The University of Queensland

Analysis of genome-wide association data

McRae, Allan F. (2017). Analysis of genome-wide association data. In Jonathan M. Keith (Ed.), Bioinformatics. Volume II: structure, function, and applications (pp. 161-173) New York, NY, United States: Humana Press. doi:10.1007/978-1-4939-6613-4_9

Trajectories of inflammatory biomarkers over the eighth decade and their associations with immune cell profiles and epigenetic ageing

Stevenson, Anna J., McCartney, Daniel L., Harris, Sarah E., Taylor, Adele M., Redmond, Paul, Starr, John M., Zhang, Qian, McRae, Allan F., Wray, Naomi R., Spires-Jones, Tara L., McColl, Barry W., McIntosh, Andrew M., Deary, Ian J. and Marioni, Riccardo E. (2018) Trajectories of inflammatory biomarkers over the eighth decade and their associations with immune cell profiles and epigenetic ageing. Clinical Epigenetics, 10 1: 159. doi:10.1186/s13148-018-0585-x

Identification of 55,000 replicated DNA methylation QTL

McRae, Allan F., Marioni, Riccardo E., Shah, Sonia, Yang, Jian, Powell, Joseph E., Harris, Sarah E., Gibson, Jude, Henders, Anjali K., Bowdler, Lisa, Painter, Jodie N., Murphy, Lee, Martin, Nicholas G., Starr, John M., Wray, Naomi R., Deary, Ian J., Visscher, Peter M. and Montgomery, Grant W. (2018) Identification of 55,000 replicated DNA methylation QTL. Scientific Reports, 8 1: . doi:10.1038/s41598-018-35871-w

Genotype effects contribute to variation in longitudinal methylome patterns in older people

Zhang, Qian, Marioni, Riccardo E., Robinson, Matthew R., Higham, Jon, Sproul, Duncan, Wray, Naomi R., Deary, Ian J., McRae, Allan F. and Visscher, Peter M. (2018) Genotype effects contribute to variation in longitudinal methylome patterns in older people. Genome Medicine, 10 1: . doi:10.1186/s13073-018-0585-7

Epigenetic prediction of complex traits and death

McCartney, Daniel L., Hillary, Robert F., Stevenson, Anna J., Ritchie, Stuart J., Walker, Rosie M., Zhang, Qian, Morris, Stewart W., Bermingham, Mairead L., Campbell, Archie, Murray, Alison D., Whalley, Heather C., Gale, Catharine R., Porteous, David J., Haley, Chris S., McRae, Allan F., Wray, Naomi R., Visscher, Peter M., McIntosh, Andrew M., Evans, Kathryn L., Deary, Ian J. and Marioni, Riccardo E. (2018) Epigenetic prediction of complex traits and death. Genome Biology, 19 1: 136. doi:10.1186/s13059-018-1514-1

Genetic regulation of disease risk and endometrial gene expression highlights potential target genes for endometriosis and polycystic ovarian syndrome

Fung, Jenny N., Mortlock, Sally, Girling, Jane E., Holdsworth-Carson, Sarah J., Teh, Wan Tinn, Zhu, Zhihong, Lukowski, Samuel W., McKinnon, Brett D., McRae, Allan, Yang, Jian, Healey, Martin, Powell, Joseph E., Rogers, Peter A. W. and Montgomery, Grant W (2018) Genetic regulation of disease risk and endometrial gene expression highlights potential target genes for endometriosis and polycystic ovarian syndrome. Scientific Reports, 8 1: 11424. doi:10.1038/s41598-018-29462-y

Genome-wide association analyses identify 143 risk variants and putative regulatory mechanisms for type 2 diabetes

Xue, Angli, Wu, Yang, Zhu, Zhihong, Zhang, Futao, Kemper, Kathryn E., Zheng, Zhili, Yengo, Loic, Lloyd-Jones, Luke R., Sidorenko, Julia, Wu, Yeda, eQTLGen Consortium, McRae, Allan F., Visscher, Peter M., Zeng, Jian and Yang, Jian (2018) Genome-wide association analyses identify 143 risk variants and putative regulatory mechanisms for type 2 diabetes. Nature Communications, 9 1: 2941. doi:10.1038/s41467-018-04951-w

DNA methylation signatures of depressive symptoms in middle-aged and elderly persons: meta-analysis of multiethnic epigenome-wide studies

Story Jovanova, Olivera, Nedeljkovic, Ivana, Derek, Spieler, Walker, Rosie M., Liu, Chunyu, Luciano, Michelle, Bressler, Jan, Brody, Jennifer, Drake, Amanda J., Evans, Kathryn L., Gondalia, Rahul, Kunze, Sonja, Kuhnel, Brigitte, Lahti, Jari, Lemaitre, Rozenn N., Marioni, Riccardo E., Swenson, Brenton, Himali, Jayandra Jung, Wu, Hongsheng, Li, Yun, McRae, Allan F., Russ, Tom C., Stewart, James, Wang, Zhiying, Zhang, Guosheng, Ladwig, Karl-Heinz, Uitterlinden, Andre G., Guo, Xiuqing, Peters, Annette, Räikkönen, Katri, Starr, John M., Waldenberger, Melanie, Wray, Naomi R., Whitsel, Eric A., Sotoodehnia, Nona, Seshadri, Sudha, Porteous, David J., van Meurs, Joyce, Mosley, Thomas H., McIntosh, Andrew M., Mendelson, Michael M., Levy, Daniel, Hou, Lifang, Eriksson, Johan G., Fornage, Myriam, Deary, Ian J., Baccarelli, Andrea, Tiemeier, Henning and Amin, Najaf (2018) DNA methylation signatures of depressive symptoms in middle-aged and elderly persons: meta-analysis of multiethnic epigenome-wide studies. JAMA Psychiatry, . doi:10.1001/jamapsychiatry.2018.1725

Identifying gene targets for brain-related traits using transcriptomic and methylomic data from blood

Qi, Ting, Wu, Yang, Zeng, Jian, Zhang, Futao, Xue, Angli, Jiang, Longda, Zhu, Zhihong, Kemper, Kathryn, Yengo, Loic, Zheng, Zhili, eQTLGen Consortium, Marioni, Riccardo E., Montgomery, Grant W., Deary, Ian J., Wray, Naomi R., Visscher, Peter M., McRae, Allan F. and Yang, Jian (2018) Identifying gene targets for brain-related traits using transcriptomic and methylomic data from blood. Nature Communications, 9 1: 2282. doi:10.1038/s41467-018-04558-1

Genome-wide survey of parent-of-origin effects on DNA methylation identifies candidate imprinted loci in humans

Cuellar Partida, Gabriel, Laurin, Charles, Ring, Susan M., Gaunt, Tom R., McRae, Allan, Visscher, Peter M., Montgomery, Grant W., Martin, Nicholas G., Hemani, Gibran, Suderman, Matthew, Relton, Caroline L., Davey Smith, George and Evans, David M. (2018) Genome-wide survey of parent-of-origin effects on DNA methylation identifies candidate imprinted loci in humans. Human Molecular Genetics, . doi:10.1093/hmg/ddy206

GWAS on family history of Alzheimer's disease

Marioni, Riccardo E., Harris, Sarah E., Zhang, Qian, McRae, Allan F., Hagenaars, Saskia P., Hill, W. David, Davies, Gail, Ritchie, Craig W., Gale, Catharine R., Starr, John M., Goate, Alison M., Porteous, David J., Yang, Jian, Evans, Kathryn L., Deary, Ian J., Wray, Naomi R. and Visscher, Peter M. (2018) GWAS on family history of Alzheimer's disease. Translational Psychiatry, 8 1: 99. doi:10.1038/s41398-018-0150-6

Genome-wide average DNA methylation is determined in utero

Li, Shuai, Wong, Ee Ming, Dugué, Pierre-Antoine, McRae, Allan F., Kim, Eunae, Joo, Ji-Hoon Eric, Nguyen, Tuong L, Stone, Jennifer, Dite, Gillian S, Armstrong, Nicola J, Mather, Karen A, Thalamuthu, Anbupalam, Wright, Margaret J., Ames, David, Milne, Roger L, Craig, Jeffrey M, Saffery, Richard, Montgomery, Grant W., Song, Yun-Mi, Sung, Joohon, Spector, Timothy D, Sachdev, Perminder S, Giles, Graham G, Southey, Melissa C and Hopper, John L (2018) Genome-wide average DNA methylation is determined in utero. International Journal of Epidemiology, 47 3: 908-916. doi:10.1093/ije/dyy028

Integrative analysis of omics summary data reveals putative mechanisms underlying complex traits

Wu, Yang, Zeng, Jian, Zhang, Futao, Zhu, Zhihong, Qi, Ting, Zheng, Zhili, Lloyd-Jones, Luke R., Marioni, Riccardo E., Martin, Nicholas G., Montgomery, Grant W., Deary, Ian J., Wray, Naomi R., Visscher, Peter M., McRae, Allan F. and Yang, Jian (2018) Integrative analysis of omics summary data reveals putative mechanisms underlying complex traits. Nature Communications, 9 918: . doi:10.1038/s41467-018-03371-0

