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Dodova RI, Mitkova AV, Dacheva DR, Hadjo LB, Vlahova AI, -Hadjieva MST, Valev SS, Caulevska MM, Popova SD, Popov IE, Dikov TI, Sedloev TA, Ionkov AS, Timcheva KV, Christova SL, Kremensky IM, Mitev VI, Kaneva RP. Spectrum and frequencies of BRCA1/2 mutations in Bulgarian high risk breast cancer patients. BMC Cancer 2015; 15:523. [PMID: 26183948 PMCID: PMC4504066 DOI: 10.1186/s12885-015-1516-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 06/26/2015] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND About 3885 women are diagnosed with breast cancer and 1285 die from the disease each year in Bulgaria. However no genetic testing to identify the mutations in high-risk families has been provided so far. METHODS We evaluated 200 Bulgarian women with primary invasive breast cancer and with personal/ family history of breast cancer for the presence of unequivocally damaging germline mutations in BRCA1/2 using Sanger sequencing. RESULTS Of the 200 patients, 39 (19.5 %) carried a disease predisposing mutation, including 28 (14 %) with a BRCA1 mutation and 11 (5.5 %) with a BRCA2 mutation. At BRCA1, 6 different mutations were identified, including 2 frameshifts, 1 nonsense and 1 missense that had been previously reported (c.5030_5033delCTAA, c.5263_5264insC, c.4603G > T, c.181 T > G), and 2 frameshifts, which were novel to this study (c.464delA, c.5397_5403delCCCTTGG). At BRCA2, 7 different frameshift mutations were identified, including 5 previously reported (5851_5854delAGTT, c.5946delT, c.5718_5719delCT, c.7910_7914delCCTTT,c.9098_9099insA) and 2 novel (c.8532_8533delAA, c.9682delA). A BRCA1 mutation was found in 18.4 % of women diagnosed with breast cancer at/or under the age of 40 compared to 11.2 % of women diagnosed at a later age; a BRCA2 mutation was found in 4 % of women diagnosed at/or under the age of 40 compared to 6.5 % of women diagnosed at a later age. A mutation was present in 26.8 % patients with a positive family history and in 14.4 % of women with a negative family history. The most prevalent mutation observed in 22 patients (11 %) was BRCA1 c.5263_5264insC, a known Slavic mutation with founder effect in Eastern European and AJ communities. Other recurrent mutations were BRCA2 c.9098-9099insA (2 %), BRCA1 c.181T > G (1 %) and BRCA2 c.5851_5854delAGTT (1 %). Notably, BRCA1 c.5263_5264insC represented 56 % of all mutations identified in this series. Of the 22 patients with BRCA1 c.5263_5264insC, 9 were diagnosed with early onset breast cancer, 11 with TNBCs, 4 with bilateral breast cancer, and 6 with both breast and ovarian cancer. CONCLUSIONS This is the first comprehensive study of the BRCA1/2 mutation spectrum in Bulgaria and will assist the establishment of efficient protocols for genetic testing and individualized risk assessment for Bulgarian breast/ovarian cancer patients and healthy individuals at a high-risk.
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Affiliation(s)
- Rumyana Ivanova Dodova
- Molecular Medicine Center, Medical University of Sofia, 2 Zdrave str., 1431, Sofia, Bulgaria.,Department of Medical Chemistry and Biochemistry, Medical Faculty, Medical University of Sofia, 2 Zdrave str., 1431, Sofia, Bulgaria
| | - Atanaska Velichkova Mitkova
- Molecular Medicine Center, Medical University of Sofia, 2 Zdrave str., 1431, Sofia, Bulgaria. .,Department of Medical Chemistry and Biochemistry, Medical Faculty, Medical University of Sofia, 2 Zdrave str., 1431, Sofia, Bulgaria.
| | - Daniela Rosenova Dacheva
- Molecular Medicine Center, Medical University of Sofia, 2 Zdrave str., 1431, Sofia, Bulgaria.,Department of Medical Chemistry and Biochemistry, Medical Faculty, Medical University of Sofia, 2 Zdrave str., 1431, Sofia, Bulgaria
| | - Lina Basam Hadjo
- Molecular Medicine Center, Medical University of Sofia, 2 Zdrave str., 1431, Sofia, Bulgaria
| | - Alexandrina Ivanova Vlahova
- General and Clinical Pathology Clinic, University Hospital "Alexandrovska", 1 Georgi Sofiiski str., 1431, Sofia, Bulgaria.,Department of General and Clinical Pathology, Medical University of Sofia, 1 Georgi Sofiiski str., 1431, Sofia, Bulgaria
| | | | - Spartak Stoyanov Valev
- Clinic of Medical Oncology (Chemotherapy), Specialized Hospital for Active Treatment in Oncology, 6 "Plovdivsko pole" str., 1756, Sofia, Bulgaria
| | - Marija Mitko Caulevska
- Molecular Medicine Center, Medical University of Sofia, 2 Zdrave str., 1431, Sofia, Bulgaria
| | | | - Ivan Emilov Popov
- Molecular Medicine Center, Medical University of Sofia, 2 Zdrave str., 1431, Sofia, Bulgaria.,Department of Medical Chemistry and Biochemistry, Medical Faculty, Medical University of Sofia, 2 Zdrave str., 1431, Sofia, Bulgaria
| | - Tihomir Iliichev Dikov
- General and Clinical Pathology Clinic, University Hospital "Alexandrovska", 1 Georgi Sofiiski str., 1431, Sofia, Bulgaria.,Department of General and Clinical Pathology, Medical University of Sofia, 1 Georgi Sofiiski str., 1431, Sofia, Bulgaria
| | - Theophil Angelov Sedloev
- Department of Surgery, University Hospital "Tsaritsa Yoana - ISUL", 8 "Byalo more" str., 1527, Sofia, Bulgaria.,Medical Faculty, 8 "Byalo more" str., 1527, Sofia, Bulgaria
| | - Atanas Stefanov Ionkov
- Department of General and Liver-Pancreatic Surgery, University Hospital "Alexandrovska", 1 Georgi Sofiiski str., 1431, Sofia, Bulgaria.,Medical Faculty, Medical University of Sofia, 1 Georgi Sofiiski str., 1431, Sofia, Bulgaria
| | - Konstanta Velinova Timcheva
- Clinic of Medical Oncology (Chemotherapy), Specialized Hospital for Active Treatment in Oncology, 6 "Plovdivsko pole" str., 1756, Sofia, Bulgaria
| | - Svetlana Liubomirova Christova
- General and Clinical Pathology Clinic, University Hospital "Alexandrovska", 1 Georgi Sofiiski str., 1431, Sofia, Bulgaria.,Department of General and Clinical Pathology, Medical University of Sofia, 1 Georgi Sofiiski str., 1431, Sofia, Bulgaria
| | - Ivo Marinov Kremensky
- Molecular Medicine Center, Medical University of Sofia, 2 Zdrave str., 1431, Sofia, Bulgaria
| | - Vanio Ivanov Mitev
- Molecular Medicine Center, Medical University of Sofia, 2 Zdrave str., 1431, Sofia, Bulgaria.,Department of Medical Chemistry and Biochemistry, Medical Faculty, Medical University of Sofia, 2 Zdrave str., 1431, Sofia, Bulgaria
| | - Radka Petrova Kaneva
