Dr Sang Hong Lee

Senior Research Fellow - School of Environmental and Rural Science

Sang Hong Lee

Phone: +61 2 6773 3665

Email: hong.lee@une.edu.au


Dr Sang Hong Lee is interested in better understanding the genetic architecture of complex traits by using advanced statistical models and methods based on the quantitative genetic theory and molecular information. He has extensive experience in developing advanced statistical methods to estimate genetic variance and individual genetic effects based on phenotype-genotype association analyses. Recently, genome-wide SNP data have been available for many traits in many species.

Dr Lee has developed advanced statistical approaches to use genome-wide SNP data to dissect the genetic architecture of complex traits, e.g. estimating genetic variances and individual genetic effects and predicting unobserved future phenotypes based on genome-wide SNP information. The developed statistical approaches were used to analyse a number of species including human, livestock and mice population, leading to the papers published in high profile journals including Nature, Nature Genetics, American Journal of Human Genetics, PLoS Genetics and many others.

Currently, Dr Lee is focused on understanding the genetic architecture of complex traits by tackling G x E interaction. He has developed an efficient statistical tool that can use genome-wide SNP information. The tool will be applied to economically important traits in livestock, health-related traits in human and many other traits of interest in many species.


  • Doctor of Philosophy, University of New England
  • Master of Agriculture, University of New England
  • Bachelor of Agriculture, DONG-A University, Pusan, Korea

Research Interests

  • Statistical Genetics
  • Quantitative Genetics
  • Population Genetics
  • Genomics
  • Medical Research


Book Chapters

Yang, J., Lee, S. H., Goddard, M. E., Visscher, P. M. (2013) Genome-Wide Complex Trait Analysis (GCTA): Methods, Data Analyses, and Interpretations Genome-Wide Association Studies and Genomic Prediction. 1019, 215-236

Peer Reviewed Journal Articles

Q= Quartile and denotes the journals relative impact within their category, e.g. Q1 = the ‘best’ 25 % of journals in that SCI Subject Category, from Journal Citation Reports, 2013 IF= 2013 5-year Impact Factor Times Cited= from Google Scholar, 12th Feb 2015

Bérénos, C., Ellis, P.A., Pilkington, J.G., Lee, S.H., Graten, J. & Pemberton, J.M. Heterogeneity of genetic architecture of body size traits in a free-living population Molecular Ecology In Press (accepted in Feb 2015). [Q1; IF 5.84, Cited 0].

Zhu, Z., Bakshi, A., Vinkhuyzen, A.A.E., Hemani, G., Lee, S.H., Nolte, I.M., van Vliet-Ostaptchouk, J.V., Snieder, H., Esko, T., Milani, L. et al. Dominance Genetic Variation Contributes Little to the Missing Heritability for Human Complex Traits. The American Journal of Human Genetics In Press (appcepted in Jan 2015). [Q1; IF 10.78, Cited 0]

Moser, G., Lee, S.H., Hayes, B.J., Goddard, M.E., Wray, N.R. & Visscher, P.M. Simultaneous discovery, estimation and prediction analysis of complex traits using a Bayesian mixture model. PLoS Genet, In Press (accepted in Jan 2015). [Q1; IF 8.90, Cited 0]

Maier, R., Moser, G., Chen, G.-B., Ripke, S., Cross disorder Working group of the Psychiatric Genomics Consortium, Coryell, W., Potash, J.B., Scheftner, W.A., Shi, J., Weissman, M.M., …,Lee, S.H. Joint analysis of psychiatric disorders increases accuracy of risk prediction for schizophrenia, bipolar disorder and major depression disorder. The American Journal of Human Genetics 96, 283-294 (2015). [Q1; IF 10.78, Cited 0]  (Last author)

