Author: "Logsdon, Benjamin A." - Searchworks@Jio Institute Digital Library Search Results

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1. Manifestations of Alzheimer’s disease genetic risk in the blood are evident in a multiomic analysis in healthy adults aged 18 to 90

Author: Heath, Laura, Earls, John C, Magis, Andrew T, Kornilov, Sergey A, Lovejoy, Jennifer C, Funk, Cory C, Rappaport, Noa, Logsdon, Benjamin A, Mangravite, Lara M, Kunkle, Brian W, Martin, Eden R, Naj, Adam C, Ertekin-Taner, Nilüfer, Golde, Todd E, Hood, Leroy, and Price, Nathan D
Subjects: Biological Sciences, Biomedical and Clinical Sciences, Genetics, Epidemiology, Health Sciences, Medical Biochemistry and Metabolomics, Dementia, Acquired Cognitive Impairment, Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD), Alzheimer's Disease, Aging, Brain Disorders, Neurodegenerative, Human Genome, Clinical Research, Prevention, 2.1 Biological and endogenous factors, Aetiology, Neurological, ATP-Binding Cassette Transporters, Adult, Alzheimer Disease, Apolipoprotein E2, Female, Genetic Predisposition to Disease, Genome-Wide Association Study, Genomics, Humans, Male, Polymorphism, Single Nucleotide, Alzheimer’s Disease Genetics Consortium
Abstract: Genetics play an important role in late-onset Alzheimer's Disease (AD) etiology and dozens of genetic variants have been implicated in AD risk through large-scale GWAS meta-analyses. However, the precise mechanistic effects of most of these variants have yet to be determined. Deeply phenotyped cohort data can reveal physiological changes associated with genetic risk for AD across an age spectrum that may provide clues to the biology of the disease. We utilized over 2000 high-quality quantitative measurements obtained from blood of 2831 cognitively normal adult clients of a consumer-based scientific wellness company, each with CLIA-certified whole-genome sequencing data. Measurements included: clinical laboratory blood tests, targeted chip-based proteomics, and metabolomics. We performed a phenome-wide association study utilizing this diverse blood marker data and 25 known AD genetic variants and an AD-specific polygenic risk score (PGRS), adjusting for sex, age, vendor (for clinical labs), and the first four genetic principal components; sex-SNP interactions were also assessed. We observed statistically significant SNP-analyte associations for five genetic variants after correction for multiple testing (for SNPs in or near NYAP1, ABCA7, INPP5D, and APOE), with effects detectable from early adulthood. The ABCA7 SNP and the APOE2 and APOE4 encoding alleles were associated with lipid variability, as seen in previous studies; in addition, six novel proteins were associated with the e2 allele. The most statistically significant finding was between the NYAP1 variant and PILRA and PILRB protein levels, supporting previous functional genomic studies in the identification of a putative causal variant within the PILRA gene. We did not observe associations between the PGRS and any analyte. Sex modified the effects of four genetic variants, with multiple interrelated immune-modulating effects associated with the PICALM variant. In post-hoc analysis, sex-stratified GWAS results from an independent AD case-control meta-analysis supported sex-specific disease effects of the PICALM variant, highlighting the importance of sex as a biological variable. Known AD genetic variation influenced lipid metabolism and immune response systems in a population of non-AD individuals, with associations observed from early adulthood onward. Further research is needed to determine whether and how these effects are implicated in early-stage biological pathways to AD. These analyses aim to complement ongoing work on the functional interpretation of AD-associated genetic variants.
Published: 2022

2. Human microglia show unique transcriptional changes in Alzheimer’s disease

Author: Prater, Katherine E., Green, Kevin J., Mamde, Sainath, Sun, Wei, Cochoit, Alexandra, Smith, Carole L., Chiou, Kenneth L., Heath, Laura, Rose, Shannon E., Wiley, Jesse, Keene, C. Dirk, Kwon, Ronald Y., Snyder-Mackler, Noah, Blue, Elizabeth E., Logsdon, Benjamin, Young, Jessica E., Shojaie, Ali, Garden, Gwenn A., and Jayadev, Suman
Published: 2023
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3. Rank and Bias in Families of Hyperelliptic Curves via Nagao's Conjecture

Author: Hammonds, Trajan, Kim, Seoyoung, Logsdon, Benjamin, Lozano-Robledo, Álvaro, and Miller, Steven J.
Subjects: Mathematics - Number Theory, 11G05, 11G20, 11G25
Abstract: Let $\mathcal{X} : y^2 = f(x)$ be a hyperelliptic curve over $\mathbb{Q}(T)$ of genus $g\geq 1$. Assume that the jacobian of $\mathcal{X}$ over $\mathbb{Q}(T)$ has no subvariety defined over $\mathbb{Q}$. Denote by $\mathcal{X}_t$ the specialization of $\mathcal{X}$ to an integer $T=t$, let $a_{\mathcal{X}_t}(p)$ be its trace of Frobenius, and $A_{\mathcal{X},r}(p) = \frac{1}{p}\sum_{t=1}^p a_{\mathcal{X}_t}(p)^r$ its $r$-th moment. The first moment is related to the rank of the jacobian $J_\mathcal{X}\left(\mathbb{Q}(T)\right)$ by a generalization of a conjecture of Nagao: $$\lim_{X \to \infty} \frac{1}{X} \sum_{p \leq X} - A_{\mathcal{X},1}(p) \log p = \operatorname{rank} J_\mathcal{X}(\mathbb{Q}(T)).$$ Generalizing a result of S. Arms, \'A. Lozano-Robledo, and S.J. Miller, we compute first moments for various families resulting in infinitely many hyperelliptic curves over $\mathbb{Q}(T)$ having jacobian of moderately large rank $4g+2$, where $g$ is the genus; by Silverman's specialization theorem, this yields hyperelliptic curves over $\mathbb{Q}$ with large rank jacobian. Note that Shioda has the best record in this directon: he constructed hyperelliptic curves of genus $g$ with jacobian of rank $4g+7$. In the case when $\mathcal{X}$ is an elliptic curve, Michel proved $p\cdot A_{\mathcal{X},2} = p^2 + O\left(p^{3/2}\right)$. For the families studied, we observe the same second moment expansion. Furthermore, we observe the largest lower order term that does not average to zero is on average negative, a bias first noted by S.J. Miller in the elliptic curve case. We prove this bias for a number of families of hyperelliptic curves., Comment: 16 pages
Published: 2019

4. Model organism development and evaluation for late-onset Alzheimer's disease: MODEL-AD.

Author: Oblak, Adrian L, Forner, Stefania, Territo, Paul R, Sasner, Michael, Carter, Gregory W, Howell, Gareth R, Sukoff-Rizzo, Stacey J, Logsdon, Benjamin A, Mangravite, Lara M, Mortazavi, Ali, Baglietto-Vargas, David, Green, Kim N, MacGregor, Grant R, Wood, Marcelo A, Tenner, Andrea J, LaFerla, Frank M, Lamb, Bruce T, and The MODEL‐AD, and Consortium
Subjects: and The MODEL‐AD, Consortium, Alzheimer's disease, LOAD, MRI, Open Science, PET, animal models, preclinical, Alzheimers disease
Abstract: Alzheimer's disease (AD) is a major cause of dementia, disability, and death in the elderly. Despite recent advances in our understanding of the basic biological mechanisms underlying AD, we do not know how to prevent it, nor do we have an approved disease-modifying intervention. Both are essential to slow or stop the growth in dementia prevalence. While our current animal models of AD have provided novel insights into AD disease mechanisms, thus far, they have not been successfully used to predict the effectiveness of therapies that have moved into AD clinical trials. The Model Organism Development and Evaluation for Late-onset Alzheimer's Disease (MODEL-AD; www.model-ad.org) Consortium was established to maximize human datasets to identify putative variants, genes, and biomarkers for AD; to generate, characterize, and validate the next generation of mouse models of AD; and to develop a preclinical testing pipeline. MODEL-AD is a collaboration among Indiana University (IU); The Jackson Laboratory (JAX); University of Pittsburgh School of Medicine (Pitt); Sage BioNetworks (Sage); and the University of California, Irvine (UCI) that will generate new AD modeling processes and pipelines, data resources, research results, standardized protocols, and models that will be shared through JAX's and Sage's proven dissemination pipelines with the National Institute on Aging-supported AD Centers, academic and medical research centers, research institutions, and the pharmaceutical industry worldwide.
Published: 2020

5. Brain proteome-wide association study implicates novel proteins in depression pathogenesis

Author: Wingo, Thomas S., Liu, Yue, Gerasimov, Ekaterina S., Gockley, Jake, Logsdon, Benjamin A., Duong, Duc M., Dammer, Eric B., Lori, Adriana, Kim, Paul J., Ressler, Kerry J., Beach, Thomas G., Reiman, Eric M., Epstein, Michael P., De Jager, Philip L., Lah, James J., Bennett, David A., Seyfried, Nicholas T., Levey, Allan I., and Wingo, Aliza P.
Published: 2021
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6. Rank and bias in families of hyperelliptic curves via Nagao's conjecture

Author: Hammonds, Trajan, Kim, Seoyoung, Logsdon, Benjamin, Lozano-Robledo, Álvaro, and Miller, Steven J.
Published: 2020
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7. Integrating human brain proteomes with genome-wide association data implicates new proteins in Alzheimer’s disease pathogenesis

Author: Wingo, Aliza P., Liu, Yue, Gerasimov, Ekaterina S., Gockley, Jake, Logsdon, Benjamin A., Duong, Duc M., Dammer, Eric B., Robins, Chloe, Beach, Thomas G., Reiman, Eric M., Epstein, Michael P., De Jager, Philip L., Lah, James J., Bennett, David A., Seyfried, Nicholas T., Levey, Allan I., and Wingo, Thomas S.
Published: 2021
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8. Crowdsourced estimation of cognitive decline and resilience in Alzheimer's disease

Author: Allen, Genevera I, Amoroso, Nicola, Anghel, Catalina, Balagurusamy, Venkat, Bare, Christopher J, Beaton, Derek, Bellotti, Roberto, Bennett, David A, Boehme, Kevin L, Boutros, Paul C, Caberlotto, Laura, Caloian, Cristian, Campbell, Frederick, Neto, Elias Chaibub, Chang, Yu‐Chuan, Chen, Beibei, Chen, Chien‐Yu, Chien, Ting‐Ying, Clark, Tim, Das, Sudeshna, Davatzikos, Christos, Deng, Jieyao, Dillenberger, Donna, Dobson, Richard JB, Dong, Qilin, Doshi, Jimit, Duma, Denise, Errico, Rosangela, Erus, Guray, Everett, Evan, Fardo, David W, Friend, Stephen H, Fröhlich, Holger, Gan, Jessica, St George‐Hyslop, Peter, Ghosh, Satrajit S, Glaab, Enrico, Green, Robert C, Guan, Yuanfang, Hong, Ming‐Yi, Huang, Chao, Hwang, Jinseub, Ibrahim, Joseph, Inglese, Paolo, Iyappan, Anandhi, Jiang, Qijia, Katsumata, Yuriko, Kauwe, John SK, Klein, Arno, Kong, Dehan, Krause, Roland, Lalonde, Emilie, Lauria, Mario, Lee, Eunjee, Lin, Xihui, Liu, Zhandong, Livingstone, Julie, Logsdon, Benjamin A, Lovestone, Simon, Ma, Tsung‐wei, Malhotra, Ashutosh, Mangravite, Lara M, Maxwell, Taylor J, Merrill, Emily, Nagorski, John, Namasivayam, Aishwarya, Narayan, Manjari, Naz, Mufassra, Newhouse, Stephen J, Norman, Thea C, Nurtdinov, Ramil N, Oyang, Yen‐Jen, Pawitan, Yudi, Peng, Shengwen, Peters, Mette A, Piccolo, Stephen R, Praveen, Paurush, Priami, Corrado, Sabelnykova, Veronica Y, Senger, Philipp, Shen, Xia, Simmons, Andrew, Sotiras, Aristeidis, Stolovitzky, Gustavo, Tangaro, Sabina, Tateo, Andrea, Tung, Yi‐An, Tustison, Nicholas J, Varol, Erdem, Vradenburg, George, Weiner, Michael W, Xiao, Guanghua, Xie, Lei, Xie, Yang, Xu, Jia, Yang, Hojin, Zhan, Xiaowei, Zhou, Yunyun, Zhu, Fan, and Zhu, Hongtu
Subjects: Biomedical and Clinical Sciences, Biological Psychology, Clinical Sciences, Neurosciences, Psychology, Acquired Cognitive Impairment, Prevention, Neurodegenerative, Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD), Dementia, Alzheimer's Disease, Aging, Brain Disorders, Neurological, Alzheimer Disease, Apolipoproteins E, Biomarkers, Cognition Disorders, Computational Biology, Databases, Bibliographic, Humans, Predictive Value of Tests, Azheimer's disease, Crowdsource, Big data, Bioinformatics, Cognitive decline, Imaging, Genetics, Alzheimer's Disease Neuroimaging Initiative, Geriatrics, Clinical sciences, Biological psychology
Abstract: Identifying accurate biomarkers of cognitive decline is essential for advancing early diagnosis and prevention therapies in Alzheimer's disease. The Alzheimer's disease DREAM Challenge was designed as a computational crowdsourced project to benchmark the current state-of-the-art in predicting cognitive outcomes in Alzheimer's disease based on high dimensional, publicly available genetic and structural imaging data. This meta-analysis failed to identify a meaningful predictor developed from either data modality, suggesting that alternate approaches should be considered for prediction of cognitive performance.
Published: 2016

9. Multi-tissue neocortical transcriptome-wide association study implicates 8 genes across 6 genomic loci in Alzheimer’s disease

Author: Gockley, Jake, Montgomery, Kelsey S., Poehlman, William L., Wiley, Jesse C., Liu, Yue, Gerasimov, Ekaterina, Greenwood, Anna K., Sieberts, Solveig K., Wingo, Aliza P., Wingo, Thomas S., Mangravite, Lara M., and Logsdon, Benjamin A.
Published: 2021
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10. Atlas of RNA editing events affecting protein expression in aged and Alzheimer’s disease human brain tissue

Author: Ma, Yiyi, Dammer, Eric B., Felsky, Daniel, Duong, Duc M., Klein, Hans-Ulrich, White, Charles C., Zhou, Maotian, Logsdon, Benjamin A., McCabe, Cristin, Xu, Jishu, Wang, Minghui, Wingo, Thomas S., Lah, James J., Zhang, Bin, Schneider, Julie, Allen, Mariet, Wang, Xue, Ertekin-Taner, Nilüfer, Seyfried, Nicholas T., Levey, Allan I., Bennett, David A., and De Jager, Philip L.
Published: 2021
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11. Genetic and multi‐omic risk assessment of Alzheimer's disease implicates core associated biological domains.

