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2. Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular Profiles

Author

Farshidfar, Farshad, Zheng, Siyuan, Gingras, Marie-Claude, Newton, Yulia, Shih, Juliann, Robertson, A Gordon, Hinoue, Toshinori, Hoadley, Katherine A, Gibb, Ewan A, Roszik, Jason, Covington, Kyle R, Wu, Chia-Chin, Shinbrot, Eve, Stransky, Nicolas, Hegde, Apurva, Yang, Ju Dong, Reznik, Ed, Sadeghi, Sara, Pedamallu, Chandra Sekhar, Ojesina, Akinyemi I, Hess, Julian M, Auman, J Todd, Rhie, Suhn K, Bowlby, Reanne, Borad, Mitesh J, Network, The Cancer Genome Atlas, Akbani, Rehan, Allotey, Loretta K, Ally, Adrian, Alvaro, Domenico, Andersen, Jesper B, Appelbaum, Elizabeth L, Arora, Arshi, Balasundaram, Miruna, Balu, Saianand, Bardeesy, Nabeel, Bathe, Oliver F, Baylin, Stephen B, Beroukhim, Rameen, Berrios, Mario, Bodenheimer, Tom, Boice, Lori, Bootwalla, Moiz S, Bowen, Jay, Bragazzi, Maria Consiglia, Brooks, Denise, Cardinale, Vincenzo, Carlsen, Rebecca, Carpino, Guido, Carvalho, Andre L, Chaiteerakij, Roongruedee, Chandan, Vishal C, Cherniack, Andrew D, Chin, Lynda, Cho, Juok, Choe, Gina, Chuah, Eric, Chudamani, Sudha, Cibulskis, Carrie, Cordes, Matthew G, Crain, Daniel, Curley, Erin, De Rose, Agostino Maria, Defreitas, Timothy, Demchok, John A, Deshpande, Vikram, Dhalla, Noreen, Ding, Li, Evason, Kimberley, Felau, Ina, Ferguson, Martin L, Foo, Wai Chin, Franchitto, Antonio, Frazer, Scott, Fronick, Catrina C, Fulton, Lucinda A, Fulton, Robert S, Gabriel, Stacey B, Gardner, Johanna, Gastier-Foster, Julie M, Gaudio, Eugenio, Gehlenborg, Nils, Genovese, Giannicola, Gerken, Mark, Getz, Gad, Giama, Nasra H, Gibbs, Richard A, Giuliante, Felice, Grazi, Gian Luca, Hayes, D Neil, Hegde, Apurva M, and Heiman, David I

Subjects
Liver Cancer, Digestive Diseases, Liver Disease, Biotechnology, Human Genome, Genetics, Cancer, Rare Diseases, Digestive Diseases - (Gallbladder), Adult, Aged, Aged, 80 and over, Bile Duct Neoplasms, Cholangiocarcinoma, Chromatin, DNA Methylation, DNA-Binding Proteins, Female, Gene Expression Regulation, Neoplastic, Genomics, Humans, Isocitrate Dehydrogenase, Liver, Liver Neoplasms, Male, Middle Aged, Mitochondria, Mutation, Nuclear Proteins, Pancreatic Neoplasms, Promoter Regions, Genetic, RNA, Long Noncoding, RNA, Messenger, Transcription Factors, Cancer Genome Atlas Network, ARID1A, DNA methylation, IDH, RNA sequencing, TCGA, cholangiocarcinoma, integrative genomics, lncRNAs, multi-omics, whole exome, Biochemistry and Cell Biology, Medical Physiology
Abstract

Cholangiocarcinoma (CCA) is an aggressive malignancy of the bile ducts, with poor prognosis and limited treatment options. Here, we describe the integrated analysis of somatic mutations, RNA expression, copy number, and DNA methylation by The Cancer Genome Atlas of a set of predominantly intrahepatic CCA cases and propose a molecular classification scheme. We identified an IDH mutant-enriched subtype with distinct molecular features including low expression of chromatin modifiers, elevated expression of mitochondrial genes, and increased mitochondrial DNA copy number. Leveraging the multi-platform data, we observed that ARID1A exhibited DNA hypermethylation and decreased expression in the IDH mutant subtype. More broadly, we found that IDH mutations are associated with an expanded histological spectrum of liver tumors with molecular features that stratify with CCA. Our studies reveal insights into the molecular pathogenesis and heterogeneity of cholangiocarcinoma and provide classification information of potential therapeutic significance.

Published
2017

3. Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular Profiles

Author

Roberts, Lewis R, Farshidfar, Farshad, Zheng, Siyuan, Gingras, Marie-Claude, Newton, Yulia, Shih, Juliann, Robertson, A Gordon, Hinoue, Toshinori, Hoadley, Katherine A, Gibbs, Richard, Roszik, Jason, Covington, Kyle, Wu, Chia-Chin, Shinbrot, Eve, Stransky, Nicolas, Hegde, Apurva M, Yang, Ju Dong, Reznik, Ed, Sadeghi, Sara, Pedamallu, Chandra Sekhar, Ojesina, Akinyemi I, Hess, Julian, Auman, J Todd, Rhie, Suhn K, Bowlby, Reanne, Borad, Mitesh J, Stuart, Josh, Sander, Chris, Akbani, Rehan, Cherniack, Andrew D, Laird, Peter W, Deshpande, Vikram, Mounajjed, Taofic, Foo, Wai Chin, Torbenson, Michael, Kleiner, David E, Wheeler, David A, Mcree, Autumn J, Bathe, Oliver F, Andersen, Jesper B, Bardeesy, Nabeel, and Kwong, Lawrence N

Subjects
Gastroenterology & Hepatology, Medical Biochemistry and Metabolomics, Clinical Sciences, Immunology
Published
2016

4. Somatic mutations of esophageal adenocarcinoma: a comparison between Black and White patients

Author

Lim, Hyeyeun, primary, Gingras, Marie-Claude, additional, Zhao, Jing, additional, Byun, Jinyoung, additional, Castro, Patricia D., additional, Tsavachidis, Spiridon, additional, Hu, Jianhong, additional, Doddapaneri, Harshavardhan, additional, Han, Yi, additional, Muzny, Donna M., additional, Gibbs, Richard A., additional, Amos, Christopher I., additional, and Thrift, Aaron P., additional

Published
2023
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6. Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes.

Author

Biankin, Andrew, Waddell, Nicola, Kassahn, Karin, Gingras, Marie-Claude, Muthuswamy, Lakshmi, Johns, Amber, Miller, David, Wilson, Peter, Patch, Ann-Marie, Wu, Jianmin, Chang, David, Cowley, Mark, Gardiner, Brooke, Song, Sarah, Harliwong, Ivon, Idrisoglu, Senel, Nourse, Craig, Nourbakhsh, Ehsan, Manning, Suzanne, Wani, Shivangi, Gongora, Milena, Pajic, Marina, Scarlett, Christopher, Gill, Anthony, Pinho, Andreia, Rooman, Ilse, Anderson, Matthew, Holmes, Oliver, Leonard, Conrad, Taylor, Darrin, Wood, Scott, Xu, Qinying, Nones, Katia, Fink, J, Christ, Angelika, Bruxner, Tim, Cloonan, Nicole, Kolle, Gabriel, Newell, Felicity, Pinese, Mark, Mead, R, Humphris, Jeremy, Kaplan, Warren, Jones, Marc, Colvin, Emily, Nagrial, Adnan, Humphrey, Emily, Chou, Angela, Chin, Venessa, Chantrill, Lorraine, Mawson, Amanda, Samra, Jaswinder, Kench, James, Lovell, Jessica, Daly, Roger, Merrett, Neil, Toon, Christopher, Epari, Krishna, Nguyen, Nam, Barbour, Andrew, Zeps, Nikolajs, Kakkar, Nipun, Zhao, Fengmei, Wu, Yuan, Wang, Min, Muzny, Donna, Fisher, William, Brunicardi, F, Hodges, Sally, Reid, Jeffrey, Drummond, Jennifer, Chang, Kyle, Han, Yi, Lewis, Lora, Dinh, Huyen, Buhay, Christian, Beck, Timothy, Timms, Lee, Sam, Michelle, Begley, Kimberly, Brown, Andrew, Pai, Deepa, Panchal, Ami, Buchner, Nicholas, De Borja, Richard, Denroche, Robert, Yung, Christina, Serra, Stefano, Onetto, Nicole, Mukhopadhyay, Debabrata, Tsao, Ming-Sound, Shaw, Patricia, Petersen, Gloria, Gallinger, Steven, Hruban, Ralph, Maitra, Anirban, Iacobuzio-Donahue, Christine, Schulick, Richard, Wolfgang, Christopher, and Morgan, Richard

