Search

Your search keyword '"Camarena, Adrian"' showing total 20 results
Start Over Author "Camarena, Adrian" Publication Year Range Last 10 years
20 results on '"Camarena, Adrian"'

4. Transcriptome and epigenome landscape of human cortical development modeled in organoids

Author

Amiri, Anahita, Coppola, Gianfilippo, Scuderi, Soraya, Wu, Feinan, Roychowdhury, Tanmoy, Liu, Fuchen, Pochareddy, Sirisha, Shin, Yurae, Safi, Alexias, Song, Lingyun, Zhu, Ying, Sousa, André MM, Gerstein, Mark, Crawford, Gregory E, Sestan, Nenad, Abyzov, Alexej, Vaccarino, Flora M, Akbarian, Schahram, An, Joon-Yong, Armoskus, Christoper, Ashley-Koch, Allison E, Beach, Thomas G, Belmont, Judson, Bendl, Jaroslav, Borrman, Tyler, Brown, Leanne, Brown, Miguel, Brown, Mimi, Brunetti, Tonya, Bryois, Julien, Burke, Emily E, Camarena, Adrian, Carlyle, Becky C, Chae, Yooree, Charney, Alexander W, Chen, Chao, Cheng, Lijun, Cherskov, Adriana, Choi, Jinmyung, Clarke, Declan, Collado-Torres, Leonardo, Dai, Rujia, De La Torre Ubieta, Luis, DelValle, Diane, Devillers, Olivia, Dracheva, Stella, Emani, Prashant S, Evgrafov, Oleg V, Farnham, Peggy J, Fitzgerald, Dominic, Flatow, Elie, Francoeur, Nancy, Fullard, John F, Gandal, Michael J, Gao, Tianliuyun, Garrett, Melanie E, Geschwind, Daniel H, Giase, Gina, Girdhar, Kiran, Giusti-Rodriguez, Paola, Goes, Fernando S, Goodman, Thomas, Grennan, Kay S, Gu, Mengting, Gürsoy, Gamze, Hadjimichael, Evi, Hahn, Chang-Gyu, Haroutunian, Vahram, Hauberg, Mads E, Hoffman, Gabriel E, Huey, Jack, Hyde, Thomas M, Ivanov, Nikolay A, Jacobov, Rivka, Jaffe, Andrew E, Jiang, Yan, Jiang, Yi, Johnson, Graham D, Kassim, Bibi S, Kefi, Amira, Kim, Yunjung, Kitchen, Robert R, Kleiman, Joel E, Knowles, James A, Kozlenkov, Alexey, Li, Mingfeng, Li, Zhen, Lipska, Barbara K, Liu, Chunyu, Liu, Shuang, Mangravite, Lara M, Mariani, Jessica, Mattei, Eugenio, Miller, Daniel J, Moore, Jill, Nairn, Angus C, Navarro, Fabio CP, Park, Royce B, Peters, Mette A, and Pinto, Dalila

Subjects
Stem Cell Research - Nonembryonic - Human, Stem Cell Research - Embryonic - Human, Stem Cell Research - Induced Pluripotent Stem Cell - Human, Stem Cell Research, Genetics, Stem Cell Research - Induced Pluripotent Stem Cell, Human Genome, Intellectual and Developmental Disabilities (IDD), Autism, Brain Disorders, Biotechnology, Clinical Research, Mental Health, Pediatric, Neurosciences, 2.1 Biological and endogenous factors, Underpinning research, Aetiology, 1.1 Normal biological development and functioning, Neurological, Cerebral Cortex, Enhancer Elements, Genetic, Epigenesis, Genetic, Gene Expression Regulation, Developmental, Humans, Induced Pluripotent Stem Cells, Models, Neurological, Neurogenesis, Organoids, Transcriptome, PsychENCODE Consortium, General Science & Technology
Abstract

Genes implicated in neuropsychiatric disorders are active in human fetal brain, yet difficult to study in a longitudinal fashion. We demonstrate that organoids from human pluripotent cells model cerebral cortical development on the molecular level before 16 weeks postconception. A multiomics analysis revealed differentially active genes and enhancers, with the greatest changes occurring at the transition from stem cells to progenitors. Networks of converging gene and enhancer modules were assembled into six and four global patterns of expression and activity across time. A pattern with progressive down-regulation was enriched with human-gained enhancers, suggesting their importance in early human brain development. A few convergent gene and enhancer modules were enriched in autism-associated genes and genomic variants in autistic children. The organoid model helps identify functional elements that may drive disease onset.

