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1. New Polygenic Risk Score to Predict High Myopia in Singapore Chinese Children

Author

Lanca, Carla, Kassam, Irfahan, Patasova, Karina, Foo, Li-Lian, Li, Jonathan, Ang, Marcus, Hoang, Quan V, Teo, Yik-Ying, Hysi, Pirro G, and Saw, Seang-Mei

Subjects
Pediatric, Clinical Research, Prevention, Good Health and Well Being, Adolescent, Child, China, Cohort Studies, Humans, Myopia, Risk Factors, Singapore, high myopia, polygenic risk score, teenagers, East Asian, Biomedical Engineering, Opthalmology and Optometry
Abstract

PurposeThe purpose of this study was to develop an Asian polygenic risk score (PRS) to predict high myopia (HM) in Chinese children in the Singapore Cohort of Risk factors for Myopia (SCORM) cohort.MethodsWe included children followed from 6 to 11 years old until teenage years (12-18 years old). Cycloplegic autorefraction, ultrasound biometry, Illumina HumanHap 550, or 550 Duo Beadarrays, demographics, and environmental factors data were obtained. The PRS was generated from the Consortium for Refractive Error and Myopia genomewide association study (n = 542,934) and the Strabismus, Amblyopia, and Refractive Error in Singapore children Study (n = 500). The Growing Up in Singapore Towards healthy Outcomes Cohort study (n = 339) was the replication cohort. The outcome was teenage HM (≤ -5.00 D) with predictive performance assessed using the area under the curve (AUC).ResultsMean baseline age ± SD was 7.85 ± 0.84 (n = 1004) and 571 attended the teenage visit; 23.3% had HM. In multivariate analysis, the PRS was associated with a myopic spherical equivalent with an incremental R2 of 0.041 (95% confidence interval [CI] = 0.010, 0.073; P < 0.001). AUC for HM (0.77 [95% CI = 0.71-0.83]) performed better (P = 0.02) with the PRS compared with a model without (0.72 [95% CI = 0.65, 0.78]). Children at the top 25% PRS risk had a 2.34-fold-greater risk of HM (95% CI = 1.53, 3.55; P < 0.001).ConclusionsThe new Asian PRS improved the predictive performance to detect children at risk of HM.Translational relevanceClinicians may use the PRS with other predictive factors to identify high risk children and guide interventions to reduce the risk of HM later in life.

Published
2021

2. Main Existing Datasets for Open Brain Research on Humans

Author

Couvy-Duchesne, Baptiste, primary, Bottani, Simona, additional, Camenen, Etienne, additional, Fang, Fang, additional, Fikere, Mulusew, additional, Gonzalez-Astudillo, Juliana, additional, Harvey, Joshua, additional, Hassanaly, Ravi, additional, Kassam, Irfahan, additional, Lind, Penelope A., additional, Liu, Qianwei, additional, Lu, Yi, additional, Nabais, Marta, additional, Rolland, Thibault, additional, Sidorenko, Julia, additional, Strike, Lachlan, additional, and Wright, Margie, additional

Published
2023
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6. Identification of novel risk loci, causal insights, and heritable risk for Parkinson's disease: a meta-analysis of genome-wide association studies

