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Silva-Fernandes IJDL, Oliveira ESD, Santos JC, Ribeiro ML, Ferrasi AC, Pardini MIDMC, Burbano RMR, Rabenhorst SHB. The intricate interplay between MSI and polymorphisms of DNA repair enzymes in gastric cancer H.pylori associated. Mutagenesis 2017; 32:471-478. [DOI: 10.1093/mutage/gex013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 04/24/2017] [Indexed: 12/15/2022] Open
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Li JH, Shi XZ, Lv S, Liu M, Xu GW. Effect of Helicobacter pylori infection on p53 expression of gastric mucosa and adenocarcinoma with microsatellite instability. World J Gastroenterol 2005; 11:4363-6. [PMID: 16038035 PMCID: PMC4434663 DOI: 10.3748/wjg.v11.i28.4363] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2004] [Revised: 12/01/2004] [Accepted: 12/03/2004] [Indexed: 02/06/2023] Open
Abstract
AIM To investigate the relationship between Helicobacter pylori (H pylori) infection, microsatellite instability and the expressions of the p53 in gastritis, intestinal metaplasia and gastric adenocarcinoma and to elucidate the mechanism of gastric carcinogenesis relating to H pylori infection. METHODS One hundred and eight endoscopic biopsies and gastric adenocarcinoma were available for the study including 33 cases of normal, 45 cases of gastritis, 30 cases of intestinal metaplasia, and 46 cases of gastric adenocarcinoma. Peripheral blood samples of these patients were also collected. H pylori infection and p53 expressions were detected by means of streptavidin-peroxidase (SP) immunohistochemical method. Microsatellite loci were studied by PCR-SSCP-CE using the markers BAT-26, D17S261, D3S1283, D2S123, and D3S1611. MSI was defined as the peak shift in the DNA of the gastric tissue compared with that of the peripheral blood samples. Based on the number of mutated MSI markers, specimens were characterized as high MSI (MSI-H) if they manifested instability at two or more markers, low MSI (MSI-L) if unstable at only one marker, and microsatellite stable (MSS) if they showed no instability at any marker. RESULTS H pylori infection was detected in the samples of gastritis, intestinal metaplasia, and gastric adenocarcinoma and the infection frequencies were 84.4%, 76.7%, and 65.2%, respectively, whereas no H pylori infection was detected in the samples of normal control. There was a significant difference in the infection rates between gastritis and carcinoma samples (P = 0.035). No MSI was detected in gastritis samples, one MSI-H and two MSI-L were detected among the 30 intestinal metaplasia samples, and 12 MSI-H and 3 MSI-L were detected in the 46 gastric carcinomas. In those gastric carcinomas, the MSI-H frequency in H pylori-positive group was significantly higher than that in H pylori-negative group. No p53 expression was detected in the normal and gastritis samples from dyspeptic patients. P53-positive immunohistochemical staining was detected in 13.3% of intestinal metaplasia samples and in 43.5% of gastric carcinoma samples. The levels of p53 in H pylori-positive samples were higher than those in the negative group when the carcinoma samples were subdivided into H pylori-positive and -negative groups (P = 0.013). Eight samples were detected with positive p53 expression out of the 11 MSI-H carcinomas with H pylori infection and no p53 expression could be seen in the H pylori-negative samples. CONCLUSION H pylori affect the p53 pattern in gastric mucosa when MMR system fails to work. Mutations of the p53 gene seem to be an early event in gastric carcinogenesis.
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Affiliation(s)
- Jian-Hua Li
- Laboratory Center of Molecular Biology, the Second Hospital of Dalian Medical University, Dalian 116027, Liaoning Province, China.
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Furitsu K, Ryo H, Yeliseeva KG, Thuy LTT, Kawabata H, Krupnova EV, Trusova VD, Rzheutsky VA, Nakajima H, Kartel N, Nomura T. Microsatellite mutations show no increases in the children of the Chernobyl liquidators. Mutat Res 2005; 581:69-82. [PMID: 15725606 DOI: 10.1016/j.mrgentox.2004.11.002] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2004] [Revised: 11/08/2004] [Accepted: 11/08/2004] [Indexed: 05/01/2023]
Abstract
We performed a study on Belarusian "liquidators", exploring whether increase in the frequencies of germline mutations at microsatellite loci could be found in their progeny. The liquidators, mostly young males, were those involved (during 1986 and 1987) in clean-up operations in the radioactively contaminated area following the Chernobyl nuclear power plant accident in 1986. Many liquidators fathered children during the clean-up period and after the work had been terminated. The numbers of families studied were 64 (liquidators) and 66 (controls). A total of 72 loci (31 autosomal, one X-linked and 40 Y-linked) were used. DNA was isolated from peripheral blood lymphocytes and the microsatellite loci were amplified by the polymerase chain reaction with fluorescence-labelled primers. Mutations were detected as variations in the length of the loci. At the Y-linked loci, the mutation rates (expressed as number of mutations among the total number of loci for the individuals included) are 2.9 x 10(-3) (4/1392) and 2.1 x 10(-3) (3/1458) in the children of exposed and control parents, respectively. This difference is not statistically significant. At the autosomal loci, the corresponding estimates are 5.9 x 10(-3) (11/1862; exposed group) and 8.5 x 10(-3) (18/2108; control). Again, the difference is not significant. The possibility that the Belarusian population might have been unexpectedly exposed to some chemical contaminants in the environment appears unlikely in view of the finding that the spontaneous mutation rates at the same set of loci in several non-Belarusian populations were similar to those in Belarus. The estimated mean radiation dose to the liquidators was small, being about 39 mSv, and this might be one reason why no increases in mutation rates due to radiation could be found.
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Affiliation(s)
- Katsumi Furitsu
- Department of Radiation Biology and Medical Genetics, Graduate School of Medicine, Osaka University, B4, 2-2, Yamada-oka, Suita, Osaka 565-0871, Japan
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Li JH, Shi XZ, Lv S, Liu M, Wang ZH, Liu LN, Jiang J, Xu GW. Microsatellite instability and loss of mismatch-repair protein expression in gastric carcinoma. Shijie Huaren Xiaohua Zazhi 2004; 12:1774-1777. [DOI: 10.11569/wcjd.v12.i8.1774] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To detect the microsatellite instability (MSI) and expression of mismatch repair (MMR) gene in gastric cancinoma, and to explore the molecular biological mechanism underlying the carcinogenesis of gastric cancinoma.
