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Luo Y, Kanai M, Choi W, Li X, Sakaue S, Yamamoto K, Ogawa K, Gutierrez-Arcelus M, Gregersen PK, Stuart PE, Elder JT, Forer L, Schönherr S, Fuchsberger C, Smith AV, Fellay J, Carrington M, Haas DW, Guo X, Palmer ND, Chen YDI, Rotter JI, Taylor KD, Rich SS, Correa A, Wilson JG, Kathiresan S, Cho MH, Metspalu A, Esko T, Okada Y, Han B, McLaren PJ, Raychaudhuri S. A high-resolution HLA reference panel capturing global population diversity enables multi-ancestry fine-mapping in HIV host response. Nat Genet 2021; 53:1504-1516. [PMID: 34611364 PMCID: PMC8959399 DOI: 10.1038/s41588-021-00935-7] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 08/02/2021] [Indexed: 02/08/2023]
Abstract
Fine-mapping to plausible causal variation may be more effective in multi-ancestry cohorts, particularly in the MHC, which has population-specific structure. To enable such studies, we constructed a large (n = 21,546) HLA reference panel spanning five global populations based on whole-genome sequences. Despite population-specific long-range haplotypes, we demonstrated accurate imputation at G-group resolution (94.2%, 93.7%, 97.8% and 93.7% in admixed African (AA), East Asian (EAS), European (EUR) and Latino (LAT) populations). Applying HLA imputation to genome-wide association study data for HIV-1 viral load in three populations (EUR, AA and LAT), we obviated effects of previously reported associations from population-specific HIV studies and discovered a novel association at position 156 in HLA-B. We pinpointed the MHC association to three amino acid positions (97, 67 and 156) marking three consecutive pockets (C, B and D) within the HLA-B peptide-binding groove, explaining 12.9% of trait variance.
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Affiliation(s)
- Yang Luo
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Division of Rheumatology, Immunology, and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Masahiro Kanai
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Wanson Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Xinyi Li
- Committee on Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Saori Sakaue
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Immunology, and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kenichi Yamamoto
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Pediatrics, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Kotaro Ogawa
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Neurology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Maria Gutierrez-Arcelus
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Immunology, and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Peter K Gregersen
- The Robert S. Boas Center for Genomics and Human Genetics, Feinstein Institute for Medical Research,North Short LIJ Health System, Manhasset, NY, USA
| | - Philip E Stuart
- Department of Dermatology, University of Michigan, Ann Arbor, MI, USA
| | - James T Elder
- Department of Dermatology, University of Michigan, Ann Arbor, MI, USA
- Ann Arbor Veterans Affairs Hospital, Ann Arbor, MI, USA
| | - Lukas Forer
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Sebastian Schönherr
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Christian Fuchsberger
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Institute for Biomedicine, Eurac Research, Bolzano, Italy
| | - Albert V Smith
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Jacques Fellay
- Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
- School of Life Sciences, EPFL, Lausanne, Switzerland
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
- Ragon Institute of MGH, MIT and Harvard, Boston, MA, USA
| | - David W Haas
- Vanderbilt University Medical Center, Nashville, TN, USA
- Meharry Medical College, Nashville, TN, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Nicholette D Palmer
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Adolfo Correa
- Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - James G Wilson
- Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS, USA
| | - Sekar Kathiresan
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Cardiology Division of the Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Andres Metspalu
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Tonu Esko
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
| | - Buhm Han
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, South Korea
| | - Paul J McLaren
- J.C. Wilt Infectious Diseases Research Centre, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Soumya Raychaudhuri
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Division of Rheumatology, Immunology, and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Centre for Genetics and Genomics Versus Arthritis, University of Manchester, Manchester, UK.
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2
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KARCHER SUSANJ. RECOMBINANT DNA CLONING. Mol Biol 1995. [DOI: 10.1016/b978-012397720-5.50036-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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3
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Whittaker PA, Wood L. Construction and features of lambda EMBL3cosW, a lambda replacement vector for detailed analysis of large regions of genomic DNA. Gene X 1994; 138:227-32. [PMID: 8125306 DOI: 10.1016/0378-1119(94)90813-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
A phage lambda replacement vector, lambda EMBL3cosW, is described which expedites detailed analysis of large regions of chromosomal DNA. Two features of the vector aid this process. Firstly, the replaceable stuffer in lambda EMBL3cosW is flanked by SP6 and T7 promoters so that end-specific hybridisation probes can be rapidly generated from cloned inserts for identification of sequentially overlapping clones in genomic libraries. Secondly, because all the phage coding sequences in the vector (which are placed to the right of the replaceable stuffer) can be removed from cloned inserts by cleavage with NotI, restriction mapping of cloned inserts using partial digest strategies is greatly facilitated. Other features of the vector are: (1) strategically placed BamHI and XhoI sites for the cloning of genomic DNA partially digested with MboI or Sau3AI by two different methods; (2) SalI and SfiI sites for the isolation of intact cloned inserts; and (3) transcription terminators to insulate vector genes from transcriptional interference from cloned insert DNAs.
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Affiliation(s)
- P A Whittaker
- University Clinical Biochemistry, Southampton General Hospital, UK
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4
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Jücker M, Günther A, Gradl G, Fonatsch C, Krueger G, Diehl V, Tesch H. The Met/hepatocyte growth factor receptor (HGFR) gene is overexpressed in some cases of human leukemia and lymphoma. Leuk Res 1994; 18:7-16. [PMID: 8289471 DOI: 10.1016/0145-2126(94)90003-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The proto-oncogene c-met encodes a heterodimeric (alpha, beta) tyrosine kinase receptor which binds the hepatocyte growth factor (HGF). Recently, overexpression of the Met/HGF receptor gene has been detected in fresh samples of carcinomas and in epithelial tumor cell lines but not in cell lines derived from human leukemia and lymphoma. Our analysis of 50 primary samples of human leukemia and lymphoma and 23 hematopoietic cell lines revealed expression of mRNA and protein of the met/HGF receptor in 6 out of the 73 hematopoietic tumor samples analyzed. Four of the six samples positive for expression of the Met/HGF receptor gene were derived from patients with Hodgkin's disease. In addition, in one Burkitt's lymphoma cell line and in one acute myeloid leukemia (AML), expression of the Met/HGF receptor gene was detected. In normal unstimulated lymphocytes, granulocytes or monocytes we did not find expression of the Met/HGF receptor gene. Upon stimulation with the phorbol ester TPA we detected a weak expression of Met/HGF receptor specific transcripts of 9.0 kb in peripheral blood mononuclear cells of a healthy donor. Cytogenetic analyses of three of the four cell lines which express the Met/HGF receptor gene revealed structural or numerical abnormalities of the long arm of chromosome 7, where the Met/HGFR gene is located, in each of the three cell lines analyzed. In one of these cell lines (L540) the Met/HGFR gene is translocated to a marker chromosome. Southern blot and pulsed field gel electrophoresis experiments did not show any rearrangement in a region of 600 kb around the Met/HGF receptor gene excluding an activation of Met/HGFR by a TPR/Met oncogenic rearrangement as described for MNNG-HOS cells and for some gastric tumors. Our data indicate that the Met/HGFR gene is deregulated in a few cases of human leukemia, Burkitt's lymphoma and Hodgkin's disease possibly by chromosomal rearrangements resulting in an overexpression of the normal Met/HGF receptor mRNA and protein without formation of a hybrid gene.
