201
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Wijmenga C, Hansen RS, Gimelli G, Björck EJ, Davies EG, Valentine D, Belohradsky BH, van Dongen JJ, Smeets DF, van den Heuvel LP, Luyten JA, Strengman E, Weemaes C, Pearson PL. Genetic variation in ICF syndrome: evidence for genetic heterogeneity. Hum Mutat 2000; 16:509-17. [PMID: 11102980 DOI: 10.1002/1098-1004(200012)16:6<509::aid-humu8>3.0.co;2-v] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
ICF syndrome is a rare autosomal recessive immunoglobulin deficiency, sometimes combined with defective cellular immunity. Other features that are frequently observed in ICF syndrome patients include facial dysmorphism, developmental delay, and recurrent infections. The most diagnostic feature of ICF syndrome is the branching of chromosomes 1, 9, and 16 due to pericentromeric instability. Positional candidate cloning recently discovered the de novo DNA methyltransferase 3B (DNMT3B) as the responsible gene by identifying seven different mutations in nine ICF patients. DNMT3B specifically methylates repeat sequences adjacent to the centromeres of chromosome 1, 9, and 16. Our panel of 14 ICF patients was subjected to mutation analysis in the DNMT3B gene. Mutations in DNMT3B were discovered in only nine of our 14 ICF patients. Moreover, two ICF patients from consanguineous families who did not show autozygosity (i.e. homozygosity by descent) for the DNMT3B locus did not reveal DNMT3B mutations, suggesting genetic heterogeneity for this disease. Mutation analysis revealed 11 different mutations, including seven novel ones: eight different missense mutations, two different nonsense mutations, and a splice-site mutation leading to the insertion of three aa's. The missense mutations occurred in or near the catalytic domain of DNMT3B protein, indicating a possible interference with the normal functioning of the enzyme. However, none of the ICF patients was homozygous for a nonsense allele, suggesting that absence of this enzyme is not compatible with life. Compound heterozygosity for a missense and a nonsense mutation did not seem to correlate with a more severe phenotype.
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Affiliation(s)
- C Wijmenga
- Department of Medical Genetics, University Medical Center Utrecht, The Netherlands
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202
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Miano MG, Jacobson SG, Carothers A, Hanson I, Teague P, Lovell J, Cideciyan AV, Haider N, Stone EM, Sheffield VC, Wright AF. Pitfalls in homozygosity mapping. Am J Hum Genet 2000; 67:1348-51. [PMID: 11007652 PMCID: PMC1288578 DOI: 10.1016/s0002-9297(07)62966-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2000] [Accepted: 09/11/2000] [Indexed: 11/26/2022] Open
Abstract
There is much interest in use of identity-by-descent (IBD) methods to map genes, both in Mendelian and in complex disorders. Homozygosity mapping provides a rapid means of mapping autosomal recessive genes in consanguineous families by identifying chromosomal regions that show homozygous IBD segments in pooled samples. In this report, we point out some potential pitfalls that arose during the course of homozygosity mapping of the enhanced S-cone syndrome gene, resulting from (1) unexpected allelic heterogeneity, so that the region containing the disease locus was missed as a result of pooling; (2) identification of a homozygous IBD region unrelated to the disease locus; and (3) the potential for inflation of LOD scores as a result of underestimation of the extent of inbreeding, which Broman and Weber suggest may be quite common.
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Affiliation(s)
- M G Miano
- MRC Human Genetics Unit, Western General Hospital, Edinburgh, UK
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203
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Goldberg EK, Glendening JM, Karanjawala Z, Sridhar A, Walker GJ, Hayward NK, Rice AJ, Kurera D, Tebha Y, Fountain JW. Localization of multiple melanoma tumor-suppressor genes on chromosome 11 by use of homozygosity mapping-of-deletions analysis. Am J Hum Genet 2000; 67:417-31. [PMID: 10877980 PMCID: PMC1287213 DOI: 10.1086/302999] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2000] [Accepted: 05/31/2000] [Indexed: 11/03/2022] Open
Abstract
Loss-of-heterozygosity (LOH) studies have implicated one or more chromosome 11 tumor-suppressor gene(s) in the development of cutaneous melanoma as well as a variety of other forms of human cancer. In the present study, we have identified multiple independent critical regions on this chromosome by use of homozygosity mapping of deletions (HOMOD) analysis. This method of analysis involved the use of highly polymorphic microsatellite markers and statistics to identify regions of hemizygous deletion in unmatched melanoma cell line DNAs. Regions of loss were defined by the presence of an extended region of homozygosity (ERH) at > or =5 adjacent markers and having a statistical probability of < or =.001. Significant ERHs were similar in nature to deletions identified by LOH analyses performed on uncultured melanomas, although a higher frequency of loss (24 [60%] of 40 vs. 16 [34%] of 47) was observed in the cell lines. Overall, six small regions of overlapping deletions (SROs) were identified on chromosome 11 flanked by the markers D11S1338/D11S907 (11p13-15.5 [SRO1]), D11S1344/D11S11385 (11p11.2 [SRO2]), D11S917/D11S1886 (11q21-22.3 [SRO3]), D11S927/D11S4094 (11q23 [SRO4]), AFM210ve3/D11S990 (11q24 [SRO5]), and D11S1351/D11S4123 (11q24-25 [SRO6]). We propose that HOMOD analysis can be used as an adjunct to LOH analysis in the localization of tumor-suppressor genes.
