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Flint J.,Oxford Genetics | Eskin E.,University of California at Los Angeles
Nature Reviews Genetics | Year: 2012

Genome-wide association studies (GWASs) have transformed the field of human genetics and have led to the discovery of hundreds of genes that are implicated in human disease. The technological advances that drove this revolution are now poised to transform genetic studies in model organisms, including mice. However, the design of GWASs in mouse strains is fundamentally different from the design of human GWASs, creating new challenges and opportunities. This Review gives an overview of the novel study designs for mouse GWASs, which dramatically improve both the statistical power and resolution compared to classical gene-mapping approaches. © 2012 Macmillan Publishers Limited. All rights reserved.

Heitzer E.,Medical University of Graz | Tomlinson I.,Oxford Genetics
Current Opinion in Genetics and Development | Year: 2014

Three DNA polymerases - Pol α, Pol δ and Pol e{open} - are essential for DNA replication. After initiation of DNA synthesis by Pol α, Pol δ or Pol e{open} take over on the lagging and leading strand respectively. Pol δ and Pol e{open} perform the bulk of replication with very high fidelity, which is ensured by Watson-Crick base pairing and 3'exonuclease (proofreading) activity. Yeast models have shown that mutations in the exonuclease domain of Pol δ and Pol e{open} homologues can cause a mutator phenotype. Recently, we identified germline exonuclease domain mutations (EDMs) in human POLD1 and POLE that predispose to 'polymerase proofreading associated polyposis' (PPAP), a disease characterised by multiple colorectal adenomas and carcinoma, with high penetrance and dominant inheritance. Moreover, somatic EDMs in POLE have also been found in sporadic colorectal and endometrial cancers. Tumors with EDMs are microsatellite stable and show an 'ultramutator' phenotype, with a dramatic increase in base substitutions. © 2014 The Authors.

Baumer D.,Oxford Genetics
Expert reviews in molecular medicine | Year: 2010

Motor neurons are large, highly polarised cells with very long axons and a requirement for precise spatial and temporal gene expression. Neurodegenerative disorders characterised by selective motor neuron vulnerability include various forms of amyotrophic lateral sclerosis (ALS) and spinal muscular atrophy (SMA). A rapid expansion in knowledge on the pathophysiology of motor neuron degeneration has occurred in recent years, largely through the identification of genes leading to familial forms of ALS and SMA. The major emerging theme is that motor neuron degeneration can result from mutation in genes that encode factors important for ribonucleoprotein biogenesis and RNA processing, including splicing regulation, transcript stabilisation, translational repression and localisation of mRNA. Complete understanding of how these pathways interact and elucidation of specialised mechanisms for mRNA targeting and processing in motor neurons are likely to produce new targets for therapy in ALS and related disorders.

Anderson C.A.,Oxford Genetics
Nature protocols | Year: 2010

This protocol details the steps for data quality assessment and control that are typically carried out during case-control association studies. The steps described involve the identification and removal of DNA samples and markers that introduce bias. These critical steps are paramount to the success of a case-control study and are necessary before statistically testing for association. We describe how to use PLINK, a tool for handling SNP data, to perform assessments of failure rate per individual and per SNP and to assess the degree of relatedness between individuals. We also detail other quality-control procedures, including the use of SMARTPCA software for the identification of ancestral outliers. These platforms were selected because they are user-friendly, widely used and computationally efficient. Steps needed to detect and establish a disease association using case-control data are not discussed here. Issues concerning study design and marker selection in case-control studies have been discussed in our earlier protocols. This protocol, which is routinely used in our labs, should take approximately 8 h to complete.

Noble D.,Oxford Genetics
Experimental Physiology | Year: 2013

New Findings: • What is the Topic of this review? Have recent experimental findings in evolutionary biology concerning the transmission of inheritance opened the way to a reintegration of physiology with evolutionary biology? • What advances does it highlight? The answer is yes, and that this requires a new synthesis between evolutionary theory and experimental physiology. The 'Modern Synthesis' (Neo-Darwinism) is a mid-20th century gene-centric view of evolution, based on random mutations accumulating to produce gradual change through natural selection. Any role of physiological function in influencing genetic inheritance was excluded. The organism became a mere carrier of the real objects of selection, its genes. We now know that genetic change is far from random and often not gradual. Molecular genetics and genome sequencing have deconstructed this unnecessarily restrictive view of evolution in a way that reintroduces physiological function and interactions with the environment as factors influencing the speed and nature of inherited change. Acquired characteristics can be inherited, and in a few but growing number of cases that inheritance has now been shown to be robust for many generations. The 21st century can look forward to a new synthesis that will reintegrate physiology with evolutionary biology. © 2013 The Physiological Society.