Subjects
Animals, Axons, Carcinoma, Pancreatic Ductal, Gene Dosage, Gene Expression Regulation, Neoplastic, Genome, Humans, Kaplan-Meier Estimate, Mice, Mutation, Pancreatic Neoplasms, Proteins, Signal Transduction
Abstract

Pancreatic cancer is a highly lethal malignancy with few effective therapies. We performed exome sequencing and copy number analysis to define genomic aberrations in a prospectively accrued clinical cohort (n = 142) of early (stage I and II) sporadic pancreatic ductal adenocarcinoma. Detailed analysis of 99 informative tumours identified substantial heterogeneity with 2,016 non-silent mutations and 1,628 copy-number variations. We define 16 significantly mutated genes, reaffirming known mutations (KRAS, TP53, CDKN2A, SMAD4, MLL3, TGFBR2, ARID1A and SF3B1), and uncover novel mutated genes including additional genes involved in chromatin modification (EPC1 and ARID2), DNA damage repair (ATM) and other mechanisms (ZIM2, MAP2K4, NALCN, SLC16A4 and MAGEA6). Integrative analysis with in vitro functional data and animal models provided supportive evidence for potential roles for these genetic aberrations in carcinogenesis. Pathway-based analysis of recurrently mutated genes recapitulated clustering in core signalling pathways in pancreatic ductal adenocarcinoma, and identified new mutated genes in each pathway. We also identified frequent and diverse somatic aberrations in genes described traditionally as embryonic regulators of axon guidance, particularly SLIT/ROBO signalling, which was also evident in murine Sleeping Beauty transposon-mediated somatic mutagenesis models of pancreatic cancer, providing further supportive evidence for the potential involvement of axon guidance genes in pancreatic carcinogenesis.

Published
2012

7. Genome-wide coancestry reveals details of ancient and recent male-driven reticulation in baboons

Author

Sørensen, Erik F., primary, Harris, R. Alan, additional, Zhang, Liye, additional, Raveendran, Muthuswamy, additional, Kuderna, Lukas F. K., additional, Walker, Jerilyn A., additional, Storer, Jessica M., additional, Kuhlwilm, Martin, additional, Fontsere, Claudia, additional, Seshadri, Lakshmi, additional, Bergey, Christina M., additional, Burrell, Andrew S., additional, Bergman, Juraj, additional, Phillips-Conroy, Jane E., additional, Shiferaw, Fekadu, additional, Chiou, Kenneth L., additional, Chuma, Idrissa S., additional, Keyyu, Julius D., additional, Fischer, Julia, additional, Gingras, Marie-Claude, additional, Salvi, Sejal, additional, Doddapaneni, Harshavardhan, additional, Schierup, Mikkel H., additional, Batzer, Mark A., additional, Jolly, Clifford J., additional, Knauf, Sascha, additional, Zinner, Dietmar, additional, Farh, Kyle K.-H., additional, Marques-Bonet, Tomas, additional, Munch, Kasper, additional, Roos, Christian, additional, and Rogers, Jeffrey, additional

Published
2023
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8. Abstract 15628: HeartCare: Improving Clinical Practice Through Comprehensive Cardiovascular Genetic Testing

Author

Murdock, David, Hadley, Trevor, Venner, Eric, Muzny, Donna, Metcalf, Ginger, Murugan, Mullai, Chander, Varuna, Jia, Xiaoming, Hussain, Aliza, Hu, Jianhong, Cohen, Michelle, Kovar, Christie, Gingras, Marie-Claude, Korchina, Viktoriya, Howard, Chad, Riconda, Daniel, Pereira, Stacey, Smith, Hadley, DeVries, Paul, Huda, Zohra, Buentello, Alexandria, Marino, Patricia, Civitello, Andrew, Chelu, Mihail, Leiber, Lee, McGuire, Amy, Balasubramanyam, Ashok, Amos, Chris, Boerwinkle, Eric, Ballantyne, Christie M, Wehrens, Xander, and Gibbs, Richard

Published
2020
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11. Genome-wide coancestry reveals details of ancient and recent male-driven reticulation in baboons

Author

Sørensen, Erik F., Harris, R. Alan, Zhang, Liye, Raveendran, Muthuswamy, Kuderna, Lukas F.K., Walker, Jerilyn A., Storer, Jessica M., Kuhlwilm, Martin, Fontsere, Claudia, Seshadri, Lakshmi, Bergey, Christina M., Burrell, Andrew S., Bergman, Juraj, Phillips-Conroy, Jane E., Shiferaw, Fekadu, Chiou, Kenneth L., Chuma, Idrissa S., Keyyu, Julius D., Fischer, Julia, Gingras, Marie Claude, Salvi, Sejal, Doddapaneni, Harshavardhan, Schierup, Mikkel H., Batzer, Mark A., Jolly, Clifford J., Knauf, Sascha, Zinner, Dietmar, Farh, Kyle K.H., Marques-Bonet, Tomas, Munch, Kasper, Roos, Christian, and Rogers, Jeffrey

Subjects
Article
Abstract

Baboons (genusPapio) are a morphologically and behaviorally diverse clade of catarrhine monkeys that have experienced hybridization between phenotypically and genetically distinct phylogenetic species. We used high coverage whole genome sequences from 225 wild baboons representing 19 geographic localities to investigate population genomics and inter-species gene flow. Our analyses provide an expanded picture of evolutionary reticulation among species and reveal novel patterns of population structure within and among species, including differential admixture among conspecific populations. We describe the first example of a baboon population with a genetic composition that is derived from three distinct lineages. The results reveal processes, both ancient and recent, that produced the observed mismatch between phylogenetic relationships based on matrilineal, patrilineal, and biparental inheritance. We also identified several candidate genes that may contribute to species-specific phenotypes.One-Sentence SummaryGenomic data for 225 baboons reveal novel sites of inter-species gene flow and local effects due to differences in admixture.

Published
2023

12. Structural variation across 138,134 samples in the TOPMed consortium

Author

Jun, Goo, primary, English, Adam, additional, Metcalf, Ginger, additional, Yang, Jianzhi, additional, Chaisson, Mark, additional, Pankratz, Nathan, additional, Menon, Vipin, additional, Salerno, William, additional, Krasheninina, Olga, additional, Smith, Albert, additional, Lane, John, additional, Blackwell, Thomas, additional, Kang, Hyun Min, additional, Salvi, Sejal, additional, Meng, Qingchang, additional, Shen, Hua, additional, Pasham, Divya, additional, Bhamidipati, Sravya, additional, Kottapalli, Kavya, additional, Arnett, Donna, additional, Ashley-Koch, Allison, additional, Auer, Paul, additional, Beutel, KAthleen, additional, Bis, Joshua, additional, Blangero, John, additional, Bowden, Donald, additional, Brody, Jennifer, additional, Cade, Brian, additional, Chen, Yii-Der Ida, additional, Cho, Michael, additional, Curran, Joanne, additional, Fornage, Myriam, additional, Frredman, Barry, additional, Fingerlin, Tasha, additional, Gelb, Bruce, additional, Hou, Lifang, additional, Hung, Yi-Jen, additional, Kane, John P, additional, Kaplan, Robert, additional, Kim, Wonji, additional, Loos, Ruth, additional, Marcus, Gregory, additional, Mathias, Rasika, additional, McGarvey, Stephen, additional, Montgomery, Courtney, additional, Naseri, Take, additional, Nouraie, Seyed, additional, Preuss, Michael, additional, Palmer, Nicholette, additional, Peyser, Patricia, additional, Raffield, Laura, additional, Ratan, Aakrosh, additional, Redline, Susan, additional, Reupena, Muagututia, additional, Rotter, Jerome, additional, Rich, Stephen, additional, Rienstra, Michiel, additional, Ruczinski, Ingo, additional, Sankaran, Vijay, additional, Schwartz, David, additional, Seidman, Christine, additional, Seidman, Jonathan, additional, Silverman, Edwin, additional, Smith, Jennifer, additional, Stilp, Adrienne, additional, Taylor, Kent, additional, Telen, Marilyn, additional, Weiss, Scott, additional, Williams, L. Keoki, additional, Wu, Baojun, additional, Yanek, Lisa, additional, Zhang, Yingze, additional, Lasky-Su, Jessica, additional, Gingras, Marie-Claude, additional, Dutcher, Susan, additional, Eichler, Evan, additional, Gabriel, Stacey, additional, Germer, Soren, additional, Kim, Ryan, additional, Martinez, Karine, additional, Nickerson, Deborah, additional, Luo, James, additional, Reiner, Alexander, additional, Gibbs, Richard, additional, Boerwinkle, Eric, additional, Abecasis, Goncaol, additional, and Sedlazeck, Fritz, additional

