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Array-Based Applications

Microarray technologies use hybridization of labeled samples onto probes of known sequence complementary to the regions of interest on a solid surface. They allow analysis of predefined locations on the genome to assess sequence base a specific positions (genotype), or quantify the number of molecules of a gene or a chromosome region (copy number analysis of DNA, expression analysis of RNA or binding of DNA or RNA associated proteins).
The number of microarray elements analyzed go from 15.000 to 5.000.000 including many species and specific applications. Assays are designed to process between 1 and 96 samples per batch, depending on the specific application.

RNA expression profiling

Profiling of total RNA, mRNA or rRNA depleted RNA can be performed using commercial as well as customized probe designs. We offer pre-made or customizable Agilent in situ synthesis probe microarrays (8x60K format) and pre-made Illumina beadarray technologies for RNA expression profiling (8x24K, 6x48K and 12x48K formats). A minimum of 8 to 24 samples may be required depending on the platform chosen.

Small RNA expression profiling

Profiling of microRNA from total RNA or small RNA fraction depleted RNA can be performed pre-made or customizable Agilent in situ synthesis probe microarrays (8x15K format) . A minimum of 8 to 24 samples may be required depending on the platform chosen.

Methylation profiling

Methylation analysis can be perfomed on bisulphite converted DNA by Infinium assay from Illumina (12x450K) or using methylcytosine immunoprecipitation (MeDIP) on Agilent promoter, CpG island or custom tiling arrays (8x60K to 2x400K). 2 to 24 samples are required depending on the platform chosen.

Copy number analysis

Analysis of chromosome rearrangements resulting in deletion, duplication, copy gain or loss may be analyzed using Agilent array comparative hybridization arrays (aCGH arrays 8x60K to 1x1M)) or with Illumina SNP beadarrays (Infinium assay 12x50K to 4x5M). A mínimum of 2 to 24 samples may be required depending on the platform chosen.

Genotyping

Single nucleotide polymorphisms (SNPs) can be determined on a global scale. This has been the major source of information used in genomewide association studies (GWAS). It can be done on Illumina SNP arrays mentioned before (Infinium 12x50K to 4x5M), which may focus on common (less than 5% MAF) to rare variants (<1% MAF). Minimum number of samples is 16 to 24 depending on platform chosen.

LOH analysis

It is possible to establish loss of heterozygosity due to uniparental disomy or duplication deletion concurrent events using Agilent aCGH+SNP arrays (2x400K) or Illumina SNP arrays (12x50K to 4x5M). Agilent arrays have a resolution of 5 Mb (ideal for low resolution LOH profiling in non-tumor samples) whereas SNP arrays can resolve down to subkb resolution (and can be applied to screen for both constitutive or somatic LOH). 4 to 24 samples are required depending on the platform chosen.

Chromatin analysis (CHIP on chip and MeDIP on chip)

By using specific antibodies against protein factors bound to chromatin (RNA polymerase subunits, histones, chromatin remodellers or transcription factors) it is possible to immunoprecipitate bound complexes that have been fixed in vivo and establish the bound regions through hybridization onto probes design specific regions or tiled along the entire genome. This can be done using Agilent promoter, CpG island or custom tiling 1x60K to 1x1M arrays. 2 to 16 samples are required depending on the platform chosen.
 

Price

Prices depend on the combination of services required. Please see general pricing guidellines


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Generalitat de Catalunya

Unió Europea

CSIC

Universitat Autònoma de Barcelona

Ajuntament de Badalona

Institut Català de la Salut

Germans Trias i Pujol Hospital

Fundació Institut d'investigació en Ciències de la Salut Germans Trias i Pujol