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Tuggle CK, Schmitz CB. Cloning and characterization of pig muscle cDNAs by an expressed sequence tag approach. Anim Biotechnol 2009. [DOI: 10.1080/10495399409525799] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- C. K. Tuggle
- a Department of Animal Science , Iowa State University , Ames, Iowa, 50011
| | - C. B. Schmitz
- a Department of Animal Science , Iowa State University , Ames, Iowa, 50011
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2
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Wang YH, McWilliam SM, Barendse W, Kata SR, Womack JE, Moore SS, Lehnert SA. Mapping of 12 bovine ribosomal protein genes using a bovine radiation hybrid panel. Anim Genet 2001; 32:269-73. [PMID: 11683713 DOI: 10.1046/j.1365-2052.2001.00791.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Twelve bovine ribosomal protein genes, for which sequence data had been acquired from complementary deoxyribonucleic acid (cDNA) clones isolated from a cattle skin cDNA library, were mapped. As ribosomal protein genes are a group of highly conserved house keeping genes, specific primers were designed to span the intron-exon splice sites and to amplify intronic sequences, in order to obtain bovine-specific polymerase chain reaction (PCR) products. Two of 12 ribosomal protein genes were genotyped in this way and the remaining 10 were mapped using additional primers designed from within the intron. Eleven previously unmapped ribosomal protein genes were localized and one previously reported ribosomal protein gene localization was confirmed. The 12 ribosomal protein genes mapped in this study are spread over 10 chromosomes, including the X chromosome. The locations show conservation of comparative map position in cattle and human.
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Affiliation(s)
- Y H Wang
- CSIRO Livestock Industries, Molecular Animal Genetics Centre, Gehrmann Laboratories, Brisbane, Australia.
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3
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Morton SM, Veile RA, Helms C, Lee M, Kuo WL, Gray J, Donis-Keller H. Subregional localization of 21 chromosome 7-specific expressed sequence tags (ESTs) by FISH using newly identified YACs and P1s. Genomics 1997; 46:491-4. [PMID: 9441757 DOI: 10.1006/geno.1997.5051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Twenty-one putative chromosome 7-derived expressed sequence tags (ESTs) identified 33 yeast artificial chromosomes (YACs) or P1 clones, which were then used as reagents for physical mapping. FISH mapping established that the ESTs contained within these clones were distributed throughout chromosome 7, with all major cytogenetic bands represented, except 7p13-p15, 7p11, 7q31.2, and 7q35. Each EST sequence identified at least one other sequence in publicly available databases (using search tools such as BLASTN, basic local alignment search tool), and many of the ESTs identified cDNAs and several genomic DNA sequences. However, 7 ESTs did not identify highly significant matches (P < 1 x 10(-5)). Only one (EST01924-D7S2281E) failed to identify any other EST from the dbEST homology searches. BLAST analysis identified at least five genes from EST sequence comparisons: protein tyrosine phosphatase zeta (PTPRZ, also known as RPTPZ) (EST02092), which we had mapped to 7q31.3, in agreement with previous studies; cAMP-dependent protein kinase regulatory subunit bI (EST01644); rat integral membrane glycoprotein (EST00085); human IFNAR gene for interferon alpha/beta receptor (EST00817); and rat 14-3.3 protein gamma subtype (putative protein kinase C regulatory protein) (EST00762). These ESTs will help to develop the map of chromosome 7, which integrates physical, transcriptional, and cytogenetic data, as well as to provide candidate disease genes for chromosome 7-specific disorders.