METHODS: A total of 56 cases of gastric cancinomas and surrounding non-cancerous tissues from surgical excision samples were collected, among which 22 cases were well and 34 cases were poorly differentiated adenocarcinoma, 20 cases were in early stage and 36 cases were in advanced stage of the disease. The microsatellite locus of BAT-26, D17S261, D3S1283, D2S123 and D3S1611 were amplified by PCR after DNA abstraction. Then PCR products were mixed together with GeneScan 500 size standard followed by heat denaturation. Microsatellites were analyzed by capillary electrophoresis with 6% SLPA and 8 moL/L-1 urea as sieving medium. Carcinoma were characterized as high MSI (MSI-H) if they manifested instability at two or more markers, low MSI (MSI-L) if unstable at only one marker, and microsatellite stable (MSS) if they showed no instability at any marker. Expression of MMR gene hMLH1 and hMSH2 were detected by immunohistochimical staining using the streptavidin-biotin-peroxidase complex method with 3, 3-diaminobenzidine as chromogen.
RESULTS: Of the 56 cases of gastric carcinomas, 14 cases (25%) showed MSI-H and 14 cases (25%) showed loss of MMR. In the 14 cases of the MSI, 11 cases (79%) were accompanied by loss of hMLH1/hMSH2 expression, whereas In the 42 cases of the MSI-L/MSS, only 3 cases (7%) were accompanied by loss of hMLH1/hMSH2 expression. MSI was significantly related with mismatch repair deficiency (P < 0.01). Of the 22 cases of well-differentiated carcinomas, 7 cases (32%) manifested MSI-H and 6 (27%) cases showed protein defection of MMR, Com-paratively, 7 cases (21%) manifested MSI-H and 8 cases (24%) showed protein defection of MMR in 34 cases poorly-differentiated carcinomas. Of the 20 cases early stage carcinomas, only 1 cases (5%) manifested MSI-H and 3 (15%) cases showed protein defection of MMR, whereas 13 cases (36%) manifested MSI-H and 11 cases (31%) showed protein defection of MMR in 36 cases advanced carcinomas. The MSI frequency was higher in advanced stage (36%) than that in early stage (5%) of gastric carcinoma and the difference was significant (P < 0.05), but no difference between well and poorly differentiated gastric carcinoma. The difference of loss frequency of hMLH1/hMSH2 expression was not significant in different stage and different differentiation of gastric carcinoma.
CONCLUSION: The defect of mismatch repair may be involved in the carcinogenesis of a subset of gastric cancer but not in the biologic behavior. MSI frequency increases with the progression of gastric carcinoma.
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Abstract
Increasing evidence suggests that human tumors sequentially accumulate multiple mutations that cannot be explained by the low rates of spontaneous mutations in normal cells (2-3 mutations/cell). The mathematical models estimate that for the solid tumors to develop, as many as 6-12 mutations are required in each tumor cell. Therefore, to account for such high mutation rates, it is proposed that tumor cells are genetically unstable, i.e. they have genome-wide mutations at short repetitive DNA sequences called microsatellites. Microsatellite repeats are scattered throughout the human genome, primarily in the non-coding regions, and can give rise to variants with increased or reduced lengths, i.e. microsatellite instability (MSI). This instability has been reported in an increasing number of cutaneous tumors including: melanocytic tumors, basal cell carcinomas and primary cutaneous T-cell lymphomas. Moreover, MSI has been observed in skin tumors arising in the context of some hereditary disorders such as Muir-Torre syndrome, Von Recklinghausen's disease and disseminated superficial porokeratosis. While MSI in some of these disorders reflects underlying DNA replication errors, the mechanism of instability in others is still unknown. Thus far, MSI is considered to be a distinct tumorigenic pathway that reveals surprising versatility. The ramifications for cutaneous neoplasms warrant further investigation.
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Affiliation(s)
- Mahmoud R Hussein
- The Department of Medicine (Dermatology), University of Wisconsin and William S. Middleton Memorial Veteran Hospital, Madison, WI 53705, USA
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Abstract
Mismatch repair (MMR) defects and microsatellite instability (MSI) are two genetic alterations that have been documented in a wide variety of human cancers, including some that involve the skin. Available evidence indicates that these two features are sometimes directly related, although their connection seems to be indirect or nonexistent in other instances. The purposes of this review are to summarize the variable relations between MMR and MSI as deduced from analysis of a diverse array of human neoplasms and to give brief insights as to the other molecular mechanisms potentially involved in the maintenance of genomic stability.
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Affiliation(s)
- Mahmoud R Hussein
- Department of Medicine (Dermatology), University of Wisconsin and William S. Middleton Memorial Veteran Hospital, Madison, Wisconsin 53705, USA
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Martins C, Kedda MA, Kew MC. Characterization of six tumor suppressor genes and microsatellite instability in hepatocellular carcinoma in southern African blacks. World J Gastroenterol 1999; 5:470-476. [PMID: 11819494 PMCID: PMC4688788 DOI: 10.3748/wjg.v5.i6.470] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To analyse cumulative loss of heterozygosity (LOH) of ch romosomal regions and tumor suppressor genes in hepatocellular carcinomas (HCCs) from 20 southern African blacks.
METHODS: p53, RB1, BRCA1, BRCA2, WT1 and E-cadherin- ge nes were analysed for LOH, and p53 gene was also analysed for the codon 249 mutation, in tumor and adjacent non-tumorous liver tissues using molecular techniques and 10 polymorphic microsatellite markers.
RESULTS: p53 codon 249 mutation was found in 25% of the subjects, as was expected, because many patients were from Mozambique, a country wit h high aflatoxin B1 exposure. LOH was found at the RB1, BRCA2 and WT1 loci in 20%(4/20) of the HCCs, supporting a possible role of these genes in HCC. No LOH was evident in any of the remaining genes. Reports of mutations of p53 and RB1 genes in combination, described in other populations, were not confirmed in this study. Change in microsatellite repeat number was noted at 9/10 microsatellite loci in different HCCs, and changes at two or more loci were detected in 15%(3/20) of subjects.
CONCLUSION: We propose that microsatellite/genomic instability may play a role in the pathogenesis of a subset of HCCs in black Africans.
