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1. A resource of lipidomics and metabolomics data from individuals with undiagnosed diseases.

Author

Kyle, Jennifer E, Kyle, Jennifer E, Stratton, Kelly G, Zink, Erika M, Kim, Young-Mo, Bloodsworth, Kent J, Monroe, Matthew E, Undiagnosed Diseases Network, Waters, Katrina M, Webb-Robertson, Bobbie-Jo M, Koeller, David M, Metz, Thomas O, Kyle, Jennifer E, Kyle, Jennifer E, Stratton, Kelly G, Zink, Erika M, Kim, Young-Mo, Bloodsworth, Kent J, Monroe, Matthew E, Undiagnosed Diseases Network, Waters, Katrina M, Webb-Robertson, Bobbie-Jo M, Koeller, David M, and Metz, Thomas O

Abstract

Every year individuals experience symptoms that remain undiagnosed by healthcare providers. In the United States, these rare diseases are defined as a condition that affects fewer than 200,000 individuals. However, there are an estimated 7000 rare diseases, and there are an estimated 25-30 million Americans in total (7.6-9.2% of the population as of 2018) affected by such disorders. The NIH Common Fund Undiagnosed Diseases Network (UDN) seeks to provide diagnoses for individuals with undiagnosed disease. Mass spectrometry-based metabolomics and lipidomics analyses could advance the collective understanding of individual symptoms and advance diagnoses for individuals with heretofore undiagnosed disease. Here, we report the mass spectrometry-based metabolomics and lipidomics analyses of blood plasma, urine, and cerebrospinal fluid from 148 patients within the UDN and their families, as well as from a reference population of over 100 individuals with no known metabolic diseases. The raw and processed data are available to the research community so that they might be useful in the diagnoses of current or future patients suffering from undiagnosed disorders.

Published
2021

2. A resource of lipidomics and metabolomics data from individuals with undiagnosed diseases.

Author

Kyle, Jennifer E, Kyle, Jennifer E, Stratton, Kelly G, Zink, Erika M, Kim, Young-Mo, Bloodsworth, Kent J, Monroe, Matthew E, Undiagnosed Diseases Network, Waters, Katrina M, Webb-Robertson, Bobbie-Jo M, Koeller, David M, Metz, Thomas O, Kyle, Jennifer E, Kyle, Jennifer E, Stratton, Kelly G, Zink, Erika M, Kim, Young-Mo, Bloodsworth, Kent J, Monroe, Matthew E, Undiagnosed Diseases Network, Waters, Katrina M, Webb-Robertson, Bobbie-Jo M, Koeller, David M, and Metz, Thomas O

Abstract

Every year individuals experience symptoms that remain undiagnosed by healthcare providers. In the United States, these rare diseases are defined as a condition that affects fewer than 200,000 individuals. However, there are an estimated 7000 rare diseases, and there are an estimated 25-30 million Americans in total (7.6-9.2% of the population as of 2018) affected by such disorders. The NIH Common Fund Undiagnosed Diseases Network (UDN) seeks to provide diagnoses for individuals with undiagnosed disease. Mass spectrometry-based metabolomics and lipidomics analyses could advance the collective understanding of individual symptoms and advance diagnoses for individuals with heretofore undiagnosed disease. Here, we report the mass spectrometry-based metabolomics and lipidomics analyses of blood plasma, urine, and cerebrospinal fluid from 148 patients within the UDN and their families, as well as from a reference population of over 100 individuals with no known metabolic diseases. The raw and processed data are available to the research community so that they might be useful in the diagnoses of current or future patients suffering from undiagnosed disorders.

Published
2021

3. CATMoS: Collaborative Acute Toxicity Modeling Suite

Author

Mansouri, K, Karmaus, A, Fitzpatrick, J, Patlewicz, G, Pradeep, P, Alberga, D, Alepee, N, Allen, T, Allen, D, Alves, V, Andrade, C, Auernhammer, T, Ballabio, D, Bell, S, Benfenati, E, Bhattacharya, S, Bastos, J, Boyd, S, Brown, J, Capuzzi, S, Chushak, Y, Ciallella, H, Clark, A, Consonni, V, Daga, P, Ekins, S, Farag, S, Fedorov, M, Fourches, D, Gadaleta, D, Gao, F, Gearhart, J, Goh, G, Goodman, J, Grisoni, F, Grulke, C, Hartung, T, Hirn, M, Karpov, P, Korotcov, A, Lavado, G, Lawless, M, Li, X, Luechtefeld, T, Lunghini, F, Mangiatordi, G, Marcou, G, Marsh, D, Martin, T, Mauri, A, Muratov, E, Myatt, G, Nguyen, D, Nicolotti, O, Note, R, Pande, P, Parks, A, Peryea, T, Polash, A, Rallo, R, Roncaglioni, A, Rowlands, C, Ruiz, P, Russo, D, Sayed, A, Sayre, R, Sheils, T, Siegel, C, Silva, A, Simeonov, A, Sosnin, S, Southall, N, Strickland, J, Tang, Y, Teppen, B, Tetko, I, Thomas, D, Tkachenko, V, Todeschini, R, Toma, C, Tripodi, I, Trisciuzzi, D, Tropsha, A, Varnek, A, Vukovic, K, Wang, Z, Wang, L, Waters, K, Wedlake, A, Wijeyesakere, S, Wilson, D, Xiao, Z, Yang, H, Zahoranszky-Kohalmi, G, Zakharov, A, Zhang, F, Zhang, Z, Zhao, T, Zhu, H, Zorn, K, Casey, W, Kleinstreuer, N, Mansouri, Kamel, Karmaus, Agnes L, Fitzpatrick, Jeremy, Patlewicz, Grace, Pradeep, Prachi, Alberga, Domenico, Alepee, Nathalie, Allen, Timothy E H, Allen, Dave, Alves, Vinicius M, Andrade, Carolina H, Auernhammer, Tyler R, Ballabio, Davide, Bell, Shannon, Benfenati, Emilio, Bhattacharya, Sudin, Bastos, Joyce V, Boyd, Stephen, Brown, J B, Capuzzi, Stephen J, Chushak, Yaroslav, Ciallella, Heather, Clark, Alex M, Consonni, Viviana, Daga, Pankaj R, Ekins, Sean, Farag, Sherif, Fedorov, Maxim, Fourches, Denis, Gadaleta, Domenico, Gao, Feng, Gearhart, Jeffery M, Goh, Garett, Goodman, Jonathan M, Grisoni, Francesca, Grulke, Christopher M, Hartung, Thomas, Hirn, Matthew, Karpov, Pavel, Korotcov, Alexandru, Lavado, Giovanna J, Lawless, Michael, Li, Xinhao, Luechtefeld, Thomas, Lunghini, Filippo, Mangiatordi, Giuseppe F, Marcou, Gilles, Marsh, Dan, Martin, Todd, Mauri, Andrea, Muratov, Eugene N, Myatt, Glenn J, Nguyen, Dac-Trung, Nicolotti, Orazio, Note, Reine, Pande, Paritosh, Parks, Amanda K, Peryea, Tyler, Polash, Ahsan H, Rallo, Robert, Roncaglioni, Alessandra, Rowlands, Craig, Ruiz, Patricia, Russo, Daniel P, Sayed, Ahmed, Sayre, Risa, Sheils, Timothy, Siegel, Charles, Silva, Arthur C, Simeonov, Anton, Sosnin, Sergey, Southall, Noel, Strickland, Judy, Tang, Yun, Teppen, Brian, Tetko, Igor V, Thomas, Dennis, Tkachenko, Valery, Todeschini, Roberto, Toma, Cosimo, Tripodi, Ignacio, Trisciuzzi, Daniela, Tropsha, Alexander, Varnek, Alexandre, Vukovic, Kristijan, Wang, Zhongyu, Wang, Liguo, Waters, Katrina M, Wedlake, Andrew J, Wijeyesakere, Sanjeeva J, Wilson, Dan, Xiao, Zijun, Yang, Hongbin, Zahoranszky-Kohalmi, Gergely, Zakharov, Alexey V, Zhang, Fagen F, Zhang, Zhen, Zhao, Tongan, Zhu, Hao, Zorn, Kimberley M, Casey, Warren, Kleinstreuer, Nicole C, Mansouri, K, Karmaus, A, Fitzpatrick, J, Patlewicz, G, Pradeep, P, Alberga, D, Alepee, N, Allen, T, Allen, D, Alves, V, Andrade, C, Auernhammer, T, Ballabio, D, Bell, S, Benfenati, E, Bhattacharya, S, Bastos, J, Boyd, S, Brown, J, Capuzzi, S, Chushak, Y, Ciallella, H, Clark, A, Consonni, V, Daga, P, Ekins, S, Farag, S, Fedorov, M, Fourches, D, Gadaleta, D, Gao, F, Gearhart, J, Goh, G, Goodman, J, Grisoni, F, Grulke, C, Hartung, T, Hirn, M, Karpov, P, Korotcov, A, Lavado, G, Lawless, M, Li, X, Luechtefeld, T, Lunghini, F, Mangiatordi, G, Marcou, G, Marsh, D, Martin, T, Mauri, A, Muratov, E, Myatt, G, Nguyen, D, Nicolotti, O, Note, R, Pande, P, Parks, A, Peryea, T, Polash, A, Rallo, R, Roncaglioni, A, Rowlands, C, Ruiz, P, Russo, D, Sayed, A, Sayre, R, Sheils, T, Siegel, C, Silva, A, Simeonov, A, Sosnin, S, Southall, N, Strickland, J, Tang, Y, Teppen, B, Tetko, I, Thomas, D, Tkachenko, V, Todeschini, R, Toma, C, Tripodi, I, Trisciuzzi, D, Tropsha, A, Varnek, A, Vukovic, K, Wang, Z, Wang, L, Waters, K, Wedlake, A, Wijeyesakere, S, Wilson, D, Xiao, Z, Yang, H, Zahoranszky-Kohalmi, G, Zakharov, A, Zhang, F, Zhang, Z, Zhao, T, Zhu, H, Zorn, K, Casey, W, Kleinstreuer, N, Mansouri, Kamel, Karmaus, Agnes L, Fitzpatrick, Jeremy, Patlewicz, Grace, Pradeep, Prachi, Alberga, Domenico, Alepee, Nathalie, Allen, Timothy E H, Allen, Dave, Alves, Vinicius M, Andrade, Carolina H, Auernhammer, Tyler R, Ballabio, Davide, Bell, Shannon, Benfenati, Emilio, Bhattacharya, Sudin, Bastos, Joyce V, Boyd, Stephen, Brown, J B, Capuzzi, Stephen J, Chushak, Yaroslav, Ciallella, Heather, Clark, Alex M, Consonni, Viviana, Daga, Pankaj R, Ekins, Sean, Farag, Sherif, Fedorov, Maxim, Fourches, Denis, Gadaleta, Domenico, Gao, Feng, Gearhart, Jeffery M, Goh, Garett, Goodman, Jonathan M, Grisoni, Francesca, Grulke, Christopher M, Hartung, Thomas, Hirn, Matthew, Karpov, Pavel, Korotcov, Alexandru, Lavado, Giovanna J, Lawless, Michael, Li, Xinhao, Luechtefeld, Thomas, Lunghini, Filippo, Mangiatordi, Giuseppe F, Marcou, Gilles, Marsh, Dan, Martin, Todd, Mauri, Andrea, Muratov, Eugene N, Myatt, Glenn J, Nguyen, Dac-Trung, Nicolotti, Orazio, Note, Reine, Pande, Paritosh, Parks, Amanda K, Peryea, Tyler, Polash, Ahsan H, Rallo, Robert, Roncaglioni, Alessandra, Rowlands, Craig, Ruiz, Patricia, Russo, Daniel P, Sayed, Ahmed, Sayre, Risa, Sheils, Timothy, Siegel, Charles, Silva, Arthur C, Simeonov, Anton, Sosnin, Sergey, Southall, Noel, Strickland, Judy, Tang, Yun, Teppen, Brian, Tetko, Igor V, Thomas, Dennis, Tkachenko, Valery, Todeschini, Roberto, Toma, Cosimo, Tripodi, Ignacio, Trisciuzzi, Daniela, Tropsha, Alexander, Varnek, Alexandre, Vukovic, Kristijan, Wang, Zhongyu, Wang, Liguo, Waters, Katrina M, Wedlake, Andrew J, Wijeyesakere, Sanjeeva J, Wilson, Dan, Xiao, Zijun, Yang, Hongbin, Zahoranszky-Kohalmi, Gergely, Zakharov, Alexey V, Zhang, Fagen F, Zhang, Zhen, Zhao, Tongan, Zhu, Hao, Zorn, Kimberley M, Casey, Warren, and Kleinstreuer, Nicole C

