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Cancer the second most common causes of death in the Czech Republic. Carriers of mutations in genes predisposing to hereditary cancers represent a small but clinically significant group of high risk individuals. Today, dozens of predisposing genes for hereditary tumor syndromes are known and targeted next generation sequencing (NGS) has become a standard approach for their analysis. NGS allows rapid acceleration diagnostics of causal mutation in high-risk individuals. To identify mutations in genes predisposing to hereditary cancers, we designed a panel NGS analysis including subsequent bioinformatics analysis allowing a reliable identification of single nucleotide variants, insertions/deletions, and large intragenic rearrangements. The bioinformatics procedures described in this thesis were used for panel NGS validation, but also for identification of alterations associating with so far undescribed hereditary tumor types. Bioinformatics analyzes have become the basis for the unified processing of large datasets from the CZECANCA consortium and enable the construction of a population-specific database of genotypes that serve to improve clinical diagnostics of cancer predisposition in Czech patients. The versatility of NGS also allows its use for RNA (cDNA-based) analyzes of splicing variants in the...

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Objetivo: Até 10% dos casos de câncer de mama estão associados com uma síndrome genética de predisposição ao câncer. A identificação de possíveis portadores dessas síndromes e o consequente encaminhamento para aconselhamento genético permitem a adoção de estratégias direcionadas de prevenção e rastreamento capazes de diminuir morbidade e mortalidade. O objetivo do presente estudo foi avaliar a proporção de pacientes com câncer de mama atendidos no Hospital Universitário de Santa Maria (HUSM) que necessitariam ser encaminhados para avaliação genética. Métodos: Pacientes com câncer de mama que iniciaram tratamento oncológico no HUSM durante o ano de 2014 foram considerados elegíveis. Uma entrevista foi conduzida com cada paciente para coleta de dados e exame físico dirigido. O questionário FSH-7 (Family Story Screening 7) e os critérios do NCCN (National Comprehensive Cancer Network) foram utilizados para identificar os pacientes que deveriam ser encaminhados para avaliação genética. Estes pacientes foram então avaliados quanto à indicação de teste genético - de acordo com as recomendações do NCCN para teste genético – e à probabilidade de mutações nos genes BRCA1 e BRCA2 através de modelos de predição de risco (BOADICEA, Penn II, sistema de escore de Manchester e tabelas da Myriad). Resultados: Dentre os 114 participantes do estudo, 65 (57%) preenchiam critérios de encaminhamento para avaliação genética de acordo com as diretrizes do NCCN. O questionário FHS-7 apresentou uma sensibilidade de 90% para identificar estes pacientes, com uma especificidade de 85%. A presença de história pessoal ou familiar de câncer de mama antes dos 50 anos foi o critério mais comum para indicar avaliação genética. Em relação aos testes genéticos, 52 pacientes (45%) deveriam ser testados para mutações nos genes BRCA1 e BRCA2 e 4 pacientes (3,5%) possuíam indicação de teste para mutações em TP53, de acordo com as recomendações do NCCN. Utilizando os modelos de predição de risco, 10,2% a 57,1% dos pacientes apresentavam uma probabilidade ≥ 10% de mutações em BRCA1 ou BRCA2. Conclusão: Este estudo revelou que a maioria dos pacientes com câncer de mama atendidos no HUSM possui indicação de encaminhamento para avaliação genética. A utilização de um questionário simples e rápido poderia identificar 90% destes pacientes. / Objective: Up to 10% of breast cancers are associated with a hereditary cancer syndrome. The identification of possible carriers of these syndromes and the subsequent referral for genetic counselling allow the adoption of tailored screening and prevention strategies capable of reducing morbidity and mortality. The aim of this study is to assess the proportion of patients with breast cancer treated at the University Hospital of Santa Maria (HUSM) that would need to be referred for