Author: Cary, Gregory A., Wiley, Jesse C., Gockley, Jake, Keegan, Stephen, Amirtha Ganesh, Sai Sruthi, Heath, Laura, Butler, Robert R., Mangravite, Lara M., Logsdon, Benjamin A., Longo, Frank M., Levey, Allan, Greenwood, Anna K., and Carter, Gregory W.
Subjects: DISEASE risk factors, GENETIC risk score, ALZHEIMER'S disease, OPEN scholarship
Abstract: INTRODUCTION: Alzheimer's disease (AD) is the predominant dementia globally, with heterogeneous presentation and penetrance of clinical symptoms, variable presence of mixed pathologies, potential disease subtypes, and numerous associated endophenotypes. Beyond the difficulty of designing treatments that address the core pathological characteristics of the disease, therapeutic development is challenged by the uncertainty of which endophenotypic areas and specific targets implicated by those endophenotypes to prioritize for further translational research. However, publicly funded consortia driving large‐scale open science efforts have produced multiple omic analyses that address both disease risk relevance and biological process involvement of genes across the genome. METHODS: Here we report the development of an informatic pipeline that draws from genetic association studies, predicted variant impact, and linkage with dementia associated phenotypes to create a genetic risk score. This is paired with a multi‐omic risk score utilizing extensive sets of both transcriptomic and proteomic studies to identify system‐level changes in expression associated with AD. These two elements combined constitute our target risk score that ranks AD risk genome‐wide. The ranked genes are organized into endophenotypic space through the development of 19 biological domains associated with AD in the described genetics and genomics studies and accompanying literature. The biological domains are constructed from exhaustive Gene Ontology (GO) term compilations, allowing automated assignment of genes into objectively defined disease‐associated biology. This rank‐and‐organize approach, performed genome‐wide, allows the characterization of aggregations of AD risk across biological domains. RESULTS: The top AD‐risk‐associated biological domains are Synapse, Immune Response, Lipid Metabolism, Mitochondrial Metabolism, Structural Stabilization, and Proteostasis, with slightly lower levels of risk enrichment present within the other 13 biological domains. DISCUSSION: This provides an objective methodology to localize risk within specific biological endophenotypes and drill down into the most significantly associated sets of GO terms and annotated genes for potential therapeutic targets. [ABSTRACT FROM AUTHOR]
Published: 2024
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12. A meta-analysis and genome-wide association study of platelet count and mean platelet volume in african americans.

Author: Qayyum, Rehan, Snively, Beverly M, Ziv, Elad, Nalls, Michael A, Liu, Yongmei, Tang, Weihong, Yanek, Lisa R, Lange, Leslie, Evans, Michele K, Ganesh, Santhi, Austin, Melissa A, Lettre, Guillaume, Becker, Diane M, Zonderman, Alan B, Singleton, Andrew B, Harris, Tamara B, Mohler, Emile R, Logsdon, Benjamin A, Kooperberg, Charles, Folsom, Aaron R, Wilson, James G, Becker, Lewis C, and Reiner, Alexander P
Subjects: Blood Platelets, Humans, Platelet Count, Platelet Aggregation, Genotype, Polymorphism, Single Nucleotide, Adult, Aged, Middle Aged, African Americans, Female, Male, Genome-Wide Association Study, Polymorphism, Single Nucleotide, Genetics, Developmental Biology
Abstract: Several genetic variants associated with platelet count and mean platelet volume (MPV) were recently reported in people of European ancestry. In this meta-analysis of 7 genome-wide association studies (GWAS) enrolling African Americans, our aim was to identify novel genetic variants associated with platelet count and MPV. For all cohorts, GWAS analysis was performed using additive models after adjusting for age, sex, and population stratification. For both platelet phenotypes, meta-analyses were conducted using inverse-variance weighted fixed-effect models. Platelet aggregation assays in whole blood were performed in the participants of the GeneSTAR cohort. Genetic variants in ten independent regions were associated with platelet count (N = 16,388) with p
Published: 2012

13. Brain microRNAs associated with late-life depressive symptoms are also associated with cognitive trajectory and dementia

Author: Wingo, Thomas S., Yang, Jingjing, Fan, Wen, Min Canon, Se, Gerasimov, Ekaterina Sergeevna, Lori, Adriana, Logsdon, Benjamin, Yao, Bing, Seyfried, Nicholas T., Lah, James J., Levey, Allan I., Boyle, Patricia A., Schneider, Julia A., De Jager, Philip L., Bennett, David A., and Wingo, Aliza P.
Published: 2020
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14. Author Correction: Molecular estimation of neurodegeneration pseudotime in older brains

Author: Mukherjee, Sumit, Heath, Laura, Preuss, Christoph, Jayadev, Suman, Garden, Gwenn A., Greenwood, Anna K., Sieberts, Solveig K., De Jager, Philip L., Ertekin-Taner, Nilüfer, Carter, Gregory W., Mangravite, Lara M., and Logsdon, Benjamin A.
Published: 2020
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15. Molecular estimation of neurodegeneration pseudotime in older brains

Author: Mukherjee, Sumit, Heath, Laura, Preuss, Christoph, Jayadev, Suman, Garden, Gwenn A., Greenwood, Anna K., Sieberts, Solveig K., De Jager, Philip L., Ertekin-Taner, Nilüfer, Carter, Gregory W., Mangravite, Lara M., and Logsdon, Benjamin A.
Published: 2020
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16. Large-scale proteomic analysis of human brain identifies proteins associated with cognitive trajectory in advanced age

Author: Wingo, Aliza P., Dammer, Eric B., Breen, Michael S., Logsdon, Benjamin A., Duong, Duc M., Troncosco, Juan C., Thambisetty, Madhav, Beach, Thomas G., Serrano, Geidy E., Reiman, Eric M., Caselli, Richard J., Lah, James J., Seyfried, Nicholas T., Levey, Allan I., and Wingo, Thomas S.
Published: 2019
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17. Genome-wide RNAseq study of the molecular mechanisms underlying microglia activation in response to pathological tau perturbation in the rTg4510 tau transgenic animal model

Author: Wang, Hong, Li, Yupeng, Ryder, John W., Hole, Justin T., Ebert, Philip J., Airey, David C., Qian, Hui-Rong, Logsdon, Benjamin, Fisher, Alice, Ahmed, Zeshan, Murray, Tracey K., Cavallini, Annalisa, Bose, Suchira, Eastwood, Brian J., Collier, David A., Dage, Jeffrey L., Miller, Bradley B., Merchant, Kalpana M., O’Neill, Michael J., and Demattos, Ronald B.
Published: 2018
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18. Transcriptomic profiling of myeloid cells in Alzheimer’s Disease brain illustrates heterogeneity of microglia endolysosomal subtypes

Author: Prater, Katherine E, primary, Green, Kevin J, additional, Sun, Wei, additional, Smith, Carole L, additional, Chiou, Kenneth L, additional, Mamde, Sainath, additional, Heath, Laura M, additional, Rose, Shannon, additional, Keene, C. Dirk, additional, Kwon, Ronald Y, additional, Snyder‐Mackler, Noah, additional, Blue, Elizabeth E, additional, Young, Jessica E., additional, Logsdon, Benjamin A, additional, Shojaie, Ali, additional, Garden, Gwenn A, additional, and Jayadev, Suman, additional
Published: 2022
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19. Transcriptomically unique endolysosomal and homeostatic microglia populations in Alzheimer’s Disease and aged human brain

Author: Prater, Katherine, primary, Green, Kevin, additional, Mamde, Sainath, additional, Sun, Wei, additional, Sotelo, Alexandra, additional, Smith, Carole, additional, Chiou, Kenneth, additional, Heath, Laura, additional, Rose, Shannon, additional, Keene, C., additional, Kwon, Ronald, additional, Snyder-Mackler, Noah, additional, Blue, Elizabeth, additional, Logsdon, Benjamin, additional, Young, Jessica, additional, Shojaie, Ali, additional, Garden, Gwenn, additional, and Jayadev, Suman, additional
Published: 2022
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20. Meta-Analysis of the Alzheimer’s Disease Human Brain Transcriptome and Functional Dissection in Mouse Models

Author: Wan, Ying-Wooi, Al-Ouran, Rami, Mangleburg, Carl G., Perumal, Thanneer M., Lee, Tom V., Allison, Katherine, Swarup, Vivek, Funk, Cory C., Gaiteri, Chris, Allen, Mariet, Wang, Minghui, Neuner, Sarah M., Kaczorowski, Catherine C., Philip, Vivek M., Howell, Gareth R., Martini-Stoica, Heidi, Zheng, Hui, Mei, Hongkang, Zhong, Xiaoyan, Kim, Jungwoo Wren, Dawson, Valina L., Dawson, Ted M., Pao, Ping-Chieh, Tsai, Li-Huei, Haure-Mirande, Jean-Vianney, Ehrlich, Michelle E., Chakrabarty, Paramita, Levites, Yona, Wang, Xue, Dammer, Eric B., Srivastava, Gyan, Mukherjee, Sumit, Sieberts, Solveig K., Omberg, Larsson, Dang, Kristen D., Eddy, James A., Snyder, Phil, Chae, Yooree, Amberkar, Sandeep, Wei, Wenbin, Hide, Winston, Preuss, Christoph, Ergun, Ayla, Ebert, Phillip J., Airey, David C., Mostafavi, Sara, Yu, Lei, Klein, Hans-Ulrich, Carter, Gregory W., Collier, David A., Golde, Todd E., Levey, Allan I., Bennett, David A., Estrada, Karol, Townsend, T. Matthew, Zhang, Bin, Schadt, Eric, De Jager, Philip L., Price, Nathan D., Ertekin-Taner, Nilüfer, Liu, Zhandong, Shulman, Joshua M., Mangravite, Lara M., Logsdon, Benjamin A., Wan, Ying-Wooi, Al-Ouran, Rami, Mangleburg, Carl G., Perumal, Thanneer M., Lee, Tom V., Allison, Katherine, Swarup, Vivek, Funk, Cory C., Gaiteri, Chris, Allen, Mariet, Wang, Minghui, Neuner, Sarah M., Kaczorowski, Catherine C., Philip, Vivek M., Howell, Gareth R., Martini-Stoica, Heidi, Zheng, Hui, Mei, Hongkang, Zhong, Xiaoyan, Kim, Jungwoo Wren, Dawson, Valina L., Dawson, Ted M., Pao, Ping-Chieh, Tsai, Li-Huei, Haure-Mirande, Jean-Vianney, Ehrlich, Michelle E., Chakrabarty, Paramita, Levites, Yona, Wang, Xue, Dammer, Eric B., Srivastava, Gyan, Mukherjee, Sumit, Sieberts, Solveig K., Omberg, Larsson, Dang, Kristen D., Eddy, James A., Snyder, Phil, Chae, Yooree, Amberkar, Sandeep, Wei, Wenbin, Hide, Winston, Preuss, Christoph, Ergun, Ayla, Ebert, Phillip J., Airey, David C., Mostafavi, Sara, Yu, Lei, Klein, Hans-Ulrich, Carter, Gregory W., Collier, David A., Golde, Todd E., Levey, Allan I., Bennett, David A., Estrada, Karol, Townsend, T. Matthew, Zhang, Bin, Schadt, Eric, De Jager, Philip L., Price, Nathan D., Ertekin-Taner, Nilüfer, Liu, Zhandong, Shulman, Joshua M., Mangravite, Lara M., and Logsdon, Benjamin A.
Abstract: © 2020 The Authors We present a consensus atlas of the human brain transcriptome in Alzheimer's disease (AD), based on meta-analysis of differential gene expression in 2,114 postmortem samples. We discover 30 brain coexpression modules from seven regions as the major source of AD transcriptional perturbations. We next examine overlap with 251 brain differentially expressed gene sets from mouse models of AD and other neurodegenerative disorders. Human-mouse overlaps highlight responses to amyloid versus tau pathology and reveal age- and sex-dependent expression signatures for disease progression. Human coexpression modules enriched for neuronal and/or microglial genes broadly overlap with mouse models of AD, Huntington's disease, amyotrophic lateral sclerosis, and aging. Other human coexpression modules, including those implicated in proteostasis, are not activated in AD models but rather following other, unexpected genetic manipulations. Our results comprise a cross-species resource, highlighting transcriptional networks altered by human brain pathophysiology and identifying correspondences with mouse models for AD preclinical studies.
Published: 2022