Abstract

Background: Humans are exposed to tens of thousands of chemical substances that need to be assessed for their potential toxicity. Acute systemic toxicity testing serves as the basis for regulatory hazard classification, labeling, and risk management. However, it is cost- and time-prohibitive to evaluate all new and existing chemicals using traditional rodent acute toxicity tests. In silica models built using existing data facilitate rapid acute tox- icity predictions without using animals. Objkctivks: The U.S. Interagency Coordinating Committee on the Validation of Alternative Methods (ICCVAM) Acute Toxicity Workgroup organ- ized an international collaboration to develop in silica models for predicting acute oral toxicity based on five different end points: Lethal Dose 50 (LD50 value, U.S. Environmental Protection Agency hazard (four) categories, Globally Harmonized System for Classification and Labeling hazard (five) categories, very toxic chemicals [LD50 (LD50 ≤ 50 mg/kg)], and nontoxic chemicals (LD50 > 2,000 mg/kg). Mkthods: An acute oral toxicity data inventory for 11,992 chemicals was compiled, split into training and evaluation sets, and made available to 35 participating international research groups that submitted a total of 139 predictive models. Predictions that fell within the applicability domains of the submitted models were evaluated using external validation sets. These were then combined into consensus models to leverage strengths of individual approaches. Results: The resulting consensus predictions, which leverage the collective strengths of each individual model, form the Collaborative Acute Toxicity Modeling Suite (CATMoS). CATMoS demonstrated high performance in terms of accuracy and robustness when compared with in viva results. Discussion: CATMoS is being evaluated by regulatory agencies for its utility and applicability as a potential replacement for in viva rat acute oral toxicity studies. CATMoS predictions for more than 800,000 chemica

Published
2021

4. Identification of rare-disease genes using blood transcriptome sequencing and large control cohorts

Author

Fresard, Laure, Smail, Craig, Ferraro, Nicole M., Teran, Nicole A., Li, Xin, Smith, Kevin S., Bonner, Devon, Kernohan, Kristin D., Marwaha, Shruti, Zappala, Zachary, Balliu, Brunilda, Davis, Joe R., Liu, Boxiang, Prybol, Cameron J., Kohler, Jennefer N., Zastrow, Diane B., Reuter, Chloe M., Fisk, Dianna G., Grove, Megan E., Davidson, Jean M., Hartley, Taila, Joshi, Ruchi, Strober, Benjamin J., Utiramerur, Sowmithri, Lind, Lars, Ingelsson, Erik, Battle, Alexis, Bejerano, Gill, Bernstein, Jonathan A., Ashley, Euan A., Boycott, Kym M., Merker, Jason D., Wheeler, Matthew T., Montgomery, Stephen B., Adams, David R., Aday, Aaron, Alejandro, Mercedes E., Allard, Patrick, Azamian, Mahshid S., Bacino, Carlos A., Baker, Eva, Balasubramanyam, Ashok, Barseghyan, Hayk, Batzli, Gabriel F., Beggs, Alan H., Behnam, Babak, Bellen, Hugo J., Berry, Gerard T., Bican, Anna, Bick, David P., Birch, Camille L., Boone, Braden E., Bostwick, Bret L., Briere, Lauren C., Brokamp, Elly, Brown, Donna M., Brush, Matthew, Burke, Elizabeth A., Burrage, Lindsay C., Butte, Manish J., Chen, Shan, Clark, Gary D., Coakley, Terra R., Cogan, Joy D., Colley, Heather A., Cooper, Cynthia M., Cope, Heidi, Craigen, William J., D'Souza, Precilla, Davids, Mariska, Dayal, Jyoti G., Dell'Angelica, Esteban C., Dhar, Shweta U., Dipple, Katrina M., Donnell-Fink, Laurel A., Dorrani, Naghmeh, Dorset, Daniel C., Douine, Emilie D., Draper, David D., Dries, Annika M., Duncan, Laura, Eckstein, David J., Emrick, Lisa T., Eng, Christine M., Enns, Gregory M., Eskin, Ascia, Esteves, Cecilia, Estwick, Tyra, Fernandez, Liliana, Ferreira, Carlos, Fieg, Elizabeth L., Fisher, Paul G., Fogel, Brent L., Friedman, Noah D., Gahl, William A., Glanton, Emily, Godfrey, Rena A., Goldman, Alica M., Goldstein, David B., Gould, Sarah E., Gourdine, Jean-Philippe F., Groden, Catherine A., Gropman, Andrea L., Haendel, Melissa, Hamid, Rizwan, Hanchard, Neil A., High, Frances, Holm, Ingrid A., Hom, Jason, Howerton, Ellen M., Huang, Yong, Jamal, Fariha, Jiang, Yong-hui, Johnston, Jean M., Jones, Angela L., Karaviti, Lefkothea, Koeller, David M., Kohane, Isaac S., Krasnewich, Donna M., Korrick, Susan, Koziura, Mary, Krier, Joel B., Kyle, Jennifer E., Lalani, Seema R., Lau, C. Christopher, Lazar, Jozef, LeBlanc, Kimberly, Lee, Brendan H., Lee, Hane, Levy, Shawn E., Lewis, Richard A., Lincoln, Sharyn A., Loo, Sandra K., Loscalzo, Joseph, Maas, Richard L., Macnamara, Ellen F., MacRae, Calum A., Maduro, Valerie V., Majcherska, Marta M., Malicdan, May Christine V., Mamounas, Laura A., Manolio, Teri A., Markello, Thomas C., Marom, Ronit, Martin, G. Martin, Martinez-Agosto, Julian A., May, Thomas, McConkie-Rosell, Allyn, McCormack, Colleen E., McCray, Alexa T., Metz, Thomas O., Might, Matthew, Moretti, Paolo M., Morimoto, Marie, Mulvihill, John J., Murdock, David R., Murphy, Jennifer L., Muzny, Donna M., Nehrebecky, Michele E., Nelson, Stan F., Newberry, J. Scott, Newman, John H., Nicholas, Sarah K., Novacic, Donna, Orange, Jordan S., Orengo, James P., Pallais, J. Carl, Palmer, Christina G. S., Papp, Jeanette C., Parker, Neil H., Pena, Loren D. M., Phillips, John A., III, Posey, Jennifer E., Postlethwait, John H., Potocki, Lorraine, Pusey, Barbara N., Renteria, Genecee, Rives, Lynette, Robertson, Amy K., Rodan, Lance H., Rosenfeld, Jill A., Sampson, Jacinda B., Samson, Susan L., Schoch, Kelly, Scott, Daryl A., Shakachite, Lisa, Sharma, Prashant, Shashi, Vandana, Signer, Rebecca, Silverman, Edwin K., Sinsheimer, Janet S., Spillmann, Rebecca C., Stoler, Joan M., Stong, Nicholas, Sullivan, Jennifer A., Sweetser, David A., Tan, Queenie K. -G., Tifft, Cynthia J., Toro, Camilo, Tran, Alyssa A., Urv, Tiina K., Vilain, Eric, Vogel, Tiphanie P., Waggott, Daryl M., Wahl, Colleen E., Walley, Nicole M., Walsh, Chris A., Walker, Melissa, Wan, Jijun, Wangler, Michael F., Ward, Patricia A., Waters, Katrina M., Webb-Robertson, Bobbie-Jo M., Westerfield, Monte, Wise, Anastasia L., Wolfe, Lynne A., Worthey, Elizabeth A., Yamamoto, Shinya, Yang, John, Yang, Yaping, Yoon, Amanda J., Yu, Guoyun, Zhao, Chunli, Zheng, Allison, Boycott, Kym, MacKenzie, Alex, Majewski, Jacek, Brudno, Michael, Bulman, Dennis, Dyment, David, Fresard, Laure, Smail, Craig, Ferraro, Nicole M., Teran, Nicole A., Li, Xin, Smith, Kevin S., Bonner, Devon, Kernohan, Kristin D., Marwaha, Shruti, Zappala, Zachary, Balliu, Brunilda, Davis, Joe R., Liu, Boxiang, Prybol, Cameron J., Kohler, Jennefer N., Zastrow, Diane B., Reuter, Chloe M., Fisk, Dianna G., Grove, Megan E., Davidson, Jean M., Hartley, Taila, Joshi, Ruchi, Strober, Benjamin J., Utiramerur, Sowmithri, Lind, Lars, Ingelsson, Erik, Battle, Alexis, Bejerano, Gill, Bernstein, Jonathan A., Ashley, Euan A., Boycott, Kym M., Merker, Jason D., Wheeler, Matthew T., Montgomery, Stephen B., Adams, David R., Aday, Aaron, Alejandro, Mercedes E., Allard, Patrick, Azamian, Mahshid S., Bacino, Carlos A., Baker, Eva, Balasubramanyam, Ashok, Barseghyan, Hayk, Batzli, Gabriel F., Beggs, Alan H., Behnam, Babak, Bellen, Hugo J., Berry, Gerard T., Bican, Anna, Bick, David P., Birch, Camille L., Boone, Braden E., Bostwick, Bret L., Briere, Lauren C., Brokamp, Elly, Brown, Donna M., Brush, Matthew, Burke, Elizabeth A., Burrage, Lindsay C., Butte, Manish J., Chen, Shan, Clark, Gary D., Coakley, Terra R., Cogan, Joy D., Colley, Heather A., Cooper, Cynthia M., Cope, Heidi, Craigen, William J., D'Souza, Precilla, Davids, Mariska, Dayal, Jyoti G., Dell'Angelica, Esteban C., Dhar, Shweta U., Dipple, Katrina M., Donnell-Fink, Laurel A., Dorrani, Naghmeh, Dorset, Daniel C., Douine, Emilie D., Draper, David D., Dries, Annika M., Duncan, Laura, Eckstein, David J., Emrick, Lisa T., Eng, Christine M., Enns, Gregory M., Eskin, Ascia, Esteves, Cecilia, Estwick, Tyra, Fernandez, Liliana, Ferreira, Carlos, Fieg, Elizabeth L., Fisher, Paul G., Fogel, Brent L., Friedman, Noah D., Gahl, William A., Glanton, Emily, Godfrey, Rena A., Goldman, Alica M., Goldstein, David B., Gould, Sarah E., Gourdine, Jean-Philippe F., Groden, Catherine A., Gropman, Andrea L., Haendel, Melissa, Hamid, Rizwan, Hanchard, Neil A., High, Frances, Holm, Ingrid A., Hom, Jason, Howerton, Ellen M., Huang, Yong, Jamal, Fariha, Jiang, Yong-hui, Johnston, Jean M., Jones, Angela L., Karaviti, Lefkothea, Koeller, David M., Kohane, Isaac S., Krasnewich, Donna M., Korrick, Susan, Koziura, Mary, Krier, Joel B., Kyle, Jennifer E., Lalani, Seema R., Lau, C. Christopher, Lazar, Jozef, LeBlanc, Kimberly, Lee, Brendan H., Lee, Hane, Levy, Shawn E., Lewis, Richard A., Lincoln, Sharyn A., Loo, Sandra K., Loscalzo, Joseph, Maas, Richard L., Macnamara, Ellen F., MacRae, Calum A., Maduro, Valerie V., Majcherska, Marta M., Malicdan, May Christine V., Mamounas, Laura A., Manolio, Teri A., Markello, Thomas C., Marom, Ronit, Martin, G. Martin, Martinez-Agosto, Julian A., May, Thomas, McConkie-Rosell, Allyn, McCormack, Colleen E., McCray, Alexa T., Metz, Thomas O., Might, Matthew, Moretti, Paolo M., Morimoto, Marie, Mulvihill, John J., Murdock, David R., Murphy, Jennifer L., Muzny, Donna M., Nehrebecky, Michele E., Nelson, Stan F., Newberry, J. Scott, Newman, John H., Nicholas, Sarah K., Novacic, Donna, Orange, Jordan S., Orengo, James P., Pallais, J. Carl, Palmer, Christina G. S., Papp, Jeanette C., Parker, Neil H., Pena, Loren D. M., Phillips, John A., III, Posey, Jennifer E., Postlethwait, John H., Potocki, Lorraine, Pusey, Barbara N., Renteria, Genecee, Rives, Lynette, Robertson, Amy K., Rodan, Lance H., Rosenfeld, Jill A., Sampson, Jacinda B., Samson, Susan L., Schoch, Kelly, Scott, Daryl A., Shakachite, Lisa, Sharma, Prashant, Shashi, Vandana, Signer, Rebecca, Silverman, Edwin K., Sinsheimer, Janet S., Spillmann, Rebecca C., Stoler, Joan M., Stong, Nicholas, Sullivan, Jennifer A., Sweetser, David A., Tan, Queenie K. -G., Tifft, Cynthia J., Toro, Camilo, Tran, Alyssa A., Urv, Tiina K., Vilain, Eric, Vogel, Tiphanie P., Waggott, Daryl M., Wahl, Colleen E., Walley, Nicole M., Walsh, Chris A., Walker, Melissa, Wan, Jijun, Wangler, Michael F., Ward, Patricia A., Waters, Katrina M., Webb-Robertson, Bobbie-Jo M., Westerfield, Monte, Wise, Anastasia L., Wolfe, Lynne A., Worthey, Elizabeth A., Yamamoto, Shinya, Yang, John, Yang, Yaping, Yoon, Amanda J., Yu, Guoyun, Zhao, Chunli, Zheng, Allison, Boycott, Kym, MacKenzie, Alex, Majewski, Jacek, Brudno, Michael, Bulman, Dennis, and Dyment, David

