312 results on '"Barbour, Andrew P"'
Search Results
2. Spatial intra-tumour heterogeneity and treatment-induced genomic evolution in oesophageal adenocarcinoma: implications for prognosis and therapy
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Brosda, Sandra, Aoude, Lauren G., Bonazzi, Vanessa F., Patel, Kalpana, Lonie, James M., Belle, Clemence J., Newell, Felicity, Koufariotis, Lambros T., Addala, Venkateswar, Naeini, Marjan M., Pearson, John V., Krause, Lutz, Waddell, Nicola, and Barbour, Andrew P.
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- 2024
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3. Relatively stable pressure effects and time-increasing thermal contraction control Heber geothermal field deformation
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Jiang, Guoyan, Barbour, Andrew J., Skoumal, Robert J., Materna, Kathryn, Taron, Joshua, and Crandall-Bear, Aren
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- 2024
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4. Multi-omic features of oesophageal adenocarcinoma in patients treated with preoperative neoadjuvant therapy
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M. Naeini, Marjan, Newell, Felicity, Aoude, Lauren G., Bonazzi, Vanessa F., Patel, Kalpana, Lampe, Guy, Koufariotis, Lambros T., Lakis, Vanessa, Addala, Venkateswar, Kondrashova, Olga, Johnston, Rebecca L., Sharma, Sowmya, Brosda, Sandra, Holmes, Oliver, Leonard, Conrad, Wood, Scott, Xu, Qinying, Thomas, Janine, Walpole, Euan, Tao Mai, G., Ackland, Stephen P., Martin, Jarad, Burge, Matthew, Finch, Robert, Karapetis, Christos S., Shannon, Jenny, Nott, Louise, Bohmer, Robert, Wilson, Kate, Barnes, Elizabeth, Zalcberg, John R., Mark Smithers, B., Simes, John, Price, Timothy, Gebski, Val, Nones, Katia, Watson, David I., Pearson, John V., Barbour, Andrew P., and Waddell, Nicola
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- 2023
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5. Direct synthesis of ordered mesoporous materials from thermoplastic elastomers
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Robertson, Mark, Guillen-Obando, Alejandro, Barbour, Andrew, Smith, Paul, Griffin, Anthony, and Qiang, Zhe
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- 2023
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6. Long-term concentration of measure and cut-off
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Barbour, Andrew, Brightwell, Graham, and Luczak, Malwina
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Mathematics - Probability ,60J75, 60C05, 60F15 - Abstract
We present new concentration of measure inequalities for Markov chains, generalising results for chains that are contracting in Wasserstein distance. These are particularly suited to establishing the cut-off phenomenon for suitable chains. We apply our discrete-time inequality to the well-studied Bernoulli-Laplace model of diffusion, and give a probabilistic proof of cut-off, recovering and improving the bounds of Diaconis and Shahshahani. We also extend the notion of cut-off to chains with an infinite state space, and illustrate this in a second example, of a two-host model of disease in continuous time. We give a third example, giving concentration results for the supermarket model, illustrating the full generality and power of our results., Comment: 60 pages; substantially revised in response to referee comments; accepted for publication in Stochastic Processes and Applications
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- 2019
7. Circulating Tumor DNA: A Promising Biomarker for Predicting Recurrence in Patients with BRAF-Negative Melanoma
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Aoude, Lauren G., Brosda, Sandra, Ng, Jessica, Lonie, James M., Belle, Clemence J., Patel, Kalpana, Koufariotis, Lambros T., Wood, Scott, Atkinson, Victoria, Smithers, B. Mark, Pearson, John V., Waddell, Nicola, Barbour, Andrew P., and Bonazzi, Vanessa F.
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- 2023
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8. Tidal response of groundwater in a leaky aquifer: application to Oklahoma
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Wang, Chi-Yuen, Doan, Mai-Linh, Xue, Lian, and Barbour, Andrew
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Physics - Geophysics - Abstract
Quantitative interpretation of the tidal response of water levels measured in wells has long been made either with a model for perfectly confined aquifers or with a model for purely unconfined aquifers. However, many aquifers may be neither totally confined nor purely unconfined at the frequencies of tidal loading but behave somewhere between the two end members. Here we present a more general model for the tidal response of groundwater in aquifers with both horizontal and vertical flow. The model has three independent parameters: the transmissivity and storativity of the aquifer and the specific leakage of the leaking aquitard. If transmissivity and storativity are known independently, this model may be used to estimate aquitard leakage from the phase shift and amplitude ratio of water level in wells obtained from tidal analysis. We apply the model to interpret the tidal response of water level in a USGS deep monitoring well installed in the Arbuckle aquifer in Oklahoma, into which massive amount of wastewater co-produced from hydrocarbon exploration has been injected. The analysis shows that the Arbuckle aquifer is leaking significantly at this site. We suggest that the present method may be effectively and economically applied to monitor leakage in groundwater systems, which bears on the safety of water resources, the security of underground waste repositories, and the outflow of wastewater during deep injection and hydrocarbon extraction., Comment: 46 pages, 8 figures
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- 2018
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9. Achieving a textbook outcome in patients undergoing gastric resections in a low incidence, high-volume Australian Upper GI unit
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Bouffler, Clare, King, Sarah, Frankel, Adam, Barbour, Andrew, Scott, Justin, Thomas, Janine, Smithers, B. Mark, and Thomson, Iain
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Textbook outcome (TBO) has been proposed as a composite measure of quality in esophagogastric surgery, and achieving a TBO has been associated with improved overall survival (OS). The Dutch Upper Gastrointestinal Cancer Audit group determined their TBO rate for gastrectomy to be 32.1%, using 10 parameters. Our study aimed to assess the TBO rate in patients who had a gastrectomy for cancer in an Australian Upper GI unit, allowing for comparisons with international specialist centers.