- Molecular Medicine Center, Medical University of Sofia, 2 Zdrave str., 1431, Sofia, Bulgaria.,Department of Medical Chemistry and Biochemistry, Medical Faculty, Medical University of Sofia, 2 Zdrave str., 1431, Sofia, Bulgaria
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Abstract
Conformation sensitive gel electrophoresis (CSGE) is a rapid screening method for the detection of DNA sequence variation, specifically single-base changes or small insertions and deletions. It has been widely used for mutation screening in genetic disorders and for the detection of single nucleotide polymorphisms (SNPs).CSGE is a simple manual method, based on heteroduplex analysis, and compares well in terms of sensitivity with other screening technologies. CSGE also lends itself to automation and such modi-fications have been useful in increasing sample throughput and sensitivity. However, manual CSGE remains a low-cost, accessible, and effective approach for mutation screening, which can be carried out with -minimal specialist equipment. This chapter describes manual CSGE, and outlines some of the uses, -modifications, and limitations of this method.
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3
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Bozhanov SS, Angelova SG, Krasteva ME, Markov TL, Christova SL, Gavrilov IG, Georgieva EI. Alterations in p53, BRCA1, ATM, PIK3CA, and HER2 genes and their effect in modifying clinicopathological characteristics and overall survival of Bulgarian patients with breast cancer. J Cancer Res Clin Oncol 2010; 136:1657-69. [DOI: 10.1007/s00432-010-0824-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2009] [Accepted: 02/04/2010] [Indexed: 02/06/2023]
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5
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Haitian Z, Yunfei L, Jian Z, Jian L, Qinghua L, Fuqiang W. Mutation screening of the BRCA1 gene in sporadic breast cancer in southern Chinese populations. Breast 2008; 17:563-7. [DOI: 10.1016/j.breast.2008.08.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2008] [Revised: 06/20/2008] [Accepted: 08/12/2008] [Indexed: 10/21/2022] Open
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Fan ZP, Zhu WS, Zhang C, Zhou YX, Li K, Liang YM, Xing ZH, Chen GQ, Bai X, Xiao JH. [SNP discovery by F-CSGE in the coding region of mitochondrial DNA in wild house mice from Shanghai suburb]. Yi Chuan 2008; 30:475-82. [PMID: 18424419 DOI: 10.3724/sp.j.1005.2008.00475] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
This study was performed to discover SNPs for genetic polymorphism analysis of mitochondrial DNA from wild house mice. Universal primer florescent PCR, fluorescence-based conformation sensitive gel electrophoresis (F-CSGE) and DNA sequencing were conducted to analyze the coding region of mitochondrial DNA. Different types of unknown mutations were recorded by variable F-CSGE patterns without false positive. Twenty-four SNPs, sixteen of which were first discovered in the coding region of mitochondrial DNA, were found in 64 wild house mice from 4 districts in Shanghai. Therefore, F-CSGE was proved to be powerful technique for SNP discovery in the coding region mitochondrial DNA. The novel SNPs can be used as molecular markers to analyze population structure and genetic polymorphisms of the wild house mice in Shanghai.
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Affiliation(s)
- Zhong-Peng Fan
- Institute of Biology Science & Technology, Donghua University, Shanghai 201620, China.
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7
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Venza M, Visalli M, Venza I, Torino C, Saladino R, Teti D. FOXE1 gene mutation screening by multiplex PCR/DHPLC in CHARGE syndrome and syndromic and non-syndromic cleft palate. J Chromatogr B Analyt Technol Biomed Life Sci 2006; 836:39-46. [PMID: 16584930 DOI: 10.1016/j.jchromb.2006.03.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2005] [Revised: 03/07/2006] [Accepted: 03/13/2006] [Indexed: 11/27/2022]
Abstract
Denaturing high-performance liquid chromatography (DHPLC) has established itself as one of the most powerful tools for DNA variation screening. FOXE1, a highly GC-rich gene involved in syndromic cleft palate, is under investigation in thyroid dysgenesis, nonsyndromic cleft palate and squamous cell carcinoma. A technique for fast and simultaneous detection of sequence variants in the entire coding region of the FOXEl gene based on multiplex PCR/DHPLC is presented here. Given its characteristics of high sensitivity and rapidity, the testing strategy developed by us appears to be a reliable approach for FOXE1 analysis in the screening of a large population at risk.
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Affiliation(s)
- Mario Venza
- Department of Odontostomatology, University of Messina, Italy
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8
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Davies H, Dicks E, Stephens P, Cox C, Teague J, Greenman C, Bignell G, O'meara S, Edkins S, Parker A, Stevens C, Menzies A, Blow M, Bottomley B, Dronsfield M, Futreal PA, Stratton MR, Wooster R. High throughput DNA sequence variant detection by conformation sensitive capillary electrophoresis and automated peak comparison. Genomics 2006; 87:427-32. [PMID: 16406726 DOI: 10.1016/j.ygeno.2005.11.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2005] [Revised: 11/10/2005] [Accepted: 11/15/2005] [Indexed: 10/25/2022]
Abstract
We report the development of a heteroduplex-based mutation detection method using multicapillary automated sequencers, known as conformation-sensitive capillary electrophoresis (CSCE). Our optimized CSCE protocol detected 93 of 95 known base substitution sequence variants. Since the optimization of the method, we have analyzed 215 Mb of DNA and identified 3397 unique variants. An analysis of this data set indicates that the sensitivity of CSCE is above 95% in the central 56% of the average PCR product. To fully exploit the mutation detection capacity of this method, we have developed software, canplot, which automatically compares normal and test results to prioritize samples that are most likely to contain variants. Using multiple fluorescent dyes, CSCE has the capacity to screen over 2.2 Mb on one ABI3730 each day. Therefore this technique is suitable for projects where a rapid and sensitive DNA mutation detection system is required.