Wray, N.R., Lee, S.H., Mehta, D., Vinkhuyzen, A.A.E., Dudbridge, F. & Middeldorp, C.M. Research Review: Polygenic methods and their application to psychiatric traits. Journal of Child Psychology and Psychiatry 55, 1068-1087 (2014). [Q1; IF 6.26, Cited 8]

Visscher, P.M., Hemani, G., Vinkhuyzen, A.A.E., Chen, G.-B., Lee, S.H., Wray, N.R., Goddard, M.E. & Yang, J. Statistical Power to Detect Genetic (Co)Variance of Complex Traits Using SNP Data in Unrelated Samples. PLoS Genet 10, e1004269 (2014). [Q1; IF 8.90, Cited 12]

Schizophrenia Working Group of the Psychiatric Genomics Consortium. Biological insights from 108 schizophrenia-associated genetic loci. Nature511, 421-427 (2014). [Q1; IF 40.78, Cited 130]

Gusev, A., Lee, S.H., Trynka, G., Finucane, H., Vilhjalmsson, B.J., Xu, H., Zang, C., Ripke, S., Bulik-Sullivan, B., Stahl, E. et al. Partitioning Heritability of Regulatory and Cell-Type-Specific Variants across 11 Common Diseases. The American Journal of Human Genetics 95, 535-552 (2014). [Q1; IF 10.78, Cited 0]

Chen, G.-B., Lee, S.H., Brion, M.-J.A., Montgomery, G.W., Wray, N.R., Radford-Smith, G.L., Visscher, P.M. & The International IBD Genetics Consortium. Estimation and partitioning of (co)heritability of inflammatory bowel disease from GWAS and immunochip data. Human Molecular Genetics 23, 4710-4720 (2014). [Q1; IF 6.97, Cited 5]

Yang, L., Neale, B.M., Liu, L., Lee, S.H., Wray, N.R., Ji, N., Li, H., Qian, Q., Wang, D., Li, J. et al. Polygenic transmission and complex neuro developmental network for attention deficit hyperactivity disorder: genome-wide association study of both common and rare variants. American Journal of Medical Genetics B Neuropsychiatric Genetics 162B, 419-430 (2013). [Q2; IF 3.42, Cited 21]

Ripke, S., O'Dushlaine, C., Chambert, K., Moran, J.L., Kahler, A.K., Akterin, S., Bergen, S.E., Collins, A.L., Crowley, J.J., Fromer, M., Kim, Y., Lee, S.H. et al. Genome-wide association analysis identifies 13 new risk loci for schizophrenia. Nature Genetics45, 1150-1159 (2013). [Q1; IF 32.14, Cited 255]

Rietveld, C.A., Medland, S.E., Derringer, J., Yang, J., Esko, T., Martin, N.W., Westra, H.-J., Shakhbazov, K., Abdellaoui, A., Agrawal, A. et al. GWAS of 126,559 Individuals Identifies Genetic Variants Associated with Educational Attainment. Science 340, 1467-1471 (2013). [Q1; IF 34.46, Cited 86]

Lee, S.H., Yang, J., Chen, G.-B., Ripke, S., Stahl, E.A., Hultman, C.M., Sklar, P., Visscher, P.M., Sullivan, P.F., Goddard, M.E. et al. Estimation of SNP heritability from dense genotype data. The American Journal of Human Genetics 93, 1151-5 (2013). [Q1; IF 10.78, Cited 11]

Lee, S.H. & Wray, N.R. Novel genetic analysis for case-control genome-wide association studies: quantification of power and genomic prediction accuracy. PLOS ONE 8, e71494 (2013). [Q1; IF 4.02, Cited 10]

Lee, S.H., Ripke, S., Neale, B.M., Faraone, S.V., Purcell, S.M., Perlis, R.H., Mowry, B.J., Thapar, A., Goddard, M.E., Witte, J.S. et al. Genetic relationship between five psychiatric disorders estimated from genome-wide SNPs. Nature Genetics 45, 984-994 (2013). [Q1; IF 32.14, Cited 212]