Published
2023
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14. Long read sequencing and expression studies ofAHDC1deletions in Xia‐Gibbs syndrome reveal a novel genetic regulatory mechanism

Author

Chander, Varuna, primary, Mahmoud, Medhat, additional, Hu, Jianhong, additional, Dardas, Zain, additional, Grochowski, Christopher M., additional, Dawood, Moez, additional, Khayat, Michael M., additional, Li, He, additional, Li, Shoudong, additional, Jhangiani, Shalini, additional, Korchina, Viktoriya, additional, Shen, Hua, additional, Weissenberger, George, additional, Meng, Qingchang, additional, Gingras, Marie‐Claude, additional, Muzny, Donna M., additional, Doddapaneni, Harsha, additional, Posey, Jennifer E., additional, Lupski, James R., additional, Sabo, Aniko, additional, Murdock, David R., additional, Sedlazeck, Fritz J., additional, and Gibbs, Richard A., additional

Published
2022
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15. Corrigendum: Whole-genome landscape of pancreatic neuroendocrine tumours

Author

Scarpa, Aldo, Chang, David K., Nones, Katia, Corbo, Vincenzo, Patch, Ann-Marie, Bailey, Peter, Lawlor, Rita T., Johns, Amber L., Miller, David K., Mafficini, Andrea, Rusev, Borislav, Scardoni, Maria, Antonello, Davide, Barbi, Stefano, Sikora, Katarzyna O., Cingarlini, Sara, Vicentini, Caterina, McKay, Skye, Quinn, Michael C. J., Bruxner, Timothy J. C., Christ, Angelika N., Harliwong, Ivon, Idrisoglu, Senel, McLean, Suzanne, Nourse, Craig, Nourbakhsh, Ehsan, Wilson, Peter J., Anderson, Matthew J., Fink, Lynn J., Newell, Felicity, Waddell, Nick, Holmes, Oliver, Kazakoff, Stephen H., Leonard, Conrad, Wood, Scott, Xu, Qinying, Nagaraj, Shivashankar Hiriyur, Amato, Eliana, Dalai, Irene, Bersani, Samantha, Cataldo, Ivana, Dei Tos, Angelo P., Capelli, Paola, Davì, Maria Vittoria, Landoni, Luca, Malpaga, Anna, Miotto, Marco, Whitehall, Vicki L. J., Leggett, Barbara A., Harris, Janelle L., Harris, Jonathan, Jones, Marc D., Humphris, Jeremy, Chantrill, Lorraine A., Chin, Venessa, Nagrial, Adnan M., Pajic, Marina, Scarlett, Christopher J., Pinho, Andreia, Rooman, Ilse, Toon, Christopher, Wu, Jianmin, Pinese, Mark, Cowley, Mark, Barbour, Andrew, Mawson, Amanda, Humphrey, Emily S., Colvin, Emily K., Chou, Angela, Lovell, Jessica A., Jamieson, Nigel B., Duthie, Fraser, Gingras, Marie-Claude, Fisher, William E., Dagg, Rebecca A., Lau, Loretta M. S., Lee, Michael, Pickett, Hilda A., Reddel, Roger R., Samra, Jaswinder S., Kench, James G., Merrett, Neil D., Epari, Krishna, Nguyen, Nam Q., Zeps, Nikolajs, Falconi, Massimo, Simbolo, Michele, Butturini, Giovanni, Van Buren, George, Partelli, Stefano, Fassan, Matteo, Khanna, Kum Kum, Gill, Anthony J., Wheeler, David A., Gibbs, Richard A., Musgrove, Elizabeth A., Bassi, Claudio, Tortora, Giampaolo, Pederzoli, Paolo, Pearson, John V., Waddell, Nicola, Biankin, Andrew V., and Grimmond, Sean M.

Published
2017
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16. Genomic analyses identify molecular subtypes of pancreatic cancer

Author

Bailey, Peter, Chang, David K., Nones, Katia, Johns, Amber L., Patch, Ann-Marie, Gingras, Marie-Claude, Miller, David K., Christ, Angelika N., Bruxner, Tim J. C., Quinn, Michael C., Nourse, Craig, Murtaugh, L. Charles, Harliwong, Ivon, Idrisoglu, Senel, Manning, Suzanne, Nourbakhsh, Ehsan, Wani, Shivangi, Fink, Lynn, Holmes, Oliver, Chin, Venessa, Anderson, Matthew J., Kazakoff, Stephen, Leonard, Conrad, Newell, Felicity, Waddell, Nick, Wood, Scott, Xu, Qinying, Wilson, Peter J., Cloonan, Nicole, Kassahn, Karin S., Taylor, Darrin, Quek, Kelly, Robertson, Alan, Pantano, Lorena, Mincarelli, Laura, Sanchez, Luis N., Evers, Lisa, Wu, Jianmin, Pinese, Mark, Cowley, Mark J., Jones, Marc D., Colvin, Emily K., Nagrial, Adnan M., Humphrey, Emily S., Chantrill, Lorraine A., Mawson, Amanda, Humphris, Jeremy, Chou, Angela, Pajic, Marina, Scarlett, Christopher J., Pinho, Andreia V., Giry-Laterriere, Marc, Rooman, Ilse, Samra, Jaswinder S., Kench, James G., Lovell, Jessica A., Merrett, Neil D., Toon, Christopher W., Epari, Krishna, Nguyen, Nam Q., Barbour, Andrew, Zeps, Nikolajs, Moran-Jones, Kim, Jamieson, Nigel B., Graham, Janet S., Duthie, Fraser, Oien, Karin, Hair, Jane, Grützmann, Robert, Maitra, Anirban, Iacobuzio-Donahue, Christine A., Wolfgang, Christopher L., Morgan, Richard A., Lawlor, Rita T., Corbo, Vincenzo, Bassi, Claudio, Rusev, Borislav, Capelli, Paola, Salvia, Roberto, Tortora, Giampaolo, Mukhopadhyay, Debabrata, Petersen, Gloria M., Munzy, Donna M., Fisher, William E., Karim, Saadia A., Eshleman, James R., Hruban, Ralph H., Pilarsky, Christian, Morton, Jennifer P., Sansom, Owen J., Scarpa, Aldo, Musgrove, Elizabeth A., Bailey, Ulla-Maja Hagbo, Hofmann, Oliver, Sutherland, Robert L., Wheeler, David A., Gill, Anthony J., Gibbs, Richard A., Pearson, John V., Waddell, Nicola, Biankin, Andrew V., and Grimmond, Sean M.

