Program in complex trait genomics

Prof Peter Visscher, Prof Naomi Wray and Prof Jian Yang together comprise the executive team of the Program in Complex Trait Genomics Group (PCTG) funded as an NHMRC Program Grant 2017-2021, and physically located in the Institute for Molecular Bioscience. The PCTG comprises a critical mass of more than 30 post-doctoral researchers plus research assistants and students, all supported by external grant funding. PCTG is structured into five research themes: statistical genomics, systems genomics, psychiatric genomics, MND genomics and genomics of cognitive ageing.

The Wray laboratory focusses on understanding the genetic contribution to psychiatric and neurological disorders. The group specialises in applying new analytical methods of genomic data to provide insights into these complex disorders, with an ultimate goal to improve diagnosis, prognosis and treatments. The lab plays a key role in the international Psychiatric Genomics Consortium and Prof Wray co-leads the sporadic ALS Australia systems genomics consortium (SALSA), funded by the IceBucket Challenge.

The Visscher laboratory specialises in developing methodology that enables analyses aimed at understanding the genetic basis of differences in risk for disease, and other phenotypes between individuals. This research crosses the boundaries of quantitative and statistical genetics, population genetics and human genetics. Applications are diverse but include the study of cognition, cognitive change, and psychiatric and neurological disorders. 

The Yang laboratory works on the interplay of genetics, genomics, statistics and computer science. The group’s research focusses on developing new statistical methods and performing large-scale analyses of high-throughput genetic and genomic data to understand the genetic architecture of complex traits in humans, with specific interests in model traits such as height, and common diseases such as obesity and schizophrenia.

Group leaders

Professor Naomi Wray

Professor Naomi Wray

Professor Peter Visscher

Professor Peter Visscher

Professor Jian Yang

Professor Jian Yang

Complex trait genomics
(2017–2021) NHMRC Program Grant

Genetic analysis of the relationship between parental age and risk of psychiatric disorders
(2016–2018) NHMRC Project Grant

Phenotypic profiling from DNA using genetic and epigenetic information
(2016–2018) ARC Discovery Projects

The genetics of ageing in human populations
(2016–2018) ARC Discovery Projects

NHMRC Research Fellowship: Neurogenetics and Statistical Genomics
(2015–2019) NHMRC Research Fellowship

Sporadic ALS Australian Systems Genomics Consortium (SALSA-SGC)
(2015–2018) Motor Neurone Disease Research Institute of Australia Inc

1/2 A Large-Scale Schizophrenia Association Study in Sweden
(2015–2017) NIH grant administered by the University of North Carolina at Chapel Hill

Analysis of Genome-Wide Data in the Health and Retirement Study
(2015–2017) NIH grant administered by the University of Southern California

Increasing the power of GxE detection by using multi-locus genome-wide predictors
(2015–2017) NIH grant administered by Harvard Medical School

Estimating the Frequencies and Population Specificities of Risk Alleles
(2013–2017) NIH grant administered by the University of Colorado

Belgian Medical Genomics Initiative (BeMGI)
(2012–2017) University of Liege

Statistical and Quantitative Genetics
(2012–2017) NIH Grant administered by the University of Washington (Seattle)

Statistical genetic analyses of social and economic outcomes
(2012–2017) Stockholm School of Economics

Theoretical Population Genetics
(2011–2017) NIH Subcontract administered by the University of Washington, Seattle


Complex trait genomics
(2017–2021) NHMRC Program Grant

New and innovative polygenic approach for understanding and modelling MNDs in zebrafish
(2017–2018) Motor Neurone Disease Research Institute of Australia Inc

Cell-free DNA and ALS; insight into disease mechanisms and progression
(2017) Motor Neurone Disease Research Institute of Australia Inc

Functional analysis of ALS candidate genes
(2017) Motor Neurone Disease Research Institute of Australia Inc

