Genotyping and annotation of Affymetrix SNP arrays

In this paper we develop a new method for genotyping Affymetrix single nucleotide polymorphism (SNP) array. The method is based on (i) using multiple arrays at the same time to determine the genotypes and (ii) a model that relates intensities of individual SNPs to each other. The latter point allows us to annotate SNPs that have poor performance, either because of poor experimental conditions or because for one of the alleles the probes do not behave in a dose–response manner. Generally, our method agrees well with a method developed by Affymetrix. When both methods make a call they agree in 99.25% (using standard settings) of the cases, using a sample of 113 Affymetrix 10k SNP arrays. In the majority of cases where the two methods disagree, our method makes a genotype call, whereas the method by Affymetrix makes a no call, i.e. the genotype of the SNP is not determined. By visualization it is indicated that our method is likely to be correct in majority of these cases. In addition, we demonstrate that our method produces more SNPs that are in concordance with Hardy–Weinberg equilibrium than the method by Affymetrix. Finally, we have validated our method on HapMap data and shown that the performance of our method is comparable to other methods

L’utilisation des réseaux sociaux (Snapchat, WhatsApp et Instagram) et le cyberbullying

100% des jeunes possèdent un téléphone portable, 99% ont un ordinateur et 97% ont accès à Internet (Waller et al., 2016). Ces nouveaux moyens technologiques font partie de notre quotidien. Depuis l’apparition de ces réseaux, un nouveau mouvement est né : le cyberbullying. Ce harcèlement par Internet consiste à l’utilisation de technologies modernes de communication afin de nuire aux autres de manière délibérée et agressive. Quand les jeunes arrivent en classe, ils apportent avec eux l’entier de leur vécu quotidien, familial ou encore émotionnel. Les problèmes liés à l’utilisation massive de ces réseaux font partie de notre quotidien d’enseignant. Malheureusement, les études faites jusqu’au jour d’aujourd’hui portent en majeure partie sur les élèves entre 13 ans et plus. Mais qu’en est-il des jeunes âgés entre 9 et 12 ans ? Notre travail de recherche porte donc sur l’utilisation des réseaux sociaux (Snapchat, Instagram et WhatsApp) et le cyberbullying. Deux outils différents ont été utilisés lors de cette recherche : des questionnaires afin d’avoir des résultats quantitatifs et deux entretiens afin d’avoir un point de vue qualitatif. Nos résultats montrent que WhatsApp est le réseau social le plus utilisé, suivi d’Instagram en deuxième position et finalement de Snapchat. Les élèves considèrent le nombre de dangers et de conflits sur les réseaux comme très faibles. Ils avouent tout de même donner plus d’informations personnelles sur WhatsApp que sur les autres réseaux choisis dans l’étude. Concernant leur vision du contrôle des parents, ils l’estiment très faible. Cependant, il s’agit uniquement de leur avis, il serait intéressant de savoir la réalité des faits en interrogeant les parents. Les deux sujets interrogés savent définir le cyberbullying et connaissent les différents acteurs agissant au sein de cette forme de harcèlement. Ils sont également conscients des différents risques, conséquences ou sentiments que peut ressentir une cyber-victime mais n’abordent pas du tout ceux concernant le témoin ou le cyber-harceleur. En conclusion, notre recherche montre que les réseaux sociaux font partie intégrante du quotidien d’un grand nombre d’élèves. Il est donc essentiel que les enseignants s’interrogent sur les moyens de gérer les problèmes que ceux-ci peuvent amener en classe mais également les moyens de les éviter

The association between genetic variants in hMLH1 and hMSH2 and the development of sporadic colorectal cancer in the Danish population

<p>Abstract</p> <p>Background</p> <p>Mutations in the mismatch repair genes <it>hMLH1 </it>and <it>hMSH2 </it>predispose to hereditary non-polyposis colorectal cancer (HNPCC). Genetic screening of more than 350 Danish patients with colorectal cancer (CRC) has led to the identification of several new genetic variants (e.g. missense, silent and non-coding) in <it>hMLH1 </it>and <it>hMSH2</it>. The aim of the present study was to investigate the frequency of these variants in <it>hMLH1 </it>and <it>hMSH2 </it>in Danish patients with sporadic colorectal cancer and in the healthy background population. The purpose was to reveal if any of the common variants lead to increased susceptibility to colorectal cancer.</p> <p>Methods</p> <p>Associations between genetic variants in <it>hMLH1 </it>and <it>hMSH2 </it>and sporadic colorectal cancer were evaluated using a case-cohort design. The genotyping was performed on DNA isolated from blood from the 380 cases with sporadic colorectal cancer and a sub-cohort of 770 individuals. The DNA samples were analyzed using Single Base Extension (SBE) Tag-arrays. A Bonferroni corrected Fisher exact test was used to test for association between the genotypes of each variant and colorectal cancer. Linkage disequilibrium (LD) was investigated using HaploView (v3.31).</p> <p>Results</p> <p>Heterozygous and homozygous changes were detected in 13 of 35 analyzed variants. Two variants showed a borderline association with colorectal cancer, whereas the remaining variants demonstrated no association. Furthermore, the genomic regions covering <it>hMLH1 </it>and <it>hMSH2 </it>displayed high linkage disequilibrium in the Danish population. Twenty-two variants were neither detected in the cases with sporadic colorectal cancer nor in the sub-cohort. Some of these rare variants have been classified either as pathogenic mutations or as neutral variants in other populations and some are unclassified Danish variants.</p> <p>Conclusion</p> <p>None of the variants in <it>hMLH1 </it>and <it>hMSH2 </it>analyzed in the present study were highly associated with colorectal cancer in the Danish population. High linkage disequilibrium in the genomic regions covering <it>hMLH1 </it>and <it>hMSH2</it>, indicate that common genetic variants in the two genes in general are not involved in the development of sporadic colorectal cancer. Nevertheless, some of the rare unclassified variants in <it>hMLH1 </it>and <it>hMSH2 </it>might be involved in the development of colorectal cancer in the families where they were originally identified.</p

Functional examination of MLH1, MSH2, and MSH6 intronic mutations identified in Danish colorectal cancer patients

BACKGROUND: Germ-line mutations in the DNA mismatch repair genes MLH1, MSH2, and MSH6 predispose to the development of colorectal cancer (Lynch syndrome or hereditary nonpolyposis colorectal cancer). These mutations include disease-causing frame-shift, nonsense, and splicing mutations as well as large genomic rearrangements. However, a large number of mutations, including missense, silent, and intronic variants, are classified as variants of unknown clinical significance. METHODS: Intronic MLH1, MSH2, or MSH6 variants were investigated using in silico prediction tools and mini-gene assay to asses the effect on splicing. RESULTS: We describe in silico and in vitro characterization of nine intronic MLH1, MSH2, or MSH6 mutations identified in Danish colorectal cancer patients, of which four mutations are novel. The analysis revealed aberrant splicing of five mutations (MLH1 c.588 + 5G > A, MLH1 c.677 + 3A > T, MLH1 c.1732-2A > T, MSH2 c.1276 + 1G > T, and MSH2 c.1662-2A > C), while four mutations had no effect on splicing compared to wild type (MLH1 c.117-34A > T, MLH1 c.1039-8 T > A, MSH2 c.2459-18delT, and MSH6 c.3439-16C > T). CONCLUSIONS: In conclusion, we classify five MLH1/MSH2 mutations as pathogenic, whereas four MLH1/MSH2/MSH6 mutations are classified as neutral. This study supports the notion that in silico prediction tools and mini-gene assays are important for the classification of intronic variants, and thereby crucial for the genetic counseling of patients and their family members