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Affiliation(s)
- S M Morton
- Department of Surgery, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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4
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Smith CM, Ma NS, Nowak NJ, Shows TB, Gerhard DS. A 3-Mb contig from D11S987 to MLK3, a gene-rich region in 11q13. Genome Res 1997; 7:835-42. [PMID: 9267807 PMCID: PMC310665 DOI: 10.1101/gr.7.8.835] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/1997] [Accepted: 06/10/1997] [Indexed: 02/05/2023]
Abstract
We have combined genetic, radiation-reduced somatic cell hybrid (RRH), fluorescent in situ hybridization (FISH), and physical mapping methods to generate a contig of overlapping YAC, PAC, and cosmid clones corresponding to > 3 continuous Mb in 11q13. A total of 15 STSs [7 genes (GSTP1, ACTN, PC, MLK3, FRA1, SEA, HNP36), 4 polymorphic loci (D11S807, D11S987, GSTP1, D11S913), 3 ESTs (D11S1956E, D11S951E, and W1-12191), and 1 anonymous STS (D11S703)], mapping to three independent RRH segregation groups, identified 26 YAC, 7 PAC, and 16 cosmid clones from the CGM, Roswell Park, CEPH Mark I, and CEPH MegaYAC YAC libraries, a 5 genome equivalent PAC library, and a chromosome II-specific cosmid library. Thirty-six Alu-PCR products derived from 10 anonymous bacteriophage lambda clones, a cosmid containing the polymorphic marker D11S460, or STS-positive YAC or cosmid clones were identified and used to screen selected libraries by hybridization, resulting in the identification of 19 additional clones. The integrity and relative position of a subset of clones was confirmed by FISH and were found to be consistent with the physical and RRH mapping results. The combination of STS and Alu-PCR-based approaches has proven to be successful in attaining contiguous cloned coverage in this very GC-rich region, thereby establishing for the first time the absolute order and distance between the markers: CEN-MLK3-(D11S1956E/D11S951E/W1-12191)-FRA1-D 11S460-SEA-HNP36/ D11S913-ACTN-PC-D11S703-GSTP1-D11S987-TEL.
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5
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Burczak JD, Wilkinson FE, Robbins DJ. Impact of genomics on diagnostic medicine. Drug Dev Res 1997. [DOI: 10.1002/(sici)1098-2299(199707/08)41:3/4<193::aid-ddr9>3.0.co;2-g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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6
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Becker KG, Nagle JW, Canning RD, Dehejia AM, Polymeropoulos MH, Gado AM, Biddison WE, Drew PD. Molecular cloning and mapping of a novel human KRAB domain-containing C2H2-type zinc finger to chromosome 7q36.1. Genomics 1997; 41:502-4. [PMID: 9169157 DOI: 10.1006/geno.1997.4678] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- K G Becker
- Neuroimmunology Branch, National Institute of Neurological Diseases and Stroke, National Institutes of Health, Bethesda, Maryland 20892, USA
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7
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Becker KG, Canning RD, Nagle JW, Dehejia AM, Polymeropoulos MH, Lee IJ, Gado AM, Biddison WE, Drew PD. Molecular cloning and mapping of a novel developmentally regulated human C2H2-type zinc finger. Mamm Genome 1997; 8:287-9. [PMID: 9096115 DOI: 10.1007/s003359900414] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- K G Becker
- Neuroimmunology Branch, Building 10, Room 5B16, National Institute of Neurological Diseases and Stroke, National Institutes of Health, Bethesda, Maryland 20892, USA
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8
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Touchman JW, Bouffard GG, Weintraub LA, Idol JR, Wang L, Robbins CM, Nussbaum JC, Lovett M, Green ED. 2006 expressed-sequence tags derived from human chromosome 7-enriched cDNA libraries. Genome Res 1997; 7:281-92. [PMID: 9074931 DOI: 10.1101/gr.7.3.281] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The establishment and mapping of gene-specific DNA sequences greatly complement the ongoing efforts to map and sequence all human chromosomes. To facilitate our studies of human chromosome 7, we have generated and analyzed 2006 expressed-sequence tags (ESTs) derived from a collection of direct selection cDNA libraries that are highly enriched for human chromosome 7 gene sequences. Similarity searches indicate that approximately two-thirds of the ESTs are not represented by sequences in the public databases, including those in dbEST. In addition, a large fraction (68%) of the ESTs do not have redundant or overlapping sequences within our collection. Human DNA-specific sequence-tagged sites (STSs) have been developed from 190 of the ESTs. Remarkably, 180 (96%) of these STSs map to chromosome 7, demonstrating the robustness of chromosome enrichment in constructing the direct selection cDNA libraries. Thus far, 140 of these EST-specific STSs have been assigned unequivocally to YAC contigs that are distributed across the chromosome. Together, these studies provide > 2000 ESTs highly enriched for chromosome 7 gene sequences, 180 new chromosome 7 STSs corresponding to ESTs, and a definitive demonstration of the ability to enrich for chromosome-specific cDNAs by direct selection. Furthermore, the libraries, sequence data, and mapping information will contribute to the construction of a chromosome 7 transcript map.