21. Large eQTL meta-analysis reveals differing patterns between cerebral cortical and cerebellar brain regions

Author: Sieberts, Solveig K., Perumal, Thanneer M., Carrasquillo, Minerva M., Allen, Mariet, Reddy, Joseph S., Hoffman, Gabriel E., Dang, Kristen K., Calley, John, Ebert, Philip J., Eddy, James, Wang, Xue, Greenwood, Anna K., Mostafavi, Sara, Akbarian, Schahram, Bendl, Jaroslav, Breen, Michael S., Brennand, Kristen, Brown, Leanne, Browne, Andrew, Buxbaum, Joseph D., Charney, Alexander, Chess, Andrew, Couto, Lizette, Crawford, Greg, Devillers, Olivia, Devlin, Bernie, Dobbyn, Amanda, Domenici, Enrico, Filosi, Michele, Flatow, Elie, Francoeur, Nancy, Fullard, John, Gil, Sergio Espeso, Girdhar, Kiran, Gulyás-Kovács, Attila, Gur, Raquel, Hahn, Chang-Gyu, Haroutunian, Vahram, Hauberg, Mads Engel, Huckins, Laura, Jacobov, Rivky, Jiang, Yan, Johnson, Jessica S., Kassim, Bibi, Kim, Yungil, Klei, Lambertus, Kramer, Robin, Lauria, Mario, Lehner, Thomas, Lewis, David A., Lipska, Barbara K., Montgomery, Kelsey, Park, Royce, Rosenbluh, Chaggai, Roussos, Panagiotis, Ruderfer, Douglas M., Senthil, Geetha, Shah, Hardik R., Sloofman, Laura, Song, Lingyun, Stahl, Eli, Sullivan, Patrick, Visintainer, Roberto, Wang, Jiebiao, Wang, Ying-Chih, Wiseman, Jennifer, Xia, Eva, Zhang, Wen, Zharovsky, Elizabeth, Addis, Laura, Addo, Sadiya N., Airey, David Charles, Arnold, Matthias, Bennett, David A., Bi, Yingtao, Biber, Knut, Blach, Colette, Bradhsaw, Elizabeth, Brennan, Paul, Canet-Aviles, Rosa, Cao, Sherry, Cavalla, Anna, Chae, Yooree, Chen, William W., Cheng, Jie, Collier, David Andrew, Dage, Jeffrey L., Dammer, Eric B., Davis, Justin Wade, Davis, John, Drake, Derek, Duong, Duc, Eastwood, Brian J., Ehrlich, Michelle, Ellingson, Benjamin, Engelmann, Brett W., Esmaeelinieh, Sahar, Felsky, Daniel, Funk, Cory, Gaiteri, Chris, Gandy, Samuel, Gao, Fan, Gileadi, Opher, Golde, Todd, Grosskurth, Shaun E., Gupta, Rishi R., Gutteridge, Alex X., Hooli, Basavaraj, Humphryes-Kirilov, Neil, Iijima, Koichi, James, Corey, Jung, Paul M., Kaddurah-Daouk, Rima, Kastenmuller, Gabi, Klein, Hans-Ulrich, Kummer, Markus, Lacor, Pascale N., Lah, James, Laing, Emma, Levey, Allan, Li, Yupeng, Lipsky, Samantha, Liu, Yushi, Liu, Jimmy, Liu, Zhandong, Louie, Gregory, Lu, Tao, Ma, Yiyi, Matsuoka, Yasuji Y., Menon, Vilas, Miller, Bradley, Misko, Thomas P., Mollon, Jennifer E., Mukherjee, Sumit, Noggle, Scott, Pao, Ping-Chieh, Pearce, Tracy Young, Pearson, Neil, Penny, Michelle, Petyuk, Vladislav A., Price, Nathan, Quarless, Danjuma X., Ravikumar, Brinda, Ried, Janina S., Ruble, Cara Lee Ann, Runz, Heiko, Saykin, Andrew J., Schadt, Eric, Scherschel, James E., Seyfried, Nicholas, Shulman, Joshua M., Snyder, Phil, Soares, Holly, Srivastava, Gyan P., Stockmann, Henning, Taga, Mariko, Tasaki, Shinya, Tenenbaum, Jessie, Tsai, Li-Huei, Vasanthakumar, Aparna, Wachter, Astrid, Wang, Yaming, Wang, Hong, Wang, Minghui, Whelan, Christopher D., White, Charles, Woo, Kara H., Wren, Paul, Wu, Jessica W., Xi, Hualin S., Yankner, Bruce A., Younkin, Steven G., Yu, Lei, Zavodszky, Maria, Zhang, Wenling, Zhang, Guoqiang, Zhang, Bin, Zhu, Jun, Omberg, Larsson, Peters, Mette A., Logsdon, Benjamin A., De Jager, Philip L., Ertekin-Taner, Nilüfer, Mangravite, Lara M., Sieberts, Solveig K., Perumal, Thanneer M., Carrasquillo, Minerva M., Allen, Mariet, Reddy, Joseph S., Hoffman, Gabriel E., Dang, Kristen K., Calley, John, Ebert, Philip J., Eddy, James, Wang, Xue, Greenwood, Anna K., Mostafavi, Sara, Akbarian, Schahram, Bendl, Jaroslav, Breen, Michael S., Brennand, Kristen, Brown, Leanne, Browne, Andrew, Buxbaum, Joseph D., Charney, Alexander, Chess, Andrew, Couto, Lizette, Crawford, Greg, Devillers, Olivia, Devlin, Bernie, Dobbyn, Amanda, Domenici, Enrico, Filosi, Michele, Flatow, Elie, Francoeur, Nancy, Fullard, John, Gil, Sergio Espeso, Girdhar, Kiran, Gulyás-Kovács, Attila, Gur, Raquel, Hahn, Chang-Gyu, Haroutunian, Vahram, Hauberg, Mads Engel, Huckins, Laura, Jacobov, Rivky, Jiang, Yan, Johnson, Jessica S., Kassim, Bibi, Kim, Yungil, Klei, Lambertus, Kramer, Robin, Lauria, Mario, Lehner, Thomas, Lewis, David A., Lipska, Barbara K., Montgomery, Kelsey, Park, Royce, Rosenbluh, Chaggai, Roussos, Panagiotis, Ruderfer, Douglas M., Senthil, Geetha, Shah, Hardik R., Sloofman, Laura, Song, Lingyun, Stahl, Eli, Sullivan, Patrick, Visintainer, Roberto, Wang, Jiebiao, Wang, Ying-Chih, Wiseman, Jennifer, Xia, Eva, Zhang, Wen, Zharovsky, Elizabeth, Addis, Laura, Addo, Sadiya N., Airey, David Charles, Arnold, Matthias, Bennett, David A., Bi, Yingtao, Biber, Knut, Blach, Colette, Bradhsaw, Elizabeth, Brennan, Paul, Canet-Aviles, Rosa, Cao, Sherry, Cavalla, Anna, Chae, Yooree, Chen, William W., Cheng, Jie, Collier, David Andrew, Dage, Jeffrey L., Dammer, Eric B., Davis, Justin Wade, Davis, John, Drake, Derek, Duong, Duc, Eastwood, Brian J., Ehrlich, Michelle, Ellingson, Benjamin, Engelmann, Brett W., Esmaeelinieh, Sahar, Felsky, Daniel, Funk, Cory, Gaiteri, Chris, Gandy, Samuel, Gao, Fan, Gileadi, Opher, Golde, Todd, Grosskurth, Shaun E., Gupta, Rishi R., Gutteridge, Alex X., Hooli, Basavaraj, Humphryes-Kirilov, Neil, Iijima, Koichi, James, Corey, Jung, Paul M., Kaddurah-Daouk, Rima, Kastenmuller, Gabi, Klein, Hans-Ulrich, Kummer, Markus, Lacor, Pascale N., Lah, James, Laing, Emma, Levey, Allan, Li, Yupeng, Lipsky, Samantha, Liu, Yushi, Liu, Jimmy, Liu, Zhandong, Louie, Gregory, Lu, Tao, Ma, Yiyi, Matsuoka, Yasuji Y., Menon, Vilas, Miller, Bradley, Misko, Thomas P., Mollon, Jennifer E., Mukherjee, Sumit, Noggle, Scott, Pao, Ping-Chieh, Pearce, Tracy Young, Pearson, Neil, Penny, Michelle, Petyuk, Vladislav A., Price, Nathan, Quarless, Danjuma X., Ravikumar, Brinda, Ried, Janina S., Ruble, Cara Lee Ann, Runz, Heiko, Saykin, Andrew J., Schadt, Eric, Scherschel, James E., Seyfried, Nicholas, Shulman, Joshua M., Snyder, Phil, Soares, Holly, Srivastava, Gyan P., Stockmann, Henning, Taga, Mariko, Tasaki, Shinya, Tenenbaum, Jessie, Tsai, Li-Huei, Vasanthakumar, Aparna, Wachter, Astrid, Wang, Yaming, Wang, Hong, Wang, Minghui, Whelan, Christopher D., White, Charles, Woo, Kara H., Wren, Paul, Wu, Jessica W., Xi, Hualin S., Yankner, Bruce A., Younkin, Steven G., Yu, Lei, Zavodszky, Maria, Zhang, Wenling, Zhang, Guoqiang, Zhang, Bin, Zhu, Jun, Omberg, Larsson, Peters, Mette A., Logsdon, Benjamin A., De Jager, Philip L., Ertekin-Taner, Nilüfer, and Mangravite, Lara M.
Abstract: © 2020, The Author(s). The availability of high-quality RNA-sequencing and genotyping data of post-mortem brain collections from consortia such as CommonMind Consortium (CMC) and the Accelerating Medicines Partnership for Alzheimer’s Disease (AMP-AD) Consortium enable the generation of a large-scale brain cis-eQTL meta-analysis. Here we generate cerebral cortical eQTL from 1433 samples available from four cohorts (identifying >4.1 million significant eQTL for >18,000 genes), as well as cerebellar eQTL from 261 samples (identifying 874,836 significant eQTL for >10,000 genes). We find substantially improved power in the meta-analysis over individual cohort analyses, particularly in comparison to the Genotype-Tissue Expression (GTEx) Project eQTL. Additionally, we observed differences in eQTL patterns between cerebral and cerebellar brain regions. We provide these brain eQTL as a resource for use by the research community. As a proof of principle for their utility, we apply a colocalization analysis to identify genes underlying the GWAS association peaks for schizophrenia and identify a potentially novel gene colocalization with lncRNA RP11-677M14.2 (posterior probability of colocalization 0.975).
Published: 2022

22. Corrigendum: Uncovering Disease Mechanisms in a Novel Mouse Model Expressing Humanized APOEε4 and Trem2*R47H

Author: Kotredes, Kevin P., primary, Oblak, Adrian, additional, Pandey, Ravi S., additional, Lin, Peter Bor-Chian, additional, Garceau, Dylan, additional, Williams, Harriet, additional, Uyar, Asli, additional, O'Rourke, Rita, additional, O'Rourke, Sarah, additional, Ingraham, Cynthia, additional, Bednarczyk, Daria, additional, Belanger, Melisa, additional, Cope, Zackary, additional, Foley, Kate E., additional, Logsdon, Benjamin A., additional, Mangravite, Lara M., additional, Sukoff Rizzo, Stacey J., additional, Territo, Paul R., additional, Carter, Gregory W., additional, Sasner, Michael, additional, Lamb, Bruce T., additional, and Howell, Gareth R., additional
Published: 2022
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23. Manifestations of Alzheimer’s Disease Genetic Risk in the Blood: A Cross-Sectional Multi-Omic Analysis in Healthy Adults Aged 18-90+

Author: Heath, Laura, primary, Earls, John, additional, Magis, Andrew, additional, Kornilov, Sergey, additional, Lovejoy, Jennifer, additional, Funk, Cory, additional, Rappaport, Noa, additional, Logsdon, Benjamin, additional, Mangravite, Lara, additional, Kunkle, Brian, additional, Martin, Eden, additional, Naj, Adam, additional, Ertekin-Taner, Nilüfer, additional, Golde, Todd, additional, Hood, Leroy, additional, and Price, Nathan, additional
Published: 2022
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24. Integrating multimodal data to support Alzheimer’s disease target prioritization

Author: Cary, Gregory A., primary, Gockley, Jake, additional, Lehallier, Benoit, additional, Leal, Karina, additional, Greenwood, Anna K, additional, Shulman, Joshua M, additional, Longo, Frank M, additional, Levey, Allan I, additional, Mangravite, Lara M, additional, Logsdon, Benjamin A, additional, and Carter, Gregory W, additional
Published: 2021
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25. Microglia subtype transcriptomes differ between Alzheimer Disease and control human postmortem brain samples

Author: Prater, Katherine E, primary, Green, Kevin J, additional, Chiou, Kenneth L, additional, Smith, Carole L, additional, Sun, Wei, additional, Shojaie, Ali, additional, Heath, Laura M, additional, Rose, Shannon, additional, Keene, C. Dirk, additional, Logsdon, Benjamin A, additional, Snyder‐Mackler, Noah, additional, Blue, Elizabeth E, additional, Young, Jessica E., additional, Garden, Gwenn A, additional, and Jayadev, Suman, additional
Published: 2021
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26. Manifestations of Alzheimer’s Disease Genetic Risk in the Blood: A Cross-Sectional Multi-Omic Analysis in Healthy Adults Aged 18-90+

Author: Heath, Laura M, primary, Earls, John C., additional, Magis, Andrew T., additional, Kornilov, Sergey A., additional, Lovejoy, Jennifer C., additional, Funk, Cory C., additional, Rappaport, Noa, additional, Logsdon, Benjamin A., additional, Mangravite, Lara M., additional, Kunkle, Brian W., additional, Martin, Eden R., additional, Naj, Adam C., additional, Ertekin-Taner, Nilüfer, additional, Golde, Todd E., additional, Hood, Leroy, additional, and Price, Nathan D., additional
Published: 2021
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27. Uncovering Disease Mechanisms in a Novel Mouse Model Expressing Humanized APOEε4 and Trem2*R47H

Author: Kotredes, Kevin P., primary, Oblak, Adrian, additional, Pandey, Ravi S., additional, Lin, Peter Bor-Chian, additional, Garceau, Dylan, additional, Williams, Harriet, additional, Uyar, Asli, additional, O’Rourke, Rita, additional, O’Rourke, Sarah, additional, Ingraham, Cynthia, additional, Bednarczyk, Daria, additional, Belanger, Melisa, additional, Cope, Zackary, additional, Foley, Kate E., additional, Logsdon, Benjamin A., additional, Mangravite, Lara M., additional, Sukoff Rizzo, Stacey J., additional, Territo, Paul R., additional, Carter, Gregory W., additional, Sasner, Michael, additional, Lamb, Bruce T., additional, and Howell, Gareth R., additional
Published: 2021
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28. Rare Variation Facilitates Inferences of Fine-Scale Population Structure in Humans

Author: OʼConnor, Timothy D., Fu, Wenqing, Mychaleckyj, Josyf C., Logsdon, Benjamin, Auer, Paul, Carlson, Christopher S., Leal, Suzanne M., Smith, Joshua D., Rieder, Mark J., Bamshad, Michael J., Nickerson, Deborah A., and Akey, Joshua M.
Published: 2015
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29. Comprehensive Evaluation of the 5XFAD Mouse Model for Preclinical Testing Applications: A MODEL-AD Study

Author: Oblak, Adrian L., primary, Lin, Peter B., additional, Kotredes, Kevin P., additional, Pandey, Ravi S., additional, Garceau, Dylan, additional, Williams, Harriet M., additional, Uyar, Asli, additional, O’Rourke, Rita, additional, O’Rourke, Sarah, additional, Ingraham, Cynthia, additional, Bednarczyk, Daria, additional, Belanger, Melisa, additional, Cope, Zackary A., additional, Little, Gabriela J., additional, Williams, Sean-Paul G., additional, Ash, Carl, additional, Bleckert, Adam, additional, Ragan, Tim, additional, Logsdon, Benjamin A., additional, Mangravite, Lara M., additional, Sukoff Rizzo, Stacey J., additional, Territo, Paul R., additional, Carter, Gregory W., additional, Howell, Gareth R., additional, Sasner, Michael, additional, and Lamb, Bruce T., additional
Published: 2021
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30. APOEe4.Trem2*R47H Mice Show Changes in Alzheimer’s Disease-Relevant Processes in the Absence of Amyloid Plaques

