Contact Details

QBI Building, UQDI

Centre for Neurogenetics and Statistical Genomics
The Queensland Brain Institute
The University of Queensland
QBI Building (#79)
St Lucia, QLD 4072

Email: a.mcrae [at]

Group Website

Brief C.V.

Positions Held

  • Research Fellow, The Queensland Brain Institute, The University of Queensland, 2014-present.
  • Visiting Scientist, QIMR Berghofer Medical Research Institute (Brisbane, Australia), 2012-present.
  • Research Fellow, University of Queensland Diamantina Institute, The University of Queensland, 2012-2013.
  • Adjunct Lecturer, School of Biological Sciences, The University of Queensland (Brisbane, Australia), 2010-2013.
  • Research Officer, then Senior Research Officer, Queensland Institute of Medical Research (Brisbane, Australia), 2006-2011.
  • Research Associate, AgReseach (Invermay, New Zealand), 2002.


  • PhD, University of Edinburgh, 2006. THESIS
  • BSc (Hons), Statistics and Genetics, University of Otago, 2002.

Research Support

  • National Health and Medical Research Council (NHMRC) Project Grant. Yang J and McRae AF. Methods and software tool for complex trait analyses using multi-omics data. 2015–2019.
  • Australian Research Council (ARC) Discover Project. Morris M, McRae AF, Youngson N. The importance of DNA methylation in response to environmental changes. 2016-2018.
  • National Health and Medical Research Council (NHMRC) Career Development Fellowship, 2015-2018.
  • National Health and Medical Research Council (NHMRC) Project Grant. Lind P, Whitfield J and McRae AF. Deep resequencing of Alcohol Dehydrogenases for alcohol use disorders and esophageal cancer. 2014-2016.
  • National Health and Medical Research Council (NHMRC) Project Grant. McRae AF and Painter JN. Inheritance of DNA methylation state in humans. 2011-2013.
  • National Health and Medical Research Council (NHRMC) Australian Based Biomedical Fellowship, 2008-2011.
  • Commonwealth Scholarship for PhD study, 2002-2005.