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Affiliation(s)
- J W Touchman
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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9
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Hayes PD, Schmitt K, Jones HB, Gyapay G, Weissenbach J, Goodfellow PN. Regional assignment of human ESTs by whole-genome radiation hybrid mapping. Mamm Genome 1996; 7:446-50. [PMID: 8662228 DOI: 10.1007/s003359900130] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The UK HGMP Resource Centre's collection of human partial cDNA sequences (ESTs) have been examined for suitability for mapping by PCR on a panel of somatic cell hybrids. The chromosomal assignments of 92 ESTs were determined with a monochromosomal hybrid panel, and a subset of 45 were linked to genetic markers with a panel of whole-genome radiation hybrids (WG-RHs). These results demonstrate the potential of WG-RHs to construct a transcript map of the human genome.
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Affiliation(s)
- P D Hayes
- HGMP Resource Centre, Hinxton, Cambridgeshire, UK
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10
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Nikolaev LG, Tsevegiyn T, Akopov SB, Ashworth LK, Sverdlov ED. Construction of a chromosome specific library of human MARs and mapping of matrix attachment regions on human chromosome 19. Nucleic Acids Res 1996; 24:1330-6. [PMID: 8614638 PMCID: PMC145782 DOI: 10.1093/nar/24.7.1330] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Using a novel procedure a representative human chromosome 19-specific library was constructed of short sequences, which bind preferentially to the nuclear matrix (matrix attachment regions, or MARs). Judging by 20 clones sequenced so far, the library contains > 50% of human inserts, about 90% of which are matrix-binding by the in vitro test. Computer analysis of sequences of eight human MARs did not reveal any significant homologies with the EMBL Nucleotide Data Base entries as well as between MARs themselves. Eight MARs were assigned to individual positions on the chromosome 19 physical map. The library constructed can serve as a good source of MAR sequences for comparative analysis and classification and for further chromosome mapping of MARs as well.
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Affiliation(s)
- L G Nikolaev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
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11
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Rouquier S, Trask BJ, Taviaux S, van den Engh G, Diriong S, Lennon GG, Giorgi D. Direct selection of cDNAs using whole chromosomes. Nucleic Acids Res 1995; 23:4415-20. [PMID: 7501464 PMCID: PMC307398 DOI: 10.1093/nar/23.21.4415] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
We have developed a method for direct selection of cDNAs using whole chromosomes as target DNA. Double-strand cDNAs were synthesized from human fetal brain polyadenylated mRNAs. Flow-sorted chromosomes 17 and 19 were amplified by degenerate oligonucleotide primed polymerase chain reaction (DOP-PCR) and used to capture ds cDNAs by an improved magnetic bead capture protocol. To demonstrate the capabilities of this method, the selected cDNAs were used as probes in FISH experiments. The selected cDNA populations specifically painted chromosomes 17 or 19 on metaphase spreads. These results demonstrate that it is possible to do chromosome painting using cDNA probes and that this method is a means to rapidly select expressed sequences encoded by any portion of the genome.
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Affiliation(s)
- S Rouquier
- Centre de Recherche de Biochimie Macromoléculaire, CNRS UPR 9008, Montpellier, France
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12
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Olavesen MG, Davies AF, Broxholme SJ, Wixon JL, Senger G, Nizetic D, Campbell RD, Ragoussis J. An integrated map of human chromosome 6p23. Genome Res 1995; 5:342-58. [PMID: 8750194 DOI: 10.1101/gr.5.4.342] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The human chromosomal band 6p23 is a Giemsa-negative (light) band that may be expected to be relatively gene rich. The genes for spinocerebellar ataxia type 1 (SCA1), guanosine monophosphate reductase (GMPR), DEK involved in a subtype of acute myeloid leukemia (AML), and the folate-sensitive fragile site FRA6A, have already been mapped to 6p23. Recent linkage data have suggested evidence for a susceptibility locus for schizophrenia in the region. We have constructed a single YAC contig of approximately 100 clones spanning the entire 6p23 band from 6p22.3 to 6p24.1 and covering 7.5-8.5 Mb of DNA. The YAC contig contains 55 markers including genetically mapped STSs, physically mapped STSs, anonymous STSs, anonymous ESTs, and ESTs from the genes mapped to the region. The order of the genetically mapped STSs is consistent with their order in the contig and some of the markers not resolved on the genetic map have been resolved by the YACs. Four of the YACs from 6p23 and covering approximately 3 Mb of DNA have been used to isolate approximately 300 cosmids from a flow-sorted human chromosome 6 cosmid library, which have been organized into pockets. The proposed susceptibility locus for schizophrenia is most closely linked to D6S260, which is located within the YAC contig along with genetic markers < or = 5 cM on either side. Therefore, the presented materials are valuable reagents for characterization of the genomic region implicated in schizophrenia.
