Our aim is to supply high quality in-house arrays for expression profiling of cells and tissues and for CGH array profiling of the human genome. We also provide expertise in designing, performing and analysing microarray experiments on each of our arrays and also on commercial array platforms.
The facility aims to make microarray technology accessible to everyone, whether they are performing their own experiments or using the lab as a service to generate data. The microarray team all contribute to the facility with their own individual projects as well as supporting the research of other teams within the Breakthrough Research Centre.
The combination of microarrays with clinical resources (such as archival tissue banks and biopsies) and other high throughput technologies (such as siRNA and tissue arrays) contributes significantly to the translational research programme at Breakthrough.
Our arrays
Human Expression ArraysThe facility prints a human expression array based upon the CRUK clone collection, from which we have produced a 20,000 gene array representing more than half of the genes in the human genome and more than 80% of well-characterized genes.
This array has been customized for its use in breast cancer and contains replicated clones for over 700 genes of primary importance in breast tumours, clones representing important published microarray gene sets predictive of long term survival in breast cancer and an extended list of genes identified in our own microarray profiling of breast cancer derived materials using other array platforms and profiling technologies.
Mouse Expression arrays
The facility continues to produce a 15K mouse expression array which has been used to phenotypically characterize purified populations of mouse mammary stem cells in Dr Matt Smalley's Team within the Breakthrough Research Centre and to examine the effects of chemical carcinogens in a number of mouse tissues in David Phillips group at ICR Sutton.
Array CGH
The 1MB-spaced clone collection used for array CGH was our most used platform in 2005. This array supported projects examining the effects of genomic rearrangements in many different aspects of breast cancer.
A great deal of work has been done using archival paraffin embedded tissues and array CGH in collaboration with the Breakthrough Molecular Pathology Team led by Dr Jorge Reis-Filho.
Full Tiling Path Array CGH
We have a full tiling path collection for array CGH. The array was created from a 32,000 BAC collection in use in a few major profiling centres around the world and covers the entire human genome at a resolution of ~50 kilobases. The array has been validated by profiling a wide panel of breast cancer cell lines and has produced a dramatic improvement in the coverage, quality and sensitivity of array CGH from our existing arrays. This array will forms the basis of several important projects for the Breakthrough Research Centre and the microarray facility.
