Ashish Kumar

AshishKumar

Statistical Analyst

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-Henschat the Swiss Tropical and Public Health Institute, University of Basel.

Research Summary:

Discovery and genotyping of genome structural polymorphism in GOT2D project
Exome Sequencing and analysis in SUMMIT project
Primary analysis of Metabochip data and meta-analysis at Oxford.
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.

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.

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 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 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^TM8000 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.

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).

Publications

E. Melen, R. Granell, M. Kogevinas, D. Strachan, J. R. Gonzalez, M. Wjst, D. Jarvis, M. Ege, C. Braun-Fahrlander, J. Genuneit, E. Horak, E. Bouzigon, F. Demenais, F. Kauffmann, V. Siroux, S. Michel, A. von Berg, A. Heinzmann, M. Kabesch, N. M. Probst-Hensch, I. Curjuric, M. Imboden, T. Rochat, J. Henderson, J. A. C. Sterne, W. L. McArdle, J. Hui, A. L. James, A. William Musk, L. J. Palmer, A. Becker, A. L. Kozyrskyj, M. Chan-Young, J. E. Park, A. Leung, D. Daley, M. B. Freidin, I. A. Deev, L. M. Ogorodova, V. P. Puzyrev, J. C. Celedon, J. M. Brehm, M. M. Cloutier, G. Canino, E. Acosta-Perez, M. Soto-Quiros, L. Avila, A. Bergstrom, J. Magnusson, C. Soderhall, I. Kull, S. Scholtens, H. Marike Boezen, G. H. Koppelman, A. H. Wijga, I. Marenholz, J. Esparza-Gordillo, S. Lau, Y.-A. Lee, M. Standl, C. M. T. Tiesler, C. Flexeder, J. Heinrich, R. A. Myers, C. Ober, D. L. Nicolae, M. Farrall, A. Kumar, M. F. Moffatt, W. O. C. M. Cookson and J. Lasky-Su (2013) 'Genome-wide association study of body mass index in 23 000 individuals with and without asthma', [Clin Exp Allergy. 2013 Apr;43(4):463-74. doi: 10.1111/cea.12054 (PMID-23517042)]
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)]
Curjuric I, Imboden M, Nadif R, Kumar A, Schindler C, Haun M, Kronenberg F, Künzli N, Phuleria H, Postma DS, Russi EW, Rochat T, Demenais F, Probst-Hensch NM (2012) 'Different genes interact with particulate matter and tobacco smoke exposure in affecting lung function decline in the general population', [PLoS One. 2012;7(7):e40175. doi: 10.1371/journal.pone.0040175. Epub 2012 Jul 6 (PMID-22792237)]
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 Kumar and Andrew P Morris (2011) 'Assessing the impact of missing genotype data in rare variant association analysis', [BMC Proceedings 2011, 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 Immunol. 2011 Nov;128(5):996-1005 (PMID-22036096)]
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. 2010 Nov 12;5(11):e13894 (PMID-21103062)]
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, type 2 diabetes, asthma, METABOCHIP, GOT2D, SUMMIT, Data quality control, GWAS

Sponsors:

EU fp6
NIH
Wellcome Trust

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

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