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MESH Headings
- Chromosome Aberrations
- Chromosomes, Human, Pair 7
- Gene Expression
- Gene Expression Regulation, Leukemic
- Gene Expression Regulation, Neoplastic
- Hematopoietic Stem Cells/metabolism
- Hodgkin Disease/genetics
- Hodgkin Disease/metabolism
- Humans
- Leukemia, Lymphoid/genetics
- Leukemia, Lymphoid/metabolism
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Lymphoma/genetics
- Lymphoma/metabolism
- Lymphoma, Non-Hodgkin/genetics
- Lymphoma, Non-Hodgkin/metabolism
- Proto-Oncogene Mas
- Proto-Oncogene Proteins c-met
- Proto-Oncogenes/genetics
- RNA, Messenger/metabolism
- Receptor Protein-Tyrosine Kinases/genetics
- Receptor Protein-Tyrosine Kinases/metabolism
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Affiliation(s)
- M Jücker
- Medizinische Klinik I, Universität Köln, F.R.G
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5
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Upcroft P, Upcroft JA. Comparison of properties of agarose for electrophoresis of DNA. JOURNAL OF CHROMATOGRAPHY 1993; 618:79-93. [PMID: 8227266 DOI: 10.1016/0378-4347(93)80028-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Agarose as a medium for separation of DNA was first introduced in 1962 and since the early 1970s agarose submarine gel electrophoresis has been synonymous with separations of DNA molecules larger than 1 kilobase pair (kb). The large pore size, low electroendosmosis and strength of the matrix have advantages over other media such as polyacrylamide for many applications. The variety of grades of agarose, developed by chemical manipulation of the substitutions on the agarose polymer, provides a range of matrices for separation of DNA molecules from a few base pairs (bp) to over 5 megabase pairs (Mb) in length. The introduction of low-melting-temperature agarose has revolutionised the extraction and manipulation of chromosome-sized molecules. On the other hand, the demand for analysis of very small quantities of DNA will most likely lead to the increasing importance of capillary electrophoresis. Many theories have been propounded to explain the electrophoretic migration of DNA in agarose. The most popular of these has been reptation theory but none can account for all of the reported anomalies in migration. However, anomalous migration has been exploited to study DNA structure, topology and catenation. An example of the use of two-dimensional electrophoresis to demonstrate the complexity of DNA migration through agarose is given. Generally, for molecules smaller than 50 kb, electrophoretic separation is a function of length. By alternately electrophoresing DNA in two different directions, molecules as large as 5.7 Mb have been effectively separated, although with such large molecules DNA structure as well as size may determine migration. In the case of separations of chromosomes from the intestinal protozoan, Giardia duodenalis, for example, a discrepancy of 1 Mb in the size of one chromosome, with an apparent size of 0.7-2.0 Mb, depended on the boundary conditions of separation. Major challenges for the molecular biologist are separation of larger chromosomal sized molecules, greater number of samples and smaller formats. Towards this challenge computer-aided technology is a key component in the control of electrophoresis parameters and analysis.
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Affiliation(s)
- P Upcroft
- Queensland Institute of Medical Research, Bancroft Center, Herston Australia
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6
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Affiliation(s)
- L Stubbs
- Biology Division, Oak Ridge National Laboratory, Tennessee 37831
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7
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Wilkinson DG. The Use of in Situ Hybridisation to Study the Molecular Genetics of Mouse Development. Development 1992. [DOI: 10.1007/978-3-642-77043-2_29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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8
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Michelmore RW, Paran I, Kesseli RV. Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations. Proc Natl Acad Sci U S A 1991; 88:9828-32. [PMID: 1682921 PMCID: PMC52814 DOI: 10.1073/pnas.88.21.9828] [Citation(s) in RCA: 1953] [Impact Index Per Article: 57.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
We developed bulked segregant analysis as a method for rapidly identifying markers linked to any specific gene or genomic region. Two bulked DNA samples are generated from a segregating population from a single cross. Each pool, or bulk, contains individuals that are identical for a particular trait or genomic region but arbitrary at all unlinked regions. The two bulks are therefore genetically dissimilar in the selected region but seemingly heterozygous at all other regions. The two bulks can be made for any genomic region and from any segregating population. The bulks are screened for differences using restriction fragment length polymorphism probes or random amplified polymorphic DNA primers. We have used bulked segregant analysis to identify three random amplified polymorphic DNA markers in lettuce linked to a gene for resistance to downy mildew. We showed that markers can be reliably identified in a 25-centimorgan window on either side of the targeted locus. Bulked segregant analysis has several advantages over the use of near-isogenic lines to identify markers in specific regions of the genome. Genetic walking will be possible by multiple rounds of bulked segregation analysis; each new pair of bulks will differ at a locus identified in the previous round of analysis. This approach will have widespread application both in those species where selfing is possible and in those that are obligatorily outbreeding.
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Affiliation(s)
- R W Michelmore
- Department of Vegetable Crops, University of California, Davis 95616
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9
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Lowe N, Edwards YH, Edwards M, Butterworth PH. Physical mapping of the human carbonic anhydrase gene cluster on chromosome 8. Genomics 1991; 10:882-8. [PMID: 1916821 DOI: 10.1016/0888-7543(91)90176-f] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A cluster of genes encoding the three cytoplasmic carbonic anhydrase isozymes CAI, CAII, and CAIII lie on the long arm of chromosome 8 (8q22) in humans. These genes have been mapped using pulsed-field gel electrophoresis. The genes lie in the order CA2, CA3, CA1. CA2 and CA3 are separated by 20 kb and are transcribed in the same direction, away from CA1. CA1 is separated from CA3 by over 80 kb and is transcribed in the direction opposite to CA2 and CA3. The arrangement of the genes is consistent with proposals that the duplication event which gave rise to CA1 predated the duplication which gave rise to CA2 and CA3. The order of these three genes differs from that suggested for the mouse based on recombination frequency.
