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Johannes M, Geyer DD, Berry R, Walter NA, Sikela JM, Bateman JB. Comparison of fluorescent genotyping methods. Anal Biochem 1998; 262:193-5. [PMID: 9750132 DOI: 10.1006/abio.1998.2778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- M Johannes
- Department of Ophthalmology, University of Colorado Health Sciences Center, Denver, Colorado, 80206, USA
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Radcliffe RA, Walter NA, Sikela JM, Erwin VG. Discovery of a new Pomc1 allele in the LS x SS recombinant inbred strains: relationship to locomotor behavior. Behav Genet 1998; 28:49-55. [PMID: 9573646 DOI: 10.1023/a:1021408815540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Various lines of evidence suggest that a polymorphism in the gene for proopiomelanocortin, Pomc1, might account for some portion of the genetic variance for open-field activity in the LS x SS RI strains. To test this hypothesis, approximately 1600 bp of Pomc1 was sequenced from genomic DNA of seven of the LS x SS strains. Two distinct alleles containing a total of five single-base pair differences were detected. A substitution was found in the coding region causing a Pro-to-Ser conversion, two substitutions occurred in the 3' untranslated region of the mRNA, and a substitution and a deletion were detected in the 3' untranscribed flanking region. The fragment containing the coding region substitution was sequenced in an additional 15 of the LS x SS strains. A total of 12 strains contained one form of the allele, while 10 had the other. The strain distribution pattern of open-field activity scores between the two allels suggests that these alleles do not contribute to the genetic variation of open-field activity in the LS x SS RI strains.
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Affiliation(s)
- R A Radcliffe
- Institute for Behavioral Genetics, University of Colorado, Boulder 80309-0447, USA.
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Schuler GD, Boguski MS, Stewart EA, Stein LD, Gyapay G, Rice K, White RE, Rodriguez-Tomé P, Aggarwal A, Bajorek E, Bentolila S, Birren BB, Butler A, Castle AB, Chiannilkulchai N, Chu A, Clee C, Cowles S, Day PJ, Dibling T, Drouot N, Dunham I, Duprat S, East C, Edwards C, Fan JB, Fang N, Fizames C, Garrett C, Green L, Hadley D, Harris M, Harrison P, Brady S, Hicks A, Holloway E, Hui L, Hussain S, Louis-Dit-Sully C, Ma J, MacGilvery A, Mader C, Maratukulam A, Matise TC, McKusick KB, Morissette J, Mungall A, Muselet D, Nusbaum HC, Page DC, Peck A, Perkins S, Piercy M, Qin F, Quackenbush J, Ranby S, Reif T, Rozen S, Sanders C, She X, Silva J, Slonim DK, Soderlund C, Sun WL, Tabar P, Thangarajah T, Vega-Czarny N, Vollrath D, Voyticky S, Wilmer T, Wu X, Adams MD, Auffray C, Walter NA, Brandon R, Dehejia A, Goodfellow PN, Houlgatte R, Hudson JR, Ide SE, Iorio KR, Lee WY, Seki N, Nagase T, Ishikawa K, Nomura N, Phillips C, Polymeropoulos MH, Sandusky M, Schmitt K, Berry R, Swanson K, Torres R, Venter JC, Sikela JM, Beckmann JS, Weissenbach J, Myers RM, Cox DR, James MR, Bentley D, Deloukas P, Lander ES, Hudson TJ. A gene map of the human genome. Science 1996; 274:540-6. [PMID: 8849440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The human genome is thought to harbor 50,000 to 100,000 genes, of which about half have been sampled to date in the form of expressed sequence tags. An international consortium was organized to develop and map gene-based sequence tagged site markers on a set of two radiation hybrid panels and a yeast artificial chromosome library. More than 16,000 human genes have been mapped relative to a framework map that contains about 1000 polymorphic genetic markers. The gene map unifies the existing genetic and physical maps with the nucleotide and protein sequence databases in a fashion that should speed the discovery of genes underlying inherited human disease. The integrated resource is available through a site on the World Wide Web at http://www.ncbi.nlm.nih.gov/SCIENCE96/.
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Affiliation(s)
- G D Schuler
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
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Berry R, Walter NA, Stevens TJ, Rubano T, Wilcox AS, Hopkins JA, Sikela JM. A strategy for the identification of candidate genes for alcohol-related phenotypes and other human disorders using rapid polymerase chain reaction mapping of gene-based sequence-tagged sites. Alcohol Clin Exp Res 1995; 19:821-3. [PMID: 7485825 DOI: 10.1111/j.1530-0277.1995.tb00952.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
We describe a method for the rapid identification and mapping of human genes, including those possibly contributing to disease and alcohol-related phenotypes. New human genes are identified from cDNA libraries through single-pass sequencing into the 3' untranslated (3'UT) regions of human brain cDNAs. Primers derived from the 3'UT region sequences [representing gene-based, sequence-tagged sites (STSs)] are used for polymerase chain reaction (PCR) analyses of the CEPH megabase insert yeast artificial chromosome (YAC) DNA pools. With this approach, approximately 18,000 megabase YACs can be screened and a single YAC identified using only 52 PCR reactions. The YAC localization in conjunction with other mapping techniques, such as PCR mapping to human chromosomes using somatic cell hybrids, allows identification of chromosomal band locations. In this manner, each gene can be associated with its own STS, which in turn specifies both a corresponding genomic clone and specific location in the genome. These locations can be compared with the purported locations of disease genes. The locations of the STSs can also be compared with those of Quantitative Trait Loci implicated for quantitative traits (e.g., alcohol-related phenotypes) on the basis of synteny between the mouse and human genes. Using this strategy, we found candidates for 78 human disease/syndrome genes among the first 220 genes mapped.
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Affiliation(s)
- R Berry
- Department of Pharmacology, University of Colorado Health Sciences Center, Denver 80262, USA
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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