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Affiliation(s)
- M G Olavesen
- Division of Medical and Molecular Genetics, United Medical School of Guy's and St. Thomas's Hospital (UMDS), London, UK.
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13
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Lamerdin JE, Athwal RS, Kansara MS, Sandhu AK, Patanjali SR, Weissman SM, Carrano AV. Chromosomal localization and expressed sequence tag generation of clones from a normalized human adult thymus cDNA library. Genome Res 1995; 5:359-67. [PMID: 8750195 DOI: 10.1101/gr.5.4.359] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Expressed sequence tags (ESTs) from 298 clones have been generated from a randomly primed, normalized human adult thymus cDNA library. We describe the chromosomal localization of 136 of these ESTs by PCR-based mapping to a human monochromosomal somatic cell hybrid panel. Data base similarities to known genes are also described. A subset (n = 18) of these randomly primed ESTs extended the sequence of ESTs from other tissues currently in dbEST. Of the nonrepetitive human adult thymus ESTs generated in this study, 237 (79.5%) have no similarity to current data base entries. This would suggest that our collection contains approximately 100 new coding regions from thymus tissue, a large proportion of which likely will represent the middle regions of genes. The mapped ESTs should prove useful as new gene-based markers for mapping and candidate gene hunting, particularly when anchored to a well-developed physical map of the human genome.
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Affiliation(s)
- J E Lamerdin
- Human Genome Center, Lawrence Livermore National Laboratory, Livermore, California 94550, USA.
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14
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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; 5:272-304. [PMID: 8593614 DOI: 10.1101/gr.5.3.272] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Detailed analysis of a set of 18,698 sequences derived from both ends of 10,979 human skeletal muscle and brain cDNA clones defined 6676 functional families, characterized by their sequence signatures over 5750 distinct human gene transcripts. About half of these genes have been assigned to specific chromosomes utilizing 2733 eSTS markers, the polymerase chain reaction, and DNA from human-rodent somatic cell hybrids. Sequence and clone clustering and a functional classification together with comprehensive data base searches and annotations made it possible to develop extensive sequence and map cross-indexes, define electronic expression profiles, identify a new set of overlapping genes, and provide numerous new candidate genes for human pathologies.
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Affiliation(s)
- R Houlgatte
- Genexpress, Centre National de la Recherche Scientifique (CNRS) UPR420, Villejuif, France.
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15
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Berry R, Stevens TJ, Walter NA, Wilcox AS, Rubano T, Hopkins JA, Weber J, Goold R, Soares MB, Sikela JM. Gene-based sequence-tagged-sites (STSs) as the basis for a human gene map. Nat Genet 1995; 10:415-23. [PMID: 7670491 DOI: 10.1038/ng0895-415] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Using our data set of 3,143 single pass sequences from human brain cDNA libraries, we have developed a strategy in which gene-based sequence-tagged-sites (STSs), derived from 3'untranslated regions of human cDNAs, are rapidly assigned to megabase-insert yeast artificial chromosomes and somatic cell hybrids to generate regional gene mapping data. Employing this approach, we have mapped 318 cDNAs, representing 308 human genes. Ninety-two of these mapped to regions implicated in human genetic diseases, identifying them as candidate genes. Extension of this strategy has the potential to result in virtually every human gene having, at its 3' end, its own associated STS, with each STS in turn specifying both a corresponding genomic clone and a specific regional location in the genome.
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Affiliation(s)
- R Berry
- Department of Pharmacology, University of Colorado Health Sciences Center, Denver 80262, USA
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17
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Mazzarella R, Ciccodicola A, Esposito T, Arcucci A, Migliaccio C, Jones C, Schlessinger D, D'Urso M, D'Esposito M. Human protein kinase C Iota gene (PRKCI) is closely linked to the BTK gene in Xq21.3. Genomics 1995; 26:629-31. [PMID: 7607695 DOI: 10.1016/0888-7543(95)80190-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- R Mazzarella
- Washington University School of Medicine, St. Louis, Missouri, USA
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18
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Kelsell DP, Rooke L, Warne D, Bouzyk M, Cullin L, Cox S, West L, Povey S, Spurr NK. Development of a panel of monochromosomal somatic cell hybrids for rapid gene mapping. Ann Hum Genet 1995; 59:233-41. [PMID: 7625768 DOI: 10.1111/j.1469-1809.1995.tb00743.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
We have assembled a panel of monochromosomal somatic cell hybrids for use in gene mapping. DNA from each individual hybrid was used as a probe on normal human metaphases to identify the human chromosome and any fragments by reverse painting. To test the efficiency of the panel PCR amplification of DNA from the monochromosomal somatic cell hybrid panel was used in combination with human specific oligonucleotide primers to assign alpha-catenin (CTNNA1) and p21/WAF1 to chromosomes 5 and 6 respectively. These genes were localized further using hybrids containing specific translocations to 5q11-qter and 6p21 respectively. We also developed primers to enable us to assign 17 ESTs sequenced by the HGMP Resource Centre. The hybrid panel was developed with support of the UK HGMP and the DNA is available to all registered users.