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Affiliation(s)
- Eleonora K. Goldberg
- Institute for Genetic Medicine, Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles; and Queensland Cancer Fund Research Unit, Joint Experimental Oncology Program of the Queensland Institute of Medical Research and the University of Queensland, Royal Brisbane Hospital, Herston, Australia
| | - J. Michael Glendening
- Institute for Genetic Medicine, Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles; and Queensland Cancer Fund Research Unit, Joint Experimental Oncology Program of the Queensland Institute of Medical Research and the University of Queensland, Royal Brisbane Hospital, Herston, Australia
| | - Zarir Karanjawala
- Institute for Genetic Medicine, Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles; and Queensland Cancer Fund Research Unit, Joint Experimental Oncology Program of the Queensland Institute of Medical Research and the University of Queensland, Royal Brisbane Hospital, Herston, Australia
| | - Anjali Sridhar
- Institute for Genetic Medicine, Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles; and Queensland Cancer Fund Research Unit, Joint Experimental Oncology Program of the Queensland Institute of Medical Research and the University of Queensland, Royal Brisbane Hospital, Herston, Australia
| | - Graeme J. Walker
- Institute for Genetic Medicine, Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles; and Queensland Cancer Fund Research Unit, Joint Experimental Oncology Program of the Queensland Institute of Medical Research and the University of Queensland, Royal Brisbane Hospital, Herston, Australia
| | - Nicholas K. Hayward
- Institute for Genetic Medicine, Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles; and Queensland Cancer Fund Research Unit, Joint Experimental Oncology Program of the Queensland Institute of Medical Research and the University of Queensland, Royal Brisbane Hospital, Herston, Australia
| | - Andrew J. Rice
- Institute for Genetic Medicine, Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles; and Queensland Cancer Fund Research Unit, Joint Experimental Oncology Program of the Queensland Institute of Medical Research and the University of Queensland, Royal Brisbane Hospital, Herston, Australia
| | - Devinda Kurera
- Institute for Genetic Medicine, Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles; and Queensland Cancer Fund Research Unit, Joint Experimental Oncology Program of the Queensland Institute of Medical Research and the University of Queensland, Royal Brisbane Hospital, Herston, Australia
| | - Yasmine Tebha
- Institute for Genetic Medicine, Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles; and Queensland Cancer Fund Research Unit, Joint Experimental Oncology Program of the Queensland Institute of Medical Research and the University of Queensland, Royal Brisbane Hospital, Herston, Australia
| | - Jane W. Fountain
- Institute for Genetic Medicine, Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles; and Queensland Cancer Fund Research Unit, Joint Experimental Oncology Program of the Queensland Institute of Medical Research and the University of Queensland, Royal Brisbane Hospital, Herston, Australia
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204
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Broman KW, Weber JL. Characterization of human crossover interference. Am J Hum Genet 2000; 66:1911-26. [PMID: 10801387 PMCID: PMC1378063 DOI: 10.1086/302923] [Citation(s) in RCA: 115] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2000] [Accepted: 03/24/2000] [Indexed: 11/04/2022] Open
Abstract
We present an analysis of crossover interference over the entire human genome, on the basis of genotype data from more than 8,000 polymorphisms in eight CEPH families. Overwhelming evidence was found for strong positive crossover interference, with average strength lying between the levels of interference implied by the Kosambi and Carter-Falconer map functions. Five mathematical models of interference were evaluated: the gamma model and four versions of the count-location model. The gamma model fit the data far better than did any of the other four models. Analysis of intercrossover distances was greatly superior to the analysis of crossover counts, in both demonstrating interference and distinguishing between the five models. In contrast to earlier suggestions, interference was found to continue uninterrupted across the centromeres. No convincing differences in the levels of interference were found between the sexes or among chromosomes; however, we did detect possible individual variation in interference among the eight mothers. Finally, we present an equation that provides the probability of the occurrence of a double crossover between two nonrecombinant, informative polymorphisms.
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Affiliation(s)
- K W Broman
- Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21205, USA.
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205
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Salzano FM. Permanence or change? The meaning of genetic variation. Proc Natl Acad Sci U S A 2000; 97:5317-21. [PMID: 10805790 PMCID: PMC25826 DOI: 10.1073/pnas.97.10.5317] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/17/2000] [Indexed: 11/18/2022] Open
Abstract
Selected aspects of the evolutionary process and more specifically of the genetic variation are considered, with an emphasis in studies performed by my group. One key aspect of evolution seems to be the concomitant occurrence of dichotomic, contradictory (dialect) processes. Genetic variation is structured, and the dynamics of change at one level is not necessarily paralleled by that in another. The pathogenesis-related protein superfamily can be cited as an example in which permanence (the maintenance of certain key genetic features) coexists with change (modifications that led to different functions in different classes of organisms). Relationships between structure and function are exemplified by studies with hemoglobin Porto Alegre. The genetic structure of tribal populations may differ in important aspects from that of industrialized societies. Evolutionary histories also may differ when considered through the investigation of patrilineal or matrilineal lineages. Global evaluations taking into consideration all of these aspects are needed if we really want to understand the meaning of genetic variation.
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Affiliation(s)
- F M Salzano
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Caixa Postal 15053, 91501-970 Porto Alegre, RS, Brazil.
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