Single Nucleotide Polymorphisms and Colorectal Cancer Risk: The First Replication Study in a South American Population

Colorectal cancer (CRC) heritability is determined by the complex interaction between inherited variants and environmental factors. CRC incidence rates have been increasing specially in developing countries, such as Brazil, where CRC is the third most frequent cancer in both genders. Genome‐wide association studies (GWAS), based on thousands of cases and controls typed at thousands of single nucleotide polymorphisms (SNPs), have identified several variants that associate with gastrointestinal cancer risk. Less of half of the familial risk has been elucidated through GWAS that identified common SNPs in almost exclusively European populations. Replication studies in admixed heterogeneous populations are scarce and most failed to replicate all the imputed SNPs. Population stratification by ethnic subgroups with different allele frequencies and so with different patterns of linkage disequilibrium may cause expurious associations. Here, we show the first replication study of CRC inherited susceptibility in South America and aimed to identify known SNPs, which are associated with CRC risk in European populations

Acessibilidade Digital em Ambientes Virtuais de Aprendizagem: uma Revisão Sistemática

Information and Communication Technologies are present in people's daily lives, causing changes in entertainment, professional personal contact, and learning. E-learning courses use these resources through Virtual Learning Environments. In this context, it is essential that this environment has accessibility resources so that people with disabilities can also follow the course. This article aims to 1) To identify the studies that are being carried out with the objective of providing digital accessibility in E-learning courses; 2) To compare the selected studies to verify possible common characteristics between the researches; 3) To present the results of the analysis done, showing the similarities and differences between the researches analyzed. A systematic review was carried out with articles, using as descriptors: "Virtual learning environment", "Accessibility" and "Disability", in which 14 articles were selected. The review found that most of the studies analyzed include people with visual impairments, use Moodle as a Virtual Learning Environment, and it was identified that the W3C and WCAG accessibility guidelines are considered in almost all articles studied. Developing proposals for accessible courses requires a multidisciplinary team, with accessibility planning from its conception. This avoids rework, costs, and expands the accessibility culture. Despite the presented studies, it is observed that accessibility in E-learning courses will still have a long way to go. Keywords: E-learning. Moodle. Inclusion.  As Tecnologias da Informação e Comunicação estão presentes na vida diária das pessoas, provocando transformações no entretenimento, contato pessoal profissional e aprendizado. Cursos à distância, empregam esses recursos, por meio de Ambientes Virtuais de Aprendizagem. Neste contexto é essencial que esse ambiente possua recursos de acessibilidade para que pessoas com deficiência também possam acompanhá-lo. Este artigo tem por objetivos 1) Identificar os estudos que estão sendo realizados com o objetivo de fornecer acessibilidade digital nos cursos à distância; 2) Comparar os trabalhos selecionados para verificar possíveis características comuns às pesquisas; 3) Apresentar os resultados da comparação feita, mostrando as semelhanças e diferenças entre as pesquisas analisadas. Foi realizada uma revisão sistemática com artigos, utilizando como descritores: “Ambiente virtual de aprendizagem”, “Acessibilidade” e “Deficiência”, tendo sido selecionados 14 trabalhos. O levantamento constatou que a maioria dos trabalhos analisados contemplam pessoas com deficiência visual e utilizam o Moodle como Ambiente Virtual de Aprendizagem, além de ter sido identificado que as diretrizes para acessibilidade W3C e WCAG são contempladas em quase todas as pesquisas. Elaborar propostas de cursos acessíveis necessita de uma equipe multidisciplinar, que planeje a acessibilidade desde a sua concepção. Isto evita retrabalho, custo e amplia a cultura da acessibilidade. Apesar dos estudos apresentados, verifica-se que a acessibilidade em cursos à distância ainda terá que percorrer um longo caminho. Palavras-chave: Educação a distância. Moodle. Inclusão

Predictive models for mutations in mismatch repair genes: implication for genetic counseling in developing countries

<p>Abstract</p> <p>Background</p> <p>Lynch syndrome (LS) is the most common form of inherited predisposition to colorectal cancer (CRC), accounting for 2-5% of all CRC. LS is an autosomal dominant disease characterized by mutations in the mismatch repair genes mutL homolog 1 (MLH1), mutS homolog 2 (MSH2), postmeiotic segregation increased 1 (PMS1), post-meiotic segregation increased 2 (PMS2) and mutS homolog 6 (MSH6). Mutation risk prediction models can be incorporated into clinical practice, facilitating the decision-making process and identifying individuals for molecular investigation. This is extremely important in countries with limited economic resources. This study aims to evaluate sensitivity and specificity of five predictive models for germline mutations in repair genes in a sample of individuals with suspected Lynch syndrome.</p> <p>Methods</p> <p>Blood samples from 88 patients were analyzed through sequencing MLH1, MSH2 and MSH6 genes. The probability of detecting a mutation was calculated using the PREMM, Barnetson, MMRpro, Wijnen and Myriad models. To evaluate the sensitivity and specificity of the models, receiver operating characteristic curves were constructed.</p> <p>Results</p> <p>Of the 88 patients included in this analysis, 31 mutations were identified: 16 were found in the MSH2 gene, 15 in the MLH1 gene and no pathogenic mutations were identified in the MSH6 gene. It was observed that the AUC for the PREMM (0.846), Barnetson (0.850), MMRpro (0.821) and Wijnen (0.807) models did not present significant statistical difference. The Myriad model presented lower AUC (0.704) than the four other models evaluated. Considering thresholds of ≥ 5%, the models sensitivity varied between 1 (Myriad) and 0.87 (Wijnen) and specificity ranged from 0 (Myriad) to 0.38 (Barnetson).</p> <p>Conclusions</p> <p>The Barnetson, PREMM, MMRpro and Wijnen models present similar AUC. The AUC of the Myriad model is statistically inferior to the four other models.</p

Clinical and Molecular Characterization of Brazilian Patients Suspected to Have Lynch Syndrome.