Published
2018

5. Integrative functional genomic analysis of human brain development and neuropsychiatric risks

Author

Li, Mingfeng, Santpere, Gabriel, Imamura Kawasawa, Yuka, Evgrafov, Oleg V, Gulden, Forrest O, Pochareddy, Sirisha, Sunkin, Susan M, Li, Zhen, Shin, Yurae, Zhu, Ying, Sousa, André MM, Werling, Donna M, Kitchen, Robert R, Kang, Hyo Jung, Pletikos, Mihovil, Choi, Jinmyung, Muchnik, Sydney, Xu, Xuming, Wang, Daifeng, Lorente-Galdos, Belen, Liu, Shuang, Giusti-Rodríguez, Paola, Won, Hyejung, de Leeuw, Christiaan A, Pardiñas, Antonio F, Hu, Ming, Jin, Fulai, Li, Yun, Owen, Michael J, O’Donovan, Michael C, Walters, James TR, Posthuma, Danielle, Reimers, Mark A, Levitt, Pat, Weinberger, Daniel R, Hyde, Thomas M, Kleinman, Joel E, Geschwind, Daniel H, Hawrylycz, Michael J, State, Matthew W, Sanders, Stephan J, Sullivan, Patrick F, Gerstein, Mark B, Lein, Ed S, Knowles, James A, Sestan, Nenad, Willsey, A Jeremy, Oldre, Aaron, Szafer, Aaron, Camarena, Adrian, Cherskov, Adriana, Charney, Alexander W, Abyzov, Alexej, Kozlenkov, Alexey, Safi, Alexias, Jones, Allan R, Ashley-Koch, Allison E, Ebbert, Amanda, Price, Amanda J, Sekijima, Amanda, Kefi, Amira, Bernard, Amy, Amiri, Anahita, Sboner, Andrea, Clark, Andrew, Jaffe, Andrew E, Tebbenkamp, Andrew TN, Sodt, Andy J, Guillozet-Bongaarts, Angie L, Nairn, Angus C, Carey, Anita, Huttner, Anita, Chervenak, Ann, Szekely, Anna, Shieh, Annie W, Harmanci, Arif, Lipska, Barbara K, Carlyle, Becky C, Gregor, Ben W, Kassim, Bibi S, Sheppard, Brooke, Bichsel, Candace, Hahn, Chang-Gyu, Lee, Chang-Kyu, Chen, Chao, Kuan, Chihchau L, Dang, Chinh, Lau, Chris, Cuhaciyan, Christine, Armoskus, Christoper, Mason, Christopher E, Liu, Chunyu, Slaughterbeck, Cliff R, Bennet, Crissa, Pinto, Dalila, Polioudakis, Damon, Franjic, Daniel, Miller, Daniel J, Bertagnolli, Darren, and Lewis, David A

Subjects
Human Genome, Genetics, Neurosciences, Biotechnology, Pediatric, Mental Health, Brain, Epigenesis, Genetic, Epigenomics, Gene Expression Regulation, Developmental, Gene Regulatory Networks, Humans, Mental Disorders, Nervous System Diseases, Neurogenesis, Single-Cell Analysis, Transcriptome, BrainSpan Consortium, PsychENCODE Consortium, PsychENCODE Developmental Subgroup, General Science & Technology
Abstract

To broaden our understanding of human neurodevelopment, we profiled transcriptomic and epigenomic landscapes across brain regions and/or cell types for the entire span of prenatal and postnatal development. Integrative analysis revealed temporal, regional, sex, and cell type-specific dynamics. We observed a global transcriptomic cup-shaped pattern, characterized by a late fetal transition associated with sharply decreased regional differences and changes in cellular composition and maturation, followed by a reversal in childhood-adolescence, and accompanied by epigenomic reorganizations. Analysis of gene coexpression modules revealed relationships with epigenomic regulation and neurodevelopmental processes. Genes with genetic associations to brain-based traits and neuropsychiatric disorders (including MEF2C, SATB2, SOX5, TCF4, and TSHZ3) converged in a small number of modules and distinct cell types, revealing insights into neurodevelopment and the genomic basis of neuropsychiatric risks.

Published
2018

6. Gene Expression in Patient-Derived Neural Progenitors Implicates WNT5A Signaling in the Etiology of Schizophrenia

Author

Evgrafov, Oleg V., Armoskus, Chris, Wrobel, Bozena B., Spitsyna, Valeria N., Souaiaia, Tade, Herstein, Jennifer S., Walker, Christopher P., Nguyen, Joseph D., Camarena, Adrian, Weitz, Jonathan R., Kim, Jae Mun “Hugo”, Lopez Duarte, Edder, Wang, Kai, Simpson, George M., Sobell, Janet L., Medeiros, Helena, Pato, Michele T., Pato, Carlos N., and Knowles, James A.