Published
2016
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17. Whole-genome landscape of pancreatic neuroendocrine tumours

Author

Scarpa, Aldo, Chang, David K., Nones, Katia, Corbo, Vincenzo, Patch, Ann-Marie, Bailey, Peter, Lawlor, Rita T., Johns, Amber L., Miller, David K., Mafficini, Andrea, Rusev, Borislav, Scardoni, Maria, Antonello, Davide, Barbi, Stefano, Sikora, Katarzyna O., Cingarlini, Sara, Vicentini, Caterina, McKay, Skye, Quinn, Michael C. J., Bruxner, Timothy J. C., Christ, Angelika N., Harliwong, Ivon, Idrisoglu, Senel, McLean, Suzanne, Nourse, Craig, Nourbakhsh, Ehsan, Wilson, Peter J., Anderson, Matthew J., Fink, Lynn J., Newell, Felicity, Waddell, Nick, Holmes, Oliver, Kazakoff, Stephen H., Leonard, Conrad, Wood, Scott, Xu, Qinying, Nagaraj, Shivashankar Hiriyur, Amato, Eliana, Dalai, Irene, Bersani, Samantha, Cataldo, Ivana, Dei Tos, Angelo P., Capelli, Paola, Davì, Maria Vittoria, Landoni, Luca, Malpaga, Anna, Miotto, Marco, Whitehall, Vicki L. J., Leggett, Barbara A., Harris, Janelle L., Harris, Jonathan, Jones, Marc D., Humphris, Jeremy, Chantrill, Lorraine A., Chin, Venessa, Nagrial, Adnan M., Pajic, Marina, Scarlett, Christopher J., Pinho, Andreia, Rooman, Ilse, Toon, Christopher, Wu, Jianmin, Pinese, Mark, Cowley, Mark, Barbour, Andrew, Mawson, Amanda, Humphrey, Emily S., Colvin, Emily K., Chou, Angela, Lovell, Jessica A., Jamieson, Nigel B., Duthie, Fraser, Gingras, Marie-Claude, Fisher, William E., Dagg, Rebecca A., Lau, Loretta M. S., Lee, Michael, Pickett, Hilda A., Reddel, Roger R., Samra, Jaswinder S., Kench, James G., Merrett, Neil D., Epari, Krishna, Nguyen, Nam Q., Zeps, Nikolajs, Falconi, Massimo, Simbolo, Michele, Butturini, Giovanni, Van Buren, George, Partelli, Stefano, Fassan, Matteo, Khanna, Kum Kum, Gill, Anthony J., Wheeler, David A., Gibbs, Richard A., Musgrove, Elizabeth A., Bassi, Claudio, Tortora, Giampaolo, Pederzoli, Paolo, Pearson, John V., Waddell, Nicola, Biankin, Andrew V., and Grimmond, Sean M.

Published
2017
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18. Genetic testing in ambulatory cardiology clinics reveals high rate of findings with clinical management implications

Author

Murdock, David R., primary, Venner, Eric, additional, Muzny, Donna M., additional, Metcalf, Ginger A., additional, Murugan, Mullai, additional, Hadley, Trevor D., additional, Chander, Varuna, additional, de Vries, Paul S., additional, Jia, Xiaoming, additional, Hussain, Aliza, additional, Agha, Ali M., additional, Sabo, Aniko, additional, Li, Shoudong, additional, Meng, Qingchang, additional, Hu, Jianhong, additional, Tian, Xia, additional, Cohen, Michelle, additional, Yi, Victoria, additional, Kovar, Christie L., additional, Gingras, Marie-Claude, additional, Korchina, Viktoriya, additional, Howard, Chad, additional, Riconda, Daniel L., additional, Pereira, Stacey, additional, Smith, Hadley S., additional, Huda, Zohra A., additional, Buentello, Alexandria, additional, Marino, Patricia R., additional, Leiber, Lee, additional, Balasubramanyam, Ashok, additional, Amos, Christopher I., additional, Civitello, Andrew B., additional, Chelu, Mihail G., additional, Maag, Ronald, additional, McGuire, Amy L., additional, Boerwinkle, Eric, additional, Wehrens, Xander H.T., additional, Ballantyne, Christie M., additional, and Gibbs, Richard A., additional

Published
2021
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19. The tumor suppressor folliculin regulates AMPK-dependent metabolic transformation

Author

Yan, Ming, Gingras, Marie-Claude, Dunlop, Elaine A., Nouet, Yann, Dupuy, Fanny, Jalali, Zahra, Possik, Elite, Coull, Barry J., Kharitidi, Dmitri, Dydensborg, Anders Bondo, Faubert, Brandon, Kamps, Miriam, Sabourin, Sylvie, Preston, Rachael S., Davies, David Mark, Roughead, Taren, Chotard, Laetitia, van Steensel, Maurice A.M., Jones, Russell, Tee, Andrew R., and Pause, Arnim

Subjects
Drug metabolism -- Genetic aspects, Estrone -- Physiological aspects, Tumor suppressor genes -- Properties, Mitochondria -- Properties, Cancer cells -- Genetic aspects, Health care industry
Abstract

The Warburg effect is a tumorigenic metabolic adaptation process characterized by augmented aerobic glycolysis, which enhances cellular bioenergetics. In normal cells, energy homeostasis is controlled by AMPK; however, its role in cancer is not understood, as both AMPK-dependent tumor-promoting and -inhibiting functions were reported. Upon stress, energy levels are maintained by increased mitochondrial biogenesis and glycolysis, controlled by transcriptional coactivator PGC-1α and HIF, respectively. In normoxia, AMPK induces PGC-1α, but how HIF is activated is unclear. Germline mutations in the gene encoding the tumor suppressor folliculin (FLCN) lead to Birt-Hogg-Dube (BHD) syndrome, which is associated with an increased cancer risk. FLCN was identified as an AMPK binding partner, and we evaluated its role with respect to AMPK-dependent energy functions. We revealed that loss of FLCN constitutively activates AMPK, resulting in PGC-1α-mediated mitochondrial biogenesis and increased ROS production. ROS induced HIF transcriptional activity and drove Warburg metabolic reprogramming, coupling AMPK-dependent mitochondrial biogenesis to HIF-dependent metabolic changes. This reprogramming stimulated cellular bioenergetics and conferred a HIF-dependent tumorigenic advantage in FLCN-negative cancer cells. Moreover, this pathway is conserved in a BHD-derived tumor. These results indicate that FLCN inhibits tumorigenesis by preventing AMPK-dependent HIF activation and the subsequent Warburg metabolic transformation., Introduction Kidney cancer is a metabolic disease, because renal cancer genes, including VHL, MET, TSC1, TSC2, FH, and SDH, are involved in metabolic sensing and adaptation to fluctuations in oxygen, [...]

Published
2014
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20. Long read sequencing and expression studies of AHDC1 deletions in Xia‐Gibbs syndrome reveal a novel genetic regulatory mechanism.

Author

Chander, Varuna, Mahmoud, Medhat, Hu, Jianhong, Dardas, Zain, Grochowski, Christopher M., Dawood, Moez, Khayat, Michael M., Li, He, Li, Shoudong, Jhangiani, Shalini, Korchina, Viktoriya, Shen, Hua, Weissenberger, George, Meng, Qingchang, Gingras, Marie‐Claude, Muzny, Donna M., Doddapaneni, Harsha, Posey, Jennifer E., Lupski, James R., and Sabo, Aniko

Abstract

Xia‐Gibbs syndrome (XGS; MIM# 615829) is a rare mendelian disorder characterized by Development Delay (DD), intellectual disability (ID), and hypotonia. Individuals with XGS typically harbor de novo protein‐truncating mutations in the AT‐Hook DNA binding motif containing 1 (AHDC1) gene, although some missense mutations can also cause XGS. Large de novo heterozygous deletions that encompass the AHDC1 gene have also been ascribed as diagnostic for the disorder, without substantial evidence to support their pathogenicity. We analyzed 19 individuals with large contiguous deletions involving AHDC1, along with other genes. One individual bore the smallest known contiguous AHDC1 deletion (∼350 Kb), encompassing eight other genes within chr1p36.11 (Feline Gardner‐Rasheed, IFI6, FAM76A, STX12, PPP1R8, THEMIS2, RPA2, SMPDL3B) and terminating within the first intron of AHDC1. The breakpoint junctions and phase of the deletion were identified using both short and long read sequencing (Oxford Nanopore). Quantification of RNA expression patterns in whole blood revealed that AHDC1 exhibited a mono‐allelic expression pattern with no deficiency in overall AHDC1 expression levels, in contrast to the other deleted genes, which exhibited a 50% reduction in mRNA expression. These results suggest that AHDC1 expression in this individual is compensated by a novel regulatory mechanism and advances understanding of mutational and regulatory mechanisms in neurodevelopmental disorders. [ABSTRACT FROM AUTHOR]

Published
2022
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21. Sequencing of a central nervous system tumor demonstrates cancer transmission in an organ transplant