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Affiliation(s)
- N Lowe
- Department of Biochemistry, University College London, United Kingdom
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10
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Cox RD, Stubbs L, Evans T, Lehrach H. A mouse specific polymerase chain reaction (PCR) primer: probe generation from somatic cell hybrids. Nucleic Acids Res 1991; 19:2503. [PMID: 2041790 PMCID: PMC329471 DOI: 10.1093/nar/19.9.2503] [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: 12/29/2022] Open
Affiliation(s)
- R D Cox
- Genome Analysis, Imperial Cancer Research Fund Laboratories, London, UK
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11
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Tsui LC, Buchwald M. Biochemical and molecular genetics of cystic fibrosis. ADVANCES IN HUMAN GENETICS 1991; 20:153-266, 311-2. [PMID: 1724873 DOI: 10.1007/978-1-4684-5958-6_4] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- L C Tsui
- Department of Genetics, Hospital for Sick Children, Toronto, Ontario, Canada
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12
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Dixon LK, Bristow C, Wilkinson PJ, Sumption KJ. Identification of a variable region of the African swine fever virus genome that has undergone separate DNA rearrangements leading to expansion of minisatellite-like sequences. J Mol Biol 1990; 216:677-88. [PMID: 2258935 DOI: 10.1016/0022-2836(90)90391-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Nucleotide sequencing identified a tandemly repeated sequence array 22 x 10(3) base-pairs from the right-hand DNA terminus of the African swine fever virus (ASFV) genome. The sequence of the repeat array and sequences closely flanking it were compared in the genomes of four groups of ASFV isolates that had very different restriction enzyme site maps. Arrays present in one group of ASFV isolates from East Zambia/Malawi varied in length and contained between 8 and 38 copies of a 17-nucleotide repeat unit. Repeat arrays in a second group of ASFV isolates from Europe were less variable in length but consisted of different types of repeat unit that were divergent in sequence. A third genetically diverse ASFV isolate. LIV 13 from a South Zambia Game Park, contained repeat unit types that were similar to those of European viruses. MFUE6 isolate from an East Zambia Game Park contained a shorter version of the European repeat unit. An eight-base-pair core sequence was conserved between the East Zambia/Malawi and European and LIV 13 repeat units. These tandemly repeated sequence arrays share a number of properties with chromosomal minisatellite DNA. Similar tandem repeat arrays have not been described in poxviruses.
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Affiliation(s)
- L K Dixon
- AFRC Institute for Animal Health, Pirbright Laboratory, Woking, Surrey, U.K
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13
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14
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Pritchard C, Casher D, Bull L, Cox DR, Myers RM. A cloned DNA segment from the telomeric region of human chromosome 4p is not detectably rearranged in Huntington disease patients. Proc Natl Acad Sci U S A 1990; 87:7309-13. [PMID: 2144903 PMCID: PMC54733 DOI: 10.1073/pnas.87.18.7309] [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: 12/30/2022] Open
Abstract
Genetic linkage studies have mapped the Huntington disease (HD) mutation to the distal region of the short arm of human chromosome 4. Analysis of recombination events in this region has produced contradictory locations for HD. One possible location is in the region distal to the D4S90 marker, which is located within 300 kilobases of the telomere. Other crossover events predict a more centromeric position for HD. Here we analyze the telomeric region of 4p in detail. Cloned DNA segments were derived from this region by utilizing a radiation-induced somatic cell hybrid as a source of DNA combined with preparative pulsed-field gel electrophoresis to enrich for the telomeric fraction. Additional DNA was obtained by using the cloned segments as multiple start points for cosmid walks. This strategy proved to be an effective method for cloning 250 kilobases of DNA in the region telomeric to D4S90. Hybridization analysis with the cloned DNA did not provide any evidence for the presence of rearrangements of 100 base pairs or greater in the DNA of individuals affected with HD. We also found no change in the size or structure of the 4p telomere in these samples.
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Affiliation(s)
- C Pritchard
- Department of Physiology, University of California, San Francisco 94143
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15
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Albertsen HM, Abderrahim H, Cann HM, Dausset J, Le Paslier D, Cohen D. Construction and characterization of a yeast artificial chromosome library containing seven haploid human genome equivalents. Proc Natl Acad Sci U S A 1990; 87:4256-60. [PMID: 2190217 PMCID: PMC54087 DOI: 10.1073/pnas.87.11.4256] [Citation(s) in RCA: 272] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Prior to constructing a library of yeast artificial chromosomes (YACs) containing very large human DNA fragments, we performed a series of preliminary experiments aimed at developing a suitable protocol. We found an inverse relationship between YAC insert size and transformation efficiency. Evidence of occasional rearrangement within YAC inserts was found resulting in clonally stable internal deletions or clonally unstable size variations. A protocol was developed for preparative electrophoretic enrichment of high molecular mass human DNA fragments from partial restriction digests and ligation with the YAC vector in agarose. A YAC library has been constructed from large fragments of DNA from an Epstein-Barr virus-transformed human lymphoblastoid cell line. The library presently contains 50,000 clones, 95% of which are greater than 250 kilobase pairs in size. The mean YAC size of the library, calculated from 132 randomly isolated clones, is 430 kilobase pairs. The library thus contains the equivalent of approximately seven haploid human genomes.
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Affiliation(s)
- H M Albertsen
- Centre d'Etude du Polymorphisme Humain, Paris, France
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16
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Harris PC, Barton NJ, Higgs DR, Reeders ST, Wilkie AO. A long-range restriction map between the alpha-globin complex and a marker closely linked to the polycystic kidney disease 1 (PKD1) locus. Genomics 1990; 7:195-206. [PMID: 2347584 DOI: 10.1016/0888-7543(90)90541-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Two polymorphic loci and two additional probes that map close to CMM65, which is tightly linked to the polycystic kidney disease 1 (PKD1) locus in chromosome band 16p13.3, are described. These new probes were isolated from a library that was enriched by preparative pulsed-field gel electrophoresis (PFGE) for sequences from a 320-kb NotI fragment that includes CMM65. Through the use of a panel of somatic cell hybrids and PFGE, the new polymorphic loci, PNL56S and NKISP1, were localized within 60 kb and approximately 250 kb distal to CMM65, respectively. A long-range restriction map linking these new probes and the distal markers EKMDA2, CMM103, and alpha-globin was constructed. These latter probes have been localized to regions approximately 900 kb, 1.2 Mb, and 1.9 Mb distal to CMM65, respectively. The entire region was found to be unusually rich in CpG dinucleotides. The new polymorphic probes and the long-range map will aid both the search for the PKD1 locus and the detailed characterization of this distal region of 16p.