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Affiliation(s)
- Helen Davies
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
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9
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Zhang XL, Liu M, Meng XH, Fu WL, Yin ZQ, Huang JF, Zhang X. Mutational analysis of the rhodopsin gene in Chinese ADRP families by conformation sensitive gel electrophoresis. Life Sci 2005; 78:1494-8. [PMID: 16229860 DOI: 10.1016/j.lfs.2005.07.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2005] [Accepted: 07/13/2005] [Indexed: 11/23/2022]
Abstract
Retinitis pigmentosa is a very heterogeneous group of retinal degenerations, with multiple genes identified in each mode of inheritance. For autosomal dominant retinitis pigmentosa (ADRP), the most common gene is the rhodopsin (RHO) gene, mutations in which contribute to about 25% of ADRP in Caucasian population. To investigate the frequency and pattern of RHO point mutations in Chinese patients with ADRP, we have screened the five coding exons and splice sites of the RHO gene in 50 unrelated probands from Chinese ADRP families and 100 normal controls to identify disease-associated mutations, using conformation sensitive gel electrophoresis (CSGE) and direct DNA sequencing. Two RHO mutations, Pro347Leu and Pro327 (1-bp del), were identified each in one family, thus the frequency of RHO mutations among ADRP families in this study is less than 14% (2/50=4%, 95% confidence interval: 1-14%), lower than that in Europe and North America, which may reflect an ethnic difference between Chinese and Caucasian populations. Loss of all phosphorylation sites at the C-terminus and a highly conserved sequence QVS(A)PA may occur because of Pro327(1-bp del). CSGE was found to be a sensitive, simple and practical method for the screening of a large number of samples under highly reproducible conditions, and could be utilized in routine molecular diagnostic laboratories.
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Affiliation(s)
- Xiao L Zhang
- Center for Molecular Diagnosis and Gene Therapy, Affiliated South-West Hospital, Third Military Medical University, Chongqing, PR China.
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Esteban-Cardeñosa E, Duran M, Infante M, Velasco E, Miner C. High-Throughput Mutation Detection Method to Scan BRCA1 and BRCA2 Based on Heteroduplex Analysis by Capillary Array Electrophoresis. Clin Chem 2004; 50:313-20. [PMID: 14684619 DOI: 10.1373/clinchem.2003.023614] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Abstract
Background: Scanning for mutations in BRCA1 and BRCA2 in a large number of samples is hampered by the large sizes of these genes and the scattering of mutations throughout their coding sequences. Automated capillary electrophoresis has been shown to be a powerful system to detect mutations by either single-strand conformation polymorphism or heteroduplex analysis (HA).
Methods: We investigated the adaptation of gel-based HA of BRCA1 and BRCA2 to a fluorescent multicapillary platform to increase the throughput of this technique. We combined multiplex PCR, three different fluorescent labels, and HA in a 16-capillary DNA sequencer and tested 57 DNA sequence variants (11 insertions/deletions and 46 single-nucleotide changes) of BRCA1 and BRCA2.
Results: We detected all 57 DNA changes in a blinded assay, and 2 additional single-nucleotide substitutions (1186 A>G of BRCA1 and 3624 A>G of BRCA2), previously unresolved by conformation-sensitive gel electrophoresis. Furthermore, different DNA changes in the same PCR fragment could be distinguished by their peak patterns.
Conclusions: Capillary-based HA is a fast, efficient, and sensitive method that considerably reduces the amount of “hands-on” time for each sample. By this approach, the entire coding regions of BRCA1 and BRCA2 from two breast cancer patients can be scanned in a single run of 90 min.
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Affiliation(s)
- Eva Esteban-Cardeñosa
- Instituto de Biología y Genética Molecular, Facultad de Medicina, Universidad de Valladolid, Valladolid, Spain
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11
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Park WD, O'Brien JF, Lundquist PA, Kraft DL, Vockley CW, Karnes PS, Patterson MC, Snow K. Identification of 58 novel mutations in Niemann-Pick disease type C: correlation with biochemical phenotype and importance of PTC1-like domains in NPC1. Hum Mutat 2003; 22:313-25. [PMID: 12955717 DOI: 10.1002/humu.10255] [Citation(s) in RCA: 140] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The two known complementation groups of Niemann-Pick Type C disease, NPC1 and NPC2, result from non-allelic protein defects. Both the NPC1 and NPC2 (HE1) gene products are intimately involved in cholesterol and glycolipid trafficking and/or transport. We describe mutation analysis on samples from 143 unrelated affected NPC patients using conformation sensitive gel electrophoresis and DNA sequencing as the primary mutation screening methods for NPC1 and NPC2, respectively. These methods are robust, sensitive, and do not require any specialized laboratory equipment. Analyses identified two NPC1 mutations for 115 (80.4%) patients, one NPC1 mutation for 10 (7.0%) patients, two NPC2 mutations for five (3.5%) patients, one NPC2 mutation for one (0.7%) patient, and no mutations for 12 (8.4%) patients. Thus, mutations were identified on 251 of 286 (88%) disease alleles, including 121 different mutations (114 in NPC1 and seven in NPC2), 58 of which are previously unreported. The most common NPC1 mutation, I1061T, was detected on 18% of NPC alleles. Other NPC1 mutations were mostly private, missense mutations located throughout the gene with clustering in the cysteine-rich luminal domain. Correlation with biochemical data suggests classification of several mutations as severe and others as moderate or variable. The region between amino acids 1038 and 1253, which shares 35% identity with Patched 1, appears to be a hot spot for mutations. Additionally, a high percentage of mutations were located at amino acids identical to the NPC1 homolog, NPC1L1. Biochemical complementation analysis of cases negative for mutations revealed a high percentage of equivocal results where the complementation group appeared to be non-NPC1 and non-NPC2. This raises the possibilities of an additional NPC complementation group(s) or non-specificity of the biochemical testing for NPC. These caveats must be considered when offering mutation testing as a clinical service.