Author

Adarmes-Gómez, Astrid D, Aguilar, Miquel, Aitkulova, Akbota, Akhmetzhanov, Vadim, Alcalay, Roy N, Alvarez, Ignacio, Alvarez, Victoria, Bandres-Ciga, Sara, Barrero, Francisco Javier, Bergareche Yarza, Jesús Alberto, Bernal-Bernal, Inmaculada, Billingsley, Kimberley, Blauwendraat, Cornelis, Blazquez, Marta, Bonilla-Toribio, Marta, Botía, Juan A, Boungiorno, María Teresa, Bras, Jose, Brice, Alexis, Brockmann, Kathrin, Bubb, Vivien, Buiza-Rueda, Dolores, Cámara, Ana, Carrillo, Fátima, Carrión-Claro, Mario, Cerdan, Debora, Chelban, Viorica, Clarimón, Jordi, Clarke, Carl, Compta, Yaroslau, Cookson, Mark R, Corvol, Jean-Christophe, Craig, David W, Danjou, Fabrice, Diez-Fairen, Monica, Dols-Icardo, Oriol, Duarte, Jacinto, Duran, Raquel, Escamilla-Sevilla, Francisco, Escott-Price, Valentina, Ezquerra, Mario, Faghri, Faraz, Feliz, Cici, Fernández, Manel, Fernández-Santiago, Rubén, Finkbeiner, Steven, Foltynie, Thomas, Gan-Or, Ziv, Garcia, Ciara, García-Ruiz, Pedro, Gasser, Thomas, Gibbs, J Raphael, Gomez Heredia, Maria Jose, Gómez-Garre, Pilar, González, Manuel Menéndez, Gonzalez-Aramburu, Isabel, Guelfi, Sebastian, Guerreiro, Rita, Hardy, John, Hassin-Baer, Sharon, Hernandez, Dena G, Heutink, Peter, Hoenicka, Janet, Holmans, Peter, Houlden, Henry, Infante, Jon, Iwaki, Hirotaka, Jesús, Silvia, Jimenez-Escrig, Adriano, Kaishybayeva, Gulnaz, Kaiyrzhanov, Rauan, Karimova, Altynay, Kia, Demis A, Kinghorn, Kerri J, Koks, Sulev, Krohn, Lynne, Kulisevsky, Jaime, Labrador-Espinosa, Miguel A, Leonard, Hampton L, Lesage, Suzanne, Lewis, Patrick, Lopez-Sendon, Jose Luis, Lovering, Ruth, Lubbe, Steven, Lungu, Codrin, Macias, Daniel, Majamaa, Kari, Manzoni, Claudia, Marín, Juan, Marinus, Johan, Marti, Maria Jose, Martinez, Maria, Martínez Torres, Irene, Martínez-Castrillo, Juan Carlos, Mata, Marina, Mencacci, Niccolo E, Méndez-del-Barrio, Carlota, Middlehurst, Ben, Mínguez, Adolfo, Mir, Pablo, Mok, Kin Y, Morris, Huw R, Muñoz, Esteban, Nalls, Mike A, Narendra, Derek, Noyce, Alastair J, Ojo, Oluwadamilola O, Okubadejo, Njideka U, Pagola, Ana Gorostidi, Pastor, Pau, Perez Errazquin, Francisco, Periñán-Tocino, Teresa, Pihlstrom, Lasse, Plun-Favreau, Helene, Quinn, John, R'Bibo, Lea, Reed, Xylena, Rezola, Elisabet Mondragon, Rizig, Mie, Rizzu, Patrizia, Robak, Laurie, Rodriguez, Antonio Sanchez, Rouleau, Guy A, Ruiz-Martínez, Javier, Ruz, Clara, Ryten, Mina, Sadykova, Dinara, Scholz, Sonja W, Schreglmann, Sebastian, Schulte, Claudia, Sharma, Manu, Shashkin, Chingiz, Shulman, Joshua M, Sierra, María, Siitonen, Ari, Simón-Sánchez, Javier, Singleton, Andrew B, Suarez-Sanmartin, Esther, Taba, Pille, Tabernero, Cesar, Tan, Manuela X, Tartari, Juan Pablo, Tejera-Parrado, Cristina, Toft, Mathias, Tolosa, Eduard, Trabzuni, Daniah, Valldeoriola, Francesc, van Hilten, Jacobus J, Van Keuren-Jensen, Kendall, Vargas-González, Laura, Vela, Lydia, Vives, Francisco, Williams, Nigel, Wood, Nicholas W, Zharkinbekova, Nazira, Zharmukhanov, Zharkyn, Zholdybayeva, Elena, Zimprich, Alexander, Ylikotila, Pauli, Shulman, Lisa M., von Coelln, Rainer, Reich, Stephen, Savitt, Joseph, Agee, Michelle, Alipanahi, Babak, Auton, Adam, Bell, Robert K., Bryc, Katarzyna, Elson, Sarah L., Fontanillas, Pierre, Furlotte, Nicholas A., Huber, Karen E., Hicks, Barry, Jewett, Ethan M., Jiang, Yunxuan, Kleinman, Aaron, Lin, Keng-Han, Litterman, Nadia K., McCreight, Jennifer C., McIntyre, Matthew H., McManus, Kimberly F., Mountain, Joanna L., Noblin, Elizabeth S., Northover, Carrie A.M., Pitts, Steven J., Poznik, G. David, Sathirapongsasuti, J. Fah, Shelton, Janie F., Shringarpure, Suyash, Tian, Chao, Tung, Joyce, Vacic, Vladimir, Wang, Xin, Wilson, Catherine H., Anderson, Tim, Bentley, Steven, Dalrymple-Alford, John, Fowdar, Javed, Gratten, Jacob, Halliday, Glenda, Henders, Anjali K., Hickie, Ian, Kassam, Irfahan, Kennedy, Martin, Kwok, John, Lewis, Simon, Mellick, George, Montgomery, Grant, Pearson, John, Pitcher, Toni, Sidorenko, Julia, Silburn, Peter A., Vallerga, Costanza L., Visscher, Peter M., Wallace, Leanne, Wray, Naomi R., Xue, Angli, Yang, Jian, Zhang, Futao, Vallerga, Costanza L, Heilbron, Karl, Chang, Diana, Tan, Manuela, Young, Emily, Pihlstrøm, Lasse, Leonard, Hampton, Botia, Juan A, Jankovic, Joseph, Shulman, Lisa M, Sutherland, Margaret, Tienari, Pentti, Andreassen, Ole A, Bangale, Tushar, Hinds, David A, Hardy, John A, Visscher, Peter M, and Graham, Robert R

Published
2019
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8. Analysis of DNA methylation associates the cystine–glutamate antiporter SLC7A11 with risk of Parkinson’s disease

