Ashish Kumar

Ashish

Post-Graduate Fellow

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:

Diabetes Research group led by Prof. Mark McCarthy, at the Wellcome Trust Centre for Human Genetics, University of Oxford.
Chronic Disease Epidemiology group, led by Prof. Nicole Probst-Hensch at the Swiss Tropical and Public Health Institute, University of Basel.

My work at Oxford (with McCarthy group) is focussed on the genetics of Type 2 Diabetes (T2D) and related phenotypes, on Metabochip - A custom iSELECT array containing ~195,000 SNPs, designed to support large scale follow up of putative associations for T2D and other metabolic and cardiovascular traits. It is spread across various international consortia like DIAGRAM (T2D genetics), EU-funded ENGAGE consortium (www.euengage.org), GIANT (anthropometric traits), MAGIC (continuous glycaemic traits), etc.

In Basel, the work is focussed on the genetics of asthma, which 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. The CDE group in Basel investigates etiology underlying chronic diseases, and is involved with large cohort studies, such as the internationally renowned Swiss SAPALDIA study (ongoing for 20 years), and other collaborations world-wide.

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.

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.

I've commissioned and manage various high computing servers like Dell^TM PowerEdge^TM R905 (four Six-Core AMD Opteron^TM 8000 Series processors, 128 GB RAM) and Sun Fire V40z server (four dual-core AMD Opteron^TM 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.

Since Jan'2010, I've moved to the McCarthy Group.

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).

Publication

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) 'Genome-wide analysis identifies HLA as strongest association with IgA nephropathy', [J Am Soc Nephrol 2010 0: ASN.2010010076 (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.

Keywords: Bioinformatics, Biostatistics, Asthma, obesity, GABRIEL, METABOCHIP, Data quality control, GWAS

Sponsors:

Wellcome Trust
EU fp6

Contact Details:

Ashish Kumar
Bioinformatics and statistical analysis
OCDEM/ WTCHG
University of Oxford
Roosevelt Drive
Oxford
OX3 7BN

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

URL: http://users.ox.ac.uk/~card0095/