(2017) Motor Neurone Disease Research Institute of Australia Inc

Identification of phenotypic modifiers in sporadic ALS through systems genomics
(2016–2017) Motor Neuron Disease Research Institute of Australia Inc project administered by Macquarie University

Multivariate whole genome estimation and prediction analysis of genomics data applied to psychiatric disorders
(2015–2019) NHMRC Project Grant

NHMRC Research Fellowship: Using genomics to understand psychiatric disorders
(2015–2019) NHMRC Research Fellowship

Tackling heterogeneity in the etiology of major depressive disorder
(2015–2019) NHMRC Project Grant administered by QIMR

Development and validation of systems genomics-based predictors for autism (Stage 1)
(2015–2018) CRC for Living with Autism Spectrum Disorders (Autism CRC Limited)

Sporadic ALS Australian Systems Genomics Consortium (SALSA-SGC)
(2015–2018) Motor Neurone Disease Research Institute of Australia Inc

1/2 A Large-Scale Schizophrenia Association Study in Sweden
(2015–2017) NIH grant administered by the University of North Carolina at Chapel Hill

Gene discovery in motor neuron disease through systems genomics
(2015–2017) NHMRC Project Grant

Complex trait genomics
(2017–2021) NHMRC Program Grant

Methods and software tool for complex trait analyses using multi-omics data
(2016–2019) NHMRC Project Grant

The role of X-chromosome inactivation in quantitative trait variation
(2016–2019) ARC Discovery Projects

The extent, causes and implications of pleiotropy among complex traits
(2016–2018) ARC Discovery Project administered by The University of Melbourne

Advanced whole-genome approaches for causative variant detection and individual risk prediction of complex traits in human populations
(2015–2017) NHMRC Project Grant administered by University of New England

Analysis of Genome-Wide Data in the Health and Retirement Study
(2015–2017) NIH grant administered by the University of Southern California

Sylvia and Charles Viertel Charitable Foundation Senior Medical Research Fellowship: Methods and large-scale genomic analyses to study the genetic basis of neuropsychiatric disorders and obesity
(2014–2019) Sylvia and Charles Viertel Charitable Foundation

Chen GB, Lee SH, Robinson MR, Trzaskowski M, Zhu ZX, Winkler TW, Day FR, Croteau-Chonka DC, Wood AR, Locke AE, Kutalik Z, Loos RJ, Frayling TM, Hirschhorn JN, Yang J, Wray NR; Genetic Investigation of Anthropometric Traits (GIANT) Consortium., Visscher PM. Across-cohort QC analyses of GWAS summary statistics from complex traits. Eur J Hum Genet. 2016 Jan;25(1):137-146. doi: 10.1038/ejhg.2016.106. PubMed PMID: 27552965; PubMed Central PMCID: PMC5159754.

Yang J, Lee SH, Wray NR, Goddard ME, Visscher PM. GCTA-GREML accounts for linkage disequilibrium when estimating genetic variance from genome-wide SNPs. Proc Natl Acad Sci U S A. 2016 Aug 9;113(32):E4579-80. doi: 10.1073/pnas.1602743113. PubMed PMID: 27457963; PubMed Central PMCID: PMC4987770.