Published
2020
Full Text
View/download PDF

8. Assessing characteristics of RNA amplification methods for single cell RNA sequencing

Author

Dueck, Hannah R, Ai, Rizi, Camarena, Adrian, Ding, Bo, Dominguez, Reymundo, Evgrafov, Oleg V, Fan, Jian-Bing, Fisher, Stephen A, Herstein, Jennifer S, Kim, Tae Kyung, Kim, Jae Mun Hugo, Lin, Ming-Yi, Liu, Rui, Mack, William J, McGroty, Sean, Nguyen, Joseph D, Salathia, Neeraj, Shallcross, Jamie, Souaiaia, Tade, Spaethling, Jennifer M, Walker, Christopher P, Wang, Jinhui, Wang, Kai, Wang, Wei, Wildberg, Andre, Zheng, Lina, Chow, Robert H, Eberwine, James, Knowles, James A, Zhang, Kun, and Kim, Junhyong

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Prevention, Underpinning research, 1.1 Normal biological development and functioning, Generic health relevance, High-Throughput Nucleotide Sequencing, Nucleic Acid Amplification Techniques, RNA, Reproducibility of Results, Sensitivity and Specificity, Sequence Analysis, RNA, Single-Cell Analysis, Single-cell RNA-sequencing, Biotechnology, Bioinformatics, Genomics, Information and Computing Sciences, Medical and Health Sciences, Biological sciences, Biomedical and clinical sciences
Abstract

BackgroundRecently, measurement of RNA at single cell resolution has yielded surprising insights. Methods for single-cell RNA sequencing (scRNA-seq) have received considerable attention, but the broad reliability of single cell methods and the factors governing their performance are still poorly known.ResultsHere, we conducted a large-scale control experiment to assess the transfer function of three scRNA-seq methods and factors modulating the function. All three methods detected greater than 70% of the expected number of genes and had a 50% probability of detecting genes with abundance greater than 2 to 4 molecules. Despite the small number of molecules, sequencing depth significantly affected gene detection. While biases in detection and quantification were qualitatively similar across methods, the degree of bias differed, consistent with differences in molecular protocol. Measurement reliability increased with expression level for all methods and we conservatively estimate measurements to be quantitative at an expression level greater than ~5-10 molecules.ConclusionsBased on these extensive control studies, we propose that RNA-seq of single cells has come of age, yielding quantitative biological information.