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Yhap M, Pyesmany AF, Ball LM, Riddle DC, Mu J, van Velzen D. Microsatellite instability assessment in prediction of drug resistance in childhood Burkitt's and large cell diffuse malignant non-Hodgkin lymphoma (MNHL). ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 1999; 457:517-25. [PMID: 10500829 DOI: 10.1007/978-1-4615-4811-9_56] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
BACKGROUND Genomic instability may, especially with DNA directed treatment, be associated with increased therapeutic response; absence may be associated with drug resistance. In childhood MNHL, drug response is variable. At present the degree of presence of microsatellite variation, i.e., intrinsic DNA instability is not known. AIMS To determine presence and range of microsatellite variability in common childhood MNHL. METHODS 1.3.1. Study Populations. Consecutive, unselected (1976-96) cases of childhood Large Cell diffuse, N = 16; (9T,7B), age range 1y5m-16y8m; Burkitt's Lymphoma, n = 13, age range 4y2m-14y. Non-malignant/pre-treatment tissue of 20 cases, 13 LC, 7 Burkitt's MNHL. 1.3.2. Molecular Pathology. Routine DNA extraction, amplifications at loci D3S 1304 and D3S1537 (both closely distal to VHL, tumour suppressor gene); ELN gene D7S1870; IFNA D1S243 (1p36) which show microsatellite variation. Isotopic labelling in amplification, non-denaturing gel electrophoresis, autoradiography. RESULTS Microsatellite variability was found 3/16 LC and 2/13 Burkitt's MNHL. LC MNHL, 4 abnormal areas: n = 1, 3 abnormal areas: n = 1, 2 abnormal areas n = 1; Burkitt's MNHL, 3 abnormal areas: n = 1, 1 abnormal area n = 1. No variability was found in the normal (constitutional) DNA of any of the 20 patients studied. CONCLUSIONS Microsatellite variability occurred in 5/29 patients with common types of childhood MNHL, indicating a limited contribution to reduced drug resistance through this mechanism.
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Affiliation(s)
- M Yhap
- Department of Clinical Haemato-Oncology, Dalhousie University, IWK Grace Health Centre
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Latil A, Bièche I, Pesche S, Volant A, Valèri A, Fournier G, Cussenot O, Lidereau R. Loss of heterozygosity at chromosome arm 13q and RB1 status in human prostate cancer. Hum Pathol 1999; 30:809-15. [PMID: 10414500 DOI: 10.1016/s0046-8177(99)90142-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Aberrations of the long arm of chromosome 13 are common in prostate cancer and were initially attributed to alterations of the RB1 gene in band q14 of the chromosome. However, prostate tumors generally yield normal p110RB1 nuclear staining despite loss of heterozygosity (LOH) at the RB1 locus. Our previous analysis of chromosome arm 13q showed allelic loss in 41% of primary prostate tumors. To refine our knowledge of 13q, we extended our previous LOH study by using more polymorphic markers to analyze more prostate tumors. Sixty human prostate carcinomas were screened for allelic loss on 13q by using 13 13q-specific markers. LOH on the long arm of chromosome 13 was found in 39 (65%) of the 60 tumors. Furthermore, 33 of these 39 tumors had evidence of allelic loss involving a region of 13q14 containing RB1. Because immunohistochemical assessment of pRb expression is controversial in prostate tumors, we used a quantitative reverse transcription polymerase chain reaction (RT-PCR) method to determine whether RB1 is the target tumor suppressor gene in this region. RB1 mRNA steady-state levels were determined in 12 prostate tumors preselected on the basis of presumed deletion at the RB1 locus and four prostate tumors without LOH at the RB1 locus; five normal prostate specimens were used as controls. One of the 12 assessable prostate tumors with presumed LOH at RB1 showed a corresponding decreased in RB1 mRNA expression, whereas none of the four tumors without LOH at RB1 locus showed such a decrease. This study, based on another technical approach, confirms that RB1 is not the main target of the observed LOH at 13q14.3, and raises the possibility that another tumor suppressor gene in this region plays a key role in prostate cancer.
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Affiliation(s)
- A Latil
- Laboratoire d'Oncogénétique, Centre René Huguenin, St Cloud, France
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Hoffman SM, Lai KS, Tomfohrde J, Bowcock A, Gordon LA, Mohrenweiser HW. JAK3 maps to human chromosome 19p12 within a cluster of proto-oncogenes and transcription factors. Genomics 1997; 43:109-11. [PMID: 9226382 DOI: 10.1006/geno.1997.4792] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- S M Hoffman
- Human Genome Center, Lawrence Livermore National Laboratory, Livermore, California 94550, USA.
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Chakraborty R, Kimmel M, Stivers DN, Davison LJ, Deka R. Relative mutation rates at di-, tri-, and tetranucleotide microsatellite loci. Proc Natl Acad Sci U S A 1997; 94:1041-6. [PMID: 9023379 PMCID: PMC19636 DOI: 10.1073/pnas.94.3.1041] [Citation(s) in RCA: 258] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/1996] [Accepted: 11/25/1996] [Indexed: 02/03/2023] Open
Abstract
Using the generalized stepwise mutation model, we propose a method of estimating the relative mutation rates of microsatellite loci, grouped by the repeat motif. Applying ANOVA to the distributions of the allele sizes at microsatellite loci from a set of populations, grouped by repeat motif types, we estimated the effect of population size differences and mutation rate differences among loci. This provides an estimate of motif-type-specific mutation rates up to a multiplicative constant. Applications to four different sets of di-, tri-, and tetranucleotide loci from a number of human populations reveal that, on average, the non-disease-causing microsatellite loci have mutation rates inversely related to their motif sizes. The dinucleotides appear to have mutation rates 1.5-2 times higher than the tetranucleotides, and the non-disease-causing trinucleotides have mutation rates intermediate between the di- and tetranucleotides. In contrast, the disease-causing trinucleotides have mutation rates 3.9-6.9 times larger than the tetranucleotides. Comparison of these estimates with the direct observations of mutation rates at microsatellites indicates that the earlier suggestion of higher mutation rates of tetranucleotides in comparison with the dinucleotides may stem from a nonrandom sampling of tetranucleotide loci in direct mutation assays.
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Affiliation(s)
- R Chakraborty
- Human Genetics Center, University of Texas Health Science Center, Houston 77225, USA
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Schug MD, Mackay TF, Aquadro CF. Low mutation rates of microsatellite loci in Drosophila melanogaster. Nat Genet 1997; 15:99-102. [PMID: 8988178 DOI: 10.1038/ng0197-99] [Citation(s) in RCA: 166] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Analysis of variation at microsatellite DNA loci is widely used in studies of parentage, linkage and evolutionary history. The utility of microsatellites is primarily due to high levels of allelic diversity, believed to reflect mutation rates orders of magnitude higher than base pair substitutions at single-copy genes. For humans, mice, rats and pigs, microsatellite mutation rates have been estimated at 10(-3)-10(-5). However, a recent study comparing microsatellite variation in humans with non-human primates suggests that microsatellite mutation rates may vary considerably across taxa. We measured mutation rates of 24 microsatellite loci in mutation accumulation lines of Drosophila melanogaster. Surprisingly, only a single mutation was detected after screening 157,680 allele-generations, yielding an estimated average mutation rate per locus of 6.3 x 10(-6), a mutation rate considerably lower than reported for various mammals. We propose that the comparatively low mutation rate is primarily a function of short microsatellite repeat lengths in the D. melanogaster genome.
