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. 1996 Jun 25;93(13):6297–6301. doi: 10.1073/pnas.93.13.6297

A bacterial artificial chromosome-based framework contig map of human chromosome 22q.

U J Kim 1, H Shizuya 1, H L Kang 1, S S Choi 1, C L Garrett 1, L J Smink 1, B W Birren 1, J R Korenberg 1, I Dunham 1, M I Simon 1
PMCID: PMC39016  PMID: 8692809

Abstract

We have constructed a physical map of human chromosome 22q using bacterial artificial chromosome (BAC) clones. The map consists of 613 chromosome 22-specific BAC clones that have been localized and assembled into contigs using 452 landmarks, 346 of which were previously ordered and mapped to specific regions of the q arm of the chromosome by means of chromosome 22-specific yeast artificial chromosome clones. The BAC-based map provides immediate access to clones that are stable and convenient for direct genome analysis. The approach to rapidly developing marker-specific BAC contigs is relatively straightforward and can be extended to generate scaffold BAC contig maps of the rest of the chromosomes. These contigs will provide substrates for sequencing the entire human genome. We discuss how to efficiently close contig gaps using the end sequences of BAC clone inserts.

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Selected References

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  1. Auffray C., Behar G., Bois F., Bouchier C., Da Silva C., Devignes M. D., Duprat S., Houlgatte R., Jumeau M. N., Lamy B. IMAGE: intégration au niveau moléculaire de l'analyse du génome humain et de son expression. C R Acad Sci III. 1995 Feb;318(2):263–272. [PubMed] [Google Scholar]
  2. Bell C. J., Budarf M. L., Nieuwenhuijsen B. W., Barnoski B. L., Buetow K. H., Campbell K., Colbert A. M., Collins J., Daly M., Desjardins P. R. Integration of physical, breakpoint and genetic maps of chromosome 22. Localization of 587 yeast artificial chromosomes with 238 mapped markers. Hum Mol Genet. 1995 Jan;4(1):59–69. doi: 10.1093/hmg/4.1.59. [DOI] [PubMed] [Google Scholar]
  3. Chumakov I. M., Rigault P., Le Gall I., Bellanné-Chantelot C., Billault A., Guillou S., Soularue P., Guasconi G., Poullier E., Gros I. A YAC contig map of the human genome. Nature. 1995 Sep 28;377(6547 Suppl):175–297. doi: 10.1038/377175a0. [DOI] [PubMed] [Google Scholar]
  4. Chumakov I., Rigault P., Guillou S., Ougen P., Billaut A., Guasconi G., Gervy P., LeGall I., Soularue P., Grinas L. Continuum of overlapping clones spanning the entire human chromosome 21q. Nature. 1992 Oct 1;359(6394):380–387. doi: 10.1038/359380a0. [DOI] [PubMed] [Google Scholar]
  5. Collins J. E., Cole C. G., Smink L. J., Garrett C. L., Leversha M. A., Soderlund C. A., Maslen G. L., Everett L. A., Rice K. M., Coffey A. J. A high-density YAC contig map of human chromosome 22. Nature. 1995 Sep 28;377(6547 Suppl):367–379. doi: 10.1038/377367a0. [DOI] [PubMed] [Google Scholar]
  6. Doggett N. A., Goodwin L. A., Tesmer J. G., Meincke L. J., Bruce D. C., Clark L. M., Altherr M. R., Ford A. A., Chi H. C., Marrone B. L. An integrated physical map of human chromosome 16. Nature. 1995 Sep 28;377(6547 Suppl):335–365. doi: 10.1038/377335a0. [DOI] [PubMed] [Google Scholar]
  7. Dumanski J. P., Geurts van Kessel A. H., Ruttledge M., Wladis A., Sugawa N., Collins V. P., Nordenskjöld M. Isolation of anonymous, polymorphic DNA fragments from human chromosome 22q12-qter. Hum Genet. 1990 Feb;84(3):219–222. doi: 10.1007/BF00200562. [DOI] [PubMed] [Google Scholar]
  8. Foote S., Vollrath D., Hilton A., Page D. C. The human Y chromosome: overlapping DNA clones spanning the euchromatic region. Science. 1992 Oct 2;258(5079):60–66. doi: 10.1126/science.1359640. [DOI] [PubMed] [Google Scholar]
