Bioinformatics

Bioinformatics Research Group

 

Databases, Software and Tools

GWAS Central Cafe Variome OmicsConnect
Data Sharing 101 The G2P Knowledge Centre Accreditation and attribution in data sharing
Osteogenesis Imperfecta Variant Database Ehlers-Danlos Syndrome Variant Database VariantValidator

Current Project Involvement

Solve-RD EPAD REQUITE
EMIF ETOX COPDMAP

 

About

The Bioinformatics Research Group focuses mainly on the use of bioinformatics for querying and analysing large datasets (so-called “big data”), generated by today’s high throughput screening technologies. Within the group, there is a wealth of experience in the development of databases, data sharing platforms and technologies that permit data discovery.

Data discovery is the ability to search resources for the presence of a particular piece or type of data without the need to reveal the underlying data in detail (unless appropriate). This work requires extensive knowledge in data harmonisation, collation and search technologies in addition to the ability to understand the issues surrounding the handling of the biomedical data itself.

We are based in both the Adrian Building on the University campus and the Data to Knowledge for Practice (DKP) Facility at the Glenfield Hospital.  This means we are ideally placed to tackle our research interests, as such the group provides bioinformatics input to several international projects (listed below).

 

Databases, Software and Tools

 

GWAS Central

GWAS Central Logo

GWAS Central (formerly HGVbaseG2P) is an enhanced graphical-based genome-wide association study (GWAS) resource which combines the best features of a database and a scientific journal. GWAS Central is the world's largest openly accessible online collection of summary-level GWAS association information.

Latest publication:

  • Beck T, Hastings RK, Gollapudi S, Free RC, Brookes AJ. (2014). GWAS Central: a comprehensive resource for the comparison and interrogation of genome-wide association studies. Eur J Hum Genet; 22(7):949-52. PubMed
  • View more in Publications.

Back to top

 

Cafe Variome

Cafe Variome Logo

Cafe Variome is a complete data discovery solution designed to provide a general-purpose, web-based tool that can be quickly installed by any genotype-phenotype data owner, or network of data owners. Cafe Variome allows safe or sensitive content to be appropriately discoverable in a manner that maintains participant anonymity by allowing data owners to set their data to one of three levels of access (hover for more information):

  • Open Access
  • Restricted Access
  • Linked Access

Latest publication:

  • Lancaster O, Beck T, Atlan D, Swertz M, Veal C, Dalgleish R, Brookes AJ. (2015). Cafe Variome: General-Purpose Software for Making Genotype-Phenotype Data Discoverable in Restricted or Open Access Contexts. Hum Mutat. PubMed
  • View more in Publications.

Back to top

 

OmicsConnect

OmicsConnect Logo

OmicsConnect is a set of tools used to assist with omics data validation, management, viewing and sharing of complex omics data.

The OmicsConnect toolkit includes:

  • Database Tools
  • DAS Server
  • Browser Server

Back to top

 

Data Sharing 101

The Data Sharing 101 website aims to be a pointer to currently available sources of information and software for analysis, interpretation and sharing of genetic data. It is also intended to be written in an accessible format to allow the non-scientific reader to gain a general overview of the various aspects of data sharing.

Back to top

 

The G2P Knowledge Centre

GEN2PHEN KC Logo

This is a cornerstone for the online genotype-to-phenotype (G2P) community. Its functions include:

  • Centralised access to distributed G2P data, acting as the GEN2PHEN project website
  • Providing dynamic online workspaces for expert knowledge exchange for the G2P community
  • Providing G2P news and meeting calendars

Latest publication:

  • Webb AJ, Thorisson GA, Brookes AJ. (2011). GEN2PHEN Consortium. An informatics project and online "Knowledge Centre" supporting modern genotype-to-phenotype research. Hum Mutat; 32(5):543-50. PubMed
  • View more in Publications.

Back to top

 

Accreditation and attribution in data sharing

The issues surrounding accreditation of researchers who deposit their data in central public databases must be addressed if this practice is to be further encouraged and the origin of a specific dataset is to be correctly determined. These issues are being tackled within the group, from the promotion of Digital Identity technologies to authenticate website membership, through to the implementation of unique researcher identifications for tracking individual’s scientific contributions. The group is actively involved in the Open Researcher and Contributor ID Initiative (ORCID).

Back to top

 

Osteogenesis Imperfecta Variant Database [Project lead: Prof. Raymond Dalgleish]

The Osteogenesis Imperfecta Variant database aims to record all published accounts of variants resulting in osteogenesis imperfecta.