Google Scholar  –  ResearcherID  –  ORCID

  1. Tseng HW, Pitt ME, Glant TT, McRae AF, Kenna TJ, Brown MA, Pettit AR, Thomas GP (2016) Inflamation-driven bone formation in a mouse model of ankylosing spondylitis: sequentia not parallel processes. Arthritis Research and Therapy 18: 35.
  2. Bui M, Benyamin B, Shah S, Henders AK, Martin NG, Montgomery GW, McRae AF (2015) Sharing a placenta is associated with a greater similarity in DNA methylation in monochorionic vs dichorionic twin pairs in blood at age 14. Twin Research and Human Genetics 18: 680-685.
  3. Peters MJ, Joehanes R, Pilling LC, Schurmann C, Conneely KN, Powell J, Reinmaa E, Sutphin GL, Zhernakova A, Schramm K, Wilson YA, Kobes S, Tukiainen T, Ramos YF, Göring HHH, Fornage M, Liu Y, Gharib SA, Stranger BE, De Jager PL, Aviv A, Levy D, Murabito JM, Munson PJ, Huan T, Hofman A, Uitterlinden AG, Rivadeneira F, van Rooij J, Stolk L, Broer L, Verbiest MMPJ, Jhamai M, Arp P, Metspalu A, Tserel L, Milani L, Samani NJ, Peterson P, Kasela S, Codd V, Peters A, Ward-Caviness CK, Herder C, Waldenberger M, Roden M, Singmann P, Zeilinger S, Illig T, Homuth G, Grabe HJ, Völzke H, Steil L, Kocher T, Murray A, Melzer D, Yaghootkar H, Bandinelli S, Moses EK, Kent JW, Curran JE, Johnson MP, Williams-Blangero S, Westra HJ, McRae AF, Smith JA, Kardia SLR, Hovatta I, Perola M, Ripatti S, Salomaa V, Henders AK, Martin NG, Smith AK, Mehta D, Binder EB, Nylocks KM, Kennedy EM, Klengel T, Ding J, Suchy-Dicey AM, Enquobahrie DA, Brody J, Rotter JI, Chen YDI, Houwing-Duistermaat J, Kloppenburg M, Slagboom PE, Helmer Q, den Hollander W, Bean S, Raj T, Bakhshi N, Wang QP, Oyston LJ, Psaty BM, Tracy RP, Montgomery GW, Turner ST, Blangero J, Meulenbelt I, Ressler KJ, Yang J, Franke L, Kettunen J, Visscher PM, Neely GG, Korstanje R, Hanson RL, Prokisch H, Ferrucci L, Esko T, Teumer A, van Meurs JBJ, Johnson AD (2015) The transcriptional landscape of age in human peripheral blood. Nature communications 6: 8570
  4. Howrigan DP, Simonson MA, Davies G, Harris SE, Tenesa A, Starr JM, Liewald DC, Deary IJ, McRae A, Wright MJ, Montgomery GW, Hansell N, Martin NG, Payton A, Horan M, Ollier WE, Abdellaoui A, Boomsma DI, DeRosse P, Knowles EEM, Glahn DC, Djurovic S, Melle I, Andreassen OA, Christoforou A, Steen VM, Hellard SL, Sundet K, Reinvang I, Espeseth T, Lundervold AJ, Giegling I, Konte B, Hartmann AM, Rujescu D, Roussos P, Giakoumaki S, Burdick KE, Bitsios P, Donohoe G, Corley RP, Visscher PM, Pendleton N, Malhotra AK, Neale BM, Lencz T, Keller MC (2015) Genome-wide autozygosity is associated with lower general cognitive ability. Molecular Psychiatry (in press)
  5. Marioni RE, Shah S, McRae AF, Ritchie SJ, Muniz-Terrera G, Harris SE, Gibson J, Redmond P, Cox SR, Pattie A, Corley J, Taylor A, Murphy L, Starr JM, Horvath S, Visscher PM, Wray NR, Deary IJ. (2015) The epigenetic clock is correlated with physical and cognitive fitness in the Lothian Birth Cohort 1936. International Journal of Epidemiology 44: 1388-1396
  6. 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, Levy D, Martin NG, Starr JM, Wijmenga C, Wray NR, Yang J, Montgomery GW, Franke L, Deary IJ, Visscher PM. (2015) Improving phenotypic prediction by combining genetic and epigenetic associations. The American Journal of Human Genetics 97: 75-85.
  7. Goldinger A, Shakhbazov K, Henders AK, McRae AF, Mongomery GW, Powell JE. (2015) Seasonal effects of gene expression. PLoS One 10: e0126995
  8. McRae AF, Visscher PM, Montgomery GW, Martin NG (2015) Large autosomal copy-number differences within unselected monozygotic twin pairs are rare. Twin Research and Human Genetics 18: 13-18.