Published
2016

11. Genome-wide association study identifies new locus associated with OCD

Author

Strom, Nora I., primary, Yu, Dongmei, additional, Gerring, Zachary F., additional, Halvorsen, Matthew W., additional, Abdellaoui, Abdel, additional, Rodriguez-Fontenla, Cristina, additional, Sealock, Julia M., additional, Bigdeli, Tim, additional, Coleman, Jonathan R. I., additional, Mahjani, Behrang, additional, Thorp, Jackson G., additional, Bey, Katharina, additional, Burton, Christie L., additional, Luykx, Jurjen J., additional, Zai, Gwyneth, additional, Askland, Kathleen D., additional, Barlassina, Cristina, additional, Nissen, Judith Becker, additional, Bellodi, Laura, additional, Bienvenu, O. Joseph, additional, Black, Donald, additional, Bloch, Michael, additional, Boberg, Julia, additional, Bosch, Rosa, additional, Breen, Michael, additional, Brennan, Brian P., additional, Brentani, Helena, additional, Buxbaum, Joseph D., additional, Bybjerg-Grauholm, Jonas, additional, Byrne, Enda M., additional, Camarena, Beatriz, additional, Camarena, Adrian, additional, Cappi, Carolina, additional, Carracedo, Angel, additional, Casas, Miguel, additional, Cavallini, Maria C., additional, Ciullo, Valentina, additional, Cook, Edwin H., additional, Coric, Vladimir, additional, Cullen, Bernadette A., additional, De Schipper, Elles J., additional, Devlin, Bernie, additional, Djurovic, Srdjan, additional, Elias, Jason A., additional, Erdman, Lauren, additional, Estivil, Xavier, additional, Falkenstein, Martha J., additional, Fundin, Bengt T., additional, Gabrielsen, Maiken E., additional, Goes, Fernando S., additional, Grados, Marco A., additional, Grove, Jakob, additional, Guo, Wei, additional, Haavik, Jan, additional, Hagen, Kristen, additional, Havdahl, Alexandra, additional, Hounie, Ana G., additional, Hucks, Donald, additional, Hultman, Christina, additional, Janecka, Magdalena, additional, Jenike, Michael, additional, Karlsson, Elinor K., additional, Klawohn, Julia, additional, Klei, Lambertus, additional, Krasnow, Janice, additional, Krebs, Kristi, additional, Krompinger, Jason, additional, Lanzagorta, Nuria, additional, Macciardi, Fabio, additional, Maher, Brion, additional, McArthur, Evonne, additional, McGregor, Nathaniel, additional, McLaughlin, Nicole C., additional, Meier, Sandra, additional, Miguel, Euripedes C., additional, Mulhern, Maureen, additional, Nestadt, Paul S., additional, Nurmi, Erika L., additional, O’Connell, Kevin S., additional, Osiecki, Lisa, additional, Palviainen, Teemu, additional, Piras, Fabrizio, additional, Piras, Federica, additional, Pulver, Ann E., additional, Rabionet, Raquel, additional, Ramirez, Alfredo, additional, Rauch, Scott, additional, Reichenberg, Abraham, additional, Reichert, Jennifer, additional, Riddle, Mark A., additional, Ripke, Stephan, additional, Sampaio, Aline S., additional, Schiele, Miriam A., additional, Sloofman, Laura G., additional, Smit, Jan, additional, Sobell, Janet L., additional, Artigas, María Soler, additional, Thomas, Laurent F., additional, Vallada, Homero, additional, Veenstra-VanderWeele, Jeremy, additional, Vulink, Nienke N. C. C., additional, Walker, Christopher P., additional, Wang, Ying, additional, Wendland, Jens R., additional, Winsvold, Bendik S., additional, Yao, Yin, additional, Alonso, Pino, additional, Berberich, Götz, additional, Bulik, Cynthia M., additional, Cath, Danielle, additional, Cusi, Daniele, additional, Delorme, Richard, additional, Denys, Damiaan, additional, Eapen, Valsamma, additional, Falkai, Peter, additional, Fernandez, Thomas V., additional, Fyer, Abby J., additional, Geller, Daniel A., additional, Grabe, Hans J., additional, Greenberg, Benjamin D., additional, Hanna, Gregory L., additional, Hickie, Ian M., additional, Hougaard, David M., additional, Kathmann, Norbert, additional, Kennedy, James, additional, Kung-Yee, Liang, additional, Landén, Mikael, additional, Le Hellard, Stéphanie, additional, Leboyer, Marion, additional, Lochner, Christine, additional, McCracken, James T., additional, Medland, Sarah E., additional, Mortensen, Preben B., additional, Neale, Benjamin, additional, Nicolini, Humberto, additional, Nordentoft, Merete, additional, Pato, Michele, additional, Pato, Carlos, additional, Pauls, David L., additional, Pedersen, Nancy L., additional, Piacentini, John, additional, Pittenger, Christopher, additional, Posthuma, Danielle, additional, Ramos-Quiroga, Josep A, additional, Rasmussen, Steven A., additional, Ressler, Kerry J., additional, Richter, Margaret A., additional, Rosário, Maria C., additional, Rosenberg, David R., additional, Ruhrmann, Stephan, additional, Samuels, Jack F., additional, Sandin, Sven, additional, Sandor, Paul, additional, Spalletta, Gianfranco, additional, Stein, Dan J., additional, Stewart, S. Evelyn, additional, Storch, Eric A., additional, Stranger, Barbara E., additional, Turiel, Maurizio, additional, Werge, Thomas, additional, Andreassen, Ole A., additional, Børglum, Anders D., additional, Walitza, Susanne, additional, Hansen, Bjarne K. A., additional, Rück, Christian P., additional, Martin, Nicholas G., additional, Milani, Lili, additional, Mors, Ole, additional, Reichborn-Kjennerud, Ted, additional, Ribasés, Marta, additional, Kvale, Gerd, additional, Mataix-Cols, David, additional, Domschke, Katharina, additional, Grünblatt, Edna, additional, Wagner, Michael, additional, Zwart, John-Anker, additional, Breen, Gerome, additional, Nestadt, Gerald, additional, Metspalu, Andres, additional, Kaprio, Jaakko, additional, Arnold, Paul D., additional, Grice, Dorothy E., additional, Knowles, James A., additional, Ask, Helga, additional, Verweij, Karin J. H., additional, Davis, Lea K., additional, Smit, Dirk J. A., additional, Crowley, James J., additional, Mathews, Carol A., additional, Derks, Eske M., additional, Scharf, Jeremiah M., additional, and Mattheisen, Manuel, additional

Published
2021
Full Text
View/download PDF

12. 48 GENE EXPRESSION OF PATIENT-DERIVED NEURAL PROGENITOR CELL LINES DEVELOPED FROM OLFACTORY NEUROEPITHELIUM IMPLICATES WNT SIGNALING IN THE ETIOLOGY OF SCHIZOPHRENIA