Lee, S.H., Harold, D., Nyholt, D.R., Goddard, M.E., Zondervan, K.T., Williams, J., Montgomery, G.W., Wray, N.R., Visscher, P.M., Consortium, A. et al. Estimation and partitioning of polygenic variation captured by common SNPs for Alzheimer's disease, multiple sclerosis and endometriosis. Human Molecular Genetics 22, 832-841 (2013). [Q1; IF 6.97, Cited 34]

de Candia, T.R., Lee, S.H., Yang, J., Browning, B.L., Gejman, P.V., Levinson, D.F., Mowry, B.J., Hewitt, J.K., Goddard, M.E., O'Donovan, M.C. et al. Additive genetic variation in schizophrenia risk is shared by populations of African and European descent. The American Journal of Human Genetics 93, 463-470 (2013). [Q1; IF 10.78, Cited 7]

Davis, L.K., Yu, D., Keenan, C.L., Gamazon, E.R., Konkashbaev, A.I., Derks, E.M., Neale, B.M., Yang, J., Lee, S.H., Evans, P. et al. Partitioning the heritability of tourette syndrome and obsessive compulsive disorder reveals differences in genetic architecture. PLoS Genet 9, e1003864 (2013). [Q1; IF 8.90, Cited 30]

Berndt, S.I., Gustafsson, S., Magi, R., Ganna, A., Wheeler, E., Feitosa, M.F., Justice, A.E., Monda, K.L., Croteau-Chonka, D.C., Day, F.R. et al. Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture. Nature Genetics 45, 501-12 (2013). [Q1; IF 32.14, Cited 87]

Wray, N.R., Lee, S.H. & Kendler, K.S. Impact of diagnostic misclassification on estimation of genetic correlations using genome-wide genotypes. European Journal of Human Genetics 20, 668-674 (2012). [Q1; IF 3.94, Cited 22]

Vinkhuyzen, A.A.E., Pedersen, N.L., Yang, J., Lee, S.H., Magnusson, P.K.E., Iacono, W.G., McGue, M., Madden, P.A.F., Heath, A.C., Luciano, M. et al. Common SNPs explain some of the variation in the personality dimensions of neuroticism and extraversion. Translational Psychiatry 2 (2012). [Q1; IF 4.36, Cited 56]

Lee, S.H., Yang, J., Goddard, M.E., Visscher, P.M. & Wray, N.R. Estimation of pleiotropy between complex diseases using single-nucleotide polymorphism-derived genomic relationships and restricted maximum likelihood. Bioinformatics 28, 2540-2542 (2012). [Q1; IF 6.97, Cited 68]

Lee, S.H., Goddard, M.E., Wray, N.R. & Visscher, P.M. A better coefficient of determination for genetic profile analysis. Genet Epidemiol 36, 214-224 (2012). [Q1; IF 3.49, Cited 14]

Lee, S.H., DeCandia, T.R., Ripke, S., Yang, J., PGC-SCZ, ISC, MGS, Sullivan, P.F., Goddard, M.E., Keller, M.C. et al. Estimating the proportion of variation in susceptibility to schizophrenia captured by common SNPs. Nature Genetics 44, 247-250 (2012). [Q1; IF 32.14, Cited 208]

Keller, M.C., Simonson, M.A., Ripke, S., Neale, B.M., Gejman, P.V., Howrigan, D.P., Lee, S.H., Lencz, T., Levinson, D.F., Sullivan, P.F. et al. Runs of Homozygosity Implicate Autozygosity as a Schizophrenia Risk Factor. Plos Genetics 8, 425-435 (2012). [Q1; IF 8.90, Cited 36]

Calvin, C.M., Deary, I.J., Webbink, D., Smith, P., Fernandes, C., Lee, S.H., Luciano, M. & Visscher, P.M. Multivariate genetic analyses of cognition and academic achievement from two population samples of 174,000 and 166,000 school children. Behavior Genetics 42, 699-710 (2012). [Q2; IF 3.09, Cited 11]

