Department of Medical Sciences

Microarray analysis

We provide all types of services for a variety of microarray analyses. We can run all standard arrays from Affymetrix for expression studies, genotyping and copynumber variations to provide you with deep insight into your samples.

Expression analysis | Genotyping | Copy-number variation

Expression Analysis

Comprehensive transcript expression profiling is crucial to study normal biology and disease processes since phenotypic abnormalities are rarely a result of expression changes in single genes. We can provide you with different microarray assay methods assaying millions of distinct sequences in parallel which allows for the regular detection and measurement of low abundance transcripts, or rare alternative splicing events.

We offer a variety of different microarrays for different organisms and multiple array types to meet your experimental needs with the Affymetrix Clariom™ and GeneChip™ microarray designs. These whole-transcript gene expression and alternative splicing solutions allow you to measure gene expression at the transcript and exon level. More information on Whole-Transcript Gene Expression & Alternative Splicing assays can be found on the Thermo Fisher Scientific website.

We provide also access to arrays based on 3' sequence based expression profiling. Such arrays, as for example the GeneChip® Human Genome U133 Plus 2.0 Array, allow better comparison with previous data that originated from the same array type.

Measuring the changes in the miRNA expression profile is extremely important for deciphering the biological context of differentially expressed genes. GeneChip™ miRNA Arrays are powerful tools for studying the role of small non-coding RNA (miRNA, snoRNA, and scaRNA) in complex diseases, such as cancer. They can be used complementary to a gene expression analysis or used separately to interrogate miRNA profiles.

We have long experience analyzing RNA from many different species and a number of tissues as well as cell cultures and sorted cells. We can assist you in selecting the best extraction protocol for your samples. Traditionally formalin-fixed, paraffin-embedded (FFPE) tissue samples were considered difficult to use for RNA. Based on our experience it is however possible to use specific extraction protocols to obtain RNA from these very valuable samples and produce reliable expression profiles using microarrays.

We can run expression analysis for any scale of project from individual samples in a cartridge format to sets of 96 well plates for large numbers of samples with the GeneTitan® Multi-Channel (MC) Instrument.

GENOTYPING

For many species and populations pre-designed Axiom Genotyping arrays are available and customized array plates with validated genomic content from the Axiom Genomic Database can be generated easily so that you get exactly the information that you need to answer your research question for example in genome-wide association, replication, fine mapping, and candidate gene studies.

COPY NUMBER ANALYSIS

- Fresh or fresh frozen samples

The Axiom and GeneChip SNP arrays are dual-purpose arrays, simultaneously providing both copy number predictions and genotypes for loss of heterozygosity (LOH) determination.

The high density of markers on these arrays enables identification of gains and losses with increased confidence because of the many data points predicting even the small copy number aberrations. The availability of genotyping data makes the detection of LOH possible.

 - Formalin fixed paraffin embedded samples

A new exciting possibility is to study allele-specific genomic copy numbers using Formalin Fixed Paraffin Embedded (FFPE) samples. Until recently fresh or fresh frozen samples have been required for genomic copy number analysis using SNP arrays. With the introduction of OncoScan™ technology based on molecular inversion probes also the many FFPE tumor samples stored in biobanks can now be analyzed.

In a pilot study we have been able to obtain allele-specific copy number information from 37 out of 52 ovarian cancer samples. These samples have been difficult to analyze with conventional methods (CN info from 10 out of 52 samples). Thus, we think that this technology will be important to obtain results from large cohorts also of relatively rare tumors. We have broad experience lab and data analysis of OncoScan™ arrays. So if you are interested in studying the genomes of tumors in FFPE samples, get in touch with us and we will be able to tell you more.

 - CytoScan HD Cytogenetics Solution

The CytoScan HD Solution provides the broadest coverage, highest performance, and most "genotype–able" single nucleotide polymorphisms (SNPs) for detecting human chromosomal aberrations associated with genes related to constitutional and cancer cytogenetics, OMIM, and RefSeq. This single array includes more than 2.6 million copy number markers of which 750,000 are "genotype–able" SNPs and 1.9 million are non–polymorphic probes.

Which array is best for you?

Dependent on the type of sample you have, the density of probes you need and the necessity for the data to be comparable to other datasets, different arrays might be the best option for your project.

We are happy to help you in selecting the best option for just your project and assist you as well in the optimal design of your study if you are unsure. You can always just send us an e-mail at arrayplatform[at]medsci.uu.se or call us at +46-18-4714485 or +46-18-4714484

Information on sample preparation, ordering and submission of biological material to our facility can be found at the "Order" page.