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Affiliation(s)
- P C Harris
- Institute of Molecular Medicine, John Radcliffe Hospital, Headington, Oxford, United Kingdom
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17
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Abstract
The protein responsible for cystic fibrosis has been identified using an approach called "reverse" genetics. This approach relies on the chromosomal map position to direct the search for a disease gene, several novel cloning strategies to isolate the gene, and the gene's sequence to define the abnormal protein. Reverse genetics, because it does not require prior knowledge of the protein's biochemical function, has wide utility and is being used to define the defects in many single-gene disorders. This update presents the reverse genetics approach and uses cystic fibrosis to illustrate the principles involved.
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Affiliation(s)
- M C Iannuzzi
- Department of Internal Medicine and Human Genetics, Howard Hughes Medical Institute, University of Michigan, Ann Arbor 48109
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18
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van de Pol TJ, Cremers FP, Brohet RM, Wieringa B, Ropers HH. Derivation of clones from the choroideremia locus by preparative field inversion gel electrophoresis. Nucleic Acids Res 1990; 18:725-31. [PMID: 1969148 PMCID: PMC330319 DOI: 10.1093/nar/18.4.725] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
By making use of preparative field inversion gel electrophoresis, we have constructed a lambda ZAP library that is highly enriched for sequences from the choroideremia locus. In vivo excision of pBluescript SK(-) constructs from lambda ZAP obviates the subcloning of DNA inserts and allows for rapid processing of several hundred recombinants. From a 625 kb Sfil fragment we isolated 7 clones that were physically mapped using microdeletions associated with the disease. One of these clones is located within, or just telomeric to, the choroideremia gene and detects two restriction fragment length polymorphisms (RFLPs). Another clone detects a RFLP which maps centromeric to the disease locus. Together these probes should improve the reliability of linkage analysis in choroideremia families and should pave the way for the isolation of the choroideremia gene.
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Affiliation(s)
- T J van de Pol
- Department of Human Genetics, Radboud Hospital, University of Nijmegen, The Netherlands
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19
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Compton DA, Weil MM, Bonetta L, Huang A, Jones C, Yeger H, Williams BR, Strong LC, Saunders GF. Definition of the limits of the Wilms tumor locus on human chromosome 11p13. Genomics 1990; 6:309-15. [PMID: 2155176 DOI: 10.1016/0888-7543(90)90571-b] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In a previous report, we described a contiguous restriction map of chromosome band 11p13 that localized the Wilms tumor locus to a small group of NotI fragments. In an effort to identify and isolate the 11p13-associated sporadic Wilms tumor locus, we developed a panel of NotI fragment-specific DNA probes. These probes were selected from genomic libraries constructed using the Chinese hamster ovary-human somatic cell hybrid carrying only human 11p. The libraries were prepared from NotI-digested DNA after size selection by pulsed-field gel electrophoresis. The selected NotI fragments had been previously targeted on the basis of deletion mapping as having a high probability of containing the Wilms tumor locus. We used these newly identified 11p13-specific probes to improve the resolution of the restriction map spanning the Wilms tumor locus. The locus has been defined by a homozygous deletion in a sporadic Wilms tumor. Using these probes, the region of homozygous deletion in this tumor and presumably all or part of the Wilms tumor gene have been confined to two small SfiI fragments spanning less than 350 kb.
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Affiliation(s)
- D A Compton
- Department of Biochemistry and Molecular Biology, University of Texas M. D. Anderson Cancer Center, Houston 77030
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20
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Bućan M, Zimmer M, Whaley WL, Poustka A, Youngman S, Allitto BA, Ormondroyd E, Smith B, Pohl TM, MacDonald M. Physical maps of 4p16.3, the area expected to contain the Huntington disease mutation. Genomics 1990; 6:1-15. [PMID: 2137426 DOI: 10.1016/0888-7543(90)90442-w] [Citation(s) in RCA: 56] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The gene for Huntington disease, a neurodegenerative disorder with autosomal dominant inheritance, has been localized to the terminal portion of the short arm of human chromosome 4 (4p16.3) by linkage analysis. Since eventual isolation of the gene requires the application of high-resolution genetic analysis coupled with long-range DNA mapping and cloning techniques, we have constructed a physical map of the chromosomal region 4p16.3 using more than 20 independently derived probes. We have grouped these markers into three clusters which have been ordered and oriented by genetic and somatic cell genetic mapping information. The mapped region extends from D4S10 (G8) toward the telomere and covers minimally 5 Mb.
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Affiliation(s)
- M Bućan
- Imperial Cancer Research Fund, London, England
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21
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Ramsay M, Wainwright BJ, Farrall M, Estivill X, Sutherland H, Ho MF, Davies R, Halford S, Tata F, Wicking C. A new polymorphic locus, D7S411, isolated by cloning from preparative pulse-field gels is close to the mutation causing cystic fibrosis. Genomics 1990; 6:39-47. [PMID: 1968045 DOI: 10.1016/0888-7543(90)90446-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The mutation causing cystic fibrosis (CF) has been localized to the DNA sequence of 700 kb bounded by the loci identified by the markers pMP6d-9 (D7S399) and pJ3.11 (D7S8). A 560-kb fragment obtained after SacII digestion of DNA from a cell line containing this region of human chromosome 7 in a mouse background was separated using pulse-field gel electrophoresis and isolated from the gel. The DNA was digested with BamHI prior to cloning into lambda EMBL3. Approximately 0.1% of the resulting clones contained human repetitive sequences, and 24 such recombinants were studied. Of these, 23 are on chromosome 7; 8 clones were duplicated, and of the 15 different recombinants, 7 are between MET and INT1L1, and a further 7 are between INT1L1 and pMP6d-9, leaving a single marker, pG2, which is between pMP6d-9 and pJ3.11. pG2 recognizes an RFLP with XbaI. A cosmid walk from pG2 has generated a further marker, H80, which recognizes an RFLP with PstI. This new locus (D7S411) divides the remaining region between the CF flanking markers, thereby making it more accessible to fine pulse-field mapping and allowing the precise localization of further clones to this region. Although it is not possible to position the CF locus unequivocally with respect to D7S411, both polymorphic markers at this locus exhibit low but significant linkage disequilibrium with CF, placing the emphasis for the search for the gene on the D7S399 to D7S411 interval of 250 kb.
