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Detection of mutations and intragenic rearrangements in BRCA1 and BRCA2 genes by sequencing and MLPA method
PECHOVÁ, Kristýna
In my bachelor thesis I dealt with the detection of mutations in BRCA genes and their effect on the development of breast cancer. Nowadays, this topic is very important, because breast cancer is the most common cancer among women in the Czech Republic (Weinberger a Zikán, 2016). In the theoretical part I focused on breast cancer, particularly on its diagnosis and consequent treatment. I also dedicated genetic counselling and examination, which is very important for the diagnosis of hereditary forms of cancer. I mentioned basic information about BRCA genes, and their protein products and I summarized the issue of mutations in these genes and their relationship to cancer, particularly breast and ovarian. In the practical part, I focused on the examination of selected areas of BRCA genes by the Sanger sequencing method. At present, BRCA genes are examined by the NGS method, because it allows for the analysis of all exons of one particular gene at once, but this testing wasn't possible to realize in my laboratory conditions, therefore I have chosen the method of Sanger sequencing, which does, however, have certain capacity limitations. By using the PCR method, I prepared samples for testing by Sanger sequencing. This testing was conducted by the firm Genseq s.r.o. In the last part of my thesis I processed the obtained sequences and I evaluated the results. I examined a total of 20 anonymized samples using the sequencing method. Mutation was present in 4 samples of the total amount - one was pathogenic, one benign and two of uncertain significance.
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Gene sequencing in patients with cancer anamnesis
MARKOVÁ, Iveta
Cancer is the second most common cause of death in the Czech Republic, of which 5-10% are occupied by hereditary cancer syndromes. They are caused by a congenital - hereditary mutation in one of the alleles of the genes, when after the second random intervention in the other allele hereditary cancer develops. It is important to distinguish between hereditary and sporadic carcinomas due to the high risk of inheritance of mutated alleles in the family. The indication may be, for example, the onset of the disease at a young age or the recurrence of the cancer in the family In my work I focused on the analysis and evaluation of data obtained by Sanger sequencing. The aim was to find mutations in the genes mentioned below and to evaluate their pathogenicity by comparison with databases. In the theoretical part of the bachelor thesis I deal with cancer in general and hereditary cancer. I specify the hereditary breast and ovarian cancer syndrome, including genes, that may cause this syndrome - BRCA1, BRCA2, TP53, PTEN, ATM, PALB2, I also deal with Lynch syndrome and the MMR gene system. Last but not least, I describe a familial adenomatous polyposis associated with the APC gene. In the research part I focused on the examination of selected areas of 18 anonymized samples in the gene PALB2 - exon 13 and in the gene BRCA2 - exon 10/4 and exon 11/12. Using the PCR method, I prepared the samples for Sanger sequencing, which then took place in GenSeq s.r.o. In the last part of my work I deal with the analysis and evaluation of the results using the BioEdit program and the NCBI database. I found a mutation in 5 samples - in 4 it was a deletion of one nucleotide with a conflicting interpretation of pathogenicity, the last mutation was pathogenic - causes hereditary breast and ovarian cancer syndrome, it was a nucleotide duplication.
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Clinical and genetic aspects of familial breast cancer: Frequency of recurrent mutations in BRCA1 and BRCA2 genes in Czech republic and the role of NBN gene
Matějů, Martin ; Novotný, Jan (advisor) ; Konopásek, Bohuslav (referee) ; Vaňásek, Jaroslav (referee)
Summary: Background: An increased risk for development of hereditary breast cancer is associated with germline mutations in BRCA1/2 and the influence of NBN mutations is also supposed. The aim of this study is to specify the frequency of recurrent mutations in BRCA1/2 in unselected breast cancer patients and the frequency of most common pathogenic mutations in NBN in Czech republic, to assess current criteria for genetic testing and to consider the addition of NBN to the tested genes. Methods: Screening for recurrent mutations 5382insC and 300T>G in BRCA1 was performed by RFLP, screening for mutations in exon 11 of BRCA1 was performed by PTT, screening for mutations in a selected region of exon 11 of BRCA2 by DHPLC, and screening for mutations in exon 6 of NBN by HRMA. All the mutations were confirmed by direct sequencing. Results: In 679 unselected breast cancer patients 7 carriers of 5382insC, 3 of 300T>G, and 4 of other mutations in BRCA1 were identified. 2 locally prevalent mutations were found in BRCA2. In 730 controls only one 5382insC BRCA1 mutation was identified. Out of 5 NBN mutations found in 600 high-risk patients two were 657del5 and one R215W. A total of 8 NBN mutation carriers were identified among 703 breast cancer patients, 2 of them 657del5 carriers and three R215W carriers. In 915...
