Abstract
Positional cloning often requires isolation of candidate genes from a large, genetically defined region. Hybrid selection (direct cDNA selection, solution hybrid capture) is a rapid, simple procedure that has been used to identify expressed sequence tags (ESTs) from cloned genomic DNA. We used hybrid selection to screen a 600-kb region that includes the BRCA1 gene. From a set of 931 sequenced clones, we obtained 118 nonoverlapping candidate ESTs from ovary and lymphocyte cDNA. We analyzed the results of our hybrid selection experiments with particular attention to the overall completeness, efficiency, and background noise of the experiment. We introduce simple parameters that serve as measures of important aspects of the hybrid selection process in the context of positional cloning.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Abe, K. (1992). Rapid isolation of desired sequences from lone linker PCR amplified cDNA mixtures: amplification to identification and recovery of expressed sequences in cloned genomic DNA. Mamm. Genome 2, 252–259.
Abe, K., Wei, J.F., Hsu, Y.C., Uehara, H., Artzt, K., Bennett, D. (1988). Searching for coding sequences in the mammalian genome: the H-2K region of the mouse MHC is replete with genes expressed in embryos. EMBO J 7, 3441–3449.
Albertson, H.M., Smith, S.A., Mazoyer, S., Fujimoto, E., et al. (1994). A physical map and candidate genes in the BRCA1 region on chromosome 17q12-21. Nature Genet. 7, 472–479.
Altschul, S.F., Gish, W., Miller, W., Myers, E.W., Lipman, D.J. (1990). Basic local alignment search tool. J. Mol. Biol. 215, 403–410.
Buckler, A.J., Chang, D.D., Graw, S.L., Brook, J.D., Haber, D.A., Sharp, P.A., Housman, D.E. (1991) Exon amplification: a strategy to isolate mammalian genes based on RNA splicing. Proc. Natl. Acad. Sci. USA. 88, 4005–4009.
Cheng, J.F., Boyartchuk, V., Zhu, Y. (1994). Isolation and mapping of human chromosome 21 cDNA: progress in constructing a chromosome 21 expression map. Genomics 23, 75–84.
Duyk, G.M., Kim, S.W., Myers, R.M., Cox, D.R. (1990). Exon trapping: a genetic screen to identify candidate transcribed sequences in cloned mammalian DNA. Proc. Natl. Acad. Sci. USA. 87, 8995–8999.
Elvin, P., Slynn, G., Black, D., Graham, A., Butler, R., Riley, J., Anand, R., Markham, A.F. (1990). Isolation of cDNA clones using yeast artificial chromosome probes. Nucleic Acids Res. 18, 3913–3917.
Fan, W.F., Wei, X., Shukla, H., Parimoo, S., Xu, H., Sankhavaram, P., Li, Z., Weissman, S.M. (1993). Application of cDNA selection techniques to regions of the human MHC. Genomics 17, 575–581.
Frothingham, R., Allen, R.L., Wilson, K.H. (1991). Rapid 16s ribosomal DNA sequencing from a single colony without DNA extraction or purification. Biotechniques 11, 40–44.
Futreal, P.A., Cochran, C., Rosenthal, J., Miki, Y., Swenson, J., Hobbs, M., Bennett, M., Haugen-Strano, A., Marks, J., Barrett, J.C., Tavtigian, S.V., Shattuck-Eidens, D., Kamb, A., Skolnick, M., Wiseman, R.W. (1994). Isolation of a diverged homeobox gene, MOX1, from the BRCA1 region of 17q21 by solution hybrid capture. Hum. Mol. Genet. 3, 1359–1364.
Green, E.D., Riethman, H.C., Dutchik, J.E., Olson, M.V. (1991). Detection and characterization of chimeric yeast artificial-chromosome clones. Genomics 11, 658–669.
Guigo, R., Knudsen, S., Drake, N., Smith, T. (1992). Prediction of gene structure. J. Mol. Biol. 266, 141–157.
harshman, K., Bell, R., Rosenthal, J., Katcher, H., Gholami, Z., Frye, C., Ding, W., Dayananth, P., Eddington, K., Miki, Y., Swenson, J., Phelps, R., Hattier, T., Stone, S., Shaffer, D., Futreal, P.A., Bayer, S., Hussey, C., Tran, T., Wiseman, R., Rosteck, P., Skolnick, M.H., Shattuck-Eidens, D., Kamb, A. (1995). Comparison of the positional cloning methods used to isolate the BRCA1 gene. Hum. Mol. Genet. 4, 1259–1266.
Korn, B., Sedlacek, Z., Manca, A., Kioschis, P., Konecki, D., Lehrach, H., Poustka, A. (1992). A strategy for the selection of transcribed sequences in the Xq28 region. Hum. Mol. Genet. 1, 235–242.
