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Boroumand N, Baghdissar C, Elihn K, Lundholm L. Nicotine interacts with DNA lesions induced by alpha radiation which may contribute to erroneous repair in human lung epithelial cells. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 284:117009. [PMID: 39244876 DOI: 10.1016/j.ecoenv.2024.117009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 08/16/2024] [Accepted: 09/02/2024] [Indexed: 09/10/2024]
Abstract
PURPOSE Epidemiological studies show that radon and cigarette smoke interact in inducing lung cancer, but the contribution of nicotine in response to alpha radiation emitted by radon is not well understood. MATERIALS AND METHODS Bronchial epithelial BEAS-2B cells were either pre-treated with 2 µM nicotine during 16 h, exposed to radiation, or the combination. DNA damage, cellular and chromosomal alterations, oxidative stress as well as inflammatory responses were assessed to investigate the role of nicotine in modulating responses. RESULTS Less γH2AX foci were detected at 1 h after alpha radiation exposure (1-2 Gy) in the combination group versus alpha radiation alone, whereas nicotine alone had no effect. Comet assay showed less DNA breaks already just after combined exposure, supported by reduced p-ATM, p-DNA-PK, p-p53 and RAD51 at 1 h, compared to alpha radiation alone. Yet the frequency of translocations was higher in the combination group at 27 h after irradiation. Although nicotine did not alter G2 arrest at 24 h, it assisted in cell cycle progression at 48 h post radiation. A slightly faster recovery was indicated in the combination group based on cell viability kinetics and viable cell counts, and significantly using colony formation assay. Pan-histone acetyl transferase inhibition using PU139 blocked the reduction in p-p53 and γH2AX activation, suggesting a role for nicotine-induced histone acetylation in enabling rapid DNA repair. Nicotine had a modest effect on reactive oxygen species induction, but tended to increase alpha particle-induced pro-inflammatory IL-6 and IL-1β (4 Gy). Interestingly, nicotine did not alter gamma radiation-induced γH2AX foci. CONCLUSIONS This study provides evidence that nicotine modulates alpha-radiation response by causing a faster but more error-prone repair, as well as rapid recovery, which may allow expansion of cells with genomic instabilities. These results hold implications for estimating radiation risk among nicotine users.
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Affiliation(s)
- Nadia Boroumand
- Centre for Radiation Protection Research, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Sweden
| | - Carol Baghdissar
- Centre for Radiation Protection Research, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Sweden
| | - Karine Elihn
- Department of Environmental Science, Stockholm University, Sweden
| | - Lovisa Lundholm
- Centre for Radiation Protection Research, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Sweden.
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2
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Barr FG. Fusions involving paired box and fork head family transcription factors in the pediatric cancer alveolar rhabdomyosarcoma. Curr Top Microbiol Immunol 1997; 220:113-29. [PMID: 9103678 DOI: 10.1007/978-3-642-60479-9_7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
MESH Headings
- Child
- Chromosomes, Human, Pair 1/genetics
- Chromosomes, Human, Pair 1/ultrastructure
- Chromosomes, Human, Pair 13/genetics
- Chromosomes, Human, Pair 13/ultrastructure
- Chromosomes, Human, Pair 2/genetics
- Chromosomes, Human, Pair 2/ultrastructure
- DNA/genetics
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/physiology
- Forkhead Box Protein O1
- Forkhead Transcription Factors
- Homeodomain Proteins
- Humans
- Muscle Proteins/genetics
- Muscle Proteins/physiology
- Nerve Tissue Proteins/genetics
- Nerve Tissue Proteins/physiology
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/physiology
- PAX3 Transcription Factor
- PAX7 Transcription Factor
- Paired Box Transcription Factors
- Rhabdomyosarcoma, Alveolar/genetics
- Rhabdomyosarcoma, Alveolar/pathology
- Transcription Factors/genetics
- Transcription Factors/physiology
- Translocation, Genetic
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Affiliation(s)
- F G Barr
- Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia 19104-6082, USA
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3
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Nakamura Y. The Japan Society of Human Genetics Award Lecture. Application of DNA markers to clinical genetics. THE JAPANESE JOURNAL OF HUMAN GENETICS 1996; 41:1-10. [PMID: 8914629 DOI: 10.1007/bf01892620] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
DNA technology using DNA sequence polymorphisms has brought a new system to the fields of medicine and forensic science, especially for the studies of genetic diseases and tumor suppressor genes, and for identification of individuals for forensic purpose. Linkage analysis based on segregation of polymorphic alleles in affected families has contributed to identification of many genetic disease. We isolated a large number of polymorphic DNA markers, called VNTR (variable number of tandem repeat) markers and identified the APC gene that is responsible for familial adenomatous polyposis (FAP) by means of a so-called "positional cloning" and characterized germline and somatic mutations of the APC gene in colorectal cancer patients. In addition, we have applied genetic information during colorectal carcinogenesis to sensitive diagnosis of lymph-node metastasis of colorectal cancer.