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Affiliation(s)
- M D Schug
- Section of Genetics and Development, Cornell University, Ithaca, New York 14853, USA
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Jin L, Macaubas C, Hallmayer J, Kimura A, Mignot E. Mutation rate varies among alleles at a microsatellite locus: phylogenetic evidence. Proc Natl Acad Sci U S A 1996; 93:15285-8. [PMID: 8986803 PMCID: PMC26396 DOI: 10.1073/pnas.93.26.15285] [Citation(s) in RCA: 92] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The understanding of the mutational mechanism that generates high levels of variation at microsatellite loci lags far behind the application of these genetic markers. A phylogenetic approach was developed to study the pattern and rate of mutations at a dinucleotide microsatellite locus tightly linked to HLA-DQB1 (DQCAR). A random Japanese population (n = 129) and a collection of multiethnic samples (n = 941) were typed at the DQB1 and DQCAR loci. The phylogeny of DQB1 alleles was then reconstructed and DQCAR alleles were superimposed onto the phylogeny. This approach allowed us to group DQCAR alleles that share a common ancestor. The results indicated that the DQCAR mutation rate varies drastically among alleles within this single microsatellite locus. Some DQCAR alleles never mutated during a long period of evolutionary time. Sequencing of representative DQCAR alleles showed that these alleles lost their ability to mutate because of nucleotide substitutions that shorten the length of uninterrupted CA repeat arrays; in contrast, all mutating alleles had relatively longer perfect CA repeat sequences.
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Affiliation(s)
- L Jin
- Department of Genetics, Stanford University, CA 94305, USA
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Schneider AS, Bischoff FZ, McCaskill C, Coady ML, Stopfer JE, Shaffer LG. Comprehensive 4-year follow-up on a case of maternal heterodisomy for chromosome 16. AMERICAN JOURNAL OF MEDICAL GENETICS 1996; 66:204-8. [PMID: 8958332 DOI: 10.1002/(sici)1096-8628(19961211)66:2<204::aid-ajmg16>3.0.co;2-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Uniparental disomy for chromosome 16 has been previously identified in fetal deaths and newborn infants with limited follow-up. Thus there is a lack of information about the long-term effects of maternal uniparental disomy 16 on growth and development. We present a case of maternal heterodisomy for chromosome 16 and a comprehensive 4-year physical and cognitive evaluation. Cytogenetic analysis of chorionic villus obtained at 10 weeks gestation for advanced maternal age showed trisomy 16. At 15 weeks, amniocentesis demonstrated low level mosaicism 47,XY,+16[1]/46,XY[25]. Decreased fetal growth was noted in the last 2 months of pregnancy and the infant was small for gestational age at birth. Molecular studies revealed only maternal alleles for chromosome 16 in a peripheral blood sample from the child, consistent with maternal uniparental heterodisomy 16. Although short stature remains a concern, there appears to be no major cognitive effects of maternal disomy 16. Clinical evaluation and follow-up on additional cases should further clarify the role of placental mosaicism and maternal disomy 16 in intrauterine growth retardation and its effects on long-term growth in childhood.
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Affiliation(s)
- A S Schneider
- Department of Pediatrics, Albert Einstein Medical Center, Philadelphia, Pennsylvania, USA
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Grierson AJ, Hodgkins MA, Hancock BW, Goepel JR, Royds J, Goyns MH. Investigation of the RB-1 tumour suppressor gene in a United Kingdom series of non-Hodgkin's lymphomas. Leuk Lymphoma 1996; 23:353-63. [PMID: 9031117 DOI: 10.3109/10428199609054839] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We have investigated the RB-1 tumour suppressor genes in a series of 20 non-Hodgkin's lymphomas (NHL). Polymerase chain reaction (PCR) amplification of polymorphic alleles indicated that there was evidence of allelic imbalance around 13q14, the site of the RB-1 gene, in at least 5 NHL. Immunohistochemical analysis of the RB-1 protein demonstrated wide variations in the percentage of cells exhibiting positive staining, but these usually correlated with differences in the proliferation index as indicated by staining of Ki67. Only 3/35 NHL exhibited significantly fewer cells expressing RB-1 protein than expressed Ki167. A comprehensive analysis of the mutation status of RB-1 in 20 NHL was carried out using PCR based strategies involving single strand conformational polymorphism (SSCP) gels. Most of the protein coding region was studied by analysing cDNA derived from its mRNA and the remaining 5'-end of the coding region investigated by analysing exon I of the gene. We also examined the promoter region of the gene. In none of the 20 NHL investigated were we able to identify a mutation: the only abnormal migrating fragment observed proved to be a polymorphism in exon I of the gene in 5 NHL. In one other case we detected instability at an intron repeat sequence, which had occurred during progression of the disease, but again no mutation of the protein coding region was found. The low levels of RB-1 protein expression that we had observed in a few of our NHL therefore did not appear to be due to mutation of the gene. These data suggest that mutation of RB-1 is not a common event in the evolution of NHL, but that there may be another, as yet unidentified, tumour suppressor gene near the RB-1 locus which is associated with NHL.
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Affiliation(s)
- A J Grierson
- Department of Clinical Oncology, Sheffield University Medical School, UK
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Laan M, Isosomppi J, Klockars T, Peltonen L, Palotie A. Utilization of FISH in positional cloning: an example on 13q22. Genome Res 1996; 6:1002-12. [PMID: 8908520 DOI: 10.1101/gr.6.10.1002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
In positional cloning the initial assignment of a gene to a specific chromosomal locus is followed by physical mapping of the critical region. The construction of a high-resolution physical map still involves considerable effort. However, new high-resolution fluorescence in situ hybridization (FISH) techniques have facilitated this process substantially. Here we summarize a strategy that combines a spectrum of FISH techniques [metaphase, interphase, mechanically stretched chromosomes (MSCs), and fiber-FISH on free chromatin] for the construction and characterization of a high-resolution physical map for a positional cloning project. The chromosomal region 13q22, containing the locus of the variant form of the neuronal ceroid lipofuscinosis (vLINCL, CLN5) disease, serves here as an example for this process. We used metaphase FISH to exclude positionally a candidate gene, to refine the locus to 13q22, and to analyze the possible chimerism of the YACs in the region. Both metaphase and interphase FISH techniques were applied to determine the low-resolution distances between the restricting markers. FISH using MSCs confirmed the centromeric-telomeric order of the clones and facilitated the estimation of the size of the gaps between the clones. Finally, fiber-FISH was found to be the method of choice for the construction of an accurate high-resolution map of the contig established over the restricted region. Thus, FISH techniques in combination with genetic mapping data enabled the refinement of the initial 4-cM region to a high-resolution map of only 400 kb in length. Here the FISH strategy replaced the need for many laborious traditional physical mapping methods, e.g., pulsed-field gel electrophoresis.
