Analysis of a 69-kb Contiguous Genomic Sequence at a Putative Tumor Suppressor Gene Locus on Human Chromosome 6q27

References

• Adams J. W., Kaufman R. E., Kretschmer P. J., Harrison M., Nienhuis A. W. A family of long reiterated DNA sequences, one copy of which is next to the human beta globin gene. Nucleic Acids Research 1980; 8: 6113–6128
   PubMedGoogle Scholar
• Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. Basic local alignment search tool. Journal of Molecular Biology 1990; 215: 403–410
   PubMed Web of Science ®Google Scholar
• Bankier A. T., Weston K. M., Barrell B. G. Random cloning and sequencing by the M13/dideoxynucleotide chain termination method. Methods in Enzymology 1987; 155: 51–93
   PubMedGoogle Scholar
• Burfoot M. S., Campbell R. D. Improved method of gene detection using exon amplification. Nucleic Acids Research 1994; 22: 5510–5511
   Google Scholar
• Burn T. C., Connors T. D., Klinger K. W., Landes G. M. Increased exon-trapping efficiency through modifications to the pSPL3 splicing vector. Gene 1995; 161: 183–187
   PubMed Web of Science ®Google Scholar
• Chappell S. A., Walsh T., Walker R. A., Shaw J. A. Loss of heterozygosity at chromosome 6q in preinvasive and early invasive breast carcinomas. British Journal of Cancer 1997; 75: 1324–1329
   Google Scholar
• Chen S. J., Chen Z., d-Auriol L., Le Coniat M., Grausz D., Berger R. Phi + bcr- acute leukemias: implication of Alu sequences in a chromosomal translocation occurring in the new cluster region within the BCR gene. Oncogene 1989; 4: 195–202
   PubMed Web of Science ®Google Scholar
• Chirgwin J. M., Przybyla A. E., MacDonald R. J., Rutter W. J. Isolation of biologically active ribonucleic acid from sources enriched in ribonuclease. Biochemistry 1979; 18: 5294–5299
   PubMed Web of Science ®Google Scholar
• Chumakov I. M., Rigault P., Le Gall I., Bellanne-Chantelot C., Billault A., Guillou S., Soularue P., Guasconi G., Poullier E., Gros I., Belova M., Sambucy J., Susini L., Gervy P., Gilbert F., Beaufils S., Bui H., Massert C., De Tand M., Dukasz F., Lecoulant S., Ougen P., Perrot V., Saumier M., Soravito C., Bahouayila R., Cohen-Akenine A., Barillot E., Bertrand S., Codani J. J., Caterina D., Georges I., Lacroix B., Lucotte G., Sahbatou M., Schmif C., Sangouard M., Tucbacher E., Dib C., Faure S., Fizames C., Gyapay G., Millasseau P., Nguyen S., Muselet D., Vignal A., Morissette J., Menninger J., Lieman J., Desai T., Banks A., Bray-Ward P., Ward D., Hudson T., Gerety S., Foote S., Stein L., Page D. C., Lander E. S., Weissenbach J., Le Paslier D., Cohen D. A YAC contig map of the human genome. Nature 1995; 377: 175–297
   PubMedGoogle Scholar
• Church D. M., Stotler C. J., Rutter J. L., Murrell J. R., Trofatter J. A., Buckler A. J. Isolation of genes from complex sources of mammalian genomic DNA using exon amplification. Nature Genetics 1994; 6: 98–105
   PubMed Web of Science ®Google Scholar
• Cliby W., Ritland S., Hartmann L., Dodson M., Hailing K. C., Keeney G., Podratz K. C., Jenkins R. B. Human epithelial ovarian cancer allelotype. Cancer Research 1993; 53: 2393–2398
   Google Scholar
• Coffey A., Gregory S., Cole C. G. Alu-PCR fingerprinting of YACs. Methods in Molecular Biology 1996; 54: 97–114
   Google Scholar
• 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., Gregory S. G., Gwilliam R., Dunham A., Davies A. F., Hassock S., Todd C. M., Lehrach H., Hulsebos T. J. M., Weissenbach J., Morrow B., Kucherlapati R. S., Wadey R., Scambler P. J., Kim U. J., Simon M. I., Peyrard M., Xie Y. G., Carter N. P., Durbin R., Dumanski J. P., Bentley D. R., Dunham I. A high-density YAC contig map of human chromosome 22. Nature 1995; 377: 367–379