Author

Evgrafov, Oleg, primary, Armoskus, Chris, additional, Spitsyna, Valeria, additional, Wrobel, Bozena, additional, Sobell, Janet, additional, Souaiaia, Tade, additional, Medeiros, Helena, additional, Wang, Kai, additional, Walker, Christopher, additional, Camarena, Adrian, additional, Simpson, George, additional, Pato, Michele, additional, Pato, Carlos, additional, and Knowles, James, additional

Published
2019
Full Text
View/download PDF

13. Using 3D epigenomic maps of primary olfactory neuronal cells from living individuals to understand gene regulation

Author

Rhie, Suhn K., primary, Schreiner, Shannon, additional, Witt, Heather, additional, Armoskus, Chris, additional, Lay, Fides D., additional, Camarena, Adrian, additional, Spitsyna, Valeria N., additional, Guo, Yu, additional, Berman, Benjamin P., additional, Evgrafov, Oleg V., additional, Knowles, James A., additional, and Farnham, Peggy J., additional

Published
2018
Full Text
View/download PDF

14. Single-Cell RNA-Seq of Neurons in the Human Nervous System

Author

Joseph D. Nguyen, Reymundo Dominguez, Robert H. Chow, William J. Mack, Christopher P Walker, James A. Knowles, Oleg V. Evgrafov, Charles Y. Liu, Ming-Yi Lin, Tade Souaiaia, Jennifer Herstein, Camarena Adrian, Maite Christi Francois, and Jae M. Kim

Subjects
Nervous system, Central nervous system, Biophysics, Anatomy, Biology, Cell biology, medicine.anatomical_structure, nervous system, Cerebral cortex, Cortex (anatomy), Subplate, Gene expression, medicine, Patch clamp, Non-spiking neuron
Abstract

The human nervous system comprises highly heterogeneous neuronal populations. Our group has applied patch clamp electrophysiology, fluorescence microscopy, and next-generation single-cell RNA sequencing to correlate function, morphology and gene expression profiles at the single-cell level in both developing and mature human central nervous system. We performed whole cell patch clamp followed by cytoplasm extraction and single-cell RNA sequencing of neurons in acute slices and organotypic brain slice cultures from human adult cerebral cortex and cerebellum; and fetal brain and spinal cord of gestational age 10-20 weeks.We sequenced the mRNA with a modified aRNA method alongside with Truseq stranded RNA kit (Vn gelder et al., 1990). On average, we can detect ∼6,000 genes for each sample. Heterogeneity in gene expression and function was evident between neurons from different types of tissue when data were analyzed for Principle Components. Cajal-Retzius neurons are of special interest, as they are morphologically distinct and large neurons, located in the outermost layer of the developing cortex, where they are believed to contribute to defining the layered structure of the cortex. We showed that Cajal-Retzius neurons separate from subplate neurons with PC analysis and identified sets of genes that are significantly differentially expressed in Cajal-Retzius neurons compared to subplate neurons. Electrophysiological recordings revealed for the first time, spontaneous synaptic activity and action potential firing in human Cajal-Retzius neurons. Our data are significant for demonstrating the synergistic potential of combining functional and transcriptome analysis at the single-cell level.

Published
2016
Full Text
View/download PDF

15. Additional file 8: of Assessing characteristics of RNA amplification methods for single cell RNA sequencing

Author

Dueck, Hannah, Rizi Ai, Camarena, Adrian, Ding, Bo, Reymundo Dominguez, Evgrafov, Oleg, Fan, Jian-Bing, Fisher, Stephen, Herstein, Jennifer, Kim, Tae, Kim, Jae, Lin, Ming-Yi, Liu, Rui, Mack, William, McGroty, Sean, Nguyen, Joseph, Salathia, Neeraj, Shallcross, Jamie, Souaiaia, Tade, Spaethling, Jennifer, Walker, Christopher, Jinhui Wang, Wang, Kai, Wang, Wei, Wildberg, Andre, Zheng, Lina, Chow, Robert, Eberwine, James, Knowles, James, Zhang, Kun, and Junhyong Kim

Subjects
health care economics and organizations
Abstract

Gene detection outliers. Genes that are problematic for detection. See Methods for classification of outliers. â Gene setâ indicates whether gene is classified as computationally unambiguous (1) or not (2). â Detected/undetectedâ indicates whether the gene is unexpectedly observed (D) or unexpectedly unobserved (U). (PDF 181 kb)