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Affiliation(s)
- M Ramsay
- Cystic Fibrosis Genetics Research Group, St. Mary's Hospital Medical School, Imperial College London, United Kingdom
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22
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Varesco L, Thomas HJ, Cottrell S, Murday V, Fennell SJ, Williams S, Searle S, Sheer D, Bodmer WF, Frischauf AM. CpG island clones from a deletion encompassing the gene for adenomatous polyposis coli. Proc Natl Acad Sci U S A 1989; 86:10118-22. [PMID: 2557613 PMCID: PMC522387 DOI: 10.1073/pnas.86.24.10118] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Adenomatous polyposis coli (APC), a dominantly inherited disorder, has been mapped to chromosome 5q15-q21 by family linkage studies. Cells from patients with deletions in this region, in one case associated with polyposis in a family, have been used to construct human hamster hybrid cell lines that retain either the normal or deleted chromosome 5. These lines have been used to identify markers from the region of the polyposis gene obtained by cloning the ends of 0.5- to 2-megabase BssHII fragments purified by pulsed-field gel electrophoresis. Three markers are described that map within the deletions and must therefore be close to the APC gene.
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Affiliation(s)
- L Varesco
- Molecular Analysis of Mammalian Mutation Laboratory, Imperial Cancer Research Fund, Lincolns Inn Fields, London, United Kingdom
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23
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Porteous DJ, Wilkinson MM, Fletcher JM, van Heyningen V. Human-mouse hybrids carrying fragments of single human chromosomes selected by tumor growth. Genomics 1989; 5:680-4. [PMID: 2687156 DOI: 10.1016/0888-7543(89)90108-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Fusion of human EJ bladder carcinoma cells to mouse C127 cells, with direct selection for tumor growth, gave rise to hybrid cells in which the human chromosome complement had been reduced dramatically, while selectively retaining the activated HRAS1 at chromosome band 11p15. A single-component hybrid retaining only part of human chromosome 11 is described in detail. Our results suggest a novel and general approach for investigating the chromosomal basis of neoplastic change and for subchromosomal mapping of and enrichment cloning for the human genome.
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Affiliation(s)
- D J Porteous
- MRC Human Genetics Unit, Western General Hospital, Edinburgh, United Kingdom
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24
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Rommens JM, Iannuzzi MC, Kerem B, Drumm ML, Melmer G, Dean M, Rozmahel R, Cole JL, Kennedy D, Hidaka N. Identification of the cystic fibrosis gene: chromosome walking and jumping. Science 1989; 245:1059-1065. [PMID: 2772657 DOI: 10.1126/science.2772657] [Citation(s) in RCA: 2085] [Impact Index Per Article: 57.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
An understanding of the basic defect in the inherited disorder cystic fibrosis requires cloning of the cystic fibrosis gene and definition of its protein product. In the absence of direct functional information, chromosomal map position is a guide for locating the gene. Chromosome walking and jumping and complementary DNA hybridization were used to isolate DNA sequences, encompassing more than 500,000 base pairs, from the cystic fibrosis region on the long arm of human chromosome 7. Several transcribed sequences and conserved segments were identified in this cloned region. One of these corresponds to the cystic fibrosis gene and spans approximately 250,000 base pairs of genomic DNA.
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Affiliation(s)
- J M Rommens
- Department of Genetics, Hospital for Sick Children, Toronto, Ontario, Canada
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25
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Dawkins HJ. Large DNA separation using field alternation agar gel electrophoresis. JOURNAL OF CHROMATOGRAPHY 1989; 492:615-39. [PMID: 2671005 DOI: 10.1016/s0378-4347(00)84481-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The techniques for large DNA separation have developed from a seminal idea for field alternation which has transformed the field of DNA electrophoresis. This single innovation of pulsed field-gradient electrophoresis (PFGE) and the subsequent modifications have made a significant impact on molecular biology, eukaryote genetics, biopolymer research and diagnostic research. The apparatus types used for large DNA separation are depicted and critically compared with relation to molecular mass separation capabilities, straight-lane migration of samples, band sharpness and ease of operation. With these criteria in mind PFGE and orthogonal field alternation gel electrophoresis systems had a number of drawbacks, the principle one being the inability of these systems to give straight-lane migration. To a large extent this has restricted the widespread use of these systems. Field inversion gel electrophoresis produces straight-lane migration but was subject to an upper molecular mass limitation of 2 megabase pairs and tended to produce broader bands in the higher-molecular-mass areas. Transverse alternating field electrophoresis, rotating gel electrophoresis and contour-clamped homogeneous electric field electrophoresis systems where superior to all the other systems. They gave straight-lane migration, separation of chromosomes up to 10 megabase pairs, good resolution of bands and were all relatively simple to operate. Very little was found to separate these three electrophoresis systems. Field alternation electrophoresis has enabled a 500-fold increase in the size of DNA molecules that can be resolved in agar gels. Consequently, electrophoretic karyotypes of a number of organisms have been produced, while genome maps, gene locations and sequences of large areas of mammalian genomes are now being undertaken. The ability to separate entire chromosomes or large DNA fragments has, in conjunction with novel molecular biology techniques, enabled scientists to work backwards from large purified fragments or entire chromosomes to construct long-range genetic maps. The time saving alone when compared with the old techniques of using very small fragments to construct a picture of the gene or gene complex is commendable. The diagnostic role of large DNA separation and electrophoretic karyotyping is beginning to be explored, while the use of this technique for clinical studies of genetic disorders is well advanced. Very few innovations in nucleic acid separation have had as marked an influence on as many areas as field alternation electrophoresis. These techniques have brought mapping of the mammalian genome into the realms of possibility and is contributing in many sphere
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Affiliation(s)
- H J Dawkins
- Department of Agriculture and Rural Affairs, Regional Veterinary Laboratory, Victoria, Australia
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26
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Sørensen MB. Mapping of the Hor2 locus in barley by pulsed field gel electrophoresis. CARLSBERG RESEARCH COMMUNICATIONS 1989; 54:109-20. [PMID: 2803483 DOI: 10.1007/bf02908303] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
High molecular weight DNA released from isolated protoplasts was digested with rare-cutting restriction enzymes and separated by pulsed field gel electrophoresis. The average size of undigested DNA was above 1500 kbp. Digests made with NotI, SfiL, Mlul and SalI was hybridized to a probe, common to all genes of the Hor2 locus encoding B-hordein polypeptides, and this revealed the maximum size of the locus to be 360 kbp. Two probes, specific for individual B-hordein genes, enabled the identification of two fragment classes in the locus, each containing an equal number of B-hordein genes. Double digests allowed ordering of sites and construction of a map covering 650 kbp around the Hor2 locus. No evidence for physical linkage of the two fragment classes was obtained. The possible assignment of the two classes of hybridizing fragments to the B1- and B3-hordein subgroups is discussed.
