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Kruzelock RP, Cuevas BD, Wiener JR, Xu FJ, Yu Y, Cabeza-Arvelaiz Y, Pershouse M, Lovell MM, Killary AM, Mills GB, Bast RC. Functional evidence for an ovarian cancer tumor suppressor gene on chromosome 22 by microcell-mediated chromosome transfer. Oncogene 2000; 19:6277-85. [PMID: 11175342 DOI: 10.1038/sj.onc.1204013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The identity of many tumor suppressor genes important in epithelial ovarian cancer tumorigenesis remains unknown. In an effort to localize a novel tumor suppressor on chromosome 22, a psv2neo tagged human chromosome 22 was transferred into the malignant epithelial ovarian cancer cell line, SKOv-3, by microcell-mediated chromosome transfer. Complete suppression of the transformed phenotype was observed in 16 of 18 individual microcell hybrid clones as evidenced by the complete abrogation of cell growth under anchorage-independent conditions. In vitro doubling times were also dramatically reduced, as was the ability to form subcutaneous tumors in CD1 nu/nu mice. Only one polymorphic marker, D22S429, segregated with decreased transformation and tumorigenic potential, suggesting that an unrecognized tumor suppressor may localize to chromosome 22q11-q12. These data provide functional support for the presence of a novel tumor suppressor locus (or loci) on chromosome 22 that is important in ovarian cancer tumorigenesis.
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Affiliation(s)
- R P Kruzelock
- Howard Hughes Medical Institute, Baylor College of Medicine, Houston, Texas, TX 77030, USA
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2
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Tai TH, Dahlbeck D, Clark ET, Gajiwala P, Pasion R, Whalen MC, Stall RE, Staskawicz BJ. Expression of the Bs2 pepper gene confers resistance to bacterial spot disease in tomato. Proc Natl Acad Sci U S A 1999; 96:14153-8. [PMID: 10570214 PMCID: PMC24206 DOI: 10.1073/pnas.96.24.14153] [Citation(s) in RCA: 282] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/1999] [Indexed: 11/18/2022] Open
Abstract
The Bs2 resistance gene of pepper specifically recognizes and confers resistance to strains of Xanthomonas campestris pv. vesicatoria that contain the corresponding bacterial avirulence gene, avrBs2. The involvement of avrBs2 in pathogen fitness and its prevalence in many X. campestris pathovars suggests that the Bs2 gene may be durable in the field and provide resistance when introduced into other plant species. Employing a positional cloning strategy, the Bs2 locus was isolated and the gene was identified by coexpression with avrBs2 in an Agrobacterium-mediated transient assay. A single candidate gene, predicted to encode motifs characteristic of the nucleotide binding site-leucine-rich repeat class of resistance genes, was identified. This gene specifically controlled the hypersensitive response when transiently expressed in susceptible pepper and tomato lines and in a nonhost species, Nicotiana benthamiana, and was designated as Bs2. Functional expression of Bs2 in stable transgenic tomatoes supports its use as a source of resistance in other Solanaceous plant species.