Lynch syndrome (LS) accounts for 3-5% of all colorectal cancers (CRC) and is inherited in an autosomal dominant fashion. This syndrome is characterized by early CRC onset, high incidence of tumors in the ascending colon, excess of synchronous/metachronous tumors and extra-colonic tumors. Nowadays, LS is regarded of patients who carry deleterious germline mutations in one of the five mismatch repair genes (MMR), mostly in MLH1 and MSH2, but also in MSH6, PMS1 and PMS2. To comprehensively characterize 116 Brazilian patients suspected for LS, we assessed the frequency of germline mutations in the three minor genes MSH6, PMS1 and PMS2 in 82 patients negative for point mutations in MLH1 and MSH2. We also assessed large genomic rearrangements by MLPA for detecting copy number variations (CNVs) in MLH1, MSH2 and MSH6 generating a broad characterization of MMR genes. The complete analysis of the five MMR genes revealed 45 carriers of pathogenic mutations, including 25 in MSH2, 15 in MLH1, four in MSH6 and one in PMS2. Eleven novel pathogenic mutations (6 in MSH2, 4 in MSH6 and one in PMS2), and 11 variants of unknown significance (VUS) were found. Mutations in the MLH1 and MSH2 genes represented 89% of all mutations (40/45), whereas the three MMR genes (MSH6, PMS1 and PMS2) accounted for 11% (5/45). We also investigated the MLH1 p.Leu676Pro VUS located in the PMS2 interaction domain and our results revealed that this variant displayed no defective function in terms of cellular location and heterodimer interaction. Additionally, we assessed the tumor phenotype of a subset of patients and also the frequency of CRC and extra-colonic tumors in 2,365 individuals of the 116 families, generating the first comprehensive portrait of the genetic and clinical aspects of patients suspected of LS in a Brazilian cohort

Characterization of germline mutations of MLH1 and MSH2 in unrelated south American suspected Lynch syndrome individuals

Lynch syndrome (LS) is an autosomal dominant syndrome that predisposes individuals to development of cancers early in life. These cancers are mainly the following: colorectal, endometrial, ovarian, small intestine, stomach and urinary tract cancers. LS is caused by germline mutations in DNA mismatch repair genes (MMR), mostly MLH1 and MSH2, which are responsible for more than 85% of known germline mutations. To search for germline mutations in MLH1 and MSH2 genes in 123 unrelated South American suspected LS patients (Bethesda or Amsterdam Criteria) DNA was obtained from peripheral blood, and PCR was performed followed by direct sequencing in both directions of all exons and intron-exon junctions regions of the MLH1 and MSH2 genes. MLH1 or MSH2 pathogenic mutations were found in 28.45% (34/123) of the individuals, where 25/57 (43.85%) fulfilled Amsterdam I, II and 9/66 (13.63%) the Bethesda criteria. The mutations found in both genes were as follows: nonsense (35.3%), frameshift (26.47%), splicing (23.52%), and missense (9%). Thirteen alterations (35.14%) were described for the first time. The data reported in this study add new information about MLH1 and MSH2 gene mutations and contribute to better characterize LS in Brazil, Uruguay and Argentina. The high rate of novel mutations demonstrates the importance of defining MLH1 and MSH2 mutations in distinct LS populations

Frequency of extra-colonic tumors in 2365 family members of 116 LS patients.

<p>Frequency of extra-colonic tumors in 2365 family members of 116 LS patients.</p

Sensitivity and specificity of clinical criteria for detecting patients with pathogenic mutations in four MMR genes (<i>MLH1</i>, <i>MSH2</i>, <i>MSH6</i> and <i>PMS2</i>).

<p>^{CI: Confidence interval}</p><p>Sensitivity and specificity of clinical criteria for detecting patients with pathogenic mutations in four MMR genes (<i>MLH1</i>, <i>MSH2</i>, <i>MSH6</i> and <i>PMS2</i>).</p

Number of CRC and extra-colonic tumors according to clinical criteria and mutation status.

<p>M:Male; F: Female</p><p>Number of CRC and extra-colonic tumors according to clinical criteria and mutation status.</p

Functional analysis of the p.Leu676Pro missense MLH1 variant.

<p>(A) Functional domains of the MLH1 protein. The new missense alteration is located in the PMS2 interaction domain. The amino acid conservation across species is presented. (B) Western blot analysis for transient transfection and immunoprecipitation of MLH1 and PMS2. Immunoprecipitation analysis showed that the protein-protein interaction between the MLH1 Leu676Pro isoform and PMS2 was equivalent to that of wild-type MLH1 and PMS2, revealing no defective interaction. SW–480 was used as a positive control. (C) Immunofluorescence staining of wild-type MLH1 and MLH1 Leu676Pro. The mutant protein was correctly imported through the nuclear pore complex (NPC) and localized almost entirely in the nucleus, similar to the wild-type MLH1 protein.</p