Author: Kotredes, Kevin P., primary, Oblak, Adrian, additional, Pandey, Ravi S., additional, Lin, Peter Bor-Chian, additional, Garceau, Dylan, additional, Williams, Harriet, additional, Uyar, Asli, additional, O’Rourke, Rita, additional, O’Rourke, Sarah, additional, Ingraham, Cynthia, additional, Bednarycek, Daria, additional, Belanger, Melisa, additional, Cope, Zackary, additional, Foley, Kate E ., additional, Logsdon, Benjamin A, additional, Mangravite, Lara M ., additional, Rizzo, Stacey J . Sukoff, additional, Territo, Paul R ., additional, Carter, Gregory W ., additional, Sasner, Michael, additional, Lamb, Bruce T ., additional, and Howell, Gareth R ., additional
Published: 2021
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31. Additional file 1 of Multi-tissue neocortical transcriptome-wide association study implicates 8 genes across 6 genomic loci in Alzheimer’s disease

Author: Gockley, Jake, Montgomery, Kelsey S., Poehlman, William L., Wiley, Jesse C., Liu, Yue, Gerasimov, Ekaterina, Greenwood, Anna K., Sieberts, Solveig K., Wingo, Aliza P., Wingo, Thomas S., Mangravite, Lara M., and Logsdon, Benjamin A.
Abstract: Additional file 1. This file contains the supplementary figures (S1-S14) and the Supplementary Methods Sections 1-4.
Published: 2021
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32. Quantitative trait loci for the circadian clock in Neurospora crassa

Author: Kim, Tae-Sung, Logsdon, Benjamin A., Park, Sohyun, Mezey, Jason G., and Lee, Kwangwon
Subjects: Quantitative genetics -- Research, Quantitative trait loci -- Evaluation, Circadian rhythms -- Genetic aspects, Neurospora -- Genetic aspects, Biological sciences
Abstract: Neurospora crassa has been a model organism for the study of circadian clocks for the past four decades. Among natural accessions of Neurospora crassa, there is significant variation in clock phenotypes. In an attempt to investigate natural allelic variants contributing to quantitative variation, we used a quantitative trait loci mapping approach to analyze three independent mapping populations whose progenitors were collected from geographically isolated locations. Two circadian clock phenotypes, free-running period and entrained phase, were evaluated in the 188 [F.sub.1] progeny of each mapping population. To identify the clock QTL, we applied two QTL mapping analyses: composite interval mapping (CIM) and Bayesian multiple QTL analysis (BMQ). When controlling false positive rates [less than or equal to] 0.05, BMQ appears to be the more sensitive of the two approaches. BMQ confirmed most of the QTL from CIM (18 QTL) and identified 23 additional QTL. While 13 QTL colocalize with previously identified clock genes, we identified 30 QTL that were not linked with any previously characterized clock genes. These are candidate regions where clock genes may be located and are expected to lead to new insights in clock regulation.
Published: 2007

33. Neutral evolution of multiple quantitative characters: a genealogical approach

Author: Griswold, Cortland K., Logsdon, Benjamin, and Gomulkiewicz, Richard
Subjects: Neutral evolution -- Research, Biological sciences
Abstract: The G matrix measures the components of phenotypic variation that are genetically heritable. The structure of G, that is, its principal components and their associated variances, determines, in part, the direction and speed of multivariate trait evolution. In this article we present a framework and results that give the structure of G under the assumption of neutrality. We suggest that a neutral expectation of the structure of G is important because it gives a null expectation for the structure of G from which the unique consequences of selection can be determined. We demonstrate how the processes of mutation, recombination, and drift shape the structure of G. Furthermore, we demonstrate how shared common ancestry between segregating alleles shapes the structure of G. Our results show that shared common ancestry, which manifests itself in the form of a gene genealogy, causes the structure of G to be nonuniform in that the variances associated with the principal components of G decline at an approximately exponential rate. Furthermore we show that the extent of the nonunifonnity in the structure of G is enhanced with declines in mutation rates, recombination rates, and numbers of loci and is dependent on the pattern and modality of mutation.
Published: 2007

34. A multi-discipline phenotyping platform for late-onset Alzheimer’s disease employed on a novel, humanized APOEε4.Trem2*R47H mouse model

Author: Kotredes, Kevin, primary, Oblak, Adrian, additional, Pandey, Ravi, additional, Lin, Peter, additional, Garceau, Dylan, additional, Williams, Harriet, additional, Uyar, Asli, additional, O'Rourke, Rita, additional, O'Rourke, Sarah, additional, Ingraham, Cynthia, additional, Bednarczyk, Daria, additional, Belanger, Melisa, additional, Cope, Zackary, additional, Foley, Kate, additional, Logsdon, Benjamin, additional, Mangravite, Lara, additional, Rizzo, Stacey Sukoff, additional, Territo, Paul, additional, Carter, Gregory, additional, Lamb, Bruce, additional, Howell, Gareth, additional, and Sasner, Michael, additional
Published: 2021
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35. Agora: An open platform for exploration of Alzheimer’s disease evidence

Author: Greenwood, Anna K., primary, Gockley, Jake, additional, Daily, Kenneth, additional, Aluthgamage, Duminda, additional, Leanza, Zoë, additional, Sieberts, Solveig K., additional, Woo, Kara H., additional, Simon, Stockard, additional, Gendel, Alina, additional, Thyer, Tess, additional, Do, Khai, additional, Doerr, Megan, additional, Peters, Mette A., additional, Omberg, Larsson, additional, Logsdon, Benjamin A., additional, and Mangravite, Lara M., additional
Published: 2020
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36. Brain transcriptome wide association study (TWAS) implicates 8 genes across 6 loci in Alzheimer’s disease

Author: Gockley, Jake, primary, Montgomery, Kelsey S., additional, Poehlman, William L., additional, Liu, Yue, additional, Gerasimov, Ekaterina S., additional, Greenwood, Anna K., additional, Wingo, Aliza P., additional, Wingo, Thomas S., additional, Mangravite, Lara M., additional, and Logsdon, Benjamin A., additional
Published: 2020
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37. N‐of‐1‐pathways transcriptomic analysis reveals distinct subtypes of Alzheimer’s disease

Author: Uyar, Asli, primary, Pandey, Ravi S., additional, Preuss, Christoph, additional, Kotredes, Kevin P., additional, Oblak, Adrian L., additional, Logsdon, Benjamin A., additional, Rizzo, Stacey J. Sukoff, additional, Howell, Gareth, additional, Lamb, Bruce T., additional, Sasner, Michael, additional, and Carter, Gregory W., additional
Published: 2020
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38. Integrating human brain proteomes and genome‐wide association results implicates new genes in Alzheimer’s disease

Author: Wingo, Aliza P., primary, Liu, Yue, additional, Gockley, Jake, additional, Logsdon, Benjamin A., additional, Duong, Duc, additional, Dammer, Eric B., additional, Robins, Chloe, additional, Cutler, David J., additional, De Jager, Philip L., additional, Lah, James J., additional, Bennett, David A., additional, Levey, Allan I., additional, Seyfried, Nicholas T., additional, and Wingo, Thomas S., additional
Published: 2020
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39. Single nuclei RNA‐seq data analysis identifies glial cell lineages associated with Alzheimer’s disease severity

Author: Elyanow, Rebecca, primary, Green, Kevin J., additional, Greenwood, Anna K., additional, Prater, Katherine E., additional, Melief, Erica J., additional, Valdmanis, Paul, additional, Blue, Elizabeth E., additional, Keene, C. Dirk, additional, Crane, Paul K., additional, Young, Jessica E., additional, Garden, Gwenn A., additional, Jayadev, Suman, additional, and Logsdon, Benjamin A., additional
Published: 2020
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40. Leveraging predicted gene expression data for recapitulation of gene coexpression network analysis associations with AD pathology and cognitive decline

Author: Seto, Mabel, primary, Janve, Vaibhav A., additional, Logsdon, Benjamin A., additional, Mostafavi, Sara, additional, Dumitrescu, Logan, additional, Mahoney, Emily R., additional, Gaiteri, Chris, additional, Schneider, Julie A., additional, Bennett, David A., additional, De Jager, Philip L., additional, and Hohman, Timothy J., additional
Published: 2020
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41. Simultaneously Testing for Marginal Genetic Association and Gene-Environment Interaction

Author: Dai, James Y., Logsdon, Benjamin A., Huang, Ying, Hsu, Li, Reiner, Alexander P., Prentice, Ross L., and Kooperberg, Charles
Published: 2012
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42. A novel variational Bayes multiple locus Z-statistic for genome-wide association studies with Bayesian model averaging

Author: Logsdon, Benjamin A., Carty, Cara L., Reiner, Alexander P., Dai, James Y., and Kooperberg, Charles
Published: 2012
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43. The AD Knowledge Portal: A Repository for Multi‐Omic Data on Alzheimer's Disease and Aging

Author: Greenwood, Anna K., primary, Montgomery, Kelsey S., additional, Kauer, Nicole, additional, Woo, Kara H., additional, Leanza, Zoe J., additional, Poehlman, William L., additional, Gockley, Jake, additional, Sieberts, Solveig K., additional, Bradic, Ljubomir, additional, Logsdon, Benjamin A., additional, Peters, Mette A., additional, Omberg, Larsson, additional, and Mangravite, Lara M., additional
Published: 2020
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44. Meta-Analysis of the Alzheimer’s Disease Human Brain Transcriptome and Functional Dissection in Mouse Models

Author: Wan, Ying-Wooi, primary, Al-Ouran, Rami, additional, Mangleburg, Carl G., additional, Perumal, Thanneer M., additional, Lee, Tom V., additional, Allison, Katherine, additional, Swarup, Vivek, additional, Funk, Cory C., additional, Gaiteri, Chris, additional, Allen, Mariet, additional, Wang, Minghui, additional, Neuner, Sarah M., additional, Kaczorowski, Catherine C., additional, Philip, Vivek M., additional, Howell, Gareth R., additional, Martini-Stoica, Heidi, additional, Zheng, Hui, additional, Mei, Hongkang, additional, Zhong, Xiaoyan, additional, Kim, Jungwoo Wren, additional, Dawson, Valina L., additional, Dawson, Ted M., additional, Pao, Ping-Chieh, additional, Tsai, Li-Huei, additional, Haure-Mirande, Jean-Vianney, additional, Ehrlich, Michelle E., additional, Chakrabarty, Paramita, additional, Levites, Yona, additional, Wang, Xue, additional, Dammer, Eric B., additional, Srivastava, Gyan, additional, Mukherjee, Sumit, additional, Sieberts, Solveig K., additional, Omberg, Larsson, additional, Dang, Kristen D., additional, Eddy, James A., additional, Snyder, Phil, additional, Chae, Yooree, additional, Amberkar, Sandeep, additional, Wei, Wenbin, additional, Hide, Winston, additional, Preuss, Christoph, additional, Ergun, Ayla, additional, Ebert, Phillip J., additional, Airey, David C., additional, Mostafavi, Sara, additional, Yu, Lei, additional, Klein, Hans-Ulrich, additional, Carter, Gregory W., additional, Collier, David A., additional, Golde, Todd E., additional, Levey, Allan I., additional, Bennett, David A., additional, Estrada, Karol, additional, Townsend, T. Matthew, additional, Zhang, Bin, additional, Schadt, Eric, additional, De Jager, Philip L., additional, Price, Nathan D., additional, Ertekin-Taner, Nilüfer, additional, Liu, Zhandong, additional, Shulman, Joshua M., additional, Mangravite, Lara M., additional, and Logsdon, Benjamin A., additional
Published: 2020
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45. Multi-Tissue Neocortical Transcriptome-Wide Association Study Implicates 8 Genes Across 6 Genomic Loci in Alzheimer’s Disease

Author: Gockley, Jake, primary, Montgomery, Kelsey S., additional, Poehlman, William L., additional, Wiley, Jesse C., additional, Liu, Yue, additional, Gerasimov, Ekaterina, additional, Greenwood, Anna K, additional, Sieberts, Solveig K., additional, Wingo, Aliza P., additional, Wingo, Thomas S., additional, Mangravite, Lara M., additional, and Logsdon, Benjamin A., additional
Published: 2020
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46. Transcriptomic stratification of late-onset Alzheimer's cases reveals novel genetic modifiers of disease pathology

Author: Milind, Nikhil, primary, Preuss, Christoph, additional, Haber, Annat, additional, Ananda, Guruprasad, additional, Mukherjee, Shubhabrata, additional, John, Cai, additional, Shapley, Sarah, additional, Logsdon, Benjamin A., additional, Crane, Paul K., additional, and Carter, Gregory W., additional
Published: 2020
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47. Gene expression imputation across multiple brain regions provides insights into schizophrenia risk