GWAS of epigenetic aging rates in blood reveals a critical role for TERT

Lu, Ake T., Xue, Luting, Salfati, Elias L., Chen, Brian H., Ferrucci, Luigi, Levy, Daniel, Joehanes, Roby, Murabito, Joanne M., Kiel, Douglas P., Tsai, Pei-Chien, Yet, Idil, Bell, Jordana T., Mangino, Massimo, Tanaka, Toshiko, McRae, Allan F., Marioni, Riccardo E., Visscher, Peter M., Wray, Naomi R., Deary, Ian J., Levine, Morgan E., Quach, Austin, Assimes, Themistocles, Tsao, Philip S., Absher, Devin, Stewart, James D., Li, Yun, Reiner, Alex P., Hou, Lifang, Baccarelli, Andrea A., Whitsel, Eric A., Aviv, Abraham, Cardona, Alexia, Day, Felix R., Wareham, Nicholas J., Perry, John R. B., Ong, Ken K., Raj, Kenneth, Lunetta, Kathryn L. and Horvath, Steve (2018) GWAS of epigenetic aging rates in blood reveals a critical role for TERT. Nature Communications, 9 1: 387. doi:10.1038/s41467-017-02697-5

Genome-wide DNA methylation profiling in whole blood reveals epigenetic signatures associated with migraine

Gerring, Zachary F., McRae, Allan F., Montgomery, Grant W. and Nyholt, Dale R. (2018) Genome-wide DNA methylation profiling in whole blood reveals epigenetic signatures associated with migraine. BMC Genomics, 19 1: 69. doi:10.1186/s12864-018-4450-2

Meta-analysis of epigenome-wide association studies of cognitive abilities

Marioni, Riccardo E., McRae, Allan F, Bressler, Jan, Colicino, Elena, Hannon, Eilis, Li, Shuo, Prada, Diddier, Smith, Jennifer A, Trevisi, Letizia, Tsai, Pei-Chien, Vojinovic, Dina, Simino, Jeannette, Levy, Daniel, Liu, Chunyu, Mendelson, Michael, Satizabal, Claudia L, Yang, Qiong, Jhun, Min A, Kardia, Sharon L R, Zhao, Wei, Bandinelli, Stefania, Ferrucci, Luigi, Hernandez, Dena G, Singleton, Andrew B, Harris, Sarah E, Starr, John M, Kiel, Douglas P, McLean, Robert R, Just, Allan C, Schwartz, Joel, Spiro, Avron, Vokonas, Pantel, Amin, Najaf, Ikram, M Arfan, Uitterlinden, Andre G, van Meurs, Joyce B J, Spector, Tim D, Steves, Claire, Baccarelli, Andrea A, Bell, Jordana T, van Duijn, Cornelia M, Fornage, Myriam, Hsu, Yi-Hsiang, Mill, Jonathan, Mosley, Thomas H, Seshadri, Sudha and Deary, Ian J (2018) Meta-analysis of epigenome-wide association studies of cognitive abilities. Molecular Psychiatry, . doi:10.1038/s41380-017-0008-y

Epigenetic influences on aging: a longitudinal genome-wide methylation study in old Swedish twins

Wang, Yunzhang, Karlsson, Robert, Lampa, Erik, Zhang, Qian, Hedman, Åsa K., Almgren, Malin, Almqvist, Catarina, McRae, Allan F., Marioni, Riccardo E., Ingelsson, Erik, Visscher, Peter M., Deary, Ian J., Lind, Lars, Morris, Tiffany, Beck, Stephan, Pedersen, Nancy L. and Hägg, Sara (2018) Epigenetic influences on aging: a longitudinal genome-wide methylation study in old Swedish twins. Epigenetics, 13 9: 1-13. doi:10.1080/15592294.2018.1526028

DNA methylation analysis identifies loci for blood pressure regulation

Richard, Melissa A., Huan, Tianxiao, Ligthart, Symen, Gondalia, Rahul, Jhun, Min A., Brody, Jennifer A., Irvin, Marguerite R., Marioni, Riccardo, Shen, Jincheng, Tsai, Pei-Chien, Montasser, May E., Jia, Yucheng, Syme, Catriona, Salfati, Elias L., Boerwinkle, Eric, Guan, Weihua, Mosley, Thomas H., Bressler, Jan, Morrison, Alanna C., Liu, Chunyu, Mendelson, Michael M., Uitterlinden, André G., van Meurs, Joyce B., Heijmans, Bastiaan T., ’t Hoen, Peter A.C., van Meurs, Joyce, Isaacs, Aaron, Jansen, Rick, Franke, Lude, Boomsma, Dorret I., Pool, René, van Dongen, Jenny, Hottenga, Jouke J., van Greevenbroek, Marleen M.J., Stehouwer, Coen D.A., van der Kallen, Carla J.H., Schalkwijk, Casper G., Wijmenga, Cisca, Zhernakova, Alexandra, Tigchelaar, Ettje F., Slagboom, P. Eline, Beekman, Marian, Deelen, Joris, van Heemst, Diana, Veldink, Jan H., van den Berg, Leonard H., van Duijn, Cornelia M., Hofman, Albert, Uitterlinden, André G., Jhamai, P. Mila, Verbiest, Michael, Suchiman, H. Eka D., Verkerk, Marijn, van der Breggen, Ruud, van Rooij, Jeroen, Lakenberg, Nico, Mei, Hailiang, van Iterson, Maarten, van Galen, Michiel, Bot, Jan, van ’t Hof, Peter, Deelen, Patrick, Nooren, Irene, Moed, Matthijs, Vermaat, Martijn, Zhernakova, Dasha V., Luijk, René, Bonder, Marc Jan, van Dijk, Freerk, Arindrarto, Wibowo, Kielbasa, Szymon M., Swertz, Morris A., van Zwet, Erik W., Franco, Oscar H., Zhang, Guosheng, Li, Yun, Stewart, James D., Bis, Joshua C., Psaty, Bruce M., Chen, Yii-Der Ida, Kardia, Sharon L.R., Zhao, Wei, Turner, Stephen T., Absher, Devin, Aslibekyan, Stella, Starr, John M., McRae, Allan F., Hou, Lifang, Just, Allan C., Schwartz, Joel D., Vokonas, Pantel S., Menni, Cristina, Spector, Tim D., Shuldiner, Alan, Damcott, Coleen M., Rotter, Jerome I., Palmas, Walter, Liu, Yongmei, Paus, Tomáš, Horvath, Steve, O'Connell, Jeffrey R., Guo, Xiuqing, Pausova, Zdenka, Assimes, Themistocles L., Sotoodehnia, Nona, Smith, Jennifer A., Arnett, Donna K., Deary, Ian J., Baccarelli, Andrea A., Bell, Jordana T., Whitsel, Eric, Dehghan, Abbas, Levy, Daniel and Fornage, Myriam (2017) DNA methylation analysis identifies loci for blood pressure regulation. American Journal of Human Genetics, 101 6: 888-902. doi:10.1016/j.ajhg.2017.09.028

Testing two evolutionary theories of human aging with DNA methylation data

Robins, Chloe, McRae, Allan F., Powell, Joseph E., Wiener, Howard W., Aslibekyan, Stella, Kennedy, Elizabeth M., Absher, Devin M., Arnett, Donna K., Montgomery, Grant W., Visscher, Peter M., Cutler, David J. and Conneely, Karen N. (2017) Testing two evolutionary theories of human aging with DNA methylation data. Genetics, 207 4: 1547-1560. doi:10.1534/genetics.117.300217

An epigenome-wide association study meta-analysis of educational attainment

Karlsson Linnér, R., Marioni, R. E., Rietveld, C. A., Simpkin, A. J., Davies, N. M., Watanabe, K., Armstrong, N. J., Auro, K., Baumbach, C., Bonder, M. J., Buchwald, J., Fiorito, G., Ismail, K., Iurato, S., Joensuu, A., Karell, P., Kasela, S, Lahti, J., McRae, A. F., Mandaviya, P. R., Seppälä, I., Wang, Y., Baglietto, L., Binder, E. B., Harris, S. E., Hodge, A. M., Horvath, S., Hurme, M., Johannesson, M., Latvala, A., Mather, K. A., Medland, S. E., Metspalu, A., Milani, L., Milne, R. L., Pattie, A., Pedersen, N. L., Peters, A., Polidoro, S., Räikkönen, K., Severi, G., Starr, J. M., Stolk, L., Waldenberger, M., BIOS Consortium, Eriksson, J. G., Esko, T., Franke, L., Gieger, C., Giles, G. G., Hägg, S., Jousilahti, P., Kaprio, J., Kähönen, M., Lehtimäki, T., Martin, N. G., van Meurs, J. B. C., Ollikainen, M., Perola, M., Posthuma, D., Raitakari, O. T., Sachdev, P. S., Taskesen, E., Uitterlinden, A. G., Vineis, P., Wijmenga, C., Wright, M. J., Relton, C., Davey Smith, G., Deary, I. J., Koellinger, P. D. and Benjamin, D. J. (2017) An epigenome-wide association study meta-analysis of educational attainment. Molecular Psychiatry, 22 12: 1680-1690. doi:10.1038/mp.2017.210

Whole exome sequencing and DNA methylation analysis in a clinical amyotrophic lateral sclerosis cohort

