Computational Genomics Analysis and Training programme (CGAT)
Lead Research Organisation:
University of Oxford
Department Name: UNLISTED
Abstract
CGAT's mission will be to reveal the significance of high-throughput sequence in health and disease, whilst providing training opportunities for pre- and post-doctoral scientists. The Programme will provide access to genome analysis for those UK biologists and clinicians who are less used to managing, manipulating and analysing extremely large sequence data sets. The Strategic Programme will aim both to fulfil the promise of high-throughput genome data in answering the most important questions in genetics and human disease, and to train a new generation of genomics researchers.
Technical Summary
CGAT will provide expertise and analytical capacity to UK-based research groups planning to use or already using next-generation sequencing data. At the same time CGAT will train post-doctoral researchers in the analysis and biological interpretation of genome-scale data sets. Each project will be highly collaborative, and focused on gleaning important biological conclusions from large data sets. Recent years have seen an accelerating growth in sequencing capacity, whilst sequencing costs have plummeted. As a result, powerful techniques and assays based on DNA sequencing (ChIP-Seq, RNA-Seq, genome resequencing etc.) are being developed that add greatly to the experimental toolkit of biologists and clinicians. However, while becoming increasingly affordable, these new methods require substantial computational infrastructure and expertise that are not available, currently, in many experimental research groups. Indeed, UK-wide there remains a considerable shortage of bioinformaticians able to process these large data sets. CGAT aims to help meet these considerable needs. For each collaboration, CGAT provides expertise in computational genomics, the computational infrastructure and a dedicated post-doctoral researcher. Collaborators contribute sequence data sets and their unique knowledge of their specific research area. Taken together, the result will be high-quality research culminating in high-profile journals under a joint-authorship model. CGAT builds on the experience of the Ponting group in comparative genomics and next-generation sequencing analysis. The group has a strong back-ground in computational sequence analysis and evolutionary biology with a proven track record of translating large scale sequencing data into diverse biological contexts. Post-doctoral trainees in the CGAT group will benefit from in-house training, but also the biological insights of collaborators. Working on a variety of projects, trainees will accumulate expertise in genome sequencing-related fields, as well as high profile publications.
Organisations
People |
ORCID iD |
Douglas Higgs (Principal Investigator) |
Publications
Anzilotti C
(2019)
An essential role for the Zn2+ transporter ZIP7 in B cell development.
in Nature immunology
Aulicino A
(2018)
Invasive Salmonella exploits divergent immune evasion strategies in infected and bystander dendritic cell subsets.
in Nature communications
Berlanga-Taylor AJ
(2018)
Genomic Response to Vitamin D Supplementation in the Setting of a Randomized, Placebo-Controlled Trial.
in EBioMedicine
Bowden R
(2019)
Sequencing of human genomes with nanopore technology.
in Nature communications
Carravilla P
(2019)
Molecular recognition of the native HIV-1 MPER revealed by STED microscopy of single virions.
in Nature communications
Cartier J
(2018)
Investigation into the role of the germline epigenome in the transmission of glucocorticoid-programmed effects across generations.
in Genome biology
Ellender T
(2019)
Embryonic progenitor pools generate diversity in fine-scale excitatory cortical subnetworks
in Nature Communications
Fry AE
(2018)
De novo mutations in GRIN1 cause extensive bilateral polymicrogyria.
in Brain : a journal of neurology
Godfrey L
(2019)
DOT1L inhibition reveals a distinct subset of enhancers dependent on H3K79 methylation.
in Nature communications
Gooding S
(2019)
Transcriptomic profiling of the myeloma bone-lining niche reveals BMP signalling inhibition to improve bone disease.
in Nature communications
Grüning B
(2018)
Bioconda: sustainable and comprehensive software distribution for the life sciences.
in Nature methods
Jaffer F
(2017)
Familial childhood-onset progressive cerebellar syndrome associated with the ATP1A3 mutation.
in Neurology. Genetics
James KL
(2019)
Low-Bias RNA Sequencing of the HIV-2 Genome from Blood Plasma.
in Journal of virology
Johnson JS
(2017)
11ß-hydroxysteroid dehydrogenase-1 deficiency alters the gut microbiome response to Western diet.
in The Journal of endocrinology
Jonikas M
(2018)
Stem cell modeling of mitochondrial parkinsonism reveals key functions of OPA1.
