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.
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.
3. Gene expression
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 no longer manufacture HT12 v4 arrays.
- UCL Genomics offer RNA-Seq for all gene expression projects (see below).
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.
- KAPA mRNA Hyper kit
- KAPA Riboerase tot-RNA kit
- NEBNext Ultra II Directional RNA Library Prep Kit for Illumina
- Clontech SMARTER low input RNA kit followed by Illumina Nextera XT DNA kit
- NEBNext Multiplex Small RNA
- QiAgen QIAseq miRNA Library Kit
- NEBNext DNA Ultra II Library prep kit
- Illumina TruSeq custom amplicons
- Agilent SureSelect
- 16S Metagenomics
- UCLG Custom assay V5-V7
- NextFlex 16S V1-V3
- NEBNext DNA Ultra II Library prep kit (choice of mechanical or enzymatic shearing)
- Illumina Nextera DNA kit
- Illumina Nextera XT DNA kit
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.
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.
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.