Author

Vallerga, Costanza L., Zhang, Futao, Fowdar, Javed, McRae, Allan F., Qi, Ting, Nabais, Marta F., Zhang, Qian, Kassam, Irfahan, Henders, Anjali K., Wallace, Leanne, Montgomery, Grant, Chuang, Yu-Hsuan, Horvath, Steve, Ritz, Beate, Halliday, Glenda, Hickie, Ian, Kwok, John B., Pearson, John, Pitcher, Toni, Kennedy, Martin, Bentley, Steven R., Silburn, Peter A., Yang, Jian, Wray, Naomi R., Lewis, Simon J. G., Anderson, Tim, Dalrymple-Alford, John, Mellick, George D., Visscher, Peter M., and Gratten, Jacob

Published
2020
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9. Supplementary Data from Integrative Profiling of T790M-Negative EGFR-Mutated NSCLC Reveals Pervasive Lineage Transition and Therapeutic Opportunities

Author

Chua, Khi Pin, primary, Teng, Yvonne H.F., primary, Tan, Aaron C., primary, Takano, Angela, primary, Alvarez, Jacob J.S., primary, Nahar, Rahul, primary, Rohatgi, Neha, primary, Lai, Gillianne G.Y., primary, Aung, Zaw Win, primary, Yeong, Joe P.S., primary, Lim, Kiat Hon, primary, Naeini, Marjan Mojtabavi, primary, Kassam, Irfahan, primary, Jain, Amit, primary, Tan, Wan Ling, primary, Gogna, Apoorva, primary, Too, Chow Wei, primary, Kanesvaran, Ravindran, primary, Ng, Quan Sing, primary, Ang, Mei Kim, primary, Rajasekaran, Tanujaa, primary, Anantham, Devanand, primary, Phua, Ghee Chee, primary, Tan, Bien Soo, primary, Lee, Yin Yeng, primary, Wang, Lanying, primary, Teo, Audrey S.M., primary, Khng, Alexis Jiaying, primary, Lim, Ming Jie, primary, Suteja, Lisda, primary, Toh, Chee Keong, primary, Lim, Wan-Teck, primary, Iyer, N. Gopalakrishna, primary, Tam, Wai Leong, primary, Tan, Eng-Huat, primary, Zhai, Weiwei, primary, Hillmer, Axel M., primary, Skanderup, Anders J., primary, and Tan, Daniel S.W., primary

Published
2023
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12. Main existing datasets for open data research on humans

Author

Couvy-Duchesne, Baptiste, Bottani, Simona, Camenen, Etienne, Fang, Fang, Fikere, Mulusew, Gonzalez-Astudillo, Juliana, Harvey, Joshua, Hassanaly, Ravi, Kassam, Irfahan, Lind, Penelope, Liu, Qianwei, Lu, Yi, Nabais, Marta, Rolland, Thibault, Sidorenko, Julia, Strike, Lachlan, Wright, Margie, Algorithms, models and methods for images and signals of the human brain (ARAMIS), Sorbonne Université (SU)-Inria de Paris, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut du Cerveau = Paris Brain Institute (ICM), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institute for Molecular Bioscience, University of Queensland [Brisbane], Institut du Cerveau = Paris Brain Institute (ICM), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Karolinska Institutet [Stockholm], University of Exeter Medical School, University of Exeter, Lee Kong Chian School of Medicine, Nanyang Technological University [Singapour], QIMR Berghofer Medical Research Institute, Queensland Brain Institute, This research was supported by the Australian National Health and Medical Research Council (1078037, 1078901, 1113400, 1161356 and 1107258), the Australian Research Council (FT180100186 and FL180100072), the Sylvia & Charles Viertel Charitable Foundation, the program 'Investissements d’avenir' ANR-10-IAIHU-06 (Agence Nationale de la Recherche-10-IA Institut Hospitalo-Universitaire-6) and reference ANR-19-P3IA-0001 (PRAIRIE 3IA Institute), the European Union H2020 program (project EuroPOND, grant number 666992, the joint NSF/NIH/ANR program 'Collaborative Research in Computational Neuroscience' (project HIPLAY7, grant number ANR-16-NEUC-0001-01), the ICM Big Brain Theory Program (project DYNAMO, project PredictICD), and the Abeona Foundation (project Brain@Scale). BCD is supported by a CJ Martin fellowship (APP1161356)., ANR-19-P3IA-0001,PRAIRIE,PaRis Artificial Intelligence Research InstitutE(2019), ANR-16-NEUC-0001,HIPLAY7,Experimental and theoretical investigation of the multi-scale emergence of parametric working memory in prefrontal cortex recurrent networks(2016), European Project: 666992,H2020 Pilier Societal Challenges,H2020-PHC-2015-two-stage,EuroPOND(2016), Couvy-Duchesne, Baptiste, PaRis Artificial Intelligence Research InstitutE - - PRAIRIE2019 - ANR-19-P3IA-0001 - P3IA - VALID, Experimental and theoretical investigation of the multi-scale emergence of parametric working memory in prefrontal cortex recurrent networks - - HIPLAY72016 - ANR-16-NEUC-0001 - CRCNS - VALID, and Data-driven models for Progression Of Neurological Disease - EuroPOND - - H2020 Pilier Societal Challenges2016-01-01 - 2019-12-31 - 666992 - VALID