Larsen, F., Gundersen, G., Lopez, R., Prydz, H. (1992). CpG islands as gene markers in the human genome. Genomics 13, 1095–1107.
Lovett, M., Kere, J., Hinton, L.M. (1991). Direct selection: a method for the isolation of cDNAs encoded by large genomic regions. Proc. Natl. Acad. Sci. USA. 88, 9628–9632.
Mercer, J.F., Livingston, J., Hall, B., Paynter, J.A., Begy, C., Chandrasekharappa, S., Lockhart, P., Grimes, A., Bhave, M., Siemieniak, D., et al. (1993). Isolation of a partial candidate gene for Menkes disease by positional cloning. Nature Genet. 3, 20–25.
Miki, Y., Swensen, J., Shattuck-Eidens, D., et al. (1994) A strong candidate for the breast and ovarian cancer susceptibility gene BRCA1. Science 266, 66–71.
Morgan, J.G., Dolganov, G.M., Robbins, S.E., Hinton, L.M., Lovett, M. (1992). The selective isolation of novel cDNAs encoded by the regions surrounding the human interleukin 4 and 5 genes. Nucleic Acids Res. 20, 5173–5179.
Neuhausen, S., Swenson, J., Miki, Y., Liu, Q., Tavtigian, S., Shattuck-Eidens, E., Kamb, A., Hobbs, M.R., Gingrich, J., Shizuya, H., Kim, U.-J., Cochran, C., Futreal, P.A., Wiseman, R.W., Lynch, H.T., Tonin, P., Narod, S., Cannon-Albright, L., Skolnick, M.H., Goldgar, D.E. (1994). A P1-based physical map of the region fom D17S776 to D17S78 containing the breast cancer susceptibility gene BRCA1. Hum. Mol. Genet. 3, 1919–1926.
Osborne-Lawrence, S., Welsch, P.L., Spillman, M., Chandrasekharappa, S.C., Gallardo, T.D., Lovett, M., Bowcock, A.M. (1995). Direct selection of expressed sequences within a 1-Mb region flanking BRCA1 on human chromosome 17q21. Genomics 25, 248–255.
Parimoo, S., Patanjali, S.R., Shukla, H., Chaplin, D.D., Weissman, S.M. (1991). cDNA selection: efficient PCR approach for the selection of cDNAs encoded in large chromosomal DNA fragments. Proc. Natl. Acad. Sci. USA 88, 9623–9627.
Parimoo, S., Patanjali, S.R., Weissman, S.M. (1993). Normalization and selection with short-fragment cDNA's. In Methods in Molecular Genetics, K.W. Adolph, ed., Vol. I. (San Diego: Academic Press), pp. 23–50.
Rommens, J.M., Iannuzzi, M.C., Kerem, B., Drumm, M.L., Melmer, G., Dean, M., Rozmahel, R., Cole, J.L., Kennedy, D., Hidaka, N., Zsiga, M., Buchwald, M., Riordan, J.R., Tsui, L.S., Collins, F.S. (1989). Identification of the cystic fibrosis gene: chromosome walking and jumping. Science 245, 1059–1065.
Shizuya, H., Birren, B., Kim, U.J., Mancino, V., Slepak, T., Tachiri, Y., Simon, M. (1992). Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA in Escherichia coli using an F-factor-based vector. Proc. Natl. Acad. Aci. USA. 89, 8794–8797.
Snyder, E.E., Stormo, G.D. (1993). Identification of coding regions in genomic DNA sequences: an application of dynamic programming and neural networks. Nucleic Acids Res. 21, 607–613.
Sternberg, N. (1990). Bacteriophage P1 cloning system for the isolation, amplification, and recovery of DNA fragments as large as 100 kilobase pairs. Proc. Natl. Acad. Aci. USA 87, 103–107.
Tagle, D.A., Swaroop, M., Lovett, M., Collins, F.S., (1993). Magnetic bead capture of expressed sequences encoded within large genomic segments. Nature 361, 751–753.
Thomas, A., Skolnick, M.H. (1994). A probalistic model for detecting coding regions in DNA sequences. J. Math. Appl. Med. Biol. 11, 149–160.
Uberbacher, E.C., Mural, R.J. (1991). Locating protein coding regions in human DNA sequences by a multiple sensor-neural network approach. Proc. Natl. Acad. Sci. USA 88, 11261–11265.
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Hattier, T., Bell, R., Shaffer, D. et al. Monitoring the efficacy of hybrid selection during positional cloning: the search for BRCA1. Mammalian Genome 6, 873–879 (1995). https://doi.org/10.1007/BF00292438
Received:
Accepted:
Issue Date:
DOI: https://doi.org/10.1007/BF00292438