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Affiliation(s)
- D P Kelsell
- Human Genetic Resources, Imperial Cancer Research Fund, Clare Hall Laboratories, South Mimms, Herts
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19
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Borodin A, Kopatnzev E, Wagner L, Volik S, Ermolaeva O, Lebedev Y, Monastyrskaya G, Kunz J, Grzeschik KH, Sverdlov E. An arrayed library enriched in hncDNA corresponding to transcribed sequences of human chromosome 19: preparation and analysis. GENETIC ANALYSIS : BIOMOLECULAR ENGINEERING 1995; 12:23-31. [PMID: 7648467 DOI: 10.1016/1050-3862(95)00106-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A simple technique for preparation of libraries of the human chromosome specific transcribed sequences is developed. It uses hnRNA from human-rodent hybrid cell lines containing particular human chromosomes or their fragments and includes three stages: (i) reverse transcription of the hnRNA with Alu-specific primers directing the transcription beyond the Alu-repeats to flanking non-repetitive sequences of the chromosome; (ii) nested primer PCR strategy with specifically designed primers; (iii) direct selective cloning of the second-stage nested primer PCR products. An arrayed hncDNA library was prepared from a hybrid cell line containing chromosome 19 and fragments of 22 and X chromosomes. The library contains around 98% of human-specific transcribed sequences. Sequences of 52 human-specific, according to PCR analysis, clones differed from each other and had no close analogs in the EMBL Data Bank. Of 17 clones assigned to certain human chromosomes, 9 belonged to chromosome 19, 5 to chromosome 22 and 3 to chromosome X. Some of the human specific clones contained repetitive elements scattered over different human chromosomes. Clones from hncDNA libraries are useful as STSs/ESTs, as probes for detecting full-size genes in genomic libraries, for RFLP analysis and for identification of chromosome specific cDNAs.
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MESH Headings
- Animals
- Base Sequence
- Chromosomes, Human, Pair 19
- Chromosomes, Human, Pair 22
- Cloning, Molecular/methods
- Cricetinae
- DNA Primers
- DNA, Complementary/biosynthesis
- DNA, Complementary/genetics
- Gene Library
- Humans
- Hybrid Cells
- Molecular Sequence Data
- Polymerase Chain Reaction/methods
- RNA, Heterogeneous Nuclear/genetics
- Repetitive Sequences, Nucleic Acid/genetics
- Sequence Analysis, DNA
- X Chromosome
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Affiliation(s)
- A Borodin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow
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20
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Affiliation(s)
- K Gardiner
- Eleanor Roosevelt Institute, Denver, CO 80206, USA
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21
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Volik S, Lebedev Y, Nikolaev L, Shevchenko Y, Vinogradova T, Kopantzev E, Kolesnik T, Monastyrskaya G, Kunz U, Grzeschik KH. Mapping of transcribed sequences on human chromosome 19. DNA SEQUENCE : THE JOURNAL OF DNA SEQUENCING AND MAPPING 1995; 6:13-26. [PMID: 8746456 DOI: 10.3109/10425179509074694] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
30 EST/STS have been mapped on human chromosome 19 using a highly specific hncDNA library as a source of transcribed sequences. In addition more than 50 sites constituting 19 families of closely related sequences containing at least one transcribed member each were mapped across the chromosome. Chromosome-19 specific hncDNA clones were hybridized to chromosome 19 cosmids that were previously assembled into contigs covering about 80% of Chr19. The hybridization results were verified by PCR. Such an approach to EST mapping provides information on possible locations of genes as transcribed units of genome and on location of repeated elements used for the priming the hncDNA synthesis. Mapped hncDNA sequences may serve as good starting points for the systematic sequencing of transcribed genomic regions.