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Affiliation(s)
- M B Sørensen
- Department of Physiology, Carlsberg Laboratory, Copenhagen Valby
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27
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Dunham I, Sargent CA, Dawkins RL, Campbell RD. Direct observation of the gene organization of the complement C4 and 21-hydroxylase loci by pulsed field gel electrophoresis. J Exp Med 1989; 169:1803-18. [PMID: 2565949 PMCID: PMC2189312 DOI: 10.1084/jem.169.5.1803] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Pulsed field gel electrophoresis and enzymes that cut genomic DNA infrequently have been used to define large RFLPs at the human C4 loci. With the enzymes BssH II or Sac II, and C4 or 21-hydroxylase DNA probes, it has been possible to observe directly the number of C4 genes present on a haplotype, and also whether the C4 genes are long (6-7-kb intron present) or short (6-7-kb intron absent). Haplotypes that have either two long C4 genes or one long and one short C4 gene generate BssH II fragments of approximately 115 or approximately 105 kb, respectively. Haplotypes that have either a single long or a single short C4 gene generate BssH II fragments of approximately 80 or approximately 70 kb, respectively. This technique has been used to analyze the DNA isolated from PBMC and allows the complete definition of the C4 gene organization of an individual without the need for family studies.
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Affiliation(s)
- I Dunham
- Department of Biochemistry, University of Oxford, United Kingdom
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28
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Crater GD, Gregg MR, Holzwarth G. Mobility surfaces for field-inversion gel electrophoresis of linear DNA. Electrophoresis 1989; 10:310-5. [PMID: 2767039 DOI: 10.1002/elps.1150100507] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The mobility of linear DNA during field-inversion gel electrophoresis was measured as a function of molecular weight Mr, pulse time t, and field strength E. Values of Mr between 48.5 and 194 kilobase pairs (kb), E from 5 to 14 V/cm and pulse times of 0.3 to 12 s were used. The data are presented as three-dimensional surfaces of mobility: E:t for fixed Mr or graphs of mobility: Mr:t for fixed E. The surfaces are not smoothly increasing functions of E, Mr, or t but instead show a valley with minimum mobility and a steep rise in mobility as t increases. For a field of 10 V/cm, 1% agarose gels, and 3:1 ratio of forward:back pulse time, the forward switching time t* at which the mobility changes most rapidly is given by t* = (0.034 +/- 0.003) Mr for Mr in kb and t* in seconds. The data and equations delineate the best conditions to achieve a particular separation.
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Affiliation(s)
- G D Crater
- Department of Physics, Wake Forest University, Winston-Salem, NC 27109
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29
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van Daelen RA, Jonkers JJ, Zabel P. Preparation of megabase-sized tomato DNA and separation of large restriction fragments by field inversion gel electrophoresis (FIGE). PLANT MOLECULAR BIOLOGY 1989; 12:341-352. [PMID: 24272869 DOI: 10.1007/bf00043211] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/1988] [Accepted: 12/08/1988] [Indexed: 06/02/2023]
Abstract
The Schwartz and Cantor technique for releasing and fractionating megabase-sized DNA from agarose-embedded cells is beginning to bridge the gap in resoluation between classical genetics and current molecular DNA techniques, particularly in mammalian systems. As yet no conditions have been described for preparing plant DNA that is of sufficient length to allow similar long-range restriction mapping experiments in plant systems. In this report, we describe the application of the Schwartz and Cantor technique for preparing high molecular weight DNA from embedded tomato leaf protoplasts, as well as conditions for generating and fractionating large restriction fragments, by field inversion gel electrophoresis (FIGE). The bulk of DNA released from lysed protoplasts was at least 2 Mb in size and amenable to restriction digestion as shown by hybridizing Southern blots with, among others, a probe for the Adh-2 gene of tomato. Restriction fragments as large as 700 kb were detected. Chloroplast DNA is isolated intact, amenable to restriction analysis and, in its native form, not mobile in FIGE.
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Affiliation(s)
- R A van Daelen
- Department for Molecular Biology, Agricultural University, Dreijenlaan 3, 6703 HA, Wageningen, Netherlands
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30
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Kere J. Chromosome 7 long arm deletion breakpoints in preleukemia: mapping by pulsed field gel electrophoresis. Nucleic Acids Res 1989; 17:1511-20. [PMID: 2922284 PMCID: PMC331818 DOI: 10.1093/nar/17.4.1511] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Chromosome 7 long arm deletions (7q-) are recurring chromosome abnormalities in leukemic bone marrow cells. In four patients we have previously localized the breakpoints in band 7q22 between the erythropoietin (EPO) and plasminogen activator inhibitor type 1 (PLANH1) genes that map 3 cM apart. The pro alpha 2(I) collagen (COL1A2, in band 7q22) and T cell receptor beta chain genes (TCRB, in band 7q35) have been found undeleted in one patient with an interstitial deletion. Pulsed field gel electrophoresis was used to map the breakpoints more accurately in two patients with a 7q- chromosome. The results suggested that lymphocytes and granulocytes give identical restriction patterns with several enzyme-probe combinations, and that a breakpoint possibly was within 195 kb of EPO in one patient but not in another. The gene order cen-COL1A2-EPO-breakpoint-tel was suggested but physical linkage between COL1A2 and EPO was not found. A new putative TCRB restriction fragment length polymorphism or inherited methylation site was detected.
