., Parham D., Webber B. L., Houghton P. J., Houghton J. A., Green A. A. A specific chromosomal abnormality in rhabdomyosarcoma. Cytogenet Cell Genet. 1987;45(3-4):148–155. doi: 10.1159/000132446. [DOI] [PubMed] [Google Scholar]
  9. Dryja T. P., Morton C. C. Mapping of seven polymorphic loci on human chromosome 13 by in situ hybridization. Hum Genet. 1985;71(3):192–195. doi: 10.1007/BF00284571. [DOI] [PubMed] [Google Scholar]
  10. Duncan A. M., Morgan C., Gallie B. l., Phillips R. A., Squire J. Re-evaluation of the sublocalization of esterase D and its relation to the retinoblastoma locus by in situ hybridization. Cytogenet Cell Genet. 1987;44(2-3):153–157. doi: 10.1159/000132361. [DOI] [PubMed] [Google Scholar]
  11. Ejima Y., Sasaki M. S., Kaneko A., Tanooka H. Types, rates, origin and expressivity of chromosome mutations involving 13q14 in retinoblastoma patients. Hum Genet. 1988 Jun;79(2):118–123. doi: 10.1007/BF00280548. [DOI] [PubMed] [Google Scholar]
  12. Fan J. B., Chikashige Y., Smith C. L., Niwa O., Yanagida M., Cantor C. R. Construction of a Not I restriction map of the fission yeast Schizosaccharomyces pombe genome. Nucleic Acids Res. 1989 Apr 11;17(7):2801–2818. doi: 10.1093/nar/17.7.2801. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Feinberg A. P., Vogelstein B. A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Anal Biochem. 1983 Jul 1;132(1):6–13. doi: 10.1016/0003-2697(83)90418-9. [DOI] [PubMed] [Google Scholar]
  14. Fischel-Ghodsian N., Nicholls R. D., Higgs D. R. Long range genome structure around the human alpha-globin complex analysed by PFGE. Nucleic Acids Res. 1987 Aug 11;15(15):6197–6207. doi: 10.1093/nar/15.15.6197. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Francke U., Holmes L. B., Atkins L., Riccardi V. M. Aniridia-Wilms' tumor association: evidence for specific deletion of 11p13. Cytogenet Cell Genet. 1979;24(3):185–192. doi: 10.1159/000131375. [DOI] [PubMed] [Google Scholar]
  16. Fulton T. R., Bowcock A. M., Smith D. R., Daneshvar L., Green P., Cavalli-Sforza L. L., Donis-Keller H. A 12 megabase restriction map at the cystic fibrosis locus. Nucleic Acids Res. 1989 Jan 11;17(1):271–284. doi: 10.1093/nar/17.1.271. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Gardiner K., Watkins P., Münke M., Drabkin H., Jones C., Patterson D. Partial physical map of human chromosome 21. Somat Cell Mol Genet. 1988 Nov;14(6):623–637. doi: 10.1007/BF01535316. [DOI] [PubMed] [Google Scholar]
  18. Gessler M., Bruns G. A. A physical map around the WAGR complex on the short arm of chromosome 11. Genomics. 1989 Jul;5(1):43–55. doi: 10.1016/0888-7543(89)90084-0. [DOI] [PubMed] [Google Scholar]
  19. Gusella J. F. DNA polymorphism and human disease. Annu Rev Biochem. 1986;55:831–854. doi: 10.1146/annurev.bi.55.070186.004151. [DOI] [PubMed] [Google Scholar]
  20. Gusella J. F., Wexler N. S., Conneally P. M., Naylor S. L., Anderson M. A., Tanzi R. E., Watkins P. C., Ottina K., Wallace M. R., Sakaguchi A. Y. A polymorphic DNA marker genetically linked to Huntington's disease. Nature. 1983 Nov 17;306(5940):234–238. doi: 10.1038/306234a0. [DOI] [PubMed] [Google Scholar]
  21. Higgins M. J., Hansen M. F., Cavenee W. K., Lalande M. Molecular detection of chromosomal translocations that disrupt the putative retinoblastoma susceptibility locus. Mol Cell Biol. 1989 Jan;9(1):1–5. doi: 10.1128/mcb.9.1.1. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Lalande M., Donlon T., Petersen R. A., Liberfarb R., Manter S., Latt S. A. Molecular detection and differentiation of deletions in band 13q14 in human retinoblastoma. Cancer Genet Cytogenet. 1986 Oct;23(2):151–157. [PubMed] [Google Scholar]
  23. Lalande M., Dryja T. P., Schreck R. R., Shipley J., Flint A., Latt S. A. Isolation of human chromosome 13-specific DNA sequences cloned from flow sorted chromosomes and potentially linked to the retinoblastoma locus. Cancer Genet Cytogenet. 1984 Dec;13(4):283–295. doi: 10.1016/0165-4608(84)90073-6. [DOI] [PubMed] [Google Scholar]
  24. Lalande M., Noolandi J., Turmel C., Rousseau J., Slater G. W. Pulsed-field electrophoresis: application of a computer model to the separation of large DNA molecules. Proc Natl Acad Sci U S A. 1987 Nov;84(22):8011–8015. doi: 10.1073/pnas.84.22.8011. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Lander E. S., Botstein D. Mapping complex genetic traits in humans: new methods using a complete RFLP linkage map. Cold Spring Harb Symp Quant Biol. 1986;51(Pt 1):49–62. doi: 10.1101/sqb.1986.051.01.007. [DOI] [PubMed] [Google Scholar]