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- 2024
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10. Targeting DNA Damage Response and Replication Stress in Pancreatic Cancer
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Allison, Sarah, Bailey, Peter J., Bailey, Ulla-Maja, Biankin, Andrew V., Beraldi, Dario, Brunton, Holly, Caligiuri, Giuseppina, Cameron, Euan, Chang, David K., Cooke, Susanna L., Cunningham, Richard, Dreyer, Stephan, Grimwood, Paul, Kelly, Shane, Lampraki, Eirini-Maria, Marshall, John, Martin, Sancha, McDade, Brian, McElroy, Daniel, Musgrove, Elizabeth A., Nourse, Craig, Paulus-Hock, Viola, Ramsay, Donna, Upstill-Goddard, Rosie, Wright, Derek, Jones, Marc D., Evers, Lisa, Rebus, Selma, Rahib, Lola, Serrels, Bryan, Hair, Jane, Jamieson, Nigel B., McKay, Colin J., Westwood, Paul, Williams, Nicola, Duthie, Fraser, Johns, Amber L., Mawson, Amanda, Scarlett, Christopher J., Brancato, Mary-Anne L., Rowe, Sarah J., Simpson, Skye H., Martyn-Smith, Mona, Thomas, Michelle T., Chantrill, Lorraine A., Chin, Venessa T., Chou, Angela, Cowley, Mark J., Humphris, Jeremy L., Mead, R. Scott, Nagrial, Adnan M., Pajic, Marina, Pettit, Jessica, Pinese, Mark, Rooman, Ilse, Wu, Jianmin, Tao, Jiang, DiPietro, Renee, Watson, Clare, Steinmann, Angela, Lee, Hong Ching, Wong, Rachel, Pinho, Andreia V., Giry-Laterriere, Marc, Daly, Roger J., Sutherland, Robert L., Grimmond, Sean M., Waddell, Nicola, Kassahn, Karin S., Miller, David K., Wilson, Peter J., Patch, Ann-Marie, Song, Sarah, Harliwong, Ivon, Idrisoglu, Senel, Nourbakhsh, Ehsan, Manning, Suzanne, Wani, Shivangi, Gongora, Milena, Anderson, Matthew, Holmes, Oliver, Leonard, Conrad, Taylor, Darrin, Wood, Scott, Xu, Christina, Nones, Katia, Fink, J. Lynn, Christ, Angelika, Bruxner, Tim, Cloonan, Nicole, Newell, Felicity, Pearson, John V., Bailey, Peter, Quinn, Michael, Nagaraj, Shivashankar, Kazakoff, Stephen, Waddell, Nick, Krisnan, Keerthana, Quek, Kelly, Wood, David, Samra, Jaswinder S., Gill, Anthony J., Pavlakis, Nick, Guminski, Alex, Toon, Christopher, Asghari, Ray, Merrett, Neil D., Pavey, Darren, Das, Amitabha, Cosman, Peter H., Ismail, Kasim, O’Connnor, Chelsie, Lam, Vincent W., McLeod, Duncan, Pleass, Henry C., Richardson, Arthur, James, Virginia, Kench, James G., Cooper, Caroline L., Joseph, David, Sandroussi, Charbel, Crawford, Michael, Gallagher, James, Texler, Michael, Forest, Cindy, Laycock, Andrew, Epari, Krishna P., Ballal, Mo, Fletcher, David R., Mukhedkar, Sanjay, Spry, Nigel A., DeBoer, Bastiaan, Chai, Ming, Zeps, Nikolajs, Beilin, Maria, Feeney, Kynan, Nguyen, Nan Q., Ruszkiewicz, Andrew R., Worthley, Chris, Tan, Chuan P., Debrencini, Tamara, Chen, John, Brooke-Smith, Mark E., Papangelis, Virginia, Tang, Henry, Barbour, Andrew P., Clouston, Andrew D., Martin, Patrick, O’Rourke, Thomas J., Chiang, Amy, Fawcett, Jonathan W., Slater, Kellee, Yeung, Shinn, Hatzifotis, Michael, Hodgkinson, Peter, Christophi, Christopher, Nikfarjam, Mehrdad, Mountain, Angela, Biobank, Victorian Cancer, Eshleman, James R., Hruban, Ralph H., Maitra, Anirban, Iacobuzio-Donahue, Christine A., Schulick, Richard D., Wolfgang, Christopher L., Morgan, Richard A., Hodgin, Mary, Scarpa, Aldo, Lawlor, Rita T., Beghelli, Stefania, Corbo, Vincenzo, Scardoni, Maria, Bassi, Claudio, Tempero, Margaret A., Graham, Janet S., Dreyer, Stephan B., Paris, Clara, Dray, Eloise, Plenker, Dennis, Galluzzo, Zachary, Tesson, Mathias, Jones, Marc, Moran-Jones, Kim, Wright, Derek W., Oien, Karin, McGregor, Grant A., Gulati, Aditi, Brough, Rachel, Bajrami, Ilirjana, Pettitt, Stephan, Dziubinski, Michele L., Candido, Juliana, Balkwill, Frances, Barry, Simon T., Grützmann, Robert, Johns, Amber, Froeling, Fieke E.M., Beer, Phillip, Petersen, Gloria M., Ashworth, Alan, Frame, Margaret C., Crawford, Howard C., Simeone, Diane M., Lord, Chris, Mukhopadhyay, Debabrata, Pilarsky, Christian, Tuveson, David A., Morton, Jennifer P., and Sansom, Owen J.
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- 2021
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11. Steins (magic) method
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Barbour, Andrew D. and Chen, Louis H. Y.
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Mathematics - Probability ,60-02, 62E17, 60F05 - Abstract
The paper presents a general introduction to the astonishing method for deriving probability approximations that was invented by Charles Stein around 50 years ago.
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- 2014
12. Glyco-centric lectin magnetic bead array (LeMBA) - proteomics dataset of human serum samples from healthy, Barrett׳s esophagus and esophageal adenocarcinoma individuals.
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Shah, Alok K, Lê Cao, Kim-Anh, Choi, Eunju, Chen, David, Gautier, Benoît, Nancarrow, Derek, Whiteman, David C, Baker, Peter R, Clauser, Karl R, Chalkley, Robert J, Saunders, Nicholas A, Barbour, Andrew P, Joshi, Virendra, and Hill, Michelle M
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Barrett׳s esophagus ,Biomarker ,Esophageal adenocarcinoma ,Glycoprotein ,Proteomics ,Rare Diseases ,Prevention ,Digestive Diseases ,Clinical Research ,Barrett's esophagus - Abstract
This data article describes serum glycoprotein biomarker discovery and qualification datasets generated using lectin magnetic bead array (LeMBA) - mass spectrometry techniques, "Serum glycoprotein biomarker discovery and qualification pipeline reveals novel diagnostic biomarker candidates for esophageal adenocarcinoma" [1]. Serum samples collected from healthy, metaplastic Barrett׳s esophagus (BE) and esophageal adenocarcinoma (EAC) individuals were profiled for glycoprotein subsets via differential lectin binding. The biomarker discovery proteomics dataset consisting of 20 individual lectin pull-downs for 29 serum samples with a spiked-in internal standard chicken ovalbumin protein has been deposited in the PRIDE partner repository of the ProteomeXchange Consortium with the data set identifier PRIDE: PXD002442. Annotated MS/MS spectra for the peptide identifications can be viewed using MS-Viewer (〈http://prospector2.ucsf.edu/prospector/cgi-bin/msform.cgi?form=msviewer〉) using search key "jn7qafftux". The qualification dataset contained 6-lectin pulldown-coupled multiple reaction monitoring-mass spectrometry (MRM-MS) data for 41 protein candidates, from 60 serum samples. This dataset is available as a supplemental files with the original publication [1].