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Affiliation(s)
- J Kere
- Department of Medical Genetics, University of Helsinki, Finland
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31
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32
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33
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Whaley WL, Michiels F, MacDonald ME, Romano D, Zimmer M, Smith B, Leavitt J, Bucan M, Haines JL, Gilliam TC. Mapping of D4S98/S114/S113 confines the Huntington's defect to a reduced physical region at the telomere of chromosome 4. Nucleic Acids Res 1988; 16:11769-80. [PMID: 2905444 PMCID: PMC339109 DOI: 10.1093/nar/16.24.11769] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The dominant gene defect in Huntington's disease (HD) is linked to the DNA marker D4S10, near the telomere of the chromosome 4 short arm. Two other markers, D4S43 and D4S95, are closer, but still proximal to the HD gene in 4p16.3. We have characterized a new locus, D4S114, identified by cloning the end of a NotI fragment resolved by pulsed-field gel electrophoresis. D4S114 was localized distal to D4S43 and D4S95 by both physical and genetic mapping techniques. The "end"-clone overlaps a previously isolated NotI "linking" clone, and is within 150 kb of a second "linking" clone defining D4S113. Restriction fragment length polymorphisms for D4S113 and D4S114, one of which is identical to a SacI polymorphism detected by the anonymous probe pBS731B-C (D4S98), were typed for key crossovers in HD and reference pedigrees. The data support the locus order D4S10-(D4S43, D4S95)-D4S98/S114/S113-HD-telomere. The D4S98/S114/S113 cluster therefore represents the nearest cloned sequences to HD, and provides a valuable new point for launching directional cloning strategies to isolate and characterize this disease gene.
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Affiliation(s)
- W L Whaley
- Neurogenetics Laboratory, Massachusetts General Hospital, Boston
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34
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Meagher RB, McLean MD, Arnold J. Recombination within a subclass of restriction fragment length polymorphisms may help link classical and molecular genetics. Genetics 1988; 120:809-18. [PMID: 2906304 PMCID: PMC1203558 DOI: 10.1093/genetics/120.3.809] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Restriction fragment length polymorphisms (RFLPs) are being used to construct complete linkage maps for many eukaryotic genomes. These RFLP maps can be used to predict the inheritance of important phenotypic loci and will assist in the molecular cloning of linked gene(s) which affect phenotypes of scientific, medical and agronomic importance. However, genetic linkage implies very little about the actual physical distances between loci. An assay is described which uses genetic recombinants to measure physical distance from a DNA probe to linked phenotypic loci. We have defined the subset of all RFLPs which have polymorphic restriction sites at both ends as class II RFLPs. The frequency of class II RFLPs is computed as a function of sequence divergence and total RFLP frequency for highly divergent genomes. Useful frequencies exist between organisms which differ by more than 7% in DNA sequence. Recombination within class II RFLPs will produce fragments of novel sizes which can be assayed by pulsed field electrophoresis to estimate physical distance in kilobase pairs between linked RFLP and phenotypic loci. This proposed assay should have particular applications to crop plants where highly divergent and polymorphic species are often genetically compatible and thus, where class II RFLPs will be most frequent.
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Affiliation(s)
- R B Meagher
- Department of Genetics, University of Georgia, Athens 30602
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35
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Anand R, Honeycombe J, Whittaker PA, Elder JK, Southern EM. Clones from an 840-kb fragment containing the 5' region of the DMD locus enriched by pulsed field gel electrophoresis. Genomics 1988; 3:177-86. [PMID: 3066744 DOI: 10.1016/0888-7543(88)90077-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Detailed analysis of a large region of genomic DNA is facilitated by generating overlapping clones covering the entire region. These clones are usually obtained by bidirectional "walking" using either bacteriophage lambda or cosmid cloning vectors. This is a slow procedure when starting from a single start site. Multiple start sites are an advantage, and here we describe a method of generating clones from an extensive region of the Duchenne muscular dystrophy locus by preparative pulsed field gel electrophoresis using the chromosome of interest isolated in a cell hybrid. We have generated 12 clones mapping to an 840-kb SfiI fragment of DNA from the Xp2.1 region of the X chromosome, where the DMD gene has been localized. Further localization of these clones to the four subregions of the 840-kb fragment indicates that the clones are distributed throughout the fragment. The feasibility of using this approach to generate probes close to other loci is discussed.
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Affiliation(s)
- R Anand
- Department of Biochemistry, University of Oxford, United Kingdom
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36
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Richards JE, Gilliam TC, Cole JL, Drumm ML, Wasmuth JJ, Gusella JF, Collins FS. Chromosome jumping from D4S10 (G8) toward the Huntington disease gene. Proc Natl Acad Sci U S A 1988; 85:6437-41. [PMID: 2901098 PMCID: PMC281987 DOI: 10.1073/pnas.85.17.6437] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The gene for Huntington disease (HD) has been localized to the distal portion of the short arm of human chromosome 4 by linkage analysis. Currently, the two closest DNA markers are D4S10 (G8), located approximately equal to 3 centimorgans centromeric to HD, and D4S43 (C4H), positioned 0-1.5 centimorgans from HD. In an effort to move closer to the HD gene, with the eventual goal of identifying the gene itself, we have applied the technique of chromosome jumping to this region. A 200-kilobase jumping library has been constructed, and a jump from D4S10 has been obtained and its approximate distance verified by pulsed field gel electrophoresis. Two restriction fragment length polymorphisms have been identified at the jump locus, which is denoted D4S81. Linkage analysis of previously identified recombinants between D4S10 and HD or D4S10 and D4S43 shows that in two of five events the jump has crossed the recombination points. This unequivocally orients D4S10 and D4S81 on the chromosome, provides additional markers for HD, and suggests that recombination frequency in this region of chromosome 4 may be increased, so that the physical distance from D4S10 to HD may not be as large as originally suspected.
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Affiliation(s)
- J E Richards
- Howard Hughes Medical Institute, Department of Internal Medicine, University of Michigan, Ann Arbor 48109
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37
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Poustka AM, Lehrach H, Williamson R, Bates G. A long-range restriction map encompassing the cystic fibrosis locus and its closely linked genetic markers. Genomics 1988; 2:337-45. [PMID: 2906041 DOI: 10.1016/0888-7543(88)90023-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The cystic fibrosis (CF) locus has been localized to the long arm of chromosome 7 by linkage analysis, and the genetic relationship between CF and the probes J3.11, met, and 7C22 has been extensively studied. To extend this genetic analysis to higher resolution, to provide information on physical distances underlying the genetic relationships, and to set limits to the position of the cystic fibrosis mutation, we have constructed a partial restriction map covering approximately 5 Mb that defines the physical relationship between these and the more recently isolated markers CS.7, XV-2c, Lcn2, and C2/5. Allelic association indicates that CS.7 and XV-2c are close to the CF locus, and an expressed sequence from this region has been described as a candidate gene for this mutation (X. Estivill et al., 1987, Nature (London) 326: 840-845). Using pulsed-field gel electrophoresis we have determined the physical order of these markers to be cen-7C22-Lcn2-met-C2/5-XV-2c-CS.7-J3.11-tel and have localized the CF mutation to an interval of less than 1500 kb. A (not unexpected) disproportionality was observed between the currently best estimates of genetic and physical distances, with the interval J3.11-met showing an approximately fourfold higher frequency of recombination than the met-7C22 interval.