Published
2016
Full Text
View/download PDF

16. Additional file 2: of Assessing characteristics of RNA amplification methods for single cell RNA sequencing

Author

Dueck, Hannah, Rizi Ai, Camarena, Adrian, Ding, Bo, Reymundo Dominguez, Evgrafov, Oleg, Fan, Jian-Bing, Fisher, Stephen, Herstein, Jennifer, Kim, Tae, Kim, Jae, Lin, Ming-Yi, Liu, Rui, Mack, William, McGroty, Sean, Nguyen, Joseph, Salathia, Neeraj, Shallcross, Jamie, Souaiaia, Tade, Spaethling, Jennifer, Walker, Christopher, Jinhui Wang, Wang, Kai, Wang, Wei, Wildberg, Andre, Zheng, Lina, Chow, Robert, Eberwine, James, Knowles, James, Zhang, Kun, and Junhyong Kim

Subjects
fungi, food and beverages
Abstract

Computationally unambiguous genes. Genes to which reads can be uniquely assigned. See the Excluded and unambiguous genes section in Methods for details on classification. (PDF 516 kb)

Published
2016
Full Text
View/download PDF

17. Additional file 3: of Assessing characteristics of RNA amplification methods for single cell RNA sequencing

Author

Dueck, Hannah, Rizi Ai, Camarena, Adrian, Ding, Bo, Reymundo Dominguez, Evgrafov, Oleg, Fan, Jian-Bing, Fisher, Stephen, Herstein, Jennifer, Kim, Tae, Kim, Jae, Lin, Ming-Yi, Liu, Rui, Mack, William, McGroty, Sean, Nguyen, Joseph, Salathia, Neeraj, Shallcross, Jamie, Souaiaia, Tade, Spaethling, Jennifer, Walker, Christopher, Jinhui Wang, Wang, Kai, Wang, Wei, Wildberg, Andre, Zheng, Lina, Chow, Robert, Eberwine, James, Knowles, James, Zhang, Kun, and Junhyong Kim

Abstract

Accuracy and robustness of estimated reference HBR and UHR RNA expression levels. A. Consistency of abundance estimates by three quantification algorithms relative to publicly available PrimePCR measurements (see Methods ). Scatters show log10 reads per million (HTSeq [22] and Maxcounts [31]), log10 transcripts per million (RSEM), or log10 molecules (PrimePCR). Upper quadrants indicate Pearson correlation (R) of log-transformed estimates. Pairwise zeros were treated as missing values. Estimates were based on combined raw reads from 3 bulk reference samples generated using ribosomal depletion for each HBR and UHR. RSEM estimates were used as reference throughout. B. Accuracy and robustness of expression estimates across library preparation methods: ribosomal-depletion (combined n = 3 samples per HBR and UHR) and poly-A RNA selection (combined n = 4 samples per source). See Methods for sample information. Scatters as in A using RSEM expression level estimates for each library preparation method. Ribosomal-depletion samples were used as reference throughout. Abbreviations: Human Brain Reference (HBR), Universal Human Reference RNA (UHR). (PDF 469 kb)

Published
2016
Full Text
View/download PDF

18. Gene expression in patient-derived neural progenitors implicates WNT5A signaling in the etiology of schizophrenia

Author

Evgrafov, Oleg V, primary, Armoskus, Chris, additional, Wrobel, Bozena B, additional, Spitsyna, Valeria N, additional, Souaiaia, Tade, additional, Herstein, Jennifer S., additional, Walker, Christopher P, additional, Nguyen, Joseph D, additional, Camarena, Adrian, additional, Weitz, Jonathan R, additional, Kim, Jae Mun ‘Hugo’, additional, Duarte, Edder Lopez, additional, Wang, Kai, additional, Simpson, George M, additional, Sobell, Janet L, additional, Medeiros, Helena, additional, Pato, Michele T, additional, Pato, Carlos N, additional, and Knowles, James A, additional

Published
2017
Full Text
View/download PDF

19. Assessing the measurement transfer function of single-cell RNA sequencing

Author

Dueck, Hannah R., primary, Ai, Rizi, additional, Camarena, Adrian, additional, Ding, Bo, additional, Dominguez, Reymundo, additional, Evgrafov, Oleg V., additional, Fan, Jian-Bing, additional, Fisher, Stephen A., additional, Hernstein, Jennifer S., additional, Kim, Tae Kyung, additional, Kim, Jae Mun (Hugo), additional, Lin, Ming-Yi, additional, Liu, Rui, additional, Mack, William J., additional, McGroty, Sean, additional, Nguyen, Joseph, additional, Salathia, Neeraj, additional, Shallcross, Jamie, additional, Souaiaia, Tade, additional, Spaethling, Jennifer, additional, Walker, Chris P., additional, Wang, Jinhui, additional, Wang, Kai, additional, Wang, Wei, additional, Wilberg, Andre, additional, Zheng, Lina, additional, Chow, Robert H., additional, Eberwine, James, additional, Knowles, James A., additional, Zhang, Kun, additional, and Kim, Junhyoung, additional