genetic evaluation. Methods: Breast cancer patients who began cancer treatment at HUSM during the year 2014 were eligible. An interview was conducted with each patient for data collection and targeted physical examination. The FSH-7 (Family Story Screening 7) questionnaire and the NCCN (National Comprehensive Cancer Network) criteria were used to identify patients who should be referred for genetic evaluation. Then these patients were assessed for genetic testing criteria - according to the NCCN recommendations for genetic testing - and the likelihood of BRCA1 and BRCA2 mutations through risk prediction models (BOADICEA, Penn II, Manchester score system and Myriad tables). Results: Among the 114 study participants, 65 (57%) meet referral criteria for genetic evaluation according to the NCCN guidelines. The FHS-7 questionnaire showed a sensitivity of 90% to identify such patients with a specificity of 85%. The presence of personal or family history of breast cancer before age 50 was the most common criteria to indicate genetic evaluation. With respect to genetic testing, 52 patients (45%) should be tested for BRCA1 and BRCA2 mutations and 4 patients (3.5%) had test indication for TP53 mutations in accordance with the recommendations of the NCCN. Using risk prediction models, 10.2% to 57.1% of patients had a BRCA1 or BRCA2 mutations probability ≥ 10%. Conclusion: This study showed that most of the patients with breast cancer treated at HUSM have referral indication for genetic evaluation. The use of a fast and simple questionnaire could identify 90% of these patients.

Objetivo: Até 10% dos casos de câncer de mama estão associados com uma síndrome genética de predisposição ao câncer. A identificação de possíveis portadores dessas síndromes e o consequente encaminhamento para aconselhamento genético permitem a adoção de estratégias direcionadas de prevenção e rastreamento capazes de diminuir morbidade e mortalidade. O objetivo do presente estudo foi avaliar a proporção de pacientes com câncer de mama atendidos no Hospital Universitário de Santa Maria (HUSM) que necessitariam ser encaminhados para avaliação genética. Métodos: Pacientes com câncer de mama que iniciaram tratamento oncológico no HUSM durante o ano de 2014 foram considerados elegíveis. Uma entrevista foi conduzida com cada paciente para coleta de dados e exame físico dirigido. O questionário FSH-7 (Family Story Screening 7) e os critérios do NCCN (National Comprehensive Cancer Network) foram utilizados para identificar os pacientes que deveriam ser encaminhados para avaliação genética. Estes pacientes foram então avaliados quanto à indicação de teste genético - de acordo com as recomendações do NCCN para teste genético – e à probabilidade de mutações nos genes BRCA1 e BRCA2 através de modelos de predição de risco (BOADICEA, Penn II, sistema de escore de Manchester e tabelas da Myriad). Resultados: Dentre os 114 participantes do estudo, 65 (57%) preenchiam critérios de encaminhamento para avaliação genética de acordo com as diretrizes do NCCN. O questionário FHS-7 apresentou uma sensibilidade de 90% para identificar estes pacientes, com uma especificidade de 85%. A presença de história pessoal ou familiar de câncer de mama antes dos 50 anos foi o critério mais comum para indicar avaliação genética. Em relação aos testes genéticos, 52 pacientes (45%) deveriam ser testados para mutações nos genes BRCA1 e BRCA2 e 4 pacientes (3,5%) possuíam indicação de teste para mutações em TP53, de acordo com as recomendações do NCCN. Utilizando os modelos de predição de risco, 10,2% a 57,1% dos pacientes apresentavam uma probabilidade ≥ 10% de mutações em BRCA1 ou BRCA2. Conclusão: Este estudo revelou que a maioria dos pacientes com câncer de mama atendidos no HUSM possui indicação de encaminhamento para avaliação genética. A utilização de um questionário simples e rápido poderia identificar 90% destes pacientes. / Objective: Up to 10% of breast cancers are associated with a hereditary cancer syndrome. The identification of possible carriers of these syndromes and the subsequent referral for genetic counselling allow the adoption of tailored screening and prevention strategies capable of reducing morbidity and mortality. The aim of this