Back to top

 

Ehlers-Danlos Syndrome Variant Database [Project lead: Prof. Raymond Dalgleish]

The Ehlers-Danlos syndrome variant database aims to record all published accounts of variants resulting in Ehlers-Danlos syndrome.

Back to top

 

VariantValidator [Project lead: Prof. Raymond Dalgleish]

VariantValidator: Accurate validation, mapping, and formatting of sequence variation descriptions. VariantValidator was designed to ensure that users are guided through the intricacies of the HGVS nomenclature, for example, if the user makes a mistake, VariantValidator automatically corrects the mistake if it can, or provides helpful guidance if it cannot. In addition, VariantValidator has the facility to interconvert genomic variant descriptions in HGVS and Variant Call Format with a degree of accuracy that surpasses most competing solutions.

Latest publication:

  • Freeman, P.J., Hart, R.K., Gretton, L.J., Brookes, A.J. and Dalgleish, R. (2018). VariantValidator: Accurate validation, mapping, and formatting of sequence variation descriptions. Hum Mutat; 39(1):61-68. Pubmed
  • View more in Publications.

Back to top

 

TraceSpace

A web-interface that provides graphical display and filtering options enabling researchers to mine extensive catalogues of human genome sequence trace files for structural variation (no public website).

Back to top

 

Current Project Involvement

 

Solve-RD

Solve-RD is an ambitious Pan European project, run by the RD-Connect organisation, which aims to develop diagnostic tests for most rare diseases by 2020. The consortia plan to combine the collective genomic and phenotypic datasets for patients suffering from rare diseases that they hold and combine them into a single database base on RD-Connect’s platform. By harmonising the datasets using standard descriptors for genotypes and phenotypes and reanalysing the resultant dataset with current bioinformatics pipelines, it is hoped that new leads will be revealed.

Back to top

 

EPAD

The EPAD project is part of a global effort in the fight against Alzheimer's disease and is a major European initiative to create a novel environment for testing numerous interventions targeted at prevention of Alzheimer's dementia.

Back to top

 

REQUITE

REQUITE is a pan-European study involving patients undergoing radiotherapy for breast, lung or prostate cancer. The project aims to identify biomarkers that can be used to predict patient sensitivity to radiotherapy, with the goal of developing a more tailored approach to radiotherapy.

Back to top

 

EMIF

EMIF is a European funded project bringing together industry, academia, healthcare and not for profit organisations with the aim to develop a secure platform for sharing electronic health data from patients and participants across Europe. The resulting platform will not only allow researchers to identify potential candidates for study participation, but also reduce the chance of duplicating work by providing access to a large database of well characterised, searchable results that can be reanalysed.

Back to top

 

ETOX

ETOX is an Innovative medicine initiative project that aims to facilitate the reductant of animal testing in drug development by improving predictive models for toxicity by bringing together academic, SME and commercial partners operating in the field of drug discovery, and collating their collective results from their 10K toxicological studies.

Back to top

 

COPDMAP

COPDMAP is a project jointly funded by the Medical Research Council and the Association of the British Pharmaceutical Industry, bringing together academia and industry to investigate the biological mechanisms that contribute to chronic obstructive pulmonary disease.

Back to top

People

Professor Anthony J. Brookes

Bioinformatics Group Leader
ajb97@le.ac.uk
People page

 

Professor Raymond Dalgleish

Collaborator, Professor of Human Genetics
raymond.dalgleish@le.ac.uk
People page

 

Dr Tim Beck

Collaborator, Research Fellow
timbeck@le.ac.uk
People page

 

Dr Peter Causey-Freeman

Leicester Wellcome Trust ISSF Early Career Fellow
pjf9@leicester.ac.uk
BSc (Manchester University); PhD (Leicester University)
Interests include: Development of software for accurate validation, mapping and describing sequence variants using HGVS, Sequence variation annotation and interpretation, Software and empirical Genomic analyses.
ORCID | ResearchGate | LinkedIn

 

Dr Spencer James Gibson

Research Associate
sg307@le.ac.uk
BSc (De Monfort); PhD (Nottingham)
Interests include: strategies for applying data usage technology and sharing platforms; method development, adaptation and application (wet lab)
ORCID

 

Dr Colin Veal

Research Associate
cdv1@le.ac.uk
BSc (Leicester); BA (Open University); PhD (Leicester)
Interests include: software development of federated discovery platforms, data mining in genomics, multidisciplinary solutions to biological problems
ORCIDResearchGate | Google scholar