Subjects
[SDV.GEN]Life Sciences [q-bio]/Genetics, PET, [INFO.INFO-DB]Computer Science [cs]/Databases [cs.DB], EEG/MEG, Brain MRI, Wearables, Genetics, [INFO.INFO-DB] Computer Science [cs]/Databases [cs.DB], Electronic health records, Omics, [SDV.GEN] Life Sciences [q-bio]/Genetics, Gene expression, Methylation
Abstract

Recent advances in technology have made possible to quantify fine-grained individual differences at many levels, such as genetic, genomics, organ level, behaviour, clinical. The wealth of data becoming available raises great promises for research on brain disorders as well as normal brain function. To name a few: systematic and agnostic study of disease risk factors (e.g. genetic variants, brain regions), the use of natural experiments (e.g. evaluate the effect of a genetic variant in a human population), and unveiling disease mechanisms across several biological levels (e.g. genetics, cellular gene expression, organ structure and function). However, this data revolution raises many challenges such as data sharing and management, the need for novel analysis methods and software, storage and computing. Here, we sought to provide an overview of some of the main existing human datasets, all accessible to researchers. Our list is far from being exhaustive and our objective is to publicise data sharing initiatives and help researchers find new data sources.

Published
2022

14. Integrative Profiling of T790M-Negative EGFR-Mutated NSCLC Reveals Pervasive Lineage Transition and Therapeutic Opportunities

Author

Chua, Khi Pin, primary, Teng, Yvonne H.F., additional, Tan, Aaron C., additional, Takano, Angela, additional, Alvarez, Jacob J.S., additional, Nahar, Rahul, additional, Rohatgi, Neha, additional, Lai, Gillianne G.Y., additional, Aung, Zaw Win, additional, Yeong, Joe P.S., additional, Lim, Kiat Hon, additional, Naeini, Marjan Mojtabavi, additional, Kassam, Irfahan, additional, Jain, Amit, additional, Tan, Wan Ling, additional, Gogna, Apoorva, additional, Too, Chow Wei, additional, Kanesvaran, Ravindran, additional, Ng, Quan Sing, additional, Ang, Mei Kim, additional, Rajasekaran, Tanujaa, additional, Anantham, Devanand, additional, Phua, Ghee Chee, additional, Tan, Bien Soo, additional, Lee, Yin Yeng, additional, Wang, Lanying, additional, Teo, Audrey S.M., additional, Khng, Alexis Jiaying, additional, Lim, Ming Jie, additional, Suteja, Lisda, additional, Toh, Chee Keong, additional, Lim, Wan-Teck, additional, Iyer, N. Gopalakrishna, additional, Tam, Wai Leong, additional, Tan, Eng-Huat, additional, Zhai, Weiwei, additional, Hillmer, Axel M., additional, Skanderup, Anders J., additional, and Tan, Daniel S.W., additional

Published
2021
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15. Additional file 2 of Impact of BMI and waist circumference on epigenome-wide DNA methylation and identification of epigenetic biomarkers in blood: an EWAS in multi-ethnic Asian individuals

Author

Chen, Yuqing, Kassam, Irfahan, Lau, Suk Hiang, Kooner, Jaspal S., Wilson, Rory, Peters, Annette, Winkelmann, Juliane, Chambers, John C., Chow, Vincent T., Khor, Chiea Chuen, van Dam, Rob M., Teo, Yik-Ying, Loh, Marie, and Sim, Xueling

Abstract

Additional file 2: Figure S1. Sensitivity analysis of control probes principal components analysis. The first five principal components were included in regression models.

Published
2021
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16. Integrative Profiling of T790M-Negative EGFR-Mutated NSCLC Reveals Pervasive Lineage Transition and Therapeutic Opportunities

Author

Chua, Khi Pin, Teng, Yvonne H. F., Tan, Aaron C., Takano, Angela, Alvarez, Jacob J. S., Nahar, Rahul, Rohatgi, Neha, Lai, Gillianne G. Y., Aung, Zaw Win, Yeong, Joe P. S., Lim, Kiat Hon, Naeini, Marjan Mojtabavi, Kassam, Irfahan, Jain, Amit, Tan, Wan Ling, Gogna, Apoorva, Too, Chow Wei, Kanesvaran, Ravindran, Ng, Quan Sing, Ang, Mei Kim, Rajasekaran, Tanujaa, Anantham, Devanand, Phua, Ghee Chee, Tan, Bien Soo, Lee, Yin Yeng, Wang, Lanying, Teo, Audrey S. M., Khng, Alexis Jiaying, Lim, Ming Jie, Suteja, Lisda, Toh, Chee Keong, Lim, Wan-Teck, Iyer, N. Gopalakrishna, Tam, Wai Leong, Tan, Eng-Huat, Zhai, Weiwei, Hillmer, Axel M., Skanderup, Anders J., Tan, Daniel S. W., Chua, Khi Pin, Teng, Yvonne H. F., Tan, Aaron C., Takano, Angela, Alvarez, Jacob J. S., Nahar, Rahul, Rohatgi, Neha, Lai, Gillianne G. Y., Aung, Zaw Win, Yeong, Joe P. S., Lim, Kiat Hon, Naeini, Marjan Mojtabavi, Kassam, Irfahan, Jain, Amit, Tan, Wan Ling, Gogna, Apoorva, Too, Chow Wei, Kanesvaran, Ravindran, Ng, Quan Sing, Ang, Mei Kim, Rajasekaran, Tanujaa, Anantham, Devanand, Phua, Ghee Chee, Tan, Bien Soo, Lee, Yin Yeng, Wang, Lanying, Teo, Audrey S. M., Khng, Alexis Jiaying, Lim, Ming Jie, Suteja, Lisda, Toh, Chee Keong, Lim, Wan-Teck, Iyer, N. Gopalakrishna, Tam, Wai Leong, Tan, Eng-Huat, Zhai, Weiwei, Hillmer, Axel M., Skanderup, Anders J., and Tan, Daniel S. W.