Published
2016
Full Text
View/download PDF

20. Genome-wide association study identifies 30 obsessive-compulsive disorder associated loci.

Author

Strom NI, Gerring ZF, Galimberti M, Yu D, Halvorsen MW, Abdellaoui A, Rodriguez-Fontenla C, Sealock JM, Bigdeli T, Coleman JR, Mahjani B, Thorp JG, Bey K, Burton CL, Luykx JJ, Zai G, Alemany S, Andre C, Askland KD, Banaj N, Barlassina C, Nissen JB, Bienvenu OJ, Black D, Bloch MH, Boberg J, Børte S, Bosch R, Breen M, Brennan BP, Brentani H, Buxbaum JD, Bybjerg-Grauholm J, Byrne EM, Cabana-Dominguez J, Camarena B, Camarena A, Cappi C, Carracedo A, Casas M, Cavallini MC, Ciullo V, Cook EH, Crosby J, Cullen BA, De Schipper EJ, Delorme R, Djurovic S, Elias JA, Estivill X, Falkenstein MJ, Fundin BT, Garner L, German C, Gironda C, Goes FS, Grados MA, Grove J, Guo W, Haavik J, Hagen K, Harrington K, Havdahl A, Höffler KD, Hounie AG, Hucks D, Hultman C, Janecka M, Jenike E, Karlsson EK, Kelley K, Klawohn J, Krasnow JE, Krebs K, Lange C, Lanzagorta N, Levey D, Lindblad-Toh K, Macciardi F, Maher B, Mathes B, McArthur E, McGregor N, McLaughlin NC, Meier S, Miguel EC, Mulhern M, Nestadt PS, Nurmi EL, O'Connell KS, Osiecki L, Ousdal OT, Palviainen T, Pedersen NL, Piras F, Piras F, Potluri S, Rabionet R, Ramirez A, Rauch S, Reichenberg A, Riddle MA, Ripke S, Rosário MC, Sampaio AS, Schiele MA, Skogholt AH, Sloofman LGSG, Smit J, Soler AM, Thomas LF, Tifft E, Vallada H, van Kirk N, Veenstra-VanderWeele J, Vulink NN, Walker CP, Wang Y, Wendland JR, Winsvold BS, Yao Y, Zhou H, Agrawal A, Alonso P, Berberich G, Bucholz KK, Bulik CM, Cath D, Denys D, Eapen V, Edenberg H, Falkai P, Fernandez TV, Fyer AJ, Gaziano JM, Geller DA, Grabe HJ, Greenberg BD, Hanna GL, Hickie IB, Hougaard DM, Kathmann N, Kennedy J, Lai D, Landén M, Le Hellard S, Leboyer M, Lochner C, McCracken JT, Medland SE, Mortensen PB, Neale BM, Nicolini H, Nordentoft M, Pato M, Pato C, Pauls DL, Piacentini J, Pittenger C, Posthuma D, Ramos-Quiroga JA, Rasmussen SA, Richter MA, Rosenberg DR, Ruhrmann S, Samuels JF, Sandin S, Sandor P, Spalletta G, Stein DJ, Stewart SE, Storch EA, Stranger BE, Turiel M, Werge T, Andreassen OA, Børglum AD, Walitza S, Hveem K, Hansen BK, Rück CP, Martin NG, Milani L, Mors O, Reichborn-Kjennerud T, Ribasés M, Kvale G, Mataix-Cols D, Domschke K, Grünblatt E, Wagner M, Zwart JA, Breen G, Nestadt G, Kaprio J, Arnold PD, Grice DE, Knowles JA, Ask H, Verweij KJ, Davis LK, Smit DJ, Crowley JJ, Scharf JM, Stein MB, Gelernter J, Mathews CA, Derks EM, and Mattheisen M

