OCDEM

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Oxford CV Medicine

Gabriel project

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I am working in the domain of complex disease medical research, with specialization in bioinformatics and statistical genetics. Currently, I am part of two research groups and share my time between:

Earlier, I was in the Department of Cardiovascular Medicine, working with Prof. Martin Farrall on a EU Framework 6 grant called GABRIEL, co-ordinated by Prof. Bill Cookson. The project aimed at investigating the genetic and environmental causes of asthma in the European Community. 

Asthma is caused by a combination of genetic and environmental effects, and despite being rare a hundred years ago; it has become increasingly common in developed societies across the world. It is believed that rural environments are strongly protective against the disease, and increasing urbanisation may be contributing to the rise in the numbers affected.

The first phase of genetic analysis involved GWAS (Genome-Wide Association Studies) across 994 cases and 1243 controls (from 2 cohorts), and led to the discovery of link between ORMDL3 and childhood asthma. The findings have been published in an article in Nature journal.

The second phase involved 22 cohorts for GWAS across approximately 25000 cases and controls. For this, the genotyping was done on Illumina 610-Quad BeadChips at CNG, Paris. These findings were recently published in an article in NEJM.

I’ve commissioned and manage various high computing servers like DellTM  PowerEdgeTM  R905 (four Six-Core AMD Opteron™ 8000 Series processors, 128 GB RAM) and Sun Fire V40z server (four dual-core AMD OpteronTM  64-bit CPUs, 16 GB RAM) with Red Hat Enterprise Linux 5. Also attached are various capacities of "Storage Array" solutions for upto 12 TB space.

Responsibility and research interests:

  • Primary analysis of Metabochip data and meta-analysis of multiple datasets.

  • Multivariate statistics like logistic regression, principal components analysis, etc. to analyse various cohort datasets.

  • Gene and environment interactions

  • Rare variants and fine mapping

  • Developing QC and analysis pipeline for genotyping and imputed SNPs

  • Managing Data centre; high-performance computing resources.

  • Large scale data storage, handling, formatting and visualisation. Towards this, I have worked with Prof. Richard Mott on projects like IGS (Integrated Genotyping System) and GSCANDB (Genome scan browser software).

  • Promotion of bioinformatics education & research in association with some Indian Institutes.

Previously, I have worked in the industry for around 8 yrs; in the UK as Bioinformatician / IT analyst with companies like Unilever & Volkswagen; in India with some promising start-ups like Omeganet India (now merged into Onicra), LinkEdge Technologies, Career Launcher and Netaquila Solutions; providing IT consultancy, project management, business development and client account management (in business process automation, ERP - Enterprise Resource Planning, database development, data migration and ware-housing, b2b).

Contact Information:

Ashish Kumar
Bioinformatcs and statistical analysis
OCDEM & Wellcome Trust Centre for Human Genetics
University of Oxford
Roosevelt Drive
Oxford
OX3 7BN
UK

Tel: +44 (0) 1865 287715
Fax: +44 (0) 1865 287586

 

Publications:        

 

  • Moffatt M F, Gut I G, Demenais F, Strachan D P, Bouzigon E, Heath S, Kumar A, et. al. (2010) 'A Large-Scale, Consortium-Based Genomewide Association Study of Asthma', [N Engl J Med 2010; 363:1211-1221 (PMID- 20860503)]

  • Feehally J, Farrall M, Boland A, Gale DP, Ivo IG, Heath S, Kumar A, et. al. (2010) 'HLA Has Strongest Association with IgA Nephropathy in Genome-Wide Analysis', [Journal of the American Society of Nephrology 2010 0: ASN.2010010076v2] (PMID - 20595679 )

  • Michel S, Liang L, Depner M, Klopp N, Ruether A, Kumar A et al. (2010) ‘Unifying candidate gene and GWAS approaches in Asthma’, [PLoS One (Submitted)]

  • Taylor M, Valdar W, Kumar A, Flint J, Mott R (2007). Management, presentation and interpretation of genome scans using GSCANDB; [Bioinformatics 2007 23(12):1545-1549; (PMID- 17400728)]

 

Industry Research - at Unilever

  • Kumar A, Bligh F, Warner G (2004). The use of phylogenetic analysis to ensure 'Genetic Diversity' in a commercial plant breeding programme. abstract