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Affiliation(s)
- Y Nakamura
- Laboratory of Molecular Medicine, University of Tokyo, Japan
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4
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Plenz G, Kügler S, Schnittger S, Rieder H, Fonatsch C, Müller PK. The human vigilin gene: identification, chromosomal localization and expression pattern. Hum Genet 1994; 93:575-82. [PMID: 8168838 DOI: 10.1007/bf00202827] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Chick vigilin cRNA clones were used to isolate the cognate human gene, by screening a pWE15 genomic library. Three independent cosmid clones were isolated and characterized by restriction mapping. The gene was identified by sequencing an internal EcoRI fragment containing two exons homologous to exon 24 and 25 of the chicken vigilin gene and corresponding to nucleotides 1973-2104 of the human HBP-cDNA. The homology between the chicken and human sequences was 77% and 82% at the cDNA level, and 91% and 100% at the amino acid level. In addition, the analyzed intron/exon boundaries were invariantly conserved. The 5' and 3' regions of the human gene were mapped by Southern analysis of the respective clones with synthetic oligonucleotides. The entire vigilin gene spans a region of about 50 kb and has been assigned to chromosome 2q36-q37.2 (FL-pter value of 0.96 +/- 0.03) by fluorescence in situ hybridization to metaphase spreads from normal peripheral blood lymphocytes. The vigilin gene is localized in a chromosomal region comprising a cluster of collagen genes (COLIVA3, COLVIA3) and the locus of the Waardenburg syndrome I. Only one mRNA species of 4.4 kb is transcribed from the human vigilin gene. In accordance with previous observations on chicken mRNA, the expression of the human vigilin mRNA depends on the stage of cytodifferentiation both in vitro and in situ.
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Affiliation(s)
- G Plenz
- Institut für Medizinische Molekularbiologie, Medizinische Universität zu Lübeck, Germany
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5
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Coon H, Jensen S, Holik J, Hoff M, Myles-Worsley M, Reimherr F, Wender P, Waldo M, Freedman R, Leppert M. Genomic scan for genes predisposing to schizophrenia. AMERICAN JOURNAL OF MEDICAL GENETICS 1994; 54:59-71. [PMID: 7909992 DOI: 10.1002/ajmg.1320540111] [Citation(s) in RCA: 139] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
We initiated a genome-wide search for genes predisposing to schizophrenia by ascertaining 9 families, each containing three to five cases of schizophrenia. The 9 pedigrees were initially genotyped with 329 polymorphic DNA loci distributed throughout the genome. Assuming either autosomal dominant or recessive inheritance, 254 DNA loci yielded lod scores less than -2.0 at theta = 0.0, 101 DNA markers gave lod scores less than -2.0 at theta = 0.05, while 5 DNA loci produced maximum lod scores greater than 1: D4S35, D14S17, D15S1, D22S84, and D22S55. Of the DNA markers yielding lod scores greater than 1, D4S35 and D22S55 also were suggestive of linkage when the Affected-Pedigree-Member method was used. The families were then genotyped with four highly polymorphic simple sequence repeat markers; possible linkage diminished with DNA markers mapping nearby D4S35, while suggestive evidence of linkage remained with loci in the region of D22S55. Although follow-up investigation of these chromosomal regions may be warranted, our linkage results should be viewed as preliminary observations, as 35 unaffected persons are not past the age of risk.