Abstract

Purpose: Despite the established role of EGFR tyrosine kinase inhibitors (TKIs) in EGFR-mutated NSCLC, drug resistance inevitably ensues, with a paucity of treatment options especially in EGFRT790M-negative resistance. Experimental Design: We performed whole-exome and transcriptome analysis of 59 patients with first- and second-generation EGFR TKI-resistant metastatic EGFR-mutated NSCLC to characterize and compare molecular alterations mediating resistance in T790M-positive (T790M(+)) and -negative (T790M(-)) disease. Results: Transcriptomic analysis revealed ubiquitous loss of adenocarcinoma lineage gene expression in T790M(-) tumors, orthogonally validated using multiplex IHC. There was enrichment of genomic features such as TP53 alterations, 3q chromosomal amplifications, whole-genome doubling and nonaging mutational signatures in T790M(-) tumors. Almost half of resistant tumors were further classified as immune(hot), with clinical outcomes conditional on immune cell-infiltration state and T790M status. Finally, using a Bayesian statistical approach, we explored how T790M(-) and T790M(+) disease might be predicted using comprehensive genomic and transcriptomic profiles of treatment-naive patients. Conclusions: Our results illustrate the interplay between genetic alterations, cell lineage plasticity, and immune microenvironment in shaping divergent TKI resistance and outcome trajectories in EGFR-mutated NSCLC. Genomic and transcriptomic profiling may facilitate the design of bespoke therapeutic approaches tailored to a tumor's adaptive potential.

Published
2021

18. Identification of novel risk loci, causal insights, and heritable risk for Parkinson's disease: a meta-analysis of genome-wide association studies