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Affiliation(s)
- S Volik
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Ras, Moscow, Russia
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22
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Pappas GJ, Polymeropoulos MH, Boyle JM, Trent JM. Regional assignment by hybrid mapping of 36 expressed sequence tags (ESTs) on human chromosome 6. Genomics 1995; 25:124-9. [PMID: 7774909 DOI: 10.1016/0888-7543(95)80117-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
We have determined the regional chromosome assignment of 36 cDNAs from infant brain libraries by assessing the concordant segregation of PCR products using a human-rodent hybrid mapping panel that subdivides chromosome 6 into 15 regions. These mapped sequences serve as markers for the physical and expression maps of chromosome 6, as well as candidate genes for various disease loci. Sequence analysis has identified putative functions and motifs for some of these genes.
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Affiliation(s)
- G J Pappas
- Department of Human Genetics, University of Michigan, Ann Arbor 48109, USA
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23
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Khan AS, Wilcox AS, Polymeropoulos MH, Hopkins JA, Stevens TJ, Robinson M, Orpana AK, Sikela JM. Single pass sequencing and physical and genetic mapping of human brain cDNAs. Nat Genet 1994; 2:180-5. [PMID: 1345165 DOI: 10.1038/ng1192-180] [Citation(s) in RCA: 128] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We have performed single pass sequencing of 1,024 human brain cDNAs, over 900 of which seem to represent new human genes. Library prescreening with total brain cDNA significantly reduced repeated sequencing of highly represented cDNAs. A subset of sequenced cDNAs were physically mapped to their chromosomal locations using gene-specific STS primers derived from 3' untranslated regions. We have also determined that human brain cDNAs represent a rich source of gene-associated polymorphic markers. Microsatellite-containing cDNAs can be physically mapped and converted to highly informative genetic markers, thus facilitating integration of the human physical, expression and genetic maps.
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Affiliation(s)
- A S Khan
- Department of Pharmacology, University of Colorado Health Sciences Center, Denver 80262
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Riess O, Winkelmann B, Epplen JT. Toward the complete genomic map and molecular pathology of human chromosome 4. Hum Genet 1994; 94:1-18. [PMID: 8034286 DOI: 10.1007/bf02272834] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The identification of disease genes via molecular DNA cloning has revolutionized human genetics and medicine. Both the candidate gene approach and positional cloning have been used successfully. The defects causing Huntington's disease, facioscapulohumeral muscular dystrophy, piebaldism, Hurler/Scheie syndrome, one form of autosomal recessive retinitis pigmentosa, and a second locus for autosomal dominant polycystic kidney disease have recently been localized to chromosome 4. In addition to the rapid progress in the cloning of the 203-megabase chromosome, the presence of more than 60 closely spaced microsatellites on this chromosome will undoubtedly lead to the localization of additional disease genes. In order to consider cloned genes as potential candidates for disorders assigned to chromosome 4, it is important to collect and order all genes with respect to their chromosomal localization. Analysis of cytogenetically visible interstitial and terminal deletions should also be helpful in defining new disease gene loci and in mapping novel genes. These data represent the status quo of the integrated molecular map for chromosome 4.
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Affiliation(s)
- O Riess
- Molekulare Humangenetik Ruhr-Universität, Bochum, Germany
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25
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Abstract
During the past year, improvements in the physical and genetic maps of the human genome, in combination with more efficient methods to isolate genes from cloned DNA, have made an increasing impact on the identification of disease genes. Sequence analysis of genomic DNA and the random sequencing and mapping of cDNA clones is helping to integrate the transcript map with the developing physical and genetic maps.
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Affiliation(s)
- A P Monaco
- Imperial Cancer Research Fund Laboratories, John Radcliffe Hospital, Headington, Oxford, UK
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26
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Chae KS, Murakawa K, Okubo K, Matsubara K. The use of overlapping and tailed short primers in the chromosomal assignment of short cDNAs by the polymerase chain reaction. Gene 1994; 142:199-205. [PMID: 8194752 DOI: 10.1016/0378-1119(94)90261-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
For the PCR-based chromosomal assignment of very short cDNA fragments specifically designed primers are required. We tested primers with very short core sequences that are identical or complementary to known cDNA sequences, with or without tails at the 5' ends. The lower limit of the core length for PCR using human chromosome templates was 14 nucleotides (nt) when they have tails. The minimal length of the tail was 2 nt when it was attached to the 5' end of a 14-nt core. In the absence of a tail, 15 nt are needed for the core to act properly. The overall size of the short cDNA fragments that could be assigned was further reduced by using a pair of primers that overlap at the 3' ends. The limits of the free energy of overlap were about -1.9 kcal/mol at 45 degrees C, -2.9 kcal/mol at 50 degrees C and -4.5 kcal/mol at 55 degrees C. A combination of these features in a primer pair allowed cDNA fragments as short as 30 nt to be assigned.