Author: Huckins, Laura M, Dobbyn, Amanda, Ruderfer, Douglas M, Hoffman, Gabriel, Wang, Weiqing, Pardinas, Antonio F, Rajagopal, Veera M, Als, Thomas D, Nguyen, Hoang T, Girdhar, Kiran, Boocock, James, Roussos, Panos, Fromer, Menachem, Kramer, Robin, Domenici, Enrico, Gamazon, Eric R, Purcell, Shaun, Demontis, Ditte, Borglum, Anders D, Walters, James TR, O'Donovan, Michael C, Sullivan, Patrick, Owen, Michael J, Devlin, Bernie, Sieberts, Solveig K, Cox, Nancy J, Im, Hae Kyung, Sklar, Pamela, Stahl, Eli A, Johnson, Jessica S, Shah, Hardik R, Klein, Lambertus L, Dang, Kristen K, Logsdon, Benjamin A, Mahajan, Milind C, Mangravite, Lara M, Toyoshiba, Hiroyoshi, Gur, Raquel E, Hahn, Chang-Gyu, Schadt, Eric, Lewis, David A, Haroutunian, Vahram, Peters, Mette A, Lipska, Barbara K, Buxbaum, Joseph D, Hirai, Keisuke, Perumal, Thanneer M, Essioux, Laurent, Rajagopal, Veera Manikandan, Mattheisen, Manuel, Grove, Jakob, Werge, Thomas, Mortensen, Preben Bo, Pedersen, Carsten Bocker, Agerbo, Esben, Pedersen, Marianne Giortz, Mors, Ole, Nordentoft, Merete, Hougaard, David M, Bybjerg-Grauholm, Jonas, Baekvad-Hansen, Marie, Hansen, Christine Soholm, Ripke, Stephan, Neale, Benjamin M, Corvin, Aiden, Farh, Kai-How, Holmans, Peter A, Lee, Phil, Bulik-Sullivan, Brendan, Collier, David A, Huang, Hailiang, Pers, Tune H, Agartz, Ingrid, Albus, Margot, Alexander, Madeline, Amin, Farooq, Bacanu, Silviu A, Begemann, Martin, Jr, Belliveau Richard A, Bene, Judit, Bergen, Sarah E, Bevilacqua, Elizabeth, Bigdeli, Tim B, Black, Donald W, Bruggeman, Richard, Buccola, Nancy G, Buckner, Randy L, Byerley, William, Cahn, Wiepke, Cai, Guiqing, Campion, Dominique, Cantor, Rita M, Carr, Vaughan J, Carrera, Noa, Catts, Stanley V, Chambert, Kimberly D, Chan, Raymond CK, Chen, Ronald YL, Chen, Eric YH, Cheng, Wei, Cheung, Eric FC, Chong, Siow Ann, Cloninger, C Robert, Cohen, David, Cohen, Nadine, Cormican, Paul, Craddock, Nick, Crowley, James J, Curtis, David, Davidson, Michael, Davis, Kenneth L, Degenhardt, Franziska, Del Favero, Jurgen, Dikeos, Dimitris, Dinan, Timothy, Djurovic, Srdjan, Donohoe, Gary, Drapeau, Elodie, Duan, Jubao, Dudbridge, Frank, Durmishi, Naser, Eichhammer, Peter, Eriksson, Johan, Escott-Price, Valentina, Fanous, Ayman H, Farrell, Martilias S, Frank, Josef, Franke, Lude, Freedman, Robert, Freimer, Nelson B, Friedl, Marion, Friedman, Joseph I, Genovese, Giulio, Georgieva, Lyudmila, Giegling, Ina, Giusti-Rodriguez, Paola, Godard, Stephanie, Goldstein, Jacqueline I, Golimbet, Vera, Gopal, Srihari, Gratten, Jacob, de Haan, Lieuwe, Hammer, Christian, Hamshere, Marian L, Hansen, Mark, Hansen, Thomas, Hartmann, Annette M, Henskens, Frans A, Herms, Stefan, Hirschhorn, Joel N, Hoffmann, Per, Hofman, Andrea, Hollegaard, Mads V, Ikeda, Masashi, Joa, Inge, Julia, Antonio, Kahn, Rene S, Kalaydjieva, Luba, Karachanak-Yankova, Sena, Karjalainen, Juha, Kavanagh, David, Keller, Matthew C, Kennedy, James L, Khrunin, Andrey, Kim, Yunjung, Klovins, Janis, Knowles, James A, Konte, Bettina, Kucinskas, Vaidutis, Kucinskiene, Zita Ausrele, Kuzelova-Ptackova, Hana, Kahler, Anna K, Laurent, Claudine, Keong, Jimmy Lee Chee, Lee, S Hong, Legge, Sophie E, Lerer, Bernard, Li, Miaoxin, Li, Tao, Liang, Kung-Yee, Lieberman, Jeffrey, Limborska, Svetlana, Loughland, Carmel M, Lubinski, Jan, Lonnqvist, Jouko, Jr, Macek Milan, Magnusson, Patrik KE, Maher, Brion S, Maier, Wolfgang, Mallet, Jacques, Marsal, Sara, Mattingsdal, Morten, McCarley, Robert W, McDonald, Colm, McIntosh, Andrew M, Meier, Sandra, Meijer, Carin J, Melegh, Bela, Melle, Ingrid, Mesholam-Gately, Raquelle I, Metspalu, Andres, Michie, Patricia T, Milani, Lili, Milanova, Vihra, Mokrab, Younes, Morris, Derek W, Murphy, Kieran C, Murray, Robin M, Myin-Germeys, Inez, Muller-Myhsok, Bertram, Nelis, Mari, Nenadic, Igor, Nertney, Deborah A, Nestadt, Gerald, Nicodemus, Kristin K, Nikitina-Zake, Liene, Nisenbaum, Laura, Nordin, Annelie, O'Callaghan, Eadbhard, O'Dushlaine, Colm, O'Neill, F Anthony, Oh, Sang-Yun, Olincy, Ann, Olsen, Line, Van Os, Jim, Pantelis, Christos, Papadimitriou, George N, Papiol, Sergi, Parkhomenko, Elena, Pato, Michele T, Paunio, Tiina, Pejovic-Milovancevic, Milica, Perkins, Diana O, Pietilainen, Olli, Pimm, Jonathan, Pocklington, Andrew J, Powell, John, Price, Alkes, Pulver, Ann E, Purcell, Shaun M, Quested, Digby, Rasmussen, Henrik B, Reichenberg, Abraham, Reimers, Mark A, Richards, Alexander L, Roffman, Joshua L, Salomaa, Veikko, Sanders, Alan R, Schall, Ulrich, Schubert, Christian R, Schulze, Thomas G, Schwab, Sibylle G, Scolnick, Edward M, Scott, Rodney J, Seidman, Larry J, Shi, Jianxin, Sigurdsson, Engilbert, Silagadze, Teimuraz, Silverman, Jeremy M, Sim, Kang, Slominsky, Petr, Smoller, Jordan W, So, Hon-Cheong, Spencer, Chris CA, Stefansson, Hreinn, Steinberg, Stacy, Stogmann, Elisabeth, Straub, Richard E, Strengman, Eric, Strohmaier, Jana, Stroup, T Scott, Subramaniam, Mythily, Suvisaari, Jaana, Svrakic, Dragan M, Szatkiewicz, Jin P, Soderman, Erik, Thirumalai, Srinivas, Toncheva, Draga, Tosato, Sarah, Veijola, Juha, Waddington, John, Walsh, Dermot, Wang, Dai, Wang, Qiang, Webb, Bradley T, Weiser, Mark, Wildenauer, Dieter B, Williams, Nigel M, Williams, Stephanie, Witt, Stephanie H, Wolen, Aaron R, Wong, Emily HM, Wormley, Brandon K, Xi, Hualin Simon, Zai, Clement C, Zheng, Xuebin, Zimprich, Fritz, Wray, Naomi R, Stefansson, Kari, Visscher, Peter M, Adolfsson, Rolf, Andreassen, Ole A, Blackwood, Douglas HR, Bramon, Elvira, Cichon, Sven, Darvasi, Ariel, Ehrenreich, Hannelore, Esko, Tonu, Gejman, Pablo V, Gill, Michael, Gurling, Hugh, Hultman, Christina M, Iwata, Nakao, Jablensky, Assen V, Jonsson, Erik G, Kendler, Kenneth S, Kirov, George, Knight, Jo, Lencz, Todd, Levinson, Douglas F, Li, Qingqin S, Liu, Jianjun, Malhotra, Anil K, McCarroll, Steven A, McQuillin, Andrew, Moran, Jennifer L, Mortensen, Preben B, Mowry, Bryan J, Nothen, Markus M, Ophoff, Roel A, Palotie, Aarno, Pato, Carlos N, Petryshen, Tracey L, Posthuma, Danielle, Rietschel, Marcella, Riley, Brien P, Rujescu, Dan, Sham, Pak C, St Clair, David, Weinberger, Daniel R, Wendland, Jens R, Daly, Mark J, Sullivan, Patrick F, Consortium, CommonMind, Consortium, Psychiat Genomics, Working, iPSYCH-GEMS Schizophrenia, Child and Adolescent Psychiatry / Psychology, ANS - Complex Trait Genetics, APH - Mental Health, Adult Psychiatry, Perceptual and Cognitive Neuroscience (PCN), Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI), Clinical Cognitive Neuropsychiatry Research Program (CCNP), Stem Cell Aging Leukemia and Lymphoma (SALL), Complex Trait Genetics, Amsterdam Neuroscience - Complex Trait Genetics, CommonMind Consortium, Psychiat Genomics Consortium, iPSYCH-GEMS Schizophrenia Working, Huckins, LM, Dobbyn, A, Ruderfer, DM, Hoffman, G, Lee, SH, Im, HK, iPSYCH-GEMS Schizophrenia Working Group, The Schizophrenia Working Group of the PsyUniversity of Copenhagenchiatric Genomics, Amsterdam Reproduction & Development (AR&D), Human genetics, RS: MHeNs - R2 - Mental Health, Psychiatrie & Neuropsychologie, and MUMC+: Hersen en Zenuw Centrum (3)
Subjects: DISORDER, Schizophrenia/genetics, iPSYCH-GEMS Schizophrenia Working Group, CHILDHOOD, Gene Expression, Genome-wide association study, VARIANTS, MOUSE, Medical and Health Sciences, ACUTE INTERMITTENT PORPHYRIA, Genome-wide association studies, 0302 clinical medicine, CommonMind Consortium, 2.1 Biological and endogenous factors, Aetiology, Prefrontal cortex, 0303 health sciences, Schizophrenia Working Group of the Psychiatric Genomics Consortium, Schizophrenia Working Group of the PsyUniversity of Copenhagenchiatric Genomics Consortium, Brain, Case-Control Studies, Genetic Predisposition to Disease, Genome-Wide Association Study, Genotype, Humans, Polymorphism, Single Nucleotide, Quantitative Trait Loci, Risk, Schizophrenia, Transcriptome, Single Nucleotide, ASSOCIATION, Transcriptome/genetics, Biological Sciences, Polymorphism, Single Nucleotide/genetics, Mental Health, Genome-Wide Association Study/methods, Medical genetics, TRAITS, Psychosis, medicine.medical_specialty, Computational biology, Quantitative trait locus, Biology, Article, 03 medical and health sciences, PSYCHOSIS, SDG 3 - Good Health and Well-being, medicine, Genetics, Polymorphism, Transcriptomics, Gene, 030304 developmental biology, Brain/physiopathology, Human Genome, medicine.disease, Brain Disorders, Gene Expression/genetics, COGNITIVE DEFICITS, Expression quantitative trait loci, Human medicine, Gene expression, Quantitative Trait Loci/genetics, 030217 neurology & neurosurgery, Imputation (genetics), Developmental Biology
Abstract: Transcriptomic imputation approaches combine eQTL reference panels with large-scale genotype data in order to test associations between disease and gene expression. These genic associations could elucidate signals in complex genome-wide association study (GWAS) loci and may disentangle the role of different tissues in disease development. We used the largest eQTL reference panel for the dorso-lateral prefrontal cortex (DLPFC) to create a set of gene expression predictors and demonstrate their utility. We applied DLPFC and 12 GTEx-brain predictors to 40,299 schizophrenia cases and 65,264 matched controls for a large transcriptomic imputation study of schizophrenia. We identified 413 genic associations across 13 brain regions. Stepwise conditioning identified 67 non-MHC genes, of which 14 did not fall within previous GWAS loci. We identified 36 significantly enriched pathways, including hexosaminidase-A deficiency, and multiple porphyric disorder pathways. We investigated developmental expression patterns among the 67 non-MHC genes and identified specific groups of pre- and postnatal expression. Working Group The Schizophrenia Working Group of the Psychiatric Genomics Consortium Stephan Ripke37,38 Benjamin M. Neale37,38,39,40 Aiden Corvin41 James T. R. Walters6 Kai-How Farh37 Peter A. Holmans6,42 Phil Lee37,38,40 Brendan Bulik-Sullivan37,38 David A. Collier43,44 Hailiang Huang37,39 Tune H. Pers39,45,46 Ingrid Agartz47,48,49 Esben Agerbo8,32,33 Margot Albus50 Madeline Alexander51 Farooq Amin52,53 Silviu A. Bacanu54 Martin Begemann55 Richard A. Belliveau Jr38 Judit Bene56,57 Sarah E. Bergen38,58 Elizabeth Bevilacqua38 Tim B. Bigdeli54 Donald W. Black59 Richard Bruggeman60 Nancy G. Buccola61 Randy L. Buckner62,63,64 William Byerley65 Wiepke Cahn66 Guiqing Cai2,3 Dominique Campion67 Rita M. Cantor10 Vaughan J. Carr68,69 Noa Carrera6 Stanley V. Catts68,70 Kimberly D. Chambert38 Raymond C. K. Chan71 Ronald Y. L. Chen72 Eric Y. H. Chen72,73 Wei Cheng15 Eric F. C. Cheung74 Siow Ann Chong75 C. Robert Cloninger76 David Cohen77 Nadine Cohen78 Paul Cormican41 Nick Craddock6,42 James J. Crowley79 David Curtis80,81 Michael Davidson82 Kenneth L. Davis3 Franziska Degenhardt83,84 Jurgen Del Favero85 Ditte Demontis7,8,9 Dimitris Dikeos86 Timothy Dinan87 Srdjan Djurovic49,88 Gary Donohoe41,89 Elodie Drapeau3 Jubao Duan90,91 Frank Dudbridge92 Naser Durmishi93 Peter Eichhammer94 Johan Eriksson95,96,97 Valentina Escott-Price6 Laurent Essioux98 Ayman H. Fanous99,100,101,102 Martilias S. Farrell79 Josef Frank103 Lude Franke104 Robert Freedman105 Nelson B. Freimer106 Marion Friedl107 Joseph I. Friedman3 Menachem Fromer1,37,38,40 Giulio Genovese38 Lyudmila Georgieva6 Ina Giegling107,108 Paola Giusti-Rodríguez79 Stephanie Godard109 Jacqueline I. Goldstein37,39 Vera Golimbet110 Srihari Gopal111 Jacob Gratten112 Lieuwe de Haan113 Christian Hammer55 Marian L. Hamshere6 Mark Hansen114 Thomas Hansen8,30 Vahram Haroutunian3,25,23 Annette M. Hartmann107 Frans A. Henskens68,115,116 Stefan Herms83,84,117 Joel N. Hirschhorn39,46,118 Per Hoffmann83,84,117 Andrea Hofman83,84 Mads V. Hollegaard36 David M. Hougaard36 Masashi Ikeda119 Inge Joa120 Antonio Julia121 Rene S. Kahn66 Luba Kalaydjieva122,123 Sena Karachanak-Yankova124 Juha Karjalainen104 David Kavanagh6 Matthew C. Keller125 James L. Kennedy126,127,128 Andrey Khrunin129 Yunjung Kim79 Janis Klovins130 James A. Knowles131 Bettina Konte107 Vaidutis Kucinskas132 Zita Ausrele Kucinskiene132 Hana Kuzelova-Ptackova133 Anna K. Kahler58 Claudine Laurent51,134 Jimmy Lee Chee Keong75,135 S. Hong Lee112 Sophie E. Legge6 Bernard Lerer136 Miaoxin Li72,73,137 Tao Li138 Kung-Yee Liang139 Jeffrey Lieberman140 Svetlana Limborska129 Carmel M. Loughland68,141 Jan Lubinski142 Jouko Lonnqvist143 Milan Macek Jr133 Patrik K. E. Magnusson58 Brion S. Maher144 Wolfgang Maier145 Jacques Mallet146 Sara Marsal121 Manuel Mattheisen7,8,9,147 Morten Mattingsdal49,148 Robert W. McCarley149,150 Colm McDonald151 Andrew M. McIntosh152,153 Sandra Meier103 Carin J. Meijer113 Bela Melegh56,57 Ingrid Melle49,154 Raquelle I. Mesholam-Gately149,155 Andres Metspalu156 Patricia T. Michie68,157 Lili Milani156 Vihra Milanova158 Younes Mokrab43 Derek W. Morris41,89 Ole Mors8,9,159 Kieran C. Murphy160 Robin M. Murray161 Inez Myin-Germeys162 Bertram Muller-Myhsok163,164,165 Mari Nelis156 Igor Nenadic166 Deborah A. Nertney167 Gerald Nestadt168 Kristin K. Nicodemus169 Liene Nikitina-Zake130 Laura Nisenbaum170 Annelie Nordin171 Eadbhard O’Callaghan172 Colm O’Dushlaine38 F. Anthony O’Neill173 Sang-Yun Oh174 Ann Olincy126 Line Olsen8,64 Jim Van Os162,175 Christos Pantelis68,176 George N. Papadimitriou86 Sergi Papiol55 Elena Parkhomenko3 Michele T. Pato131 Tiina Paunio177,178 Milica Pejovic-Milovancevic179 Diana O. Perkins180 Olli Pietiläinen178,181 Jonathan Pimm81 Andrew J. Pocklington6 John Powell161 Alkes Price39,182 Ann E. Pulver168 Shaun M. Purcell1 Digby Quested183 Henrik B. Rasmussen30,43 Abraham Reichenberg3 Mark A. Reimers184 Alexander L. Richards6 Joshua L. Roffman62,64 Panos Roussos1,4 Douglas M. Ruderfer1,5,6 Veikko Salomaa97 Alan R. Sanders90,91 Ulrich Schall68,141 Christian R. Schubert185 Thomas G. Schulze103,186 Sibylle G. Schwab187 Edward M. Scolnick38 Rodney J. Scott68,188,189 Larry J. Seidman144,155 Jianxin Shi190 Engilbert Sigurdsson191 Teimuraz Silagadze192 Jeremy M. Silverman3,193 Kang Sim75 Petr Slominsky129 Jordan W. Smoller38,40 Hon-Cheong So72 Chris C. A. Spencer194 Eli A. Stahl1,2,3,4 Hreinn Stefansson195 Stacy Steinberg195 Elisabeth Stogmann196 Richard E. Straub197 Eric Strengman66,198 Jana Strohmaier103 T. Scott Stroup140 Mythily Subramaniam75 Jaana Suvisaari143 Dragan M. Svrakic76 Jin P. Szatkiewicz79 Erik Soderman47 Srinivas Thirumalai199 Draga Toncheva124 Sarah Tosato200 Juha Veijola201,202 John Waddington203 Dermot Walsh204 Dai Wang111 Qiang Wang138 Bradley T. Webb54 Mark Weiser82 Dieter B. Wildenauer205 Nigel M. Williams6 Stephanie Williams79 Stephanie H. Witt103 Aaron R. Wolen184 Emily H. M. Wong72 Brandon K. Wormley54 Hualin Simon Xi206 Clement C. Zai126,127 Xuebin Zheng207 Fritz Zimprich196 Naomi R. Wray112 Kari Stefansson195 Peter M. Visscher112 Rolf Adolfsson171 Ole A. Andreassen49,154 Douglas H. R. Blackwood153 Elvira Bramon208 Joseph D. Buxbaum2,3,24,25 Anders D. Børglum7,8,9,159 Sven Cichon83,84,117,209 Ariel Darvasi210 Enrico Domenici211 Hannelore Ehrenreich55 Tonu Esko39,46,118,156 Pablo V. Gejman90,91 Michael Gill41 Hugh Gurling81 Christina M. Hultman58 Nakao Iwata119 Assen V. Jablensky68,123,205,212 Erik G. Jonsson47,49 Kenneth S. Kendler213 George Kirov6 Jo Knight125,127,128 Todd Lencz214,215,216 Douglas F. Levinson51 Qingqin S. Li111 Jianjun Liu207,217 Anil K. Malhotra214,215,216 Steven A. McCarroll38,118 Andrew McQuillin81 Jennifer L. Moran38 Preben B. Mortensen8,32,33 Bryan J. Mowry112,218 Markus M. Nothen83,84 Roel A. Ophoff10,66,105 Michael J. Owen6,42 Aarno Palotie38,40,181 Carlos N. Pato131 Tracey L. Petryshen38,149,219 Danielle Posthuma220,221,222 Marcella Rietschel103 Brien P. Riley213 Dan Rujescu107,108 Pak C. Sham72,73,137 Pamela Sklar1,2,3,4,25 David St Clair223 Daniel R. Weinberger197,224 Jens R. Wendland185 Thomas Werge8,30,225 Mark J. Daly37,38,39 Patrick F. Sullivan58,79,180 Michael C. O’Donovan6,42 20Integrated Technology Research Laboratories, Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, Fujisawa, Japan. 21Neuropsychiatry Section, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. 22Neuropsychiatric Signaling Program, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. 23Psychiatry, JJ Peters Virginia Medical Center, Bronx, NY, USA. 24Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, NY, USA. 25Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA. 26Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA. 27CNS Drug Discovery Unit, Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, Fujisawa, Japan. 28F. Hoffman-La Roche Ltd, Basel, Switzerland. 29Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark. 30Institute of Biological Psychiatry, MHC Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark. 31Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark. 32National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark. 33Centre for Integrated Registerbased Research, Aarhus University, Aarhus, Denmark. 34Psychosis Research Unit, Aarhus University Hospital, Risskov, Denmark. 35Mental Health Services in the Capital Region of Denmark, Mental Health Center Copenhagen, University of Copenhagen, Copenhagen, Denmark. 36Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark. 37Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA. 38Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA. 39Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA. 40Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, USA. 41Neuropsychiatric Genetics Research Group, Department of Psychiatry, Trinity College Dublin, Dublin, Ireland. 42NationalCentre for Mental Health, Cardiff University, Cardiff, UK. 43Eli Lilly and Company Limited, Erl Wood Manor, Sunninghill Road, Windlesham, Surrey, UK. 44Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King’s College London, London, UK. 45Center for BiologicalSequence Analysis, Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark. 46Division of Endocrinology and Center for Basic and Translational Obesity Research, Boston Children’s Hospital, Boston, MA, USA. 47Department of Clinical Neuroscience, Psychiatry Section, Karolinska Institutet, Stockholm, Sweden. 48Department of Psychiatry, Diakonhjemmet Hospital, Oslo, Norway. 49NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway. 50State Mental Hospital, Haar, Germany. 51Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA. 52Department of Psychiatry and Behavioral Sciences, Atlanta Veterans Affairs Medical Center, Atlanta, GA, USA. 53Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, USA. 54Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA. 55Clinical Neuroscience, Max Planck Institute of Experimental Medicine, Gottingen, Germany. 56Department of Medical Genetics, University of Pécs, Pécs, Hungary. 57Szentagothai Research Center, University of Pécs, Pécs, Hungary. 58Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden. 59Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, USA. 60University Medical Center Groningen, Department of Psychiatry, University of Groningen, Groningen, the Netherlands. 61School of Nursing, Louisiana State University Health Sciences Center, New Orleans, LA, USA. 62Athinoula A. Martinos Center, Massachusetts General Hospital, Boston, MA, USA. 63Center for Brain Science, Harvard University, Cambridge, MA, USA. 64Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA. 65Department of Psychiatry, University of California at San Francisco, San Francisco, CA, USA. 66University Medical Center Utrecht, Department of Psychiatry, Rudolf Magnus Institute of Neuroscience, Utrecht, the Netherlands. 67Centre Hospitalier du Rouvray and INSERM U1079 Faculty of Medicine, Rouen, France. 68Schizophrenia Research Institute, Sydney, New South Wales, Australia. 69School of Psychiatry, University of New South Wales, Sydney, New South Wales, Australia. 70Royal Brisbane and Women’s Hospital, University of Queensland, Brisbane, Queensland, Australia. 71Institute of Psychology, Chinese Academy of Science, Beijing, China. 72Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China. 73State Key Laboratory for Brain and Cognitive Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China. 74Castle Peak Hospital, Hong Kong, China. 75Institute of Mental Health, Singapore, Singapore. 76Department of Psychiatry, Washington University, St. Louis, MO, USA. 77Department of Child and Adolescent Psychiatry, Assistance Publique Hopitaux de Paris, Pierre and Marie Curie Faculty of Medicine and Institute for Intelligent Systems and Robotics, Paris, France. 78Blue Note Biosciences, Princeton, NJ, USA. 79Department of Genetics, University of North Carolina, Chapel Hill, NC, USA. 80Department of Psychological Medicine, Queen Mary University of London, London, UK. 81Molecular Psychiatry Laboratory, Division of Psychiatry, University College London, London, UK. 82Sheba Medical Center, Tel Hashomer, Israel. 83Department of Genomics, Life and Brain Center, Bonn, Germany. 84Institute of Human Genetics, University of Bonn, Bonn, Germany. 85AppliedMolecular Genomics Unit, VIB Department of Molecular Genetics, University of Antwerp, Antwerp, Belgium. 86First Department of Psychiatry, University of Athens Medical School, Athens, Greece. 87Department of Psychiatry, University College Cork, Co, Cork, Ireland. 88Department of Medical Genetics, Oslo University Hospital, Oslo, Norway. 89Cognitive Genetics and Therapy Group, School of Psychology and Discipline of Biochemistry, National University of Ireland Galway, Co, Galway, Ireland. 90Department of Psychiatry and Behavioral Neuroscience, University of Chicago, Chicago, IL, USA. 91Department of Psychiatry and Behavioral Sciences, North Shore University Health System, Evanston, IL, USA. 92Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK. 93Department of Child and Adolescent Psychiatry, University Clinic of Psychiatry, Skopje, Republic of Macedonia. 94Department of Psychiatry, University of Regensburg, Regensburg, Germany. 95Department of General Practice, Helsinki University Central Hospital, University of Helsinki, Helsinki, Finland. 96Folkhälsan Research Center, Helsinki, Finland, Biomedicum Helsinki, Helsinki, Finland. 97National Institute for Health and Welfare, Helsinki, Finland. 98Translational Technologies and Bioinformatics, Pharma Research and Early Development, F. Hoffman-La Roche, Basel, Switzerland. 99Department of Psychiatry, Georgetown University School of Medicine, Washington, DC, USA. 100Department of Psychiatry, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA. 101Department of Psychiatry, Virginia Commonwealth University School of Medicine, Richmond, VA, USA. 102Mental Health Service Line, Washington VA Medical Center, Washington, DC, USA. 103Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Heidelberg, Mannheim, Germany. 104Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands. 105Department of Psychiatry, University of Colorado Denver, Aurora, CO, USA. 106Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA, USA. 107Department of Psychiatry, University of Halle, Halle, Germany. 108Department of Psychiatry, University of Munich, Munich, Germany. 109Departments of Psychiatry and Human and Molecular Genetics, INSERM, Institut de Myologie, Hôpital de la Pitiè-Salpêtrière, Paris, France. 110Mental Health Research Centre, Russian Academy of Medical Sciences, Moscow, Russia. 111Neuroscience Therapeutic Area, Janssen Research and Development, Raritan, NJ, USA. 112Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia. 113Academic Medical Centre University of Amsterdam, Department of Psychiatry, Amsterdam, the Netherlands. 114Illumina, La Jolla, CA, USA. 115Priority Research Centre for Health Behaviour, University of Newcastle, Newcastle, New South Wales, Australia. 116School of Electrical Engineering and Computer Science, University of Newcastle, Newcastle, New South Wales, Australia. 117Division of Medical Genetics, Department of Biomedicine, University of Basel, Basel, Switzerland. 118Department of Genetics, Harvard Medical School, Boston, MA, USA. 119Department of Psychiatry, Fujita Health University School of Medicine, Toyoake, Japan. 120Regional Centre for Clinical Researchin Psychosis, Department of Psychiatry, Stavanger University Hospital, Stavanger, Norway. 121Rheumatology Research Group, Vall d’Hebron Research Institute, Barcelona, Spain. 122Centre for Medical Research, The University of Western Australia, Perth, Western Australia, Australia. 123The Perkins Institute for Medical Research, The University of Western Australia, Perth, Western Australia, Australia. 124Department of Medical Genetics, Medical University, Sofia, Bulgaria. 125Department of Psychology, University of Colorado Boulder, Boulder, CO, USA. 126Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada. 127Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada. 128Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada. 129Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia. 130Latvian Biomedical Research and Study Centre, Riga, Latvia. 131Department of Psychiatry and Zilkha Neurogenetics Institute, Keck School of Medicine at University of Southern California, Los Angeles, CA, USA. 132Faculty of Medicine, Vilnius University, Vilnius, Lithuania. 133Department of Biology and Medical Genetics, 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic. 134Department of Child and Adolescent Psychiatry, Pierre and Marie Curie Faculty of Medicine, Paris, France. 135Duke-NUS Graduate Medical School, Singapore, Singapore. 136Department of Psychiatry, Hadassah-Hebrew University Medical Center, Jerusalem, Israel. 137Centre for Genomic Sciences, The University of Hong Kong, Hong Kong, China. 138Mental Health Centre and Psychiatric Laboratory, West China Hospital, Sichuan University, Chengdu, Sichuan, China. 139Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA. 140Department of Psychiatry, Columbia University, New York, New York, NY, USA. 141Priority Centre for Translational Neuroscience and Mental Health, University of Newcastle, Newcastle, New South Wales, Australia. 142Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University in Szczecin, Szczecin, Poland. 143Department of Mental Health and Substance Abuse Services, National Institute for Health and Welfare, Helsinki, Finland. 144Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA. 145Department of Psychiatry, University of Bonn, Bonn, Germany. 146Centre National de la Recherche Scientifique, Laboratoire de Génétique Moléculaire de la Neurotransmission et des Processus Neurodénégératifs, Hôpital de la Pitiè-Salpêtrière, Paris, France. 147Department of Genomics Mathematics, University of Bonn, Bonn, Germany. 148Research Unit, Sørlandet Hospital, Kristiansand, Norway. 149Department of Psychiatry, Harvard Medical School, Boston, MA, USA. 150VA Boston Health Care System, Brockton, MA, USA. 151Department of Psychiatry, National University of Ireland Galway, Co, Galway, Ireland. 152Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK. 153Division of Psychiatry, University of Edinburgh, Edinburgh, UK. 154Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway. 155Massachusetts Mental Health Center Public Psychiatry Division of the Beth Israel Deaconess Medical Center, Boston, MA, USA. 156Estonian Genome Center, University of Tartu, Tartu, Estonia. 157School of Psychology, University of Newcastle, Newcastle, New South Wales, Australia. 158First Psychiatric Clinic, Medical University, Sofia, Bulgaria. 159Department P, Aarhus University Hospital, Risskov, Denmark. 160Department of Psychiatry, Royal College of Surgeons in Ireland, Dublin, Ireland. 161King’s College London, London, UK. 162Maastricht University Medical Centre, South Limburg Mental Health Research and TeachingNetwork, EURON, Maastricht, the Netherlands. 163Institute of Translational Medicine, University of Liverpool, Liverpool, UK. 164Max Planck Institute of Psychiatry, Munich, Germany. 165Munich Cluster for Systems Neurology (SyNergy), Munich, Germany. 166Department of Psychiatry and Psychotherapy, Jena University Hospital, Jena, Germany. 167Department of Psychiatry, Queensland Brain Institute and Queensland Centre for Mental Health Research, University of Queensland, Brisbane, Queensland, Australia. 168Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA. 169Department of Psychiatry, Trinity College Dublin, Dublin, Ireland. 170Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN, USA. 171Department of Clinical Sciences, Psychiatry, Umeå University, Umeå, Sweden. 172DETECT Early Intervention Service for Psychosis, Blackrock, Co, Dublin, Ireland. 173Centre for Public Health, Institute of Clinical Sciences, Queen’s University Belfast, Belfast, UK. 174Lawrence Berkeley National Laboratory, University of California at Berkeley, Berkeley, CA, USA. 175Institute of Psychiatry, King’s College London, London, UK. 176Melbourne Neuropsychiatry Centre, University of Melbourne & Melbourne Health, Melbourne, Victoria, Australia. 177Department of Psychiatry, University of Helsinki, Helsinki, Finland. 178Public Health Genomics Unit, National Institute for Health and Welfare, Helsinki, Finland. 179Medical Faculty, University of Belgrade, Belgrade, Serbia. 180Department of Psychiatry, University of North Carolina, Chapel Hill, NC, USA. 181Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Helsinki, Finland. 182Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA. 183Department of Psychiatry, University of Oxford, Oxford, UK. 184Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, USA. 185Pharma Therapeutics Clinical Research, Pfizer Worldwide Research and Development, Cambridge, MA, USA. 186Department of Psychiatry and Psychotherapy, University of Gottingen, Göttingen, Germany. 187Psychiatry and Psychotherapy Clinic, University of Erlangen, Erlangen, Germany. 188Hunter New England Health Service, Newcastle, New South Wales, Australia. 189School of Biomedical Sciences, University of Newcastle, Newcastle, New South Wales, Australia. 190Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA. 191University of Iceland, Landspitali, National University Hospital, Reykjavik, Iceland. 192Department of Psychiatry and Drug Addiction, Tbilisi State Medical University (TSMU), Tbilisi, Georgia. 193Research and Development, Bronx Veterans Affairs Medical Center, New York, NY, USA. 194WellcomeTrust Centre for Human Genetics, Oxford, UK. 195deCODE Genetics, Reykjavik, Iceland. 196Department of Clinical Neurology, Medical University of Vienna, Wien, Austria. 197Lieber Institute for Brain Development, Baltimore, MD, USA. 198Department of Medical Genetics, University Medical Centre Utrecht, Utrecht, the Netherlands. 199Berkshire Healthcare NHS Foundation Trust, Bracknell, UK. 200Section of Psychiatry, University of Verona, Verona, Italy. 201Department of Psychiatry, University of Oulu, Oulu, Finland. 202University Hospital of Oulu, Oulu, Finland. 203Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland. 204Health Research Board, Dublin, Ireland. 205School of Psychiatry and Clinical Neurosciences, The University of Western Australia, Perth, Western Australia, Australia. 206Computational Sciences CoE, Pfizer Worldwide Research and Development, Cambridge, MA, USA. 207Human Genetics, Genome Institute of Singapore, A*STAR, Singapore, Singapore. 208University College London, London, UK. 209Institute of Neuroscience and Medicine (INM-1), Research Center Juelich, Juelich, Germany. 210Department of Genetics, The Hebrew University of Jerusalem, Jerusalem, Israel. 211NeuroscienceDiscovery and Translational Area, Pharma Research and Early Development, F. Hoffman-La Roche, Basel, Switzerland. 212Centre for Clinical Research in Neuropsychiatry, School of Psychiatry and Clinical Neurosciences, The University of Western Australia, Medical Research Foundation Building, Perth, Western Australia, Australia. 213Virginia Institute for Psychiatric and Behavioral Genetics, Departments of Psychiatry and Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA, USA. 214The Feinstein Institute for Medical Research, Manhasset, NY, USA. 215The Hofstra NS-LIJ School of Medicine, Hempstead, NY, USA. 216The Zucker Hillside Hospital, Glen Oaks, NY, USA. 217Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore. 218Queensland Centre for Mental Health Research, University of Queensland, Brisbane, Queensland, Australia. 219Center for HumanGenetic Research and Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA. 220Department of Child and Adolescent Psychiatry, Erasmus University Medical Centre, Rotterdam, the Netherlands. 221Department of Complex Trait Genetics, Neuroscience Campus Amsterdam, VU University Medical Center Amsterdam, Amsterdam, the Netherlands. 222Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, Amsterdam, the Netherlands. 223University of Aberdeen, Institute of Medical Sciences, Aberdeen, UK. 224Departments of Psychiatry, Neurology, Neuroscience and Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA. 225Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark.
Published: 2019