Author

Nalls, Mike A, primary, Blauwendraat, Cornelis, additional, Vallerga, Costanza L, additional, Heilbron, Karl, additional, Bandres-Ciga, Sara, additional, Chang, Diana, additional, Tan, Manuela, additional, Kia, Demis A, additional, Noyce, Alastair J, additional, Xue, Angli, additional, Bras, Jose, additional, Young, Emily, additional, von Coelln, Rainer, additional, Simón-Sánchez, Javier, additional, Schulte, Claudia, additional, Sharma, Manu, additional, Krohn, Lynne, additional, Pihlstrøm, Lasse, additional, Siitonen, Ari, additional, Iwaki, Hirotaka, additional, Leonard, Hampton, additional, Faghri, Faraz, additional, Gibbs, J Raphael, additional, Hernandez, Dena G, additional, Scholz, Sonja W, additional, Botia, Juan A, additional, Martinez, Maria, additional, Corvol, Jean-Christophe, additional, Lesage, Suzanne, additional, Jankovic, Joseph, additional, Shulman, Lisa M, additional, Sutherland, Margaret, additional, Tienari, Pentti, additional, Majamaa, Kari, additional, Toft, Mathias, additional, Andreassen, Ole A, additional, Bangale, Tushar, additional, Brice, Alexis, additional, Yang, Jian, additional, Gan-Or, Ziv, additional, Gasser, Thomas, additional, Heutink, Peter, additional, Shulman, Joshua M, additional, Wood, Nicholas W, additional, Hinds, David A, additional, Hardy, John A, additional, Morris, Huw R, additional, Gratten, Jacob, additional, Visscher, Peter M, additional, Graham, Robert R, additional, Singleton, Andrew B, additional, Adarmes-Gómez, Astrid D, additional, Aguilar, Miquel, additional, Aitkulova, Akbota, additional, Akhmetzhanov, Vadim, additional, Alcalay, Roy N, additional, Alvarez, Ignacio, additional, Alvarez, Victoria, additional, Barrero, Francisco Javier, additional, Bergareche Yarza, Jesús Alberto, additional, Bernal-Bernal, Inmaculada, additional, Billingsley, Kimberley, additional, Blazquez, Marta, additional, Bonilla-Toribio, Marta, additional, Botía, Juan A, additional, Boungiorno, María Teresa, additional, Brockmann, Kathrin, additional, Bubb, Vivien, additional, Buiza-Rueda, Dolores, additional, Cámara, Ana, additional, Carrillo, Fátima, additional, Carrión-Claro, Mario, additional, Cerdan, Debora, additional, Chelban, Viorica, additional, Clarimón, Jordi, additional, Clarke, Carl, additional, Compta, Yaroslau, additional, Cookson, Mark R, additional, Craig, David W, additional, Danjou, Fabrice, additional, Diez-Fairen, Monica, additional, Dols-Icardo, Oriol, additional, Duarte, Jacinto, additional, Duran, Raquel, additional, Escamilla-Sevilla, Francisco, additional, Escott-Price, Valentina, additional, Ezquerra, Mario, additional, Feliz, Cici, additional, Fernández, Manel, additional, Fernández-Santiago, Rubén, additional, Finkbeiner, Steven, additional, Foltynie, Thomas, additional, Garcia, Ciara, additional, García-Ruiz, Pedro, additional, Gomez Heredia, Maria Jose, additional, Gómez-Garre, Pilar, additional, González, Manuel Menéndez, additional, Gonzalez-Aramburu, Isabel, additional, Guelfi, Sebastian, additional, Guerreiro, Rita, additional, Hardy, John, additional, Hassin-Baer, Sharon, additional, Hoenicka, Janet, additional, Holmans, Peter, additional, Houlden, Henry, additional, Infante, Jon, additional, Jesús, Silvia, additional, Jimenez-Escrig, Adriano, additional, Kaishybayeva, Gulnaz, additional, Kaiyrzhanov, Rauan, additional, Karimova, Altynay, additional, Kinghorn, Kerri J, additional, Koks, Sulev, additional, Kulisevsky, Jaime, additional, Labrador-Espinosa, Miguel A, additional, Leonard, Hampton L, additional, Lewis, Patrick, additional, Lopez-Sendon, Jose Luis, additional, Lovering, Ruth, additional, Lubbe, Steven, additional, Lungu, Codrin, additional, Macias, Daniel, additional, Manzoni, Claudia, additional, Marín, Juan, additional, Marinus, Johan, additional, Marti, Maria Jose, additional, Martínez Torres, Irene, additional, Martínez-Castrillo, Juan Carlos, additional, Mata, Marina, additional, Mencacci, Niccolo E, additional, Méndez-del-Barrio, Carlota, additional, Middlehurst, Ben, additional, Mínguez, Adolfo, additional, Mir, Pablo, additional, Mok, Kin Y, additional, Muñoz, Esteban, additional, Nalls, Mike A, additional, Narendra, Derek, additional, Ojo, Oluwadamilola O, additional, Okubadejo, Njideka U, additional, Pagola, Ana Gorostidi, additional, Pastor, Pau, additional, Perez Errazquin, Francisco, additional, Periñán-Tocino, Teresa, additional, Pihlstrom, Lasse, additional, Plun-Favreau, Helene, additional, Quinn, John, additional, R'Bibo, Lea, additional, Reed, Xylena, additional, Rezola, Elisabet Mondragon, additional, Rizig, Mie, additional, Rizzu, Patrizia, additional, Robak, Laurie, additional, Rodriguez, Antonio Sanchez, additional, Rouleau, Guy A, additional, Ruiz-Martínez, Javier, additional, Ruz, Clara, additional, Ryten, Mina, additional, Sadykova, Dinara, additional, Schreglmann, Sebastian, additional, Shashkin, Chingiz, additional, Sierra, María, additional, Suarez-Sanmartin, Esther, additional, Taba, Pille, additional, Tabernero, Cesar, additional, Tan, Manuela X, additional, Tartari, Juan Pablo, additional, Tejera-Parrado, Cristina, additional, Tolosa, Eduard, additional, Trabzuni, Daniah, additional, Valldeoriola, Francesc, additional, van Hilten, Jacobus J, additional, Van Keuren-Jensen, Kendall, additional, Vargas-González, Laura, additional, Vela, Lydia, additional, Vives, Francisco, additional, Williams, Nigel, additional, Zharkinbekova, Nazira, additional, Zharmukhanov, Zharkyn, additional, Zholdybayeva, Elena, additional, Zimprich, Alexander, additional, Ylikotila, Pauli, additional, Shulman, Lisa M., additional, Reich, Stephen, additional, Savitt, Joseph, additional, Agee, Michelle, additional, Alipanahi, Babak, additional, Auton, Adam, additional, Bell, Robert K., additional, Bryc, Katarzyna, additional, Elson, Sarah L., additional, Fontanillas, Pierre, additional, Furlotte, Nicholas A., additional, Huber, Karen E., additional, Hicks, Barry, additional, Jewett, Ethan M., additional, Jiang, Yunxuan, additional, Kleinman, Aaron, additional, Lin, Keng-Han, additional, Litterman, Nadia K., additional, McCreight, Jennifer C., additional, McIntyre, Matthew H., additional, McManus, Kimberly F., additional, Mountain, Joanna L., additional, Noblin, Elizabeth S., additional, Northover, Carrie A.M., additional, Pitts, Steven J., additional, Poznik, G. David, additional, Sathirapongsasuti, J. Fah, additional, Shelton, Janie F., additional, Shringarpure, Suyash, additional, Tian, Chao, additional, Tung, Joyce, additional, Vacic, Vladimir, additional, Wang, Xin, additional, Wilson, Catherine H., additional, Anderson, Tim, additional, Bentley, Steven, additional, Dalrymple-Alford, John, additional, Fowdar, Javed, additional, Halliday, Glenda, additional, Henders, Anjali K., additional, Hickie, Ian, additional, Kassam, Irfahan, additional, Kennedy, Martin, additional, Kwok, John, additional, Lewis, Simon, additional, Mellick, George, additional, Montgomery, Grant, additional, Pearson, John, additional, Pitcher, Toni, additional, Sidorenko, Julia, additional, Silburn, Peter A., additional, Vallerga, Costanza L., additional, Visscher, Peter M., additional, Wallace, Leanne, additional, Wray, Naomi R., additional, and Zhang, Futao, additional