study is to assess the proportion of patients with breast cancer treated at the University Hospital of Santa Maria (HUSM) that would need to be referred for genetic evaluation. Methods: Breast cancer patients who began cancer treatment at HUSM during the year 2014 were eligible. An interview was conducted with each patient for data collection and targeted physical examination. The FSH-7 (Family Story Screening 7) questionnaire and the NCCN (National Comprehensive Cancer Network) criteria were used to identify patients who should be referred for genetic evaluation. Then these patients were assessed for genetic testing criteria - according to the NCCN recommendations for genetic testing - and the likelihood of BRCA1 and BRCA2 mutations through risk prediction models (BOADICEA, Penn II, Manchester score system and Myriad tables). Results: Among the 114 study participants, 65 (57%) meet referral criteria for genetic evaluation according to the NCCN guidelines. The FHS-7 questionnaire showed a sensitivity of 90% to identify such patients with a specificity of 85%. The presence of personal or family history of breast cancer before age 50 was the most common criteria to indicate genetic evaluation. With respect to genetic testing, 52 patients (45%) should be tested for BRCA1 and BRCA2 mutations and 4 patients (3.5%) had test indication for TP53 mutations in accordance with the recommendations of the NCCN. Using risk prediction models, 10.2% to 57.1% of patients had a BRCA1 or BRCA2 mutations probability ≥ 10%. Conclusion: This study showed that most of the patients with breast cancer treated at HUSM have referral indication for genetic evaluation. The use of a fast and simple questionnaire could identify 90% of these patients.

Objetivo: Até 10% dos casos de câncer de mama estão associados com uma síndrome genética de predisposição ao câncer. A identificação de possíveis portadores dessas síndromes e o consequente encaminhamento para aconselhamento genético permitem a adoção de estratégias direcionadas de prevenção e rastreamento capazes de diminuir morbidade e mortalidade. O objetivo do presente estudo foi avaliar a proporção de pacientes com câncer de mama atendidos no Hospital Universitário de Santa Maria (HUSM) que necessitariam ser encaminhados para avaliação genética. Métodos: Pacientes com câncer de mama que iniciaram tratamento oncológico no HUSM durante o ano de 2014 foram considerados elegíveis. Uma entrevista foi conduzida com cada paciente para coleta de dados e exame físico dirigido. O questionário FSH-7 (Family Story Screening 7) e os critérios do NCCN (National Comprehensive Cancer Network) foram utilizados para identificar os pacientes que deveriam ser encaminhados para avaliação genética. Estes pacientes foram então avaliados quanto à indicação de teste genético - de acordo com as recomendações do NCCN para teste genético – e à probabilidade de mutações nos genes BRCA1 e BRCA2 através de modelos de predição de risco (BOADICEA, Penn II, sistema de escore de Manchester e tabelas da Myriad). Resultados: Dentre os 114 participantes do estudo, 65 (57%) preenchiam critérios de encaminhamento para avaliação genética de acordo com as diretrizes do NCCN. O questionário FHS-7 apresentou uma sensibilidade de 90% para identificar estes pacientes, com uma especificidade de 85%. A presença de história pessoal ou familiar de câncer de mama antes dos 50 anos foi o critério mais comum para indicar avaliação genética. Em relação aos testes genéticos, 52 pacientes (45%) deveriam ser testados para mutações nos genes BRCA1 e BRCA2 e 4 pacientes (3,5%) possuíam indicação de teste para mutações em TP53, de acordo com as recomendações do NCCN. Utilizando os modelos de predição de risco, 10,2% a 57,1% dos pacientes apresentavam uma probabilidade ≥ 10% de mutações em BRCA1 ou BRCA2. Conclusão: Este estudo revelou que a maioria dos pacientes com câncer de mama atendidos no HUSM possui indicação de encaminhamento para avaliação genética. A utilização de um questionário simples e rápido poderia identificar 90% destes pacientes. / Objective: Up to 10% of breast cancers are associated with a hereditary cancer syndrome. The identification of possible carriers of these syndromes and the subsequent