  26. Lathrop G. M., Lalouel J. M., Julier C., Ott J. Multilocus linkage analysis in humans: detection of linkage and estimation of recombination. Am J Hum Genet. 1985 May;37(3):482–498. [PMC free article] [PubMed] [Google Scholar]
  27. Lebo R. V., Chakravarti A., Buetow K. H., Cheung M. C., Cann H., Cordell B., Goodman H. Recombination within and between the human insulin and beta-globin gene loci. Proc Natl Acad Sci U S A. 1983 Aug;80(15):4808–4812. doi: 10.1073/pnas.80.15.4808. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. MORTON N. E. Sequential tests for the detection of linkage. Am J Hum Genet. 1955 Sep;7(3):277–318. [PMC free article] [PubMed] [Google Scholar]
  29. Nakamura Y., Mathew C. G., Sobol H., Easton D. F., Telenius H., Bragg T., Chin K., Clark J., Jones C., Lenoir G. M. Linked markers flanking the gene for multiple endocrine neoplasia type 2A. Genomics. 1989 Aug;5(2):199–203. doi: 10.1016/0888-7543(89)90046-3. [DOI] [PubMed] [Google Scholar]
  30. Noolandi J., Slater G. W., Lim H. A., Viovy J. L. Generalized tube model of biased reptation for gel electrophoresis of DNA. Science. 1989 Mar 17;243(4897):1456–1458. doi: 10.1126/science.2928779. [DOI] [PubMed] [Google Scholar]
  31. Nussbaum R. L., Lewis R. A., Lesko J. G., Ferrell R. Choroideremia is linked to the restriction fragment length polymorphism DXYS1 at XQ13-21. Am J Hum Genet. 1985 May;37(3):473–481. [PMC free article] [PubMed] [Google Scholar]
  32. Rao D. C., Keats B. J., Lalouel J. M., Morton N. E., Yee S. A maximum likelihood map of chromosome 1. Am J Hum Genet. 1979 Nov;31(6):680–696. [PMC free article] [PubMed] [Google Scholar]
  33. Reeders S. T., Breuning M. H., Davies K. E., Nicholls R. D., Jarman A. P., Higgs D. R., Pearson P. L., Weatherall D. J. A highly polymorphic DNA marker linked to adult polycystic kidney disease on chromosome 16. Nature. 1985 Oct 10;317(6037):542–544. doi: 10.1038/317542a0. [DOI] [PubMed] [Google Scholar]
  34. Reeders S. T., Keith T., Green P., Germino G. G., Barton N. J., Lehmann O. J., Brown V. A., Phipps P., Morgan J., Bear J. C. Regional localization of the autosomal dominant polycystic kidney disease locus. Genomics. 1988 Aug;3(2):150–155. doi: 10.1016/0888-7543(88)90146-2. [DOI] [PubMed] [Google Scholar]
  35. SMITH C. A. Some comments on the statistical methods used in linkage investigations. Am J Hum Genet. 1959 Dec;11:289–304. [PMC free article] [PubMed] [Google Scholar]
  36. Scheffer H., Kema I. P., Kondo I., van der Veen A. Y., Ikeuchi T., Buys C. H. Localization at a subband level of polymorphic 13q14 DNA probes for diagnosis of hereditary retinoblastoma and Wilson disease. Hum Genet. 1987 Dec;77(4):335–337. doi: 10.1007/BF00291421. [DOI] [PubMed] [Google Scholar]
  37. Scheffer H., van der Lelie D., Aanstoot G. H., Goor N., Nienhaus A. J., van der Hout A. H., Pearson P. L., Buys C. H. A straightforward approach to isolate DNA sequences with potential linkage to the retinoblastoma locus. Hum Genet. 1986 Nov;74(3):249–255. doi: 10.1007/BF00282543. [DOI] [PubMed] [Google Scholar]
  38. Schwartz D. C., Cantor C. R. Separation of yeast chromosome-sized DNAs by pulsed field gradient gel electrophoresis. Cell. 1984 May;37(1):67–75. doi: 10.1016/0092-8674(84)90301-5. [DOI] [PubMed] [Google Scholar]
  39. Simpson N. E., Kidd K. K., Goodfellow P. J., McDermid H., Myers S., Kidd J. R., Jackson C. E., Duncan A. M., Farrer L. A., Brasch K. Assignment of multiple endocrine neoplasia type 2A to chromosome 10 by linkage. Nature. 1987 Aug 6;328(6130):528–530. doi: 10.1038/328528a0. [DOI] [PubMed] [Google Scholar]
  40. Smith C. L., Lawrance S. K., Gillespie G. A., Cantor C. R., Weissman S. M., Collins F. S. Strategies for mapping and cloning macroregions of mammalian genomes. Methods Enzymol. 1987;151:461–489. doi: 10.1016/s0076-6879(87)51038-2. [DOI] [PubMed] [Google Scholar]
  41. Tsui L. C., Buchwald M., Barker D., Braman J. C., Knowlton R., Schumm J. W., Eiberg H., Mohr J., Kennedy D., Plavsic N. Cystic fibrosis locus defined by a genetically linked polymorphic DNA marker. Science. 1985 Nov 29;230(4729):1054–1057. doi: 10.1126/science.2997931. [DOI] [PubMed] [Google Scholar]
  42. Yunis J. J., Ramsay N. Retinoblastoma and subband deletion of chromosome 13. Am J Dis Child. 1978 Feb;132(2):161–163. doi: 10.1001/archpedi.1978.02120270059012. [DOI] [PubMed] [Google Scholar]

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