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Affiliation(s)
- M Laan
- Department of Clinical Chemistry, University of Helsinki, Finland
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Lorigan PC, Grierson AJ, Goepel JR, Coleman RE, Goyns MH. Gestational choriocarcinoma of the ovary diagnosed by analysis of tumour DNA. Cancer Lett 1996; 104:27-30. [PMID: 8640741 DOI: 10.1016/0304-3835(96)04219-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Gestational choriocarcinoma of the ovary is a rare form of malignancy which can be difficult to distinguish from primary ovarian choriocarcinoma. The ability to make such a diagnosis could, however, have important implications for therapy. We report here a case of choriocarcinoma whose origins were difficult to determine and which behaved clinically more like a primary rather than a gestational choriocarcinoma. We have analysed DNA from this tumour by using polymerase chain reaction (PCR) amplification of a range of polymorphic alleles and have demonstrated that the tumour was in fact gestational. Furthermore, the lack of chromosome Y sequences and the presence of heterozygosity of the spouse's alleles, indicated that this tumour arose as a result of dispermic fertilisation of an empty ovum by sperm carrying the X chromosome.
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Affiliation(s)
- P C Lorigan
- YCRC Department of Clinical Oncology, Weston Park Hospital, Sheffield, UK
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18
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Allen PJ, Amos W, Pomeroy PP, Twiss SD. Microsatellite variation in grey seals (Halichoerus grypus) shows evidence of genetic differentiation between two British breeding colonies. Mol Ecol 1995; 4:653-62. [PMID: 8564005 DOI: 10.1111/j.1365-294x.1995.tb00266.x] [Citation(s) in RCA: 162] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Eight highly variable microsatellite loci were used to examine the genetic variability and differentiation of grey seals (Halichoerus grypus) at two widely spaced British breeding colonies. Samples were collected from adults and pups on the island of North Rona, off the north-west coast of Scotland, and on the Isle of May, situated at the mouth of the Firth of Forth on the east coast. Highly significant differences in allele frequencies between these two sites were found for all eight loci, indicating considerable genetic differentiation. Thus, although grey seals are known to range over very large areas outside the breeding season, site fidelity of adults and philopatry of pups for these breeding colonies must be sufficiently common to have effects, through genetic drift, at the sub-population level. Migration rate was estimated using Wright's fixation index (FST), Slatkin's private alleles model and the new statistic, RST, which is analogous to FST but which takes into account the process of microsatellite mutation. An almost 8-fold discrepancy between the values we obtained provides cautionary evidence that microsatellite loci may contravene one or more of the assumptions on which these methods are based.
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Affiliation(s)
- P J Allen
- Department of Genetics, University of Cambridge, UK
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19
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Dietzsch E, Ramsay M, Christianson AL, Henderson BD, de Ravel TJ. Maternal origin of extra haploid set of chromosomes in third trimester triploid fetuses. AMERICAN JOURNAL OF MEDICAL GENETICS 1995; 58:360-4. [PMID: 8533847 DOI: 10.1002/ajmg.1320580412] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Twenty-six highly polymorphic markers were used to determine the origin of the extra haploid chromosome set in 6 triploid fetuses of type II phenotype. All had reached the third trimester of pregnancy. The extra set was maternal in origin in all cases, supporting previous research indicating longer in utero survival of maternally-derived triploid fetuses. These findings provide evidence for an instance of genomic imprinting in humans.
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Affiliation(s)
- E Dietzsch
- Department of Human Genetics, School of Pathology, South African Institute for Medical Research, Johannesburg, South Africa
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20
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Jones C, Booth C, Rita D, Jazmines L, Spiro R, McCulloch B, McCaskill C, Shaffer LG. Identification of a case of maternal uniparental disomy of chromosome 10 associated with confined placental mosaicism. Prenat Diagn 1995; 15:843-8. [PMID: 8559755 DOI: 10.1002/pd.1970150909] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
We report a case of maternal uniparental disomy of chromosome 10 discovered after chorionic villus sampling (CVS). Direct preparations revealed mosaic trisomy 10, while cultured CVS cells, as well as amniotic fluid cells, showed only a normal 46,XY complement. DNA analysis using microsatellite markers showed both chromosomes 10 to have been inherited from the mother. The pregnancy was complicated by polyhydramnios. A phenotypically normal male infant of appropriate size was delivered by Caesarean section at 41 weeks' gestation. Since only the direct preparations showed trisomy 10, this case illustrates the importance of CVS direct preparations in the detection of pregnancies at risk of uniparental disomy (UPD). Although the increased frequency of confined placental mosaicism (CPM) diagnosed when direct preparations are performed has been viewed negatively, identification of both CPM and UPD may have biological and clinical significance for a pregnancy. Even though only a single case of maternal disomy 10 is reported here, the apparently normal phenotype provides evidence that there are no major imprinted loci on chromosome 10 that affect in utero growth and development. However, other potential effects such as mental retardation will require long-term follow-up of this as well as additional cases.
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Affiliation(s)
- C Jones
- Department of Genetics, Lutheran General Hospital, Park Ridge, Illinois, USA
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21
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Van Camp G, Van Thienen MN, Handig I, Van Roy B, Rao VS, Milunsky A, Read AP, Baldwin CT, Farrer LA, Bonduelle M. Chromosome 13q deletion with Waardenburg syndrome: further evidence for a gene involved in neural crest function on 13q. J Med Genet 1995; 32:531-6. [PMID: 7562965 PMCID: PMC1050545 DOI: 10.1136/jmg.32.7.531] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Waardenburg syndrome (WS) is an autosomal dominant disorder characterised by pigmentary abnormalities and sensorineural deafness. It is subcategorised into type 1 (WS1) and type 2 (WS2) on the basis of the presence (WS1) or absence (WS2) of dystopia canthorum. WS1 is always caused by mutations in the PAX3 gene, whereas WS2 is caused by mutations in the microphthalmia (MITF) gene in some but not all families. An association of WS symptoms with Hirschsprung disease (HSCR) has been reported in many families. We report here a patient with characteristics of WS2 and a de novo interstitial deletion of chromosome 13q. We also describe a family with two sibs who have both WS2 and HSCR. In this family, all possible genes for WS and HSCR, but not chromosome 13q, could be excluded. As an association between chromosome 13q and HSCR/WS has been reported previously, these data suggest that there is a gene on chromosome 13q that is responsible for WS or HSCR or both.