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Affiliation(s)
- Walter D Park
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic and Foundation, Rochester, Minnesota 55905, USA
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12
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Jayandharan G, Shaji RV, Chandy M, Srivastava A. Identification of factor IX gene defects using a multiplex PCR and CSGE strategy-a first report. J Thromb Haemost 2003; 1:2051-4. [PMID: 12941051 DOI: 10.1046/j.1538-7836.2003.00347.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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13
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Chen ST, Chen RA, Kuo SJ, Chien YC. Mutational screening of breast cancer susceptibility gene 1 from early onset, bi-lateral, and familial breast cancer patients in Taiwan. Breast Cancer Res Treat 2003; 77:133-43. [PMID: 12602912 DOI: 10.1023/a:1021386026051] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The BRCA1 gene has been shown to be strongly associated with the occurrence of familial breast cancer. The spectrum of BRCA1 gene mutations in breast cancer patients in various populations has been investigated. In this study, patients in Central Taiwan with breast cancer were screened for BRCA1 mutations by sequencing PCR products spanning the coding region and partial intronic regions of the BRCA1 gene. Twelve polymorphisms in four exons and three introns were found. One mutation was found in one patient with familial breast cancer. Two patients showed LOH at the locus of BRCA1. Also found in the Taiwanese population were two common haplotypes and one rare haplotype of BRCA1. These results suggest that the mutation of BRCA1 contributes little to the occurrence of breast cancer in the Taiwanese population.
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Affiliation(s)
- Shou-Tung Chen
- Department of Surgery, Changhua Christian Hospital, Taiwan, ROC
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14
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Abstract
DNA repair is essential for the maintenance of genomic integrity. Consequently, altered repair capacity may impact individual health in such areas as aging and susceptibility to certain diseases. Defects in some DNA repair genes, for example, have been shown to increase cancer risk, accelerate aging and impair neurological functions. Now that over 115 genes directly involved in human DNA repair have been characterized at the DNA sequence level, the identification of single nucleotide polymorphisms (SNPs) in DNA repair genes is becoming a reality. This information will likely lead to the identification of alleles, or combinations of alleles that affect disease predisposition. This communication summarizes SNPs identified to date in the coding region of 24 human double-strand break repair (DSBR) genes. SNP data for four of these genes were obtained by screening at least 100 individuals in our laboratory. For each SNP, the codon number, amino acid substitution, allele frequency and population information is supplied.
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Affiliation(s)
- Cindy C Ruttan
- Centre for Biomedical Research, University of Victoria, P.O. Box 3020 STN CSC,Victoria, BC, Canada V8W 3N5
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Velasco Sampedro E, Esteban Cardeñosa E, Infante Sanz M, Durán Domínguez M, Lastra Aras E, García Girón C, Miner Pino C. [Molecular study of the BRCA1 and BRCA2 genes in 153 breast cancer families from Castilla and León (Spain): new nine unclassified variants identified]. Med Clin (Barc) 2002; 119:441-5. [PMID: 12385650 DOI: 10.1016/s0025-7753(02)73450-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
BACKGROUND It is estimated that 5-10% of breast cancers have an hereditary origin, germline mutations of BRCA1 and BRCA2 genes causing a predisposition. In the present study we analyzed BRCA1 and BRCA2 mutations in moderate to high risk breast cancer patients in order to find out the types and frequency of these mutations in the Spanish regional community of Castilla y León. PATIENTS AND METHOD We studied 207 moderate to high risk patients from 153 selected families. Genomic DNA was extracted from peripheral blood and analyzed by multiplex polymerase chain reaction-heteroduplexes-conformation sensitive gel electrophoresis (multiplex PCR-HA-CSGE). All variants detected were sequenced to further verify the mutation. RESULTS 45 alterations (23 in BRCA1 and 22 in BRCA2) were identified in 74 families (48.4%), corresponding to 13 polymorphisms (29 families), 19 unclassified variants (26 families) of which 9 have not been previously described and 13 cancer-prone mutations (19 families; 12.42% of all families). Eight out of the 19 deleterious mutations (42.1%) were detected in the BRCA1 gene and 11 (57.9%) in the BRCA2 gene. The most prevalent mutation was 3036delACAA, which was detected in four unrelated families. CONCLUSIONS The high proportion of mutations, polymorphisms and unclassified variants we have detected may be the result of the sensitive procedure and the risk selection criteria used in this study. There is a high proportion of unclassified variants. Their role in the disease must be clarified through more studies, including their typing in control samples.
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Ezzeldin H, Okamoto Y, Johnson MR, Diasio RB. A high-throughput denaturing high-performance liquid chromatography method for the identification of variant alleles associated with dihydropyrimidine dehydrogenase deficiency. Anal Biochem 2002; 306:63-73. [PMID: 12069415 DOI: 10.1006/abio.2002.5666] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Dihydropyrimidine dehydrogenase (DPD) is the initial, rate-limiting enzyme in the catabolism of 5-fluorouracil (5-FU). A pharmacogenetic syndrome has been described in which DPD-deficient patients are at risk for toxicity following administration of 5-FU. To date, there are at least 21 previously described mutations and/or polymorphisms that have been associated with DPD deficiency. In this study we describe the development of a highly specific, sensitive, inexpensive, and robust denaturing HPLC (DHPLC) method for rapidly identifying sequence variations (mutations and/or polymorphisms) in the gene (DPYD) that codes for the DPD enzyme. DHPLC conditions were optimized at three temperatures for analysis of the 23 exons of the DPYD gene using 25 amplicons representing the entire coding sequence, including all intron/exon boundaries (splice sites). Resolution of all 25 amplicons at the optimized temperature can be performed in 4.2 h. All 21 previously described sequence variations (mutations and/or polymorphisms) were prepared using site-directed mutagenesis from the wild-type DPYD gene, confirmed by sequence analysis, and subsequently resolved by DHPLC using the optimized conditions. These analyses generated reference chromatogram patterns for all known sequence variations previously encountered in DPD-deficient patients. In order to examine the utility and sensitivity of this approach, samples from patients with known sequence variations in the DPYD gene were analyzed. This DHPLC technique resolved 100% of the known DPYD sequence variations and differentiated between homozygous and heterozygous genotypes. We conclude that this DHPLC method is a highly specific and sensitive technique for rapidly detecting known sequence variations in the DPYD gene. In addition, this approach can be used to identify currently unrecognized unknown sequence variations in the DPYD gene and should be useful in future pharmacogenetic studies examining DPD deficiency.