Abstract

It is estimated that 350 million individuals worldwide suffer from rare diseases, which are predominantly caused by mutation in a single gene(1). The current molecular diagnostic rate is estimated at 50%, with whole-exome sequencing (WES) among the most successful approaches(2-5). For patients in whom WES is uninformative, RNA sequencing (RNA-seq) has shown diagnostic utility in specific tissues and diseases(6-8). This includes muscle biopsies from patients with undiagnosed rare muscle disorders(6,9), and cultured fibroblasts from patients with mitochondrial disorders(7). However, for many individuals, biopsies are not performed for clinical care, and tissues are difficult to access. We sought to assess the utility of RNA-seq from blood as a diagnostic tool for rare diseases of different pathophysiologies. We generated whole-blood RNA-seq from 94 individuals with undiagnosed rare diseases spanning 16 diverse disease categories. We developed a robust approach to compare data from these individuals with large sets of RNA-seq data for controls (n = 1,594 unrelated controls and n = 49 family members) and demonstrated the impacts of expression, splicing, gene and variant filtering strategies on disease gene identification. Across our cohort, we observed that RNA-seq yields a 7.5% diagnostic rate, and an additional 16.7% with improved candidate gene resolution., Group Authors: Undiagnosed Dis Network ; Care4Rare Canada Consortium

Published
2019
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5. Spectrum of neurodevelopmental disease associated with the GNAO1 guanosine triphosphate-binding region

Author

Kelly, McKenna, Park, Meredith, Mihalek, Ivana, Rochtus, Anne, Gramm, Marie, Perez-Palma, Eduardo, Axeen, Erika Takle, Hung, Christina Y., Olson, Heather, Swanson, Lindsay, Anselm, Irina, Briere, Lauren C., High, Frances A., Sweetser, David A., Kayani, Saima, Snyder, Molly, Calvert, Sophie, Scheffer, Ingrid E., Yang, Edward, Waugh, Jeff L., Lal, Dennis, Bodamer, Olaf, Poduri, Annapurna, Adams, David R., Aday, Aaron, Alejandro, Mercedes E., Allard, Patrick, Ashley, Euan A., Azamian, Mahshid S., Bacino, Carlos A., Baker, Eva, Balasubramanyam, Ashok, Barseghyan, Hayk, Batzli, Gabriel F., Beggs, Alan H., Behnam, Babak, Bellen, Hugo J., Bernstein, Jonathan A., Bican, Anna, Bick, David P., Birch, Camille L., Bonner, Devon, Boone, Braden E., Bostwick, Bret L., Brokamp, Elly, Brown, Donna M., Brush, Matthew, Burke, Elizabeth A., Burrage, Lindsay C., Butte, Manish J., Chen, Shan, Clark, Gary D., Coakley, Terra R., Cogan, Joy D., Colley, Heather A., Cooper, Cynthia M., Cope, Heidi, Craigen, William J., D'Souza, Precilla, Davids, Mariska, Davidson, Jean M., Dayal, Jyoti G., Dell'Angelica, Esteban C., Dhar, Shweta U., Dipple, Katrina M., Donnell-Fink, Laurel A., Dorrani, Naghmeh, Dorset, Daniel C., Douine, Emilie D., Draper, David D., Dries, Annika M., Eckstein, David J., Emrick, Lisa T., Eng, Christine M., Enns, Gre-Gory M., Eskin, Ascia, Esteves, Cecilia, Estwick, Tyra, Fairbrother, Laura, Fernandez, Liliana, Ferreira, Carlos, Fieg, Elizabeth L., Fisher, Paul G., Fogel, Brent L., Friedman, Noah D., Gahl, William A., Glanton, Emily, Godfrey, Rena A., Goldman, Alica M., Goldstein, David B., Gould, Sarah E., Gourdine, Jean-Philippe F., Groden, Catherine A., Gropman, Andrea L., Haendel, Melissa, Hamid, Rizwan, Hanchard, Neil A., High, Francis, Holm, Ingrid A., Horn, Jason, Howerton, Ellen M., Huang, Yong, Jamal, Fariha, Jiang, Yong-hui, Johnston, Jean M., Jones, Angela L., Karaviti, Lefkothea, Koeller, David M., Kohane, Isaac S., Kohler, Jennefer N., Konick, Susan, Koziura, Mary, Krasnewich, Donna M., Krier, Joel B., Kyle, Jennifer E., Lalani, Seema R., Lau, C. Christopher, Lazar, Jozef, LeBlanc, Kimberly, Lee, Brendan H., Lee, Hane, Levy, Shawn E., Lewis, Richard A., Lincoln, Sharyn A., Loo, Sandra K., Loscalzo, Joseph, Maas, Richard L., Macnamara, Ellen F., MacRae, Calum A., Maduro, Valerie V., Majch-erska, Marta M., Malicdan, May Christine, V, Mamounas, Laura A., Manolio, Teri A., Markello, Thomas C., Marom, Ronit, Martin, Martin G., Martinez-Agosto, Julian A., Mar-waha, Shruti, May, Thomas, McConkie-Rosell, Allyn, McCormack, Colleen E., McCray, Alexa F., Merker, Jason D., Metz, Thomas O., Might, Matthew, Moretti, Paolo M., Morimoto, Marie, Mulvihill, John J., Murdock, David R., Murphy, Jennifer L., Muzny, Donna M., Nehrebecky, Michele E., Nelson, Stan F., Newberry, J. Scott, Newman, John H., Nicholas, Sarah K., Novacic, Donna, Orange, Jordan S., Orengo, James P., Pallais, J. Carl, Palmer, Christina G. S., Papp, Jeanette C., Parker, Neil H., Pena, Loren D. M., Phillips, John A., III, Posey, Jennifer E., Postlethwait, John H., Potocki, Lorraine, Pusey, Barbara N., Reuter, Chloe M., Rives, Lynette, Robertson, Amy K., Rodan, Lance H., Rosenfeld, Jill A., Sampson, Jacinda B., Samson, Susan L., Schoch, Kelly, Scott, Daryl A., Shakachite, Lisa, Sharma, Prashant, Shashi, Vandana, Signer, Rebecca, Silverman, Edwin K., Sinsheimer, Janet S., Smith, Kevin S., Spillmann, Rebecca C., Stoler, Joan M., Stong, Nicholas, Sullivan, Jennifer A., Tan, Queenie K-G, Tifft, Cynthia J., Toro, Camilo, Tran, Alyssa A., Urv, Tiina K., Vilain, Eric, Vogel, Tiphanie P., Waggott, Daryl M., Wahl, Colleen E., Walker, Melissa, Walley, Nicole M., Walsh, Chris A., Wan, Jijun, Wangler, Michael F., Ward, Patricia A., Waters, Katrina M., Webb-Robertson, Bobbie-Jo M., Westerfield, Monte, Wheeler, Matthew T., Wise, Anastasia L., Wolfe, Lynne A., Worthey, Elizabeth A., Yamamoto, Shinya, Yang, Yaping, Yoon, Amanda J., Yu, Guoyun, Zastrow, Diane B., Zhao, Chunli, Zheng, Allison, Kelly, McKenna, Park, Meredith, Mihalek, Ivana, Rochtus, Anne, Gramm, Marie, Perez-Palma, Eduardo, Axeen, Erika Takle, Hung, Christina Y., Olson, Heather, Swanson, Lindsay, Anselm, Irina, Briere, Lauren C., High, Frances A., Sweetser, David A., Kayani, Saima, Snyder, Molly, Calvert, Sophie, Scheffer, Ingrid E., Yang, Edward, Waugh, Jeff L., Lal, Dennis, Bodamer, Olaf, Poduri, Annapurna, Adams, David R., Aday, Aaron, Alejandro, Mercedes E., Allard, Patrick, Ashley, Euan A., Azamian, Mahshid S., Bacino, Carlos A., Baker, Eva, Balasubramanyam, Ashok, Barseghyan, Hayk, Batzli, Gabriel F., Beggs, Alan H., Behnam, Babak, Bellen, Hugo J., Bernstein, Jonathan A., Bican, Anna, Bick, David P., Birch, Camille L., Bonner, Devon, Boone, Braden E., Bostwick, Bret L., Brokamp, Elly, Brown, Donna M., Brush, Matthew, Burke, Elizabeth A., Burrage, Lindsay C., Butte, Manish J., Chen, Shan, Clark, Gary D., Coakley, Terra R., Cogan, Joy D., Colley, Heather A., Cooper, Cynthia M., Cope, Heidi, Craigen, William J., D'Souza, Precilla, Davids, Mariska, Davidson, Jean M., Dayal, Jyoti G., Dell'Angelica, Esteban C., Dhar, Shweta U., Dipple, Katrina M., Donnell-Fink, Laurel A., Dorrani, Naghmeh, Dorset, Daniel C., Douine, Emilie D., Draper, David D., Dries, Annika M., Eckstein, David J., Emrick, Lisa T., Eng, Christine M., Enns, Gre-Gory M., Eskin, Ascia, Esteves, Cecilia, Estwick, Tyra, Fairbrother, Laura, Fernandez, Liliana, Ferreira, Carlos, Fieg, Elizabeth L., Fisher, Paul G., Fogel, Brent L., Friedman, Noah D., Gahl, William A., Glanton, Emily, Godfrey, Rena A., Goldman, Alica M., Goldstein, David B., Gould, Sarah E., Gourdine, Jean-Philippe F., Groden, Catherine A., Gropman, Andrea L., Haendel, Melissa, Hamid, Rizwan, Hanchard, Neil A., High, Francis, Holm, Ingrid A., Horn, Jason, Howerton, Ellen M., Huang, Yong, Jamal, Fariha, Jiang, Yong-hui, Johnston, Jean M., Jones, Angela L., Karaviti, Lefkothea, Koeller, David M., Kohane, Isaac S., Kohler, Jennefer N., Konick, Susan, Koziura, Mary, Krasnewich, Donna M., Krier, Joel B., Kyle, Jennifer E., Lalani, Seema R., Lau, C. Christopher, Lazar, Jozef, LeBlanc, Kimberly, Lee, Brendan H., Lee, Hane, Levy, Shawn E., Lewis, Richard A., Lincoln, Sharyn A., Loo, Sandra K., Loscalzo, Joseph, Maas, Richard L., Macnamara, Ellen F., MacRae, Calum A., Maduro, Valerie V., Majch-erska, Marta M., Malicdan, May Christine, V, Mamounas, Laura A., Manolio, Teri A., Markello, Thomas C., Marom, Ronit, Martin, Martin G., Martinez-Agosto, Julian A., Mar-waha, Shruti, May, Thomas, McConkie-Rosell, Allyn, McCormack, Colleen E., McCray, Alexa F., Merker, Jason D., Metz, Thomas O., Might, Matthew, Moretti, Paolo M., Morimoto, Marie, Mulvihill, John J., Murdock, David R., Murphy, Jennifer L., Muzny, Donna M., Nehrebecky, Michele E., Nelson, Stan F., Newberry, J. Scott, Newman, John H., Nicholas, Sarah K., Novacic, Donna, Orange, Jordan S., Orengo, James P., Pallais, J. Carl, Palmer, Christina G. S., Papp, Jeanette C., Parker, Neil H., Pena, Loren D. M., Phillips, John A., III, Posey, Jennifer E., Postlethwait, John H., Potocki, Lorraine, Pusey, Barbara N., Reuter, Chloe M., Rives, Lynette, Robertson, Amy K., Rodan, Lance H., Rosenfeld, Jill A., Sampson, Jacinda B., Samson, Susan L., Schoch, Kelly, Scott, Daryl A., Shakachite, Lisa, Sharma, Prashant, Shashi, Vandana, Signer, Rebecca, Silverman, Edwin K., Sinsheimer, Janet S., Smith, Kevin S., Spillmann, Rebecca C., Stoler, Joan M., Stong, Nicholas, Sullivan, Jennifer A., Tan, Queenie K-G, Tifft, Cynthia J., Toro, Camilo, Tran, Alyssa A., Urv, Tiina K., Vilain, Eric, Vogel, Tiphanie P., Waggott, Daryl M., Wahl, Colleen E., Walker, Melissa, Walley, Nicole M., Walsh, Chris A., Wan, Jijun, Wangler, Michael F., Ward, Patricia A., Waters, Katrina M., Webb-Robertson, Bobbie-Jo M., Westerfield, Monte, Wheeler, Matthew T., Wise, Anastasia L., Wolfe, Lynne A., Worthey, Elizabeth A., Yamamoto, Shinya, Yang, Yaping, Yoon, Amanda J., Yu, Guoyun, Zastrow, Diane B., Zhao, Chunli, and Zheng, Allison