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- 2016
13. Tumour microenvironment influences response to treatment in oesophageal adenocarcinoma
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Belle, Clemence J., primary, Lonie, James M., additional, Brosda, Sandra, additional, and Barbour, Andrew P., additional
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- 2023
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14. AGITG MASTERPLAN: a randomised phase II study of modified FOLFIRINOX alone or in combination with stereotactic body radiotherapy for patients with high-risk and locally advanced pancreatic cancer
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Oar, Andrew, Lee, Mark, Le, Hien, Wilson, Kate, Aiken, Chris, Chantrill, Lorraine, Simes, John, Nguyen, Nam, Barbour, Andrew, Samra, Jaswinder, Sjoquist, Katrin M., Moore, Alisha, Espinoza, David, Gebski, Val, Yip, Sonia, Chu, Julie, Kneebone, Andrew, and Goldstein, David
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- 2021
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15. International Multicenter Experience of Isolated Limb Infusion for In-Transit Melanoma Metastases in Octogenarian and Nonagenarian Patients
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Teras, Jüri, Kroon, Hidde M., Miura, John T., Kenyon-Smith, Tim, Beasley, Georgia M., Mullen, Dean, Farrow, Norma E., Mosca, Paul J., Lowe, Michael C., Farley, Clara R., Potdar, Aishwarya, Daou, Hala, Sun, James, Carr, Michael, Farma, Jeffrey M., Henderson, Michael A., Speakman, David, Serpell, Jonathan, Delman, Keith A., Smithers, B. Mark, Barbour, Andrew, Tyler, Douglas S., Coventry, Brendon J., Zager, Jonathan S., and Thompson, John F.
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- 2020
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16. The oesophageal adenocarcinoma tumour immune microenvironment dictates outcomes with different modalities of neoadjuvant therapy – results from the AGITG DOCTOR trial and the cancer evolution biobank
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Lonie, James M., primary, Brosda, Sandra, additional, Bonazzi, Vanessa F., additional, Aoude, Lauren G., additional, Patel, Kalpana, additional, Brown, Ian, additional, Sharma, Sowmya, additional, Lampe, Guy, additional, Addala, Venkateswar, additional, Koufariotis, Lambros T., additional, Wood, Scott, additional, Waddell, Nicola, additional, Dolcetti, Riccardo, additional, and Barbour, Andrew P., additional
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- 2023
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17. Circulating Tumor DNA
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Aoude, Lauren G., primary, Brosda, Sandra, additional, Ng, Jessica, additional, Lonie, James M., additional, Belle, Clemence J., additional, Patel, Kalpana, additional, Koufariotis, Lambros T., additional, Wood, Scott, additional, Atkinson, Victoria, additional, Smithers, B. Mark, additional, Pearson, John V., additional, Waddell, Nicola, additional, Barbour, Andrew P., additional, and Bonazzi, Vanessa F., additional
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- 2023
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18. On Stein's method and perturbations
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Barbour, Andrew D., Cekanavicius, Vydas, and Xia, Aihua
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Mathematics - Probability ,62E17 ,60F05 - Abstract
Stein's (1972) method is a very general tool for assessing the quality of approximation of the distribution of a random element by another, often simpler, distribution. In applications of Stein's method, one needs to establish a Stein identity for the approximating distribution, solve the Stein equation and estimate the behaviour of the solutions in terms of the metrics under study. For some Stein equations, solutions with good properties are known; for others, this is not the case. Barbour and Xia (1999) introduced a perturbation method for Poisson approximation, in which Stein identities for a large class of compound Poisson and translated Poisson distributions are viewed as perturbations of a Poisson distribution. In this paper, it is shown that the method can be extended to very general settings, including perturbations of normal, Poisson, compound Poisson, binomial and Poisson process approximations in terms of various metrics such as the Kolmogorov, Wasserstein and total variation metrics. Examples are provided to illustrate how the general perturbation method can be applied., Comment: 34 pages
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- 2007
19. Regenerative Compositions in the Case of Slow Variation
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Barbour, Andrew D. and Gnedin, Alexander V.
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Mathematics - Probability ,60G09, 60C05 - Abstract
For $S$ a subordinator and $\Pi_n$ an independent Poisson process of intensity $ne^{-x}, x>0,$ we are interested in the number $K_n$ of gaps in the range of $S$ that are hit by at least one point of $\Pi_n$. Extending previous studies in \cite{Bernoulli, GPYI, GPYII} we focus on the case when the tail of the L{\'e}vy measure of $S$ is slowly varying. We view $K_n$ as the terminal value of a random process ${\cal K}_n$, and provide an asymptotic analysis of the fluctuations of ${\cal K}_n$, as $n\to\infty$, for a wide spectrum of situations.
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- 2005
20. Neoadjuvant therapy reduces cardiopulmunary function in patients undegoing oesophagectomy
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Thomson, Iain G., Wallen, Matthew P., Hall, Adrian, Ferris, Rebekah, Gotley, David C., Barbour, Andrew P., Lee, Andrew, Thomas, Janine, and Smithers, Bernard M.
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- 2018
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21. The Impact of Signet Ring Cell Differentiation on Outcome in Patients with Esophageal and Gastroesophageal Junction Adenocarcinoma
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van Hootegem, Sander J. M., Smithers, B. Mark, Gotley, David C., Brosda, Sandra, Thomson, Iain G., Thomas, Janine M., Gartside, Michael, van Lanschot, Jan J. B., Lagarde, Sjoerd M., Wijnhoven, Bas P. L., and Barbour, Andrew P.
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- 2019
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22. Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes.
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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
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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.