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Affiliation(s)
- T H Tai
- Department of Plant Biology, University of California, Berkeley, CA 94720, USA
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3
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Van Leuven F, Torrekens S, Moechars D, Hilliker C, Buellens M, Bollen M, Delabie J. Molecular cloning of a gene on chromosome 19q12 coding for a novel intracellular protein: analysis of expression in human and mouse tissues and in human tumor cells, particularly Reed-Sternberg cells in Hodgkin disease. Genomics 1998; 54:511-20. [PMID: 9878255 DOI: 10.1006/geno.1998.5609] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A novel protein, named NNX3, was molecularly characterized by cloning its cDNA, and its gene was mapped to chromosome 19q12. The equivalent mouse cDNA and gene were also cloned to allow us to analyze expression in murine in addition to human cells and tissues. Human and mouse NNX3 genes are composed of nine exons coding for proteins that are unrelated to any known protein. Signal peptides and hydrophobic domains are absent, corroborating their localization in the cytoplasm in transfected Cos cells. In Western blotting and immunoprecipitation, human NNX3 appeared as a doublet of Mr 64K-66K, while mouse NNX3 was a 70-kDa protein, both apparently much larger than the predicted 50 kDa, due in part to a stretch of 16-18 acidic residues hinging two nearly equally sized domains. In addition, phosphorylation of serine residues was demonstrated. Putative nuclear targeting signals were predicted, but NNX3 protein and two truncated versions remained localized in the cytoplasm of transfected Cos cells. NNX3 was expressed in embryonic and adult mouse tissues, particularly in brain, muscle, and lung. The expression of human NNX3 was most notable in human skeletal muscle and in ganglion cells and was also evident in human tumors and derived cell lines. This was confirmed by entries appearing in the GenBank EST database during the later phase of this study, representing partial NNX3 cDNA isolated from diverse neoplastic and developing tissues. Surprisingly, NNX3 was immunochemically detected in Reed-Sternberg cells of Hodgkin disease, in parallel with restin, a cytoplasmic protein we previously characterized (J. Delabie et al., 1993, Leuk. Lymphoma 12, 21-26). The cloning and comprehensive molecular analysis of NNX3 as presented will form the basis for elucidating its function and, conversely, will constitute a marker for Reed-Sternberg cells in Hodgkin disease.
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Affiliation(s)
- F Van Leuven
- Experimental Genetics Group, Center for Human Genetics, Flemish Institute for Biotechnology, Department of Biochemistry, K.U. Leuven, Campus Gasthuisberg, Louvain, B-3000, Belgium.
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4
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Abstract
While celebrating its fifth official birthday last year it seems that the Human Genome Project (HGP) has and will continue to yield important biochemical information to mankind. It is exhilarating to think about the transition from studying genome structure to understanding genome function. The collective actions of information dessimination, technology development for efficient and faster sequencing, high-volume sequencing and developing model organisms has led to its success sofar. Various genome-wide STS-based human maps were completed in 1995, including a genetic map, a YAC map, a RH map with, and an integrated YAC-RH genetic map. These maps provide comprehensive frameworks for positioning additional loci, with the current genetic and RH maps spanning essentially 100% of the human genome and the YAC maps covering 95%. Few genes, however, have yet been localized on these framework maps. To date the Human Genome Project has experienced gratifying success. The technology and data produced by the genome project will provide a strong stimulus to broad areas of biological research and biotechnology. However, enormous challenges remain.
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Affiliation(s)
- U Kelavkar
- Department of Biological Sciences, Clark Atlanta University, GA 30314, USA
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5
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Elkahloun AG, Bittner M, Hoskins K, Gemmill R, Meltzer PS. Molecular cytogenetic characterization and physical mapping of 12q13-15 amplification in human cancers. Genes Chromosomes Cancer 1996; 17:205-14. [PMID: 8946202 DOI: 10.1002/(sici)1098-2264(199612)17:4<205::aid-gcc2>3.0.co;2-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Amplification of sequences derived from 12q13-15 is frequent in human sarcomas and brain tumors. Detailed mapping studies of the amplified region are necessary for definition of the impact of these amplification events on the tumor cell phenotype. By using the genes in this region and genomic fragments isolated by chromosome microdissection, we have established a series of ordered probes from 12q13-15 for fluorescence in situ hybridization (FISH) and Southern blot analysis. These probes have been used for physical mapping of two portions of the interval from GLI to D12S8. The centromeric region extends 1.8 Mb from GLI to microclone M79 and contains at least five genes, including the cyclin-dependent kinase gene CDK4. The more telomeric region includes the p53 regulator MDM2 and covers 1.1 Mb. We used the same group of probes to determine the pattern of amplification in three cell lines and three tumor specimens carrying amplified sequences from 12q13-15. In addition, we used a yeast artificial chromosome (YAC) contig of several megabases covering the entire region from SAS to D12S8 for FISH to determine the pattern of amplification in the neuroblastoma cell line NGP-127. The results suggest that the MDM2 and CDK4 regions may be either coamplified or amplified independently, and they illustrate how the map positions of genes and their functions may interact to determine the pattern of DNA amplification in human malignancies.