Paterson D.J.,Oxford Genetics
Journal of Physiology | Year: 2014

One hundred years ago in this journal, Krogh and Lindhard published a seminal paper highlighting the importance of the brain in the control of breathing during exercise. This symposium report reviews the historical developments that have taken place since 1913, and attempts to place the detailed neurocircuitry thought to underpin exercise hyperpnoea into context by focusing on key structures that might form the command network. With the advent of enhanced neuroimaging and functional neurosurgical techniques, a unique window of opportunity has recently arisen to target potential circuits in humans. Animal studies have identified a priori sites of interest in mid-brain structures, in particular the subthalamic locomotor region (subthalamic nucleus, STN) and the periaqueductal grey (PAG), which have now been recorded from in humans during exercise. When all data are viewed in an integrative manner, the PAG, in particular the lateral PAG, and aspects of the dorsal lateral PAG, appear to be key communicating circuitry for 'central command'. Moreover, the PAG also fulfils many requirements of a command centre. It has functional connectivity to higher centres (dorsal lateral prefrontal cortex) and the basal ganglia (in particular, the STN), and receives a sensory input from contracting muscle, but, importantly, it sends efferent information to brainstem nuclei involved in cardiorespiratory control. © 2013 The Physiological Society.

Lunter G.,Oxford Genetics | Goodson M.,Oxford Genetics
Genome Research | Year: 2011

High-volume sequencing of DNA and RNA is now within reach of any research laboratory and is quickly becoming established as a key research tool. In many workflows, each of the short sequences ("reads") resulting from a sequencing run are first "mapped" (aligned) to a reference sequence to infer the read from which the genomic location derived, a challenging task because of the high data volumes and often large genomes. Existing read mapping software excel in either speed (e.g., BWA, Bowtie, ELAND) or sensitivity (e.g., Novoalign), but not in both. In addition, performance often deteriorates in the presence of sequence variation, particularly so for short insertions and deletions (indels). Here, we present a read mapper, Stampy, which uses a hybrid mapping algorithm and a detailed statistical model to achieve both speed and sensitivity, particularly when reads include sequence variation. This results in a higher useable sequence yield and improved accuracy compared to that of existing software. © 2011 by Cold Spring Harbor Laboratory Press.

Morris A.P.,Oxford Genetics
Genetic Epidemiology | Year: 2011

The detection of loci contributing effects to complex human traits, and their subsequent fine-mapping for the location of causal variants, remains a considerable challenge for the genetics research community. Meta-analyses of genomewide association studies, primarily ascertained from European-descent populations, have made considerable advances in our understanding of complex trait genetics, although much of their heritability is still unexplained. With the increasing availability of genomewide association data from diverse populations, transethnic meta-analysis may offer an exciting opportunity to increase the power to detect novel complex trait loci and to improve the resolution of fine-mapping of causal variants by leveraging differences in local linkage disequilibrium structure between ethnic groups. However, we might also expect there to be substantial genetic heterogeneity between diverse populations, both in terms of the spectrum of causal variants and their allelic effects, which cannot easily be accommodated through traditional approaches to meta-analysis. In order to address this challenge, I propose novel transethnic meta-analysis methodology that takes account of the expected similarity in allelic effects between the most closely related populations, while allowing for heterogeneity between more diverse ethnic groups. This approach yields substantial improvements in performance, compared to fixed-effects meta-analysis, both in terms of power to detect association, and localization of the causal variant, over a range of models of heterogeneity between ethnic groups. Furthermore, when the similarity in allelic effects between populations is well captured by their relatedness, this approach has increased power and mapping resolution over random-effects meta-analysis. © 2011 Wiley Periodicals, Inc.

Newbury D.F.,Oxford Genetics | Monaco A.P.,Oxford Genetics
Neuron | Year: 2010

Developmental speech and language disorders cover a wide range of childhood conditions with overlapping but heterogeneous phenotypes and underlying etiologies. This characteristic heterogeneity hinders accurate diagnosis, can complicate treatment strategies, and causes difficulties in the identification of causal factors. Nonetheless, over the last decade, genetic variants have been identified that may predispose certain individuals to different aspects of speech and language difficulties. In this review, we summarize advances in the genetic investigation of stuttering, speech-sound disorder (SSD), specific language impairment (SLI), and developmental verbal dyspraxia (DVD). We discuss how the identification and study of specific genes and pathways, including FOXP2, CNTNAP2, ATP2C2, CMIP, and lysosomal enzymes, may advance our understanding of the etiology of speech and language disorders and enable us to better understand the relationships between the different forms of impairment across the spectrum. © 2010 Elsevier Inc.

Agency: GTR | Branch: Innovate UK | Program: | Phase: Feasibility Study | Award Amount: 186.68K | Year: 2015

Many different factors influence whether a piece of DNA will work in a biological setting, to express the protein it encodes. Proteins represent a broad new class of exciting but expensive new medicines. Poor DNA activity is particularly problematic when manufacturers of proteins need to produce large quantities by industrial manufacture. At Oxford Genetics we have developed a wide range of tools and expertise to allow us to design and build DNA sequences that produce high amounts of proteins. In this project we aim to industrialise a large proportion of our existing work flow and make the assembly of complex DNA an automated high-throughput process. This will enable the rapid and efficient development of DNA sequences that are optimal for producing proteins in any system, and should lead to major improvements in protein manufacture. This will benefit many aspects of commerce and medicine in the UK.

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