48. Gene expression imputation across multiple brain regions provides insights into schizophrenia risk

Author: Huckins, Laura M. Dobbyn, Amanda Ruderfer, Douglas M. and Hoffman, Gabriel Wang, Weiqing Pardinas, Antonio F. and Rajagopal, Veera M. Als, Thomas D. Nguyen, Hoang T. Girdhar, Kiran Boocock, James Roussos, Panos Fromer, Menachem and Kramer, Robin Domenici, Enrico Gamazon, Eric R. Purcell, Shaun Demontis, Ditte Borglum, Anders D. Walters, James T. R. O'Donovan, Michael C. Sullivan, Patrick Owen, Michael J. and Devlin, Bernie Sieberts, Solveig K. Cox, Nancy J. Im, Hae Kyung Sklar, Pamela Stahl, Eli A. Johnson, Jessica S. and Shah, Hardik R. Klein, Lambertus L. Dang, Kristen K. and Logsdon, Benjamin A. Mahajan, Milind C. Mangravite, Lara M. and Toyoshiba, Hiroyoshi Gur, Raquel E. Hahn, Chang-Gyu Schadt, Eric Lewis, David A. Haroutunian, Vahram Peters, Mette A. and Lipska, Barbara K. Buxbaum, Joseph D. Hirai, Keisuke and Perumal, Thanneer M. Essioux, Laurent Rajagopal, Veera Manikandan Mattheisen, Manuel Grove, Jakob Werge, Thomas and Mortensen, Preben Bo Pedersen, Carsten Bocker Agerbo, Esben and Pedersen, Marianne Giortz Mors, Ole Nordentoft, Merete and Hougaard, David M. Bybjerg-Grauholm, Jonas Baekvad-Hansen, Marie and Hansen, Christine Soholm Ripke, Stephan Neale, Benjamin M. and Corvin, Aiden Farh, Kai-How Holmans, Peter A. Lee, Phil and Bulik-Sullivan, Brendan Collier, David A. Huang, Hailiang and Pers, Tune H. Agartz, Ingrid Albus, Margot Alexander, Madeline Amin, Farooq Bacanu, Silviu A. Begemann, Martin and Belliveau, Jr., Richard A. Bene, Judit Bergen, Sarah E. and Bevilacqua, Elizabeth Bigdeli, Tim B. Black, Donald W. and Bruggeman, Richard Buccola, Nancy G. Buckner, Randy L. and Byerley, William Cahn, Wiepke Cai, Guiqing Campion, Dominique Cantor, Rita M. Carr, Vaughan J. Carrera, Noa and Catts, V, Stanley Chambert, Kimberly D. Chan, Raymond C. K. and Chen, Ronald Y. L. Chen, Eric Y. H. Cheng, Wei Cheung, Eric F. C. Chong, Siow Ann Cloninger, C. Robert Cohen, David and Cohen, Nadine Cormican, Paul Craddock, Nick Crowley, James J. Curtis, David Davidson, Michael Davis, Kenneth L. and Degenhardt, Franziska Del Favero, Jurgen Dikeos, Dimitris and Dinan, Timothy Djurovic, Srdjan Donohoe, Gary Drapeau, Elodie Duan, Jubao Dudbridge, Frank Durmishi, Naser and Eichhammer, Peter Eriksson, Johan Escott-Price, Valentina and Essioux, Laurent Fanous, Ayman H. Farrell, Martilias S. and Frank, Josef Franke, Lude Freedman, Robert Freimer, Nelson B. Friedl, Marion Friedman, I, Joseph Fromer, Menachem and Genovese, Giulio Georgieva, Lyudmila Giegling, Ina and Giusti-Rodriguez, Paola Godard, Stephanie Goldstein, I, Jacqueline Golimbet, Vera Gopal, Srihari Gratten, Jacob and de Haan, Lieuwe Hammer, Christian Hamshere, Marian L. and Hansen, Mark Hansen, Thomas Haroutunian, Vahram Hartmann, Annette M. Henskens, Frans A. Herms, Stefan Hirschhorn, Joel N. Hoffmann, Per Hofman, Andrea Hollegaard, V, Mads and Ikeda, Masashi Joa, Inge Julia, Antonio Kahn, Rene S. and Kalaydjieva, Luba Karachanak-Yankova, Sena Karjalainen, Juha and Kavanagh, David Keller, Matthew C. Kennedy, James L. and Khrunin, Andrey Kim, Yunjung Klovins, Janis Knowles, James A. Konte, Bettina Kucinskas, Vaidutis Kucinskiene, Zita Ausrele Kuzelova-Ptackova, Hana Kahler, Anna K. Laurent, Claudine Keong, Jimmy Lee Chee Lee, S. Hong Legge, Sophie E. and Lerer, Bernard Li, Miaoxin Li, Tao Liang, Kung-Yee and Lieberman, Jeffrey Limborska, Svetlana Loughland, Carmel M. and Lubinski, Jan Lonnqvist, Jouko Macek, Jr., Milan Magnusson, Patrik K. E. Maher, Brion S. Maier, Wolfgang Mallet, Jacques and Marsal, Sara Mattingsdal, Morten McCarley, Robert W. and McDonald, Colm McIntosh, Andrew M. Meier, Sandra Meijer, Carin J. Melegh, Bela Melle, Ingrid Mesholam-Gately, I, Raquelle Metspalu, Andres Michie, Patricia T. Milani, Lili and Milanova, Vihra Mokrab, Younes Morris, Derek W. Mors, Ole Murphy, Kieran C. Murray, Robin M. Myin-Germeys, Inez and Muller-Myhsok, Bertram Nelis, Mari Nenadic, Igor and Nertney, Deborah A. Nestadt, Gerald Nicodemus, Kristin K. and Nikitina-Zake, Liene Nisenbaum, Laura Nordin, Annelie and O'Callaghan, Eadbhard O'Dushlaine, Colm O'Neill, F. Anthony and Oh, Sang-Yun Olincy, Ann Olsen, Line Van Os, Jim and Pantelis, Christos Papadimitriou, George N. Papiol, Sergi and Parkhomenko, Elena Pato, Michele T. Paunio, Tiina and Pejovic-Milovancevic, Milica Perkins, Diana O. Pietilainen, Olli and Pimm, Jonathan Pocklington, Andrew J. Powell, John and Price, Alkes Pulver, Ann E. Purcell, Shaun M. Quested, Digby and Rasmussen, Henrik B. Reichenberg, Abraham Reimers, Mark A. and Richards, Alexander L. Roffman, Joshua L. Ruderfer, Douglas M. Salomaa, Veikko Sanders, Alan R. Schall, Ulrich and Schubert, Christian R. Schulze, Thomas G. Schwab, Sibylle G. and Scolnick, Edward M. Scott, Rodney J. Seidman, Larry J. Shi, Jianxin Sigurdsson, Engilbert Silagadze, Teimuraz Silverman, Jeremy M. Sim, Kang Slominsky, Petr Smoller, Jordan W. and So, Hon-Cheong Spencer, Chris C. A. Stefansson, Hreinn and Steinberg, Stacy Stogmann, Elisabeth Straub, Richard E. and Strengman, Eric Strohmaier, Jana Stroup, T. Scott and Subramaniam, Mythily Suvisaari, Jaana Svrakic, Dragan M. and Szatkiewicz, Jin P. Soderman, Erik Thirumalai, Srinivas and Toncheva, Draga Tosato, Sarah Veijola, Juha Waddington, John and Walsh, Dermot Wang, Dai Wang, Qiang Webb, Bradley T. and Weiser, Mark Wildenauer, Dieter B. Williams, Nigel M. and Williams, Stephanie Witt, Stephanie H. Wolen, Aaron R. Wong, Emily H. M. Wormley, Brandon K. Xi, Hualin Simon Zai, Clement C. Zheng, Xuebin Zimprich, Fritz Wray, Naomi R. and Stefansson, Kari Visscher, Peter M. Adolfsson, Rolf and Andreassen, Ole A. Blackwood, Douglas H. R. Bramon, Elvira and Buxbaum, Joseph D. Borglum, Anders D. Cichon, Sven Darvasi, Ariel Domenici, Enrico Ehrenreich, Hannelore Esko, Tonu and Gejman, V, Pablo Gill, Michael Gurling, Hugh Hultman, Christina M. Iwata, Nakao Jablensky, V, Assen Jonsson, Erik G. Kendler, Kenneth S. Kirov, George Knight, Jo Lencz, Todd Levinson, Douglas F. Li, Qingqin S. Liu, Jianjun and Malhotra, Anil K. McCarroll, Steven A. McQuillin, Andrew and Moran, Jennifer L. Mortensen, Preben B. Mowry, Bryan J. and Nothen, Markus M. Ophoff, Roel A. Owen, Michael J. Palotie, Aarno Pato, Carlos N. Petryshen, Tracey L. Posthuma, Danielle Rietschel, Marcella Riley, Brien P. Rujescu, Dan and Sham, Pak C. St Clair, David Weinberger, Daniel R. and Wendland, Jens R. Werge, Thomas Daly, Mark J. Sullivan, Patrick F. CommonMind Consortium Psychiat Genomics Consortium and iPSYCH-GEMS Schizophrenia Working
Abstract: Transcriptomic imputation approaches combine eQTL reference panels with large-scale genotype data in order to test associations between disease and gene expression. These genic associations could elucidate signals in complex genome-wide association study (GWAS) loci and may disentangle the role of different tissues in disease development. We used the largest eQTL reference panel for the dorso-lateral prefrontal cortex (DLPFC) to create a set of gene expression predictors and demonstrate their utility. We applied DLPFC and 12 GTEx-brain predictors to 40,299 schizophrenia cases and 65,264 matched controls for a large transcriptomic imputation study of schizophrenia. We identified 413 genic associations across 13 brain regions. Stepwise conditioning identified 67 non-MHC genes, of which 14 did not fall within previous GWAS loci. We identified 36 significantly enriched pathways, including hexosaminidase-A deficiency, and multiple porphyric disorder pathways. We investigated developmental expression patterns among the 67 non-MHC genes and identified specific groups of pre- and postnatal expression.
Published: 2019

