Oxford CV Medicine
Ashish Kumar's Home Page
I am working in the domain of complex disease medical
research, with specialization in bioinformatics and statistical
Currently, I am part of two research groups and share my time
Responsibility and research interests:
Variant discovery/genotyping from sequencing data in
projects like GoT2D and SUMMIT.
Specifically structural variants/CNVs and Indels.
Gene and environment interactions, in
relation to rare variants.
Developing analysis and QC pipeline for
Primary analysis of Metabochip data and
meta-analysis of multiple datasets.
statistics like logistic regression, principal components
analysis, etc. to analyse various cohort datasets.
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)
(Genome scan browser software).
Promotion of bioinformatics education & research in
association with some Indian Institutes.
My work at Oxford (with McCarthy group) is focussed on the
genetics of Type 2 Diabetes (T2D) and related phenotypes on
GoT2D and Metabochip projects.
GoT2D project is looking into the genetic architecture of type 2
diabetes (T2D) using a combination of low-coverage sequencing
data, exome data and 2.5M Omni chip array from Illumina.
The various projects are spread across various international consortia like
DIAGRAM (T2D genetics), EU-funded ENGAGE consortium (www.euengage.org),
GIANT (anthropometric traits), MAGIC (continuous glycaemic
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 and developing societies across
the world. The Chronic Disease Epidemiology 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
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 DellTM
R905 (four Six-Core AMD OpteronTM8000
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
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
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).
Andrew P Morris, Benjamin F Voight, Tanya M Teslovich,
Teresa Ferreira, Ayellet V Segrè, Valgerdur Steinthorsdottir,
Rona J Strawbridge, Hassan Khan, Harald Grallert, Anubha
Mahajan, Inga Prokopenko, Hyun Min Kang, Christian Dina,
Tonu Esko, Ross M Fraser, Stavroula Kanoni, Ashish
Kumar, Vasiliki Lagou, Claudia Langenberg, Jian'an
Luan, Cecilia M Lindgren, Martina Müller-Nurasyid, Sonali
Pechlivanis, N William Rayner, Laura J Scott et al. (2012)
'Large-scale association analysis provides insights into the
genetic architecture and pathophysiology of type 2
diabetes', [Nature Genetics 44,
981–990 (2012) doi:10.1038/ng.2383 (PMID-22885922)]
- Imboden M, Bouzigon E,
Curjuric I, Ramasamy A, Kumar A, et al.
(2012) ‘Genome wide association study of lung function
decline in adults with and without asthma’, [J
Allergy Clin Immunol. 2012 May;129(5):1218-28 (PMID-22424883)]
- Reedik Mägi*, Ashish
Andrew P Morris (2011) 'Assessing the impact of missing
genotype data in rare variant association analysis', [BMC
5(Suppl 9):S107 doi:10.1186/1753-6561-5-S9-S107 (PMID-22373025)]
- Ramasamy A, Curjuric I, Coin
LJ, Kumar A, McArdle WL, et al. (2011) 'A
genome-wide meta-analysis of genetic variants associated
with allergic rhinitis and grass sensitization, and their
interaction with birth order', [J Allergy Clin
- Moffatt M F, Gut I G,
Demenais F, Strachan D P, Bouzigon E, Heath S, Kumar
al. (2010) 'A Large-Scale, Consortium-Based Genomewide
Association Study of Asthma', [N Engl J Med 2010;
Feehally J, Farrall M, Boland A, Gale DP, Ivo IG, Heath S, Kumar
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
al. (2010) 'Unifying candidate gene and GWAS approaches in
Asthma', [PLoS One. 2010 Nov
- 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-
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
Bioinformatcs and statistical analysis
Wellcome Trust Centre for Human Genetics
University of Oxford
Tel: +44 (0) 1865 287715
Fax: +44 (0) 1865 287586