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Affiliation(s)
- Hany Ezzeldin
- Division of Clinical Pharmacology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
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Geisler JP, Hatterman-Zogg MA, Rathe JA, Lallas TA, Kirby P, Buller RE. Ovarian cancer BRCA1 mutation detection: Protein truncation test (PTT) outperforms single strand conformation polymorphism analysis (SSCP). Hum Mutat 2001; 18:337-44. [PMID: 11668617 DOI: 10.1002/humu.1195] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Recent studies have shown that the BRCA1 tumor suppressor gene plays a role in the development of both hereditary and sporadic ovarian cancer. Since several different mechanisms may give rise to tumor gene defects, a better understanding of these mechanisms may identify BRCA1 as an attractive therapeutic target in ovarian cancer. Sequencing this large gene is not practical on a population-wide basis. The optimal screening strategy is yet to be determined. The purpose of our study is to compare two common screening techniques: the protein truncation test (PTT) and single strand conformational polymorphism analysis (SSCP). Ninety-four patients with epithelial ovarian cancer and available snap-frozen tissue were screened for BRCA1 mutations by both PTT (five individual PCR reactions with complete translation of the product in the TNT System (Promega, Madison, WI)) and SSCP (41 individual PCR reactions covering the entire coding sequence). All abnormal results were confirmed by sequencing. A paired peripheral blood DNA sample was utilized to determine if the sequence abnormality was a germline mutation. Twenty-three mutations in BRCA1 were found in 22 patients (14 germline, eight somatic, one unknown) including four novel mutations: E489X, 3558delT, 3871delGTCT, del exon 7-10. Although the predictive value of a negative test was close for the two methods (PTT 99.1%, SSCP 99.8%), the comparison of positive predictive value overwhelmingly favored PTT (100.0%, vs. 26.4%, respectively). The specificity for PTT was 100.0% while the sensitivity was 82.6%. While for SSCP, the specificity was 99.0% and the sensitivity was only 60.9%. The concordance rate for the two screening tests was 88.9%. Only SSCP can detect missense mutations. PTT is a superior screening test for truncating BRCA1 mutations that are expected to be of clinical significance.
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Affiliation(s)
- J P Geisler
- Division of Gynecologic Oncology, University of Iowa Hospitals and Clinics, Iowa City, Iowa, USA
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19
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Sun X, Marks DL, Park WD, Wheatley CL, Puri V, O’Brien JF, Kraft DL, Lundquist PA, Patterson MC, Pagano RE, Snow K. Niemann-Pick C variant detection by altered sphingolipid trafficking and correlation with mutations within a specific domain of NPC1. Am J Hum Genet 2001; 68:1361-72. [PMID: 11349231 PMCID: PMC1226123 DOI: 10.1086/320599] [Citation(s) in RCA: 116] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2001] [Accepted: 04/03/2001] [Indexed: 11/04/2022] Open
Abstract
Niemann-Pick disease type C (NPC) is a fatal, autosomal recessive lipidosis characterized by lysosomal accumulation of unesterified cholesterol and multiple neurological symptoms, such as vertical supranuclear ophthalmoplegia, progressive ataxia, and dementia. More than 90% of cases of NPC are due to a defect in Niemann-Pick C1 (NPC1), a late endosomal, integral membrane protein that plays a role in cholesterol transport or homeostasis. Biochemical diagnosis of NPC has relied on the use of patient skin fibroblasts in an assay to demonstrate delayed low-density lipoprotein (LDL)-derived cholesterol esterification and a cytological technique-filipin staining-to demonstrate the intracellular accumulation of cholesterol. A small percentage of patients, referred to as "NPC variants," present with clinical symptoms of NPC but show near-normal results of these biochemical tests, making laboratory confirmation of NPC disease problematic. Here, we demonstrate that NPC-variant fibroblast samples can be detected as sphingolipid storage disease cells, using a fluorescent sphingolipid analog, BODIPY-lactosylceramide. This lipid accumulated in endosomes/lysosomes in variant cells preincubated with LDL cholesterol but targeted to the Golgi complex in normal cells under these conditions. The reproducibility of this technique was validated in a blinded study. In addition, we performed mutation analysis of the NPC1 gene in NPC variant and "classical" NPC cell samples and found a high incidence of specific mutations within the cysteine-rich region of NPC1 in variants. We also found that 5 of the 12 variant cell samples had no apparent defect in NPC1 but were otherwise indistinguishable from other variant cells. This is a surprising result, since, in general, approximately 90% of patients with NPC possess defects in NPC1. Our findings should be useful for the detection of NPC variants and also may provide significant new insight regarding NPC1 genotype/phenotype correlations.