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MESH Headings
- Animals
- Chromosome Deletion
- Chromosome Mapping
- Chromosomes, Human, Pair 13/ultrastructure
- Chromosomes, Human, Pair 3
- DNA-Binding Proteins/genetics
- Female
- Gene Expression Regulation, Developmental
- Genes, Homeobox
- Genetic Heterogeneity
- Hirschsprung Disease/genetics
- Humans
- Infant, Newborn
- Lod Score
- Male
- Mice
- Mice, Mutant Strains
- Microphthalmia-Associated Transcription Factor
- Microsatellite Repeats
- Neural Crest/abnormalities
- PAX3 Transcription Factor
- Paired Box Transcription Factors
- Receptor, Endothelin B
- Receptors, Endothelin/genetics
- Species Specificity
- Transcription Factors
- Waardenburg Syndrome/classification
- Waardenburg Syndrome/embryology
- Waardenburg Syndrome/genetics
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Affiliation(s)
- G Van Camp
- Department of Medical Genetics, University of Antwerp, Belgium
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22
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Eiberg H, Berendt I, Mohr J. Assignment of dominant inherited nocturnal enuresis (ENUR1) to chromosome 13q. Nat Genet 1995; 10:354-6. [PMID: 7670476 DOI: 10.1038/ng0795-354] [Citation(s) in RCA: 131] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Nocturnal enuresis, or nightly bedwetting in children more than seven years of age affects about 10% of seven-year-old children, with a wide range of frequencies between populations. The affliction is often linked to major social maladjustments and occupies considerable time in general practice. From the age of seven there is a spontaneous cure rate of 15% per year, such that few remain affected after the age of 16 years. There are two types of nocturnal enuresis: type I (PEN1, primary) with at least three nightly episodes in children above seven years, where the child has always had the disorder and type II (secondary) where the child has been dry for at least six months, but enuresis has recurred. Among some 400 Danish, mostly three-generation families, we have found 17 families with nocturnal enuresis. Eleven of these family had type I nocturnal enuresis (PEN1) that appeared to follow an autosomal dominant mode of inheritance with penetrance above 90%. We now describe strong evidence of linkage with the DNA polymorphisms D13S291 (Z = 3.55; theta M = F = 0.07) and D13S263 (Z = 2.67; theta M = F = 0.08). Multipoint analysis indicates that these markers flank the disease locus at chromosome 13q13-q14.3.
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Affiliation(s)
- H Eiberg
- University Institute of Medical Biochemistry & Genetics, Department of Medical Genetics, Danish Centre for Genome Research, Copenhagen, Denmark
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23
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Stallard R, Krueger S, James RS, Schwartz S. Uniparental isodisomy 13 in a normal female due to transmission of a maternal t(13q13q). AMERICAN JOURNAL OF MEDICAL GENETICS 1995; 57:14-8. [PMID: 7645591 DOI: 10.1002/ajmg.1320570105] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Chromosomes from a normal 23-year-old, primigravid woman were examined at 10 weeks of gestation because of her mother's history: 8 miscarriages and two liveborn infants (the proposita and a brother who died at 3 days with multiple anomalies). Karyotypes of the proposita and her normal mother were 45,XX,t(13q13q). No evidence of mosaicism was encountered. When the proposita inherited the t(13q13q), she received two copies of 13q from her mother. Moreover, she and her mother shared the same homozygous pattern of alleles from 7 highly polymorphic microsatellite repeats localized along 13q. No evidence of paternal markers from 13 was detected, although biparental inheritance was demonstrated with DNA markers from chromosomes 2 and 17. Cytogenetic and molecular findings indicated that the proposita's chromosomal complement included mUPD 13q. The proposita's normal phenotype suggested that no maternally imprinted genes map to 13q.
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Affiliation(s)
- R Stallard
- Department of Genetics, Case Western Reserve University, Cleveland, Ohio, USA
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24
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Loudianos G, Figus AL, Loi A, Angius A, Dessì V, Deiana M, De Virgiliis S, Monni G, Cao A, Pirastu M. Improvement of prenatal diagnosis of Wilson disease using microsatellite markers. Prenat Diagn 1994; 14:999-1002. [PMID: 7899276 DOI: 10.1002/pd.1970141018] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
This paper describes a case of prenatal diagnosis for Wilson disease (WD) carried out in an at-risk couple of Sardinian descent, following non-directive genetic counselling. Diagnosis was obtained by using eight microsatellites located within or flanking the WD locus, six of which were 100 per cent and two 50 per cent informative. The use of several markers may limit the occurrence of misdiagnosis resulting from recombination or instability of repeats.
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Affiliation(s)
- G Loudianos
- Ospedale Regionale per le Microcitemie USL 21, Cagliari, Italy
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25
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Zaragoza MV, Jacobs PA, James RS, Rogan P, Sherman S, Hassold T. Nondisjunction of human acrocentric chromosomes: studies of 432 trisomic fetuses and liveborns. Hum Genet 1994; 94:411-7. [PMID: 7927339 DOI: 10.1007/bf00201603] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The present report summarizes molecular studies on the parent and meiotic stage of origin of the additional chromosome in 432 fetuses or liveborns with an additional chromosome 13, 14, 15, 21, or 22. Our studies suggest that there is little variation in the origin of nondisjunction among the five acrocentric trisomies and that there is no association between the origin of nondisjunction and the likelihood of survival to term of the trisomic conceptus. The proportion of cases of paternal origin was similar among the five trisomies: 12% for trisomy 13, 17% for trisomy 14, 12% for trisomy 15, 9% for trisomy 21, and 11% for trisomy 22. The stage of nondisjunction was also similar among the five trisomies, with the majority of cases of maternal origin being due to nondisjunction at meiosis I, whereas for paternally derived cases, nondisjunction occurred primarily at meiosis II.
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MESH Headings
- Adult
- Chromosomes, Human, Pair 13
- Chromosomes, Human, Pair 14
- Chromosomes, Human, Pair 15
- Chromosomes, Human, Pair 21
- Chromosomes, Human, Pair 22
- Fetus
- Genetic Markers
- Humans
- Infant, Newborn
- Middle Aged
- Nondisjunction, Genetic
- Parents
- Polymerase Chain Reaction
- Polymorphism, Genetic
- Trisomy/genetics
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Affiliation(s)
- M V Zaragoza
- Department of Genetics, Case Western Reserve University School of Medicine, Cleveland, OH 44106
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26
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Gyapay G, Morissette J, Vignal A, Dib C, Fizames C, Millasseau P, Marc S, Bernardi G, Lathrop M, Weissenbach J. The 1993-94 Généthon human genetic linkage map. Nat Genet 1994; 7:246-339. [PMID: 7545953 DOI: 10.1038/ng0694supp-246] [Citation(s) in RCA: 1250] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
In 1992, we described a second-generation genetic linkage map of the human genome. Using 1,267 new microsatellite markers, we now present a new genetic linkage map containing a total of 2,066 (AC)n short tandem repeats, 60% of which show a heterozygosity of over 0.7. Statistical linkage analysis based on the genotyping of eight large CEPH families placed these markers in the 23 linkage groups. The map includes 1,266 intervals and spans a total distance of 3690 centiMorgans (cM). A total of 1,041 markers could be ordered with odds ratios greater than 1000:1. About 56% of this map is at a distance of 1 cM or less from one of its markers.