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Affiliation(s)
- H Coon
- Department of Psychiatry, University of Utah Medical Center, Salt Lake City 84132
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6
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Ewart AK, Morris CA, Atkinson D, Jin W, Sternes K, Spallone P, Stock AD, Leppert M, Keating MT. Hemizygosity at the elastin locus in a developmental disorder, Williams syndrome. Nat Genet 1993; 5:11-6. [PMID: 7693128 DOI: 10.1038/ng0993-11] [Citation(s) in RCA: 674] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Williams syndrome (WS) is a developmental disorder affecting connective tissue and the central nervous system. A common feature of WS, supravalvular aortic stenosis, is also a distinct autosomal dominant disorder caused by mutations in the elastin gene. In this study, we identified hemizygosity at the elastin locus using genetic analyses in four familial and five sporadic cases of WS. Fluorescent in situ hybridization and quantitative Southern analyses confirmed these findings, demonstrating inherited and de novo deletions of the elastin gene. These data indicate that deletions involving one elastin allele cause WS and implicate elastin hemizygosity in the pathogenesis of the disease.
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Affiliation(s)
- A K Ewart
- Department of Human Genetics, University of Utah, Salt Lake City 84112
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7
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Antignac C, Arduy CH, Beckmann JS, Benessy F, Gros F, Medhioub M, Hildebrandt F, Dufier JL, Kleinknecht C, Broyer M. A gene for familial juvenile nephronophthisis (recessive medullary cystic kidney disease) maps to chromosome 2p. Nat Genet 1993; 3:342-5. [PMID: 7981755 DOI: 10.1038/ng0493-342] [Citation(s) in RCA: 85] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Familial juvenile nephronophthisis (NPH) is a chronic autosomal recessive kidney disease responsible for 15% of end stage renal failure in children. NPH is frequently (16% of cases) associated with Leber amaurosis (termed Senior-Løken syndrome, SLS). Linkage analyses, performed in 22 multiplex NPH families (18 without and 4 with ocular abnormalities), have localized the gene to a region between D2S48 and D2S51 on chromosome 2p. This was confirmed using adjacent microsatellite markers, one of which (AFM220ze3 at the D2S160 locus) gave a lod score of 4.78 at theta = 0.05 in the 18 families with isolated NPH, whereas the same marker excluded linkage with SLS. These results demonstrate linkage of the purely renal form of NPH to chromosome 2p, and suggest that there may be genetic heterogeneity between NPH and SLS.
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8
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Aschauer HN, Fischer G, Isenberg KE, Meszaros K, Willinger U, Todd RD, Beran H, Strobl R, Lang M, Fuchs K. No proof of linkage between schizophrenia-related disorders including schizophrenia and chromosome 2q21 region. Eur Arch Psychiatry Clin Neurosci 1993; 243:193-8. [PMID: 8117764 DOI: 10.1007/bf02190727] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We examined linkage between schizophrenia and schizophrenia-related disorders and five genetic markers on chromosome 2 in fourteen families ascertained through affected probands in St. Louis and Vienna. The chromosomal region 2q21 was considered a candidate locus for schizophrenia because of a report of a balanced translocation 2;18 (q21;q23) in a schizophrenia family. Linkage analyses were conducted for three disease models: a narrow model including schizophrenia only; an intermediate model including a spectrum of schizophrenia-related disorders; and a broad model including major affective disorders. Multipoint linkage analyses excluded linkage across the region (about 50 cM) for the intermediate disease model. The same was generally true for the broad affection status model. None of the two-point and multipoint analyses showed definite linkage of schizophrenia to any marker. The most prominent positive association was between D2S44 and a broad affection status model, giving a two-point lod score of 1.71 at 0.20 recombination fraction.