Author

Gingras, Marie-Claude, primary, Sabo, Aniko, additional, Cardenas, Maria, additional, Rana, Abbas, additional, Dhingra, Sadhna, additional, Meng, Qingchang, additional, Hu, Jianhong, additional, Muzny, Donna M, additional, Doddapaneni, Harshavardhan, additional, Perez, Lesette, additional, Korchina, Viktoriya, additional, Nessner, Caitlin, additional, Liu, Xiuping, additional, Chao, Hsu, additional, Goss, John, additional, and Gibbs, Richard A, additional

Published
2021
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22. Transmission event of SARS-CoV-2 Delta variant reveals multiple vaccine breakthrough infections

Author

Farinholt, Timothy, primary, Doddapaneni, Harsha, additional, Qin, Xiang, additional, Menon, Vipin, additional, Meng, Qingchang, additional, Metcalf, Ginger, additional, Chao, Hsu, additional, Gingras, Marie-Claude, additional, Farinholt, Paige, additional, Agrawal, Charu, additional, Muzny, Donna M., additional, Piedra, Pedro A., additional, Gibbs, Richard A., additional, and Petrosino, Joseph, additional

Published
2021
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24. DNA methylation patterns identify subgroups of pancreatic neuroendocrine tumors with clinical association

Author

Lakis, Vanessa, Lawlor, Rita T., Newell, Felicity, Patch, Ann-Marie, Mafficini, Andrea, Sadanandam, Anguraj, Koufariotis, Lambros T., Johnston, Rebecca L., Leonard, Conrad, Wood, Scott, Rusev, Borislav, Corbo, Vincenzo, Luchini, Claudio, Cingarlini, Sara, Landoni, Luca, Salvia, Roberto, Milella, Michele, Chang, David, Bailey, Peter, Jamieson, Nigel B., Duthie, Fraser, Gingras, Marie-Claude, Muzny, Donna M., Wheeler, David A., Gibbs, Richard A., Milione, Massimo, Pederzoli, Paolo, Samra, Jaswinder S., Gill, Anthony J., Johns, Amber L., Pearson, John V., Biankin, Andrew V., Grimmond, Sean M., Waddell, Nicola, Nones, Katia, Scarpa, Aldo, Chantrill, Lorraine A., Timpson, Paul, Chou, Angela, Pajic, Marina, Murphy, Angela, Dwarte, Tanya, Hermann, David, Vennin, Claire, Cox, Thomas R., Pereira, Brooke, Ritchie, Shona, Reed, Daniel A., Chambers, Cecilia R., Metcalf, Xanthe, Nobis, Max, Mukhopadhyay, Pamela, Addala, Venkateswar, Kazakoff, Stephen, Holmes, Oliver, Xu, Qinying, Hofmann, Oliver, Pavlakis, Nick, Arena, Jennifer, High, Hilda A., Asghari, Ray, Merrett, Neil D., Pavey, Darren, Das, Amitabha, Cosman, Peter H., Ismail, Kasim, O’Connnor, Chelsie, Stoita, Alina, Williams, David, Spigellman, Allan, Lam, Vincent W., McLeod, Duncan, Kirk, Judy, Kench, James G., Grimison, Peter, Sandroussi, Charbel, Goodwin, Annabel, Mead, R. Scott, Tucker, Katherine, Andrews, Lesley, Texler, Michael, Forest, Cindy, Ballal, Mo, Fletcher, David R., Zeps, Nikolajs, Nguyen, Nan Q., Ruszkiewicz, Andrew R., Worthley, Chris, Chen, John, Brooke-Smith, Mark E., Papangelis, Virginia, Clouston, Andrew D., Barbour, Andrew P., O’Rourke, Thomas J., Fawcett, Jonathan W., Slater, Kellee, Hatzifotis, Michael, Hodgkinson, Peter, Nikfarjam, Mehrdad, Eshleman, James R., Hruban, Ralph H., Wolfgang, Christopher L., Dixon, Judith, Scardoni, Maria, Bassi, Claudio, Grimaldi, Sonia, Cantù, Cinzia, Bonizzato, Giada, Bersani, Samantha, Antonello, Davide, Piredda, Liliana, Sperandio, Nicola, Barbi, Stefano, and Merlini, Paola

Abstract

Here we report the DNA methylation profile of 84 sporadic pancreatic neuroendocrine tumors (PanNETs) with associated clinical and genomic information. We identified three subgroups of PanNETs, termed T1, T2 and T3, with distinct patterns of methylation. The T1 subgroup was enriched for functional tumors and ATRX, DAXX and MEN1 wild-type genotypes. The T2 subgroup contained tumors with mutations in ATRX, DAXX and MEN1 and recurrent patterns of chromosomal losses in half of the genome with no association between regions with recurrent loss and methylation levels. T2 tumors were larger and had lower methylation in the MGMT gene body, which showed positive correlation with gene expression. The T3 subgroup harboured mutations in MEN1 with recurrent loss of chromosome 11, was enriched for grade G1 tumors and showed histological parameters associated with better prognosis. Our results suggest a role for methylation in both driving tumorigenesis and potentially stratifying prognosis in PanNETs.

Published
2021

25. Additional file 2 of Transmission event of SARS-CoV-2 delta variant reveals multiple vaccine breakthrough infections

Author

Farinholt, Timothy, Doddapaneni, Harsha, Qin, Xiang, Menon, Vipin, Meng, Qingchang, Metcalf, Ginger, Chao, Hsu, Gingras, Marie-Claude, Avadhanula, Vasanthi, Farinholt, Paige, Agrawal, Charu, Muzny, Donna M., Piedra, Pedro A., Gibbs, Richard A., and Petrosino, Joseph

Abstract

Additional file 2:. Supplementary table 1. Swift Ampilicon Normalize Panel sequencing metrics

Published
2021
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33. Germline mutation in POLR2A: a heterogeneous, multi-systemic developmental disorder characterized by transcriptional dysregulation

Author

Hansen, Adam W., primary, Arora, Payal, additional, Khayat, Michael M., additional, Smith, Leah J., additional, Lewis, Andrea M., additional, Rossetti, Linda Z., additional, Jayaseelan, Joy, additional, Cristian, Ingrid, additional, Haynes, Devon, additional, DiTroia, Stephanie, additional, Meeks, Naomi, additional, Delgado, Mauricio R., additional, Rosenfeld, Jill A., additional, Pais, Lynn, additional, White, Susan M., additional, Meng, Qingchang, additional, Pehlivan, Davut, additional, Liu, Pengfei, additional, Gingras, Marie-Claude, additional, Wangler, Michael F., additional, Muzny, Donna M., additional, Lupski, James R., additional, Kaplan, Craig D., additional, and Gibbs, Richard A., additional

Published
2021
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34. NF-κB and STAT3 co-operation enhances high glucose induced aggressiveness of cholangiocarcinoma cells

Author

Saengboonmee, Charupong, primary, Phoomak, Chatchai, additional, Supabphol, Suangson, additional, Covington, Kyle R., additional, Hampton, Oliver, additional, Wongkham, Chaisiri, additional, Gibbs, Richard A., additional, Umezawa, Kazuo, additional, Seubwai, Wunchana, additional, Gingras, Marie-Claude, additional, and Wongkham, Sopit, additional

Published
2020
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35. Phenotypic expansion in KIF1A ‐related dominant disorders: A description of novel variants and review of published cases

Author

Montenegro‐Garreaud, Ximena, primary, Hansen, Adam W., additional, Khayat, Michael M., additional, Chander, Varuna, additional, Grochowski, Christopher M., additional, Jiang, Yunyun, additional, Li, He, additional, Mitani, Tadahiro, additional, Kessler, Elena, additional, Jayaseelan, Joy, additional, Shen, Hua, additional, Gezdirici, Alper, additional, Pehlivan, Davut, additional, Meng, Qingchang, additional, Rosenfeld, Jill A., additional, Jhangiani, Shalini N., additional, Madan‐Khetarpal, Suneeta, additional, Scott, Daryl A., additional, Abarca‐Barriga, Hugo, additional, Trubnykova, Milana, additional, Gingras, Marie‐Claude, additional, Muzny, Donna M., additional, Posey, Jennifer E., additional, Liu, Pengfei, additional, Lupski, James R., additional, and Gibbs, Richard A., additional