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Clinical and genetic aspects of familial breast cancerFrequency of recurrent mutations in BRCA1 and BRCA2 genes in Czech republic and the role of NBN gene
Matějů, Martin ; Novotný, Jan (advisor) ; Konopásek, Bohuslav (referee) ; Vaňásek, Jaroslav (referee)
Summary: Background: An increased risk for development of hereditary breast cancer is associated with germline mutations in BRCA1/2 and the influence of NBN mutations is also supposed. The aim of this study is to specify the frequency of recurrent mutations in BRCA1/2 in unselected breast cancer patients and the frequency of most common pathogenic mutations in NBN in Czech republic, to assess current criteria for genetic testing and to consider the addition of NBN to the tested genes. Methods: Screening for recurrent mutations 5382insC and 300T>G in BRCA1 was performed by RFLP, screening for mutations in exon 11 of BRCA1 was performed by PTT, screening for mutations in a selected region of exon 11 of BRCA2 by DHPLC, and screening for mutations in exon 6 of NBN by HRMA. All the mutations were confirmed by direct sequencing. Results: In 679 unselected breast cancer patients 7 carriers of 5382insC, 3 of 300T>G, and 4 of other mutations in BRCA1 were identified. 2 locally prevalent mutations were found in BRCA2. In 730 controls only one 5382insC BRCA1 mutation was identified. Out of 5 NBN mutations found in 600 high-risk patients two were 657del5 and one R215W. A total of 8 NBN mutation carriers were identified among 703 breast cancer patients, 2 of them 657del5 carriers and three R215W carriers. In 915...
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Intracellular signalling of Chk2 kinase and impact of its defects in oncogenesis
Stolařová, Lenka ; Kleibl, Zdeněk (advisor) ; Brábek, Jan (referee)
Chk2 (checkpoint kinase 2), a regulatory protein of the cell cycle checkpoints, is coded by CHEK2 gene. Chk2 belongs to serine/threonine kinase family and its dominant activity is in regulation and signal distribution of intracellular response to DNA damage. The upstream regulator of Chk2 protein is the ATM kinase that activates Chk2 by its phosphorylation on Thr68 localized in FHA domain. This in turn leads to the conformation change inducing homodimerization of Chk2 protomers and their activating phosphorylation within their kinase domains. Upon phosphorylation, catalytically active Chk2 protomers dissociate and phosphorylate various intracellular proteins (incl. p53, E2F-1, BRCA1, Cdc25A a C, BRCA2 a PLK3). By regulation of these proteins, Chk2 contributes to the cell cycle arrest, regulation of DNA repair and apoptosis. Germline mutations in CHEK2 gene were identified with the increased frequency in many human cancers, including breast and colorectal cancer. Hence, the failure of Chk2 intracellular activity contributes to the process of malignant transformation.
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Detection of mutations associated with increased incidence of breast and ovarian tumors using modern molecular biology methods
RÁJOVÁ, Kristýna
Breast cancer and ovarian cancer is one of the most common malignancies what women have in the Czech Republic and the incidence of new diagnoses has a tendency to increase. It is estimated that 5-10 per cent of these tumours is cause by pathogenic mutations in highly penetrance tumour suppressor genes BRCA1 or BRCA2. The main function of these genes are repair of double strand DNA breaks and another function is control of cell division and participate on regulation of transcription and chromatin remodeling. The aim of this bachelors thesis is to summarize current knowledge of the "Gene mutations" topic, the function of the genes BRCA1 and BRCA 2 and their link with hereditary breast and ovarian cancer, an overview of possible detection methods and particularly also the summary of the Czech studies of detection mutations in the Czech Republic. It pointed out to the strong effect of the founder mutation. Among the most frequently found mutations are mutations as c.5266dupC, c.181T> G and c.3700_3704del5 in the gene BRCA1 and c.7913_7917del5 and c.8537_8538del2 in the BRCA2 gene. In the experimental part of the work I have tried to optimize ARMS PCR method for point mutation c.5266dupC. This mutation has proved to be one of the most common mutations not only in the Czech Republic but also in Europe. The objective was to optimize the PCR ARMS in the conditions of the GENLABS Ltd. laboratory. The main goal of the optimization was the selection of appropriate PCR mix and optimal temperature of PCR profile at which the quality and quantity of the yield was visualized on gel electrophoresis as specific and highest as it is possible. The aim of this part is also practically to do the DNA isolation from peripheral blood and buccal swab, preparation and execution of the PCR reaction and detection of PCR products by gel electrophoresis. Eventually, we managed to optimize a method for the two different matrices for the DNA isolates, and peripheral blood. Unfortunately the method for the buccal swab was not successful. During gradually temperature increasing, we started the process of annealing at 55°C, the best results were achieved at a temperature of 65.5 ° C using gb Basic PCR Master Mix from the Generi Biotech firm. In the future this optimization might allow the using of method for mutation in the gene BRCA1 c.5266dupC for the routine practise in the laboratory.
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