   Google Scholar
• Cooke I. E., Cox S. A., Shelling A. N., Le Meuth V. G., Spurr N. K., Ganesan T. S. An integrated genetic map of Chromosome 6. Mammalian Genome 1996a; 7: 157–159
   PubMed Web of Science ®Google Scholar
• Cooke I. E., Shelling A. N., Le Meuth V. G., Charnock M. L., Ganesan T. S. Allele loss on chromosome arm 6q and fine mapping of the region at 6q27 in epithelial ovarian cancer. Genes, Chromosomes & Cancer 1996b; 15: 223–233
   Google Scholar
• Cross S. H., Bird A. P. CpG islands and genes. Current Opinion in Genetics and Development 1995; 5: 309–314
   PubMed Web of Science ®Google Scholar
• Cross S. H., Charlton J. A., Nan X., Bird A. P. Purification of CpG islands using a methylated DNA binding column. Nature Genetics 1994; 6: 236–244
   PubMed Web of Science ®Google Scholar
• De Souza A. T., Hankins G. R., Washington M. K., Fine R. L., Orton T. C., Jirtle R. L. Frequent loss of heterozygosity on 6q at the mannose 6-phosphate/insulin-like growth factor II receptor locus in human hepatocellular tumors. Oncogene 1995; 10: 1725–1729
   PubMedGoogle Scholar
• Deininger P. L. Random subcloning of sonicated DNA: application to shotgun DNA sequence analysis. Analytical Biochemistry 1983; 129: 216–223
   PubMedGoogle Scholar
• Devilee P., van Vliet M., van Sloun P., Dijkshoorn Kuipers N., Hermans J., Pearson P. L., Cornelisse C. J. Allelotype of human breast carcinoma: a second major site for loss of heterozygosity is on chromosome 6q. Oncogene 1991; 6: 1705–1711
   PubMedGoogle Scholar
• Dib C., Faure S., Fizames C., Samson D., Drouot N., Vignal A., Millasseau P., Marc S., Hazan J., Seboun E., Lathrop M., Gyapay G., Morissette J., Weissenbach J. A comprehensive genetic map of the human genome based on 5,264 microsatellites. Nature 1996; 380: 152–154
   PubMed Web of Science ®Google Scholar
• Ehlen T., Dubeau L. Loss of heterozygosity on chromosomal segments 3p, 6q and lip in human ovarian carcinomas-. Oncogene 1990; 5: 219–223
   PubMed Web of Science ®Google Scholar
• Fanning T. G., Singer M. F. LINE-1: a mammalian transposable element. Biochimica et Biophysica Acta 1987; 910: 203–212
   PubMedGoogle Scholar
• Feinberg A. P., Vogelstein B. A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Analytical Biochemistry 1983; 132: 6–13
   PubMed Web of Science ®Google Scholar
• Foulkes W. D., Ragoussis J., Stamp G. W., Allan G. J., Trowsdale J. Frequent loss of heterozygosity on chromosome 6 in human ovarian carcinoma. British Journal of Cancer 1993; 67: 551–559
   Google Scholar
• Gaidano G., Hauptschein R. S., Parsa N. Z., Offit K., Rao P. H., Lenoir G., Knowles D. M., Chaganti R. S., Dalla-Favera R. Deletions involving two distinct regions of 6q in B-cell non-Hodgkin lymphoma. Blood 1992; 80: 1781–1787
   PubMed Web of Science ®Google Scholar
• Gish W., States D. J. Identification of protein coding regions by database similarity search. Nature Genetics 1993; 3: 266–272
   PubMed Web of Science ®Google Scholar
• Hauptschein R. S., Gamberi B., Rao P. H., Frigeri F., Scotto L., Venkatraj V. S., Gaidano G., Rutner T., Edwards Y. H., Chaganti R. S. K., Dalla-Favera R. Cloning and mapping of human chromosome 6q26-q27 deleted in B-cell non-Hodgkin-s lymphoma and multiple tumor types. Genomics 1998, in press
   Google Scholar
• Hochgeschwender U. Toward a transcriptional map of the human genome. Trends in Genetics 1992; 8: 41–44