van Rheenen W, Shatunov A, Dekker AM, McLaughlin RL, Diekstra FP, Pulit SL, van der Spek RA, Võsa U, de Jong S, Robinson MR, Yang J, Fogh I, van Doormaal PT, Tazelaar GH, Koppers M, Blokhuis AM, Sproviero W, Jones AR, Kenna KP, van Eijk KR, Harschnitz O, Schellevis RD, Brands WJ, Medic J, Menelaou A, Vajda A, Ticozzi N, Lin K, Rogelj B, Vrabec K, Ravnik-Glavač M, Koritnik B, Zidar J, Leonardis L,  Grošelj LD, Millecamps S, Salachas F, Meininger V, de Carvalho M, Pinto S, Mora JS, Rojas-García R, Polak M, Chandran S, Colville S, Swingler R, Morrison KE, Shaw PJ, Hardy J, Orrell RW, Pittman A, Sidle K, Fratta P, Malaspina A, Topp S, Petri S, Abdulla S, Drepper C, Sendtner M, Meyer T, Ophoff RA, Staats KA, Wiedau-Pazos M, Lomen-Hoerth C, Van Deerlin VM, Trojanowski JQ, Elman L, McCluskey L, Basak AN, Tunca C, Hamzeiy H, Parman Y, Meitinger T, Lichtner P, Radivojkov-Blagojevic M, Andres CR, Maurel C, Bensimon G, Landwehrmeyer B, Brice  A, Payan CA, Saker-Delye S, Dürr A, Wood NW, Tittmann L, Lieb W, Franke A, Rietschel M, Cichon S, Nöthen MM, Amouyel P, Tzourio C, Dartigues JF, Uitterlinden AG, Rivadeneira F, Estrada K, Hofman A, Curtis C, Blauw HM, van der  Kooi AJ, de Visser M, Goris A, Weber M, Shaw CE, Smith BN, Pansarasa O, Cereda C, Del Bo R, Comi GP, D'Alfonso S, Bertolin C, Sorarù G, Mazzini L, Pensato V, Gellera C, Tiloca C, Ratti A, Calvo A, Moglia C, Brunetti M, Arcuti S, Capozzo R, Zecca C, Lunetta C, Penco S, Riva N, Padovani A, Filosto M, Muller B, Stuit RJ; PARALS Registry.; SLALOM Group.; SLAP Registry.; FALS Sequencing Consortium.; SLAGEN Consortium.; NNIPPS Study Group., Blair I, Zhang K, McCann EP, Fifita JA,  Nicholson GA, Rowe DB, Pamphlett R, Kiernan MC, Grosskreutz J, Witte OW, Ringer T, Prell T, Stubendorff B, Kurth I, Hübner CA, Leigh PN, Casale F, Chio A, Beghi  E, Pupillo E, Tortelli R, Logroscino G, Powell J, Ludolph AC, Weishaupt JH, Robberecht W, Van Damme P, Franke L, Pers TH, Brown RH, Glass JD, Landers JE, Hardiman O, Andersen PM, Corcia P, Vourc'h P, Silani V, Wray NR, Visscher PM, de  Bakker PI, van Es MA, Pasterkamp RJ, Lewis CM, Breen G, Al-Chalabi A, van den Berg LH, Veldink JH. Genome-wide association analyses identify new risk variants  and the genetic architecture of amyotrophic lateral sclerosis. Nat Genet. 2016 Sep;48(9):1043-8. doi: 10.1038/ng.3622. PubMed PMID: 27455348.

Zhu Z, Zhang F, Hu H, Bakshi A, Robinson MR, Powell JE, Montgomery GW, Goddard ME, Wray NR, Visscher PM, Yang J. Integration of summary data from GWAS and eQTL  studies predicts complex trait gene targets. Nat Genet. 2016 May;48(5):481-7. doi: 10.1038/ng.3538. PubMed PMID: 27019110.