  9. Marioni RE*, Shah S*, McRae AF*, Chen BH, Colicino E, Harris SE, Gibson J, Henders AK, Redmond P, Cox SR, Pattie A, Corley J, Murphy L, Martin NG, Montgomery GW, Feinberg AP, Fallin M, Multhaup ML, Jaffe AE, Joehanes R, Schwartz J, Just AC, Lunetta KL, Murabito JM, Starr JM, Horvath S, Baccarelli AA, Levy D, Visscher PM, Wray NR, Deary IJ. (2015) DNA methylation age of blood predicts all-cause mortality in later life. Genome Biology 16: 25. (* joint first authors)
  10. Shah S*, McRae AF*, Marioni RE, Harris SE, Gibson J, Henders AK, Redmond P, Cox SR, Pattie A, Corley J, Murphy L, Martin NG, Montgomery GW, Starr JM, Wray NR, Deary IJ, Visscher PM (2014) Genetic and environmental exposures constrain epigenetic drift over the human life course. Genome Research 24: 1725-1733. (* joint first authors)
  11. Hemani G, Shakhbazov K, Westra H-J, Esko T, Henders AK, McRae AF, Yang J, Gibson G, Martin NG, Metspalu A, Franke L, Montgomery GW, Visscher PM, Powell JE. (2014) Hemani et al. reply. Nature 514: E5-E6.
  12. Thomson P*, Parla JS*, McRae AF*, Kramer M, Ranakrishnan K, Yao J, Soares DC, McCarthy S, Morris SW, Cardone L, Cass S, Ghiban E, Hennah W, Evans KL, Rebolini D, Millar JK, Harris SE, Starr JM, MacIntyre DJ, Generation Scotland, McIntosh AM, Watson JD, Deary IJ, Visscher PM, Blackwood DH, McCombie WR, Porteous DJ. (2013) 708 common and 2,010 rare DISC1 locus variants identified in 1,542 subjects: Analysis for association with psychiatric disorder and cognitive traits. Molecular Psychiatry 19: 668-675. (* joint first authors) PDF
  13. McRae AF, Powell JE, Henders AK, Bowdler L, Hemani G, Shah S, Painter JN, Martin NG, Visscher PM, Mongomery GW. (2014) Contribution of genetic variation to transgenerational inheritance of DNA methylation. Genome Biology 15: R73. PDF
  14. Hemani G, Shakhbazov K, Westra H-J, Esko T, Henders AK, McRae AF, Yang J, Gibson G, Martin NG, Metspalu A, Franke L, Montgomery GW, Visscher PM, Powell JE. (2014) Detection and replication of epistasis influencing transcription in humans. Nature 508:249-253 PDF
  15. Derks EM, Ayub M, Chambert K, Del Favero J, Johnstone M, Macgregor S, Maclean A, McKechanie AG, McRae AF, Moran JL, Pickard BS, Purcell S, Sklar P, Stclair DM, Wray NR, Visscher PM, Blackwood DH. (2013) A genome wide survey supports the involvement of large copy number variants in schizophrenia with and without intellectual disability. American Journal of Medical Genetics Part B: Neuropsychiatric Genetics 162: 847-854. PDF
  16. Goldinger A, Henders AK, McRae AF, Martin NG, Gibson G, Montgomery GW, Visscher PM, Powell JE. (2013) Genetic and nongenetic variation revealed for the principal components of human gene expression. Genetics 195:1117-28. PDF
  17. McRae AF, Richter MM, Lind PA. (2013) Case-control association testing of common variants from sequencing of DNA pools. PLoS One 8:e65410. PDF
  18. Byrne EM, Carillo-Roa T, Henders AK, Bowdler L, McRae AF, Heath AC, Martin NG, Montgomery GW, Krause L, Wray NR. (2013) Monozygotic Twins affected with Major Depressive Disorder have greater variance in methylation than their unaffected co-twin. Translational Psychiatry 3: e269. PDF
  19. Powell JE, Henders AK, McRae AF, Kim J, Hemani G, Martin NG, Dermitzakis ET, Gibson G, Montgomery GW, Visscher PM. (2103) Congruence of additive and non-additive effects on gene expression estimated from pedigree and SNP data. PLoS Genetics 9:e1003502. PDF