Garton, Fleur C., Benyamin, Beben, Zhao, Qiongyi, Liu, Zhijun, Gratten, Jacob, Henders, Anjali K., Zhang, Zong-Hong, Edson, Janette, Furlong, Sarah, Morgan, Sarah, Heggie, Susan, Thorpe, Kathryn, Pfluger, Casey, Mather, Karen A., Sachdev, Perminder S., McRae, Allan F., Robinson, Matthew R., Shah, Sonia, Visscher, Peter M., Mangelsdorf, Marie, Henderson, Robert D., Wray, Naomi R. and McCombe, Pamela A. (2017) Whole exome sequencing and DNA methylation analysis in a clinical amyotrophic lateral sclerosis cohort. Molecular Genetics and Genomic Medicine, 5 4: 418-428. doi:10.1002/mgg3.302

Role of DNA methylation in type 2 diabetes etiology: using genotype as a causal anchor

Elliott, Hannah R., Shihab, Hashem A., Lockett, Gabrielle A., Holloway, John W., McRae, Allan F., Smith, George Davey, Ring, Susan M., Gaunt, Tom R. and Relton, Caroline L. (2017) Role of DNA methylation in type 2 diabetes etiology: using genotype as a causal anchor. Diabetes, 66 6: 1713-1722. doi:10.2337/db16-0874

Epigenetic patterns in blood associated with lipid traits predict incident coronary heart disease events and are enriched for results from genome-wide association studies

Hedman, Åsa K., Mendelson, Michael M., Marioni, Riccardo E., Gustafsson, Stefan, Joehanes, Roby, Irvin, Marguerite R., Zhi, Degui, Sandling, Johanna K., Yao, Chen, Liu, Chunyu, Liang, Liming, Huan, Tianxiao, McRae, Allan F., Demissie, Serkalem, Shah, Sonia, Starr, John M., Cupples, L. Adrienne, Deloukas, Panos, Spector, Timothy D., Sundstrom, Johan, Krauss, Ronald M., Arnett, Donna K., Deary, Ian J., Lind, Lars, Levy, Daniel and Ingelsson, Erik (2017) Epigenetic patterns in blood associated with lipid traits predict incident coronary heart disease events and are enriched for results from genome-wide association studies. Circulation: Cardiovascular Genetics, 10 1: . doi:10.1161/CIRCGENETICS.116.001487

The Genetic Architecture of Gene Expression in Peripheral Blood (vol 100, pg 228, 2017)

Lloyd-Jones, Luke R., Holloway, Alexander, McRae, Allan, Yang, Jian, Small, Kerrin, Zhao, Jing, Zeng, Biao, Bakshi, Andrew, Metspalu, Andres, Dermitzakis, Manolis, Gibson, Greg, Spector, Tim, Montgomery, Grant, Esko, Tonu, Visscher, Peter M. and Powell, Joseph E. (2017) The Genetic Architecture of Gene Expression in Peripheral Blood (vol 100, pg 228, 2017). American Journal of Human Genetics, 100 2: 371-371. doi:10.1016/j.ajhg.2017.01.026

The genetic architecture of gene expression in peripheral blood

Lloyd-Jones, Luke R., Holloway, Alexander, McRae, Allan, Yang, Jian, Small, Kerrin, Zeng, Biao, Bakshi, Andrew, Metspalu, Andres, Dermitzakis, Manolis, Gibson, Greg, Spector, Tim, Montgomery, Grant, Esko, Tonu, Visscher, Peter M. and Powell, Joseph E. (2017) The genetic architecture of gene expression in peripheral blood. American Journal of Human Genetics, 100 2: 228-237. doi:10.1016/j.ajhg.2016.12.008

DNA methylation signatures of chronic low-grade inflammation are associated with complex diseases

Ligthart, Symen, Marzi, Carola, Aslibekyan, Stella, Mendelson, Michael M., Conneely, Karen N., Tanaka, Toshiko, Colicino, Elena, Waite, Lindsay L., Joehanes, Roby, Guan, Weihua, Brody, Jennifer A., Elks, Cathy, Marioni, Riccardo, Jhun, Min A., Agha, Golareh, Bressler, Jan, Ward-Caviness, Cavin K., Chen, Brian H., Huan, Tianxiao, Bakulski, Kelly, Salfati, Elias L., Fiorito, Giovanni, Wahl, Simone, Schramm, Katharina, Sha, Jin, Hernandez, Dena G., Just, Allan C., Smith, Jennifer A., Sotoodehnia, Nona, Pilling, Luke C., Pankow, James S., Tsao, Phil S., Liu, Chunyu, Zhao, Wei, Guarrera, Simonetta, Michopoulos, Vasiliki J., Smith, Alicia K., Peters, Marjolein J., Melzer, David, Vokonas, Pantel, Fornage, Myriam, Prokisch, Holger, Bis, Joshua C., Chu, Audrey Y., Herder, Christian, Grallert, Harald, Yao, Chen, Shah, Sonia, McRae, Allan F., Lin, Honghuang, Horvath, Steve, Fallin, Daniele, Hofman, Albert, Wareham, Nicholas J., Wiggins, Kerri L., Feinberg, Andrew P., Starr, John M., Visscher, Peter M., Murabito, Joanne M., Kardia, Sharon L. R., Absher, Devin M., Binder, Elisabeth B., Singleton, Andrew B., Bandinelli, Stefania, Peters, Annette, Waldenberger, Melanie, Matullo, Giuseppe, Schwartz, Joel D., Demerath, Ellen W., Uitterlinden, André G., Van Meurs, Joyce B. J., Franco, Oscar H., Chen, Yii-Der Ida, Levy, Daniel, Turner, Stephen T., Deary, Ian J., Ressler, Kerry J., Dupuis, Josée, Ferrucci, Luigi, Ong, Ken K., Assimes, Themistocles L., Boerwinkle, Eric, Koenig, Wolfgang, Arnett, Donna K., Baccarelli, Andrea A., Benjamin, Emelia J. and Dehghan, Abbas (2016) DNA methylation signatures of chronic low-grade inflammation are associated with complex diseases. Genome Biology, 17 1: 255-255. doi:10.1186/s13059-016-1119-5

Autosomal genetic control of human gene expression does not differ across the sexes

Kassam, Irfahan, Lloyd-Jones, Luke, Holloway, Alexander, Small, Kerrin S., Zeng, Biao, Bakshi, Andrew, Metspalu, Andres, Gibson, Greg, Spector, Tim D., Esko, Tonu, Montgomery, Grant W., Powell, Joseph E., Yang, Jian, Visscher, Peter M. and McRae, Allan F. (2016) Autosomal genetic control of human gene expression does not differ across the sexes. Genome Biology, 17 1: 248.1-248.10. doi:10.1186/s13059-016-1111-0

A DNA methylation biomarker of alcohol consumption

Liu, C., Marioni, R. E., Hedman, K., Pfeiffer, L., Tsai, P. -C., Reynolds, L. M., Just, A. C., Duan, Q., Boer, C. G., Tanaka, T., Elks, C. E., Aslibekyan, S., Brody, J. A., Kuhnel, B., Herder, C., Almli, L. M., Zhi, D., Wang, Y., Huan, T., Yao, C., Mendelson, M. M., Joehanes, R., Liang, L., Love, S. -A., Guan, W., Shah, S., McRae, A. F., Kretschmer, A., Prokisch, H., Strauch, K., Peters, A., Visscher, P. M., Wray, N. R., Guo, X., Wiggins, K. L., Smith, A. K., Binder, E. B., Ressler, K. J., Irvin, M. R., Absher, D. M., Hernandez, D., Ferrucci, L., Bandinelli, S., Lohman, K., Ding, J., Trevisi, L., Gustafsson, S., Sandling, J. H., Stolk, L., Uitterlinden, A. G., Yet, I., Castillo-Fernandez, J. E., Spector, T. D., Schwartz, J. D., Vokonas, P., Lind, L., Li, Y., Fornage, M., Arnett, D. K., Wareham, N. J., Sotoodehnia, N., Ong, K. K., van Meurs, J. B. J., Conneely, K. N., Baccarelli, A. A., Deary, I. J., Bell, J. T., North, K. E., Liu, Y., Waldenberger, M., London, S. J., Ingelsson, E. and Levy, D. (2016) A DNA methylation biomarker of alcohol consumption. Molecular Psychiatry, 23 2: 422-433. doi:10.1038/mp.2016.192

Evidence for mitochondrial genetic control of autosomal gene expression

Kassam, Irfahan, Qi, Tuan, Lloyd-Jones, Luke, Holloway, Alexander, Bonder, Marc Jan, Henders, Anjali K., Martin, Nicholas G., Powell, Joseph E., Franke, Lude, Montgomery, Grant W., Visscher, Peter M. and McRae, Allan F. (2016) Evidence for mitochondrial genetic control of autosomal gene expression. Human Molecular Genetics, 25 24: 5332-5338. doi:10.1093/hmg/ddw347

