Skip to main content
SpringerLink
Log in

YAC analysis and minimal tiling path construction for chromosome 21q

  • Published:
Somatic Cell and Molecular Genetics

Abstract

We have undertaken a detailed analysis of several hundred YACs from widely available YAC libraries which map to human chromosome 21 with the goal of improving the physical map of chromosome 21 and determining the feasibility of producing a minimal tiling path of well characterized, stable, non-chimeric YACs spanning the long arm of the chromosome (21q). We report information on over 500 YACs known to contain STS from 21q including information on size, stability, chimerism, marker content, and NotI restriction sites. YACs derive from the CEPH and St. Louis YAC libraries, and STSs include the set of 198 markers originally used do assemble a YAC contig of 21q, as well as additional anonymous probes and gene markers. This information has assisted in refinements of STS order, has defined a region of general instability in 21q22.3, has identified an increased number of NotI restriction sites, and has defined cryptic gaps, particularly in 21q21, for which few or no markers are available. These results have allowed us to develop and assess a minimal tiling path of overlapping YACs consisting of 59 YACs (and two P1 clones), largely non chimeric, stable, and of verified STS content. They total 30 mb of non-overlapping DNA, and contain all chromosome 21 specific STSs originally used to define the 810 YAC 21q YAC contig. When integrated with the analysis of a somatic cell hybrid mapping panel of chromosome 21 reported in the accompanying manuscript, a greatly enhanced understanding of the physical map of chromosome 21 is obtained.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  1. Albertsen, H.M., Abderrahim, H., Cann, H.M., Dausset, J., Le Paslier, D., and Cohen, D. (1990).Proc. Natl. Acad. Sci. U.S.A. 87:4256–4260.

    CAS  PubMed  Google Scholar 

  2. Bellanne-Chantelot, C., Lacroix, B., Ougen, P., Billault, A., Beaufils, S., Bertrand, S., Georges, I., Glibert, F., Gros, I., Lucotte, G., Susini, L., Codani, J-J., Gesnouin, P., Pook, S., Vaysseix, G., Lu-Kuo, J., Ried, T., Ward, D., Chumakov, I., Le Paslier, D., Barillot, E., and Cohen, D. (1992).Cell 70:1059–1068.

    CAS  PubMed  Google Scholar 

  3. Burke, D.T., Carle, G.F., and Olson, M.V. (1987).Science 236:806–812.

    CAS  PubMed  Google Scholar 

  4. Imai, T., and Olson, M.V. (1990).Genomics 8:297–303.

    Article  CAS  PubMed  Google Scholar 

  5. Chumakov, I., Rigault, P., Guillou, S., Ougen, P., Billaut, A., Guasconi, G., Gervy, P., LeGall, I., Soularue, P., Grinas, L., Bougueleret, L., Bellanne-Chantelot, C., Lacroix, B., Barillot, E., Gesnouin, P., Pook, S., Vaysseix, G., Frelat, G., Shmitz, A., Sambucy, J-L., Bosch, A., Estivill, X., Weissenbach, J., Vignal, A., Riethman, H., Cox, D., Patterson, D., Gardiner, K., Hattori, M., Sakaki, Y., Ichikawa, H., Ohki, M., Le Paslier, D., Hellig, R., Antonarakis, S., and Cohen, D.Nature 359:380–387.

  6. Delabar, J-M., Creau, N., Sinet, P-M., Ritter, O., Antonarakis, S.E., Burmeister, M., Chakravarti, A., Nizetic, D., Ohki, M., Patterson, D., Petersen, M.B., Reeves, R.G., and Van Broechkoven, C. (1993).Genomics 18:735–745.

    Article  CAS  PubMed  Google Scholar 

  7. Shimizu, M., Antonarakis, S.E., Van Broeckhoven, C., Patterson, D., Gardiner, K., Nizetic, D., Creau, N., Delabar, J-M., Korenberg, J., Reeves, R., Doering, J., Chakravati, A., Minoshima, S., Ritter, O., and Cuticchia, J. (1995).Cytogenet. Cell Genet. 70:148–182.