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38
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Park M, Testa JR, Blair DG, Parsa NZ, Vande Woude GF. Two rearranged MET alleles in MNNG-HOS cells reveal the orientation of MET on chromosome 7 to other markers tightly linked to the cystic fibrosis locus. Proc Natl Acad Sci U S A 1988; 85:2667-71. [PMID: 3282234 PMCID: PMC280059 DOI: 10.1073/pnas.85.8.2667] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
We have found that two alleles of the MET locus are rearranged in the human cell line MNNG-HOS. One allele is the previously characterized TPR-MET oncogene and the other is found on a der(7)t(1;7)(q23;q32) marker chromosome. These data and in situ chromosomal hybridization analysis would indicate that MET and, therefore, the cystic fibrosis locus are located at bands q31-q32 on human chromosome 7. Using somatic cell hybrids, we show that the chromosome containing the TPR-MET oncogene is grossly rearranged and contains both the upstream and downstream portions of the MET protooncogene locus. These results demonstrate that the TPR-MET oncogene rearrangement involving chromosomes 1 and 7 is either due to an insertion of TPR sequences into the MET locus or is more complex. We also show that the upstream MET protooncogene locus is deleted on der(7), while the downstream portion is retained. We cannot exclude that this is due to an interstitial chromosomal deletion or to a more complex rearrangement, but if MET maps at the breakpoint in der(7), then the 3' end of the MET transcription unit should be oriented towards the centromere. We also show that other DNA restriction fragment length polymorphism markers tightly linked with the inheritance of cystic fibrosis are deleted on der(7).
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Affiliation(s)
- M Park
- Bionetics Research, Inc., Basic Research Program, National Cancer Institute, Frederick Cancer Research Facility, MD 21701
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Burmeister M, Monaco AP, Gillard EF, van Ommen GJ, Affara NA, Ferguson-Smith MA, Kunkel LM, Lehrach H. A 10-megabase physical map of human Xp21, including the Duchenne muscular dystrophy gene. Genomics 1988; 2:189-202. [PMID: 3397058 DOI: 10.1016/0888-7543(88)90002-x] [Citation(s) in RCA: 82] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Using pulsed-field gel electrophoresis and 12 Xp21-derived DNA probes, we have constructed a continuous restriction map spanning more than 4 million base pairs (4 Mbp), including the Duchenne muscular dystrophy gene of more than 2 Mbp. This detailed map is part of a less detailed map spanning 10 Mbp, also spanning the genes for glycerol kinase and congenital adrenal hypoplasia, constructed under electrophoresis conditions which separated DNA fragments in the range 200 to 4000 kbp. DNA from three different tissues was analyzed, and differential methylation was observed.
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Affiliation(s)
- M Burmeister
- European Molecular Biology Laboratory, Heidelberg, West Germany
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40
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Myklebost O, Rogne S. A physical map of the apolipoprotein gene cluster on human chromosome 19. Hum Genet 1988; 78:244-7. [PMID: 2894348 DOI: 10.1007/bf00291670] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
We have generated a restriction map around the cloned genes for human apolipoproteins CI, CII, and E by pulsed-field gel analysis. We show that the genes are clustered within an area of about 50 kb on chromosome 19. The genes are all oriented in the same direction, head to tail.
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Affiliation(s)
- O Myklebost
- Research Institute of Internal Medicine, Rikshospitalet, Oslo, Norway
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41
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Ragoussis J, Bloemer K, Weiss EH, Ziegler A. Localization of the genes for tumor necrosis factor and lymphotoxin between the HLA class I and III regions by field inversion gel electrophoresis. Immunogenetics 1988; 27:66-9. [PMID: 3257100 DOI: 10.1007/bf00404447] [Citation(s) in RCA: 35] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- J Ragoussis
- Medizinische Klinik, University of Tübingen, Federal Republic of Germany
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42
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Stubbs L, Poustka A, Rohme D, Russell LB, Lehrach H. Approaching the mouse Steel locus from closely linked molecular markers. Curr Top Microbiol Immunol 1988; 137:47-52. [PMID: 3166418 DOI: 10.1007/978-3-642-50059-6_8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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43
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Westphal EM, Burmeister M, Wienker TF, Lehrach H, Bender K, Scherer G. Tyrosine aminotransferase and chymotrypsinogen B are linked to haptoglobin on human chromosome 16q: comparison of genetic and physical distances. Genomics 1987; 1:313-9. [PMID: 2896626 DOI: 10.1016/0888-7543(87)90030-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The loci for haptoglobin (HP) and tyrosine aminotransferase (TAT) are known to reside at 16q22. Chymotrypsinogen B (CTRB), which is syntenic with TAT and HP on mouse chromosome 8, has also been assigned to human chromosome 16 but has not been mapped regionally. A linkage analysis was carried out in 13 informative families using RFLPs for these three markers. For CTRB, two TaqI RFLPs with a polymorphism information content of 0.60 derived from haplotype frequencies are described. The most likely order of loci, deduced from triple informative crosses, and their map distances, obtained by pair-wise linkage analysis, are HP-7 cM-TAT-9 cM-CTRB. By pulsed-field gel electrophoresis, a physical map covering more than 2000 kb was constructed. A maximum physical distance of about 700 kb was obtained for HP and TAT, which contrasts with the genetic distance of 7 cM (approximate confidence limits 2-18 cM). CTRB is at least 800 kb away from these two markers.
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Affiliation(s)
- E M Westphal
- Institute of Human Genetics, Freiburg i. Br., Federal Republic of Germany
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Molecular Techniques in Mammalian Genetics: A New Era in Genetic Analysis. Hum Genet 1987. [DOI: 10.1007/978-3-642-71635-5_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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