Abstract

Objective To characterize the phenotypic spectrum associated with GNAO1 variants and establish genotype-protein structure-phenotype relationships. Methods We evaluated the phenotypes of 14 patients with GNAO1 variants, analyzed their variants for potential pathogenicity, and mapped them, along with those in the literature, on a three-dimensional structural protein model. Results The 14 patients in our cohort, including one sibling pair, had 13 distinct, heterozygous GNAO1 variants classified as pathogenic or likely pathogenic. We attributed the same variant in two siblings to parental mosaicism. Patients initially presented with seizures beginning in the first 3 months of life (8/14), developmental delay (4/14), hypotonia (1/14), or movement disorder (1/14). All patients had hypotonia and developmental delay ranging from mild to severe. Nine had epilepsy, and nine had movement disorders, including dystonia, ataxia, chorea, and dyskinesia. The 13 GNAO1 variants in our patients are predicted to result in amino acid substitutions or deletions in the GNAO1 guanosine triphosphate (GTP)-binding region, analogous to those in previous publications. Patients with variants affecting amino acids 207-221 had only movement disorder and hypotonia. Patients with variants affecting the C-terminal region had the mildest phenotypes.

Published
2019

6. Spectrum of neurodevelopmental disease associated with the GNAO1 guanosine triphosphate-binding region

Author

Kelly, McKenna, Park, Meredith, Mihalek, Ivana, Rochtus, Anne, Gramm, Marie, Perez-Palma, Eduardo, Axeen, Erika Takle, Hung, Christina Y., Olson, Heather, Swanson, Lindsay, Anselm, Irina, Briere, Lauren C., High, Frances A., Sweetser, David A., Kayani, Saima, Snyder, Molly, Calvert, Sophie, Scheffer, Ingrid E., Yang, Edward, Waugh, Jeff L., Lal, Dennis, Bodamer, Olaf, Poduri, Annapurna, Adams, David R., Aday, Aaron, Alejandro, Mercedes E., Allard, Patrick, Ashley, Euan A., Azamian, Mahshid S., Bacino, Carlos A., Baker, Eva, Balasubramanyam, Ashok, Barseghyan, Hayk, Batzli, Gabriel F., Beggs, Alan H., Behnam, Babak, Bellen, Hugo J., Bernstein, Jonathan A., Bican, Anna, Bick, David P., Birch, Camille L., Bonner, Devon, Boone, Braden E., Bostwick, Bret L., Brokamp, Elly, Brown, Donna M., Brush, Matthew, Burke, Elizabeth A., Burrage, Lindsay C., Butte, Manish J., Chen, Shan, Clark, Gary D., Coakley, Terra R., Cogan, Joy D., Colley, Heather A., Cooper, Cynthia M., Cope, Heidi, Craigen, William J., D'Souza, Precilla, Davids, Mariska, Davidson, Jean M., Dayal, Jyoti G., Dell'Angelica, Esteban C., Dhar, Shweta U., Dipple, Katrina M., Donnell-Fink, Laurel A., Dorrani, Naghmeh, Dorset, Daniel C., Douine, Emilie D., Draper, David D., Dries, Annika M., Eckstein, David J., Emrick, Lisa T., Eng, Christine M., Enns, Gre-Gory M., Eskin, Ascia, Esteves, Cecilia, Estwick, Tyra, Fairbrother, Laura, Fernandez, Liliana, Ferreira, Carlos, Fieg, Elizabeth L., Fisher, Paul G., Fogel, Brent L., Friedman, Noah D., Gahl, William A., Glanton, Emily, Godfrey, Rena A., Goldman, Alica M., Goldstein, David B., Gould, Sarah E., Gourdine, Jean-Philippe F., Groden, Catherine A., Gropman, Andrea L., Haendel, Melissa, Hamid, Rizwan, Hanchard, Neil A., High, Francis, Holm, Ingrid A., Horn, Jason, Howerton, Ellen M., Huang, Yong, Jamal, Fariha, Jiang, Yong-hui, Johnston, Jean M., Jones, Angela L., Karaviti, Lefkothea, Koeller, David M., Kohane, Isaac S., Kohler, Jennefer N., Konick, Susan, Koziura, Mary, Krasnewich, Donna M., Krier, Joel B., Kyle, Jennifer E., Lalani, Seema R., Lau, C. Christopher, Lazar, Jozef, LeBlanc, Kimberly, Lee, Brendan H., Lee, Hane, Levy, Shawn E., Lewis, Richard A., Lincoln, Sharyn A., Loo, Sandra K., Loscalzo, Joseph, Maas, Richard L., Macnamara, Ellen F., MacRae, Calum A., Maduro, Valerie V., Majch-erska, Marta M., Malicdan, May Christine, V, Mamounas, Laura A., Manolio, Teri A., Markello, Thomas C., Marom, Ronit, Martin, Martin G., Martinez-Agosto, Julian A., Mar-waha, Shruti, May, Thomas, McConkie-Rosell, Allyn, McCormack, Colleen E., McCray, Alexa F., Merker, Jason D., Metz, Thomas O., Might, Matthew, Moretti, Paolo M., Morimoto, Marie, Mulvihill, John J., Murdock, David R., Murphy, Jennifer L., Muzny, Donna M., Nehrebecky, Michele E., Nelson, Stan F., Newberry, J. Scott, Newman, John H., Nicholas, Sarah K., Novacic, Donna, Orange, Jordan S., Orengo, James P., Pallais, J. Carl, Palmer, Christina G. S., Papp, Jeanette C., Parker, Neil H., Pena, Loren D. M., Phillips, John A., III, Posey, Jennifer E., Postlethwait, John H., Potocki, Lorraine, Pusey, Barbara N., Reuter, Chloe M., Rives, Lynette, Robertson, Amy K., Rodan, Lance H., Rosenfeld, Jill A., Sampson, Jacinda B., Samson, Susan L., Schoch, Kelly, Scott, Daryl A., Shakachite, Lisa, Sharma, Prashant, Shashi, Vandana, Signer, Rebecca, Silverman, Edwin K., Sinsheimer, Janet S., Smith, Kevin S., Spillmann, Rebecca C., Stoler, Joan M., Stong, Nicholas, Sullivan, Jennifer A., Tan, Queenie K-G, Tifft, Cynthia J., Toro, Camilo, Tran, Alyssa A., Urv, Tiina K., Vilain, Eric, Vogel, Tiphanie P., Waggott, Daryl M., Wahl, Colleen E., Walker, Melissa, Walley, Nicole M., Walsh, Chris A., Wan, Jijun, Wangler, Michael F., Ward, Patricia A., Waters, Katrina M., Webb-Robertson, Bobbie-Jo M., Westerfield, Monte, Wheeler, Matthew T., Wise, Anastasia L., Wolfe, Lynne A., Worthey, Elizabeth A., Yamamoto, Shinya, Yang, Yaping, Yoon, Amanda J., Yu, Guoyun, Zastrow, Diane B., Zhao, Chunli, Zheng, Allison, Kelly, McKenna, Park, Meredith, Mihalek, Ivana, Rochtus, Anne, Gramm, Marie, Perez-Palma, Eduardo, Axeen, Erika Takle, Hung, Christina Y., Olson, Heather, Swanson, Lindsay, Anselm, Irina, Briere, Lauren C., High, Frances A., Sweetser, David A., Kayani, Saima, Snyder, Molly, Calvert, Sophie, Scheffer, Ingrid E., Yang, Edward, Waugh, Jeff L., Lal, Dennis, Bodamer, Olaf, Poduri, Annapurna, Adams, David R., Aday, Aaron, Alejandro, Mercedes E., Allard, Patrick, Ashley, Euan A., Azamian, Mahshid S., Bacino, Carlos A., Baker, Eva, Balasubramanyam, Ashok, Barseghyan, Hayk, Batzli, Gabriel F., Beggs, Alan H., Behnam, Babak, Bellen, Hugo J., Bernstein, Jonathan A., Bican, Anna, Bick, David P., Birch, Camille L., Bonner, Devon, Boone, Braden E., Bostwick, Bret L., Brokamp, Elly, Brown, Donna M., Brush, Matthew, Burke, Elizabeth A., Burrage, Lindsay C., Butte, Manish J., Chen, Shan, Clark, Gary D., Coakley, Terra R., Cogan, Joy D., Colley, Heather A., Cooper, Cynthia M., Cope, Heidi, Craigen, William J., D'Souza, Precilla, Davids, Mariska, Davidson, Jean M., Dayal, Jyoti G., Dell'Angelica, Esteban C., Dhar, Shweta U., Dipple, Katrina M., Donnell-Fink, Laurel A., Dorrani, Naghmeh, Dorset, Daniel C., Douine, Emilie D., Draper, David D., Dries, Annika M., Eckstein, David J., Emrick, Lisa T., Eng, Christine M., Enns, Gre-Gory M., Eskin, Ascia, Esteves, Cecilia, Estwick, Tyra, Fairbrother, Laura, Fernandez, Liliana, Ferreira, Carlos, Fieg, Elizabeth L., Fisher, Paul G., Fogel, Brent L., Friedman, Noah D., Gahl, William A., Glanton, Emily, Godfrey, Rena A., Goldman, Alica M., Goldstein, David B., Gould, Sarah E., Gourdine, Jean-Philippe F., Groden, Catherine A., Gropman, Andrea L., Haendel, Melissa, Hamid, Rizwan, Hanchard, Neil A., High, Francis, Holm, Ingrid A., Horn, Jason, Howerton, Ellen M., Huang, Yong, Jamal, Fariha, Jiang, Yong-hui, Johnston, Jean M., Jones, Angela L., Karaviti, Lefkothea, Koeller, David M., Kohane, Isaac S., Kohler, Jennefer N., Konick, Susan, Koziura, Mary, Krasnewich, Donna M., Krier, Joel B., Kyle, Jennifer E., Lalani, Seema R., Lau, C. Christopher, Lazar, Jozef, LeBlanc, Kimberly, Lee, Brendan H., Lee, Hane, Levy, Shawn E., Lewis, Richard A., Lincoln, Sharyn A., Loo, Sandra K., Loscalzo, Joseph, Maas, Richard L., Macnamara, Ellen F., MacRae, Calum A., Maduro, Valerie V., Majch-erska, Marta M., Malicdan, May Christine, V, Mamounas, Laura A., Manolio, Teri A., Markello, Thomas C., Marom, Ronit, Martin, Martin G., Martinez-Agosto, Julian A., Mar-waha, Shruti, May, Thomas, McConkie-Rosell, Allyn, McCormack, Colleen E., McCray, Alexa F., Merker, Jason D., Metz, Thomas O., Might, Matthew, Moretti, Paolo M., Morimoto, Marie, Mulvihill, John J., Murdock, David R., Murphy, Jennifer L., Muzny, Donna M., Nehrebecky, Michele E., Nelson, Stan F., Newberry, J. Scott, Newman, John H., Nicholas, Sarah K., Novacic, Donna, Orange, Jordan S., Orengo, James P., Pallais, J. Carl, Palmer, Christina G. S., Papp, Jeanette C., Parker, Neil H., Pena, Loren D. M., Phillips, John A., III, Posey, Jennifer E., Postlethwait, John H., Potocki, Lorraine, Pusey, Barbara N., Reuter, Chloe M., Rives, Lynette, Robertson, Amy K., Rodan, Lance H., Rosenfeld, Jill A., Sampson, Jacinda B., Samson, Susan L., Schoch, Kelly, Scott, Daryl A., Shakachite, Lisa, Sharma, Prashant, Shashi, Vandana, Signer, Rebecca, Silverman, Edwin K., Sinsheimer, Janet S., Smith, Kevin S., Spillmann, Rebecca C., Stoler, Joan M., Stong, Nicholas, Sullivan, Jennifer A., Tan, Queenie K-G, Tifft, Cynthia J., Toro, Camilo, Tran, Alyssa A., Urv, Tiina K., Vilain, Eric, Vogel, Tiphanie P., Waggott, Daryl M., Wahl, Colleen E., Walker, Melissa, Walley, Nicole M., Walsh, Chris A., Wan, Jijun, Wangler, Michael F., Ward, Patricia A., Waters, Katrina M., Webb-Robertson, Bobbie-Jo M., Westerfield, Monte, Wheeler, Matthew T., Wise, Anastasia L., Wolfe, Lynne A., Worthey, Elizabeth A., Yamamoto, Shinya, Yang, Yaping, Yoon, Amanda J., Yu, Guoyun, Zastrow, Diane B., Zhao, Chunli, and Zheng, Allison