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Affiliation(s)
- H N Aschauer
- Department of Psychiatry, University of Vienna, Austria
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9
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Blumenfeld A, Axelrod FB, Trofatter JA, Maayan C, Lucente DE, Slaugenhaupt SA, Liebert CB, Ozelius LJ, Haines JL, Breakefield XO. Exclusion of familial dysautonomia from more than 60% of the genome. J Med Genet 1993; 30:47-52. [PMID: 8093738 PMCID: PMC1016234 DOI: 10.1136/jmg.30.1.47] [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] [Indexed: 01/28/2023]
Abstract
Familial dysautonomia (FD) is a recessive neurological disorder that affects the development of the sensory and autonomic nervous system. The gene defect appears to be limited to the Ashkenazi Jewish population, where the carrier frequency is 1 in 30. One hundred and ninety-one marker loci representing all autosomes were tested for linkage with the FD genetic defect in 23 families. A combination of pairwise and multipoint analyses excluded the FD gene from at least 60% of the autosomal genome. The program EXCLUDE predicted regions of chromosomes 2, 4, 5q, 9, or 10 as the most promising locations for future analyses.
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MESH Headings
- Chromosome Mapping/methods
- Chromosomes, Human, 4-5
- Chromosomes, Human, Pair 10
- Chromosomes, Human, Pair 9
- Dysautonomia, Familial/genetics
- Europe, Eastern/ethnology
- Female
- Genetic Linkage
- Genetic Markers
- Genome, Human
- Humans
- Jews
- Likelihood Functions
- Lod Score
- Male
- New York
- Pedigree
- Polymorphism, Restriction Fragment Length
- Software
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Affiliation(s)
- A Blumenfeld
- Molecular Neurogenetics Laboratory, Massachusetts General Hospital, Boston 02129
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10
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Spurr NK, Cox S, Bryant SP, Attwood J, Robson EB, Shields DC, Steinbrueck T, Jenkins T, Murray JC, Kidd KK. The CEPH consortium linkage map of human chromosome 2. Genomics 1992; 14:1055-63. [PMID: 1478647 DOI: 10.1016/s0888-7543(05)80129-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
This paper describes the Centre d'Etude du Polymorphisme Humain (CEPH) consortium linkage map of chromosome 2. The map contains 36 loci defined by genotyping generated from the CEPH family DNAs. A total of 73 different markers were typed by 14 contributing laboratories; of these, 36 loci are ordered on the map with likelihood support of at least 1000:1. Markers are placed along the length of the chromosome but no markers were available to anchor the map at either telomere or the centromere. Multilocus linkage analysis has produced male, female, and sex-averaged maps extending for 261, 430, and 328 cM, respectively. The sex-averaged map contains five intervals greater than 15 cM and the mean genetic distance between the 36 uniquely placed loci is 9.1 cM.
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Affiliation(s)
- N K Spurr
- Human Genetic Resources Unit, Imperial Cancer Research Fund, Potters Bar, Herts, England
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11
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Barr FG, Holick J, Nycum L, Biegel JA, Emanuel BS. Localization of the t(2;13) breakpoint of alveolar rhabdomyosarcoma on a physical map of chromosome 2. Genomics 1992; 13:1150-6. [PMID: 1505949 DOI: 10.1016/0888-7543(92)90030-v] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A characteristic translocation t(2;13)(q35;q14) has been previously identified in the pediatric soft tissue tumor alveolar rhabdomyosarcoma. We have assembled a panel of lymphoblast, fibroblast, and somatic cell hybrid cell lines with deletions and unbalanced translocations involving chromosome 2 to develop a physical map of the distal 2q region. Twenty-two probes were localized on this physical map by Southern blot analysis of the mapping panel. The position of these probes with respect to the t(2;13) rhabdomyosarcoma breakpoint was then determined by quantitative Southern blot analysis of an alveolar rhabdomyosarcoma cell line with two copies of the derivative chromosome 13 and one copy of the derivative chromosome 2 and by analysis of somatic cell hybrid clones derived from an alveolar rhabdomyosarcoma cell line. We demonstrate that the t(2;13) breakpoint is situated within a map interval delimited by the distal deletion breakpoint in fibroblast line GM09892 and the t(X;2) breakpoint in somatic cell hybrid GM11022. Furthermore, from a comparison of our data with the linkage map of the syntenic region on mouse chromosome 1, we conclude that the t(2;13) breakpoint is most closely flanked by loci INHA and ALPI within this map interval.