Published
2020
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43. Erratum: Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular Profiles (Cell Reports (2017) 18(11) (2780–2794) (S2211124717302140) (10.1016/j.celrep.2017.02.033))

Author

Farshidfar, Farshad, Zheng, Siyuan, Gingras, Marie-Claude, Newton, Yulia, Shih, Juliann, Robertson, A. Gordon, Hinoue, Toshinori, Hoadley, Katherine A., Gibb, Ewan A., Roszik, Jason, Covington, Kyle R., Wu, Chia-Chin, Shinbrot, Eve, Stransky, Nicolas, Hegde, Apurva, Yang, Ju Dong, Reznik, Ed, Sadeghi, Sara, Pedamallu, Chandra Sekhar, Ojesina, Akinyemi I., Hess, Julian M., Auman, J. Todd, Rhie, Suhn K., Bowlby, Reanne, Borad, Mitesh J., Akbani, Rehan, Allotey, Loretta K., Ally, Adrian, Alvaro, Domenico, Andersen, Jesper B., Appelbaum, Elizabeth L., Arora, Arshi, Balasundaram, Miruna, Balu, Saianand, Bardeesy, Nabeel, Bathe, Oliver F., Baylin, Stephen B., Beroukhim, Rameen, Berrios, Mario, Bodenheimer, Tom, Boice, Lori, Bootwalla, Moiz S., Bowen, Jay, Bragazzi, Maria Consiglia, Brooks, Denise, Cardinale, Vincenzo, Carlsen, Rebecca, Carpino, Guido, Carvalho, Andre L., Chaiteerakij, Roongruedee, Chandan, Vishal C., Cherniack, Andrew D., Chin, Lynda, Cho, Juok, Choe, Gina, Chuah, Eric, Chudamani, Sudha, Cibulskis, Carrie, Cordes, Matthew G., Crain, Daniel, Curley, Erin, De Rose, Agostino Maria, Defreitas, Timothy, Demchok, John A., Deshpande, Vikram, Dhalla, Noreen, Ding, Li, Evason, Kimberley, Felau, Ina, Ferguson, Martin L., Foo, Wai Chin, Franchitto, Antonio, Frazer, Scott, Fronick, Catrina C., Fulton, Lucinda A., Fulton, Robert S., Gabriel, Stacey B., Gardner, Johanna, Gastier-Foster, Julie M., Gaudio, Eugenio, Gehlenborg, Nils, Genovese, Giannicola, Gerken, Mark, Getz, Gad, Giama, Nasra H., Gibbs, Richard A., Giuliante, Felice, Grazi, Gian Luca, Hayes, D. Neil, Hegde, Apurva M., Heiman, David I., Holbrook, Andrea, Holt, Robert A., Hoyle, Alan P., Huang, Mei, Hutter, Carolyn M., Jefferys, Stuart R., Jones, Steven J. M., Jones, Corbin D., Kasaian, Katayoon, Kelley, Robin K., Kim, Jaegil, Kleiner, David E., Kocher, Jean-Pierre A., Kwong, Lawrence N., Lai, Phillip H., Laird, Peter W., Lawrence, Michael S., Leraas, Kristen M., Lichtenberg, Tara M., Lin, Pei, Liu, Wenbin, Liu, Jia, Lolla, Laxmi, Lu, Yiling, Ma, Yussanne, Mallery, David, Mardis, Elaine R., Marra, Marco A., Matsushita, Marcus M., Mayo, Michael, McLellan, Michael D., McRee, Autumn J., Meier, Sam, Meng, Shaowu, Meyerson, Matthew, Mieczkowski, Piotr A., Miller, Christopher A., Mills, Gordon B., Moore, Richard A., Morris, Scott, Mose, Lisle E., Moser, Catherine D., Mounajjed, Taofic, Mungall, Andrew J., Mungall, Karen, Murray, Bradley A., Naresh, Rashi, Noble, Michael S., O'Brien, Daniel R., Parker, Joel S., Patel, Tushar C., Paulauskis, Joseph, Penny, Robert, Perou, Charles M., Perou, Amy H., Pihl, Todd, Radenbaugh, Amie J., Ramirez, Nilsa C., Rathmell, W. Kimryn, Roach, Jeffrey, Roberts, Lewis R., Saksena, Gordon, Sander, Chris, Schein, Jacqueline E., Schmidt, Heather K., Schumacher, Steven E., Shelton, Candace, Shelton, Troy, Shen, Ronglai, Sheth, Margi, Shi, Yan, Shroff, Rachna, Simons, Janae V., Sipahimalani, Payal, Skelly, Tara, Sofia, Heidi J., Soloway, Matthew G., Stoppler, Hubert, Stuart, Josh, Sun, Qiang, Tam, Angela, Tan, Donghui, Tarnuzzer, Roy, Thiessen, Nina, Thorne, Leigh B., Torbenson, Michael S., Van Den Berg, David J., Veluvolu, Umadevi, Verhaak, Roel G. W., Voet, Doug, Wan, Yunhu, Wang, Zhining, Weinstein, John N., Weisenberger, Daniel J., Wheeler, David A., Wilson, Richard K., Wise, Lisa, Wong, Tina, Wu, Ye, Xi, Liu, Yang, Liming, Zenklusen, Jean C., Zhang, Hailei, Zhang, Jiashan (Julia), Zmuda, Erik, Zhu, Andrew X., Stuart, Josh M., Farshidfar, Farshad, Zheng, Siyuan, Gingras, Marie-Claude, Newton, Yulia, Shih, Juliann, Robertson, A. Gordon, Hinoue, Toshinori, Hoadley, Katherine A., Gibb, Ewan A., Roszik, Jason, Covington, Kyle R., Chia-Chin, Wu, Shinbrot, Eve, Stransky, Nicola, Hegde, Apurva, Yang, Ju Dong, Reznik, Ed, Sadeghi, Sara, Pedamallu, Chandra Sekhar, Ojesina, Akinyemi I., Hess, Julian M., Auman, J. Todd, Rhie, Suhn K., Bowlby, Reanne, Borad, Mitesh J., Akbani, Rehan, Allotey, Loretta K., Ally, Adrian, Alvaro, Domenico, Andersen, Jesper B., Appelbaum, Elizabeth L., Arora, Arshi, Balasundaram, Miruna, Balu, Saianand, Bardeesy, Nabeel, Bathe, Oliver F., Baylin, Stephen B., Beroukhim, Rameen, Berrios, Mario, Bodenheimer, Tom, Boice, Lori, Bootwalla, Moiz S., Bowen, Jay, Bragazzi, Maria Consiglia, Brooks, Denise, Cardinale, Vincenzo, Carlsen, Rebecca, Guido, Carpino, Carvalho, Andre L., Chaiteerakij, Roongruedee, Chandan, Vishal C., Cherniack, Andrew D., Chin, Lynda, Cho, Juok, Choe, Gina, Chuah, Eric, Chudamani, Sudha, Cibulskis, Carrie, Cordes, Matthew G., Crain, Daniel, Curley, Erin, De Rose, Agostino Maria, Defreitas, Timothy, Demchok, John A., Deshpande, Vikram, Dhalla, Noreen, Ding, Li, Evason, Kimberley, Felau, Ina, Ferguson, Martin L., Foo, Wai Chin, Franchitto, Antonio, Frazer, Scott, Fronick, Catrina C., Fulton, Lucinda A., Fulton, Robert S., Gabriel, Stacey B., Gardner, Johanna, Gastier-Foster, Julie M., Gaudio, Eugenio, Gehlenborg, Nil, Genovese, Giannicola, Gerken, Mark, Getz, Gad, Giama, Nasra H., Gibbs, Richard A., Giuliante, Felice, Grazi, Gian Luca, Hayes, D. Neil, Hegde, Apurva M., Heiman, David I., Holbrook, Andrea, Holt, Robert A., Hoyle, Alan P., Huang, Mei, Hutter, Carolyn M., Jefferys, Stuart R., Jones, Steven J. M., Jones, Corbin D., Kasaian, Katayoon, Kelley, Robin K., Kim, Jaegil, Kleiner, David E., Kocher, Jean-Pierre A., Kwong, Lawrence N., Lai, Phillip H., Laird, Peter W., Lawrence, Michael S., Leraas, Kristen M., Lichtenberg, Tara M., Lin, Pei, Liu, Wenbin, Liu, Jia, Lolla, Laxmi, Yiling, Lu, Yussanne, Ma, Mallery, David, Mardis, Elaine R., Marra, Marco A., Matsushita, Marcus M., Mayo, Michael, Mclellan, Michael D., Mcree, Autumn J., Meier, Sam, Meng, Shaowu, Meyerson, Matthew, Mieczkowski, Piotr A., Miller, Christopher A., Mills, Gordon B., Moore, Richard A., Morris, Scott, Mose, Lisle E., Moser, Catherine D., Mounajjed, Taofic, Mungall, Andrew J., Mungall, Karen, Murray, Bradley A., Naresh, Rashi, Noble, Michael S., O'Brien, Daniel R., Parker, Joel S., Patel, Tushar C., Paulauskis, Joseph, Penny, Robert, Perou, Charles M., Perou, Amy H., Pihl, Todd, Radenbaugh, Amie J., Ramirez, Nilsa C., Rathmell, W. Kimryn, Roach, Jeffrey, Roberts, Lewis R., Saksena, Gordon, Sander, Chri, Schein, Jacqueline E., Schmidt, Heather K., Schumacher, Steven E., Shelton, Candace, Shelton, Troy, Shen, Ronglai, Sheth, Margi, Shi, Yan, Shroff, Rachna, Simons, Janae V., Sipahimalani, Payal, Skelly, Tara, Sofia, Heidi J., Soloway, Matthew G., Stoppler, Hubert, Stuart, Josh, Sun, Qiang, Tam, Angela, Tan, Donghui, Tarnuzzer, Roy, Thiessen, Nina, Thorne, Leigh B., Torbenson, Michael S., Van Den Berg, David J., Veluvolu, Umadevi, Verhaak, Roel G. W., Voet, Doug, Wan, Yunhu, Wang, Zhining, Weinstein, John N., Weisenberger, Daniel J., Wheeler, David A., Wilson, Richard K., Wise, Lisa, Wong, Tina, Ye, Wu, Liu, Xi, Yang, Liming, Zenklusen, Jean C., Zhang, Hailei, Zhang, Jiashan (Julia), Zmuda, Erik, Zhu, Andrew X., and Stuart, Josh M.