Mehta D, Tropf FC, Gratten J, Bakshi A, Zhu Z, Bacanu SA, Hemani G, Magnusson  PK, Barban N, Esko T, Metspalu A, Snieder H, Mowry BJ, Kendler KS, Yang J, Visscher PM, McGrath JJ, Mills MC, Wray NR, Lee SH; Schizophrenia Working Group of the Psychiatric Genomics Consortium, LifeLines Cohort Study, and TwinsUK., Andreassen OA, Bramon E, Bruggeman R, Buxbaum JD, Cairns MJ, Cantor RM, Cloninger CR, Cohen D, Crespo-Facorro B, Darvasi A, DeLisi LE, Dinan T, Djurovic S, Donohoe G, Drapeau E, Escott-Price V, Freimer NB, Georgieva L, de Haan L, Henskens FA, Joa I, Julià A, Khrunin A, Lerer B, Limborska S, Loughland CM, Macek M Jr, Magnusson PK, Marsal S, McCarley RW, McIntosh AM, McQuillin A, Melegh B, Michie PT, Morris DW, Murphy KC, Myin-Germeys I, Olincy A, Van Os J, Pantelis C, Posthuma D, Quested D, Schall U, Scott RJ, Seidman LJ, Toncheva D, Tooney PA, Waddington J, Weinberger DR, Weiser M, Wu JQ. Evidence for Genetic Overlap Between Schizophrenia and Age at First Birth in Women. JAMA Psychiatry. 2016 May  1;73(5):497-505. doi: 10.1001/jamapsychiatry.2016.0129. PubMed PMID: 27007234.

Yang J, Bakshi A, Zhu Z, Hemani G, Vinkhuyzen AA, Lee SH, Robinson MR, Perry JR, Nolte IM, van Vliet-Ostaptchouk JV, Snieder H; LifeLines Cohort Study., Esko  T, Milani L, Mägi R, Metspalu A, Hamsten A, Magnusson PK, Pedersen NL, Ingelsson  E, Soranzo N, Keller MC, Wray NR, Goddard ME, Visscher PM. Genetic variance estimation with imputed variants finds negligible missing heritability for human  height and body mass index. Nat Genet. 2015 Oct;47(10):1114-20. doi: 10.1038/ng.3390. PubMed PMID: 26323059; PubMed Central PMCID: PMC4589513.

Shah S, Bonder MJ, Marioni RE, Zhu Z, McRae AF, Zhernakova A, Harris SE, Liewald D, Henders AK, Mendelson MM, Liu C, Joehanes R, Liang L; BIOS Consortium., Levy D, Martin NG, Starr JM, Wijmenga C, Wray NR, Yang J, Montgomery GW, Franke L, Deary IJ, Visscher PM. Improving Phenotypic Prediction by Combining Genetic and Epigenetic Associations. Am J Hum Genet. 2015 Jul 2;97(1):75-85. doi: 10.1016/j.ajhg.2015.05.014. PubMed PMID: 26119815; PubMed Central PMCID: PMC4572498.

Visscher PM, Hemani G, Vinkhuyzen AA, Chen GB, Lee SH, Wray NR, Goddard ME, Yang J. Statistical power to detect genetic (co)variance of complex traits using  SNP data in unrelated samples. PLoS Genet. 2014 Apr 10;10(4):e1004269. doi: 10.1371/journal.pgen.1004269. PubMed PMID: 24721987; PubMed Central PMCID: PMC3983037.

Lee SH, Yang J, Chen GB, Ripke S, Stahl EA, Hultman CM, Sklar P, Visscher PM,  Sullivan PF, Goddard ME, Wray NR. Estimation of SNP heritability from dense genotype data. Am J Hum Genet. 2013 Dec 5;93(6):1151-5. doi: 10.1016/j.ajhg.2013.10.015. PubMed PMID: 24314550; PubMed Central PMCID: PMC3852919.

Wray NR, Yang J, Hayes BJ, Price AL, Goddard ME, Visscher PM. Author reply to A commentary on Pitfalls of predicting complex traits from SNPs. Nat Rev Genet. 2013 Dec;14(12):894. doi: 10.1038/nrg3457-c2. PubMed PMID: 24240515; PubMed Central PMCID: PMC4266985.