   Google Scholar
• Honchel R., McDonnell S., Schaid D. J., Thibodeau S. N. Tumor necrosis factor-α allelic frequency and chromosome 6 allelic imbalance in patients with colorectal cancer. Cancer Research 1996; 56: 145–149
   PubMedGoogle Scholar
• Ioannou P. A., Amemiya C. T., Games J., Kroisel P. M., Shizuya H., Chen C., Batzer M. A., de Jong P. J. A new bacteriophage P1-derived vector for the propagation of large human DNA fragments. Nature Genetics 1994; 6: 84–89
   PubMed Web of Science ®Google Scholar
• Kenwrick S., Levinson B., Taylor S., Shapiro A., Gitschier J. Isolation and sequence of two genes associated with a CpG island 5′ of the factor VIII gene. Human Molecular Genetics 1992; 1: 179–186
   Google Scholar
• Kwiatkowski D. J., Dib C., Slaugenhaupt S. A., Povey S., Gusella J. F., Haines J. L. An index marker map of chromosome 9 provides strong evidence for positive interference. American Journal of Human Genetics 1993; 53: 1279–1288
   Google Scholar
• Larsen F., Gundersen G., Lopez R., Prydz H. CpG islands as gene markers in the human genome. Genomics 1992; 13: 1095–1107
   PubMed Web of Science ®Google Scholar
• Lehrach H., Drmanac R., Hoheisel J., Larin Z., Lennon G., Monaco A. P., Nizetic D., Zeherner G., Poustka A. Hybridization fingerprinting in genome mapping and sequencing. Genome Analysis, K. E. Davies, S. M. Tilghman. Cold Spring Harbor Laboratory Press, Plainview, NY 1990; Volume I: 39–81
   Google Scholar
• Liu P., Siciliano J., Seong D., Craig J., Zhao Y., de Jong P. J., Siciliano M. J. Dual Alu polymerase chain reaction primers and conditions for isolation of human chromosome painting probes from hybrid cells. Cancer Genetics & Cytogenetics 1993; 65: 93–99
   PubMedGoogle Scholar
• Longmire J. L., Brown N. C., Meincke L. J., Campbell M. L., Albright K. L., Fawcett J. J., Campbell E. W., Moyzis R. K., Hildebrand C. E., Evans G. A., Deaven L. L. Construction and characterization of partial digest DNA libraries made from flow-sorted human chromosome 16. Genetic Analysis, Techniques & Applications 1993; 10: 69–76
   PubMedGoogle Scholar
• Menasce L. P., Orphanos V., Santibanez-Koref M., Boyle J. M., Harrison C. J. Common region of deletion on the long arm of chromosome 6 in non-Hodgkin-s lymphoma and acute lymphoblastic leukaemia. Genes, Chromosomes & Cancer 1994; 10: 286–288
   PubMed Web of Science ®Google Scholar
• Miki Y., Nishisho I., Horii A., Miyoshi Y., Utsunomiya J., Kinzler K. W., Vogelstein B., Nakamura Y. Disruption of the APC gene by a retrotransposal insertion of LI sequence in a colon cancer. Cancer Research 1992; 52: 643–645
   PubMed Web of Science ®Google Scholar
• Miltikin D., Meese E., Vogelstein B., Witkowski C., Trent J. Loss of heterozygosity for loci on the long arm of chromosome 6 in human malignant melanoma. Cancer Research 1991; 51: 5449–5453
   Google Scholar
• Mitelman F. Catalog of Chromosomal Aberrations in Cancer4th ed. Wiley-Liss, New York, NY 1991; Volume 1: 393–474
   Google Scholar
• Morita R., Saito S., Ishikawa J., Ogawa O., Yoshida O., Yamakawa K., Nakamura Y. Common regions of deletion on chromosomes 5q, 6q, and 10q in renal cell carcinoma. Cancer Research 1991; 51: 5817–5820
   PubMedGoogle Scholar
• Morse B., Rotherg P. G., South V. J., Spandorfer J. M., Astrin S. M. Insertional mutagenesis of the myc locus by a LINE-1 sequence in a human breast carcinoma. Nature 1988; 333: 87–90
   PubMed Web of Science ®Google Scholar