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- 2012
23. Mechanical Powers: Engineering and Romantic Poetics in the Early Anthropocene
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Barbour, Andrew John
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English literature ,Engineering ,Anthropocene studies ,climate change ,engineering ,literature ,poetry ,Romanticism - Abstract
My dissertation, Mechanical Powers: Engineering and Romantic Poetics in the Early Anthropocene, retrieves how poetic and technological making converge at the onset of industrial modernity to produce an early industrial consciousness of humanity’s terrestrial agency. One of the proposed start dates for the Anthropocene is James Watt’s 1784 steam engine design, widely taken to mark the emergence of humankind as a geomorphic force with the Romantic advent of engineering and fossil capitalism. Contrary to Anthropocene narratives identifying this planetary power solely with the detrimental effects of industrial capitalism that we have remained unconscious of until the late twentieth and early twenty-first centuries, Mechanical Powers unearths how Romantic poets and engineers in fact developed an early form of Anthropocene consciousness of humankind’s newfound planetary powers as ones that should not be applied for industrial capitalist ends. Dismantling critical narratives of the late eighteenth and early nineteenth century as unreflexively capitalist and unconscious of humankind’s newfound planetary powers, and of poetry as anti-instrumental and anti-industrial, I show how Romantic poets such as Darwin, Wordsworth, Blake, and Byron came to re-envision poetic making in relation to the worldmaking powers of machinery to reckon with the emergence of humankind as a geomorphic force and counteract industrial capitalism’s planetary damages. If today we no longer expect poetic and technological making to intersect, what allowed for this early industrial confluence was the fact that poetry (from poiesis, making) and engineering both came to stand in for humanity’s terrestrial agency as a whole. Chapter 1, “Blake’s Industrial Revolutions,” begins by recovering a critically neglected confluence between Blake’s poetics and Romantic era industrial socialists, the Owenites and Mechanics Institutes, who attempt to develop forms of industry outside of industrial capitalism. In the final chapters of The Making of the English Working Class, best known for documenting industrial capitalism’s damage to labor, E.P. Thompson turns to the Romantic era radical traditions that developed the first forms of industrial socialism. Such radical movements, Thompson writes, applied machinery’s “force to the context of working-class struggle” to fight industrial capitalism for socialist industry. Thompson laments the loss of this radical Romantic era tradition, and its failure to come into contact with Romantic poetry: “After William Blake, no mind was at home in both cultures nor had the genius to interpret the two traditions to each other… In the failure of the two traditions – to come to a point of junction, something was lost. How much we cannot be sure, for we are among the losers.” What we have lost is the possibility of thinking industry outside of capitalism. Yet Blake and the radical elements of the Mechanics Institutes were far closer together than Thompson realizes, even coming into direct contact and sharing a desire to scale up the labor power of machinery for socialist industry. Rejecting the emergence of capitalist factories, Blake develops an industrial poetics that prefigures what he calls a “sweet industry” after capitalism, in which even the labor of making and using heavy machinery such as the mill would be poetic, pleasurable, and lyrical, and the benefits of the worldmaking powers of industry would be extended to “every population over the world” rather than unevenly distributed and extracted from the earth.Chapter 2, “Wordsworth’s Green Industry,” recovers how railway and steamship earthworks prompted Romantic poets and engineers to develop an early Anthropocene consciousness of the human power to shape the earth as a geological force. Against railway capitalists who advocated for blasting through the earth to construct railway earthworks such as viaducts and tunnels as cheaply as possible regardless of ecological cost, William Wordsworth and an environmentally conscious group of railway engineers pioneer a strain of steamboat and railway poetry to develop ecologically sustainable forms of earthworks. Wordsworth and Romantic engineers came to reject the ecological devastation of fossil capitalism, instead imagining alternative forms of green industry figured in the earth’s image. Rather than reading Wordsworth’s persistent naturalization of poetic and industrial technologies as a symptom of productivist ideology, the nineteenth-century belief in the seamless continuity between nature and industry that fueled the ecological crises of industrial capitalism, I argue that this ecocritical drive of Wordsworth’s poetics fuels his attempt to envision a form of green industry over his poetic career realized most fully in his late steamboat and railway poetry. Even in protesting the expansion of the Windermere Railroad into the Lake Distinct, often considered one of the nineteenth-century origins of the environmental movement, Wordsworth cites his steamboat and railway poetry as evidence that he is not against the railway but rather against fossil capitalism’s disfiguring the environment, one year after the utopian-socialist Chevalier imagined the railway as a means of “universal association” between humanity and nature. Protesting the ecological crises of industrial capitalism, Wordsworth prefigures forms of green industry that anticipate the eco-socialist hopes of the Green New Deal.Chapter 3, “The Rise of Thermodynamics: Mechanical Engineering and Byron’s Poetic Machinery,” charts the first history of Byron’s and Romantic engineers’ attempts to grapple with how the new concept of energy that emerges out of the steam engine did not in fact merely fuel industrial capitalism’s visions of limitless steam power – as existing critical narratives assume – but radically erodes it, as Romantic era engineers discover that the universal dissipation of energy through friction sets strict material constraints on any mechanical power. Excavating the Romantic rise of thermodynamics in early nineteenth-century engineering and its impact on Romantic aesthetics, I show how Byron develops an engineering poetics directly influenced by early nineteenth-century engineering, calling his poetic vocation “my post as an engineer” and pioneering a new thermodynamic form of poetic machinery. Romantic poetry and engineering shared a mutual question fueling their thermodynamic aesthetics: what work can mechanical powers achieve under strict constraints of perpetual energy loss and unavoidable physical attrition? This question continues to bear on how we approach poetry and machinery today, and what we might anticipate from poetry and engineering in the industrial age we share with Romanticism. As Byron explores through his engineering poetics, although the endless loss of energy erodes capitalist visions of limitless steam power, it can also provide tools for combating planetary scale dissipation in a time of climate change. A final coda, “Geopoetic Futures,” considers the fate and futures of Romantic industrialism. While by the late nineteenth century, this early form of Anthropocene consciousness where Romantic poetry and engineering intersected was eclipsed by the Victorian consolidation of industrial capitalism, it persists in a counter-modernity that runs from Romantic industrialism to contemporary Green New Deal and eco-socialist movements. This final coda also considers the promises and limits of Anthropocene narratives, and of an all too white and male strain of engineering that becomes bound up with the consolidation of industrial capitalism over the nineteenth century. Romantic poets and engineers begin to envision how the abolition of this white male strain of engineering is necessary for dismantling industrial capitalism. Turning from the metropole to the peripheries of British industrialization to the colonial subjects excluded from Anthropocene history, I show how Romantic poets and industrial socialists such as Robert Southey, Robert Owen, and George Numa Des Sources envision industrial socialist projects of global abolition to dismantle the plantation form that structured the dependency of British industrialization on slavery and sugar. Romantic poets and industrial socialists prefigure how to decolonize industrial modernity by abolishing the racialized logic of industrial capitalism, with its constitutive white industrialism and black other, forgotten Romantic possibilities which Victorian liberals such as Samuel Smiles work to suppress. Finally, I turn to Byron’s daughter Ada Lovelace’s rejection of Charles Babbage’s narrowly masculinist and capitalist application of early computing machinery. Lovelace pioneers a “poetical science” between Romantic poetry and engineering that repurposes the worldmaking powers of poetry and machinery for progressive-gender political ends. Romanticism anticipates one of the most pressing theoretical questions of our own late moment in Anthropocene history that lives on in contemporary critical theory and eco-socialist projects like the Green New Deal and environmental justice movements: how to remake industrial modernity to combat our planetary crises by and for the sake of those whom capitalism has denied or excluded from having any such worldmaking powers in the first place. Returning to this early moment of Anthropocene history where Romantic poetry and engineering intersect provides access to imaginative tools to develop forms of human agency outside capitalism that might renew rather than exhaust the planet.
