Laboratory for Genetic Epidemiology


http://www.genepi.org.au

Dr Pamela McCaskie

Pamela McCaskie

Pamela is a genetic statistician with applied and methodological interests in the genetics of complex human disease. Completed her PhD at UWA in 2008 and is currently an Assistant Professor with the CGEB and the School of Mathematics and Statistics. Her current research involves applied and methodological statistical aspects of genetic data analysis and software development for such analyses. Pamela’s current research interest primarily surround cardiovascular disease and depression.

Qualifications

2002BSc - Double major in Human Biology and Applied Statistics, University of Western Australia
2003BSc (Hons, first class) - Applied Statistics, School of Mathematics and Statistics, University of Western Australia
2007PhD (Genetic Statistics) – School of Population Health, University of Western Australia

Research Interests

  • Applied and methodological research in genetic statistics and bioinformatics
  • Epidemiology and genetic epidemiology of complex human diseases

Recent Awards and Honours

2003Applied Probability Trust Richard Tweedie Memorial Prize
2003AMSI Student Travel Scholarship to BioInfoSummer: AMSI Summer Symposium in Bioinformatics
2004-presentAustralian Postgraduate Award, University of Western Australia
2004-presentDepartmental Ad Hoc Scholarship
2004Western Australian Institute for Medical Research Travel Award
2004International Genetic Epidemiology Society Travel award to attend the 13th annual meeting
2004Genetic Analysis Workshop Travel Award to attend the 14th Genetic Analysis Workshop
2005Postgraduate Research School Travel Award
2005Western Australian Institute for Medical Research Travel Award
2005International Genetic Epidemiology Society Travel award to attend the 14th annual meeting
2005Convocation Postgraduate Research Travel Award for 2006

Scientific Involvement

  • Statistical Society of Australia Inc - Member 2003 onwards, Young Statistician Representative for Western Australia 2005 to 2006, WA Branch Secretary 2007, National Young Statistician Representative 2007.
  • International Genetic Epidemiology Society - Member 2004, Memberships Committee 2005 onwards.

Publications

Examined Theses

  1. McCaskie PA. A statistical analysis of microarray data: the effect of the HOX11 gene on other genes. BSc Honours Thesis. Faculty of Life and Physical Sciences, University of Western Australia, 2003.
  2. McCaskie PA. A multiple imputation approach to haplotypic analysis of population-based data with applications to cardiovascular disease. PhD Thesis. School of Population Health, University of Western Australia, 2008.

Conference Presentations

  1. McCaskie PA. A haplotype of the oxidizing enzyme 15-lipoxygenase is associated with cardiovascular outcomes in a Perth community population. Australasian Human Gene Mapping Meeting, Perth, 10-11 August 2004.
  2. McCaskie PA. The effect of missing data on linkage disequilibrium mapping. Genetic Analysis Workshop 14, Noordwijkerhout, The Netherlands, 7-10 September 2004.

Published Abstracts

  1. McCaskie PA, Carter KW, Hazelton M, Palmer LJ. SimHap: A comprehensive modeling framework and simulation-based approach to haplotype analysis for population data. Genetic Epidemiology 2005; 29(3):268.
  2. McCaskie PA, Beilby JP, Chapman CML, McQuillan BM, Thompson PL, Hung J, Palmer LJ. Association between haplotypes in the cholesteryl ester transfer protein (CETP) gene and high density lipoprotein (HDL) levels: Results from three separate populations. Genetic Epidemiology 2004; 27(3):285.
  3. McCaskie PA, Chapman CML, Beilby JP, Hung J, McQuillan BM, Carter KW, Thompson PL, Palmer LJ. SNPs and haplotypes in the 15-LOX gene are associated with intermediate phenotypes but not risk of coronary heart disease. Genetic Epidemiology 2007; 31(5):488.
  4. McCaskie PA, Palmer LJ. Too correlated to be true? Complete separation and the problem of "bouncing betas". Genetic Epidemiology 2007; 31(5):489.