Yang, J., Lee, S.H., Goddard, M. & Visscher, P. GCTA: A tool for genome-wide complex trait analysis. The American Journal of Human Genetics 88, 76-82 (2011). [Q1; IF 10.78, Cited 526]

Painter, J., Anderson, C., Nyholt, D., Macgregor, S., Lin, J., Lee, S.H., Lambert, A., Zhao, Z., Roseman, F., Guo, Q. et al. Genome-wide association study identifies a locus at 7p15.2 associated with endometriosis. Nature Genetics43, 51-U69 (2011). [Q1; IF 32.14, Cited 136]

Martin, N.W., Medland, S.E., Verweij, K.J.H., Lee, S.H., Nyholt, D.R., Madden, P.A., Heath, A.C., Montgomery, G.W., Wright, M.J. & Martin, N.G. Educational Attainment: A Genome Wide Association Study in 9538 Australians. PLoS ONE 6 (2011). [Q1; IF 4.02, Cited 11]

Lee, S.H., van der Werf, J.H.J., Kim, N.K., Lee, S.H., Gondro, C., Park, E.W., Oh, S.J., Gibson, J.P. & Thompson, J.M. QTL and gene expression analyses identify genes affecting carcass weight and marbling on BTA14 in Hanwoo (Korean Cattle). Mammalian Genome22, 589-601 (2011). [Q2; IF 2.60, Cited 6]

Lee, S.H., Wray, N., Goddard, M. & Visscher, P. Estimating Missing Heritability for Disease from Genome-wide Association Studies. The American Journal of Human Genetics 88, 294-305 (2011). [Q1; IF 10.78, Cited 282]

Goddard, M.E., Lee, S.H., Yang, J., Wray, N.R. & Visscher, P.M. Population Structure Can Inflate SNP-Based Heritability Estimates (Response). The American Journal of Human Genetics 89, 193-195 (2011). [Q1; IF 10.78, Cited 6]

Lee, S.H., van der Werf, J., Lee, S.H., Park, E., Oh, S., Gibson, J. & Thompson, J. Genetic polymorphisms of the bovine Fatty acid binding protein 4 gene are significantly associated with marbling and carcass weight in Hanwoo (Korean Cattle). Animal Genetics 41, 442-444 (2010). [Q1; IF 2.68, Cited 30]

Lee, S.H., Nyholt, D., Macgregor, S., Henders, A., Zondervan, K., Montgomery, G. & Visscher, P. A Simple and Fast Two-Locus Quality Control Test to Detect False Positives Due to Batch Effects in Genome-Wide Association Studies. Genetic Epidemiology 34, 854-862 (2010). [Q1; IF 3.49, Cited 10]

Lee, S.H., Goddard, M., Visscher, P. & van der Werf, J. Using the realized relationship matrix to disentangle confounding factors for the estimation of genetic variance components of complex traits. Genetics Selection Evolution 42(2010). [Q1; IF 3.37, Cited 29]

Idaghdour, Y., Czika, W., Shianna, K., Lee, S.H., Visscher, P., Martin, H., Miclaus, K., Jadallah, S., Goldstein, D., Wolfinger, R. et al. Geographical genomics of human leukocyte gene expression variation in southern Morocco. Nature Genetics 42, 62-67 (2010). [Q1; IF 32.14, Cited 88]

Marshall, K., Maddox, J., Lee, S.H., Zhang, Y., Kahn, L., Graser, H., Gondro, C., Walkden-Brown, S. & van der Werf, J. Genetic mapping of quantitative trait loci for resistance to Haemonchus contortus in sheep. Animal Genetics 40, 262-272 (2009). [Q1; IF 2.68, Cited 33]

Lee, S.H., Van der Werf, J. & Kinghorn, B. Using an evolutionary algorithm and parallel computing for haplotyping in a general complex pedigree with multiple marker loci. BMC Bioinformatics 9(2008). [Q1; IF 3.49, Cited 5]