Epigenetic signatures of cigarette smoking

Joehanes, Roby, Just, Allan C., Marioni, Riccardo E., Pilling, Luke C., Reynolds, Lindsay M., Mandaviya, Pooja R., Guan, Weihua, Xu, Tao, Elks, Cathy E., Aslibekyan, Stella, Moreno-Macias, Hortensia, Smith, Jennifer A., Brody, Jennifer A., Dhingra, Radhika, Yousefi, Paul, Pankow, James S., Kunze, Sonja, Shah, Sonia H., McRae, Allan F., Lohman, Kurt, Sha, Jin, Absher, Devin M., Ferrucci, Luigi, Zhao, Wei, Demerath, Ellen W., Bressler, Jan, Grove, Megan L., Huan, Tianxiao, Liu, Chunyu, Mendelson, Michael M., Yao, Chen, Kiel, Douglas P., Peters, Annette, Wang-Sattler, Rui, Visscher, Peter M., Wray, Naomi R., Starr, John M., Ding, Jingzhong, Rodriguez, Carlos J., Wareham, Nicholas J., Irvin, Marguerite R., Zhi, Degui, Barrdahl, Myrto, Vineis, Paolo, Ambatipudi, Srikant, Uitterlinden, André G., Hofman, Albert, Schwartz, Joel, Colicino, Elena, Hou, Lifang, Vokonas, Pantel S., Hernandez, Dena G., Singleton, Andrew B., Bandinelli, Stefania, Turner, Stephen T., Ware, Erin B., Smith, Alicia K., Klengel, Torsten, Binder, Elisabeth B., Psaty, Bruce M., Taylor, Kent D., Gharib, Sina A., Swenson, Brenton R., Liang, Liming, Demeo, Dawn L., O'Connor, George T., Herceg, Zdenko, Ressler, Kerry J., Conneely, Karen N., Sotoodehnia, Nona, Kardia, Sharon L. R., Melzer, David, Baccarelli, Andrea A., Van Meurs, Joyce B. J., Romieu, Isabelle, Arnett, Donna K., Ong, Ken K., Liu, Yongmei, Waldenberger, Melanie, Deary, Ian J., Fornage, Myriam, Levy, Daniel and London, Stephanie J. (2016) Epigenetic signatures of cigarette smoking. Circulation: Cardiovascular Genetics, 9 5: 436-447. doi:10.1161/CIRCGENETICS.116.001506

Fast set-based association analysis using summary data from GWAS identifies novel gene loci for human complex traits

Bakshi, Andrew, Zhu, Zhihong, Vinkhuyzen, Anna A. E., Hill, W. David, Mcrae, Allan F., Visscher, Peter M. and Yang, Jian (2016) Fast set-based association analysis using summary data from GWAS identifies novel gene loci for human complex traits. Scientific Reports, 6 32894. doi:10.1038/srep32894

The autosomal genetic control of sexually dimorphic traits in humans is largely the same across the sexes

Kassam, Irfahan and McRae, Allan F. (2016) The autosomal genetic control of sexually dimorphic traits in humans is largely the same across the sexes. Genome Biology, 17 1: . doi:10.1186/s13059-016-1035-8

Predicting gene targets from integrative analyses of summary data from GWAS and eQTL studies for 28 human complex traits

Pavlides, Jennifer M. Whitehead, Zhu, Zhihong, Gratten, Jacob, Mcrae, Allan F., Wray, Naomi R. and Yang, Jian (2016) Predicting gene targets from integrative analyses of summary data from GWAS and eQTL studies for 28 human complex traits. Genome Medicine, 8 1: 84. doi:10.1186/s13073-016-0338-4

Identification of common genetic variants influencing spontaneous dizygotic twinning and female fertility

Mbarek, Hamdi, Steinberg, Stacy, Nyholt, Dale R., Gordon, Scott D., Miller, Michael B., McRae, Allan F, Hottenga, Jouke Jan, Day, Felix R., Willemsen, Gonneke, de Geus, Eco J., Davies, Gareth E, Martin, Hilary C, Penninx, Brenda W, Jansen, Rick, McAloney, Kerrie, Vink, Jacqueline M., Kaprio, Jaakko, Plomin, Robert, Spector, Tim D., Magnusson, Patrik K., Reversade, Bruno, Harris, R. Alan, Aagaard, Kjersti, Kristjansson, Ragnar P., Olafsson, Isleifur, Eyjolfsson, Gudmundur Ingi, Sigurdardottir, Olof, Iacono, William G., Lambalk, Cornelis B, Montgomery, Grant W., McGue , Matt, Ong, Ken K., Perry, John R.B., Martin, Nicholas G., Stefansson, Hreinn, Stefansson, Kari and Boomsman, Dorret I. (2016) Identification of common genetic variants influencing spontaneous dizygotic twinning and female fertility. American Journal of Human Genetics, 98 5: 898-908. doi:10.1016/j.ajhg.2016.03.008

Corrigendum: The epigenetic clock and telomere length are independently associated with chronological age and mortality [Int J Epidemiol., 45, 2, (424-432)(2016)] DOI: 10.1093/ije/dyw041

Marioni, Riccardo E., Harris, Sarah E., Shah, Sonia, McRae, Allan F., von Zglinicki, Thomas, Martin-Ruiz, Carmen, Wray, Naomi R., Visscher, Peter M. and Deary, Ian J. (2016) Corrigendum: The epigenetic clock and telomere length are independently associated with chronological age and mortality [Int J Epidemiol., 45, 2, (424-432)(2016)] DOI: 10.1093/ije/dyw041. International Journal of Epidemiology, 47 1: 356-356. doi:10.1093/ije/dyx233

The epigenetic clock and telomere length are independently associated with chronological age and mortality

Marioni, Riccardo E., Harris, Sarah E., Shah, Sonia, McRae, Allan F., von Zglinicki, Thomas, Martin-Ruiz, Carmen, Wray, Naomi R., Visscher, Peter M. and Deary, Ian J. (2016) The epigenetic clock and telomere length are independently associated with chronological age and mortality. International Journal of Epidemiology, 45 2: 424-432. doi:10.1093/ije/dyw041

Shared genetic control of expression and methylation in peripheral blood

Shakhbazov, Konstantin, Powell, Joseph E., Hemani, Gibran, Henders, Anjali K., Martin, Nicholas G., Visscher, Peter M., Montgomery, Grant W. and McRae, Allan F. (2016) Shared genetic control of expression and methylation in peripheral blood. BMC Genomics, 17 1: . doi:10.1186/s12864-016-2498-4

Inflammation-driven bone formation in a mouse model of ankylosing spondylitis: sequential not parallel processes

Tseng, Hsu-Wen, Pitt, Miranda E., Glant, Tibor T., McRae, Allan F., Kenna, Tony J., Brown, Matthew A., Pettit, Allison R. and Thomas, Gethin P. (2016) Inflammation-driven bone formation in a mouse model of ankylosing spondylitis: sequential not parallel processes. Arthritis Research and Therapy, 18 1: . doi:10.1186/s13075-015-0805-0

DNA methylation-based measures of biological age: meta-analysis predicting time to death

Chen, Brian H., Marioni, Riccardo E., Colicino, Elena, Peters, Marjolein J., Ward-Caviness, Cavin K., Tsai, Pei-Chien, Roetker, Nicholas S., Just, Allan C., Demerath, Ellen W., Guan, Weihua, Bressler, Jan, Fornage, Myriam, Studenski, Stephanie, Vandiver, Amy R., Moore, Ann Zenobia, Tanaka, Toshiko, Kiel, Douglas P., Liang, Liming, Vokonas, Pantel, Schwartz, Joel, Lunetta, Kathryn L., Murabito, Joanne M., Bandinelli, Stefania, Hernandez, Dena G., Melzer, David, Nalls, Michael, Pilling, Luke C., Price, Timothy R., Singleton, Andrew B., Gieger, Christian, Holle, Rolf, Kretschmer, Anja, Kronenberg, Florian, Kunze, Sonja, Linseisen, Jakob, Meisinger, Christine, Rathmann, Wolfgang, Waldenberger, Melanie, Visscher, Peter M., Shah, Sonia, Wray, Naomi R., McRae, Allan F., Franco, Oscar H., Hofman, Albert, Uitterlinden, Andre G., Absher, Devin, Assimes, Themistocles, Levine, Morgan E., Lu, Ake T., Tsao, Philip S., Hou, Lifang, Manson, JoAnn E., Carty, Cara L., LaCroix, Andrea Z., Reiner, Alexander P., Spector, Tim D., Feinberg, Andrew P., Levy, Daniel, Baccarelli, Andrea, van Meurs, Joyce, Bell, Jordana T., Peters, Annette, Deary, Ian J., Pankow, James S., Ferrucci, Luigi and Horvath, Steve (2016) DNA methylation-based measures of biological age: meta-analysis predicting time to death. Aging, 8 9: 1844-1865. doi:10.18632/aging.101020

Sharing a placenta is associated with a greater similarity in DNA methylation in monochorionic versus dichorionic twin pars in blood at age 14

Bui, Masato, Benyamin, Beben, Shah, Sonia, Henders, Anjali K., Martin, Nicholas G., Montgomery, Grant W. and McRae, Allan F. (2015) Sharing a placenta is associated with a greater similarity in DNA methylation in monochorionic versus dichorionic twin pars in blood at age 14. Twin Research and Human Genetics, 18 6: 680-685. doi:10.1017/thg.2015.87