- Published
- 2021
24. Pathogenic germline variants are associated with poor survival in stage III/IV melanoma patients
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Aoude, Lauren G., Bonazzi, Vanessa F., Brosda, Sandra, Patel, Kalpana, Koufariotis, Lambros T., Oey, Harald, Nones, Katia, Wood, Scott, Pearson, John V., Lonie, James M., Arneil, Melissa, Atkinson, Victoria, Smithers, B. Mark, Waddell, Nicola, and Barbour, Andrew P.
- Published
- 2020
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25. Supplementary Data from Comparative Genomics Provides Etiologic and Biological Insight into Melanoma Subtypes
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Newell, Felicity, primary, Johansson, Peter A., primary, Wilmott, James S., primary, Nones, Katia, primary, Lakis, Vanessa, primary, Pritchard, Antonia L., primary, Lo, Serigne N., primary, Rawson, Robert V., primary, Kazakoff, Stephen H., primary, Colebatch, Andrew J., primary, Koufariotis, Lambros T., primary, Ferguson, Peter M., primary, Wood, Scott, primary, Leonard, Conrad, primary, Law, Matthew H., primary, Brooks, Kelly M., primary, Broit, Natasa, primary, Palmer, Jane M., primary, Couts, Kasey L., primary, Vergara, Ismael A., primary, Long, Georgina V., primary, Barbour, Andrew P., primary, Nieweg, Omgo E., primary, Shivalingam, Brindha, primary, Robinson, William A., primary, Stretch, Jonathan R., primary, Spillane, Andrew J., primary, Saw, Robyn P.M., primary, Shannon, Kerwin F., primary, Thompson, John F., primary, Mann, Graham J., primary, Pearson, John V., primary, Scolyer, Richard A., primary, Waddell, Nicola, primary, and Hayward, Nicholas K., primary
- Published
- 2023
- Full Text
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26. Data from Comparative Genomics Provides Etiologic and Biological Insight into Melanoma Subtypes
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Newell, Felicity, primary, Johansson, Peter A., primary, Wilmott, James S., primary, Nones, Katia, primary, Lakis, Vanessa, primary, Pritchard, Antonia L., primary, Lo, Serigne N., primary, Rawson, Robert V., primary, Kazakoff, Stephen H., primary, Colebatch, Andrew J., primary, Koufariotis, Lambros T., primary, Ferguson, Peter M., primary, Wood, Scott, primary, Leonard, Conrad, primary, Law, Matthew H., primary, Brooks, Kelly M., primary, Broit, Natasa, primary, Palmer, Jane M., primary, Couts, Kasey L., primary, Vergara, Ismael A., primary, Long, Georgina V., primary, Barbour, Andrew P., primary, Nieweg, Omgo E., primary, Shivalingam, Brindha, primary, Robinson, William A., primary, Stretch, Jonathan R., primary, Spillane, Andrew J., primary, Saw, Robyn P.M., primary, Shannon, Kerwin F., primary, Thompson, John F., primary, Mann, Graham J., primary, Pearson, John V., primary, Scolyer, Richard A., primary, Waddell, Nicola, primary, and Hayward, Nicholas K., primary
- Published
- 2023
- Full Text
- View/download PDF
27. Data from Radiomics Biomarkers Correlate with CD8 Expression and Predict Immune Signatures in Melanoma Patients
- Author
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Aoude, Lauren G., primary, Wong, Bernadette Z.Y., primary, Bonazzi, Vanessa F., primary, Brosda, Sandra, primary, Walters, Shaun B., primary, Koufariotis, Lambros T., primary, Naeini, Marjan M., primary, Pearson, John V., primary, Oey, Harald, primary, Patel, Kalpana, primary, Bradford, Julia J., primary, Bloxham, Conor J., primary, Atkinson, Victoria, primary, Law, Phillip, primary, Strutton, Geoffrey, primary, Bayley, Gerard, primary, Yang, Samuel, primary, Smithers, B. Mark, primary, Waddell, Nicola, primary, Miles, Kenneth, primary, and Barbour, Andrew P., primary
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- 2023
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28. Supplementary Figure 3 from Radiomics Biomarkers Correlate with CD8 Expression and Predict Immune Signatures in Melanoma Patients
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Aoude, Lauren G., primary, Wong, Bernadette Z.Y., primary, Bonazzi, Vanessa F., primary, Brosda, Sandra, primary, Walters, Shaun B., primary, Koufariotis, Lambros T., primary, Naeini, Marjan M., primary, Pearson, John V., primary, Oey, Harald, primary, Patel, Kalpana, primary, Bradford, Julia J., primary, Bloxham, Conor J., primary, Atkinson, Victoria, primary, Law, Phillip, primary, Strutton, Geoffrey, primary, Bayley, Gerard, primary, Yang, Samuel, primary, Smithers, B. Mark, primary, Waddell, Nicola, primary, Miles, Kenneth, primary, and Barbour, Andrew P., primary
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- 2023
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29. Supplementary Figure 1 from Radiomics Biomarkers Correlate with CD8 Expression and Predict Immune Signatures in Melanoma Patients
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Aoude, Lauren G., primary, Wong, Bernadette Z.Y., primary, Bonazzi, Vanessa F., primary, Brosda, Sandra, primary, Walters, Shaun B., primary, Koufariotis, Lambros T., primary, Naeini, Marjan M., primary, Pearson, John V., primary, Oey, Harald, primary, Patel, Kalpana, primary, Bradford, Julia J., primary, Bloxham, Conor J., primary, Atkinson, Victoria, primary, Law, Phillip, primary, Strutton, Geoffrey, primary, Bayley, Gerard, primary, Yang, Samuel, primary, Smithers, B. Mark, primary, Waddell, Nicola, primary, Miles, Kenneth, primary, and Barbour, Andrew P., primary
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- 2023
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30. Supplementary Tables 1-4 from Radiomics Biomarkers Correlate with CD8 Expression and Predict Immune Signatures in Melanoma Patients
