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Welcome to Genomics

Welcome to the Genomics Core facility pages

Hopefully our website is easy to navigate and you can find the information you are looking for. If you'd like more of an introduction to what we do then please read on...

The Genomics core facility allows researchers at the CI access to state-of-the-art DNA and RNA analysis instruments, methods and applications; particularly NGS. 

Nearly all data are today generated using next-generation DNA sequencing (NGS) and we have multiple Illumina NGS instruments. These allow users to carry out unbiased genome-wide experiments and see, at base-pair resolution, what the underlying sequence differences are in cancer genomes, transcriptomes, methylomes, etc... 

New investments in single-cell sequencing capabilities include the Fluidigm C1 and 10X Genomics instruments. These can be used today to generate single-cell RNA-seq data, and we're working on making sure you can use them for copy-number and other applications in the future.

Other technologies we have include: Real-time PCR is carried out using two Life Technologies QuantStudio6 instruments; commonly for lower throughput gene expression analysis but SNP genotyping, allelic expression and copy number are also run.  The Fluidigm Biomark instrument that allows analysis of 2,000-10,000ish gene expression data-points in a single run, single cell gene expression analysis and digital PCR. The Fluidigm Access Array for target enrichment and library preparation prior to NGS. The Agilent Bioanalyser capillary electrophoresis system for QC of samples before genomic analysis, an Invitrogen Qubit for fluorometric quantification of nucleic acids, a Covaris DNA sonicator, an Agilent Bravo robot for automated liquid handling, and Qiagen robotics for nucleic acid extraction.

These tools in Genomics help researchers to understand the cancer genome, unravel the genetic causes of cancer and develop new methods for diagnosis, treatment, etc.  Cancer genomics has been revolutionised by next-generation sequencing (NGS) technology and the people and instruments in the Genomics core help CI scientists answer their research questions.

Highlights from the last years genomics research include work from the Balasubramanian group who have shown that it is possible to capture and sequence double-strand DNA breaks (DSBs) in situ and directly map these at single-nucleotide resolution, enabling the study of DSB origin (Lensing et al. Nature Methods 2016); and the Caldas group who have profiled almost 2500 Breast Cancer patients for mutational analysis of 173 genes using a targeted pull-down (Pereira et al Nature Communications 2016). The rapid speed and unbiased nature of the genome-wide experiments being completed in the Genomics core continue to increase our understanding cancer genomes.

An important component of the Genomics core facility is our staff.  The technologies we use are complicated and we undertake projects for the Institute’s research groups as well as training individuals to use Genomics core equipment.