The transcriptional landscape of age in human peripheral blood

Peters, Marjolein J., Joehanes, Roby, Pilling, Luke C., Schurmann, Claudia, Conneely, Karen N., Powell, Joseph, Reinmaa, Eva, Sutphin, George L., Zhernakova, Alexandra, Schramm, Katharina, Wilson, Yana A., Kobes, Sayuko, Tukiainen, Taru, Ramos, Yolande F., Goring, Harald H. H., Fornage, Myriam, Liu, Yongmei, Gharib, Sina A., Stranger, Barbara E., De Jager, Philip L., Aviv, Abraham, Levy, Daniel, Murabito, Joanne M., Munson, Peter J., Huan, Tianxiao, Hofman, Albert, Uitterlinden, Andre G., Rivadeneira, Fernando, Van Rooij, Jeroen, Stolk, Lisette, Broer, Linda, Verbiest, Michael M. P. J., Jhamai, Mila, Arp, Pascal, Metspalu, Andres, Tserel, Liina, Milani, Lili, Samani, Nilesh J., Peterson, Part, Kasela, Silva, Codd, Veryan, Peters, Annette, Ward-Caviness, Cavin K., Herder, Christian, Waldenberger, Melanie, Roden, Michael, Singmann, Paula, Zeilinger, Sonja, Illig, Thomas, Homuth, Georg, Grabe, Hans-Jorgen, Volzke, Henry, Steil, Leif, Kocher, Thomas, Murray, Anna, Melzer, David, Yaghootkar, Hanieh, Bandinelli, Stefania, Moses, Eric K., Kent, Jack W., Curran, Joanne E., Johnson, Matthew P., Williams-Blangero, Sarah, Westra, Harm-Jan, McRae, Allan F., Smith, Jennifer A., Kardia, Sharon L. R., Hovatta, Iiris, Perola, Markus, Ripatti, Samuli, Salomaa, Veikko, Henders, Anjali K., Martin, Nicholas G., Smith, Alicia K., Mehta, Divya, Binder, Elisabeth B., Nylocks, K. Maria, Kennedy, Elizabeth M., Klengel, Torsten, Ding, Jingzhong, Suchy-Dicey, Astrid M., Enquobahrie, Daniel A., Brody, Jennifer, Rotter, Jerome I., Chen, Yii-Der I., Houwing-Duistermaat, Jeanine, Kloppenburg, Margreet, Slagboom, P. Eline, Helmer, Quinta, Den Hollander, Wouter, Bean, Shannon, Raj, Towfique, Bakhshi, Noman, Wang, Qiao Ping, Oyston, Lisa J., Psaty, Bruce M., Tracy, Russell P., Montgomery, Grant W., Turner, Stephen T., Blangero, John, Meulenbelt, Ingrid, Ressler, Kerry J., Yang, Jian, Franke, Lude, Kettunen, Johannes, Visscher, Peter M., Neely, G. Gregory, Korstanje, Ron, Hanson, Robert L., Prokisch, Holger, Ferrucci, Luigi, Esko, Tonu, Teumer, Alexander, Van Meurs, Joyce B. J., Johnson, Andrew D., Nalls, Michael A., Hernandez, Dena G., Cookson, Mark R., Gibbs, Raphael J., Hardy, John, Ramasamy, Adaikalavan, Zonderman, Alan B., Dillman, Allissa, Traynor, Bryan, Smith, Colin, Longo, Dan L., Trabzuni, Daniah, Troncoso, Juan, Van Der Brug, Marcel, Weale, Michael E., O'Brien, Richard, Johnson, Robert, Walker, Robert, Zielke, Ronald H., Arepalli, Sampath, Ryten, Mina, Singleton, Andrew B. and NABEC/UKBEC Consortium (2015) The transcriptional landscape of age in human peripheral blood. Nature Communications, 6 1: 8570.1-8570.14. doi:10.1038/ncomms9570

Genome-wide autozygosity is associated with lower general cognitive ability

Howrigan, D.P., Simonson, M.A., Davies, G., Harris, S.E., Tenesa, A., Starr, J.M., Liewald, D.C., Deary, I.J., McRae, A., Wright, M.J., Montgomery, G.W., Hansell, N., Martin, N.G., Payton, A., Horan, M., Ollier, W.E., Abdellaoui, A., Boomsma, D.I., DeRosse, P., Knowles, E.E.M., Glahn, D.C., Djurovic, S., Melle, I., Andreassen, O.A., Christoforou, A., Steen, V.M., Hellard, S.L., Sundet, K., Reinvang, I., Espeseth, T., Lundervold, A.J., Giegling, I., Konte, B., Hartmann, A.M., Rujescu, D., Roussos, P., Giakoumaki, S., Burdick, K.E., Bitsios, P., Donohoe, G., Corley, R.P., Visscher, P.M., Pendleton, N., Malhotra, A.K., Neale, B.M., Lencz, T. and Keller, M.C. (2015) Genome-wide autozygosity is associated with lower general cognitive ability. Molecular Psychiatry, 21 6: 837-843. doi:10.1038/mp.2015.120

The epigenetic clock is correlated with physical and cognitive fitness in the Lothian Birth Cohort 1936

Marioni, Riccardo E., Shah, Sonia, McRae, Allan F., Ritchie, Stuart J., Muniz-Terrera, Graciela, Harris, Sarah E., Gibson, Jude, Redmond, Paul, Cox, Simon R., Pattie, Alison, Corley, Janie, Taylor, Adele, Murphy, Lee, Starr, John M., Horvath, Steve, Visscher, Peter M., Wray, Naomi R. and Deary, Ian J. (2015) The epigenetic clock is correlated with physical and cognitive fitness in the Lothian Birth Cohort 1936. International Journal of Epidemiology, 44 4: 1388-1396. doi:10.1093/ije/dyu277

Improving phenotypic prediction by combining genetic and epigenetic associations

Shah, Sonia, Bonder, Marc J., Marioni, Riccardo E., Zhu, Zhihong, McRae, Allan F., Zhernakova, Alexandra, Harris, Sarah E., Liewald, Dave, Henders, Anjali K., Mendelson, Michael M., Liu, Chunyu, Joehanes, Roby, Liang, Liming, Levy, Daniel, Martin, Nicholas G., Starr, John M., Wijmenga, Cisca, Wray, Naomi R., Yang, Jian, Montgomery, Grant W., Franke, Luke, Deary, Ian J., Visscher, Peter M. and BIOS Consortium (2015) Improving phenotypic prediction by combining genetic and epigenetic associations. American Journal of Human Genetics, 97 1: 75-85. doi:10.1016/j.ajhg.2015.05.014

Seasonal effects on gene expression

Goldinger, Anita, Shakhbazov, Konstantin, Henders, Anjali K., McRae, Allan F., Montgomery, Grant W. and Powell, Joseph E. (2015) Seasonal effects on gene expression. PLoS ONE, 10 5: 1-16. doi:10.1371/journal.pone.0126995

Large autosomal copy-number differences within unselected monozygotic twin pairs are rare

Mcrae, Allan F., Visscher, Peter M., Montgomery, Grant W. and Martin, Nicholas G. (2015) Large autosomal copy-number differences within unselected monozygotic twin pairs are rare. Twin Research and Human Genetics, 18 1: 13-18. doi:10.1017/thg.2014.85

DNA methylation age of blood predicts all-cause mortality in later life

Marioni, Riccardo E., Shah, Sonia, McRae, Allan F., Chen, Brian H., Colicino, Elena, Harris, Sarah E., Gibson, Jude, Henders, Anjali K., Redmond, Paul, Cox, Simon R., Pattie, Alison, Corley, Janie, Murphy, Lee, Martin, Nicholas G., Montgomery, Grant W., Feinberg, Andrew P., Fallin, M. Daniele, Multhaup, Michael L., Jaffe, Andrew E., Joehanes, Roby, Schwartz, Joel, Just, Allan C., Lunetta, Kathryn L., Murabito, Joanne M., Starr, John M., Horvath, Steve, Baccarelli, Andrea A., Levy, Daniel, Visscher, Peter M., Wray, Naomi R. and Deary, Ian J. (2015) DNA methylation age of blood predicts all-cause mortality in later life. Genome Biology, 16 1: 25.1-25.12. doi:10.1186/s13059-015-0584-6

Genetic and environmental exposures constrain epigenetic drift over the human life course

Shah, Sonia, McRae, Allan F., Marioni, Riccardo E., Harris, Sarah E., Gibson, Jude, Henders, Anjali K., Redmond, Paul, Cox, Simon R., Pattie, Alison, Corley, Janie, Murphy, Lee, Martin, Nicholas G., Montgomery, Grant W., Starr, John M., Wray, Naomi R., Deary, Ian J. and Visscher, Peter M. (2014) Genetic and environmental exposures constrain epigenetic drift over the human life course. Genome Research, 24 11: 1725-1733. doi:10.1101/gr.176933.114

Another explanation for apparent epistasis: reply

Hemani, Gibran, Shakhbazov, Konstantin, Westra, Harm-Jan, Esko, Tonu, Henders, Anjali K., McRae, Allan F., Yang, Jian, Gibson, Greg, Martin, Nicholas G., Metspalu, Andres, Franke, Lude, Montgomery, Grant W., Visscher, Peter M. and Powell, Joseph E. (2014) Another explanation for apparent epistasis: reply. Nature, 514 7520: E5-E6. doi:10.1038/nature13692

Contribution of genetic variation to transgenerational inheritance of DNA methylation

McRae, Allan F., Powell, Joseph E., Henders, Anjali K., Bowdler, Lisa, Hemani, Gibran, Shah, Sonia, Painter, Jodie N., Martin, Nicholas G., Visscher, Peter M. and Montgomery, Grant W. (2014) Contribution of genetic variation to transgenerational inheritance of DNA methylation. Genome Biology, 15 5: 1-10. doi:10.1186/gb-2014-15-5-r73

