Applications

The Oxford Genomics Centre has been specifically set up to support a wide range of applications aimed at accelerating the pace of research into the underlying genetic cause of common diseases. The main applications supported are summarized below but the Centre is constantly working with scientists to develop new ways to exploit the power of the high throughput technologies.

DNA

Where the focus is on the discovery of causal variants, copy number changes or structural rearrangements associated with a particular disease condition the following DNA based applications are supported:

Whole-Genome Resequencing: This is the sequencing of whole genomes where the sequenced reads can be mapped against a published reference sequence. 

De-novo Sequencing: If the genome of interest does not have a published reference sequence it will require de novo assembly from the sequenced reads.   

When a target region has already been defined through classical mapping approaches or a microarray based GWAS study, follow-up work can be done utilizing more targeted approaches:

Targeted Re-sequencing: Where only specific regions of the genome are to be investigated, there are a wide range of possibilities, from whole exome analysis to more custom designs of targeted capture or PCR based approaches.  Great for follow-up or as a cheaper alternative for discovery, where budget precludes whole genome sequencing. There are many techniques available for targeted re-sequencing. Please contact us and we will provide you with some suitable options for your experiment.

Large-scale SNP genotyping and Whole Genome genotyping: Still a highly relevant option and supported with a new range of chips from Illumina, supporting all budgets. This approach looks at known variants across all, or most, of the genome and is a good discovery tool.

Low to Mid- range SNP genotyping: Useful for candidate gene analysis or following genome wide association studies and is ideally carried out using Sequenom based assays to investigate variants in a targeted region of the genome.

RNA

Although the analysis of a transcriptome is still supported by expression arrays, High-Throughput Sequencing is rapidly expanding as the gold standard.  Sequencing allows the analysis of both coding and non-coding messages and provides a digital count of expression levels while also allowing the identification of splice variants and coding mutations. 

 RNA-SEQ: Allows the determination of the relative abundance of transcripts, the discovery of transcript isoforms, and the characterisation of splice junctions.

Gene Expression Array: Allows gene expression levels of known transcripts to be quantitated.

Gene regulation

Gene regulation can occur at any stage during the process of gene expression and is essential because it allows greater control and flexibility in gene expression.

Methylation status: The methylome can be characterised to a single base resolution by sequencing bisulphite-treated DNA. A less precise but cheaper option is to perform MeDIP-Seq. The methylation status of target regions can also be determined from arrays.

ChIP-SEQ: This technique combines chromatin immunoprecipitation and High-Throughput sequencing to accurately quantify in vivo protein-DNA interactions on a genome-wide scale.

Small RNA Discovery and Analysis: Determine the abundance of small RNA populations such as microRNAs and discover rare small RNA.