Peer-Reviewed Papers

  1. McCaskie PA, Carter KW, McCaskie SR, Palmer LJ, The effect of missing data on linkage disequilibrium mapping and haplotype association analysis in the GAW 14 simulated data sets, BMC Genetics 2005; 6 Suppl 1:S151.
  2. Carter KW, McCaskie PA, Palmer LJ, Genome wide linkage and association mapping of disease genes with the GAW14 simulated datasets, BMC Genetics 2006; 6 Suppl 1:S41.
  3. Carter KW, McCaskie PA, Palmer LJ. JLIN:A Java based linkage disequilibrium plotter, BMC Bioinformatics 2006; 7:60.
  4. McCaskie PA, Cadby G, Hung J, McQuillan BM, Chapman CML, Carter KW, Thompson PL, Palmer LJ, Beilby JP. The C-480T hepatic lipase polymorphism is associated with HDL-C but not with risk of coronary heart disease, Clinical Genetics 2006; 70:114-121.
  5. McCaskie PA, Beilby JP, Chapman CM, Hung J, McQuillan BM, Thomson PL, Palmer LJ. Cholesteryl ester transfer protein gene haplotyles, plasma high-density lipoprotein levels and the risk of coronary heart disease, Human Genetics 2007; 121:401-411.
  6. Thompson SR, McCaskie PA , Beilby JP, Hung J, Jennens M, Chapman C, Thompson P, Humphries SE. IL18 haplotypes are associated with serum IL-18 concentrations in a population-based study and a cohort of individuals with premature coronary heart disease. Clinical Chemistry 2007; 53(12):2078-85.
  7. Xiao J, Zhang F, Wiltshire S, Hung J, Jennens M, Beilby JP, Thompson PL, McQuillan BM, McCaskie PA, Carter KW, Palmer LJ, Powell BL. The apolipoprotein AII rs5082 variant is associated with reduced risk of coronary artery disease in an Australian male population. Atherosclerosis 2008; 199(2):333-9.
  8. Wiltshire S, Powell BL, Jennens M, McCaskie PA, Carter KW, Palmer LJ, Thompson PL, McQuillan BM, Hung J, Beilby JP. Investigating the association between K198N coding polymorphism in EDN1 and hypertension, lipoprotein levels, the metabolic syndrome and cardiovascular disease. Human Genetics 2008; 123(3):307-13.
  9. McCaskie PA, Beilby JP, Hung J, Chapman CM, McQuillan BM, Powell BL, Thompson PL, Palmer LJ. 15-Lipoxygenase gene variants are associated with carotid plaque but not carotid intima-media thickness. Human Genetics 2008; 123(5):445-53.
  10. Carter KW, Hung J, Powell BL, Wiltshire S, Foo BT, Leow YC, McQuillan BM, Jennens M,McCaskie PA, Thompson PL, Beilby JP, Palmer LJ. Association of Interleukin-1 gene polymorphisms with central obesity and metabolic syndrome in a coronary heart disease population. Human Genetics 2008; 124(3):199-206.
  11. Powell BL, Wiltshire S, Arscott G, McCaskie PA, Hung J, McQuillan BM, Thompson PL, Carter KW, Palmer LJ, Beilby JP. Association of PARL rs3732581 genetic variant with insulin levels, metabolic syndrome and coronary artery disease. Human Genetics 2008; 124(3):263-70.
  12. Webster RJ, Warrington NM, Weedon MN, Hattersley AT, McCaskie PA, Beilby JP, Palmer LJ, Frayling TM. The association of common genetic variants in the APOA5, LPL and GCK genes with longitudinal changes in metabolic and cardiovascular traits. Diabetologia 2009; 52(1):106-14.
  13. Carter KW, McCaskie PA, Palmer LJ. SimHap GUI: an intuitive graphical user interface for genetic association analysis. BMC Bioinformatics 2008; 25(9):557.
  14. Daley D, Lemire M, Akhabir L, Chan-Yeung M, He JQ, McDonald T, Sandford A, Stefanowicz D, Tripp B, Zamar D, Bosse Y, Ferretti V, Montpetit A, Tessier MC, Becker A, Kozyrskyj AL, Beilby J, McCaskie PA , Musk B, Warrington N, James A, Laprise C, Palmer LJ, Paré PD, Hudson TJ. Analyses of associations with asthma in four asthma population samples from Canada and Australia. Human Genetics 2009; 125(4):445-59.
  15. Moran CS, Clancy P, Biros E, Blanco-Martin B, McCaskie PA, Palmer LJ, Coomans D, Norman PE, Golledge J. Association of PPARgamma Allelic Variation, osteoprotegerin and abdominal aortic aneurysm. Clinical Endocrinology (Oxf) 2009; Apr 25 (Epub).

Reviewing for Scientific Journals

  • Genetic Epidemiology
  • International Journal of Epidemiology

Invited Lectures

2004Haplotype analysis: More black boxes than Boeing. Statistical Society of Australia, WA Branch, Perth, Australia.
2005Introduction to Genetic Epidemiology. Summer School Short Course, University of Western Australia, Perth, Australia.
2005Genetic Epidemiology for Epidemiologists. Short course, University of Bristol, UK.
2005Linkage Disequilibrium and Haplotyping: Applications to Genetic Epidemiology. School of Population Health, University of Western Australia, Perth, Australia.
2005Postgraduate Research Opportunities: Wining, dining and international Stardom. 2005 Workshop for Western Australian Young Statisticians, Tompkins Park, Alfred Cove, Western Australia.
2005Haplotype analysis for the masses. Western Australian Institute for Medical Research, Nedlands, Western Australia.
2006SNP and Haplotype Analysis: Numbers to Nature. Department of Cardiovascular Medicine, University College London, UK.
2006Genetic Epidemiology for Epidemiologists. Conference Workshop, North American Congress of Epidemiology, Seattle, WA, USA.