Published
2019
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19. Moving beyond neurons: the role of cell type-specific gene regulation in Parkinson's disease heritability

Author

Reynolds, Regina H, Botía, Juan, Gibbs, J Raphael, Duarte, Jacinto, Clarimón, Jordi, Dols-Icardo, Oriol, Infante, Jon, Marín, Juan, Kulisevsky, Jaime, Pagonabarraga, Javier, Gonzalez-Aramburu, Isabel, Rodriguez, Antonio Sanchez, Sierra, María, Hernandez, Dena G, Duran, Raquel, Ruz, Clara, Vives, Francisco, Escamilla-Sevilla, Francisco, Mínguez, Adolfo, Cámara, Ana, Compta, Yaroslau, Ezquerra, Mario, Marti, Maria Jose, Fernández, Manel, Singleton, Andrew B, Muñoz, Esteban, Fernández-Santiago, Rubén, Tolosa, Eduard, Valldeoriola, Francesc, García-Ruiz, Pedro, Heredia, Maria Jose Gomez, Errazquin, Francisco Perez, Hoenicka, Janet, Jimenez-Escrig, Adriano, Martínez-Castrillo, Juan Carlos, Reed, Xylena, Lopez-Sendon, Jose Luis, Torres, Irene Martínez, Tabernero, Cesar, Vela, Lydia, Zimprich, Alexander, Pihlstrom, Lasse, Koks, Sulev, Taba, Pille, Majamaa, Kari, Siitonen, Ari, Leonard, Hampton, Okubadejo, Njideka U, Ojo, Oluwadamilola O, Pitcher, Toni, Anderson, Tim, Bentley, Steven, Fowdar, Javed, Mellick, George, Dalrymple-Alford, John, Henders, Anjali K, Kassam, Irfahan, Blauwendraat, Cornelis, Montgomery, Grant, Sidorenko, Julia, Zhang, Futao, Xue, Angli, Vallerga, Costanza L, Wallace, Leanne, Wray, Naomi R, Yang, Jian, Visscher, Peter M, Gratten, Jacob, Faghri, Faraz, Silburn, Peter A, Halliday, Glenda, Hickie, Ian, Kwok, John, Lewis, Simon, Kennedy, Martin, Pearson, John, Bras, Jose, Guerreiro, Rita, Tucci, Arianna, Nalls, Mike A, Kia, Demis A, Houlden, Henry, Plun-Favreau, Helene, Mok, Kin Y, Wood, Nicholas W, Lovering, Ruth, R'Bibo, Lea, Rizig, Mie, Chelban, Viorica, Trabzuni, Daniah, Hardy, John, Tan, Manuela, Morris, Huw R, Middlehurst, Ben, Quinn, John, Billingsley, Kimberley, Holmans, Peter, Kinghorn, Kerri J, Lewis, Patrick, Escott-Price, Valentina, Williams, Nigel, Gagliano Taliun, Sarah A, Foltynie, Thomas, Brice, Alexis, Danjou, Fabrice, Lesage, Suzanne, Corvol, Jean-Christophe, Martinez, Maria, Giri, Anamika, Schulte, Claudia, Brockmann, Kathrin, Simon Sanchez, Javier, Ryten, Mina, Heutink, Peter, Gasser, Thomas, Rizzu, Patrizia, Sharma, Manu, Shulman, Joshua M, Robak, Laurie, Lubbe, Steven, Mencacci, Niccolo E, Finkbeiner, Steven, Lungu, Codrin, Noyce, Alastair J, Scholz, Sonja W, Gan-Or, Ziv, Rouleau, Guy A, Krohan, Lynne, van Hilten, Jacobus J, Marinus, Johan, Adarmes-Gómez, Astrid D, Bernal-Bernal, Inmaculada, Bonilla-Toribio, Marta, Buiza-Rueda, Dolores, Nicolas, Aude, Carrillo, Fátima, Carrión-Claro, Mario, Mir, Pablo, Gómez-Garre, Pilar, Jesús, Silvia, Labrador-Espinosa, Miguel A, Macias, Daniel, Vargas-González, Laura, Méndez-Del-Barrio, Carlota, Periñán-Tocino, Teresa, Cookson, Mark R, Tejera-Parrado, Cristina, Diez-Fairen, Monica, Aguilar, Miquel, Alvarez, Ignacio, Boungiorno, María Teresa, Carcel, Maria, Pastor, Pau, Tartari, Juan Pablo, Alvarez, Victoria, González, Manuel Menéndez, Bandres-Ciga, Sara, Blazquez, Marta, Garcia, Ciara, Suarez-Sanmartin, Esther, Barrero, Francisco Javier, Rezola, Elisabet Mondragon, Yarza, Jesús Alberto Bergareche, Pagola, Ana Gorostidi, de Munain Arregui, Adolfo López, Ruiz-Martínez, Javier, and Cerdan, Debora

