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snp array experiments  (Integragen sa)
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Integragen sa snp array experiments
( a ) An integrative ‘cluster of cluster' approach was used to define robust molecular subtypes of 141 oligodendroglial tumours. Consensus clustering was used to assign molecular classes on the basis of mRNA <t>data,</t> <t>DNA</t> methylation data and microRNA data independently. Consensus ‘clusters of clusters' were subsequently identified on the basis of the classes labels resulting from previous independent classifications. ( b ) Clinical annotations and common genomic alterations associated to each subtype. Genomic alterations were identified through the analysis of <t>SNP</t> arrays. For each clinical and molecular characteristic we performed χ 2 tests to assess the strength of association with the five-class system.
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( a ) An integrative ‘cluster of cluster' approach was used to define robust molecular subtypes of 141 oligodendroglial tumours. Consensus clustering was used to assign molecular classes on the basis of mRNA data, DNA methylation data and microRNA data independently. Consensus ‘clusters of clusters' were subsequently identified on the basis of the classes labels resulting from previous independent classifications. ( b ) Clinical annotations and common genomic alterations associated to each subtype. Genomic alterations were identified through the analysis of SNP arrays. For each clinical and molecular characteristic we performed χ 2 tests to assess the strength of association with the five-class system.

Journal: Nature Communications

Article Title: Integrated multi-omics analysis of oligodendroglial tumours identifies three subgroups of 1p/19q co-deleted gliomas

doi: 10.1038/ncomms11263

Figure Lengend Snippet: ( a ) An integrative ‘cluster of cluster' approach was used to define robust molecular subtypes of 141 oligodendroglial tumours. Consensus clustering was used to assign molecular classes on the basis of mRNA data, DNA methylation data and microRNA data independently. Consensus ‘clusters of clusters' were subsequently identified on the basis of the classes labels resulting from previous independent classifications. ( b ) Clinical annotations and common genomic alterations associated to each subtype. Genomic alterations were identified through the analysis of SNP arrays. For each clinical and molecular characteristic we performed χ 2 tests to assess the strength of association with the five-class system.

Article Snippet: A 1-μg volume from each DNA and RNA sample was used for SNP array experiments (outsourced to the Integragen Company Paris, France) and to perform the gene expression analysis, respectively.

Techniques: DNA Methylation Assay