Abstract

Objective To characterize the phenotypic spectrum associated with GNAO1 variants and establish genotype-protein structure-phenotype relationships. Methods We evaluated the phenotypes of 14 patients with GNAO1 variants, analyzed their variants for potential pathogenicity, and mapped them, along with those in the literature, on a three-dimensional structural protein model. Results The 14 patients in our cohort, including one sibling pair, had 13 distinct, heterozygous GNAO1 variants classified as pathogenic or likely pathogenic. We attributed the same variant in two siblings to parental mosaicism. Patients initially presented with seizures beginning in the first 3 months of life (8/14), developmental delay (4/14), hypotonia (1/14), or movement disorder (1/14). All patients had hypotonia and developmental delay ranging from mild to severe. Nine had epilepsy, and nine had movement disorders, including dystonia, ataxia, chorea, and dyskinesia. The 13 GNAO1 variants in our patients are predicted to result in amino acid substitutions or deletions in the GNAO1 guanosine triphosphate (GTP)-binding region, analogous to those in previous publications. Patients with variants affecting amino acids 207-221 had only movement disorder and hypotonia. Patients with variants affecting the C-terminal region had the mildest phenotypes.

Published
2019

7. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

Author

Wang, Mingxun, Carver, Jeremy J., Phelan, Vanessa V., Sanchez, Laura M., Garg, Neha, Peng, Yao, Don Duy Nguyen, Watrous, Jeramie, Kapono, Clifford A., Luzzatto-knaan, Tal, Porto, Carla, Bouslimani, Amina, Melnik, Alexey V., Meehan, Michael J., Liu, Wei -ting, Criisemann, Max, Boudreau, Paul D., Esquenazi, Eduardo, Sandoval-calderon, Mario, Kersten, Roland D., Pace, Laura A., Quinn, Robert A., Duncan, Katherine R., Hsu, Cheng-chih, Floros, Dimitrios J., Gavilan, Ronnie G., Kleigrewe, Karin, Northen, Trent, Dutton, Rachel J., Parrot, Delphine, Carlson, Erin E., Aigle, Bertrand, Michelsen, Charlotte F., Jelsbak, Lars, Sohlenkamp, Christian, Pevzner, Pavel, Edlund, Anna, Mclean, Jeffrey, Piel, Jorn, Murphy, Brian T., Gerwick, Lena, Liaw, Chih-chuang, Yang, Yu-liang, Humpf, Hans-ulrich, Maansson, Maria, Keyzers, Robert A., Sims, Amy C., Johnson, Andrew R., Sidebottom, Ashley M., Sedio, Brian E., Klitgaard, Andreas, Larson, Charles B., Boya P, Cristopher A., Torres-mendoza, Daniel, Gonzalez, David J., Silva, Denise B., Marques, Lucas M., Demarque, Daniel P., Pociute, Egle, O'Neill, Ellis C., Briand, Enora, Helfrich, Eric J. N., Granatosky, Eve A., Glukhov, Evgenia, Ryffel, Florian, Houson, Hailey, Mohimani, Hosein, Kharbush, Jenan J., Zeng, Yi, Vorholt, Julia A., Kurita, Kenji L., Charusanti, Pep, Mcphail, Kerry L., Nielsen, Kristian Fog, Vuong, Lisa, Elfeki, Maryam, Traxler, Matthew F., Engene, Niclas, Koyama, Nobuhiro, Vining, Oliver B., Baric, Ralph, Silva, Ricardo R., Mascuch, Samantha J., Tomasi, Sophie, Jenkins, Stefan, Macherla, Venkat, Hoffman, Thomas, Agarwal, Vinayak, Williams, Philip G., Dai, Jingqui, Neupane, Ram, Gurr, Joshua, Rodriguez, Andres M. C., Lamsa, Anne, Zhang, Chen, Dorrestein, Kathleen, Duggan, Brendan M., Almaliti, Jehad, Allard, Pierre-marie, Phapale, Prasad, Nothias, Louis-felix, Alexandrovr, Theodore, Litaudon, Marc, Wolfender, Jean-luc, Kyle, Jennifer E., Metz, Thomas O., Peryea, Tyler, Dac-trung Nguyen, Vanleer, Danielle, Shinn, Paul, Jadhav, Ajit, Muller, Rolf, Waters, Katrina M., Shi, Wenyuan, Liu, Xueting, Zhang, Lixin, Knight, Rob, Jensen, Paul R., Palsson, Bernhard O., Pogliano, Kit, Linington, Roger G., Gutierrez, Marcelino, Lopes, Norberto P., Gerwick, William H., Moore, Bradley S., Dorrestein, Pieter C., Bandeira, Nuno, Wang, Mingxun, Carver, Jeremy J., Phelan, Vanessa V., Sanchez, Laura M., Garg, Neha, Peng, Yao, Don Duy Nguyen, Watrous, Jeramie, Kapono, Clifford A., Luzzatto-knaan, Tal, Porto, Carla, Bouslimani, Amina, Melnik, Alexey V., Meehan, Michael J., Liu, Wei -ting, Criisemann, Max, Boudreau, Paul D., Esquenazi, Eduardo, Sandoval-calderon, Mario, Kersten, Roland D., Pace, Laura A., Quinn, Robert A., Duncan, Katherine R., Hsu, Cheng-chih, Floros, Dimitrios J., Gavilan, Ronnie G., Kleigrewe, Karin, Northen, Trent, Dutton, Rachel J., Parrot, Delphine, Carlson, Erin E., Aigle, Bertrand, Michelsen, Charlotte F., Jelsbak, Lars, Sohlenkamp, Christian, Pevzner, Pavel, Edlund, Anna, Mclean, Jeffrey, Piel, Jorn, Murphy, Brian T., Gerwick, Lena, Liaw, Chih-chuang, Yang, Yu-liang, Humpf, Hans-ulrich, Maansson, Maria, Keyzers, Robert A., Sims, Amy C., Johnson, Andrew R., Sidebottom, Ashley M., Sedio, Brian E., Klitgaard, Andreas, Larson, Charles B., Boya P, Cristopher A., Torres-mendoza, Daniel, Gonzalez, David J., Silva, Denise B., Marques, Lucas M., Demarque, Daniel P., Pociute, Egle, O'Neill, Ellis C., Briand, Enora, Helfrich, Eric J. N., Granatosky, Eve A., Glukhov, Evgenia, Ryffel, Florian, Houson, Hailey, Mohimani, Hosein, Kharbush, Jenan J., Zeng, Yi, Vorholt, Julia A., Kurita, Kenji L., Charusanti, Pep, Mcphail, Kerry L., Nielsen, Kristian Fog, Vuong, Lisa, Elfeki, Maryam, Traxler, Matthew F., Engene, Niclas, Koyama, Nobuhiro, Vining, Oliver B., Baric, Ralph, Silva, Ricardo R., Mascuch, Samantha J., Tomasi, Sophie, Jenkins, Stefan, Macherla, Venkat, Hoffman, Thomas, Agarwal, Vinayak, Williams, Philip G., Dai, Jingqui, Neupane, Ram, Gurr, Joshua, Rodriguez, Andres M. C., Lamsa, Anne, Zhang, Chen, Dorrestein, Kathleen, Duggan, Brendan M., Almaliti, Jehad, Allard, Pierre-marie, Phapale, Prasad, Nothias, Louis-felix, Alexandrovr, Theodore, Litaudon, Marc, Wolfender, Jean-luc, Kyle, Jennifer E., Metz, Thomas O., Peryea, Tyler, Dac-trung Nguyen, Vanleer, Danielle, Shinn, Paul, Jadhav, Ajit, Muller, Rolf, Waters, Katrina M., Shi, Wenyuan, Liu, Xueting, Zhang, Lixin, Knight, Rob, Jensen, Paul R., Palsson, Bernhard O., Pogliano, Kit, Linington, Roger G., Gutierrez, Marcelino, Lopes, Norberto P., Gerwick, William H., Moore, Bradley S., Dorrestein, Pieter C., and Bandeira, Nuno

Abstract

The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry (MS) techniques are well-suited to high-throughput characterization of NP, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social Molecular Networking (GNPS; http://gnps.ucsd.edu), an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS, crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of 'living data' through continuous reanalysis of deposited data.

Published
2016
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8. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

