Senior postdoctoral researcher
I am involved in Mark McCarthy's research group focussed on type 2 diabetes and related traits. I am interested in the storage, processing, quality control and delivery to users of the very large data sets now being generated.
With file sizes now in the multi-gigabyte range and growing rapidly I have been developing systems to store and process the data using databases, Perl programs, scripting and publicly available tools e.g plink. I have developed an extensive range of tools to process, reformat and validate data files from a wide variety of sources including data in all the major current file formats. I also provide support, software, data and experience of data handling and QC to affiliated groups, national and international collaborators as well as the main research groups.
To date work has been focussed on dealing with data from the genome-wide genotyping scans and imputed data sets derived from these scans but the focus is changing to include the data now being generated both in-house and publicly from the new high throughput sequencing efforts.
My work also involves efforts to develop data analysis pipelines and to integrate and display data from these with publicly available data.
Click here to access strand files for various genotyping arrays.
Family-based analysis of tumor necrosis factor and lymphotoxin-alpha tag polymorphisms with type 1 diabetes in the population of South Croatia. Boraska V, Zeggini E, Groves CJ, Rayner NW, Skrabic V, Diakite M, Rockett KA, Kwiatkowski D, McCarthy MI, Zemunik T. Hum Immunol. 2009 Mar;70(3):195-9. Epub 2009 Jan 22. PMID: 19167443
Adiposity-related heterogeneity in patterns of type 2 diabetes susceptibility observed in genome-wide association data. Timpson NJ, Lindgren CM, Weedon MN, Randall J, Ouwehand WH, Strachan DP, Rayner NW, Walker M, Hitman GA, Doney AS, Palmer CN, Morris AD, Hattersley AT, Zeggini E, Frayling TM, McCarthy MI. Diabetes. 2009 Feb;58(2):505-10. Epub 2008 Dec 3. PMID: 19056611
Common variants near MC4R are associated with fat mass, weight and risk of obesity. Loos RJ, Lindgren CM, Li S, Wheeler E, Zhao JH, et al. Nat Genet. 2008 Jun;40(6):768-75. Epub 2008 May 4. PMID: 18454148
Genetic determinants of ulcerative colitis include the ECM1 locus and five loci implicated in Crohn's disease. Fisher SA, Tremelling M, Anderson CA, Gwilliam R, Bumpstead S, et al. Nat Genet. 2008 Jun;40(6):710-2. Epub 2008 Apr 27. PMID: 18438406
Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes. Zeggini E, Scott LJ, Saxena R, Voight BF, Marchini JL, et al. Nat Genet. 2008 May;40(5):638-45. Epub 2008 Mar 30. PMID: 18372903
Association scan of 14,500 nonsynonymous SNPs in four diseases identifies autoimmunity variants. Wellcome Trust Case Control Consortium; Australo-Anglo-American Spondylitis Consortium (TASC), Burton PR, Clayton DG, Cardon LR, et al. Nat Genet. 2007 Nov;39(11):1329-37. Epub 2007 Oct 21. PMID: 17952073
A common variant of HMGA2 is associated with adult and childhood height in the general population. Weedon MN, Lettre G, Freathy RM, Lindgren CM, Voight BF, et al. Nat Genet. 2007 Oct;39(10):1245-50. Epub 2007 Sep 2. PMID: 17767157
Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Wellcome Trust Case Control Consortium. Nature. 2007;447;661-78. PMID: 17554300
Replication of genome-wide association signals in UK samples reveals risk loci for type 2 diabetes. Zeggini E, Weedon MN, Lindgren CM, Frayling TM, Elliott KS, et al. Science. 2007 Jun 1;316(5829):1336-41. Epub 2007 Apr 26. Erratum in: Science. 2007 Aug 24;317(5841):1035-6. PMID: 17463249
A common variant in the FTO gene is associated with body mass index and predisposes to childhood and adult obesity. Frayling TM, Timpson NJ, Weedon MN, Zeggini E, Freathy RM, et al. Science. 2007 May 11;316(5826):889-94. Epub 2007 Apr 12. PMID: 17434869
The mountainous Cretan dietary patterns and their relationship with cardiovascular risk factors: the Hellenic Isolated Cohorts MANOLIS study
Farmaki A-E. et al, (2017), Public Health Nutrition, 20, 1063 - 1074
Low-frequency and rare exome chip variants associate with fasting glucose and type 2 diabetes susceptibility
Wessel J. et al, (2015), Nature Communications, 6
Using genomic information to differentiate aetiology in young adult onset diabetes
Kavvoura FK. et al, (2015), DIABETIC MEDICINE, 32, 18 - 18
Genetic studies of body mass index yield new insights for obesity biology
Locke AE. et al, (2015), Nature, 518, 197 - 206
New genetic loci link adipose and insulin biology to body fat distribution
Shungin D. et al, (2015), Nature, 518, 187 - 196