  20. McRae AF, Wright MJ, Hansell NK, Montgomery GW, Martin NG. (2013) No association between general cognitive ability and rare copy number variation. Behavior Genetics 43: 202-207. PDF
  21. Jablensky A, Angelicheva D, Donohoe GJ, Cruickshank M, Azmanov DN, Morris DW, McRae AF, Weickert CS, Carter KW, Chandler D, Alexandrov B, Usheva A, Morar B, Verbrugghe PL, Filipovska A, Rackham O, Bishop AR, Rasmussen KØ, Dragovic M, Cooper M, Phillips M, Badcock J, Bramon-Bosch E, Almeida OP, Flicker L, Gill M, Corvin A, MacGregor S, Kalaydjieva L. (2012) Promoter polymorphisms in two overlapping 6p25 genes implicate mitochondrial proteins in cognitive deficit in schizophrenia. Molecular Psychiatry 17: 1328–1339. PDF
  22. Byrne EM, Johnson J, McRae AF, Nyholt DR, Medland SE, Gehrman PR, Heath AC, Madden PAF, Montgomery GW, Chenevix-Trench G, Martin NG. (2012) A genome-wide association study of caffeine-related sleep disturbance: Confirmation of a role for the adenosine receptor. Sleep 35: 967-975. PDF
  23. Powell JE, Henders AK, McRae AF, Wright MJ, Martin NG, Dermitzakis ET, Visscher PM, Montgomery GW. (2012) The Brisbane Systems Genetics Study: Genetical genomics meets complex trait genetic. PLoS ONE 7: e35430. PDF
  24. Powell JE, Henders AK, McRae AF, Wright MJ, Martin NG, Dermitzakis ET, Montgomery GW, Visscher PM. (2012) Genetic control of gene expression in whole blood and lymphoblastoid cell lines is largely independent. Genome Research 22: 456-466. PDF
  25. Mosing MA, Medland SE, McRae AF, Landers G, Wright MJ, Martin NG. (2012) Genetic influences on life-span and its relationship to personality: A 16 year follow-up study of a sample of ageing twins. Psychosomatic Medicine 74: 16-22. PDF
  26. Luong HTT, Chaplin J, McRae AF, Medland SE, Willemsen G, Nyholt DR, Henders AK, Hoekstra C, Duffy DL, Martin NG, Boomsma DI, Montgomery GW, Painter JN. (2011) Variation in BMPR1B, TGFRB1 and BMPR2 and control of dizygotic twinning. Twin Research and Human Genetics 14: 408-16 PDF
  27. Larsson M, Duffy DL, Zhu G, Liu JZ, Macgregor S, McRae AF, Wright MJ, Sturm RA, Mackey DA, Mongomery GW, Martin NG, Medland SE. (2011) GWAS findings for human iris patterns: Associations with variants in genes that influence normal neuronal pattern development. American Journal of Human Genetics 89: 334-343. PDF
  28. Frank RAW*, McRae AF*, Pocklington AJ, van de Lagemaat, LN, Navarro, P, Croning MDR, Komiyama NH, Armstrong JD, Finn RD, Malloy MP, MacLean AW, Harris SE, Starr JM, Bhaskar SS, Howard EK, Hunt SE, Coffey AJ, Ranganath V, Deloukas P, Rogers J, Muir WJ, Deary IJ, Blackwood DH, Visscher PM, Grant SGN. (2011) Clustered coding variants in the synaptic receptor complexes of individuals with schizophrenia and bipolar disorder. PLoS ONE 6: e19011. (* joint first authors) PDF
  29. Ferreira MA, McRae AF, Medland SE, Nyholt DR, Gordon SD, Wright MJ, Henders AK, Madden PA, Visscher PM, Wray NR, Heath AC, Montgomery GW, Duffy DL, Martin NG. (2011) Association between ORMDL3, IL1RL1 and a deletion on chromosome 17q21 with asthma risk in Australia. European Journal of Human Genetics 19: 458-464. PDF
  30. Gratten J, Wilson AJ, McRae AF, Beraldi D, Visscher PM, Pemberton JM, Slate J. No evidence for warming climate theory of coat colour change in Soay sheep: a comment on Maloney et al. Biology Letters 6: 678-679 (2010) PDF
  31. Sommerlad S, McRae AF, McDonald B, Johnstone I, Cuttell L, Seddon JM, O’Leary CA. (2010) Congenital sensorineural deafness in Australian Stumpy-Tail Cattle Dogs is an autosomal recessive trait that maps to CFA10. PLoS ONE 5: e13364. PDF
