Genome Centre

Single Cell Genomics

Single cell genomics is used to unpack cell heterogeneity, often within a tissue or cancer biology.  We have been running chemistry from 10X genomics since 2018. A modular approach means whole transcriptome information can be augmented with a combination of T and B cell receptor profiling, surface bound protein, and chromatin accessibility.

Talk to the team about single cell genomics

Spatial Biology

Using Spatial biology technologies it is possible to analyse RNA and Protein  whilst retaining their two dimension position information in the original tissues. We can offer solutions from both 10X Genomics (Visium Chemistry), for which we are the only certified supplier in the South of England, and Nanostring (GeoMX DSP).

Talk to the team about spatial biology

RNA Analysis

We run a range of different platforms and implement or develop methods that cover all scales of genomic questions.

Talk to the team about RNA profiling

Technology		Assay
	Next Generation Sequencing - Illumina NovaSeq, NextSeq, and MiSeq	Whole Transcriptome Analysis, options to profile protein coding RNA, total RNA and miRNA from bulk samples.  See our guide to RNA seq
	Real-time PCR - ABI QuantStudio 7 Flex Real-Time PCR System	qPCR (real time PCR) is still the gold standard to analyze individual RNA. Learn more about our qPCR service . Find out about booking time on the QS7 Equipment booking guide

DNA Analysis

We run a range of different platforms and implement or develop methods that cover all scales of genomic questions.

Talk to the team about spatial DNA analysis

Technology		Assay
	Next Generation Sequencing - Illumina NextSeq and MiSeq	Whole Genome Sequencing (WGS)
		Whole Exome Sequencing (WES) using  Agilent Sure Select or similar
		Targeted Region Sequencing with either Fluidigm Access Array or Agilent Sure Select
		Metagenomics with either 16s DNA or whole genome sequencing
	Arrays  - Illumina Bead Arrays	To run genome wide association studies (GWS) Genome Wide or Custom SNP arrays
	Real-time PCR - ABI QuantStudio 7 Flex Real-Time PCR System	Genotyping individual single nucleotide polymorphisms (SNP) in large cohorts we use SNP genotyping Taqman
	Sanger Sequencing - ABI 3730	Sequencing individual plasmids or PCR products see our Sanger Sequencing guide
	Microsatellite (Short Tandem Repeat (STR)) Genotyping - ABI - 3730	Off the shelf panels can be used for human identification and cell line validation.  Custom panels are often used to study population genetics

Epigenome Analysis

Understanding the control of gene expression through DNA methylation and chromatin accessibility is key to decoding cell circuits.  We offer a range of scales to study DNA methylation of which the most cost effective approach is using Infinium arrays form Illumina  targeting hundreds of thousands of GpG sites.

Talk to the team about epigenomics

Technology		Assay
	Next Generation Sequencing - Illumina NextSeq and MiSeq	DNA Methylation Analysis Whole Genome Bisulphite Sequencing
		DNA Methylation Analysis (WGBS)Reduced Representation Bisuplhite Sequencing
		DNA Methylation Analysis (RRBS)Targeted Bisulphite
		DNA Methylation Analysis Targeted Region Sequencing with Fluidigm Access Array or individually
	Arrays  - Illumina Bead Arrays	DNA Methylation Analysis Infinium EPIC Arrays (human 850,000 CpG sites) Infinium mouse methylation arrays (mouse 265,000 CpG sites)
	Next Generation Sequencing - Illumina NextSeq and MiSeq	Chromatin Accessibility Assay for Transposase-Accessible Chromatin (ATACseq).

Bioinformatics

Genetics and genomics studies produce ever larger data sets.  Having a strategy to analyse the results of a project is all important. 

The Centre can help with a guided analysis for RNAseq, Single Cell Sequencing, and Spatial Genomics using a commercial solution from Partek (Partek Flow) for which QMUL has a cloud based instance.  We run a preliminary analysis and provide a user login to view and interrogate the results. Partek Flow requires no prior coding experience and uses a point and click based interface making it a great solution for many users.

For more bespoke applications we have bioinfomatics support to answer novel questions and to develop new tools. We take advantage of the QMUL High Performance Cluster (Apocrita) and run computationally intense processes in order to analyse data that cannot be analysed on a standalone desktop. We have experience in Bash, R and Python programming languages and associated packages, and have worked on bespoke analyses for Flow Cytometry, DNA sequencing (variant calling), single cell and spatial transcriptomics and metagenomics to name a few. We are open to and love to analyse new data types in order to answer specific biological questions.

Talk to the team about bioinformatics

We have a dedicated team of very experienced scientists

Professor Patricia Munroe, Director Patricia became Director of the Bart's and The London Genome Centre in 2016, taking over from David vanHeel. Patricia is internationally renowned geneticist with research interests in cardiovascular and blood pressure phenotypes. Publications	Dr Charles Mein, Manager Charles studied Genetics at undergraduate level before working on the Genetics of Type 1 Diabetes for his Dphil. He was recruited in 2000 to establish the Centre which focused on the genetics of complex disease. Under his leadership the Centre has kept pace with the rapid technological changes in the genomics field. Publications	Eva Wozniak, Deputy Manager Eva joined our team in 2011 after working on research into women’s cancers at the Institute for Women’s Health at UCL for 6 years.  Her areas of expertise are many, covering all of the activities we specialise in. She has established many services at our Centre, including Spatial Genomics, Single Cell genomics, and RNA seq. She's a member of the QMUL Technician Commitment Steering Group. Publications
Ben Jones, Senior Technician Ben has been part of our team since the summer of 2023, joining us with previous stints at Liverpool University and KCL.  His current areas of responsibility include single cell, and spatial genomics  along with managing service contracts.  Publications	Paul Stevens, Technician Paul has developed a great deal of experience in single cell genomics and spatial biology, working with the Visium and Visium HD technology from 10X genomics.  He joined us in spring 2021 having worked previously at UCL for many years running their Sanger sequencing service. Publications	Salina Thapa, Technician Salina joined our team, in Jun 2022, having recently gained her MSc Medical Microbiology followed by service in one of the COVID testing centres.  She's now an expert in Illumina Infinium protocols, and is developing competence in transcriptomics. Publications
Bryna McCarthy Bryna joined the team us at the end of June 2022, having previously worked with the BGI in their COVID testing facility.  She has an MSc in  "Cancer, Molecular Pathology and Genomics" from Barts Cancer Institute.  She's now a wealth of experience in transcriptomics, metagenomics, and genotyping array protocols.

Genome Centre
Faculty of Medicine and Dentistry
Queen Mary University of London
Blizard Institute, 4 Newark Street, London, E1 2AT

Tel +44 207 882 2055 (Manager)
Tel +44 207 882 2058 (Lab Staff)

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