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Aoude, Lauren G., primary, Wong, Bernadette Z.Y., primary, Bonazzi, Vanessa F., primary, Brosda, Sandra, primary, Walters, Shaun B., primary, Koufariotis, Lambros T., primary, Naeini, Marjan M., primary, Pearson, John V., primary, Oey, Harald, primary, Patel, Kalpana, primary, Bradford, Julia J., primary, Bloxham, Conor J., primary, Atkinson, Victoria, primary, Law, Phillip, primary, Strutton, Geoffrey, primary, Bayley, Gerard, primary, Yang, Samuel, primary, Smithers, B. Mark, primary, Waddell, Nicola, primary, Miles, Kenneth, primary, and Barbour, Andrew P., primary
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- 2023
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31. Supplementary Figure 2 from Radiomics Biomarkers Correlate with CD8 Expression and Predict Immune Signatures in Melanoma Patients
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Aoude, Lauren G., primary, Wong, Bernadette Z.Y., primary, Bonazzi, Vanessa F., primary, Brosda, Sandra, primary, Walters, Shaun B., primary, Koufariotis, Lambros T., primary, Naeini, Marjan M., primary, Pearson, John V., primary, Oey, Harald, primary, Patel, Kalpana, primary, Bradford, Julia J., primary, Bloxham, Conor J., primary, Atkinson, Victoria, primary, Law, Phillip, primary, Strutton, Geoffrey, primary, Bayley, Gerard, primary, Yang, Samuel, primary, Smithers, B. Mark, primary, Waddell, Nicola, primary, Miles, Kenneth, primary, and Barbour, Andrew P., primary
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- 2023
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32. Pancreatic cancer: Is the surgeon still relevant?
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Butler, Nick, Samra, Jaswinder, Nikfarjam, Mehrdad, and Barbour, Andrew P
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- 2016
33. Complex structural rearrangements are present in high-grade dysplastic Barrett’s oesophagus samples
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Newell, Felicity, Patel, Kalpana, Gartside, Michael, Krause, Lutz, Brosda, Sandra, Aoude, Lauren G., Loffler, Kelly A., Bonazzi, Vanessa F., Patch, Ann-Marie, Kazakoff, Stephen H., Holmes, Oliver, Xu, Qinying, Wood, Scott, Leonard, Conrad, Lampe, Guy, Lord, Reginald V., Whiteman, David C., Pearson, John V., Nones, Katia, Waddell, Nicola, and Barbour, Andrew P.
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- 2019
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34. A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns
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Jiao, Wei, Atwal, Gurnit, Polak, Paz, Karlic, Rosa, Cuppen, Edwin, Al-Shahrour, Fatima, Bailey, Peter J, Biankin, Andrew V, Boutros, Paul C, Campbell, Peter J, Chang, David K, Cooke, Susanna L, Deshpande, Vikram, Faltas, Bishoy M, Faquin, William C, Garraway, Levi, Getz, Gad, Grimmond, Sean M, Haider, Syed, Hoadley, Katherine A, Kaiser, Vera B, Kato, Mamoru, Kübler, Kirsten, Lazar, Alexander J, Li, Constance H, Louis, David N, Margolin, Adam, Martin, Sancha, Nahal-Bose, Hardeep K, Nielsen, G Petur, Nik-Zainal, Serena, Omberg, Larsson, P’ng, Christine, Perry, Marc D, Rheinbay, Esther, Rubin, Mark A, Semple, Colin A, Sgroi, Dennis C, Shibata, Tatsuhiro, Siebert, Reiner, Smith, Jaclyn, Stein, Lincoln D, Stobbe, Miranda D, Sun, Ren X, Thai, Kevin, Wright, Derek W, Wu, Chin-Lee, Yuan, Ke, Zhang, Junjun, Danyi, Alexandra, de Ridder, Jeroen, van Herpen, Carla, Lolkema, Martijn P, Steeghs, Neeltje, Morris, Quaid D, Aaltonen, Lauri A, Abascal, Federico, Abeshouse, Adam, Aburatani, Hiroyuki, Adams, David J, Agrawal, Nishant, Ahn, Keun Soo, Ahn, Sung-Min, Aikata, Hiroshi, Akbani, Rehan, Akdemir, Kadir C, Al-Ahmadie, Hikmat, Al-Sedairy, Sultan T, Alawi, Malik, Albert, Monique, Aldape, Kenneth, Alexandrov, Ludmil B, Ally, Adrian, Alsop, Kathryn, Alvarez, Eva G, Amary, Fernanda, Amin, Samirkumar B, Aminou, Brice, Ammerpohl, Ole, Anderson, Matthew J, Ang, Yeng, Antonello, Davide, Anur, Pavana, Aparicio, Samuel, Appelbaum, Elizabeth L, Arai, Yasuhito, Aretz, Axel, Arihiro, Koji, Ariizumi, Shun-ichi, Armenia, Joshua, Arnould, Laurent, Asa, Sylvia, Assenov, Yassen, Aukema, Sietse, Auman, J Todd, Aure, Miriam RR, Awadalla, Philip, Aymerich, Marta, Bader, Gary D, Baez-Ortega, Adrian, Bailey, Matthew H, Balasundaram, Miruna, Balu, Saianand, Bandopadhayay, Pratiti, Banks, Rosamonde E, Barbi, Stefano, Barbour, Andrew P, Barenboim, Jonathan, Barnholtz-Sloan, Jill, Barr, Hugh, Barrera, Elisabet, Bartlett, John, Bartolome, Javier, Bassi, Claudio, Bathe, Oliver F, Baumhoer, Daniel, Bavi, 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Deurzen, Carolien HM, van de Vijver, Marc J, Veer, L van’t, and von Mering, Christian
- Subjects
Human Biology & Physiology ,Ecology,Evolution & Ethology ,Tumour Biology ,Genetics & Genomics ,Structural Biology & Biophysics ,Computational & Systems Biology - Abstract
In cancer, the primary tumour’s organ of origin and histopathology are the strongest determinants of its clinical behaviour, but in 3% of cases a patient presents with a metastatic tumour and no obvious primary. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, we train a deep learning classifier to predict cancer type based on patterns of somatic passenger mutations detected in whole genome sequencing (WGS) of 2606 tumours representing 24 common cancer types produced by the PCAWG Consortium. Our classifier achieves an accuracy of 91% on held-out tumor samples and 88% and 83% respectively on independent primary and metastatic samples, roughly double the accuracy of trained pathologists when presented with a metastatic tumour without knowledge of the primary. Surprisingly, adding information on driver mutations reduced accuracy. Our results have clinical applicability, underscore how patterns of somatic passenger mutations encode the state of the cell of origin, and can inform future strategies to detect the source of circulating tumour DNA.