  32. Liu JZ, McRae AF, Nyholt DR, Medland SE, Wray NR, Brown KM; AMFS Investigators, Hayward NK, Montgomery GW, Visscher PM, Martin NG, Macgregor S. (2010) A Versatile Gene-Based Test for Genome-wide Association Studies. American Journal of Human Genetics 87: 139-145. PDF
  33. Liu JZ, Medland SE, Wright MJ, Henders AK, Heath AC, Madden PA, Duncan A, Montgomery GW, Martin NG, McRae AF. (2010) Genome-wide association study of height and body mass index in Australian twin families. Twin Research and Human Genetics 13: 179-193. PDF
  34. Johnston SE, Beraldi D, McRae AF, Pemberton JM, Slate J. (2010) Horn type and horn length genes map to the same chromosomal region in Soay sheep. Heredity 104: 196-205. PDF
  35. Knight HM, Pickard BS, Maclean A, Malloy MP, Soares DC, McRae AF, Condie A, White A, Hawkins W, McGhee K, van Beck M, Macintyre D, Starr JM, Deary IJ, Visscher PM, Porteous DJ, Cannon RE, St Clair D, Muir WJ, Blackwood DHR. (2009) A cytogenetic abnormality and rare coding variants identify ABCA13 as a candidate gene in schizophrenia, bipolar disorder and depression. American Journal of Human Genetics 85: 833-846. PDF
  36. Medland SE, Nyholt DR, Painter JN, McEvoy BP, McRae AF, Zhu G, Gordon SD, Wray NR, Ferreira MAR, Wright MJ, Henders AK, Campbell MJ, Duffy DL, Hansell NK, Macgregor S, Slutske WS, Heath AC, Montgomery GW, Martin NG. (2009) Common variants in the Trichohyalin gene are associated with straight hair in Europeans. American Journal of Human Genetics 85: 750-755. PDF
  37. Byrne EM, McRae AF, Duffy DL, Zhao ZZ, Martin NG, Whitfield JB, Visscher PM, Montgomery GW. (2009) Family-based mitochondrial association study of traits related to type 2 diabetes and the metabolic syndrome in adolescents. Diabetologia 52: 2359-2368. PDF
  38. Byrne EM, McRae AF, Duffy DL, Zhao ZZ, Martin NG, Wright MJ, Montgomery GW, Visscher PM. (2009) Association study of common mitochondrial variants and cognitive ability. Behavior Genetics 39: 504-512. PDF
  39. Keller MC, McRae AF, McGaughran JM, Visscher PM, Martin NG, Montgomery GW. (2009) Paternal isodisomy of Chromosome 2 with no apparent phenotypic effects detected using genomewide association data. American Journal of Medical Genetics Part A 149: 1823-1826. PDF
  40. McEvoy BP, Montgomery GW, McRae AF, Ripatti S, Perola M, Spector TD, Cherkas L, Ahmadi KR, Boomsma D, Willemsen G, Hottenga JJ, Pederson NL, Magnusson PKE, Ohm Kyvik K, Christensen K, Kaprio J, Heikkilä K, Palotie A, Widen E, Muilu J, Syvänen AC, Liljedahl U, Hardiman O, Cronin S, Peltonen L, Martin NG, Visscher PM. (2009) Geographical structure and differential natural selection amongst North European populations. Genome Research 19: 804-814. PDF
  41. Benyamin B, Visscher PM, McRae AF. (2009) Family-based genome-wide association studies. Pharmacogenomics 10: 181-190. PDF
  42. Kaminsky ZA, Tang T, Wang SC, Ptak C, Oh GHT, Wong AHC, Feldcamp LA, Virtanen C, Halfvarson J, Tysk C, McRae AF, Visscher PM, Montgomery GW, Gottesman II, Martin NG, Petronis A. (2009) DNA methylation profiles in monozygotic and dizygotic twins. Nature Genetics 41: 240-245. PDF
  43. Benyamin B*, McRae AF*, Zhu G, Gordon S, Henders AK, Palotie A, Peltonen L, Martin NG, Montgomery GW, Whitfield JB, Visscher PM. (2009) Variants in TF and HFE explain ~40% of genetic variation in serum transferrin levels. American Journal of Human Genetics 85: 60-65. (* joint first authors) PDF
  44. Sved JA, McRae AF, Visscher PM. (2008) Divergence between human populations estimated from linkage disequilibrium. American Journal of Human Genetics 83: 737-743. PDF