Subjects
Regulation of gene expression, 0303 health sciences, Cell type, Parkinson's disease, Microglia, Dopaminergic, Genomics, Disease, Biology, medicine.disease, Article, 03 medical and health sciences, 0302 clinical medicine, medicine.anatomical_structure, medicine, ddc:610, Neuroscience, Gene, 030217 neurology & neurosurgery, 030304 developmental biology
Abstract

Parkinson’s disease (PD), with its characteristic loss of nigrostriatal dopaminergic neurons and deposition of α-synuclein in neurons, is often considered a neuronal disorder. However, in recent years substantial evidence has emerged to implicate glial cell types, such as astrocytes and microglia. In this study, we used stratified LD score regression and expression-weighted cell-type enrichment together with several brain-related and cell-type-specific genomic annotations to connect human genomic PD findings to specific brain cell types. We found that PD heritability attributable to common variation does not enrich in global and regional brain annotations or brain-related cell-type-specific annotations. Likewise, we found no enrichment of PD susceptibility genes in brain-related cell types. In contrast, we demonstrated a significant enrichment of PD heritability in a curated lysosomal gene set highly expressed in astrocytic, microglial, and oligodendrocyte subtypes, and in LoF-intolerant genes, which were found highly expressed in almost all tested cellular subtypes. Our results suggest that PD risk loci do not lie in specific cell types or individual brain regions, but rather in global cellular processes detectable across several cell types.

Published
2019

21. The effect of X-linked dosage compensation on complex trait variation

Author

Sidorenko, Julia, primary, Kassam, Irfahan, additional, Kemper, Kathryn, additional, Zeng, Jian, additional, Lloyd-Jones, Luke, additional, Montgomery, Grant W., additional, Gibson, Greg, additional, Metspalu, Andres, additional, Esko, Tonu, additional, Yang, Jian, additional, McRae, Allan F., additional, and Visscher, Peter M., additional

Published
2018
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22. Blood triglyceride levels are associated with DNA methylation at the serine metabolism gene PHGDH

Author

Truong, Vinh, primary, Huang, Siying, additional, Dennis, Jessica, additional, Lemire, Mathieu, additional, Zwingerman, Nora, additional, Aïssi, Dylan, additional, Kassam, Irfahan, additional, Perret, Claire, additional, Wells, Philip, additional, Morange, Pierre-Emmanuel, additional, Wilson, Michael, additional, Trégouët, David-Alexandre, additional, and Gagnon, France, additional

Published
2017
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24. Autosomal genetic control of human gene expression does not differ across the sexes

Author

Kassam, Irfahan, primary, Lloyd-Jones, Luke, additional, Holloway, Alexander, additional, Small, Kerrin S., additional, Zeng, Biao, additional, Bakshi, Andrew, additional, Metspalu, Andres, additional, Gibson, Greg, additional, Spector, Tim D., additional, Esko, Tonu, additional, Montgomery, Grant W., additional, Powell, Joseph E., additional, Yang, Jian, additional, Visscher, Peter M., additional, and McRae, Allan F., additional

Published
2016
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25. Evidence for mitochondrial genetic control of autosomal gene expression

Author

Kassam, Irfahan, primary, Qi, Tuan, additional, Lloyd-Jones, Luke, additional, Holloway, Alexander, additional, Jan Bonder, Marc, additional, Henders, Anjali K., additional, Martin, Nicholas G., additional, Powell, Joseph E., additional, Franke, Lude, additional, Montgomery, Grant W., additional, Visscher, Peter M., additional, and McRae, Allan F., additional

Published
2016
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28. Long-range epigenetic regulation is conferred by genetic variation located at thousands of independent loci

Author

Lemire, Mathieu, primary, Zaidi, Syed H.E., additional, Ban, Maria, additional, Ge, Bing, additional, Aïssi, Dylan, additional, Germain, Marine, additional, Kassam, Irfahan, additional, Wang, Mike, additional, Zanke, Brent W., additional, Gagnon, France, additional, Morange, Pierre-Emmanuel, additional, Trégouët, David-Alexandre, additional, Wells, Philip S., additional, Sawcer, Stephen, additional, Gallinger, Steven, additional, Pastinen, Tomi, additional, and Hudson, Thomas J., additional

Published
2015
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