Detection and replication of epistasis influencing transcription in humans

Hemani, Gibran, Shakhbazov, Konstantin, Westra, Harm-Jan, Esko, Tonu, Henders, Anjali K., McRae, Allan F., Yang, Jian, Gibson, Greg, Martin, Nicholas G., Metspalu, Andres, Franke, Lude, Montgomery, Grant W., Visscher, Peter M. and Powell, Joseph E. (2014) Detection and replication of epistasis influencing transcription in humans. Nature, 508 7495: 249-253. doi:10.1038/nature13005

A genome wide survey supports the involvement of large copy number variants in schizophrenia with and without intellectual disability

Derks, Eske M., Ayub, Muhammad, Chambert, Kimberly, Del Favero, Jurgen, Johnstone, Mandy, Macgregor, Stuart, Maclean, Alan, McKechanie, Andrew G., McRae, Allan F., Moran, Jennifer L., Pickard, Benjamin S., Purcell, Shaun, Sklar, Pamela, St Clair, David M., Wray, Naomi R., Visscher, Peter M. and Blackwood, Douglas H. R. (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 8: 847-854. doi:10.1002/ajmg.b.32189

708 common and 2010 rare DISC1 locus variants identified in 1542 subjects: analysis for association with psychiatric disorder and cognitive traits

Thomson, P. A., Parla, J. S., McRae, A. F., Kramer, M., Ramakrushnan, K., Yao, J., Soares, D. C., McCarthy, S., Morris, S. W., Cardone, L., Cass, S., Ghiban, E., Hennah, W., Evans, K. L., Rebolini, D., Millar, J. K., Harris, S. E., Starr, J. M., MacIntyre, J., Generation Scotland, McIntosh, A. M., Watson, J. D., Deary, I. J., Visscher, P. M., Blackwood, D. H., McCombie, W. R. and Porteous, D. J. (2013) 708 common and 2010 rare DISC1 locus variants identified in 1542 subjects: analysis for association with psychiatric disorder and cognitive traits. Molecular Psychiatry, Advance online publication 6: 1-8. doi:10.1038/mp.2013.68

Case-control association testing of common variants from sequencing of DNA pools

McRae, Allan F., Richter, Melinda M. and Lind, Penelope A. (2013) Case-control association testing of common variants from sequencing of DNA pools. PLoS One, 8 6: e65410.1-e65410.4. doi:10.1371/journal.pone.0065410

Monozygotic twins affected with major depressive disorder have greater variance in methylation than their unaffected co-twin

Byrne, E. M., Carrillo-Roa, T., Henders, A. K., Bowdler, L., McRae, A. F., Heath, A. C., Martin, N. G., Montgomery, G. W., Krause, L. and Wray, N. R. (2013) Monozygotic twins affected with major depressive disorder have greater variance in methylation than their unaffected co-twin. Translational Psychiatry, 3 6: e269.1-e269.6. doi:10.1038/tp.2013.45

Congruence of additive and non-additive effects on gene expression estimated from pedigree and SNP data

Powell, Joseph E., Henders, Anjali K., McRae, Allan F., Kim, Jinhee, Hemani, Gibran, Martin, Nicholas G., Dermitzakis, Emmanouil T., Gibson, Greg, Montgomery, Grant W. and Visscher, Peter M. (2013) Congruence of additive and non-additive effects on gene expression estimated from pedigree and SNP data. PLoS Genetics, 9 5: e1003502.1-e1003502.10. doi:10.1371/journal.pgen.1003502

No association between general cognitive ability and rare copy number variation

McRae, Allan F., Wright, Margaret J., Hansell, Narelle K., Montgomery, Grant W. and Martin, Nicholas G. (2013) No association between general cognitive ability and rare copy number variation. Behavior Genetics, 43 3: 202-207. doi:10.1007/s10519-013-9587-9

Genetic and nongenetic variation revealed for the principal components of human gene expression

Goldinger, Anita, Henders, Anjali K., McRae, Allan F., Martin, Nicholas G., Gibson, Greg, Montgomery, Grant W., Visscher, Peter M. and Powell, Joseph E. (2013) Genetic and nongenetic variation revealed for the principal components of human gene expression. Genetics, 195 3: 1117-1128. doi:10.1534/genetics.113.153221

A genome-wide association study of caffeine-related sleep disturbance: confirmation of a role for a common variant in the adenosine receptor

Byrne, Enda M., Johnson, Julie, McRae, Allan F., Nyholt, Dale R., Medland, Sarah E., Gehrman, Philip R., Heath, Andrew C., Madden, Pamela A. F., Montgomery, Grant W., Chenevix-Trench, Georgia and Martin, Nicholas G. (2012) A genome-wide association study of caffeine-related sleep disturbance: confirmation of a role for a common variant in the adenosine receptor. Sleep, 35 7: 967-975. doi:10.5665/sleep.1962

The Brisbane systems genetics study: genetical genomics meets complex trait genetics

Powell, Joseph E., Henders, Anjali K., McRae, Allan F., Caracella, Anthony, Smith, Sara, Wright, Margaret J., Whitfield, John B., Dermitzakis, Emmanouil T., Martin, Nicholas G., Visscher, Peter M. and Montgomery, Grant W. (2012) The Brisbane systems genetics study: genetical genomics meets complex trait genetics. PLoS One, 7 4: e35430.1-e35430.9. doi:10.1371/journal.pone.0035430

Genetic control of gene expression in whole blood and lymphoblastoid cell lines is largely independent

Powell, Joseph E., Henders, Anjali K., McRae, Allan F., Wright, Margaret J., Martin, Nicholas G., Dermitzakis, Emmanouil T., Montgomery, Grant W. and Visscher, Peter M. (2012) Genetic control of gene expression in whole blood and lymphoblastoid cell lines is largely independent. Genome Research, 22 3: 456-466. doi:10.1101/gr.126540.111

Genetic influences on life span and its relationship to personality: A 16-year follow-up study of a sample of aging twins

Mosing, Miriam A., Medland, Sarah E., McRae, Allan, Landers, Joseph George, Wright, Margaret J. and Martin, Nicholas G. (2012) Genetic influences on life span and its relationship to personality: A 16-year follow-up study of a sample of aging twins. Psychosomatic Medicine, 74 1: 16-22. doi:10.1097/PSY.0b013e3182385784

Promoter polymorphisms in two overlapping 6p25 genes implicate mitochondrial proteins in cognitive deficit in schizophrenia

Jablensky, A ., Angelicheva, D ., Donohoe, G. J., Cruickshank, M., Azmanov, D. N., Morris, D. W., McRae, A., Weickert, C. S., Carter, K. W., Chandler, D., Alexandrov, B., Usheva, A., Morar, B., Verbrugghe, P. L., Filipovska, A., Rackham, O., Bishop, A. R., Rasmussen, K. Ø., Dragovic, M., Cooper, M., Phillips, M., Badcock, J., Bramon-Bosch, E., Almeida, O. P., Flicker, L., Gill, M., Corvin, A., MacGregor, S. and Kalaydjieva, L. (2012) Promoter polymorphisms in two overlapping 6p25 genes implicate mitochondrial proteins in cognitive deficit in schizophrenia. Molecular Psychiatry, 17 12: 1328-1339. doi:10.1038/mp.2011.129

Variation in BMPR1B, TGFRB1 and BMPR2 and control of dizygotic twinning

Luong, Hein T. T., Chaplin, Justin, McRae, Allan F., Medland, Sarah E., Willemsen, Gonneke, Nyholt, Dale R., Henders, Anjali K., Hoekstra, Chantal, Duffy, David L., Martin, Nicholas G., Boomsma, Dorret I., Montgomery, Grant W. and Painter, Jodie N. (2011) Variation in BMPR1B, TGFRB1 and BMPR2 and control of dizygotic twinning. Twin Research and Human Genetics, 14 5: 408-416. doi:10.1375/twin.14.5.408

GWAS findings for human iris patterns: Associations with variants in genes that influence normal neuronal pattern development

Larsson, Mats, Duffy, David L., Zhu, Gu, Liu, Jimmy Z., Macgregor, Stuart, McRae, Allan F., Wright, Margaret J., Sturm, Richard A., Mackey, David A., Montgomery, Grant W., Martin, Nicholas G. and Medland, Sarah E. (2011) GWAS findings for human iris patterns: Associations with variants in genes that influence normal neuronal pattern development. American Journal of Human Genetics, 89 2: 334-343. doi:10.1016/j.ajhg.2011.07.011

Association between ORMDL3, IL1RL1 and a deletion on chromosome 17q21 with asthma risk in Australia

Ferreira, Manuel A. R., McRae, Allan F., Medland, Sarah E., Nyholt, Dale R., Gordon, Scott D., Wright, Margaret J., Henders, Anjali K., Madden, Pamela A., Visscher, Peter M., Wray, Naomi R., Heath, Andrew C., Montgomery, Grant W., Duffy, David L. and Martin, Nicholas G. (2011) Association between ORMDL3, IL1RL1 and a deletion on chromosome 17q21 with asthma risk in Australia. European Journal of Human Genetics, 19 4: 458-464. doi:10.1038/ejhg.2010.191

Clustered coding variants in the glutamate receptor complexes of individuals with schizophrenia and bipolar disorder

Frank, Rene A. W., McRae, Allan F., Pocklington, Andrew J., van de Lagemaat, Louie N., Navarro, Pau, Croning, Mike D. R., Komiyama, Noboru H., Bradley, Sophie J., Challiss, R. A. John, Armstrong, J. Douglas, Finn, Robert D., Malloy, Mary P., MacLean, Alan W., Harris, Sarah E., Starr, John M., Bhaskar, Sanjeev S., Howard, Eleanor K., Hunt, Sarah E., Coffey, Alison J., Ranganath, Venkatesh, Deloukas, Panos, Rogers, Jane, Muir, Walter J., Deary, Ian J., Blackwood, Douglas H., Visscher, Peter M. and Grant, Seth G. N. (2011) Clustered coding variants in the glutamate receptor complexes of individuals with schizophrenia and bipolar disorder. PLoS One, 6 4: e19011.1-e19011.9. doi:10.1371/journal.pone.0019011

No evidence for warming climate theory of coat colour change in Soay sheep: A comment on Maloney et al.