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Affiliation(s)
- Xiaofeng Sun
- Thoracic Diseases Research Unit, Department of Biochemistry and Molecular Biology; Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology; and Division of Child and Adolescent Neurology, Department of Neurology, Mayo Clinic and Foundation, Rochester, MN
| | - David L. Marks
- Thoracic Diseases Research Unit, Department of Biochemistry and Molecular Biology; Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology; and Division of Child and Adolescent Neurology, Department of Neurology, Mayo Clinic and Foundation, Rochester, MN
| | - Walter D. Park
- Thoracic Diseases Research Unit, Department of Biochemistry and Molecular Biology; Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology; and Division of Child and Adolescent Neurology, Department of Neurology, Mayo Clinic and Foundation, Rochester, MN
| | - Christine L. Wheatley
- Thoracic Diseases Research Unit, Department of Biochemistry and Molecular Biology; Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology; and Division of Child and Adolescent Neurology, Department of Neurology, Mayo Clinic and Foundation, Rochester, MN
| | - Vishwajeet Puri
- Thoracic Diseases Research Unit, Department of Biochemistry and Molecular Biology; Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology; and Division of Child and Adolescent Neurology, Department of Neurology, Mayo Clinic and Foundation, Rochester, MN
| | - John F. O’Brien
- Thoracic Diseases Research Unit, Department of Biochemistry and Molecular Biology; Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology; and Division of Child and Adolescent Neurology, Department of Neurology, Mayo Clinic and Foundation, Rochester, MN
| | - Daniel L. Kraft
- Thoracic Diseases Research Unit, Department of Biochemistry and Molecular Biology; Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology; and Division of Child and Adolescent Neurology, Department of Neurology, Mayo Clinic and Foundation, Rochester, MN
| | - Patrick A. Lundquist
- Thoracic Diseases Research Unit, Department of Biochemistry and Molecular Biology; Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology; and Division of Child and Adolescent Neurology, Department of Neurology, Mayo Clinic and Foundation, Rochester, MN
| | - Marc C. Patterson
- Thoracic Diseases Research Unit, Department of Biochemistry and Molecular Biology; Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology; and Division of Child and Adolescent Neurology, Department of Neurology, Mayo Clinic and Foundation, Rochester, MN
| | - Richard E. Pagano
- Thoracic Diseases Research Unit, Department of Biochemistry and Molecular Biology; Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology; and Division of Child and Adolescent Neurology, Department of Neurology, Mayo Clinic and Foundation, Rochester, MN
| | - Karen Snow
- Thoracic Diseases Research Unit, Department of Biochemistry and Molecular Biology; Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology; and Division of Child and Adolescent Neurology, Department of Neurology, Mayo Clinic and Foundation, Rochester, MN
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20
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Wang T, Lerer I, Gueta Z, Sagi M, Kadouri L, Peretz T, Abeliovich D. A deletion/insertion mutation in the BRCA2 gene in a breast cancer family: a possible role of the Alu-polyA tail in the evolution of the deletion. Genes Chromosomes Cancer 2001; 31:91-5. [PMID: 11284040 DOI: 10.1002/gcc.1110] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Patients with breast and/or ovarian cancer were screened for gross rearrangements in the BRCA2 gene by Southern hybridization, with exon 10 and a fragment of exon 11 used as probes. One breast cancer patient with a positive family history had a 6.2-kb deletion including exons 12 and 13. The deletion breakpoint in intron 11 was in the 3' polyA tail of an Alu element, where a track of approximately 60 adenine nucleotide residues was inserted. Expansion of the Alu-polyA tail may have resulted from polymerase slippage during replication, representing a novel mechanism in which Alu elements mediate deletion/insertion mutations.
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Affiliation(s)
- T Wang
- Department of Human Genetics, Hadassah Hebrew University Hospital and Medical School, Jerusalem, Israel
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21
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Tian H, Brody LC, Mao D, Landers JP. Effective capillary electrophoresis-based heteroduplex analysis through optimization of surface coating and polymer networks. Anal Chem 2000; 72:5483-92. [PMID: 11080904 DOI: 10.1021/ac0004916] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The efficacy of capillary electrophoresis for detecting DNA mutations via heteroduplex analysis (HDA) is dependent upon both the effective passivition of the capillary surface and the choice of the correct polymer network for sieving. Using HDA with laser-induced fluorescence detection of fluorescently labeled DNA fragments, an effective coating and optimal polymer matrix were sought. Optimized separation conditions were determined through the methodological evaluation of a number of different silanizing reagents, polymeric coatings, and polymer networks for resolving the PCR-amplified DNA fragments associated with five mutations (185delAG, 1294del40, 4446C > G, 5382insC, 5677insA) in the breast cancer susceptibility gene (BRCA1). For capillary coating, allyldimethylchlorosilane, 4-chlorobutyldimethylchlorosilane, (gamma-methacryloxypropyl)trimethoxysilane, chlorodimethyloctylsilane (OCT), and 7-octenyltrimethoxysilane were evaluated as silanizing reagents in combination with poly(vinylprrolidone) (PVP) and polyacrylamide (PA) as the polymeric coat. The HDA results were compared with those obtained using a commercial (FC) coated capillary. Of these, the OCT-PVP combination was found to be most effective. Using this modified capillary, HDA with polymer networks that included hydroxyethylcellulose (HEC), linear polyacrylamide, and PVP showed that a PVP-, PA-, or FC-coated capillary, in combination with HEC as the sieving polymer, could be used effectively to discriminate the mutations in less than 10 min. However, optimal performance was observed with the OCT-PVP-coated capillary and HEC as the polymer network.
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Affiliation(s)
- H Tian
- Department of Chemistry, University of Pittsburgh, Pennsylvania 15260, USA
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22
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Witt CS, Martin A, Christiansen FT. Detection of KIR2DL4 alleles by sequencing and SSCP reveals a common allele with a shortened cytoplasmic tail. Tissue Antigens 2000; 56:248-57. [PMID: 11034561 DOI: 10.1034/j.1399-0039.2000.560307.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Single-stranded conformation polymorphism (SSCP) by capillary electrophoresis was assessed as a screening and typing method for alleles of KIR2DL4. Exon 6 was investigated as this exon was reported to include three polymorphic nucleotides. Exon 6, intron 6 and exon 7 were amplified as a single polymerase chain reaction (PCR) product of 650 bp from genomic DNA. The PCR product was sequenced and analysed by SSCP. Exon 7 was found to be invariant. Only two nucleotides were found to be polymorphic in exon 6 and another three were found in intron 6. Strong linkage disequilibrium was found between the polymorphic nucleotides resulting in the presence of three alleles in a panel of 20 cell lines. Two alleles differed within intron 6 while the third allele differed at two nucleotides in exon 6. All six possible genotypes were distinguishable by SSCP providing information from both the forward and reverse primers was used. Exon 6 of one allele was one nucleotide shorter than that of the other alleles and the resulting frame shift is predicted to produce a truncated cytoplasmic tail due to a premature stop codon four codons into exon 7. SSCP was found to be an efficient method of typing exons 6 and 7 in a panel of 46 bone marrow donors. All three alleles were found to be common and one was in strong linkage disequilibrium with the presence of another KIR sequence KIR3DS1.