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Affiliation(s)
- A G Elkahloun
- Laboratory of Cancer Genetics, National Center for Human Genome Research, National Institutes of Health, Bethesda, Maryland 20892-4470, USA
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6
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Venditti CP, Lawlor DA, Sharma P, Chorney MJ. Structure and content of the major histocompatibility complex (MHC) class I regions of the great anthropoid apes. Hum Immunol 1996; 49:71-84. [PMID: 8872161 DOI: 10.1016/0198-8859(96)00017-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The origins of the functional class I genes predated human speciation, a phenomenon known as trans-speciation. The retention of class Ia orthologues within the great apes, however, has not been paralleled by studies designed to examine the pseudogene content, organization, and structure of their class I regions. Therefore, we have begun the systematic characterization of the Old World primate MHCs. The numbers and sizes of fragments harboring class I sequences were similar among the chimpanzee, gorilla, and human genomes tested. Both of the gorillas included in our study possessed genomic fragments carrying orthologues of the recently evolved HLA-H pseudogene identical to those found in the human. The overall megabase restriction fragment patterns of humans and chimpanzees appeared slightly more similar to each other, although the HLA-A subregional megabase variants may have been generated following the emergence of Homo sapiens. Based on the results of this initial study, it is difficult to generate a firm species tree and to determine human's closest evolutionary neighbor. Nevertheless, an analysis of MHC subregional similarities and differences in the hominoid apes may ultimately aid in localizing and identifying MHC haplotype-associated disease genes such as idiopathic hemochromatosis.
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Affiliation(s)
- C P Venditti
- Department of Microbiology and Immunology, Pennsylvania State University College of Medicine, Hershey 17033, USA
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7
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Mendez MJ, Abderrahim H, Noguchi M, David NE, Hardy MC, Green LL, Tsuda H, Yoast S, Maynard-Currie CE, Garza D. Analysis of the structural integrity of YACs comprising human immunoglobulin genes in yeast and in embryonic stem cells. Genomics 1995; 26:294-307. [PMID: 7601456 DOI: 10.1016/0888-7543(95)80214-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
With the goal of creating a strain of mice capable of producing human antibodies, we are cloning and reconstructing the human immunoglobulin germline repertoire in yeast artificial chromosomes (YACs). We describe the identification of YACs containing variable and constant region sequences from the human heavy chain (IgH) and kappa light chain (IgK) loci and the characterization of their integrity in yeast and in mouse embryonic stem (ES) cells. The IgH locus-derived YAC contains five variable (VH) genes, the major diversity (D) gene cluster, the joining (JH) genes, the intronic enhancer (EH), and the constant region genes, mu (C mu) and delta (C delta). Two IgK locus-derived YACs each contain three variable (V kappa) genes, the joining (J kappa) region, the intronic enhancer (E kappa), the constant gene (C kappa), and the kappa deleting element (kde). The IgH YAC was unstable in yeast, generating a variety of deletion derivatives, whereas both IgK YACs were stable. YACs encoding heavy chain and kappa light chain, retrofitted with the mammalian selectable marker, hypoxanthine phosphoribosyltransferase (HPRT), were each introduced into HPRT-deficient mouse ES cells. Analysis of YAC integrity in ES cell lines revealed that the majority of DNA inserts were integrated in substantially intact form.
