Array and Analysis Facility

Regional facility of national interest

The Array and Analysis facility provides access to microarray technology and bioinformatics support for applications in both research and healthcare in Sweden. We offer all types of support from the initial consultation, performing the complete array experiments to analyzing the results. We perform array-based diagnostics of children with suspected mental retardation in collaboration with Clinical genetics. We also develop methods for copy number analysis of tumor samples with the goal to identify aberrations in tumor cells in clinical tumor samples. We provide bioinformatic support for the development and introduction of both array-based and sequencing-based clinical analyses throughout Sweden.

SERVICES

  • Clinical diagnostics. Array-based analysis of 300 patients/year with suspected mental retardation, in collaboration with Clinical genetics
  • Data analysis and bioinformatic support. experimental design, quality control, normalization, visualization, data integration and higher-level analysis
  • Genome analysis. SNP genotyping and copy number analysis, in both fresh frozen and FFPE samples
  • Method development. Bioinformatic tools for copy number analysis of tumor samples using either whole genome sequenced data or array data
  • Transcriptome analysis. Analysis of mRNA, long non-coding transcripts and miRNA, in both fresh frozen and FFPE samples

APPLICATIONS

  • Genomic analysis of 120 samples from patients with colon cancer.
  • Developing bioinformatic tools for allele-specific copy number analysis in tumor samples.
  • Genome-wide expression analysis of 400 drosophila samples.

EQUIPMENT

 

  • ABI 9700 Thermocycler.
  • Affymetrix Fluidic stations FS 450.
  • Affymetrix Gene Chip System 3000 7G.
  • Affymetrix GeneTitan MC system.
  • Affymetrix Hybridization ovens 640/645.
  • Agilent 2100 Bioanalyzer.
  • Labconco CentriVap Concentrator.

RECENT PROJECTS

Science. 2011 May 13;332(6031):845-8. doi: 10.1126/science.1201157. Experimental evidence supports a sex-specific selective sieve in mitochondrial genome evolution. Innocenti P, Morrow EH, Dowling DK.

 

Mayrhofer M, DiLorenzo S, Isaksson A. 2013. Patchwork: allele-specific copy number analysis of whole genome sequenced tumor tissue. Genome Biol. Mar 25;14(3):R24

 

Gunnarsson R, Isaksson A, Mansouri M, Göransson H, Jansson M, Cahill N, Rasmussen M, Staaf J, Lundin J, Norin, Buhl AM, Ekström Smedby K, Hjalgrim H, Karlsson K, Jurlander J, Juliusson G and Rosenquist R. 2010. Large but not small copy-number alterations correlate to high-risk genomic aberrations and survival in chronic lymphocytic leukemia: A high-resolution genomic screening of newly diagnosed patients. Leukemia. Jan;24(1):211-5

 

Skirnisdottir I, Mayrhofer M, Rydåker M, Åkerud H and Isaksson A. 2012.Loss-of-heterozygosity on chromosome 19q in early-stage serous ovarian cancer is associated with recurrent disease. BMC Cancer2012, 12:407doi:10.1186/1471-2407-12-407

 

Rasmussen M, Sundström M, Kultima HG, Botling J, Micke P, Birgisson H, Glimelius B, Isaksson A. Allele-specific copy number analysis of tumor samples with aneuploidy and tumor heterogeneity. Genome Biol. 2011 Oct 24;12(10):R108.