Abstract

Obsessive-compulsive disorder (OCD) affects ~1% of the population and exhibits a high SNP-heritability, yet previous genome-wide association studies (GWAS) have provided limited information on the genetic etiology and underlying biological mechanisms of the disorder. We conducted a GWAS meta-analysis combining 53,660 OCD cases and 2,044,417 controls from 28 European-ancestry cohorts revealing 30 independent genome-wide significant SNPs and a SNP-based heritability of 6.7%. Separate GWAS for clinical, biobank, comorbid, and self-report sub-groups found no evidence of sample ascertainment impacting our results. Functional and positional QTL gene-based approaches identified 249 significant candidate risk genes for OCD, of which 25 were identified as putatively causal, highlighting WDR6 , DALRD3 , CTNND1 and genes in the MHC region. Tissue and single-cell enrichment analyses highlighted hippocampal and cortical excitatory neurons, along with D1- and D2-type dopamine receptor-containing medium spiny neurons, as playing a role in OCD risk. OCD displayed significant genetic correlations with 65 out of 112 examined phenotypes. Notably, it showed positive genetic correlations with all included psychiatric phenotypes, in particular anxiety, depression, anorexia nervosa, and Tourette syndrome, and negative correlations with a subset of the included autoimmune disorders, educational attainment, and body mass index.. This study marks a significant step toward unraveling its genetic landscape and advances understanding of OCD genetics, providing a foundation for future interventions to address this debilitating disorder., Competing Interests: Chris German is employed by and hold stock or stock options in 23andMe, Inc. Erika L. Nurmi is on the Scientific Advisory Board for Myriad Genetics and Medical Advisory Board for Tourette Association of America and received Clinical trial funding from Emalex and Octapharma Pharmaceuticals. Jeremy Veenstra-VanderWeele has served on advisory boards or consulted with Roche, Novartis, and SynapDx; received research funding from Roche, Novartis, SynapDx, Seaside Therapeutics, Forest, Janssen, Acadia, Yamo, and MapLight; received stipends for editorial work from Wiley and Springer. Jens R. Wendland is a current employee and shareholder of Takeda Pharmaceuticals and a past employee and shareholder of F. Hoffmann-La Roche, Pfizer and Nestle Health Science. Cynthia M. Bulik reports: Pearson (author, royalty recipient).Peter Falkai reports no conflict of interest regarding this study and reports to have received financial support and Advisory Board: Richter, Recordati, Boehringer-Ingelheim, Otsuka, Janssen and Lundbeck. Hans J. Grabe has received travel grants and speakers honoraria from Fresenius Medical Care, Neuraxpharm, Servier and Janssen Cilag as well as research funding from Fresenius Medical Care. Ian B. Hickie is the Co-Director, Health and Policy at the Brain and Mind Centre (BMC) University of Sydney, Australia. The BMC operates an early-intervention youth services at Camperdown under contract to headspace. Professor Hickie has previously led community-based and pharmaceutical industry-supported (Wyeth, Eli Lily, Servier, Pfizer, AstraZeneca, Janssen Cilag) projects focused on the identification and better management of anxiety and depression. He is the Chief Scientific Advisor to, and a 3.2% equity shareholder in, InnoWell Pty Ltd which aims to transform mental health services through the use of innovative technologies. Benjamin M. Neale is a member of the scientific advisory board at Deep Genomics and Neumora. Christopher Pittenger consults and/or receives research support from Biohaven Pharmaceuticals, Freedom Biosciences, Ceruvia Lifesciences, Transcend Therapeutics, UCB BioPharma, and F-Prime Capital Partners. He owns equity in Alco Therapeutics. These relationships are not related to the current work. Dan J. Stein has received consultancy honoraria from Discovery Vitality, Johnson & Johnson, Kanna, L’Oreal, Lundbeck, Orion, Sanofi, Servier, Takeda and Vistagen. Eric A. Storch reports receiving research funding to his institution from the Ream Foundation, International OCD Foundation, and NIH. He was formerly a consultant for Brainsway and Biohaven Pharmaceuticals in the past 12 months. He owns stock less than $5000 in NView/Proem for distribution related to the YBOCS scales. He receives book royalties from Elsevier, Wiley, Oxford, American Psychological Association, Guildford, Springer, Routledge, and Jessica Kingsley. Ole A. Andreasson reports to be a consultant to Cortechs.ai, Precision Health AS, speakers honorarium from Otsuka, Lundbeck, Sunovion, Janssen. Anders D. Børglum has received speaker fee from Lundbeck. David Mataix-Cols receives royalties for contributing articles to UpToDate, Wolters Kluwer Health, and personal fees for editorial work from Elsevier, all unrelated to the current work. Murray B. Stein has in the past 3 years received consulting income from Acadia Pharmaceuticals, BigHealth, Biogen, Bionomics, Boehringer Ingelheim, Clexio, Eisai, EmpowerPharm, Engrail Therapeutics, Janssen, Jazz Pharmaceuticals, NeuroTrauma Sciences, Otsuka, PureTech Health, Sage Therapeutics, Sumitomo Pharma, and Roche/Genentech. Dr. Stein has stock options in Oxeia Biopharmaceuticals and EpiVario. He has been paid for his editorial work on Depression and Anxiety (Editor-in-Chief), Biological Psychiatry (Deputy Editor), and UpToDate (Co-Editor-in-Chief for Psychiatry). Joel Gelernter is paid for editorial work by the journal Complex Psychiatry. Pino Alonso has received funding from Biohaven, Boston Scientific, Medtronic. All other authors report no conflicts of interest.

Published
2024
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results