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. 1996 Jan 23;93(2):690–694. doi: 10.1073/pnas.93.2.690

A high-resolution annotated physical map of the human chromosome 13q12-13 region containing the breast cancer susceptibility locus BRCA2.

S G Fischer 1, E Cayanis 1, M de Fatima Bonaldo 1, A M Bowcock 1, L L Deaven 1, I S Edelman 1, T Gallardo 1, S Kalachikov 1, L Lawton 1, J L Longmire 1, M Lovett 1, S Osborne-Lawrence 1, R Rothstein 1, J J Russo 1, M B Soares 1, I Sunjevaric 1, V S Venkatraj 1, D Warburton 1, P Zhang 1, A Efstratiadis 1
PMCID: PMC40114  PMID: 8570617

Abstract

Various types of physical mapping data were assembled by developing a set of computer programs (Integrated Mapping Package) to derive a detailed, annotated map of a 4-Mb region of human chromosome 13 that includes the BRCA2 locus. The final assembly consists of a yeast artificial chromosome (YAC) contig with 42 members spanning the 13q12-13 region and aligned contigs of 399 cosmids established by cross-hybridization between the cosmids, which were selected from a chromosome 13-specific cosmid library using inter-Alu PCR probes from the YACs. The end sequences of 60 cosmids spaced nearly evenly across the map were used to generate sequence-tagged sites (STSs), which were mapped to the YACs by PCR. A contig framework was generated by STS content mapping, and the map was assembled on this scaffold. Additional annotation was provided by 72 expressed sequences and 10 genetic markers that were positioned on the map by hybridization to cosmids.

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Selected References

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

  1. Bonaldo M. F., Yu M. T., Jelenc P., Brown S., Su L., Lawton L., Deaven L., Efstratiadis A., Warburton D., Soares M. B. Selection of cDNAs using chromosome-specific genomic clones: application to human chromosome 13. Hum Mol Genet. 1994 Sep;3(9):1663–1673. doi: 10.1093/hmg/3.9.1663. [DOI] [PubMed] [Google Scholar]
  2. Claus E. B., Risch N., Thompson W. D. Genetic analysis of breast cancer in the cancer and steroid hormone study. Am J Hum Genet. 1991 Feb;48(2):232–242. [PMC free article] [PubMed] [Google Scholar]
  3. Collins N., McManus R., Wooster R., Mangion J., Seal S., Lakhani S. R., Ormiston W., Daly P. A., Ford D., Easton D. F. Consistent loss of the wild type allele in breast cancers from a family linked to the BRCA2 gene on chromosome 13q12-13. Oncogene. 1995 Apr 20;10(8):1673–1675. [PubMed] [Google Scholar]
  4. Easton D. F., Ford D., Bishop D. T. Breast and ovarian cancer incidence in BRCA1-mutation carriers. Breast Cancer Linkage Consortium. Am J Hum Genet. 1995 Jan;56(1):265–271. [PMC free article] [PubMed] [Google Scholar]
  5. Easton D., Ford D., Peto J. Inherited susceptibility to breast cancer. Cancer Surv. 1993;18:95–113. [PubMed] [Google Scholar]
  6. Fischer S. G., Cayanis E., Russo J. J., Sunjevaric I., Boukhgalter B., Zhang P., Yu M. T., Rothstein R., Warburton D., Edelman I. S. Assembly of ordered contigs of cosmids selected with YACs of human chromosome 13. Genomics. 1994 Jun;21(3):525–537. doi: 10.1006/geno.1994.1311. [DOI] [PubMed] [Google Scholar]
  7. Hall J. M., Lee M. K., Newman B., Morrow J. E., Anderson L. A., Huey B., King M. C. Linkage of early-onset familial breast cancer to chromosome 17q21. Science. 1990 Dec 21;250(4988):1684–1689. doi: 10.1126/science.2270482. [DOI] [PubMed] [Google Scholar]
  8. Lovett M. Fishing for complements: finding genes by direct selection. Trends Genet. 1994 Oct;10(10):352–357. doi: 10.1016/0168-9525(94)90131-7. [DOI] [PubMed] [Google Scholar]
  9. Lovett M., Kere J., Hinton L. M. Direct selection: a method for the isolation of cDNAs encoded by large genomic regions. Proc Natl Acad Sci U S A. 1991 Nov 1;88(21):9628–9632. doi: 10.1073/pnas.88.21.9628. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Miki Y., Swensen J., Shattuck-Eidens D., Futreal P. A., Harshman K., Tavtigian S., Liu Q., Cochran C., Bennett L. M., Ding W. A strong candidate for the breast and ovarian cancer susceptibility gene BRCA1. Science. 1994 Oct 7;266(5182):66–71. doi: 10.1126/science.7545954. [DOI] [PubMed] [Google Scholar]
  11. Morgan J. G., Dolganov G. M., Robbins S. E., Hinton L. M., Lovett M. The selective isolation of novel cDNAs encoded by the regions surrounding the human interleukin 4 and 5 genes. Nucleic Acids Res. 1992 Oct 11;20(19):5173–5179. doi: 10.1093/nar/20.19.5173. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Neuhausen S. L., Swensen J., Miki Y., Liu Q., Tavtigian S., Shattuck-Eidens D., Kamb A., Hobbs M. R., Gingrich J., Shizuya H. A P1-based physical map of the region from D17S776 to D17S78 containing the breast cancer susceptibility gene BRCA1. Hum Mol Genet. 1994 Nov;3(11):1919–1926. doi: 10.1093/hmg/3.11.1919. [DOI] [PubMed] [Google Scholar]
  13. Schutte M., da Costa L. T., Hahn S. A., Moskaluk C., Hoque A. T., Rozenblum E., Weinstein C. L., Bittner M., Meltzer P. S., Trent J. M. Identification by representational difference analysis of a homozygous deletion in pancreatic carcinoma that lies within the BRCA2 region. Proc Natl Acad Sci U S A. 1995 Jun 20;92(13):5950–5954. doi: 10.1073/pnas.92.13.5950. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Shaw S. H., Farr J. E., Thiel B. A., Matise T. C., Weissenbach J., Chakaravarti A., Richard C. W., 3rd A radiation hybrid map of 95 STSs spanning human chromosome 13q. Genomics. 1995 Jun 10;27(3):502–510. doi: 10.1006/geno.1995.1083. [DOI] [PubMed] [Google Scholar]
  15. Sobol H., Birnbaum D., Eisinger F. Evidence for a third breast-cancer susceptibility gene. Lancet. 1994 Oct 22;344(8930):1151–1152. doi: 10.1016/s0140-6736(94)90655-6. [DOI] [PubMed] [Google Scholar]
  16. Wooster R., Neuhausen S. L., Mangion J., Quirk Y., Ford D., Collins N., Nguyen K., Seal S., Tran T., Averill D. Localization of a breast cancer susceptibility gene, BRCA2, to chromosome 13q12-13. Science. 1994 Sep 30;265(5181):2088–2090. doi: 10.1126/science.8091231. [DOI] [PubMed] [Google Scholar]
  17. Zhang P., Schon E. A., Fischer S. G., Cayanis E., Weiss J., Kistler S., Bourne P. E. An algorithm based on graph theory for the assembly of contigs in physical mapping of DNA. Comput Appl Biosci. 1994 Jun;10(3):309–317. doi: 10.1093/bioinformatics/10.3.309. [DOI] [PubMed] [Google Scholar]

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