Gratten, J., Wilson, A. J., McRae, A. F., Beraldi, D., Visscher, P. M., Pemberton, J. M. and Slate, J. (2010) No evidence for warming climate theory of coat colour change in Soay sheep: A comment on Maloney et al.. Biology Letters, 6 5: 678-679. doi:10.1098/rsbl.2010.0160

Congenital sensorineural deafness in Australian Stumpy-tail Cattle Dogs is an autosomal recessive trait that maps to CFA10

Sommerlad, Susan, McRae, Allan F., McDonald, Brenda, Johnstone, Isobel, Cuttell, Leigh, Seddon, Jennifer M. and O'Leary, Caroline A. (2010) Congenital sensorineural deafness in Australian Stumpy-tail Cattle Dogs is an autosomal recessive trait that maps to CFA10. PLoS One, 5 10: e13364. doi:10.1371/journal.pone.0013364

A versatile gene-based test for genome-wide association studies

Liu, Jimmy Z., McRae, Allan F., Nyholt, Dale R., Medland, Sarah E., Wray, Naomi R., Brown, Kevin M., AMFS Investigators, Hayward, Nicholas K., Montgomery, Grant W., Visscher, Peter M., Martin, Nicholas G. and Macgregor, Stuart (2010) A versatile gene-based test for genome-wide association studies. American Journal of Human Genetics, 87 1: 139-145. doi:10.1016/j.ajhg.2010.06.009

Genome-wide association study of height and body mass index in Australian twin families

Liu, Jimmy Z., Medland, Sarah E., Wright, Margaret J., Henders, Anjali K., Heath, Andrew C., Madden, Pamela A. F., Duncan, Alexis, Montgomery, Grant W., Martin, Nicholas G. and McRae, Allan F. (2010) Genome-wide association study of height and body mass index in Australian twin families. Twin Research And Human Genetics, 13 2: 179-193. doi:10.1375/twin.13.2.179

Horn type and horn length genes map to the same chromosomal region in Soay sheep

Johnston, S. E., Beraldi, D., McRae, A. F., Pemberton, J. M. and Slate, J. (2010) Horn type and horn length genes map to the same chromosomal region in Soay sheep. Heredity, 104 2: 196-205. doi:10.1038/hdy.2009.109

Common Variants in the Trichohyalin Gene Are Associated with Straight Hair in Europeans

Medland, S, Nyholt, D, Painter, JN, McEnvoy, BP, Allan McRae, Zhu, G, Gordon, SD, Ferreira, MAR, Wright, MJ, Henders, AK, Campbell MJ, Duffy, D, Hansell, N K, Macgregor, S, Slutske, WS, Heath, AC, Montgomery, GW and Martin, NG (2009) Common Variants in the Trichohyalin Gene Are Associated with Straight Hair in Europeans. American Journal of Human Genetics, 85 5: 750-755. doi:10.1016/j.ajhg.2009.10.009

Family-based mitochondrial association study of traits related to type 2 diabetes and the metabolic syndrome in adolescents

E. M. Byrne, A. F. McRae, D. L. Duffy, Z. Z. Zhao, N. G. Martin, J. B. Whitfield, P. M. Visscher and G. W. Montgomery (2009) Family-based mitochondrial association study of traits related to type 2 diabetes and the metabolic syndrome in adolescents. Diabetologia, 52 11: 2359-2368. doi:10.1007/s00125-009-1510-9

Association Study of Common Mitochondrial Variants and Cognitive Ability

Byrne, EM, McRae, AF, Duffy, DL, Zhao, ZZ, Martin, NG, Wright, MJ, Montgomery, GW and Visscher, PM (2009) Association Study of Common Mitochondrial Variants and Cognitive Ability. BEHAVIOR GENETICS, 39 5: 504-512. doi:10.1007/s10519-009-9276-x

Non-pathological paternal isodisomy of chromosome 2 detected from a genome-wide SNP scan.

Matthew C. Keller, Allan F. McRae, Julie M. McGaughran, Peter M. Visscher, Nicholas G. Martin and Grant W. Montgomery (2009) Non-pathological paternal isodisomy of chromosome 2 detected from a genome-wide SNP scan.. American Journal of Medical Genetics. Part A, 149A 8: 1823-1826. doi:10.1002/ajmg.a.32973

Geographical structure and differential natural selection among North European populations

Brian P. McEvoy, Grant W. Montgomery, Allan F. McRae, Samuli Ripatti, Markus Perola, Tim D. Spector, Lynn Cherkas, Kourosh R. Ahmadi, Dorret Boomsma, Gonneke Willemsen, Jouke J. Hottenga, Nancy L. Pedersen, Patrik K.E. Magnusson, Kirsten Ohm Kyvik, Kaare Christensen, Jaakko Kaprio, Kauko Heikkilä, Aarno Palotie, Elisabeth Widen, Juha Muilu, Ann-Christine Syvänen, Ulrika Liljedahl, Orla Hardiman, Simon Cronin, Leena Peltonen, Nicholas G. Martin and Peter M. Visscher (2009) Geographical structure and differential natural selection among North European populations. Genome Research, 19 5: 804-814. doi:10.1101/gr.083394.108

Family-based genome-wide association studies

Benyamin, Beben, Visscher, Peter M. and McRae, Allan F. (2009) Family-based genome-wide association studies. Pharmacogenomics, 10 2: 181-190. doi:10.2217/14622416.10.2.181

DNA methylation profiles in monozygotic and dizygotic twins

Zachary A Kaminsky, Thomas Tang, Sun-Chong Wang, Carolyn Ptak, Gabriel H T Oh, Albert H C Wong, Laura A Feldcamp, Carl Virtanen, Jonas Halfvarson, Curt Tysk, Allan F McRae, Peter M Visscher, Grant W Montgomery, Irving I Gottesman, Nicholas G Martin and Art Petronis (2009) DNA methylation profiles in monozygotic and dizygotic twins. Nature Genetics, 41 2: 240-245. doi:10.1038/ng.286

Variants in TF and HFE Explain 40% of Genetic Variation in Serum-Transferrin Levels

Beben Benyamin, Allan F. McRae, Gu Zhu, Scott Gordon, Anjali K. Henders, Aarno Palotie, Leena Peltonen, Nicholas G. Martin, Grant W. Montgomery, John B. Whitfield and Peter M. Visscher (2009) Variants in TF and HFE Explain 40% of Genetic Variation in Serum-Transferrin Levels. American Journal of Human Genetics, 84 1: 60-65. doi:10.1016/j.ajhg.2008.11.011

A cytogenetic abnormality and rare coding variants identify ABCA13 as a candidate gene in schizophrenia, bipolar disorder, and depression

Knight, Helen M., Pickard, Benjamin S., Maclean, Alan, Malloy, Mary P., Soares, Dinesh C., McRae, Allan F., Condie, Alison, White, Angela, Hawkins, William, McGhee, Kevin, van Beck, Margaret, MacIntyre, Donald J., Starr, John M., Deary, Ian J., Visscher, Peter M., Porteous, David J., Cannon, Ronald E., St Clair, David, Muir, Walter J. and Blackwood, Douglas H. R. (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 6: 833-846. doi:10.1016/j.ajhg.2009.11.003

Divergence between human populations estimated from linkage disequilibrium

Sved, John A., McRae, Allan F. and Visscher, Peter M. (2008) Divergence between human populations estimated from linkage disequilibrium. American Journal of Human Genetics, 83 6: 737-743. doi:10.1016/j.ajhg.2008.10.019

Linkage and Association Analyses of Longitudinally Measured Lipid Phenotypes in Adolescence

Middelberg, Rita P., Gordon, Scott D., Zhu, Gu, McRae, Allan, Montgomery, Grant W., Martin, Nicholas G. and Whitfield, John B. (2008) Linkage and Association Analyses of Longitudinally Measured Lipid Phenotypes in Adolescence. Twin Research and Human Genetics, 11 6: 603-620. doi:10.1375/twin.11.6.603

The use of common mitochondrial variants to detect and characterise population structure in the Australian population: Implications for genome-wide association studies

Byrne, Enda M., Mcrae, Allan F., Zhao, Zhen-Zhen, Martin, Nicholas G., Montgomery, Grant W. and Visscher, Peter M. (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 11: 1396-1403. doi:10.1038/ejhg.2008.117

Calculation of IBD probabilities with dense SNP or sequence data

Keith, Jonathan M., McRae, Allan, Duffy, David, Mengersen, Kerrie and Visscher, Peter M. (2008) Calculation of IBD probabilities with dense SNP or sequence data. Genetic Epidemiology, 32 6: 513-519. doi:10.1002/gepi.20324