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Affiliation(s)
- K S Chae
- Institute for Molecular and Cellular Biology, Osaka University, Japan
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27
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Meezaman D, Charles P, Daskal E, Polymeropoulos M, Martin B, Rose M. Cloning and analysis of cDNA encoding a major airway glycoprotein, human tracheobronchial mucin (MUC5). J Biol Chem 1994. [DOI: 10.1016/s0021-9258(18)99965-5] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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28
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Riess O, Epplen C, Siedlaczck I, Epplen JT. Chromosomal assignment of the human smg GDP dissociation stimulator gene to human chromosome 4q21-q25. Hum Genet 1993; 92:629-30. [PMID: 8262526 DOI: 10.1007/bf00420952] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The 3'-end of the cDNA encoding the smg GDP dissociation stimulator (smg GDS) protein shares 100% homology with the previously published expressed sequence tag 00038 site. This site extends the 3'-end of the smg GDS gene by 212 bp. It has been localized to human chromosome 4. Here, we have refined the localization of smg GDP to human chromosome 4q21-q25 using a mapping panel of rodent/human somatic cell hybrids containing different parts of chromosome 4. This chromosomal localization of smg GDP to 4q21-25 overlaps with a region of allele loss in primary hepatocellular carcinoma (4q13-q26).
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Affiliation(s)
- O Riess
- Abteilung für Molekulare Humangenetik, Ruhr Universität, Bochum, Germany
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29
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Matsubara K, Okubo K. Identification of new genes by systematic analysis of cDNAs and database construction. Curr Opin Biotechnol 1993; 4:672-7. [PMID: 7764463 DOI: 10.1016/0958-1669(93)90048-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The large-scale collection of partial cDNA sequences is becoming a powerful tool in biology. Similarity or motif searches in DNA databases using these partial cDNA sequences have facilitated the discovery of new genes of interest. By collecting and registering large numbers of partial sequences with a well designed non-biased cDNA library, an expression profile of active genes in a particular tissue can be obtained. Tissue-specific or stage-specific genes can be discovered by comparing the profiles from different tissues or from a tissue at different stages of development, respectively. The compilation of such expression profiles enables genes to be mapped to the tissue(s) where they are actively transcribed. The large-scale collation of gene sequences actively expressed in the body into databases complements efforts directed towards the structural analysis of the genome, with the ultimate aim of decoding all the genetic information carried in the human genome. This cDNA strategy is also being widely applied to organisms other than man.
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Affiliation(s)
- K Matsubara
- Institute for Molecular and Cellular Biology, Osaka University, Japan
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30
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Polymeropoulos MH, Xiao H, Sikela JM, Adams M, Venter JC, Merril CR. Chromosomal distribution of 320 genes from a brain cDNA library. Nat Genet 1993; 4:381-6. [PMID: 8401586 DOI: 10.1038/ng0893-381] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
We have determined the chromosomal assignment of 320 brain expressed genes by studying the segregation of polymerase chain reaction (PCR) products in human rodent somatic cell hybrids and by genetically mapping polymorphic cDNAs using the CEPH (Centre d'Etude du Polymophisme Humaine) reference pedigrees and database. These mapped genes can function as markers on the physical map of the human genome, as well as serve as candidate disease gene loci. Distribution of these genes to the human chromosomes correlates well with the GC content of the chromosomes. However, the distribution of these genes does not correlate well with the cytogenetic length of each chromosome.
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Affiliation(s)
- M H Polymeropoulos
- Laboratory of Biochemical Genetics, National Institute of Mental Health, Neuroscience Center at St. Elizabeths, Washington, DC 20032
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31
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Abstract
The recently published, detailed cytogenetic-based physical map of chromosome 16 has the highest resolution of any autosomal cytogenetic map thus far constructed. The genetic map has been integrated with the cytogenetic map to facilitate the regional localization of disease genes by linkage. Disease genes for tuberous sclerosis, familial Mediterranean fever, Rubinstein-Taybi syndrome and Morquio A syndrome have now been assigned to chromosome 16. The search for the adult polycystic kidney disease gene has recently been narrowed to the analysis of candidate loci on chromosome 16, and localization of the gene determining juvenile Batten disease has been further refined by disequilibrium mapping.