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Affiliation(s)
- F G Barr
- Division of Human Genetics and Molecular Biology, Children's Hospital of Philadelphia, Pennsylvania
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12
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Abstract
There are CEPH genetic maps on each homologous human chromosome pair. Genotypes for these maps have been generated in 88 laboratories that receive DNA from a reference panel of large nuclear pedigrees/families supplied by the Centre d'Etude du Polymorphisme Humain. These maps serve as useful tools for the localization of both disease genes and other genes of interest.
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Affiliation(s)
- H M Cann
- Centre d'Etude du Polymorphisme Humain, Paris, France
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13
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Mays PK, Tromp G, Kuivaniemi H, Ryynänen M, Prockop DJ. A 15 base-pair AT-rich variable number tandem repeat in the type III procollagen gene (COL3A1) as an informative marker for 2q31-2q32.3. MATRIX (STUTTGART, GERMANY) 1992; 12:44-9. [PMID: 1560789 DOI: 10.1016/s0934-8832(11)80103-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Segments of repeating DNA, termed variable number tandem repeats, within the genome are often used as polymorphic markers. Here we report such a repeat in the intervening sequence 25 of the type III procollagen gene (COL3A1) located at 2q31-q32.3. The region containing intervening sequence 25 of the COL3A1 gene was amplified using the polymerase chain reaction and the products were analyzed by agarose gel electrophoresis and dideoxynucleotide sequencing. The repeat consisted of an AT-rich unit of 15 base-pairs (ATATATATATGAGAC). Seven different alleles were identified containing between three and nine repeats of the 15 base-pair unit. The allele heterozygosity was 73% in 117 unrelated individuals. The alleles were shown to be inherited in a Mendelian fashion in three large families. This marker should prove useful in linkage studies for COL3A1, and for linkage studies of other genes on the long arm of chromosome 2. The information extends and complements a report on the same repeat recently published by Lee et al. (J. Biol. Chem. 266: 5256, 1991 a).
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Affiliation(s)
- P K Mays
- Department of Biochemistry and Molecular Biology, Jefferson Medical College, Thomas Jefferson University, Philadelphia, PA 19107
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14
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Heliö T, Palotie A, Tötterman KJ, Ott J, Kauppinen-Mäkelin R, Tikkanen MJ. Lack of association between the apolipoprotein B gene 3' hypervariable region alleles and coronary artery disease in Finnish patients with angiographically documented coronary artery disease. J Intern Med 1992; 231:49-57. [PMID: 1732399 DOI: 10.1111/j.1365-2796.1992.tb00498.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Previous studies have suggested that some apolipoprotein B (apoB) 3' variable number of tandem repeats (3'VNTR) locus alleles are associated with coronary artery disease (CAD). We examined the possible association between the apoB 3'VNTR alleles and CAD in 387 Finnish subjects. Using the polymerase chain reaction and polyacrylamide gel electrophoresis, the 3'VNTR genotype was determined in 187 individuals with severe CAD confirmed by coronary angiography (patients), in 121 individuals with normal coronary angiograms (controls), and in 79 apparently healthy subjects (normals). In contrast to previous reports from other populations, the larger apoB 3'VNTR alleles were not significantly more frequent among CAD patients than among controls or normals. In addition, there was no significant association between the 3'VNTR alleles and serum lipid levels in this Finnish population.