Subjects
Genetics and Molecular Biology (all), Biochemistry, Genetics and Molecular Biology (all), Biochemistry
Abstract

Cholangiocarcinoma (CCA) is an aggressive malignancy of the bile ducts, with poor prognosis and limited treatment options. Here, we describe the integrated analysis of somatic mutations, RNA expression, copy number, and DNA methylation by The Cancer Genome Atlas of a set of predominantly intrahepatic CCA cases and propose a molecular classification scheme. We identified an IDH mutant-enriched subtype with distinct molecular features including low expression of chromatin modifiers, elevated expression of mitochondrial genes, and increased mitochondrial DNA copy number. Leveraging the multi-platform data, we observed that ARID1A exhibited DNA hypermethylation and decreased expression in the IDH mutant subtype. More broadly, we found that IDH mutations are associated with an expanded histological spectrum of liver tumors with molecular features that stratify with CCA. Our studies reveal insights into the molecular pathogenesis and heterogeneity of cholangiocarcinoma and provide classification information of potential therapeutic significance.

Published
2017

44. Corrigendum: Whole-genome landscape of pancreatic neuroendocrine tumours (Nature (2017) 543 (65-71) DOI: 10.1038/nature21063)

Author

Scarpa, Aldo, Chang, David K, Nones, Katia, Corbo, Vincenzo, Patch, Ann-Marie, Bailey, Peter, Lawlor, Rita T, Johns, Amber L, Miller, David K, Mafficini, Andrea, Rusev, Borislav, Scardoni, Maria, Antonello, Davide, Barbi, Stefano, Sikora, Katarzyna O, Cingarlini, Sara, Vicentini, Caterina, McKay, Skye, Quinn, Michael C J, Bruxner, Timothy J C, Christ, Angelika N, Harliwong, Ivon, Idrisoglu, Senel, McLean, Suzanne, Nourse, Craig, Nourbakhsh, Ehsan, Wilson, Peter J, Anderson, Matthew J, Fink, J Lynn, Newell, Felicity, Waddell, Nick, Holmes, Oliver, Kazakoff, Stephen H, Leonard, Conrad, Wood, Scott, Xu, Qinying, Hiriyur Nagaraj, Shivashankar, Amato, Eliana, Dalai, Irene, Bersani, Samantha, Cataldo, Ivana, Dei Tos, Angelo P, Capelli, Paola, Vittoria Davì, Maria, Landoni, Luca, Malpaga, Anna, Miotto, Marco, Whitehall, Vicki L J, Leggett, Barbara A, Harris, Janelle L, Harris, Jonathan, Jones, Marc D, Humphris, Jeremy, Chantrill, Lorraine A, Chin, Venessa, Nagrial, Adnan M, Pajic, Marina, Scarlett, Christopher J, Pinho, Andreia, Rooman, Ilse, Toon, Christopher, Wu, Jianmin, Pinese, Mark, Cowley, Mark, Barbour, Andrew, Mawson, Amanda, Humphrey, Emily S, Colvin, Emily K, Chou, Angela, Lovell, Jessica A, Jamieson, Nigel B, Duthie, Fraser, Gingras, Marie-Claude, Fisher, William E, Dagg, Rebecca A, Lau, Loretta M S, Lee, Michael, Pickett, Hilda A, Reddel, Roger R, Samra, Jaswinder S, Kench, James G, Merrett, Neil D, Epari, Krishna, Nguyen, Nam Q, Zeps, Nikolajs, Falconi, Massimo, Simbolo, Michele, Butturini, Giovanni, Van Buren, George, Partelli, Stefano, Fassan, Matteo, Khanna, Kum Kum, Gill, Anthony J, Wheeler, David A, Gibbs, Richard A, Musgrove, Elizabeth A, Bassi, Claudio, Tortora, Giampaolo, Pederzoli, Paolo, Pearson, John V, Waddell, Nicola, Biankin, Andrew V, Grimmond, Sean M, Scarpa, Aldo, Chang, David K, Nones, Katia, Corbo, Vincenzo, Patch, Ann-Marie, Bailey, Peter, Lawlor, Rita T, Johns, Amber L, Miller, David K, Mafficini, Andrea, Rusev, Borislav, Scardoni, Maria, Antonello, Davide, Barbi, Stefano, Sikora, Katarzyna O, Cingarlini, Sara, Vicentini, Caterina, Mckay, Skye, Quinn, Michael C J, Bruxner, Timothy J C, Christ, Angelika N, Harliwong, Ivon, Idrisoglu, Senel, Mclean, Suzanne, Nourse, Craig, Nourbakhsh, Ehsan, Wilson, Peter J, Anderson, Matthew J, Fink, J Lynn, Newell, Felicity, Waddell, Nick, Holmes, Oliver, Kazakoff, Stephen H, Leonard, Conrad, Wood, Scott, Xu, Qinying, Hiriyur Nagaraj, Shivashankar, Amato, Eliana, Dalai, Irene, Bersani, Samantha, Cataldo, Ivana, Dei Tos, Angelo P, Capelli, Paola, Vittoria Davì, Maria, Landoni, Luca, Malpaga, Anna, Miotto, Marco, Whitehall, Vicki L J, Leggett, Barbara A, Harris, Janelle L, Harris, Jonathan, Jones, Marc D, Humphris, Jeremy, Chantrill, Lorraine A, Chin, Venessa, Nagrial, Adnan M, Pajic, Marina, Scarlett, Christopher J, Pinho, Andreia, Rooman, Ilse, Toon, Christopher, Wu, Jianmin, Pinese, Mark, Cowley, Mark, Barbour, Andrew, Mawson, Amanda, Humphrey, Emily S, Colvin, Emily K, Chou, Angela, Lovell, Jessica A, Jamieson, Nigel B, Duthie, Fraser, Gingras, Marie-Claude, Fisher, William E, Dagg, Rebecca A, Lau, Loretta M S, Lee, Michael, Pickett, Hilda A, Reddel, Roger R, Samra, Jaswinder S, Kench, James G, Merrett, Neil D, Epari, Krishna, Nguyen, Nam Q, Zeps, Nikolaj, Falconi, Massimo, Simbolo, Michele, Butturini, Giovanni, Van Buren, George, Partelli, Stefano, Fassan, Matteo, Khanna, Kum Kum, Gill, Anthony J, Wheeler, David A, Gibbs, Richard A, Musgrove, Elizabeth A, Bassi, Claudio, Tortora, Giampaolo, Pederzoli, Paolo, Pearson, John V, Waddell, Nicola, Biankin, Andrew V, and Grimmond, Sean M