• Moyzis R. K., Torney D. C., Meyne J., Buckingham J. M., Wu J. R., Burks C., Sirotkin K. M., Goad W. B. The distribution of interspersed repetitive DNA sequences in the human genome. Genomics 1989; 4: 273–289
   PubMedGoogle Scholar
• Munroe D. J., Haas M., Brie E., Whitton T., Aburatani H., Hunter K., Ward D., Housman D. E. IRE-bubble PCR: a rapid method for efficient and representative amplification of human genomic DNA sequences from complex sources. Genomics 1994; 19: 506–514
   Web of Science ®Google Scholar
• Negrini M., Sabbioni S., Possati L., Rattan S., Corallini A., Barbanti-Brodano G., Croce G. M. Suppression of tumorigenicity of breast cancer cells by micro-cell-mediated chromosome transfer: studies on chromosomes 6 and 11. Cancer Research 1994; 54: 1331–1336
   PubMedGoogle Scholar
• Nizetic D., Monard S., Young B., Cotter F., Zehetner G., Lehrach H. Construction of cosmid libraries from flow-sorted human chromosomes 1, 6, 7, 11, 13, and 18 for reference library resources. Mammalian Genome 1994; 5: 801–802
   Google Scholar
• Nystrom-Lahti M., Kristo P., Nicolaides N. C., Chang S. Y., Aaltonen L. A., Moisio A. L., Jarvinen H. J., Mecklin J. P., Kinzler K. W., Vogelstein B., de la Chapelle A., Peltomaki P. Founding mutations and Alu-mediated recombination in hereditary colon cancer. Nature Medicine 1995; 1: 1203–1206
   PubMedGoogle Scholar
• Orphanos V., McGown G., Hey Y., Boyle J. M., Santibanez-Koref M. Proximal 6q, a region showing allele loss in primary breast cancer. British Journal of Cancer 1995a; 71: 290–293
   PubMed Web of Science ®Google Scholar
• Orphanos V., McGown G., Hey Y., Thorncroft M., Santibanez-Koref M., Russell S. E., Hickey I., Atkinson R. J., Boyle J. M. Allelic imbalance of chromosome 6q in ovarian tumours. British Journal of Cancer 1995b; 71: 666–669
   Google Scholar
• Pearson W. R., Lipman D. J. Improved tools for biological sequence comparison. Proceedings of the National Academy of Sciences of the United States of America 1988; 85: 2444–2448
   PubMed Web of Science ®Google Scholar
• Puget N., Torchard D., Serova-Sinilnikova O. M., Lynch H. T., Feunteun J., Lenoir G. M., Mazoyer S. A 1-kb Alu-mediated germ-line deletion removing BRCA1 exon 17. Cancer Research 1997; 57: 828–831
   PubMed Web of Science ®Google Scholar
• Queimado L., Seruca R., Costa-Pereira A., Castedo S. Identification of two distinct regions of deletion at 6q in gastric carcinoma. Genes, Chromosomes & Cancer 1995; 14: 28–34
   Google Scholar
• Reese M. G., Harris N. L., Eeckman F. H. (1996) Large scale sequencing: specific neural networks for promoter and splice site recognition. Proceedings of the Pacific Symposium on Biocomputing. 1996, L. Hunter, T. Klein. Kona, HI
   Google Scholar
• Rinehart F. P., Ritch T. G., Deininger P. L., Schmid G. W. Renaturation rate studies of a single family of interspersed repeated sequences in human deoxyribonucleic acid. Biochemistry 1981; 20: 3003–3010
   PubMedGoogle Scholar
• Rodabaugh K. J., Blanchard G., Welch W. R., Bell D. A., Berkowitz R. S., Mok S. G. Detailed deletion mapping of chromosome 6q in borderline epithelial ovarian tumors. Cancer Research 1995; 55: 2169–2172
   Google Scholar
• Russo J. J., Bohenzky R. A., Chien M. G., Chen J., Yan M., Maddalena D., Parry J. P., Peruzzi D., Edelman I. S., Chang Y., Moore P. S. Nucleotide sequence of the Kaposi sarcoma-associated herpesvirus (HHV8). Proceedings of the National Academy of Sciences of the United States of America 1996; 93: 14862–14867
   PubMed Web of Science ®Google Scholar
• Saito S., Nakamura Y. A genetic linkage map with 16 RFLP loci on the distal long arm of human chromosome 6. Genomics 1993; 15: 103–106