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Affiliation(s)
- G Gyapay
- Centre d'Etudes du Polymorphisme Humain, Paris, France
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27
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Tomfohrde J, Silverman A, Barnes R, Fernandez-Vina MA, Young M, Lory D, Morris L, Wuepper KD, Stastny P, Menter A. Gene for familial psoriasis susceptibility mapped to the distal end of human chromosome 17q. Science 1994; 264:1141-5. [PMID: 8178173 DOI: 10.1126/science.8178173] [Citation(s) in RCA: 275] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
A gene involved in psoriasis susceptibility was localized to the distal region of human chromosome 17q as a result of a genome-wide linkage analysis with polymorphic microsatellites and eight multiply affected psoriasis kindreds. In the family which showed the strongest evidence for linkage, the recombination fraction between a psoriasis susceptibility locus and D17S784 was 0.04 with a maximum two-point lod score of 5.33. There was also evidence for genetic heterogeneity and although none of the linked families showed any association with HLA-Cw6, two unlinked families showed weak levels of association. This study demonstrates that in some families, psoriasis susceptibility is due to variation at a single major genetic locus other than the human lymphocyte antigen locus.
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Affiliation(s)
- J Tomfohrde
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas 75235-8591
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28
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Di Rienzo A, Peterson AC, Garza JC, Valdes AM, Slatkin M, Freimer NB. Mutational processes of simple-sequence repeat loci in human populations. Proc Natl Acad Sci U S A 1994; 91:3166-70. [PMID: 8159720 PMCID: PMC43536 DOI: 10.1073/pnas.91.8.3166] [Citation(s) in RCA: 911] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Mutational processes of simple sequence repeats (SSRs) in complex genomes are poorly understood. We examined these processes by introducing a two-phase mutation model. In this model, most mutations are single-step changes, but infrequent large jumps in repeat number also occur. We used computer simulations to determine expected values of statistics that reflect frequency distributions of allele size for the two-phase model and two alternatives, the one-step and geometric models. The theoretical expectations for each model were tested by comparison with observed values for 10 SSR loci genotyped in the Sardinian population, whose genetic and demographic histories have been previously reconstructed. The two-phase model provided the best fit to the data for most of these loci in this population. In the analysis we assumed that the loci were neutral and that this population had undergone rapid population growth. Recent observations made for unstable trinucleotide repeats support our suggestion that frequent small changes and rare large changes in repeat number represent two distinct classes of mutation at SSR loci. We genotyped the same 10 loci in Egyptian and sub-Saharan African samples to assess the utility of SSRs for studying the divergence of populations and found that estimates of interpopulation distances from SSRs were similar to those derived from analysis of mitochondrial DNA.
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Affiliation(s)
- A Di Rienzo
- Neurogenetics Laboratory, University of California, San Francisco 94143
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29
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Bowcock AM, Ruiz-Linares A, Tomfohrde J, Minch E, Kidd JR, Cavalli-Sforza LL. High resolution of human evolutionary trees with polymorphic microsatellites. Nature 1994; 368:455-7. [PMID: 7510853 DOI: 10.1038/368455a0] [Citation(s) in RCA: 1000] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Genetic variation at hypervariable loci is being used extensively for linkage analysis and individual identification, and may be useful for inter-population studies. Here we show that polymorphic microsatellites (primarily CA repeats) allow trees of human individuals to be constructed that reflect their geographic origin with remarkable accuracy. This is achieved by the analysis of a large number of loci for each individual, in spite of the small variations in allele frequencies existing between populations. Reliable evolutionary relationships could also be established in comparisons among human populations but not among great ape species, probably because of constraints on allele length variation. Among human populations, diversity of microsatellites is highest in Africa, which is in contrast to other nuclear markers and supports the hypothesis of an African origin for humans.
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Affiliation(s)
- A M Bowcock
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas 75235-8591
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30
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Moore SS, Byrne K, Berger KT, Barendse W, McCarthy F, Womack JE, Hetzel DJ. Characterization of 65 bovine microsatellites. Mamm Genome 1994; 5:84-90. [PMID: 8180478 DOI: 10.1007/bf00292333] [Citation(s) in RCA: 95] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Microsatellites or simple sequence repeat (SSR) polymorphisms are used widely in the construction of linkage maps in many species. High levels of polymorphism coupled with the ease of analysis of the polymerase chain reaction (PCR) have resulted in this type of maker being one of the most widely used for genetic analysis. In this paper we describe 58 polymorphic bovine microsatellites that were isolated from insert size selected bovine genomic libraries. Primer sequences, number of alleles, and heterozygosity levels in cattle reference families are reported. Chromosomal locations for 47 of these microsatellites as well as for 7 previously described systems derived from entries in the Genbank or EMBL databases have been determined. The markers map to 24 syntenic or chromosomal locations. Polymorphic bovine microsatellites were estimated to occur, on average, every 320 kb, and there is no evidence of clustering in the genome. Thirty of the bovine-derived microsatellite systems gave specific and polymorphic products in sheep, adding to the number of useful markers in that species.