Vinkhuyzen AA, Wray NR, Yang J, Goddard ME, Visscher PM. Estimation and partition of heritability in human populations using whole-genome analysis methods. Annu Rev Genet. 2013;47:75-95. doi: 10.1146/annurev-genet-111212-133258. Review. PubMed PMID: 23988118; PubMed Central PMCID: PMC4037293.

de Candia TR, Lee SH, Yang J, Browning BL, Gejman PV, Levinson DF, Mowry BJ,  Hewitt JK, Goddard ME, O'Donovan MC, Purcell SM, Posthuma D; International Schizophrenia Consortium.; Molecular Genetics of Schizophrenia Collaboration., Visscher PM, Wray NR, Keller MC. Additive genetic variation in schizophrenia risk is shared by populations of African and European descent. Am J Hum Genet. 2013 Sep 5;93(3):463-70. doi: 10.1016/j.ajhg.2013.07.007. PubMed PMID: 23954163; PubMed Central PMCID: PMC3845872.

Wray NR, Yang J, Hayes BJ, Price AL, Goddard ME, Visscher PM. Pitfalls of predicting complex traits from SNPs. Nat Rev Genet. 2013 Jul;14(7):507-15. doi: 10.1038/nrg3457. Review. PubMed PMID: 23774735; PubMed Central PMCID: PMC4096801.

Lee SH, DeCandia TR, Ripke S, Yang J; Schizophrenia Psychiatric Genome-Wide Association Study Consortium (PGC-SCZ).; International Schizophrenia Consortium (ISC).; Molecular Genetics of Schizophrenia Collaboration (MGS)., Sullivan PF, Goddard ME, Keller MC, Visscher PM, Wray NR. Estimating the proportion of variation in susceptibility to schizophrenia captured by common SNPs. Nat Genet.  2012 Feb 19;44(3):247-50. doi: 10.1038/ng.1108. PubMed PMID: 22344220; PubMed Central PMCID: PMC3327879.

Wray NR, Yang J, Goddard ME, Visscher PM. The genetic interpretation of area  under the ROC curve in genomic profiling. PLoS Genet. 2010 Feb 26;6(2):e1000864.  doi: 10.1371/journal.pgen.1000864. PubMed PMID: 20195508; PubMed Central PMCID: PMC2829056.

Yang J, Wray NR, Visscher PM. Comparing apples and oranges: equating the power of case-control and quantitative trait association studies. Genet Epidemiol. 2010 Apr;34(3):254-7. doi: 10.1002/gepi.20456. PubMed PMID: 19918758.

Yang J, Visscher PM, Wray NR. Sporadic cases are the norm for complex disease. Eur J Hum Genet. 2010 Sep;18(9):1039-43. doi: 10.1038/ejhg.2009.177. Erratum in: Eur J Hum Genet. 2010 Sep;18(9):1044. PubMed PMID: 19826454; PubMed Central PMCID: PMC2987426.

Genomics of Motor Neuron Disease ALS genomics in collaboration with Prof Pam McCombe, UQCCR and A/Prof Rob Henderson, RBWH. The Sporadic ALS Australia Systems Genomics Consortium, funded by the MNDRIA IceBucket Challenge Grant, to implement consistent collection of clinical data and biological samples across Australia, and to use genetic and genomic date to understand the etiology of ALS motor neurone disease.

Genomics of autism spectrum disorders, funded by the Autism CRC with the ultimate goal of early predictors of autism spectrum disorders

Genomics of Parkinson’s Disease in collaboration with Prof George Mellick, Griffith University and Prof Peter Silburn, QBI

Genomics of major depressive disorder, funded by NHMRC, in collaboration with Prof Nick Martin QIMR Berghofer Medical Research Institute we are establishing an online collection of MDD cases and controls asking participants to provide a spit sample for DNA.

Genomics of Postpartum Depression – the PPD-ACT study, in collaboration with A/Prof Samantha Meltzer-Brody, University of North Carolina

Genomics of schizophrenia, the Sweden3 study, in collaboration with Prof Patrick Sullivan, Karolinska Institutet and University of North Carolina

Research Areas

  • Genomics
  • Quantitative genetics
  • Psychiatric Disorders
  • Neurological Disorders
  • Cognitive Ageing

Our team

Group Leaders

Research Members