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Genomics core facility
We provide access to state-of-the-art DNA and RNA analysis instruments, methods and applications, and in particular next generation sequencing.
Genomics has access to the latest sequencing and microarray technologies to analyse genomic data. Currently nearly all data are generated using next-generation DNA sequencing (NGS), microarrays or quantitative real-time PCR (qPCR). We have multiple Illumina NGS instruments, allowing unbiased genome-wide experiments to be performed that enable researchers to see, at base-pair resolution, what the underlying sequence differences are in cancer genomes. We are currently using commercial microarray systems from Illumina, Agilent and Affymetrix to analyse, among others: gene expression, gene copy number, methylation, and microRNA expression. Much of this work is being supplanted by NGS.
We use two Applied Biosystems 7900s to carry out real-time PCR, mostly for lower throughput gene expression analysis but also for SNP genotyping, allelic expression and copy number. We have a Fluidigm Biomark™ instrument that allows analysis of approximately 2,000-10,000 gene expression data-points in a single run, single cell gene expression analysis and digital PCR. We use the Fluidigm Access Array™ for target enrichment and library preparation prior to NGS.
Other technologies in the facility include the Agilent Bioanalyzer capillary electrophoresis system for QC of samples before genomic analysis, an Invitrogen Qubit® for fluorometric quantification of nucleic acids, a Covaris DNA sonicator, a Tecan Freedom EVO® 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 and treatment. Cancer genomics has been revolutionised by NGS technology and we help CRUK CI scientists answer their research questions in this area.
In 2013 Institute researchers showed that it is possible to sequence the exome of a tumour from circulating DNA (Murtaza et al., Nature 2013: 497; 108). Another proof-of-concept study showed that ctDNA can be used as a ‘liquid biopsy’ during the course of a patient’s treatment (Dawson et al., NEJM 2013: 368; 1199). It is likely to be several years before these technical advances become clinical tools. However, we can now sequence a cancer genome in 24 hours, last year this took five days and two years ago several weeks.
Illumina NGS: We make extensive use of the Illumina NGS instruments, which keep the CRUK CI at the forefront of genomic research. However, the technology continues to develop and Jason Carroll’s group recently published a novel method called RIME (rapid immunoprecipitation mass spectrometry of endogenous proteins) to detect interacting proteins in ChIP complexes using NGS and mass spectrometry (Mohammed et al., Cell Rep. 2013; 3: 342).
Microarray: Arrays continue to be used by many other groups at the CRUK CI. The Caldas group explored the differential expression of microRNAs across breast cancer subtypes in 1300 tumours using Agilent microarrays, and showed they have oncogenic and tumour-suppressive roles. (Dvinge et al., Nature. 2013; 497; 378).
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.