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Affiliation(s)
- S S Moore
- CSIRO, Division of Tropical Animal Production, Gehrmann Laboratories, University of Queensland, Brisbane, Australia
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31
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Banchs I, Bosch A, Guimerà J, Lázaro C, Puig A, Estivill X. New alleles at microsatellite loci in CEPH families mainly arise from somatic mutations in the lymphoblastoid cell lines. Hum Mutat 1994; 3:365-72. [PMID: 8081390 DOI: 10.1002/humu.1380030407] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
In the analysis of 40 CEPH families, under the EUROGEM project, with a total of 29 microsatellites (26 CA-repeats, a TCTA-repeat within the vWFII-3 gene, a TTA-repeat within the PLA-2 gene, and an AAAT-repeat intragenic to the NF1 gene) from human chromosomes 12, 17, and 21, we have detected 21 cases of abnormal segregation of alleles in 16 pedigrees for a total of 14 markers (48%). In 11 cases, the abnormal transmissions were of somatic origin, 10 of which (91%) occurred in the lymphoblastoid cell lines. In 9 other cases, it was not possible to determine if the origin of the new alleles was somatic or germline, and in one case hemizygosity in several family members was observed, so its origin was germline. The 20 new mutations detected in the 22,852 meioses analysed represent a mutation frequency of 8.7 x 10(-4) per locus per allele. The germline mutation rate could be as high as 3.9 x 10(-4) per locus per gamete (from 0 to 3.9 x 10(-4)), but the rate of somatic mutations detected in the study was much higher (4.8 x 10(-4) to 8.7 x 10(-4) per locus per allele). Individual mutation rates ranged from 0 to 3.8 x 10(-3). Among the markers analysed, all three that were tri- or tetranucleotide repeats showed one or two new alleles, compared to only 10 of the 26 (38%) CA-repeats showing mutations. Three CEPH families (102, 45 and 1333) each had several mutational events, and one individual (10210) had somatic mutations for two microsatellites from different chromosomes.(ABSTRACT TRUNCATED AT 250 WORDS)
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MESH Headings
- Adult
- Alleles
- Cell Line
- Child
- Chromosome Mapping/methods
- Chromosomes, Human, Pair 12
- Chromosomes, Human, Pair 17
- Chromosomes, Human, Pair 21
- DNA Mutational Analysis
- DNA, Satellite/genetics
- Databases, Factual
- Fathers
- Female
- Gene Frequency
- Genes, Neurofibromatosis 1/genetics
- Genetic Markers
- Germ-Line Mutation
- Humans
- Lymphocytes
- Male
- Molecular Epidemiology
- Mothers
- Mutation
- Pancreas/enzymology
- Pedigree
- Phospholipases A/genetics
- Polymerase Chain Reaction
- Polymorphism, Genetic
- Repetitive Sequences, Nucleic Acid
- von Willebrand Factor/genetics
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Affiliation(s)
- I Banchs
- Molecular Genetics Department, Hospitalet de Llobregat, Barcelona, Catalunya, Spain
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32
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Abstract
BACKGROUND Alteration of the ras family of oncogenes and of the tumor suppressor genes p53 and RB are the most common genetic events in human tumors. Although there have been no reports of the prevalence of these alterations in Wilms tumors, overexpression of the N-myc and insulin-like growth factor-II (IGF-II) genes have been observed, and alteration of another tumor suppressor gene (WT1) has been demonstrated. METHODS Forty-four Wilms tumor specimens were tested for the presence of N-, K-, and H-ras mutations in codons 12, 13, and 61 by single-strand conformation polymorphism (SSCP) analysis and direct DNA sequence analysis. Sixteen tumors were tested for abnormalities of WT1 by Southern and northern blot analysis and reverse transcriptase polymerase chain reaction (RT-PCR). N-myc, c-myc, WT1, and IGF-II mRNA expression was measured in 16 tumors by Northern blot analysis. Thirty-eight tumors were screened for p53 mutations by SSCP analysis and direct DNA sequence analysis. Nine tumors were analyzed for loss of heterozygosity (LOH) of RB. RESULTS Although the authors confirmed that N-myc and IGF-II are overexpressed in Wilms tumors, no mutations of ras family, p53, or RB genes were identified, and no gross alterations of WT1 were detected by Southern or Northern blot analysis. CONCLUSIONS These findings suggest that H-ras, K-ras, N-ras, p53, and RB are not involved in the pathogenesis of Wilms tumor.
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Affiliation(s)
- P G Waber
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas 75235-9063
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33
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Washington SS, Bowcock AM, Gerken S, Matsunami N, Lesh D, Osborne-Lawrence SL, Cowell J, Ledbetter DH, White RL, Chakravarti A. A somatic cell hybrid map of human chromosome 13. Genomics 1993; 18:486-95. [PMID: 8307557 DOI: 10.1016/s0888-7543(11)80004-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
We have constructed a chromosome 13 somatic cell hybrid map using seven cell lines: PGMEA6, a hybrid containing the entire chromosome 13, and six hybrids containing various deletions of chromosome 13 (BARF7, PPF22, KBF11, KSF39, CF25, and CF27). We have mapped 80 markers that define 10 regions of chromosome 13 with respect to 10 breakpoints in the mapping panel; these regions range in size from 4 to 24 Mb, with an average size of 8 Mb. The 80 markers sublocalized on our mapping panel include 10 Alu-PCR clones, 6 of which were converted to sequence-tagged sites; 40 (CA)n repeat-containing clones, 27 of which are microsatellite PCR markers; 8 (AAAG)n repeat-containing PCR markers, 1 two-allele PCR marker, 4 genes or expressed sequences, and 17 anonymous DNA probes. This low-resolution physical map can be used as a backbone map for more refined physical mapping using radiation hybrids or yeast artificial chromosomes.
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Affiliation(s)
- S S Washington
- Department of Human Genetics, University of Pittsburgh, Pennsylvania 15261
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34
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White A, Tomfohrde J, Stewart E, Barnes R, Le Paslier D, Weissenbach J, Cavalli-Sforza L, Farrer L, Bowcock A. A 4.5-megabase yeast artificial chromosome contig from human chromosome 13q14.3 ordering 9 polymorphic microsatellites (22 sequence-tagged sites) tightly linked to the Wilson disease locus. Proc Natl Acad Sci U S A 1993; 90:10105-9. [PMID: 8234264 PMCID: PMC47722 DOI: 10.1073/pnas.90.21.10105] [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: 01/29/2023] Open
Abstract
We have previously performed a genetic analysis of multiply affected families to map a locus responsible for Wilson disease (WND) to a 0.3-centimorgan (cM) region within chromosome 13q14.3, between D13S31 and D13S59. Here we describe the construction of a contig of approximately 4.5 Mb, which spans this region and extends from D13S25 to D13S59. This contig consists of 28 genomic yeast artificial chromosome (YAC) clones. Five critical crossover events have been defined in this interval in two unaffected (Centre d'Etudes du Polymorphisme Humain) and three WND families. The combination of sequence tagged site content mapping of YACs with both polymorphic and nonpolymorphic markers and recombination breakpoint mapping resulted in the following order of polymorphic markers: centromere-RB1-D13S25-AFM205vh2-D13S31-D13S22 7-D13S228-AFM238vc3-D13S133- AFM084xc5-D13S137-D13S169, D13S155-D13S59-telomere. The recombination/physical distance ratio varies from approximately 3000 kb per cM in the region between D13S31 and D13S25 to 6000 kb per cM in the region between D13S31 and D13S59. Three WND families exhibiting recombination between the disease locus and D13S31 or D13S59 were genotyped for additional markers in this region and further refined the location of the WND gene to between D13S155 and D13S133. Nine of the markers in this region of < 1 cM are polymorphic microsatellites (seven have observed heterozygosities of 70% or above) that will be extremely useful in prenatal and preclinical diagnosis of this disease. This physical map is an essential step in the isolation of the WND gene and is a framework for the identification of candidate genes.
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Affiliation(s)
- A White
- Department of Pediatrics, University of Southwestern Medical Center, Dallas, TX 75235
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