referral for genetic counselling allow the adoption of tailored screening and prevention strategies capable of reducing morbidity and mortality. The aim of this study is to assess the proportion of patients with breast cancer treated at the University Hospital of Santa Maria (HUSM) that would need to be referred for genetic evaluation. Methods: Breast cancer patients who began cancer treatment at HUSM during the year 2014 were eligible. An interview was conducted with each patient for data collection and targeted physical examination. The FSH-7 (Family Story Screening 7) questionnaire and the NCCN (National Comprehensive Cancer Network) criteria were used to identify patients who should be referred for genetic evaluation. Then these patients were assessed for genetic testing criteria - according to the NCCN recommendations for genetic testing - and the likelihood of BRCA1 and BRCA2 mutations through risk prediction models (BOADICEA, Penn II, Manchester score system and Myriad tables). Results: Among the 114 study participants, 65 (57%) meet referral criteria for genetic evaluation according to the NCCN guidelines. The FHS-7 questionnaire showed a sensitivity of 90% to identify such patients with a specificity of 85%. The presence of personal or family history of breast cancer before age 50 was the most common criteria to indicate genetic evaluation. With respect to genetic testing, 52 patients (45%) should be tested for BRCA1 and BRCA2 mutations and 4 patients (3.5%) had test indication for TP53 mutations in accordance with the recommendations of the NCCN. Using risk prediction models, 10.2% to 57.1% of patients had a BRCA1 or BRCA2 mutations probability ≥ 10%. Conclusion: This study showed that most of the patients with breast cancer treated at HUSM have referral indication for genetic evaluation. The use of a fast and simple questionnaire could identify 90% of these patients.

Abstract Approximately 5–10% of all breast cancer cases are estimated to result from a hereditary predisposition to the disease. Currently no more than 25–30% of these familial cases can be explained by mutations in the known susceptibility genes, BRCA1 and BRCA2 being the major ones. Additional predisposing genes are therefore likely to be discovered. This study evaluates whether germline alterations in three BRCA1-associated genes, BACH1 (i.e. BRIP1/FANCJ), BARD1 and TOPBP1, contribute to familial breast cancer. Altogether 214 Finnish patients having breast and/or ovarian cancer were analysed for germline mutations in the BACH1 gene. Nine alterations were observed, four of which located in the protein-encoding region. The previously unidentified Pro1034Leu was considered a possible cancer-associated alteration as it appeared with two-fold higher frequency among cancer cases compared to controls. All the other observed alterations were classified as harmless polymorphisms. Mutation analysis of the BARD1 gene among 126 Finnish patients having family history of breast and/or ovarian cancer revealed seven alterations in the protein-encoding region. The Cys557Ser alteration was seen at an elevated frequency among familial cancer cases compared to controls (p = 0.005, odds ratio [OR] 4.2, 95% confidence interval [CI] 1.7–10.7). The other alterations appeared to be harmless polymorphisms. To evaluate further the possible effect of Cys557Ser on cancer risk, a large case-control study was performed, consisting of 3,956 cancer patients from the Nordic countries. The highest prevalence of Cys557Ser was found among breast and ovarian cancer patients from BRCA1/BRCA2 mutation-negative families (p < 0.001, OR 2.6, 95% CI 1.7–4.0). In contrast, no significant association with male breast cancer, ovarian, colorectal or prostate cancer was observed. The current study is the first evaluating the role of TOPBP1 mutations in familial cancer predisposition. The analysis of 125 Finnish patients having breast and/or ovarian cancer revealed one putative pathogenic alteration. The commonly occurring Arg309Cys allele was observed at a significantly higher frequency among familial cancer cases compared to controls (p = 0.002, OR 2.4, 95% CI 1.3–4.2). The other 18 alterations observed were classified as harmless polymorphisms.