  9. Gemmill R. M., Chumakov I., Scott P., Waggoner B., Rigault P., Cypser J., Chen Q., Weissenbach J., Gardiner K., Wang H. A second-generation YAC contig map of human chromosome 3. Nature. 1995 Sep 28;377(6547 Suppl):299–319. doi: 10.1038/377299a0. [DOI] [PubMed] [Google Scholar]
  10. Green E. D., Riethman H. C., Dutchik J. E., Olson M. V. Detection and characterization of chimeric yeast artificial-chromosome clones. Genomics. 1991 Nov;11(3):658–669. doi: 10.1016/0888-7543(91)90073-n. [DOI] [PubMed] [Google Scholar]
  11. Houlgatte R., Mariage-Samson R., Duprat S., Tessier A., Bentolila S., Lamy B., Auffray C. The Genexpress Index: a resource for gene discovery and the genic map of the human genome. Genome Res. 1995 Oct;5(3):272–304. doi: 10.1101/gr.5.3.272. [DOI] [PubMed] [Google Scholar]
  12. Hudson T. J., Stein L. D., Gerety S. S., Ma J., Castle A. B., Silva J., Slonim D. K., Baptista R., Kruglyak L., Xu S. H. An STS-based map of the human genome. Science. 1995 Dec 22;270(5244):1945–1954. doi: 10.1126/science.270.5244.1945. [DOI] [PubMed] [Google Scholar]
  13. Kim U. J., Shizuya H., Birren B., Slepak T., de Jong P., Simon M. I. Selection of chromosome 22-specific clones from human genomic BAC library using a chromosome-specific cosmid library pool. Genomics. 1994 Jul 15;22(2):336–339. doi: 10.1006/geno.1994.1392. [DOI] [PubMed] [Google Scholar]
  14. Kim U. J., Shizuya H., Chen X. N., Deaven L., Speicher S., Solomon J., Korenberg J., Simon M. I. Characterization of a human chromosome 22 enriched bacterial artificial chromosome sublibrary. Genet Anal. 1995 Oct;12(2):73–79. doi: 10.1016/1050-3862(95)00121-2. [DOI] [PubMed] [Google Scholar]
  15. Kim U. J., Shizuya H., de Jong P. J., Birren B., Simon M. I. Stable propagation of cosmid sized human DNA inserts in an F factor based vector. Nucleic Acids Res. 1992 Mar 11;20(5):1083–1085. doi: 10.1093/nar/20.5.1083. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Kouprina N., Eldarov M., Moyzis R., Resnick M., Larionov V. A model system to assess the integrity of mammalian YACs during transformation and propagation in yeast. Genomics. 1994 May 1;21(1):7–17. doi: 10.1006/geno.1994.1218. [DOI] [PubMed] [Google Scholar]
  17. Krauter K., Montgomery K., Yoon S. J., LeBlanc-Straceski J., Renault B., Marondel I., Herdman V., Cupelli L., Banks A., Lieman J. A second-generation YAC contig map of human chromosome 12. Nature. 1995 Sep 28;377(6547 Suppl):321–333. doi: 10.1038/377321a0. [DOI] [PubMed] [Google Scholar]
  18. Larionov V., Kouprina N., Nikolaishvili N., Resnick M. A. Recombination during transformation as a source of chimeric mammalian artificial chromosomes in yeast (YACs). Nucleic Acids Res. 1994 Oct 11;22(20):4154–4162. doi: 10.1093/nar/22.20.4154. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Shizuya H., Birren B., Kim U. J., Mancino V., Slepak T., Tachiiri Y., Simon M. Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA in Escherichia coli using an F-factor-based vector. Proc Natl Acad Sci U S A. 1992 Sep 15;89(18):8794–8797. doi: 10.1073/pnas.89.18.8794. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Sulston J., Mallett F., Durbin R., Horsnell T. Image analysis of restriction enzyme fingerprint autoradiograms. Comput Appl Biosci. 1989 Apr;5(2):101–106. doi: 10.1093/bioinformatics/5.2.101. [DOI] [PubMed] [Google Scholar]
  21. Sulston J., Mallett F., Staden R., Durbin R., Horsnell T., Coulson A. Software for genome mapping by fingerprinting techniques. Comput Appl Biosci. 1988 Mar;4(1):125–132. doi: 10.1093/bioinformatics/4.1.125. [DOI] [PubMed] [Google Scholar]

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