Abstract

It has been brought to our attention that in Fig. 2d of this Article, an incorrect Sanger trace was used to represent the breakpoint of the EWSR1 and FLI1 type 2 fusion. This was due to an error during manuscript preparation, when we inadvertently inserted the electrophoretic trace referring to EWSR1 splicing variants. Figure 2d has been corrected in the online versions of the Article. We apologize for the confusion. In addition, in the first sentence of the 'Somatic driver mutation' section on page 67, the sentence: 'A total of 15,751 somatic coding mutations (7,703 non-silent) were detected in 2,787 genes (Supplementary Tables 4, 5)", should have stated "A total of 3,097 somatic coding mutations (2,498 non-silent) were detected in 2,567 genes (Supplementary Tables 4, 5)". Note that the numbers in the Supplementary Tables are correct. This sentence has been corrected in the online versions of the Article.

Published
2017

48. Integrated Genomic Characterization of Pancreatic Ductal Adenocarcinoma

Author

Raphael, Benjamin J., primary, Hruban, Ralph H., additional, Aguirre, Andrew J., additional, Moffitt, Richard A., additional, Yeh, Jen Jen, additional, Stewart, Chip, additional, Robertson, A. Gordon, additional, Cherniack, Andrew D., additional, Gupta, Manaswi, additional, Getz, Gad, additional, Gabriel, Stacey B., additional, Meyerson, Matthew, additional, Cibulskis, Carrie, additional, Fei, Suzanne S., additional, Hinoue, Toshinori, additional, Shen, Hui, additional, Laird, Peter W., additional, Ling, Shiyun, additional, Lu, Yiling, additional, Mills, Gordon B., additional, Akbani, Rehan, additional, Loher, Phillipe, additional, Londin, Eric R., additional, Rigoutsos, Isidore, additional, Telonis, Aristeidis G., additional, Gibb, Ewan A., additional, Goldenberg, Anna, additional, Mezlini, Aziz M., additional, Hoadley, Katherine A., additional, Collisson, Eric, additional, Lander, Eric, additional, Murray, Bradley A., additional, Hess, Julian, additional, Rosenberg, Mara, additional, Bergelson, Louis, additional, Zhang, Hailei, additional, Cho, Juok, additional, Tiao, Grace, additional, Kim, Jaegil, additional, Livitz, Dimitri, additional, Leshchiner, Ignaty, additional, Reardon, Brendan, additional, Van Allen, Eliezer, additional, Kamburov, Atanas, additional, Beroukhim, Rameen, additional, Saksena, Gordon, additional, Schumacher, Steven E., additional, Noble, Michael S., additional, Heiman, David I., additional, Gehlenborg, Nils, additional, Lawrence, Michael S., additional, Adsay, Volkan, additional, Petersen, Gloria, additional, Klimstra, David, additional, Bardeesy, Nabeel, additional, Leiserson, Mark D.M., additional, Bowlby, Reanne, additional, Kasaian, Katayoon, additional, Birol, Inanc, additional, Mungall, Karen L., additional, Sadeghi, Sara, additional, Weinstein, John N., additional, Spellman, Paul T., additional, Liu, Yuexin, additional, Amundadottir, Laufey T., additional, Tepper, Joel, additional, Singhi, Aatur D., additional, Dhir, Rajiv, additional, Paul, Drwiega, additional, Smyrk, Thomas, additional, Zhang, Lizhi, additional, Kim, Paula, additional, Bowen, Jay, additional, Frick, Jessica, additional, Gastier-Foster, Julie M., additional, Gerken, Mark, additional, Lau, Kevin, additional, Leraas, Kristen M., additional, Lichtenberg, Tara M., additional, Ramirez, Nilsa C., additional, Renkel, Jeremy, additional, Sherman, Mark, additional, Wise, Lisa, additional, Yena, Peggy, additional, Zmuda, Erik, additional, Shih, Juliann, additional, Ally, Adrian, additional, Balasundaram, Miruna, additional, Carlsen, Rebecca, additional, Chu, Andy, additional, Chuah, Eric, additional, Clarke, Amanda, additional, Dhalla, Noreen, additional, Holt, Robert A., additional, Jones, Steven J.M., additional, Lee, Darlene, additional, Ma, Yussanne, additional, Marra, Marco A., additional, Mayo, Michael, additional, Moore, Richard A., additional, Mungall, Andrew J., additional, Schein, Jacqueline E., additional, Sipahimalani, Payal, additional, Tam, Angela, additional, Thiessen, Nina, additional, Tse, Kane, additional, Wong, Tina, additional, Brooks, Denise, additional, Auman, J. Todd, additional, Balu, Saianand, additional, Bodenheimer, Tom, additional, Hayes, D. Neil, additional, Hoyle, Alan P., additional, Jefferys, Stuart R., additional, Jones, Corbin D., additional, Meng, Shaowu, additional, Mieczkowski, Piotr A., additional, Mose, Lisle E., additional, Perou, Charles M., additional, Perou, Amy H., additional, Roach, Jeffrey, additional, Shi, Yan, additional, Simons, Janae V., additional, Skelly, Tara, additional, Soloway, Matthew G., additional, Tan, Donghui, additional, Veluvolu, Umadevi, additional, Parker, Joel S., additional, Wilkerson, Matthew D., additional, Korkut, Anil, additional, Senbabaoglu, Yasin, additional, Burch, Patrick, additional, McWilliams, Robert, additional, Chaffee, Kari, additional, Oberg, Ann, additional, Zhang, Wei, additional, Gingras, Marie-Claude, additional, Wheeler, David A., additional, Xi, Liu, additional, Albert, Monique, additional, Bartlett, John, additional, Sekhon, Harman, additional, Stephen, Yeager, additional, Howard, Zaren, additional, Judy, Miller, additional, Breggia, Anne, additional, Shroff, Rachna T., additional, Chudamani, Sudha, additional, Liu, Jia, additional, Lolla, Laxmi, additional, Naresh, Rashi, additional, Pihl, Todd, additional, Sun, Qiang, additional, Wan, Yunhu, additional, Wu, Ye, additional, Jennifer, Smith, additional, Roggin, Kevin, additional, Becker, Karl-Friedrich, additional, Behera, Madhusmita, additional, Bennett, Joseph, additional, Boice, Lori, additional, Burks, Eric, additional, Carlotti Junior, Carlos Gilberto, additional, Chabot, John, additional, Pretti da Cunha Tirapelli, Daniela, additional, Sebastião dos Santos, Jose, additional, Dubina, Michael, additional, Eschbacher, Jennifer, additional, Huang, Mei, additional, Huelsenbeck-Dill, Lori, additional, Jenkins, Roger, additional, Karpov, Alexey, additional, Kemp, Rafael, additional, Lyadov, Vladimir, additional, Maithel, Shishir, additional, Manikhas, Georgy, additional, Montgomery, Eric, additional, Noushmehr, Houtan, additional, Osunkoya, Adeboye, additional, Owonikoko, Taofeek, additional, Paklina, Oxana, additional, Potapova, Olga, additional, Ramalingam, Suresh, additional, Rathmell, W. 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Published
2017
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50. Haploinsufficiency of the ESCRT Component HD-PTP Predisposes to Cancer

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Manteghi, Sanaz, primary, Gingras, Marie-Claude, additional, Kharitidi, Dmitri, additional, Galarneau, Luc, additional, Marques, Maud, additional, Yan, Ming, additional, Cencic, Regina, additional, Robert, Francis, additional, Paquet, Marilène, additional, Witcher, Michael, additional, Pelletier, Jerry, additional, and Pause, Arnim, additional

Published
2016
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