    CAS  Google Scholar 

  8. Tassone, F., Cheng, S., and Gardiner, K. (1992).Am. J. Hum. Genet. 51:1251–1264.

    CAS  PubMed  Google Scholar 

  9. Dufresne-Zacharia, M.-C., Dahmane, N., Theophile, D., Orti, R., Chettouh, Z., Sinet, P.-M., and Delabar, J.-M. (1994).Genomics 19:462–469.

    Article  CAS  PubMed  Google Scholar 

  10. Nizetic, D., Gellen, L., Hamvas, R.M.J., Mott, R., Grigoriev, A., Vatcheva, R., Zehetner, G., Yaspo, M.-L., Dutriaux, A., Lopes, C., Delabar, J.-M., Van Broeckhoven, C., Potier, M.-C., and Lehrach, H. (1994).Hum. Mol. Genet. 3:759–770.

    CAS  PubMed  Google Scholar 

  11. Sherman, F., Fink, G.R., and Hicks, J.B. (1986).Methods in Yeast Genetics. Cold Spring Harbor Laboratory, Cold Spring Harbor Press.

  12. Feinberg, A.P., and Vogelstein, B. (1989).Anal. Biochem. 137:266–267.

    Google Scholar 

  13. Ichikawa, H., Hosoda, F., Arai, Y., Shimizu, K., Ohira, M., and Ohki, M. (1993).Nat. Genet. 4:361–365.

    Article  CAS  PubMed  Google Scholar 

  14. Gao, J., Erickson, P., Patterson, D., Jones, C., and Drabkin, H. (1991).Genomics 10:166–172.

    Article  CAS  PubMed  Google Scholar 

  15. Gardiner, K., Horisberger, M., Kraus, J., Tantravahi, U., Korenberg, J., Rao, V., Reddy, S., and Patterson, D. (1990).EMBO J. 9:25–34.

    CAS  PubMed  Google Scholar 

  16. Gardiner K. Physical mapping of the long arm of chromosome 21. (1990). InMolecular Genetics of Chromosome 21 and Down Syndrome. (eds.), Patterson, D., and Epstein, C.J. Wiley-Liss, Inc., pp 1–14.

  17. Trask, B., Pinkel, D., and Van Den Engh, G. (1989).Genomics 5:710–717.

    Article  CAS  PubMed  Google Scholar 

  18. Pahl, P., Berger, R., Hart, I., Chae, H.Z., Rhee, S.G., and Patterson, D. (1995).Genomics 26:602–606.

    Article  CAS  PubMed  Google Scholar 

  19. Shepherd, N.S., Pfrogner, B.D., Coulby, J.N., Ackerman, S.L., Vaidyanathan, G., Sauer, R.H., Balkenhol, T.C., and Sternberg, N. (1994).Proc. Natl. Acad. Sci. U.S.A. 91:2629–2633.

    CAS  PubMed  Google Scholar 

  20. Lutfalla G., Gardiner, K., Proudhon, D., Vielh, E., and Uze, G. (1992).J. Biol. Chem. 267:2802–2809.

    CAS  PubMed  Google Scholar 

  21. Patil, N., Peterson, A., Rothman, A., de Jong, J., Myers, R.M., and Cox, D.R. (1994).Hum. Mol. Genet. 3:1811–1817.

    CAS  PubMed  Google Scholar 

  22. Burmeister, M., Kim, S., Price, E.R., de Lange, T., Tantravahi, U., Myers, R.M., and Cox, D.R. (1991).Genomics 9:19–30.