   Google Scholar
• Saito S., Saito H., Koi S., Sagae S., Kudo R., Saito J., Noda K., Nakamura Y. Fine-scale deletion mapping of the distal long arm of chromosome 6 in 70 human ovarian cancers. Cancer Research 1992; 52: 5815–5817
   Google Scholar
• Sambrook J., Fritsch E. F., Maniatis T. Molecular Cloning: A Laboratory Manual2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY 1989
   Google Scholar
• Sargent C. A., Dunham I., Campbell R. D. Identification of multiple HTF-island associated genes in the human major histocompatibility complex class III region. EMBO Journal 1989; 8: 2305–2312
   PubMed Web of Science ®Google Scholar
• Shepherd N. S., Pfrogner B. D., Coulby J. N., Ackerman S. L., Vaidyanathan G., Sauer R. H., Balkenhol T. C., Sternberg N. Preparation and screening of an arrayed human genomic library generated with the PI cloning system. Proceedings of the National Academy of Sciences of the United States of America 1994; 91: 2629–2633
   Google Scholar
• Solovyev V. V., Salamov A. A., Lawrence G. B. Predicting internal exons by oligonucleotide composition and discriminant analysis of spliceable open reading frames. Nucleic Acids Research 1994; 22: 5156–5163
   PubMedGoogle Scholar
• Stenman G., Sandros J., Mark J., Edstrom S. Partial 6q deletion in a human salivary gland adenocarcinoma. Cancer Genetics & Cytogenetics 1989; 39: 153–156
   PubMedGoogle Scholar
• Strachan T., Read A. P. Human Molecular Genetics. BIOS Scientific Publishers Limited, OxfordUK 1996
   Google Scholar
• Tahara H., Smith A. P., Gas R. D., Cryns V. L., Arnold A. Genomic localization of novel candidate tumor suppressor gene loci in human parathyroid adenomas. Cancer Research 1996; 56: 599–605
   Google Scholar
• Theile M., Seitz S., Arnold W., Jandrig B., Frege R., Schlag P. M., Haensch W., Guski H., Winzer K. J., Barrett J. C., Scherneck S. A defined chromosome 6q fragment (at D6S310) harbors a putative tumor suppressor gene for breast cancer. Oncogene 1996; 13: 677–685
   PubMed Web of Science ®Google Scholar
• Tibiletti M. G., Bernasconi B., Taborelli M., Furlan D., Fabbri A., Franchi M., Taramelli R., Trubia M., Capella G. Involvement of chromosome 6 in endometrial cancer. British Journal of Cancer 1997; 75: 1831–1835
   Google Scholar
• Vogelstein B., Fearon E. R., Kern S. E., Hamilton S. R., Preisinger A. G., Nakamura Y., White R. Allelo-type of colorectal carcinoma. Science 1989; 66: 207–211
   Google Scholar
• Walker G. J., Palmer J. M., Walters M. K., Nancarrow D. J., Parsons P. G., Hayward N. K. Simple tandem repeat allelic deletions confirm the preferential loss of distal chromosome 6q in melanoma. International Journal of Cancer 1994; 58: 203–206
   Google Scholar
• Wilson R. K. High-throughput purification of M13 templates for DNA sequencing. Biotechniques 1993; 15: 414–416
   Google Scholar
• Xu Y., Mural R., Shah M., Uberbacher E. Recognizing exons in genomic sequence using GRAIL II. Genetic Engineering 1994; 16: 241–253
   Google Scholar
• Zhang J., Madden T. L. PowerBLAST: a new network BLAST application for interactive or automated sequence analysis and annotation. Genome Research 1997; 7: 649–656
   PubMed Web of Science ®Google Scholar
• Zheng J. P., Robinson W. R., Ehlen T., Yu M. C., Dubeau L. Distinction of low grade from high grade human ovarian carcinomas on the basis of losses of heterozygosity on chromosomes 3, 6, and 11 and HER-2/neu gene amplification. Cancer Research 1991; 51: 4045–4051
   Google Scholar