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Affiliation(s)
- T Heliö
- First Department of Medicine, University of Helsinki, Finland
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15
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Affiliation(s)
- P D'Eustachio
- Department of Biochemistry, Kaplan Cancer Center, New York University Medical Center, New York 10016
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16
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Yamakawa K, Morita R, Takahashi E, Hori T, Lathrop M, Nakamura Y. A genetic linkage map of 41 restriction fragment length polymorphism markers for human chromosome 3. Genomics 1991; 11:565-72. [PMID: 1685476 DOI: 10.1016/0888-7543(91)90063-k] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A genetic linkage map for human chromosome 3 has been constructed using 41 polymorphic DNA markers genotyped in 40 CEPH reference families. The map spans a genetic distance of 261 cM in males and 413 cM in females; the ratio of these distances (approximately 1.6 in favor of female meioses) was fairly constant across the map. Frequency of recombination was relatively uniform throughout much of the chromosome, except that in both telomeric regions recombination was more frequent than the physical distances would predict. The genetic map was basically in agreement with physical localization of 24 loci that were mapped by fluorescent in situ hybridization. This map can be used for linkage studies for genetic diseases, and it will serve as a step toward a high-resolution map for human chromosome 3.
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Affiliation(s)
- K Yamakawa
- Division of Biochemistry, Cancer Institute, Tokyo, Japan
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17
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Vergnaud G, Mariat D, Apiou F, Aurias A, Lathrop M, Lauthier V. The use of synthetic tandem repeats to isolate new VNTR loci: cloning of a human hypermutable sequence. Genomics 1991; 11:135-44. [PMID: 1765371 DOI: 10.1016/0888-7543(91)90110-z] [Citation(s) in RCA: 98] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Synthetic tandem repeats (STRs) of oligonucleotides have previously been shown to detect polymorphic loci in the human genome. Here, we report results from the use of three such probes to screen a human cosmid library. Nine of the 45 positive clones that were analyzed appear to contain highly polymorphic minisatellite or VNTR loci. The degree of enrichment for minisatellite sequences varied with the choice of STR: one provided a 15- to 20-fold enrichment (4 polymorphic loci among 10 clones), whereas 2 others gave a 3- to 5-fold enrichment (5 polymorphic probes in a total of 35 clones) compared to random screening. The 9 VNTR markers have been localized by linkage analysis in the CEPH panel and/or by in situ hybridization. Eight probes identify new loci, one of which maps to an interstitial region. One of the VNTR loci (identified by probe CEB1) was found to be hypermutable, with 52 mutation events identified among 310 children characterized in 40 CEPH families. The parental origin of the mutation could be identified in all instances, and only one mutation was found to be of maternal origin. The mutation rate in males was estimated to be approximately 15%. Segregation analysis of flanking markers suggests that mutations are not associated with crossing over. As the only previously described hypermutable minisatellite loci in humans have equal rates of male and female mutations, these observations establish that a second type of hypermutable minisatellite exists in the human genome. In neither case does the generation of new alleles appear to be associated with unequal crossing over.
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Affiliation(s)
- G Vergnaud
- Centre d'Etudes du Bouchet, Vert le Petit, France
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18
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Affiliation(s)
- A P Read
- Department of Medical Genetics, University of Manchester, St. Mary's Hospital, United Kingdom
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19
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Affiliation(s)
- P D'Eustachio
- Department of Biochemistry, New York University Medical Center, NY 10016
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20
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Cox DR, Burmeister M, Price ER, Kim S, Myers RM. Radiation hybrid mapping: a somatic cell genetic method for constructing high-resolution maps of mammalian chromosomes. Science 1990; 250:245-50. [PMID: 2218528 DOI: 10.1126/science.2218528] [Citation(s) in RCA: 462] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Radiation hybrid (RH) mapping, a somatic cell genetic technique, was developed as a general approach for constructing long-range maps of mammalian chromosomes. This statistical method depends on x-ray breakage of chromosomes to determine the distances between DNA markers, as well as their order on the chromosome. In addition, the method allows the relative likelihoods of alternative marker orders to be determined. The RH procedure was used to map 14 DNA probes from a region of human chromosome 21 spanning 20 megabase pairs. The map was confirmed by pulsed-field gel electrophoretic analysis. The results demonstrate the effectiveness of RH mapping for constructing high-resolution, contiguous maps of mammalian chromosomes.