    Article  CAS  PubMed  Google Scholar 

  23. Ferrin, L.J., and Camerini-Otero, R.D. (1991).Science 254:1494–1497.

    CAS  PubMed  Google Scholar 

  24. Negorev, D.G., Macina, R.A., Spais, C., Ruthig, I.A., Hu, X.-L., and Riethman, H.C. (1994).Genomics 22:569–578.

    Article  CAS  PubMed  Google Scholar 

  25. Barnes, W.M. (1994).Proc. Natl. Acad. Sci. U.S.A. 91:2216–2220.

    CAS  PubMed  Google Scholar 

  26. Cheng, S., Fockler, C., Barnes, W.M., and Higuchi, R. (1994).Proc. Natl. Acad. Sci. U.S.A. 91:5695–5699.

    CAS  PubMed  Google Scholar 

  27. Xu, H., Wel, H., Tassone, F., Graw S., Gardiner, K., and Weissman, S.M. (1995).Genomics 27:1–8.

    CAS  PubMed  Google Scholar 

  28. Nasir, J., Maconochie, M.K., and Brown, S.D.M. (1991).Nucl. Acids Res. 19:3255–3260.

    CAS  PubMed  Google Scholar 

  29. Gardiner, K., Aissani, B., and Bernardi, G. (1990).EMBO J 9:1853–1858.

    CAS  PubMed  Google Scholar 

  30. Cheng, J-F., Boyartchuk, V., and Zhu, Y. (1994).Genomics 23:75–84.

    Article  CAS  PubMed  Google Scholar 

  31. Gardiner, K., Ichikawa, H., Ohki, M., Patterson, D., and Cheng, J-F. (1995). Localization of cDNAs to a region poorly represented in the CEPH chromosome 21 YAC contig: candidate genes for genetic diseases mapped to 21q22.3.Genomics 30:376–379.

    Article  CAS  PubMed  Google Scholar 

  32. Guiseppe, P., Roman, G., Ciccodicola, A., Casamassimi, A., Campanile, C., Esposito, T., Cappa, V., Lania, A., Johnson, S., Reinbold, R., Pousta, A., Schlessinger, D., and D'Urso, M. (1994).Genomics 24:149–158.

    Google Scholar 

  33. Pekarsky, Y., Zabarovsky, E., Kashuba, V., Drabkin, H., Sandberg, A., Morgan, R. Rynditch, A., and Gardiner, K. (1995).Cancer Genet. Cytogenet. 80:1–8.

    Article  CAS  PubMed  Google Scholar 

  34. Ioannou, P.A., Amemiya, C.T., Garnes, J., Kroisel, P.M., Shizuya, H., Chen, C., Batzer, M.A., and de Jong, P.J. (1994).Nat. Genet. 6:84–89.

    CAS  PubMed  Google Scholar 

  35. Sheperd, N.S., Pfrogner, B.D., Coulby, J.N., Ackerman, S.L., Vaidyanathan, G., Sauer, R.H., Balkenhol, T.C., and Sternberg, N. (1994).Proc. Natl. Acad. Sci. U.S.A. 91:2629–2633.

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Eleanor Roosevelt Institute, 1899 Gaylord Street, 80206, Denver, Colorado

    Katheleen Gardiner, Sharon Graw, Anthony Joetham & David Patterson

  2. National Cancer Center Research Institute, Tokyo, Japan

    Hitoshi Ichikawa & Misao Ohki

  3. Fondation Jean Dausset-CEPH, Paris, France

    Partricia Gervy & Ilya Chumakov

Authors
  1. Katheleen Gardiner
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Sharon Graw
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Hitoshi Ichikawa
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Misao Ohki
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Anthony Joetham
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Partricia Gervy
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Ilya Chumakov
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. David Patterson
    View author publications

    You can also search for this author in PubMed Google Scholar

Rights and permissions

Reprints and permissions

About this article

Cite this article

Gardiner, K., Graw, S., Ichikawa, H. et al. YAC analysis and minimal tiling path construction for chromosome 21q. Somat Cell Mol Genet 21, 399–414 (1995). https://doi.org/10.1007/BF02310207

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1007/BF02310207

Keywords

Search

Navigation