49. Publisher Correction:Gene expression imputation across multiple brain regions provides insights into schizophrenia risk (Nature Genetics, (2019), 51, 4, (659-674), 10.1038/s41588-019-0364-4)

Author: Huckins, Laura M., Dobbyn, Amanda, Ruderfer, Douglas M., Hoffman, Gabriel, Wang, Weiqing, Pardiñas, Antonio F., Rajagopal, Veera M., Als, Thomas D., T. Nguyen, Hoang, Girdhar, Kiran, Boocock, James, Roussos, Panos, Fromer, Menachem, Kramer, Robin, Domenici, Enrico, Gamazon, Eric R., Purcell, Shaun, Johnson, Jessica S., Shah, Hardik R., Klein, Lambertus L., Dang, Kristen K., Logsdon, Benjamin A., Mahajan, Milind C., Agerbo, Esben, Demontis, Ditte, Hansen, Mark, Hansen, Thomas, Hollegaard, Mads V., Mattheisen, Manuel, Meier, Sandra, Mors, Ole, Rasmussen, Henrik B., Stahl, Eli A., Børglum, Anders D., Mortensen, Preben Bo, Grove, Jakob, Pedersen, Carsten Bøcker, Pedersen, Marianne Giørtz, and Hansen, Christine Søholm
Abstract: In the HTML version of the article originally published, the author group ‘The Schizophrenia Working Group of the Psychiatric Genomics Consortium’ was displayed incorrectly. The error has been corrected in the HTML version of the article.
Published: 2019

50. Gene expression imputation across multiple brain regions provides insights into schizophrenia risk

Author: Huckins, Laura M., Dobbyn, Amanda, Ruderfer, Douglas M., Hoffman, Gabriel, Wang, Weiqing, Pardinas, Antonio F., Rajagopal, Veera M., Als, Thomas D., Nguyen, Hoang T., Girdhar, Kiran, Boocock, James, Roussos, Panos, Fromer, Menachem, Kramer, Robin, Domenici, Enrico, Gamazon, Eric R., Purcell, Shaun, Demontis, Ditte, Borglum, Anders D., Walters, James T. R., O'Donovan, Michael C., Sullivan, Patrick, Owen, Michael J., Devlin, Bernie, Sieberts, Solveig K., Cox, Nancy J., Im, Hae Kyung, Sklar, Pamela, Stahl, Eli A., Johnson, Jessica S., Shah, Hardik R., Klein, Lambertus L., Dang, Kristen K., Logsdon, Benjamin A., Mahajan, Milind C., Mangravite, Lara M., Toyoshiba, Hiroyoshi, Gur, Raquel E., Hahn, Chang-Gyu, Schadt, Eric, Lewis, David A., Haroutunian, Vahram, Peters, Mette A., Lipska, Barbara K., Buxbaum, Joseph D., Hirai, Keisuke, Perumal, Thanneer M., Essioux, Laurent, Rajagopal, Veera Manikandan, Mattheisen, Manuel, Grove, Jakob, Werge, Thomas, Mortensen, Preben Bo, Pedersen, Carsten Bocker, Agerbo, Esben, Pedersen, Marianne Giortz, Mors, Ole, Nordentoft, Merete, Hougaard, David M., Bybjerg-Grauholm, Jonas, Baekvad-Hansen, Marie, Hansen, Christine Soholm, Ripke, Stephan, Neale, Benjamin M., Corvin, Aiden, Farh, Kai-How, Holmans, Peter A., Lee, Phil, Bulik-Sullivan, Brendan, Collier, David A., Huang, Hailiang, Pers, Tune H., Agartz, Ingrid, Albus, Margot, Alexander, Madeline, Amin, Farooq, Bacanu, Silviu A., Begemann, Martin, Belliveau, Richard A., Jr., Bene, Judit, Bergen, Sarah E., Bevilacqua, Elizabeth, Bigdeli, Tim B., Black, Donald W., Bruggeman, Richard, Buccola, Nancy G., Buckner, Randy L., Byerley, William, Cahn, Wiepke, Cai, Guiqing, Campion, Dominique, Cantor, Rita M., Carr, Vaughan J., Carrera, Noa, Catts, Stanley, V, Chambert, Kimberly D., Chan, Raymond C. K., Chen, Ronald Y. L., Chen, Eric Y. H., Cheng, Wei, Cheung, Eric F. C., Chong, Siow Ann, Cloninger, C. Robert, Cohen, David, Cohen, Nadine, Cormican, Paul, Craddock, Nick, Crowley, James J., Curtis, David, Davidson, Michael, Davis, Kenneth L., Degenhardt, Franziska, Del Favero, Jurgen, Dikeos, Dimitris, Dinan, Timothy, Djurovic, Srdjan, Donohoe, Gary, Drapeau, Elodie, Duan, Jubao, Dudbridge, Frank, Durmishi, Naser, Eichhammer, Peter, Eriksson, Johan, Escott-Price, Valentina, Fanous, Ayman H., Farrell, Martilias S., Frank, Josef, Franke, Lude, Freedman, Robert, Freimer, Nelson B., Friedl, Marion, Friedman, Joseph, I, Genovese, Giulio, Georgieva, Lyudmila, Giegling, Ina, Giusti-Rodriguez, Paola, Godard, Stephanie, Goldstein, Jacqueline, I, Golimbet, Vera, Gopal, Srihari, Gratten, Jacob, de Haan, Lieuwe, Hammer, Christian, Hamshere, Marian L., Hansen, Mark, Hansen, Thomas, Hartmann, Annette M., Henskens, Frans A., Herms, Stefan, Hirschhorn, Joel N., Hoffmann, Per, Hofman, Andrea, Hollegaard, Mads, V, Ikeda, Masashi, Joa, Inge, Julia, Antonio, Kahn, Rene S., Kalaydjieva, Luba, Karachanak-Yankova, Sena, Karjalainen, Juha, Kavanagh, David, Keller, Matthew C., Kennedy, James L., Khrunin, Andrey, Kim, Yunjung, Klovins, Janis, Knowles, James A., Konte, Bettina, Kucinskas, Vaidutis, Kucinskiene, Zita Ausrele, Kuzelova-Ptackova, Hana, Kahler, Anna K., Laurent, Claudine, Keong, Jimmy Lee Chee, Lee, S. Hong, Legge, Sophie E., Lerer, Bernard, Li, Miaoxin, Li, Tao, Liang, Kung-Yee, Lieberman, Jeffrey, Limborska, Svetlana, Loughland, Carmel M., Lubinski, Jan, Lonnqvist, Jouko, Macek, Milan, Jr., Magnusson, Patrik K. E., Maher, Brion S., Maier, Wolfgang, Mallet, Jacques, Marsal, Sara, Mattingsdal, Morten, McCarley, Robert W., McDonald, Colm, McIntosh, Andrew M., Meier, Sandra, Meijer, Carin J., Melegh, Bela, Melle, Ingrid, Mesholam-Gately, Raquelle, I, Metspalu, Andres, Michie, Patricia T., Milani, Lili, Milanova, Vihra, Mokrab, Younes, Morris, Derek W., Murphy, Kieran C., Murray, Robin M., Myin-Germeys, Inez, Muller-Myhsok, Bertram, Nelis, Mari, Nenadic, Igor, Nertney, Deborah A., Nestadt, Gerald, Nicodemus, Kristin K., Nikitina-Zake, Liene, Nisenbaum, Laura, Nordin Adolfsson, Annelie, O'Callaghan, Eadbhard, O'Dushlaine, Colm, O'Neill, F. Anthony, Oh, Sang-Yun, Olincy, Ann, Olsen, Line, Van Os, Jim, Pantelis, Christos, Papadimitriou, George N., Papiol, Sergi, Parkhomenko, Elena, Pato, Michele T., Paunio, Tiina, Pejovic-Milovancevic, Milica, Perkins, Diana O., Pietilainen, Olli, Pimm, Jonathan, Pocklington, Andrew J., Powell, John, Price, Alkes, Pulver, Ann E., Purcell, Shaun M., Quested, Digby, Rasmussen, Henrik B., Reichenberg, Abraham, Reimers, Mark A., Richards, Alexander L., Roffman, Joshua L., Salomaa, Veikko, Sanders, Alan R., Schall, Ulrich, Schubert, Christian R., Schulze, Thomas G., Schwab, Sibylle G., Scolnick, Edward M., Scott, Rodney J., Seidman, Larry J., Shi, Jianxin, Sigurdsson, Engilbert, Silagadze, Teimuraz, Silverman, Jeremy M., Sim, Kang, Slominsky, Petr, Smoller, Jordan W., So, Hon-Cheong, Spencer, Chris C. A., Stefansson, Hreinn, Steinberg, Stacy, Stogmann, Elisabeth, Straub, Richard E., Strengman, Eric, Strohmaier, Jana, Stroup, T. Scott, Subramaniam, Mythily, Suvisaari, Jaana, Svrakic, Dragan M., Szatkiewicz, Jin P., Soderman, Erik, Thirumalai, Srinivas, Toncheva, Draga, Tosato, Sarah, Veijola, Juha, Waddington, John, Walsh, Dermot, Wang, Dai, Wang, Qiang, Webb, Bradley T., Weiser, Mark, Wildenauer, Dieter B., Williams, Nigel M., Williams, Stephanie, Witt, Stephanie H., Wolen, Aaron R., Wong, Emily H. M., Wormley, Brandon K., Xi, Hualin Simon, Zai, Clement C., Zheng, Xuebin, Zimprich, Fritz, Wray, Naomi R., Stefansson, Kari, Visscher, Peter M., Adolfsson, Rolf, Andreassen, Ole A., Blackwood, Douglas H. R., Bramon, Elvira, Cichon, Sven, Darvasi, Ariel, Ehrenreich, Hannelore, Esko, Tonu, Gejman, Pablo, V, Gill, Michael, Gurling, Hugh, Hultman, Christina M., Iwata, Nakao, Jablensky, Assen, V, Jonsson, Erik G., Kendler, Kenneth S., Kirov, George, Knight, Jo, Lencz, Todd, Levinson, Douglas F., Li, Qingqin S., Liu, Jianjun, Malhotra, Anil K., McCarroll, Steven A., McQuillin, Andrew, Moran, Jennifer L., Mortensen, Preben B., Mowry, Bryan J., Nothen, Markus M., Ophoff, Roel A., Palotie, Aarno, Pato, Carlos N., Petryshen, Tracey L., Posthuma, Danielle, Rietschel, Marcella, Riley, Brien P., Rujescu, Dan, Sham, Pak C., St Clair, David, Weinberger, Daniel R., Wendland, Jens R., Daly, Mark J., Sullivan, Patrick F., Huckins, Laura M., Dobbyn, Amanda, Ruderfer, Douglas M., Hoffman, Gabriel, Wang, Weiqing, Pardinas, Antonio F., Rajagopal, Veera M., Als, Thomas D., Nguyen, Hoang T., Girdhar, Kiran, Boocock, James, Roussos, Panos, Fromer, Menachem, Kramer, Robin, Domenici, Enrico, Gamazon, Eric R., Purcell, Shaun, Demontis, Ditte, Borglum, Anders D., Walters, James T. R., O'Donovan, Michael C., Sullivan, Patrick, Owen, Michael J., Devlin, Bernie, Sieberts, Solveig K., Cox, Nancy J., Im, Hae Kyung, Sklar, Pamela, Stahl, Eli A., Johnson, Jessica S., Shah, Hardik R., Klein, Lambertus L., Dang, Kristen K., Logsdon, Benjamin A., Mahajan, Milind C., Mangravite, Lara M., Toyoshiba, Hiroyoshi, Gur, Raquel E., Hahn, Chang-Gyu, Schadt, Eric, Lewis, David A., Haroutunian, Vahram, Peters, Mette A., Lipska, Barbara K., Buxbaum, Joseph D., Hirai, Keisuke, Perumal, Thanneer M., Essioux, Laurent, Rajagopal, Veera Manikandan, Mattheisen, Manuel, Grove, Jakob, Werge, Thomas, Mortensen, Preben Bo, Pedersen, Carsten Bocker, Agerbo, Esben, Pedersen, Marianne Giortz, Mors, Ole, Nordentoft, Merete, Hougaard, David M., Bybjerg-Grauholm, Jonas, Baekvad-Hansen, Marie, Hansen, Christine Soholm, Ripke, Stephan, Neale, Benjamin M., Corvin, Aiden, Farh, Kai-How, Holmans, Peter A., Lee, Phil, Bulik-Sullivan, Brendan, Collier, David A., Huang, Hailiang, Pers, Tune H., Agartz, Ingrid, Albus, Margot, Alexander, Madeline, Amin, Farooq, Bacanu, Silviu A., Begemann, Martin, Belliveau, Richard A., Jr., Bene, Judit, Bergen, Sarah E., Bevilacqua, Elizabeth, Bigdeli, Tim B., Black, Donald W., Bruggeman, Richard, Buccola, Nancy G., Buckner, Randy L., Byerley, William, Cahn, Wiepke, Cai, Guiqing, Campion, Dominique, Cantor, Rita M., Carr, Vaughan J., Carrera, Noa, Catts, Stanley, V, Chambert, Kimberly D., Chan, Raymond C. K., Chen, Ronald Y. L., Chen, Eric Y. H., Cheng, Wei, Cheung, Eric F. C., Chong, Siow Ann, Cloninger, C. 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Abstract: Transcriptomic imputation approaches combine eQTL reference panels with large-scale genotype data in order to test associations between disease and gene expression. These genic associations could elucidate signals in complex genome-wide association study (GWAS) loci and may disentangle the role of different tissues in disease development. We used the largest eQTL reference panel for the dorso-lateral prefrontal cortex (DLPFC) to create a set of gene expression predictors and demonstrate their utility. We applied DLPFC and 12 GTEx-brain predictors to 40,299 schizophrenia cases and 65,264 matched controls for a large transcriptomic imputation study of schizophrenia. We identified 413 genic associations across 13 brain regions. Stepwise conditioning identified 67 non-MHC genes, of which 14 did not fall within previous GWAS loci. We identified 36 significantly enriched pathways, including hexosaminidase-A deficiency, and multiple porphyric disorder pathways. We investigated developmental expression patterns among the 67 non-MHC genes and identified specific groups of pre- and postnatal expression.
Published: 2019
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