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Affiliation(s)
- C S Witt
- Department of Clinical Immunology and Biochemical Genetics, Royal Perth Hospital, Western Australia, Australia
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23
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Tian H, Brody LC, Landers JP. Rapid detection of deletion, insertion, and substitution mutations via heteroduplex analysis using capillary- and microchip-based electrophoresis. Genome Res 2000; 10:1403-13. [PMID: 10984458 PMCID: PMC310899 DOI: 10.1101/gr.132700] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
In this report, we explore the potential of capillary and microchip electrophoresis for heteroduplex analysis- (HDA) based mutation detection. Fluorescent dye-labeled primers (6-FAM-tagged) were used to amplify the DNA fragments ranging from 130 to 400 bp. The effects of DNA fragment length, matrix additives, pH, and salt were evaluated for capillary electrophoresis- (CE) and/or microchip electrophoresis-based HDA, using six heterozygous mutations, 185delAG, E1250X (3867GT), R1443G (4446CG), 5382insC, 5677insA in BRCA1, and 6174delT in BRCA2. For this system, the effective fragment size for CE-based HDA was found in the range of 200-300 bp, however, the effective range was 150-260 bp for microchip-based HDA. Sensitivity studies show CE-based HDA could detect a mutated DNA present at only 1%-10% of the total DNA. Discrimination between wild-type and deletion or insertion mutations in BRCA1 and BRCA2 with CE-based HDA could be achieved in <8 min, while the substitution mutations required 14 min of analysis time. For each mutation region, 15 samples were run to confirm the accuracy and reproducibility of the method. Using the method described, two previously reported mutations, E1038G (3232AG, missense) and 4427 C/T (4427CT, polymorphism), were detected in the tested samples and confirmed by DNA sequencing. Translation of the CE-based methodology to the microchip format allowed the analysis time for each mutation to be decreased to 130 sec. Based on the results obtained with this model system, it is possible that CE-based HDA methodologies can be developed and used effectively in genetic testing. The fast separation time and automated operation afforded with CE instrumentation provide a powerful system for screening mutations that include small deletions, insertions, and point mutations. Translation to the microchip platform, especially to a multichannel microchip system, would allow for screening mutations with high throughput.
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Affiliation(s)
- H Tian
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
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24
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Spitzer E, Abbaszadegan MR, Schmidt F, Hauser A, Buwitt U, Lauter FR, Pötschick K, Krocker J, Elling D, Grosse R. Detection of BRCA1 and BRCA2 mutations in breast cancer families by a comprehensive two-stage screening procedure. Int J Cancer 2000; 85:474-81. [PMID: 10699917 DOI: 10.1002/(sici)1097-0215(20000215)85:4<474::aid-ijc5>3.0.co;2-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We have developed a 2-stage protocol for BRCA1 and BRCA2 mutation screening from blood spot paper. Stage 1 screening was aimed to analyze patients at highest risk for the most common disease-associated sequence variants listed in the BIC database. Accordingly, stage1 testing implied detection of 18 disease- associated BRCA1 and 9 BRCA2 mutations by adapting the 5' nuclease assay to heterozygote screening. For stage 2 screening, we applied the conformation sensitive gel electrophoresis (CSGE) method by adapting this technique to automated heteroduplex analysis of BRCA1 and BRCA2 using fragment scanning on an ABI 377 sequencing device. Of the 120 patients with a family history of breast and ovarian cancer who took part in this study so far, 45 entered stage 1 testing. Disease-associated mutations were detected in 6 patients by stage 1 testing (13%). For these patients, the final result was available within 10 days. Mutation 300T-->G was found in 2 patients. One patient with mutation 3036delACAA in BRCA2 reported only 1 sister with a multifocal bilateral breast cancer. New disease-associated mutations were detected in 2 of the 114 patients who entered the stage 2 test (1.7%). Of particular interest was 1 patient who was diagnosed with a medullary breast carcinoma at age 39 and who had no family history of breast cancer. We conclude that pre-screening by 5' nuclease assay for the mutations most frequently seen in a given population represents a relatively effective first line of analysis. Subsequent detailed analysis by fluorescence conformation sensitive gel electrophoresis (F-CSGE) and fragment sequencing is a sensitive alternative to full nucleotide sequencing.
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Affiliation(s)
- E Spitzer
- Institute of Medical Molecular Diagnostics Ltd., Berlin, Germany
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25
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Tian H, Jaquins-Gerstl A, Munro N, Trucco M, Brody LC, Landers JP. Single-strand conformation polymorphism analysis by capillary and microchip electrophoresis: a fast, simple method for detection of common mutations in BRCA1 and BRCA2. Genomics 2000; 63:25-34. [PMID: 10662541 DOI: 10.1006/geno.1999.6067] [Citation(s) in RCA: 93] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
As a result of intensive studies on hereditary breast and ovarian cancers, two breast cancer susceptibility genes, BRCA1 and BRCA2, have been identified. In each gene, a small number of specific mutations have been found at relatively high frequency in certain ethnic populations. The mutations, 185delAG and 5382insC in BRCA1 and 6174delT in BRCA2, have been identified as common mutations in the Ashkenazi Jewish population, with a combined frequency of 2.0 to 2.5%. Women who have one of the above three common mutations are at a high risk of developing breast or ovarian cancer. Consequently, accurate and cost-effective detection of these three mutations may have important implications for risk assessment in susceptible women and men. In this report, we describe a fast and simple capillary electrophoresis (CE)-based method using a polymer network for screening the three common mutations in BRCA1 and BRCA2. Fluorescent dye-labeled primers (6-FAM-tagged) were used to amplify three DNA fragments of 258, 296, and 201 bp for detection of the 185delAG, 5382insC, and 6174delT mutations, respectively. After the PCR products were denatured, a single-strand conformation polymorphism (SSCP) profile could be obtained for each mutation in less than 10 min by CE in a polymer network. We demonstrate the potential provided by translating this assay to the microchip format where the SSCP analysis is complete in 120 s, representing only a fraction of the reduction in analysis time that can be achieved with microchip technology. The speed and simplicity of the SSCP methodology for detection of these mutations make it attractive for use in the clinical diagnostic laboratory.
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Affiliation(s)
- H Tian
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
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26
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Arnold N, Gross E, Schwarz-Boeger U, Pfisterer J, Jonat W, Kiechle M. A highly sensitive, fast, and economical technique for mutation analysis in hereditary breast and ovarian cancers. Hum Mutat 1999. [PMID: 10502781 DOI: 10.1002/(sici)1098-1004(199910)14:4%3c333::aid-humu9%3e3.0.co;2-c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Mutation analysis of complex genes without hotspots for sequence variations, such as BRCA1, is time-consuming and expensive. Of all currently available methods, direct sequencing has the highest sensitivity, but also the highest costs. Other techniques, such as SSCP, DGGE, and PTT, are more economical but, depending on the experience of the investigator, have at best a sensitivity of 90%. We investigated in a prospective study the feasibility and accuracy of the DHPLC technique. We present the application of the DHPLC protocol for BRCA1 mutation detection on a HPLC device from Bio-Tek Kontron Instruments (Neufahrn, Germany). DNA from 46 women with hereditary breast and ovarian cancer undergoing genetic testing for BRCA1 mutations were tested. Of 1,518 amplicons analyzed by DHPLC, corresponding to 33 fragments spanning the entire BRCA1 gene, 626 were also directly sequenced. The comparison demonstrated that DHPLC detected all alterations found by direct sequencing. No false-positive signals were seen in cases of homozygous sequences. Further, no false-negative results were ever obtained in women with mutations or polymorphisms, or both. In cases of known genetic variations, the nature of the alterations could be predicted by DHPLC. We also compared different separation matrices. Up to about 500 injections, no significant differences in sensitivity could be observed between poly(styrene divinylbenzene) and end-capped silica based columns. However, after more than 500 injections, the resolution of hetero- from homoduplex deteriorated rapidly on silica columns.