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Affiliation(s)
- M J Mendez
- Cell Genesys, Inc., Foster City, California 94404, USA
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8
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Todd S, Roche J, Hahner L, Bolin R, Drabkin HA, Gemmill RM. YAC contigs covering an 8-megabase region of 3p deleted in the small-cell lung cancer cell line U2020. Genomics 1995; 25:19-28. [PMID: 7774917 DOI: 10.1016/0888-7543(95)80105-u] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Somatic deletions of chromosome 3p occur at high frequencies in cancers of kidney, breast, cervix, head and neck, nasopharynx, and lung. The frequency of 3p deletion in lung cancer approaches 100% among small cell lesions and 70 to 80% in non-small cell lesions. This evidence strongly implies that one or more tumor suppressor genes of potentially widespread significance reside within the deleted region(s). Precise definition of the deleted target region(s) has been difficult due to the extensive area(s) lost and use of markers with low informativeness. However, improved definition remains essential to permit isolation of putative tumor suppressor genes from 3p. The identification of several small, homozygous 3p deletions in lung cancer cell lines has provided a critical resource that will assist this search. The U2020 cell line contains a small homozygous deletion that maps to a very proximal region of 3p and includes the marker D3S3. We previously identified a subset of DNA markers located within the deleted region and determined their relative order by pulsed-field gel mapping studies. In the present report, we describe the development of YAC contigs that span the majority of the deleted region and link up to flanking markers on both sides. The centromere proximal portion of the contig crosses the breakpoint from an X;3 translocation located within 3p12 providing both location and orientation to the map. PCR-based (CA)n microsatellite polymorphisms have been localized within and flanking the deletion region. These markers should greatly facilitate loss-of-heterozygosity studies of this region in human cancer. The contig provides a direct means for isolation of putative tumor suppressor genes from this segment of 3p.
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Affiliation(s)
- S Todd
- Eleanor Roosevelt Institute for Cancer Research, Denver, Colorado 80206, USA
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9
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Siden TS, Kumlien J, Drumheller T, Smith SE, Röhme D, Lehrach H, Smith DI. Identification of human chromosome region 3p14.2-21.3-specific YAC clones using Alu-PCR products from a radiation hybrid. SOMATIC CELL AND MOLECULAR GENETICS 1994; 20:137-142. [PMID: 8009367 DOI: 10.1007/bf02290683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Deletion of DNA sequences from at least three different regions on the short arm of human chromosome 3 (3p13-14, 3p21 and 3p25) are frequently observed during the development of many solid tumors, including lung cancers and renal cell carcinomas. In order to physically characterize the 3p21 region, we previously identified a radiation fusion hybrid that contained about 20 megabases of DNA from chromosome region 3p14.2-p21.3. In this study total Alu-PCR products from this hybrid were used as a probe to isolate 86 yeast artificial chromosomes (YAC) clones from a 620-kb average insert YAC library (ICRF). Sixty-nine Alu-PCR markers, generated from the YACs, and seven PCR primers were used to screen for overlaps between individual clones. Seven contigs were identified encompassing 32 YAC clones. Based on previous information about localization of the PCR primers, the three largest contigs could be assigned to smaller subregions between 3p14.2 and 3p21.3. By this work a large proportion of the 3p14.2-21.3 region is covered with large-insert YAC clones.
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Affiliation(s)
- T S Siden
- Department of Internal Medicine, Wayne State University School of Medicine, Detroit, Michigan 48201
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10
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Kao FT. Microdissection and microcloning of human chromosome regions in genome and genetic disease analysis. Bioessays 1993; 15:141-6. [PMID: 8471059 DOI: 10.1002/bies.950150212] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- F T Kao
- Eleanor Roosevelt Institute for Cancer Research, Denver, CO 80206
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11
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Gemmill RM, Mendez MJ, Dougherty CM, Paulien S, Liao M, Mitchell D, Jankowski SA, Trent JM, Berger C, Sandberg AA. Isolation of a yeast artificial chromosome clone that spans the (12;16) translocation breakpoint characteristic of myxoid liposarcoma. CANCER GENETICS AND CYTOGENETICS 1992; 62:166-70. [PMID: 1394104 DOI: 10.1016/0165-4608(92)90257-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Cytogenetic analysis of liposarcomas has demonstrated that translocation (12;16) (q13.3;p11.2) is characteristic of the myxoid subtype of this adipose tissue tumor. Our previous results suggested that the GLI gene is close to the translocation breakpoint on chromosome 12. We now describe a yeast artificial chromosome (YAC) that contains GLI and spans the chromosome 12 region involved in the t(12;16) breakpoint. This clone will permit rapid definition of the genetic region surrounding the breakpoint and allow isolation of the gene presumably affected by the translocation.