- Published
- 2023
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35. Combined burden and functional impact tests for cancer driver discovery using DriverPower
- Author
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Human Biology & Physiology ,Ecology,Evolution & Ethology ,Tumour Biology ,Genetics & Genomics ,Structural Biology & Biophysics ,Computational & Systems Biology - Abstract
The discovery of driver mutations is one of the key motivations for cancer genome sequencing. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumour types, we describe DriverPower, a software package that uses mutational burden and functional impact evidence to identify driver mutations in coding and non-coding sites within cancer whole genomes. Using a total of 1373 genomic features derived from public sources, DriverPower’s background mutation model explains up to 93% of the regional variance in the mutation rate across multiple tumour types. By incorporating functional impact scores, we are able to further increase the accuracy of driver discovery. Testing across a collection of 2583 cancer genomes from the PCAWG project, DriverPower identifies 217 coding and 95 non-coding driver candidates. Comparing to six published methods used by the PCAWG Drivers and Functional Interpretation Working Group, DriverPower has the highest F1 score for both coding and non-coding driver discovery. This demonstrates that DriverPower is an effective framework for computational driver discovery.
- Published
- 2023
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36. Integrative pathway enrichment analysis of multivariate omics data
- Author
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Paczkowska, Marta, Barenboim, Jonathan, Sintupisut, Nardnisa, Fox, Natalie S, Zhu, Helen, Abd-Rabbo, Diala, Mee, Miles W, Boutros, Paul C, Abascal, Federico, Amin, Samirkumar B, Bader, Gary D, Beroukhim, Rameen, Bertl, Johanna, Boroevich, Keith A, Brunak, Søren, Campbell, Peter J, Carlevaro-Fita, Joana, Chakravarty, Dimple, Chan, Calvin Wing Yiu, Chen, Ken, Choi, Jung Kyoon, Deu-Pons, Jordi, Dhingra, Priyanka, Diamanti, Klev, Feuerbach, Lars, Fink, J Lynn, Fonseca, Nuno A, Frigola, Joan, Gambacorti-Passerini, Carlo, Garsed, Dale W, Gerstein, Mark, Getz, Gad, Gonzalez-Perez, Abel, Guo, Qianyun, Gut, Ivo G, Haan, David, Hamilton, Mark P, Haradhvala, Nicholas J, Harmanci, Arif O, Helmy, Mohamed, Herrmann, Carl, Hess, Julian M, Hobolth, Asger, Hodzic, Ermin, Hong, Chen, Hornshøj, Henrik, Isaev, Keren, Izarzugaza, Jose MG, Johnson, Rory, Johnson, Todd A, Juul, Malene, Juul, Randi Istrup, Kahles, Andre, Kahraman, Abdullah, Kellis, Manolis, Khurana, Ekta, Kim, Jaegil, Kim, Jong K, Kim, 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Vijver, Marc J, and Veer, L van’t
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Human Biology & Physiology ,Ecology,Evolution & Ethology ,Tumour Biology ,Genetics & Genomics ,Structural Biology & Biophysics ,Computational & Systems Biology - Abstract
Multi-omics datasets represent distinct aspects of the central dogma of molecular biology. Such high-dimensional molecular profiles pose challenges to data interpretation and hypothesis generation. ActivePathways is an integrative method that discovers significantly enriched pathways across multiple datasets using statistical data fusion, rationalizes contributing evidence and highlights associated genes. As part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumor types, we integrated genes with coding and non-coding mutations and revealed frequently mutated pathways and additional cancer genes with infrequent mutations. We also analyzed prognostic molecular pathways by integrating genomic and transcriptomic features of 1780 breast cancers and highlighted associations with immune response and anti-apoptotic signaling. Integration of ChIP-seq and RNA-seq data for master regulators of the Hippo pathway across normal human tissues identified processes of tissue regeneration and stem cell regulation. ActivePathways is a versatile method that improves systems-level understanding of cellular organization in health and disease through integration of multiple molecular datasets and pathway annotations.