Lee, S.H., van der Werf, J., Hayes, B., Goddard, M. & Visscher, P. Predicting unobserved phenotypes for complex traits from whole-genome SNP data. PLOS Genet 4, e1000231 (2008). [Q1; IF 8.90, Cited 124]

Lee, S.H. & van der Werf, J. Simultaneous fine mapping of closely linked epistatic quantitative trait loci using combined linkage disequilibrium and linkage with a general pedigree. Genetics Selection Evolution 40, 265-278 (2008). [Q1; IF 3.37, Cited 6]

Lee, S.H., Cho, Y., Lee, S.H., Kim, B., Kim, N., Choy, Y., Kim, K., Yoon, D., Im, S., Oh, S. & Park, E. Identification of marbling-related candidate genes in M-longissimus dorsi of high- and low marbled Hanwoo (Korean Native Cattle) steers. BMB Reports 41, 846-851 (2008). [Q3; IF 1.95, Cited 28]

van der Werf, J., Marshall, K. & Lee, S.H. Methods and experimental designs for detection of QTL in sheep and goats. Small Ruminant Research 70, 21-31 (2007). [Q2; IF 1.34, Cited 23]

Kijas, J., McCulloch, R., Edwards, J., Oddy, V., Lee, S.H. & van der Werf, J. Evidence for multiple alleles effecting muscling and fatness at the Ovine GDF8 locus. BMC Genetics 8(2007). [Q3; IF 2.81, Cited 58]

Lee, S. H.; van der Werf, J. H. Fine mapping of multiple interacting quantitative trait loci using combined linkage disequilibrium and linkage information. Journal of Zhejiang Universicty Science B (2007) 8: 787-791. [Q3; IF 1.42, Cited 1]

Lee, S.H. & Van der Werf, J. Using dominance relationship coefficients based on linkage disequilibrium and linkage with a general complex pedigree to increase mapping resolution. Genetics 174, 1009-1016 (2006). [Q1; IF 4.50, Cited 17]

Lee, S. H.; Van der Werf, J. H. J. Simultaneous fine mapping of multiple closely linked quantitative trait loci using combined linkage disequilibrium and linkage with a general pedigree. Genetics 173: 2329-2337 (2006). [Q1; IF 4.50, Cited 19]

Lee, S. H.; Van der Werf, J. H. J. An efficient variance component approach implementing an average information REML suitable for combined LD and linkage mapping with a general complex pedigree. Genetics Selection Evolution  38: 25-43 (2006). [Q1; IF 3.37, Cited 36]

Lee, S.H., Van der Werf, J. & Tier, B. Combining the meiosis Gibbs sampler with the random walk approach for linkage and association studies with a general complex pedigree and multimarker loci. Genetics 171, 2063-2072 (2005). [Q1; IF 4.50, Cited 14]

Lee, S.H. & Van der Werf, J. The role of pedigree information in combined linkage disequilibrium and linkage mapping of quantitative trait loci in a general complex pedigree. Genetics 169, 455-466 (2005). [Q1; IF 4.50, Cited 29]

Refereed Conference Papers

Lee, S. H. and van der Werf, J. H. J. Fine mapping of multiple QTL using a reversible jump MCMC. 8th World Congress Genetics Applied Livestock Production. Communication 21-08 (2006).

Marshall, K., Lee, S. H. and van der Werf, J. H. J. Information sources in linkage disequilibrium – linkage mapping using half-sib designs. 8th World Congress Genetics Applied Livestock Production. Communication 21-09 (2006).

Lee, S. H., van der Werf, J. H. J. and Tier, B. Combining two Markov chain Monte Carlo approaches for linkage and association studies with a complex pedigree and multi marker loci. Proceedings of the Association for the Advancement of Animal Breeding and Genetics 16: 107-110 (2005).