Power and SNP tagging in whole mitochondrial genome association studies

McRae, Allan F., Byrne, Enda M., Zhao, Zhen Zhen, Montgomery, Grant W. and Visscher, Peter M. (2008) Power and SNP tagging in whole mitochondrial genome association studies. Genome Research, 18 6: 911-917. doi:10.1101/gr.074872.107

A localized negative genetic correlation constrains microevolution of coat color in wild sheep

Gratten, J., Wilson, A. J., McRae, A. F., Beraldi, D., Visscher, P. M., Pemberton, J. M. and Slate, J. (2008) A localized negative genetic correlation constrains microevolution of coat color in wild sheep. Science, 319 5861: 318-320. doi:10.1126/science.1151182

Mapping quantitative trait loci underlying fitness-related traits in a free-living sheep population

Beraldi, Dario, McRae, Allan F., Gratten, Jacob, Slate, Jon, Visscher, Peter M. and Pemberton, Josephine M. (2007) Mapping quantitative trait loci underlying fitness-related traits in a free-living sheep population. Evolution, 61 6: 1403-1416. doi:10.1111/j.1558-5646.2007.00106.x

Compelling evidence that a single nucleotide substitution in TYRP1 is responsible for coat-colour polymorphism in a free-living population of Soay sheep

Gratten, J., Beraldi, D., Lowder, B. V., McRae, A. F., Visscher, P. M., Pemberton, J. M. and 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 of London: Biological Sciences, 274 1610: 619-626. doi:10.1098/rspb.2006.3762

Replicated effects of sex and genotype on gene expression in human lymphoblastoid cell lines

McRae, A. F., Matigian, N. A., Vadlamudi, L., Mulley, J. C., Mowry, B., Martin, N. G., Berkovic, S. F., Hayward, N. K. and Visscher, P. M. (2007) Replicated effects of sex and genotype on gene expression in human lymphoblastoid cell lines. Human Molecular Genetics, 16 4: 364-373. doi:10.1093/hmg/ddl456

Quantitative trait loci (QTL) mapping of resistance to strongyles and coccidia in the free-living Soay sheep (Ovis aries)

Beraldi, Dario, McRae, Allan F., Gratten, Jacob, Slate, Jon, Visscher, Peter M., Pemberton, Josephine M. and Pilkington, Jill G. (2007) Quantitative trait loci (QTL) mapping of resistance to strongyles and coccidia in the free-living Soay sheep (Ovis aries). Journal of Parasitology, 37 1: 121-129. doi:10.1016/j.ijpara.2006.09.007

A simple linear regression method for quantitative trait loci linkage analysis with censored observations

Anderson, Carl A., McRae, Allan F. and Visscher, Peter M. (2006) A simple linear regression method for quantitative trait loci linkage analysis with censored observations. Genetics, 173 3: 1735-1745. doi:10.1534/genetics.106.055921

Development of a linkage map and mapping of phenotypic polymorphisms in a free-living population of Soay sheep (Ovis aries)

Beraldi, Dario, McRae, Allan F., Gratten, Jacob, Slate, Jon, Visscher, Peter M. and Pemberton, Josephine M. (2006) Development of a linkage map and mapping of phenotypic polymorphisms in a free-living population of Soay sheep (Ovis aries). Genetics, 173 3: 1521-1537. doi:10.1534/genetics.106.057141

Examination of a region showing linkage map discrepancies across sheep breeds

McRae, AF and Beraldi, D (2006) Examination of a region showing linkage map discrepancies across sheep breeds. Mammalian Genome, 17 4: 346-353. doi:10.1007/s00335-005-0087-y

Modeling linkage disequilibrium in natural populations: The example of the Soay sheep population of St. Kilda, Scotland

McRae, AF, Pemberton, JM and Visscher, PM (2005) Modeling linkage disequilibrium in natural populations: The example of the Soay sheep population of St. Kilda, Scotland. Genetics, 171 1: 251-258. doi:10.1534/genetics.105.040972

Mapping of multiple quantitative trait loci for growth and carcass traits in a complex commercial sheep pedigree

McRae, AF, Bishop, SC, Walling, GA, Wilson, AD and Visscher, PM (2005) Mapping of multiple quantitative trait loci for growth and carcass traits in a complex commercial sheep pedigree. Animal Science, 80 8: 135-141.

Bone density in sheep: genetic variation and quantitative trait loci localisation

Campbell, AW, Bain, WE, McRae, AF, Broad, TE, Johnstone, PD, Dodds, KG, Veenvliet, BA, Greer, GJ, Glass, BC, Beattie, AE, Jopson, NB and McEwan, JC (2003) Bone density in sheep: genetic variation and quantitative trait loci localisation. Bone, 33 4: 540-548. doi:10.1016/S8756-3282(03)00228-X

Linkage disequilibrium in domestic sheep

McRae, AF, McEwan, JC, Dodds, KG, Wilson, T, Crawford, AM and Slate, J (2002) Linkage disequilibrium in domestic sheep. Genetics, 160 3: 1113-1122.

Signatures of negative selection in the genetic architecture of human complex traits

Zeng, Jian, de Vlaming, Ronald, Wu, Yang, Robinson, Matthew R., Lloyd-Jones, Luke R., Yengo, Loic, Yap, Chloe X., Xue, Angli, Sidorenko, Julia, Mcrae, Allan F., Powell, Joseph E., Montgomery, Grant W., Metspalu, Andres, Esko, Tonu, Gibson, Greg, Wray, Naomi R., Visscher, Peter M. and Yang, Jian (2018). Signatures of negative selection in the genetic architecture of human complex traits. In: 48th Annual Meeting of the Behavior-Genetics-Association (BGA), Boston MA, United States, (525-525). 20-23 June 2018.

Comparison of Faecal Microbe Diversity Between Motor Neurone Disease (Mnd) and Control Participants

Steyn, Frederik J., Restuadi, Restuadi, Ioannides, Zara, Ngo, Shyuan T., McRae, Allan, Wray, Naomi R., Henderson, Robert and McCombe, Pamela (2017). Comparison of Faecal Microbe Diversity Between Motor Neurone Disease (Mnd) and Control Participants. In: Annual Scientific Meeting of the Australian-and-New-Zealand-Association-of-Neurologists (ANZAN), Gold Coast, Australia, (). 9-12 May 2017. doi:10.1136/jnnp-2017-316074.81

Comparison of faecal microbe diversity between motor neurone disease (MND) and control participants

Steyn, Frederik J., Restuadi, Restuadi, Ioannides, Zara, Ngo, Shyuan T., McRae, Allan, Wray, Naomi R., Henderson, Robert and McCombe, Pamela (2017). Comparison of faecal microbe diversity between motor neurone disease (MND) and control participants. In: Annual Scientific Meeting of the Australian and New Zealand Association of Neurologists (ANZAN), Gold Coast Australia, (). May 9-12, 2017. doi:10.1136/jnnp-2017-316074.81

Genome-wide association study identifies the SLC2A14 gene on chromosome 12P13 as a trans-acting locus for methylation of MAPT gene

Kwok, J., Coupland, K., Mellick, G., Mather, K., Thalamuthu, A., Armstrong, N., Sachdev, P., Brodaty, H., Wright, M., Ames, D., Allen, M., Ertekin-Taner, N., McRae, A., Bennett, D., Jager, P. D., Kim, W., Halliday, G. and Dobson-Stone, C. (2015). Genome-wide association study identifies the SLC2A14 gene on chromosome 12P13 as a trans-acting locus for methylation of MAPT gene. In: Special Issue: 25th Biennial Meeting of the International Society for Neurochemistry Jointly with the 13th Meeting of the Asian Pacific Society for Neurochemistry in Conjunction with the 35th Meeting of the Australasian Neuroscience Society. 25th Biennial Meeting of the International Society for Neurochemistry Jointly with the 13th Meeting of the Asian Pacific Society for Neurochemistry in Conjunction with the 35th Meeting of the Australasian Neuroscience Society, Cairns, QLD Australia, (113-114). 23-27 August 2015. doi:10.1111/jnc.13188

Endochondral Bone Formation and Advanced Enthesitis Are Key Features Of Proteoglycan Induced Spondylitis Mouse Model Of Ankylosing Spondylitis

Thomas, Gethin P., Tseng, Hsu-Wen, Pettit, Allison, Glant, Tibor T., McRae, Allan and Brown, Matthew A. (2013). Endochondral Bone Formation and Advanced Enthesitis Are Key Features Of Proteoglycan Induced Spondylitis Mouse Model Of Ankylosing Spondylitis. In: Abstract Supplement 2013 Annual Meeting. 77th Annual Meeting of the American College of Rheumatology / 48th Annual Meeting of the Association of Rheumatology Health Professionals, San Diego CA, United States, (S231-S231). 25-30 October 2013. doi:10.1002/art.38216

Common variants in the Trichohyalin gene are associated with straight hair in Europeans genetics and genodermatoses

Medland, S. E., Nyholt, D. R., Painter, J. N., McEvoy, B. P., McRae, A. F., Montgomery, G. W. and Martin, N. G. (2010). Common variants in the Trichohyalin gene are associated with straight hair in Europeans genetics and genodermatoses. In: 6th World Congress for Hair Research, Cairns, QLD, Australia, (563-563). 16-19 June 2010. doi:10.1111/j.1600-0625.2010.01097.x