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Affiliation(s)
- N Arnold
- Department of Gynecology and Obstetrics, Christian-Albrechts-Universität, Kiel, Germany
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27
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Abstract
Mutation analysis of complex genes without hotspots for sequence variations, such as BRCA1, is time-consuming and expensive. Of all currently available methods, direct sequencing has the highest sensitivity, but also the highest costs. Other techniques, such as SSCP, DGGE, and PTT, are more economical but, depending on the experience of the investigator, have at best a sensitivity of 90%. We investigated in a prospective study the feasibility and accuracy of the DHPLC technique. We present the application of the DHPLC protocol for BRCA1 mutation detection on a HPLC device from Bio-Tek Kontron Instruments (Neufahrn, Germany). DNA from 46 women with hereditary breast and ovarian cancer undergoing genetic testing for BRCA1 mutations were tested. Of 1,518 amplicons analyzed by DHPLC, corresponding to 33 fragments spanning the entire BRCA1 gene, 626 were also directly sequenced. The comparison demonstrated that DHPLC detected all alterations found by direct sequencing. No false-positive signals were seen in cases of homozygous sequences. Further, no false-negative results were ever obtained in women with mutations or polymorphisms, or both. In cases of known genetic variations, the nature of the alterations could be predicted by DHPLC. We also compared different separation matrices. Up to about 500 injections, no significant differences in sensitivity could be observed between poly(styrene divinylbenzene) and end-capped silica based columns. However, after more than 500 injections, the resolution of hetero- from homoduplex deteriorated rapidly on silica columns.
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Affiliation(s)
- N Arnold
- Department of Gynecology and Obstetrics, Christian-Albrechts-Universität, Kiel, Germany
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28
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Highsmith WE, Jin Q, Nataraj AJ, O'Connor JM, Burland VD, Baubonis WR, Curtis FP, Kusukawa N, Garner MM. Use of a DNA toolbox for the characterization of mutation scanning methods. I: construction of the toolbox and evaluation of heteroduplex analysis. Electrophoresis 1999; 20:1186-94. [PMID: 10380758 DOI: 10.1002/(sici)1522-2683(19990101)20:6<1186::aid-elps1186>3.0.co;2-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
A systematic characterization of the effects of important physical parameters on the sensitivity and specificity of methods in searching for unknown base changes (mutations or single nucleotide polymorphisms) over a relatively long DNA segment has not been previously reported. To this end, we have constructed a set of molecules of varying G+C content (40, 50, and 60% GC) having all possible base changes at a particular location - the "DNA toolbox". Exhaustive confirmatory sequencing demonstrated that there were no other base changes in any of the clones. Using this set of clones as polymerase chain reaction (PCR) templates, amplicons of various lengths with the same base mutated to all other bases were generated. The behavior of these constructs in manual and automated heteroduplex analysis was analyzed as a function of the size and overall base content of the fragment, the nature and location of the base change. Our results show that in heteroduplex analysis, the nature of the mismatched base pair is the overriding determinant for the ability to detect the mutation, regardless of fragment length, GC content, or the location of the mutation.
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Affiliation(s)
- W E Highsmith
- Department of Pathology, University of Maryland Medical School, Baltimore, USA
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29
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Abstract
Cleavage-based methods of mutation detection offer a simple and intuitive means to detect and in most cases locate mutations within DNA fragment sizes ranging from 500 to 1500 bases. Their main advantages as a presequencing screening technology when scanning for unknown mutations is the potential to increase throughput by multiplexing. Combined with lower reagent costs per sample, mutation scanning methods offer significant advantages over currently available sequencing techniques and are likely to be of increasing importance as genomic sequence data becomes more readily available. Although enzymatic methods offer the advantages of simpler and less hazardous protocols, at present the most robust cleavage methods are based around chemical methods.
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Affiliation(s)
- G R Taylor
- Regional DNA Laboratory, St. James's University Hospital, Leeds, UK.
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30
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Hinks JL, Winship PR, Makris M, Preston FE, Peake IR, Goodeve AC. A rapid method for haemophilia B mutation detection using conformation sensitive gel electrophoresis. Br J Haematol 1999; 104:915-8. [PMID: 10192459 DOI: 10.1046/j.1365-2141.1999.01274.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Conformation sensitive gel electrophoresis (CSGE) was confirmed as an effective procedure for screening the factor IX (FIX) gene by detecting 10/10 previously known FIX gene mutations. The FIX genes of a further 11 haemophilia B patients with unknown mutations were then screened and an abnormal CSGE profile was identified in all cases. Subsequent DNA sequencing demonstrated one of these to be a novel mutation (31133insT, Arg338Fs), the remaining 10 having been previously reported on the haemophilia B database. Mutation screening of the FIX gene using CSGE was demonstrated to be a rapid and efficient means of carrier analysis in families with haemophilia B.
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Affiliation(s)
- J L Hinks
- Division of Molecular and Genetic Medicine, University of Sheffield, Royal Hallamshire Hospital
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31
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Abstract
The neuronal ceroid lipofuscinoses (NCLs), also referred to as Batten disease, are a group of neurodegenerative disorders characterised by the accumulation of an autofluorescent lipopigment in many cell types. Different NCL types are distinguished according to age of onset, clinical phenotype, ultrastructural characterisation of the storage material, and chromosomal location of the disease gene. At least eight genes underlie the NCLs, of which four have been isolated and mutations characterised: CLN1, CLN2, CLN3, CLN5. Two of these genes encode lysosomal enzymes, and two encode transmembrane proteins, at least one of which is likely to be in the lysosomal membrane. The basic defect in the NCLs appears to be associated with lysosomal function.
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Affiliation(s)
- S E Mole
- Department of Paediatrics, Royal Free and University College Medical School, University College London, The Rayne Institute, London, United Kingdom.
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