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Affiliation(s)
- D R Cox
- Department of Psychiatry, University of California, San Francisco 94143
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21
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Abstract
The human genome has already been the subject of extensive research activity even though the Human Genome Project is only just officially starting. This review and the accompanying wall chart attempt to provide an integrated, quantitative, and detailed summary of the status of knowledge on the human genome in mid-1990. The analysis has highlighted the rudimentary nature of many of the information links needed for the task. While this overview could not be fully comprehensive and required simplifying assumptions, the results have provided estimates of relative progress on a region-by-region basis throughout the genome.
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Affiliation(s)
- J C Stephens
- Laboratory of Viral Carcinogenesis, National Cancer Institute, Frederick, MD 21701
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22
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Abstract
Genetic mapping provides a means of understanding the molecular basis of inherited diseases whose biochemistry is unknown. Adequate pedigrees, informative genetic markers, and accurate identification of the disease phenotype are necessary. For dominant inheritance, mapping studies can be done in a single large pedigree; the larger the number of affected individuals sampled the better the estimate of recombination between the gene causing the disease and one or more nearby genetic markers. For recessive inheritance, nuclear families with more than one affected sibling provide the best information. The development of many polymorphic DNA markers on the human genome has contributed to the success of mapping unknown genes because, as the genome is now densely covered with markers, the probability is good that at least one marker will be linked to the disease locus in a family that is segregating a disease allele. Most genetic markers now in use depend upon restriction fragment length polymorphisms (RFLPs), which are either the result of single-base-pair substitution or the presence of a variable number of tandemly repeated oligonucleotide units at a locus (VNTRs). RFLPs can be recognized by digesting DNA with restriction enzymes and separating the fragments by size on an electrophoretic gel. VNTRs can vary widely among individuals, and they provide more linkage information than single-site polymorphic markers because family members are more likely to be heterozygous. Genetic maps of each chromosome, constructed from linkage data relating marker loci to one another in normal reference families, permit rational choices of markers for disease-mapping studies.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- M F Leppert
- Howard Hughes Medical Institute, University of Utah, Salt Lake City 84132
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Julier C, Nakamura Y, Lathrop M, O'Connell P, Leppert M, Mohandas T, Lalouel JM, White R. A primary map of 24 loci on human chromosome 16. Genomics 1990; 6:419-27. [PMID: 2328986 DOI: 10.1016/0888-7543(90)90471-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A primary genetic map of chromosome 16 has been constructed by linkage analysis of 24 polymorphic loci, typed in 59 reference families. These loci form a continuous map that covers the whole chromosome and spans genetic distances of 187 cM in males and 226 cM in females. Most of the sex-specific recombination rate difference comes from a nontelomeric region that covers 10 cM in males and 74 cM in females. Both telomeric regions show the opposite trend, with a significant increase in the male recombination rate.
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Affiliation(s)
- C Julier
- Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City 84132
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24
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Nakamura Y, Leppert M, O'Connell P, Lathrop M, Lalouel JM, White R. A genetic linkage map of markers for human chromosome 20. Genomics 1989; 5:945-7. [PMID: 2591973 DOI: 10.1016/0888-7543(89)90139-0] [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: 01/01/2023]
Abstract
A continuous genetic linkage map with five polymorphic DNA markers, including one that defines a locus containing a variable number of tandem repeats (VNTR), has been constructed from genotypic analysis of 59 large reference families. The map spans a genetic distance of 105 cM in males and 115 cM in females and provides initial anchor points for a high-resolution map of human chromosome 20.
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Affiliation(s)
- Y Nakamura
- Howard Hughes Medical Institute, University of Utah Medical School, Salt Lake City 84132
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