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Affiliation(s)
- J C Mulley
- Department of Cytogenetics and Molecular Genetics, Women's and Children's Hospital, North Adelaide, Australia
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33
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Lefebvre S, Bureau JF, Muscatelli F, Mattei MG, Brahic M. A new human brain cDNA molecule: assignment to chromosome 11q21-q23.1 and description of two polymorphisms studied by the polymerase chain reaction. Hum Genet 1993; 91:148-50. [PMID: 8462974 DOI: 10.1007/bf00222715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
A new human brain cDNA molecule was mapped by in situ hybridization to the 11q21-q23.1 region of the human genome, probably to the 11q22 band. An EcoRI restriction site and a (GT)n repeat element within the gene were shown to be polymorphic. Both polymorphisms were readily studied by the polymerase chain reaction. A two-allele polymorphism was described for the EcoRI restriction site, whereas four different alleles were detected for the second genetic marker. The observed heterozygosities were 37% and 42% for the former and the latter polymorphism, respectively. The combined heterozygosity index was estimated to be 0.56. These new genetic markers will be useful for linkage analysis of neurogenetic diseases that have been mapped to this chromosomal region.
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Affiliation(s)
- S Lefebvre
- Unité des Virus Lents (CNRS UA 1157), Institut Pasteur, Paris, France
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34
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Carstea ED, Polymeropoulos MH, Parker CC, Detera-Wadleigh SD, O'Neill RR, Patterson MC, Goldin E, Xiao H, Straub RE, Vanier MT. Linkage of Niemann-Pick disease type C to human chromosome 18. Proc Natl Acad Sci U S A 1993; 90:2002-4. [PMID: 8446622 PMCID: PMC46008 DOI: 10.1073/pnas.90.5.2002] [Citation(s) in RCA: 90] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
We analyzed the involvement of chromosome 18 in Niemann-Pick disease type C (NPC), an autosomal recessive cholesterol-processing disorder. Within affected offspring, the chromosome 18 parental contributions were identified by using allele-specific microsatellite markers. Significant linkage of NPC to an 18p genomic marker, D18S40, was indicated by a two-point lod score of 3.84. Analysis of meiotic chromosomal breakpoint patterns among the affected individuals indicated that the NPC gene is pericentromerically localized on human chromosome 18.
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Affiliation(s)
- E D Carstea
- Developmental and Metabolic Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892
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McClelland M, Chada K, Welsh J, Ralph D. Arbitrary primed PCR fingerprinting of RNA applied to mapping differentially expressed genes. EXS 1993; 67:103-15. [PMID: 7691286 DOI: 10.1007/978-3-0348-8583-6_10] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Differential gene expression between various tissues and developmental stages or between cells in vitro under different growth conditions can be rapidly and efficiently compared using the RNA arbitrarily primed polymerase chain reaction (RAP) fingerprinting method (Welsh et al., 1992b; Liang and Pardee, 1992). In RAP, a primer of arbitrary sequence primes both first and second strand cDNA synthesis. The mixture of products is then PCR amplified and resolved electrophoretically, yielding highly reproducible fingerprints that are tissue-specific or growth condition-specific. Differences between fingerprints arise from differentially expressed genes, as verified by Northern blot analysis. RAP can be performed on the RNA samples using various DNA primers. Each two day experiment yields a sample of approximately twenty cDNA products per lane making the identification of differentially or developmentally regulated genes no longer rate limiting. Those PCR products representing genes that are regulated can be cloned from the gel and sequenced. Sequences can be compared to the DNA and protein sequence databases to identify homologs, motifs and members of gene families. The clones can be placed on the genetic map as Expression Tagged Sites (ETS, Adams et al., 1991a).
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Affiliation(s)
- M McClelland
- California Institute of Biological Research, La Jolla 92037
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37
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38
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Durkin AS, Maglott DR, Nierman WC. Chromosomal assignment of 38 human brain expressed sequence tags (ESTs) by analyzing fluorescently labeled PCR products from hybrid cell panels. Genomics 1992; 14:808-10. [PMID: 1427913 DOI: 10.1016/s0888-7543(05)80194-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We have localized 38 human brain cDNA sequences to individual human chromosomes. PCR primers were designed from expressed sequence tags and tested for specific amplification from human genomic DNA. The sizes of amplification products from DNA of somatic cell hybrid mapping panels were determined electrophoretically using an automated fluorescence detection system. Chromosomal assignments were made by discordancy analysis.
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Affiliation(s)
- A S Durkin
- Department of Molecular Biology, American Type Culture Collection, Rockville, Maryland 20852-1776
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