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Applications

Applications

Microarrays

1. Genotyping 

Genotyping arrays allow for powerful genome-wide association studies, and can accurately detect: 

  • point mutations 
  • copy number variants 
  • chromosome aberrations 

Genotyping is a popular and effective way to identifying single nucleotide polymorphism (SNP) among alleles within or between populations. SNP detection is important in genotyping as well as measuring predisposition to disease, identifying drug-candidates, assessing loss if heterozygosity or genetic linkage.

2. Methylation 

DNA methylation plays an important and dynamic role in regulating gene expression. Methylation arrays are used to interrogate methylation sites across the genome at single-nucleotide resolution, analysing multiple samples in parallel making these arrays ideal for epigenome-wide association studies (EWAS).

UCL Genomics runs a weekly methylation clinic using Illumina Human MethylationEPIC 850k beadarrays. 

Contact UCL Genomics for more information and also to register an interest in Mouse Methylation microarrays.

3. Gene expression

Affymetrix 

We offer Affymetrix arrays for legacy projects only. If you require Affymetrix array processing, please contact the centre manager in the first instance to discuss your requirements

Illumina 
  • Illumina no longer manufacture HT12 v4 arrays.
  • UCL Genomics offer RNA-Seq for all gene expression projects (see below).

Sequencing

UCL Genomics offers support at every stage of the sequencing pipeline: experimental design, in-depth sample quality control, library preparation, sequencing on Illumina platform and data analysis. All samples must be submitted with a sample submission form which can be accessed here.

1. Quality Control 

Sample Quality Control is the first step of the sequencing pipeline and one of the crucial steps for a successful sequencing experiment. 

2. Library preparation 

UCL Genomics offers a wide range of library preparation kits for a range of next-generation sequencing applications. In the table below are shown some of the more popular kits we are currently using in our facility. UCL Genomics is constantly updating and testing new kits on the sequencing market to find better solutions.

RNA-seq
ChiP-seq
Targeted-seq
16S Metagenomics
DNA-seq

3. Sequencing 

UCL Genomics currently houses an Illumina NextSeq 500 and a Illumina MiSeq. 

4. Data Analysis

We offer a tiered system for data analysis of sequencing projects. 


Quality Control

UCL Genomics can perform QC on your samples

  • Agilent Bioanalyzer 
  • Agilent Tapestation 
  • Nanodrop ND-1000 
  • Life Technologies Qubit 

However, if you would like to be trained to use our QC equipment yourself, please get in contact with Dr Paola Niola for further information.


Analysis

UCL Genomics offers a number of ways to help you analyse your data. 

Software available for use at UCL Genomics include:

  • GenomeStudio and Bluefuse (for microarray data analysis, linkage and homozygosity mapping) 
  • Strand NGS (Agilent) 
  • Ingenuity Pathway Analysis (QIAGEN) [*for a fee]
  • Please contact us for access to Ingenuity Variant Analysis (Qiagen) for identification of causal variants from exome sequencing data (UCL only). Please contact us for costs and access codes

Sequencing analysis packages 

We offer tiered system for data analysis of sequencing projects including in depth analysis with a dedicated bioinformatician.