 

Dr Adam Webb

Research Associate
ajw51@le.ac.uk
BSc (Leicester); PhD (Leicester)
Interests include: human molecular genetics, DNA variation, G2P data handling
ORCID

 

Vagelis Ladas

Research Assistant
vl62@le.ac.uk
BSc (Lamia, Greece); MSc (Leicester)
Interests include: data warehousing, ETL processes, data mining

 

Dhiwagaran Thangavelu

Research Assistant
dt185@leicester.ac.uk
BEng (Anna University, Chennai); MSc (Leicester)
Interests include: sequence alignment, data analysis, software development

 

Tom Shorter

Research Assistant
ts329@le.ac.uk
BSc (Bangor); MSc (Leicester University)
Interests include: machine learning, software development

 

Gregory Warren

Research Assistant
gw154@le.ac.uk
BSc (Keele); MSc (Leicester University)
Interests include: Big Data management and presentation

Peter Causey-Freeman

Leicester Wellcome Trust ISSF Early Career Fellow

GWAS Central Logo

GWAS Central Logo
GWAS Central Logo
Full-size image: 8.2 KB | View image View Download image Download

GEN2PHEN KC Logo

GEN2PHEN KC Logo
GEN2PHEN KC Logo
Full-size image: 4.9 KB | View image View Download image Download

Cafe Variome Logo

Cafe Variome Logo
Cafe Variome Logo
Full-size image: 15.3 KB | View image View Download image Download

OmicsConnect Logo

OmicsConnect Logo
OmicsConnect Logo
Full-size image: 5.0 KB | View image View Download image Download

Publications and Media

Publications and media announcements from the Bioinformatics Research Group.

GWAS Central

Journals

  • Beck T, Hastings RK, Gollapudi S, Free RC, Brookes AJ. (2014). GWAS Central: a comprehensive resource for the comparison and interrogation of genome-wide association studies. Eur J Hum Genet; 22(7):949-52. PubMed
  • Beck T, Free RC, Thorisson GA, Brookes AJ. (2012). Semantically enabling a genome-wide association study database. J Biomed Semantics; 3(1):9. PubMed
  • Beck, T., Thorisson, G.A. and Brookes, A.J. (2011). December. Applying ontologies and exploring nanopublishing in a genome-wide association study database. In Proceedings of the 4th International Workshop on Semantic Web Applications and Tools for the Life Sciences (pp. 1-2). ACM
  • Thorisson GA, Lancaster O, Free RC, Hastings RK, Sarmah P, Dash D, Brahmachari SK, Brookes AJ. (2009). HGVbaseG2P: a central genetic association database. Nucleic Acids Res; 37(Database issue):D797-802. PubMed

Cafe Variome

Journals

  • Lancaster O, Beck T, Atlan D, Swertz M, Veal C, Dalgleish R, Brookes AJ. (2015). Cafe Variome: General-Purpose Software for Making Genotype-Phenotype Data Discoverable in Restricted or Open Access Contexts. Hum Mutat. PubMed

 

The G2P Knowledge Centre

Journals

  • Webb AJ, Thorisson GA, Brookes AJ. (2011). GEN2PHEN Consortium. An informatics project and online "Knowledge Centre" supporting modern genotype-to-phenotype research. Hum Mutat; 32(5):543-50. PubMed

VariantValidator

Journals

  • Freeman, P.J., Hart, R.K., Gretton, L.J., Brookes, A.J. and Dalgleish, R. (2018). VariantValidator: Accurate validation, mapping, and formatting of sequence variation descriptions. Hum Mutat; 39(1):61-68. Pubmed

 

Ontology tree view

Part of the GWAS Central MeSH tree navigation
Ontology tree view
Full-size image: 36.6 KB | View image View Download image Download

Ontology graph view 2

A graph database visualisation of part of SNOMED CT
Ontology graph view 2
Full-size image: 37.2 KB | View image View Download image Download

Share this page:

Contact Details

Department of Genetics
University of Leicester

Adrian Building
University Road
Leicester
LE1 7RH
United Kingdom

Tel: +44 (0)116 252 3374
E Mail: genetics@le.ac.uk

Head of Department
Professor Alison Goodall

Student complaints procedure

Accessibility

DisabledGo logo

The University of Leicester is committed to equal access to our facilities. DisabledGo has a detailed accessibility guide for the Adrian Building.