Bioinformatic Microarray Services

BEA offers bioinformatic support for various microarray platforms, including arrays for gene expression, miRNA expression, methylation and cytogenetics. All bioinformatic services are free of charge. A basic analysis is always included, and for additional services (see below) we will assist depending on time and opportunity.

Basic Services

The analysis methods and output differ is depending on platform, but our aim is to provide the customer with results in a format that is easy to interpret and adjusted to the customers wishes. Below is a summary of the basic analysis provided for the microarray platforms BEA provides.

Gene Expression Analysis

BEA provide the Thermo Fisher/Affymetrix and Agilent array platforms. Our basic services include quality control, processing of raw data, comparisons of sample groups and annotations. The results will be summarized in Excel spreadsheets.

The Affymetrix XTA/Clariom deep platform also allows exon-level analysis and alternative splicing analysis.

miRNA Expression Analysis

The analysis methods and output is similar to the gene expression analysis, and both Thermo Fisher/Affymetrix and Agilent offers array platforms for miRNA analysis. Both of the platforms generate a quantitative signal and a qualitative detection call, and the same downstream analysis methods can be applied.

The freeware Transcriptome Analysis Console (TAC) allows integration of gene and miRNA expression analysis.

Methylation Analysis

Illumina provides the Infinium Methylation EPIC BeadChip platform for epigenome-wide association studies. BEA offers BeadStudio analysis and/or additional analysis using the R package ChAMP which allows various analysis methods for normalization, CpG and region finding etc. Analysis results are usually delivered in Excel spreadsheets.

Cytogenetic Analysis

Thermo Fisher/Affymetrix OncoScan assay enables the detection of relevant copy number variations (CNVs) such as copy number gain and loss, loss of heterozygosity (LOH), copy neutral loss of heterozygosity (cnLOH), ploidy, allele specific changes, break point determination, mosaicism, clonal heterogeneity, and chromotripsis, as well as a panel of driver somatic mutations.

BEA can provide results from analysis in Chromosome Analysis Suite (ChAS) Software, but we encourage customers to perform their own ChAS analysis, with our support if needed.

Additional Bioinformatic Services

Additional services may be visualizations like heatmaps and clusterings, enrichment analysis, various statistical methods, GEO submissions of data etc. Please contact the core facility for details.