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Affiliation(s)
- R M Gemmill
- Eleanor Roosevelt Institute, Denver, Colorado 80206
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12
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Strauss WM, Jaenisch E, Jaenisch R. A strategy for rapid production and screening of yeast artificial chromosome libraries. Mamm Genome 1992; 2:150-7. [PMID: 1347474 DOI: 10.1007/bf00302873] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
We describe methods for rapid production and screening of yeast artificial chromosome (YAC) libraries. Utilizing complete restriction digests of mouse genomic DNA for ligations in agarose, a 32,000-clone library was produced and screened in seven weeks. Screening was accomplished by subdividing primary transformation plates into pools of approximately 100 clones which were transferred into a master glycerol stock. These master stocks were used to inoculate liquid cultures to produce culture "pools," and ten pools of 100 clones were then combined to yield superpools of 1,000 clones. Both pool and superpool DNA was screened by polymerase chain reaction (PCR) and positive pools representing 100 clones were then plated on selective medium and screened by in situ hybridization. Screening by the two tiered PCR assay and by in situ hybridization was completed in 4-5 days. Utilizing this methodology we have isolated a 150 kb clone spanning the alpha 1(I) collagen (Col1a1) gene as well as 40 kb clones from the Hox-2 locus. To characterize the representation of the YAC library, the size distribution of genomic Sal I fragments was compared to that of clones picked at random from the library. The results demonstrate significant biasing of the cloned fragment distribution, resulting in a loss of representation for larger fragments.
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Affiliation(s)
- W M Strauss
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge 02142
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13
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Affiliation(s)
- L Stubbs
- Biology Division, Oak Ridge National Laboratory, Tennessee 37831
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14
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Evans GA, McElligott DL. Physical mapping of human chromosomes. GENETIC ENGINEERING 1992; 14:269-78. [PMID: 1368280 DOI: 10.1007/978-1-4615-3424-2_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
Affiliation(s)
- G A Evans
- Molecular Genetics Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037
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15
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Green ED, Green P. Sequence-tagged site (STS) content mapping of human chromosomes: theoretical considerations and early experiences. PCR METHODS AND APPLICATIONS 1991; 1:77-90. [PMID: 1842934 DOI: 10.1101/gr.1.2.77] [Citation(s) in RCA: 75] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The magnitude of the effort required to complete the human genome project will require constant refinements of the tools available for the large-scale study of DNA. Such improvements must include both the development of more powerful technologies and the reformulation of the theoretical strategies that account for the changing experimental capabilities. The two technological advances described here, PCR and YAC cloning, have rapidly become incorporated into the standard armamentarium of genome analysis and represent key examples of how technological developments continue to drive experimental strategies in molecular biology. Because of its high sensitivity, specificity, and potential for automation, PCR is transforming many aspects of DNA mapping. Similarly, by providing the means to isolate and study larger pieces of DNA, YAC cloning has made practical the achievement of megabase-level continuity in physical maps. Taken together, these two technologies can be envisioned as providing a powerful strategy for constructing physical maps of whole chromosomes. Undoubtedly, future technological developments will promote even more effective mapping strategies. Nonetheless, the theoretical projections and practical experience described here suggest that constructing YAC-based STS-content maps of whole human chromosomes is now possible. Random STSs can be efficiently generated and used to screen collections of YAC clones, and contiguous YAC coverage of regions exceeding 2 Mb can be readily obtained. While the predicted laboratory effort required for mapping whole human chromosomes remains daunting, it is clearly feasible.
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Affiliation(s)
- E D Green
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110
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