Author

Wang, Mingxun, Carver, Jeremy J., Phelan, Vanessa V., Sanchez, Laura M., Garg, Neha, Peng, Yao, Don Duy Nguyen, Watrous, Jeramie, Kapono, Clifford A., Luzzatto-knaan, Tal, Porto, Carla, Bouslimani, Amina, Melnik, Alexey V., Meehan, Michael J., Liu, Wei -ting, Criisemann, Max, Boudreau, Paul D., Esquenazi, Eduardo, Sandoval-calderon, Mario, Kersten, Roland D., Pace, Laura A., Quinn, Robert A., Duncan, Katherine R., Hsu, Cheng-chih, Floros, Dimitrios J., Gavilan, Ronnie G., Kleigrewe, Karin, Northen, Trent, Dutton, Rachel J., Parrot, Delphine, Carlson, Erin E., Aigle, Bertrand, Michelsen, Charlotte F., Jelsbak, Lars, Sohlenkamp, Christian, Pevzner, Pavel, Edlund, Anna, Mclean, Jeffrey, Piel, Jorn, Murphy, Brian T., Gerwick, Lena, Liaw, Chih-chuang, Yang, Yu-liang, Humpf, Hans-ulrich, Maansson, Maria, Keyzers, Robert A., Sims, Amy C., Johnson, Andrew R., Sidebottom, Ashley M., Sedio, Brian E., Klitgaard, Andreas, Larson, Charles B., Boya P, Cristopher A., Torres-mendoza, Daniel, Gonzalez, David J., Silva, Denise B., Marques, Lucas M., Demarque, Daniel P., Pociute, Egle, O'Neill, Ellis C., Briand, Enora, Helfrich, Eric J. N., Granatosky, Eve A., Glukhov, Evgenia, Ryffel, Florian, Houson, Hailey, Mohimani, Hosein, Kharbush, Jenan J., Zeng, Yi, Vorholt, Julia A., Kurita, Kenji L., Charusanti, Pep, Mcphail, Kerry L., Nielsen, Kristian Fog, Vuong, Lisa, Elfeki, Maryam, Traxler, Matthew F., Engene, Niclas, Koyama, Nobuhiro, Vining, Oliver B., Baric, Ralph, Silva, Ricardo R., Mascuch, Samantha J., Tomasi, Sophie, Jenkins, Stefan, Macherla, Venkat, Hoffman, Thomas, Agarwal, Vinayak, Williams, Philip G., Dai, Jingqui, Neupane, Ram, Gurr, Joshua, Rodriguez, Andres M. C., Lamsa, Anne, Zhang, Chen, Dorrestein, Kathleen, Duggan, Brendan M., Almaliti, Jehad, Allard, Pierre-marie, Phapale, Prasad, Nothias, Louis-felix, Alexandrovr, Theodore, Litaudon, Marc, Wolfender, Jean-luc, Kyle, Jennifer E., Metz, Thomas O., Peryea, Tyler, Dac-trung Nguyen, Vanleer, Danielle, Shinn, Paul, Jadhav, Ajit, Muller, Rolf, Waters, Katrina M., Shi, Wenyuan, Liu, Xueting, Zhang, Lixin, Knight, Rob, Jensen, Paul R., Palsson, Bernhard O., Pogliano, Kit, Linington, Roger G., Gutierrez, Marcelino, Lopes, Norberto P., Gerwick, William H., Moore, Bradley S., Dorrestein, Pieter C., Bandeira, Nuno, Wang, Mingxun, Carver, Jeremy J., Phelan, Vanessa V., Sanchez, Laura M., Garg, Neha, Peng, Yao, Don Duy Nguyen, Watrous, Jeramie, Kapono, Clifford A., Luzzatto-knaan, Tal, Porto, Carla, Bouslimani, Amina, Melnik, Alexey V., Meehan, Michael J., Liu, Wei -ting, Criisemann, Max, Boudreau, Paul D., Esquenazi, Eduardo, Sandoval-calderon, Mario, Kersten, Roland D., Pace, Laura A., Quinn, Robert A., Duncan, Katherine R., Hsu, Cheng-chih, Floros, Dimitrios J., Gavilan, Ronnie G., Kleigrewe, Karin, Northen, Trent, Dutton, Rachel J., Parrot, Delphine, Carlson, Erin E., Aigle, Bertrand, Michelsen, Charlotte F., Jelsbak, Lars, Sohlenkamp, Christian, Pevzner, Pavel, Edlund, Anna, Mclean, Jeffrey, Piel, Jorn, Murphy, Brian T., Gerwick, Lena, Liaw, Chih-chuang, Yang, Yu-liang, Humpf, Hans-ulrich, Maansson, Maria, Keyzers, Robert A., Sims, Amy C., Johnson, Andrew R., Sidebottom, Ashley M., Sedio, Brian E., Klitgaard, Andreas, Larson, Charles B., Boya P, Cristopher A., Torres-mendoza, Daniel, Gonzalez, David J., Silva, Denise B., Marques, Lucas M., Demarque, Daniel P., Pociute, Egle, O'Neill, Ellis C., Briand, Enora, Helfrich, Eric J. N., Granatosky, Eve A., Glukhov, Evgenia, Ryffel, Florian, Houson, Hailey, Mohimani, Hosein, Kharbush, Jenan J., Zeng, Yi, Vorholt, Julia A., Kurita, Kenji L., Charusanti, Pep, Mcphail, Kerry L., Nielsen, Kristian Fog, Vuong, Lisa, Elfeki, Maryam, Traxler, Matthew F., Engene, Niclas, Koyama, Nobuhiro, Vining, Oliver B., Baric, Ralph, Silva, Ricardo R., Mascuch, Samantha J., Tomasi, Sophie, Jenkins, Stefan, Macherla, Venkat, Hoffman, Thomas, Agarwal, Vinayak, Williams, Philip G., Dai, Jingqui, Neupane, Ram, Gurr, Joshua, Rodriguez, Andres M. C., Lamsa, Anne, Zhang, Chen, Dorrestein, Kathleen, Duggan, Brendan M., Almaliti, Jehad, Allard, Pierre-marie, Phapale, Prasad, Nothias, Louis-felix, Alexandrovr, Theodore, Litaudon, Marc, Wolfender, Jean-luc, Kyle, Jennifer E., Metz, Thomas O., Peryea, Tyler, Dac-trung Nguyen, Vanleer, Danielle, Shinn, Paul, Jadhav, Ajit, Muller, Rolf, Waters, Katrina M., Shi, Wenyuan, Liu, Xueting, Zhang, Lixin, Knight, Rob, Jensen, Paul R., Palsson, Bernhard O., Pogliano, Kit, Linington, Roger G., Gutierrez, Marcelino, Lopes, Norberto P., Gerwick, William H., Moore, Bradley S., Dorrestein, Pieter C., and Bandeira, Nuno

Abstract

The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry (MS) techniques are well-suited to high-throughput characterization of NP, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social Molecular Networking (GNPS; http://gnps.ucsd.edu), an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS, crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of 'living data' through continuous reanalysis of deposited data.

Published
2016
Full Text
View/download PDF

9. Integrated Omics Analysis of Pathogenic Host Responses during Pandemic H1N1 Influenza Virus Infection: The Crucial Role of Lipid Metabolism.

Author

Tisoncik-Go, Jennifer, Tisoncik-Go, Jennifer, Gasper, David J, Kyle, Jennifer E, Eisfeld, Amie J, Selinger, Christian, Hatta, Masato, Morrison, Juliet, Korth, Marcus J, Zink, Erika M, Kim, Young-Mo, Schepmoes, Athena A, Nicora, Carrie D, Purvine, Samuel O, Weitz, Karl K, Peng, Xinxia, Green, Richard R, Tilton, Susan C, Webb-Robertson, Bobbie-Jo, Waters, Katrina M, Metz, Thomas O, Smith, Richard D, Kawaoka, Yoshihiro, Suresh, M, Josset, Laurence, Katze, Michael G, Tisoncik-Go, Jennifer, Tisoncik-Go, Jennifer, Gasper, David J, Kyle, Jennifer E, Eisfeld, Amie J, Selinger, Christian, Hatta, Masato, Morrison, Juliet, Korth, Marcus J, Zink, Erika M, Kim, Young-Mo, Schepmoes, Athena A, Nicora, Carrie D, Purvine, Samuel O, Weitz, Karl K, Peng, Xinxia, Green, Richard R, Tilton, Susan C, Webb-Robertson, Bobbie-Jo, Waters, Katrina M, Metz, Thomas O, Smith, Richard D, Kawaoka, Yoshihiro, Suresh, M, Josset, Laurence, and Katze, Michael G

Abstract

Pandemic influenza viruses modulate proinflammatory responses that can lead to immunopathogenesis. We present an extensive and systematic profiling of lipids, metabolites, and proteins in respiratory compartments of ferrets infected with either 1918 or 2009 human pandemic H1N1 influenza viruses. Integrative analysis of high-throughput omics data with virologic and histopathologic data uncovered relationships between host responses and phenotypic outcomes of viral infection. Proinflammatory lipid precursors in the trachea following 1918 infection correlated with severe tracheal lesions. Using an algorithm to infer cell quantity changes from gene expression data, we found enrichment of distinct T cell subpopulations in the trachea. There was also a predicted increase in inflammatory monocytes in the lung of 1918 virus-infected animals that was sustained throughout infection. This study presents a unique resource to the influenza research community and demonstrates the utility of an integrative systems approach for characterization of lipid metabolism alterations underlying respiratory responses to viruses.

Published
2016

10. Integrated Omics Analysis of Pathogenic Host Responses during Pandemic H1N1 Influenza Virus Infection: The Crucial Role of Lipid Metabolism.

Author

Tisoncik-Go, Jennifer, Tisoncik-Go, Jennifer, Gasper, David J, Kyle, Jennifer E, Eisfeld, Amie J, Selinger, Christian, Hatta, Masato, Morrison, Juliet, Korth, Marcus J, Zink, Erika M, Kim, Young-Mo, Schepmoes, Athena A, Nicora, Carrie D, Purvine, Samuel O, Weitz, Karl K, Peng, Xinxia, Green, Richard R, Tilton, Susan C, Webb-Robertson, Bobbie-Jo, Waters, Katrina M, Metz, Thomas O, Smith, Richard D, Kawaoka, Yoshihiro, Suresh, M, Josset, Laurence, Katze, Michael G, Tisoncik-Go, Jennifer, Tisoncik-Go, Jennifer, Gasper, David J, Kyle, Jennifer E, Eisfeld, Amie J, Selinger, Christian, Hatta, Masato, Morrison, Juliet, Korth, Marcus J, Zink, Erika M, Kim, Young-Mo, Schepmoes, Athena A, Nicora, Carrie D, Purvine, Samuel O, Weitz, Karl K, Peng, Xinxia, Green, Richard R, Tilton, Susan C, Webb-Robertson, Bobbie-Jo, Waters, Katrina M, Metz, Thomas O, Smith, Richard D, Kawaoka, Yoshihiro, Suresh, M, Josset, Laurence, and Katze, Michael G

Abstract

Pandemic influenza viruses modulate proinflammatory responses that can lead to immunopathogenesis. We present an extensive and systematic profiling of lipids, metabolites, and proteins in respiratory compartments of ferrets infected with either 1918 or 2009 human pandemic H1N1 influenza viruses. Integrative analysis of high-throughput omics data with virologic and histopathologic data uncovered relationships between host responses and phenotypic outcomes of viral infection. Proinflammatory lipid precursors in the trachea following 1918 infection correlated with severe tracheal lesions. Using an algorithm to infer cell quantity changes from gene expression data, we found enrichment of distinct T cell subpopulations in the trachea. There was also a predicted increase in inflammatory monocytes in the lung of 1918 virus-infected animals that was sustained throughout infection. This study presents a unique resource to the influenza research community and demonstrates the utility of an integrative systems approach for characterization of lipid metabolism alterations underlying respiratory responses to viruses.