in Annals of neurology
Labuhn M
(2019)
Mechanisms of Progression of Myeloid Preleukemia to Transformed Myeloid Leukemia in Children with Down Syndrome.
in Cancer cell
Li X
(2019)
A Comprehensive Analysis of Key Immune Checkpoint Receptors on Tumor-Infiltrating T Cells From Multiple Types of Cancer.
in Frontiers in oncology
Mettananda S
(2019)
Synergistic silencing of a-globin and induction of ?-globin by histone deacetylase inhibitor, vorinostat as a potential therapy for ß-thalassaemia.
in Scientific reports
Morgan MD
(2018)
Genome-wide study of hair colour in UK Biobank explains most of the SNP heritability.
in Nature communications
Morotti M
(2019)
Hypoxia-induced switch in SNAT2/SLC38A2 regulation generates endocrine resistance in breast cancer.
in Proceedings of the National Academy of Sciences of the United States of America
Rajan D
(2022)
Autosomal Recessive Cerebellar Atrophy and Spastic Ataxia in Patients With Pathogenic Biallelic Variants in GEMIN5
in Frontiers in Cell and Developmental Biology
Sandor C
(2017)
Transcriptomic profiling of purified patient-derived dopamine neurons identifies convergent perturbations and therapeutics for Parkinson's disease.
in Human molecular genetics
Smith T
(2017)
UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy.
in Genome research
Stamatopoulos B
(2018)
The Light Chain IgLV3-21 Defines a New Poor Prognostic Subgroup in Chronic Lymphocytic Leukemia: Results of a Multicenter Study.
in Clinical cancer research : an official journal of the American Association for Cancer Research
Tanudjojo B
(2021)
Phenotypic manifestation of a-synuclein strains derived from Parkinson's disease and multiple system atrophy in human dopaminergic neurons.
in Nature communications
Turnpenny PD
(2018)
Missense Mutations of the Pro65 Residue of PCGF2 Cause a Recognizable Syndrome Associated with Craniofacial, Neurological, Cardiovascular, and Skeletal Features.
in American journal of human genetics
Van Bemmel JG
(2019)
The bipartite TAD organization of the X-inactivation center ensures opposing developmental regulation of Tsix and Xist.
in Nature genetics
Villegas-Mendez A
(2020)
Exhausted CD4+ T Cells during Malaria Exhibit Reduced mTORc1 Activity Correlated with Loss of T-bet Expression
in The Journal of Immunology
Viphakone N
(2019)
Co-transcriptional Loading of RNA Export Factors Shapes the Human Transcriptome.
in Molecular cell
Watson LM
(2017)
Dominant Mutations in GRM1 Cause Spinocerebellar Ataxia Type 44.
in American journal of human genetics
Williams RM
(2019)
Reconstruction of the Global Neural Crest Gene Regulatory Network In Vivo.
in Developmental cell
Xu X
(2020)
An ontogenetic switch drives the positive and negative selection of B cells
in Proceedings of the National Academy of Sciences
Zarei M
(2019)
Incidence and Risk Factors for Post-Intravitreal Injection Endophthalmitis in a Modified Operating Room Setting.
in Ocular immunology and inflammation
Zhang P
(2021)
Germline and Somatic Genetic Variants in the p53 Pathway Interact to Affect Cancer Risk, Progression, and Drug Response
in Cancer Research
Description | Capital Prioritisation for MRC Units and Institutes |
Amount | £300,000 (GBP) |
Organisation | Medical Research Council (MRC) |
Sector | Public |
Country | United Kingdom |
Start | 04/2018 |
End | 04/2019 |
Description | Provision for Public Engagement within Research Grants application. DNA Origami: How do you fold a genome? |
Amount | £36 (GBP) |
Funding ID | 106130/Z/14/B |
Organisation | Wellcome Trust |
Sector | Charity/Non Profit |
Country | United Kingdom |
Start | 06/2017 |
End | 02/2019 |
Description | Support for the Computational Genomic Analysis and Training Programme (CGAT) |
Amount | £854,000 (GBP) |
Organisation | Medical Research Council (MRC) |
Sector | Public |
Country | United Kingdom |
Start | 07/2016 |
End | 05/2019 |
Description | Royal Society Summer Exhibition |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Schools |
Results and Impact | The presentation was part of the Royal Society Summer Exhibition attended by schoolchildren, members of the public and members of the scientific community. This exhibition is probably the largest of the year in terms of attendees over the course of a week. |
Year(s) Of Engagement Activity | 2017 |