  45. Middelberg RP, Gordon SD, Zhu G, McRae AF, Montgomery GW, Martin NG, Whitfield JB. (2008) Linkage and association analyses of longitudinally measured lipid phenotypes in adolescence. Twin Research and Human Genetics 11: 603-620. PDF
  46. Byrne EM, McRae AF, Zhao ZZ, Martin NG, Montgomery GW, Visscher PM. (2008) The use of common mitochondrial variants to detect and characterise population structure in the Australian population: Implications for genome-wide association studies. European Journal of Human Genetics 16: 1396-1403. PDF
  47. Keith JM, McRae AF, Duffy D, Mengersen K, Visscher PM. (2008) Calculation of IBD probabilities with dense SNP or sequence data. Genetic Epidemiology 32: 513-519. PDF
  48. McRae AF, Byrne EM, Zhao ZZ, Montgomery GW, Visscher PM. (2008) Power and SNP tagging in whole mitochondrial genome association studies. Genome Research 18: 911-917. PDF
  49. Gratten J, Wilson AJ, McRae AF, Beraldi D, Visscher PM, Pemberton JM, Slate J. (2008) A localized negative genetic correlation constrains microevolution of coal color in wild sheep. Science, 319: 318-320. PDF
  50. Beraldi D, McRae AF, Gratten J, Slate J, Visscher PM, Pemberton JM. (2007) Mapping QTL underlying fitness-related traits in a free-living sheep population. Evolution 61: 1403-1416. PDF
  51. Gratten J, Beraldi D, Lowder DV, McRae AF, Visscher PM, Pemberton JM, Slate J. (2007) Compelling evidence that a single nucleotide substitution in TYRP1 is responsible for coat-colour polymorphism in a free-living population of Soay sheep. Proceedings of the Royal Society B: Biological Sciences 274: 619-626. PDF
  52. McRae AF, Matigan NA, Vadlamudi L, Mulley JC, Mowry B, Martin NG, Berkovic SF, Hayward NK, Visscher PM. (2007) Replicated effects of sex and genotyping on gene expression in human lymphoblastoid cell lines. Human Molecular Genetics 16: 364-373. PDF
  53. Beraldi D, McRae AF, Gratten J, Pilkington JG, Slate J, Visscher PM, Pemberton JM. (2007) Quantitative trait loci (QTL) mapping of resistance to strongyles and coccidia in the free-living Soay sheep (Ovis aries). International Journal for Parasitology 37: 121-129. PDF
  54. Anderson CA, McRae AF, Visscher PM. (2006) A simple linear regression method for QTL linkage analysis with censored observations. Genetics 173: 1735-1745. PDF
  55. Beraldi D, McRae AF, Gratten J, Slate J, Visscher PM, Pemberton JM. (2006) Development of a linkage map and mapping of phenotypic polymorphisms in a free living population of Soay sheep (Ovis aries). Genetics 173: 1521-1537. PDF
  56. McRae AF, Beraldi D. (2006) Examination of a region showing linkage map discrepancies across sheep breeds. Mammalian Genome, 17: 346-353. PDF
  57. McRae AF, Pemberton JM, Visscher PM. (2005) Modeling linkage disequilibrium in natural populations: The example of the Soay sheep population of St. Kilda, Scotland. Genetics 171: 251-258. PDF
  58. McRae AF, Bishop SC, Walling GA, Wilson AD, Visscher PM. (2005) Mapping of multiple quantitative trait loci for growth and carcass traits in a complex commercial sheep pedigree. Animal Science 80: 135-142. PDF
  59. Campbell AW, Bain WE, McRae AF, Broad TE, Johnstone PD, Dodds KG, Veenvliet B, Greer GJ, Glass BC, Beattie AE, Jopson NB, McEwan JC. (2003) Bone density in sheep: Genetic variation and quantitative trait localization. Bone 33: 540-548. PDF
  60. McRae AF, McEwan JC, Dodds KG, Wilson T, Crawford AM, Slate J. (2002) Linkage disequilibrium in domestic sheep. Genetics 160: 1113-1122. PDF

Last updated: 12 March 2014