Published
2016

11. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

Author

Wang, Mingxun, Carver, Jeremy J., Phelan, Vanessa V., Sanchez, Laura M., Garg, Neha, Peng, Yao, Don Duy Nguyen, Watrous, Jeramie, Kapono, Clifford A., Luzzatto-knaan, Tal, Porto, Carla, Bouslimani, Amina, Melnik, Alexey V., Meehan, Michael J., Liu, Wei -ting, Criisemann, Max, Boudreau, Paul D., Esquenazi, Eduardo, Sandoval-calderon, Mario, Kersten, Roland D., Pace, Laura A., Quinn, Robert A., Duncan, Katherine R., Hsu, Cheng-chih, Floros, Dimitrios J., Gavilan, Ronnie G., Kleigrewe, Karin, Northen, Trent, Dutton, Rachel J., Parrot, Delphine, Carlson, Erin E., Aigle, Bertrand, Michelsen, Charlotte F., Jelsbak, Lars, Sohlenkamp, Christian, Pevzner, Pavel, Edlund, Anna, Mclean, Jeffrey, Piel, Jorn, Murphy, Brian T., Gerwick, Lena, Liaw, Chih-chuang, Yang, Yu-liang, Humpf, Hans-ulrich, Maansson, Maria, Keyzers, Robert A., Sims, Amy C., Johnson, Andrew R., Sidebottom, Ashley M., Sedio, Brian E., Klitgaard, Andreas, Larson, Charles B., Boya P, Cristopher A., Torres-mendoza, Daniel, Gonzalez, David J., Silva, Denise B., Marques, Lucas M., Demarque, Daniel P., Pociute, Egle, O'Neill, Ellis C., Briand, Enora, Helfrich, Eric J. N., Granatosky, Eve A., Glukhov, Evgenia, Ryffel, Florian, Houson, Hailey, Mohimani, Hosein, Kharbush, Jenan J., Zeng, Yi, Vorholt, Julia A., Kurita, Kenji L., Charusanti, Pep, Mcphail, Kerry L., Nielsen, Kristian Fog, Vuong, Lisa, Elfeki, Maryam, Traxler, Matthew F., Engene, Niclas, Koyama, Nobuhiro, Vining, Oliver B., Baric, Ralph, Silva, Ricardo R., Mascuch, Samantha J., Tomasi, Sophie, Jenkins, Stefan, Macherla, Venkat, Hoffman, Thomas, Agarwal, Vinayak, Williams, Philip G., Dai, Jingqui, Neupane, Ram, Gurr, Joshua, Rodriguez, Andres M. C., Lamsa, Anne, Zhang, Chen, Dorrestein, Kathleen, Duggan, Brendan M., Almaliti, Jehad, Allard, Pierre-marie, Phapale, Prasad, Nothias, Louis-felix, Alexandrovr, Theodore, Litaudon, Marc, Wolfender, Jean-luc, Kyle, Jennifer E., Metz, Thomas O., Peryea, Tyler, Dac-trung Nguyen, Vanleer, Danielle, Shinn, Paul, Jadhav, Ajit, Muller, Rolf, Waters, Katrina M., Shi, Wenyuan, Liu, Xueting, Zhang, Lixin, Knight, Rob, Jensen, Paul R., Palsson, Bernhard O., Pogliano, Kit, Linington, Roger G., Gutierrez, Marcelino, Lopes, Norberto P., Gerwick, William H., Moore, Bradley S., Dorrestein, Pieter C., Bandeira, Nuno, Wang, Mingxun, Carver, Jeremy J., Phelan, Vanessa V., Sanchez, Laura M., Garg, Neha, Peng, Yao, Don Duy Nguyen, Watrous, Jeramie, Kapono, Clifford A., Luzzatto-knaan, Tal, Porto, Carla, Bouslimani, Amina, Melnik, Alexey V., Meehan, Michael J., Liu, Wei -ting, Criisemann, Max, Boudreau, Paul D., Esquenazi, Eduardo, Sandoval-calderon, Mario, Kersten, Roland D., Pace, Laura A., Quinn, Robert A., Duncan, Katherine R., Hsu, Cheng-chih, Floros, Dimitrios J., Gavilan, Ronnie G., Kleigrewe, Karin, Northen, Trent, Dutton, Rachel J., Parrot, Delphine, Carlson, Erin E., Aigle, Bertrand, Michelsen, Charlotte F., Jelsbak, Lars, Sohlenkamp, Christian, Pevzner, Pavel, Edlund, Anna, Mclean, Jeffrey, Piel, Jorn, Murphy, Brian T., Gerwick, Lena, Liaw, Chih-chuang, Yang, Yu-liang, Humpf, Hans-ulrich, Maansson, Maria, Keyzers, Robert A., Sims, Amy C., Johnson, Andrew R., Sidebottom, Ashley M., Sedio, Brian E., Klitgaard, Andreas, Larson, Charles B., Boya P, Cristopher A., Torres-mendoza, Daniel, Gonzalez, David J., Silva, Denise B., Marques, Lucas M., Demarque, Daniel P., Pociute, Egle, O'Neill, Ellis C., Briand, Enora, Helfrich, Eric J. N., Granatosky, Eve A., Glukhov, Evgenia, Ryffel, Florian, Houson, Hailey, Mohimani, Hosein, Kharbush, Jenan J., Zeng, Yi, Vorholt, Julia A., Kurita, Kenji L., Charusanti, Pep, Mcphail, Kerry L., Nielsen, Kristian Fog, Vuong, Lisa, Elfeki, Maryam, Traxler, Matthew F., Engene, Niclas, Koyama, Nobuhiro, Vining, Oliver B., Baric, Ralph, Silva, Ricardo R., Mascuch, Samantha J., Tomasi, Sophie, Jenkins, Stefan, Macherla, Venkat, Hoffman, Thomas, Agarwal, Vinayak, Williams, Philip G., Dai, Jingqui, Neupane, Ram, Gurr, Joshua, Rodriguez, Andres M. C., Lamsa, Anne, Zhang, Chen, Dorrestein, Kathleen, Duggan, Brendan M., Almaliti, Jehad, Allard, Pierre-marie, Phapale, Prasad, Nothias, Louis-felix, Alexandrovr, Theodore, Litaudon, Marc, Wolfender, Jean-luc, Kyle, Jennifer E., Metz, Thomas O., Peryea, Tyler, Dac-trung Nguyen, Vanleer, Danielle, Shinn, Paul, Jadhav, Ajit, Muller, Rolf, Waters, Katrina M., Shi, Wenyuan, Liu, Xueting, Zhang, Lixin, Knight, Rob, Jensen, Paul R., Palsson, Bernhard O., Pogliano, Kit, Linington, Roger G., Gutierrez, Marcelino, Lopes, Norberto P., Gerwick, William H., Moore, Bradley S., Dorrestein, Pieter C., and Bandeira, Nuno

Abstract

The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry (MS) techniques are well-suited to high-throughput characterization of NP, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social Molecular Networking (GNPS; http://gnps.ucsd.edu), an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS, crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of 'living data' through continuous reanalysis of deposited data.

Published
2016
Full Text
View/download PDF

12. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

Author

Wang, Mingxun, Carver, Jeremy J, Phelan, Vanessa V, Sanchez, Laura M, Garg, Neha, Peng, Yao, Nguyen, Don Duy, Watrous, Jeramie, Kapono, Clifford A, Luzzatto-Knaan, Tal, Porto, Carla, Bouslimani, Amina, Melnik, Alexey V, Meehan, Michael J, Liu, Wei-Ting, Crüsemann, Max, Boudreau, Paul D, Esquenazi, Eduardo, Sandoval-Calderón, Mario, Kersten, Roland D, Pace, Laura A, Quinn, Robert A, Duncan, Katherine R, Hsu, Cheng-Chih, Floros, Dimitrios J, Gavilan, Ronnie G, Kleigrewe, Karin, Northen, Trent, Dutton, Rachel J, Parrot, Delphine, Carlson, Erin E, Aigle, Bertrand, Michelsen, Charlotte F, Jelsbak, Lars, Sohlenkamp, Christian, Pevzner, Pavel, Edlund, Anna, McLean, Jeffrey, Piel, Jörn, Murphy, Brian T, Gerwick, Lena, Liaw, Chih-Chuang, Yang, Yu-Liang, Humpf, Hans-Ulrich, Maansson, Maria, Keyzers, Robert A, Sims, Amy C, Johnson, Andrew R, Sidebottom, Ashley M, Sedio, Brian E, Klitgaard, Andreas, Larson, Charles B, Boya P, Cristopher A, Torres-Mendoza, Daniel, Gonzalez, David J, Silva, Denise B, Marques, Lucas M, Demarque, Daniel P, Pociute, Egle, O'Neill, Ellis C, Briand, Enora, Helfrich, Eric J N, Granatosky, Eve A, Glukhov, Evgenia, Ryffel, Florian, Houson, Hailey, Mohimani, Hosein, Kharbush, Jenan J, Zeng, Yi, Vorholt, Julia A, Kurita, Kenji L, Charusanti, Pep, McPhail, Kerry L, Nielsen, Kristian Fog, Vuong, Lisa, Elfeki, Maryam, Traxler, Matthew F, Engene, Niclas, Koyama, Nobuhiro, Vining, Oliver B, Baric, Ralph, Silva, Ricardo R, Mascuch, Samantha J, Tomasi, Sophie, Jenkins, Stefan, Macherla, Venkat, Hoffman, Thomas, Agarwal, Vinayak, Williams, Philip G, Dai, Jingqui, Neupane, Ram, Gurr, Joshua, Rodríguez, Andrés M C, Lamsa, Anne, Zhang, Chen, Dorrestein, Kathleen, Duggan, Brendan M, Almaliti, Jehad, Allard, Pierre-Marie, Phapale, Prasad, Nothias, Louis-Felix, Alexandrov, Theodore, Litaudon, Marc, Wolfender, Jean-Luc, Kyle, Jennifer E, Metz, Thomas O, Peryea, Tyler, Nguyen, Dac-Trung, VanLeer, Danielle, Shinn, Paul, Jadhav, Ajit, Müller, Rolf, Waters, Katrina M, Shi, Wenyuan, Liu, Xueting, Zhang, Lixin, Knight, Rob, Jensen, Paul R, Palsson, Bernhard Ø, Pogliano, Kit, Linington, Roger G, Gutiérrez, Marcelino, Lopes, Norberto P, Gerwick, William H, Moore, Bradley S, Dorrestein, Pieter C, Bandeira, Nuno, Wang, Mingxun, Carver, Jeremy J, Phelan, Vanessa V, Sanchez, Laura M, Garg, Neha, Peng, Yao, Nguyen, Don Duy, Watrous, Jeramie, Kapono, Clifford A, Luzzatto-Knaan, Tal, Porto, Carla, Bouslimani, Amina, Melnik, Alexey V, Meehan, Michael J, Liu, Wei-Ting, Crüsemann, Max, Boudreau, Paul D, Esquenazi, Eduardo, Sandoval-Calderón, Mario, Kersten, Roland D, Pace, Laura A, Quinn, Robert A, Duncan, Katherine R, Hsu, Cheng-Chih, Floros, Dimitrios J, Gavilan, Ronnie G, Kleigrewe, Karin, Northen, Trent, Dutton, Rachel J, Parrot, Delphine, Carlson, Erin E, Aigle, Bertrand, Michelsen, Charlotte F, Jelsbak, Lars, Sohlenkamp, Christian, Pevzner, Pavel, Edlund, Anna, McLean, Jeffrey, Piel, Jörn, Murphy, Brian T, Gerwick, Lena, Liaw, Chih-Chuang, Yang, Yu-Liang, Humpf, Hans-Ulrich, Maansson, Maria, Keyzers, Robert A, Sims, Amy C, Johnson, Andrew R, Sidebottom, Ashley M, Sedio, Brian E, Klitgaard, Andreas, Larson, Charles B, Boya P, Cristopher A, Torres-Mendoza, Daniel, Gonzalez, David J, Silva, Denise B, Marques, Lucas M, Demarque, Daniel P, Pociute, Egle, O'Neill, Ellis C, Briand, Enora, Helfrich, Eric J N, Granatosky, Eve A, Glukhov, Evgenia, Ryffel, Florian, Houson, Hailey, Mohimani, Hosein, Kharbush, Jenan J, Zeng, Yi, Vorholt, Julia A, Kurita, Kenji L, Charusanti, Pep, McPhail, Kerry L, Nielsen, Kristian Fog, Vuong, Lisa, Elfeki, Maryam, Traxler, Matthew F, Engene, Niclas, Koyama, Nobuhiro, Vining, Oliver B, Baric, Ralph, Silva, Ricardo R, Mascuch, Samantha J, Tomasi, Sophie, Jenkins, Stefan, Macherla, Venkat, Hoffman, Thomas, Agarwal, Vinayak, Williams, Philip G, Dai, Jingqui, Neupane, Ram, Gurr, Joshua, Rodríguez, Andrés M C, Lamsa, Anne, Zhang, Chen, Dorrestein, Kathleen, Duggan, Brendan M, Almaliti, Jehad, Allard, Pierre-Marie, Phapale, Prasad, Nothias, Louis-Felix, Alexandrov, Theodore, Litaudon, Marc, Wolfender, Jean-Luc, Kyle, Jennifer E, Metz, Thomas O, Peryea, Tyler, Nguyen, Dac-Trung, VanLeer, Danielle, Shinn, Paul, Jadhav, Ajit, Müller, Rolf, Waters, Katrina M, Shi, Wenyuan, Liu, Xueting, Zhang, Lixin, Knight, Rob, Jensen, Paul R, Palsson, Bernhard Ø, Pogliano, Kit, Linington, Roger G, Gutiérrez, Marcelino, Lopes, Norberto P, Gerwick, William H, Moore, Bradley S, Dorrestein, Pieter C, and Bandeira, Nuno

Abstract

The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry (MS) techniques are well-suited to high-throughput characterization of NP, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social Molecular Networking (GNPS; http://gnps.ucsd.edu), an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS, crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of 'living data' through continuous reanalysis of deposited data.

Published
2016
Full Text
View/download PDF

13. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

Author

Wang, Mingxun, Carver, Jeremy J., Phelan, Vanessa V., Sanchez, Laura M., Garg, Neha, Peng, Yao, Don Duy Nguyen, Watrous, Jeramie, Kapono, Clifford A., Luzzatto-knaan, Tal, Porto, Carla, Bouslimani, Amina, Melnik, Alexey V., Meehan, Michael J., Liu, Wei -ting, Criisemann, Max, Boudreau, Paul D., Esquenazi, Eduardo, Sandoval-calderon, Mario, Kersten, Roland D., Pace, Laura A., Quinn, Robert A., Duncan, Katherine R., Hsu, Cheng-chih, Floros, Dimitrios J., Gavilan, Ronnie G., Kleigrewe, Karin, Northen, Trent, Dutton, Rachel J., Parrot, Delphine, Carlson, Erin E., Aigle, Bertrand, Michelsen, Charlotte F., Jelsbak, Lars, Sohlenkamp, Christian, Pevzner, Pavel, Edlund, Anna, Mclean, Jeffrey, Piel, Jorn, Murphy, Brian T., Gerwick, Lena, Liaw, Chih-chuang, Yang, Yu-liang, Humpf, Hans-ulrich, Maansson, Maria, Keyzers, Robert A., Sims, Amy C., Johnson, Andrew R., Sidebottom, Ashley M., Sedio, Brian E., Klitgaard, Andreas, Larson, Charles B., Boya P, Cristopher A., Torres-mendoza, Daniel, Gonzalez, David J., Silva, Denise B., Marques, Lucas M., Demarque, Daniel P., Pociute, Egle, O'Neill, Ellis C., Briand, Enora, Helfrich, Eric J. N., Granatosky, Eve A., Glukhov, Evgenia, Ryffel, Florian, Houson, Hailey, Mohimani, Hosein, Kharbush, Jenan J., Zeng, Yi, Vorholt, Julia A., Kurita, Kenji L., Charusanti, Pep, Mcphail, Kerry L., Nielsen, Kristian Fog, Vuong, Lisa, Elfeki, Maryam, Traxler, Matthew F., Engene, Niclas, Koyama, Nobuhiro, Vining, Oliver B., Baric, Ralph, Silva, Ricardo R., Mascuch, Samantha J., Tomasi, Sophie, Jenkins, Stefan, Macherla, Venkat, Hoffman, Thomas, Agarwal, Vinayak, Williams, Philip G., Dai, Jingqui, Neupane, Ram, Gurr, Joshua, Rodriguez, Andres M. C., Lamsa, Anne, Zhang, Chen, Dorrestein, Kathleen, Duggan, Brendan M., Almaliti, Jehad, Allard, Pierre-marie, Phapale, Prasad, Nothias, Louis-felix, Alexandrovr, Theodore, Litaudon, Marc, Wolfender, Jean-luc, Kyle, Jennifer E., Metz, Thomas O., Peryea, Tyler, Dac-trung Nguyen, Vanleer, Danielle, Shinn, Paul, Jadhav, Ajit, Muller, Rolf, Waters, Katrina M., Shi, Wenyuan, Liu, Xueting, Zhang, Lixin, Knight, Rob, Jensen, Paul R., Palsson, Bernhard O., Pogliano, Kit, Linington, Roger G., Gutierrez, Marcelino, Lopes, Norberto P., Gerwick, William H., Moore, Bradley S., Dorrestein, Pieter C., Bandeira, Nuno, Wang, Mingxun, Carver, Jeremy J., Phelan, Vanessa V., Sanchez, Laura M., Garg, Neha, Peng, Yao, Don Duy Nguyen, Watrous, Jeramie, Kapono, Clifford A., Luzzatto-knaan, Tal, Porto, Carla, Bouslimani, Amina, Melnik, Alexey V., Meehan, Michael J., Liu, Wei -ting, Criisemann, Max, Boudreau, Paul D., Esquenazi, Eduardo, Sandoval-calderon, Mario, Kersten, Roland D., Pace, Laura A., Quinn, Robert A., Duncan, Katherine R., Hsu, Cheng-chih, Floros, Dimitrios J., Gavilan, Ronnie G., Kleigrewe, Karin, Northen, Trent, Dutton, Rachel J., Parrot, Delphine, Carlson, Erin E., Aigle, Bertrand, Michelsen, Charlotte F., Jelsbak, Lars, Sohlenkamp, Christian, Pevzner, Pavel, Edlund, Anna, Mclean, Jeffrey, Piel, Jorn, Murphy, Brian T., Gerwick, Lena, Liaw, Chih-chuang, Yang, Yu-liang, Humpf, Hans-ulrich, Maansson, Maria, Keyzers, Robert A., Sims, Amy C., Johnson, Andrew R., Sidebottom, Ashley M., Sedio, Brian E., Klitgaard, Andreas, Larson, Charles B., Boya P, Cristopher A., Torres-mendoza, Daniel, Gonzalez, David J., Silva, Denise B., Marques, Lucas M., Demarque, Daniel P., Pociute, Egle, O'Neill, Ellis C., Briand, Enora, Helfrich, Eric J. N., Granatosky, Eve A., Glukhov, Evgenia, Ryffel, Florian, Houson, Hailey, Mohimani, Hosein, Kharbush, Jenan J., Zeng, Yi, Vorholt, Julia A., Kurita, Kenji L., Charusanti, Pep, Mcphail, Kerry L., Nielsen, Kristian Fog, Vuong, Lisa, Elfeki, Maryam, Traxler, Matthew F., Engene, Niclas, Koyama, Nobuhiro, Vining, Oliver B., Baric, Ralph, Silva, Ricardo R., Mascuch, Samantha J., Tomasi, Sophie, Jenkins, Stefan, Macherla, Venkat, Hoffman, Thomas, Agarwal, Vinayak, Williams, Philip G., Dai, Jingqui, Neupane, Ram, Gurr, Joshua, Rodriguez, Andres M. C., Lamsa, Anne, Zhang, Chen, Dorrestein, Kathleen, Duggan, Brendan M., Almaliti, Jehad, Allard, Pierre-marie, Phapale, Prasad, Nothias, Louis-felix, Alexandrovr, Theodore, Litaudon, Marc, Wolfender, Jean-luc, Kyle, Jennifer E., Metz, Thomas O., Peryea, Tyler, Dac-trung Nguyen, Vanleer, Danielle, Shinn, Paul, Jadhav, Ajit, Muller, Rolf, Waters, Katrina M., Shi, Wenyuan, Liu, Xueting, Zhang, Lixin, Knight, Rob, Jensen, Paul R., Palsson, Bernhard O., Pogliano, Kit, Linington, Roger G., Gutierrez, Marcelino, Lopes, Norberto P., Gerwick, William H., Moore, Bradley S., Dorrestein, Pieter C., and Bandeira, Nuno

Abstract

The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry (MS) techniques are well-suited to high-throughput characterization of NP, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social Molecular Networking (GNPS; http://gnps.ucsd.edu), an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS, crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of 'living data' through continuous reanalysis of deposited data.

Published
2016
Full Text
View/download PDF

14. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

Author

Wang, Mingxun, Carver, Jeremy J, Phelan, Vanessa V, Sanchez, Laura M, Garg, Neha, Peng, Yao, Nguyen, Don Duy, Watrous, Jeramie, Kapono, Clifford A, Luzzatto-Knaan, Tal, Porto, Carla, Bouslimani, Amina, Melnik, Alexey V, Meehan, Michael J, Liu, Wei-Ting, Crüsemann, Max, Boudreau, Paul D, Esquenazi, Eduardo, Sandoval-Calderón, Mario, Kersten, Roland D, Pace, Laura A, Quinn, Robert A, Duncan, Katherine R, Hsu, Cheng-Chih, Floros, Dimitrios J, Gavilan, Ronnie G, Kleigrewe, Karin, Northen, Trent, Dutton, Rachel J, Parrot, Delphine, Carlson, Erin E, Aigle, Bertrand, Michelsen, Charlotte F, Jelsbak, Lars, Sohlenkamp, Christian, Pevzner, Pavel, Edlund, Anna, McLean, Jeffrey, Piel, Jörn, Murphy, Brian T, Gerwick, Lena, Liaw, Chih-Chuang, Yang, Yu-Liang, Humpf, Hans-Ulrich, Maansson, Maria, Keyzers, Robert A, Sims, Amy C, Johnson, Andrew R, Sidebottom, Ashley M, Sedio, Brian E, Klitgaard, Andreas, Larson, Charles B, Boya P, Cristopher A, Torres-Mendoza, Daniel, Gonzalez, David J, Silva, Denise B, Marques, Lucas M, Demarque, Daniel P, Pociute, Egle, O'Neill, Ellis C, Briand, Enora, Helfrich, Eric J N, Granatosky, Eve A, Glukhov, Evgenia, Ryffel, Florian, Houson, Hailey, Mohimani, Hosein, Kharbush, Jenan J, Zeng, Yi, Vorholt, Julia A, Kurita, Kenji L, Charusanti, Pep, McPhail, Kerry L, Nielsen, Kristian Fog, Vuong, Lisa, Elfeki, Maryam, Traxler, Matthew F, Engene, Niclas, Koyama, Nobuhiro, Vining, Oliver B, Baric, Ralph, Silva, Ricardo R, Mascuch, Samantha J, Tomasi, Sophie, Jenkins, Stefan, Macherla, Venkat, Hoffman, Thomas, Agarwal, Vinayak, Williams, Philip G, Dai, Jingqui, Neupane, Ram, Gurr, Joshua, Rodríguez, Andrés M C, Lamsa, Anne, Zhang, Chen, Dorrestein, Kathleen, Duggan, Brendan M, Almaliti, Jehad, Allard, Pierre-Marie, Phapale, Prasad, Nothias, Louis-Felix, Alexandrov, Theodore, Litaudon, Marc, Wolfender, Jean-Luc, Kyle, Jennifer E, Metz, Thomas O, Peryea, Tyler, Nguyen, Dac-Trung, VanLeer, Danielle, Shinn, Paul, Jadhav, Ajit, Müller, Rolf, Waters, Katrina M, Shi, Wenyuan, Liu, Xueting, Zhang, Lixin, Knight, Rob, Jensen, Paul R, Palsson, Bernhard Ø, Pogliano, Kit, Linington, Roger G, Gutiérrez, Marcelino, Lopes, Norberto P, Gerwick, William H, Moore, Bradley S, Dorrestein, Pieter C, Bandeira, Nuno, Wang, Mingxun, Carver, Jeremy J, Phelan, Vanessa V, Sanchez, Laura M, Garg, Neha, Peng, Yao, Nguyen, Don Duy, Watrous, Jeramie, Kapono, Clifford A, Luzzatto-Knaan, Tal, Porto, Carla, Bouslimani, Amina, Melnik, Alexey V, Meehan, Michael J, Liu, Wei-Ting, Crüsemann, Max, Boudreau, Paul D, Esquenazi, Eduardo, Sandoval-Calderón, Mario, Kersten, Roland D, Pace, Laura A, Quinn, Robert A, Duncan, Katherine R, Hsu, Cheng-Chih, Floros, Dimitrios J, Gavilan, Ronnie G, Kleigrewe, Karin, Northen, Trent, Dutton, Rachel J, Parrot, Delphine, Carlson, Erin E, Aigle, Bertrand, Michelsen, Charlotte F, Jelsbak, Lars, Sohlenkamp, Christian, Pevzner, Pavel, Edlund, Anna, McLean, Jeffrey, Piel, Jörn, Murphy, Brian T, Gerwick, Lena, Liaw, Chih-Chuang, Yang, Yu-Liang, Humpf, Hans-Ulrich, Maansson, Maria, Keyzers, Robert A, Sims, Amy C, Johnson, Andrew R, Sidebottom, Ashley M, Sedio, Brian E, Klitgaard, Andreas, Larson, Charles B, Boya P, Cristopher A, Torres-Mendoza, Daniel, Gonzalez, David J, Silva, Denise B, Marques, Lucas M, Demarque, Daniel P, Pociute, Egle, O'Neill, Ellis C, Briand, Enora, Helfrich, Eric J N, Granatosky, Eve A, Glukhov, Evgenia, Ryffel, Florian, Houson, Hailey, Mohimani, Hosein, Kharbush, Jenan J, Zeng, Yi, Vorholt, Julia A, Kurita, Kenji L, Charusanti, Pep, McPhail, Kerry L, Nielsen, Kristian Fog, Vuong, Lisa, Elfeki, Maryam, Traxler, Matthew F, Engene, Niclas, Koyama, Nobuhiro, Vining, Oliver B, Baric, Ralph, Silva, Ricardo R, Mascuch, Samantha J, Tomasi, Sophie, Jenkins, Stefan, Macherla, Venkat, Hoffman, Thomas, Agarwal, Vinayak, Williams, Philip G, Dai, Jingqui, Neupane, Ram, Gurr, Joshua, Rodríguez, Andrés M C, Lamsa, Anne, Zhang, Chen, Dorrestein, Kathleen, Duggan, Brendan M, Almaliti, Jehad, Allard, Pierre-Marie, Phapale, Prasad, Nothias, Louis-Felix, Alexandrov, Theodore, Litaudon, Marc, Wolfender, Jean-Luc, Kyle, Jennifer E, Metz, Thomas O, Peryea, Tyler, Nguyen, Dac-Trung, VanLeer, Danielle, Shinn, Paul, Jadhav, Ajit, Müller, Rolf, Waters, Katrina M, Shi, Wenyuan, Liu, Xueting, Zhang, Lixin, Knight, Rob, Jensen, Paul R, Palsson, Bernhard Ø, Pogliano, Kit, Linington, Roger G, Gutiérrez, Marcelino, Lopes, Norberto P, Gerwick, William H, Moore, Bradley S, Dorrestein, Pieter C, and Bandeira, Nuno

Abstract

The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry (MS) techniques are well-suited to high-throughput characterization of NP, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social Molecular Networking (GNPS; http://gnps.ucsd.edu), an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS, crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of 'living data' through continuous reanalysis of deposited data.

Published
2016
Full Text
View/download PDF

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