- Published
- 2023
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37. Pathway and network analysis of more than 2500 whole cancer genomes
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Reyna, Matthew A, Haan, David, Paczkowska, Marta, Verbeke, Lieven PC, Vazquez, Miguel, Kahraman, Abdullah, Pulido-Tamayo, Sergio, Barenboim, Jonathan, Wadi, Lina, Dhingra, Priyanka, Shrestha, Raunak, Getz, Gad, Lawrence, Michael S, Pedersen, Jakob Skou, Rubin, Mark A, Wheeler, David A, Brunak, Søren, Izarzugaza, Jose MG, Khurana, Ekta, Marchal, Kathleen, von Mering, Christian, Sahinalp, S Cenk, Valencia, Alfonso, Abascal, Federico, Amin, Samirkumar B, Bader, Gary D, Bandopadhayay, Pratiti, Beroukhim, Rameen, Bertl, Johanna, Boroevich, Keith A, Busanovich, John, Campbell, Peter J, Carlevaro-Fita, Joana, Chakravarty, Dimple, Chan, Calvin Wing Yiu, Chen, Ken, Choi, Jung Kyoon, Deu-Pons, Jordi, Diamanti, Klev, Feuerbach, Lars, Fink, J Lynn, Fonseca, Nuno A, Frigola, Joan, Gambacorti-Passerini, Carlo, Garsed, Dale W, Gerstein, Mark, Guo, Qianyun, Gut, Ivo G, Hamilton, Mark P, Haradhvala, Nicholas J, Harmanci, Arif O, Helmy, Mohamed, Herrmann, Carl, Hess, Julian M, Hobolth, Asger, Hodzic, Ermin, Hong, Chen, Hornshøj, Henrik, Isaev, Keren, Johnson, Rory, Johnson, Todd A, Juul, Malene, Juul, Randi Istrup, Kahles, Andre, Kellis, Manolis, Kim, Jaegil, Kim, Jong K, Kim, Youngwook, Komorowski, Jan, Korbel, Jan O, Kumar, Sushant, Lanzós, Andrés, Larsson, Erik, Lee, Donghoon, Lehmann, Kjong-Van, Li, Shantao, Li, Xiaotong, Lin, Ziao, Liu, Eric Minwei, Lochovsky, Lucas, Lou, Shaoke, Madsen, Tobias, Martincorena, Iñigo, Martinez-Fundichely, Alexander, Maruvka, Yosef E, McGillivray, Patrick D, Meyerson, William, Muiños, Ferran, Mularoni, Loris, Nakagawa, Hidewaki, Nielsen, Morten Muhlig, Park, Keunchil, Park, Kiejung, Pons, Tirso, Reyes-Salazar, Iker, Rheinbay, Esther, Rubio-Perez, Carlota, Saksena, Gordon, Salichos, Leonidas, Sander, Chris, Schumacher, Steven E, Shackleton, Mark, Shapira, Ofer, Shen, Ciyue, Shuai, Shimin, Sidiropoulos, Nikos, Sieverling, Lina, Sinnott-Armstrong, Nasa, Stein, Lincoln D, Tamborero, David, Tiao, Grace, Tsunoda, Tatsuhiko, Umer, Husen M, Uusküla-Reimand, Liis, Wadelius, Claes, Wang, Jiayin, Warrell, Jonathan, Waszak, Sebastian M, Weischenfeldt, Joachim, Wu, Guanming, Yu, Jun, Zhang, Jing, Zhang, Xuanping, Zhang, Yan, Zhao, Zhongming, Zou, Lihua, Reimand, Jüri, Stuart, Joshua M, Raphael, Benjamin J, Aaltonen, Lauri A, Abeshouse, Adam, Aburatani, Hiroyuki, Adams, David J, Agrawal, Nishant, Ahn, Keun Soo, Ahn, Sung-Min, Aikata, Hiroshi, Akbani, Rehan, Akdemir, Kadir C, Al-Ahmadie, Hikmat, Al-Sedairy, Sultan T, Al-Shahrour, Fatima, Alawi, Malik, Albert, Monique, Aldape, Kenneth, Alexandrov, Ludmil B, Ally, Adrian, Alsop, Kathryn, Alvarez, Eva G, Amary, Fernanda, Aminou, Brice, Ammerpohl, Ole, Anderson, Matthew J, Ang, Yeng, Antonello, Davide, Anur, Pavana, Aparicio, Samuel, Appelbaum, Elizabeth L, Arai, Yasuhito, Aretz, Axel, Arihiro, Koji, Ariizumi, Shun-ichi, Armenia, Joshua, Arnould, Laurent, Asa, Sylvia, Assenov, Yassen, Atwal, Gurnit, Aukema, Sietse, Auman, J Todd, Aure, Miriam RR, Awadalla, Philip, Aymerich, Marta, Baez-Ortega, Adrian, Bailey, Matthew H, Bailey, Peter J, Balasundaram, Miruna, Balu, Saianand, Banks, Rosamonde E, Barbi, Stefano, Barbour, Andrew P, Barnholtz-Sloan, Jill, Barr, Hugh, Barrera, Elisabet, Bartlett, John, Bartolome, Javier, Bassi, Claudio, Bathe, Oliver F, Baumhoer, Daniel, Bavi, Prashant, Baylin, Stephen B, Bazant, Wojciech, Beardsmore, Duncan, Beck, Timothy A, Behjati, Sam, Behren, Andreas, Niu, Beifang, Bell, Cindy, Beltran, Sergi, Benz, Christopher, Berchuck, Andrew, Bergmann, Anke K, Bergstrom, Erik N, Berman, Benjamin P, Berney, Daniel M, Bernhart, Stephan H, Berrios, Mario, Bersani, Samantha, Betancourt, Miguel, Bhandari, Vinayak, Bhosle, Shriram G, Biankin, Andrew V, Bieg, Matthias, Bigner, Darell, Binder, Hans, Birney, Ewan, Birrer, Michael, Biswas, Nidhan K, Bjerkehagen, Bodil, Bodenheimer, Tom, Boice, Lori, Bonizzato, Giada, De Bono, Johann S, Boot, Arnoud, Bootwalla, Moiz S, Borg, Ake, Borkhardt, Arndt, Borozan, Ivan, Borst, Christoph, Bosenberg, Marcus, Bosio, Mattia, Boultwood, Jacqueline, Bourque, Guillaume, Boutros, Paul C, Bova, G Steven, Bowen, David T, Bowlby, Reanne, Bowtell, David DL, Boyault, Sandrine, Boyce, Rich, Boyd, Jeffrey, Brazma, Alvis, Brennan, Paul, Brewer, Daniel S, Brinkman, Arie B, Bristow, Robert G, Broaddus, Russell R, Brock, Jane E, Brock, Malcolm, Broeks, Annegien, Brooks, Angela N, Brooks, Denise, Brors, Benedikt, Bruxner, Timothy JC, Bruzos, Alicia L, Buchanan, Alex, Buchhalter, Ivo, Buchholz, Christiane, Bullman, Susan, Burke, Hazel, Burkhardt, Birgit, Burns, Kathleen H, Bustamante, Carlos D, Butler, Adam P, Butte, Atul J, Byrne, Niall J, Børresen-Dale, Anne-Lise, Caesar-Johnson, Samantha J, Cafferkey, Andy, Cahill, Declan, Calabrese, Claudia, Caldas, Carlos, Calvo, Fabien, Camacho, Niedzica, Campo, Elias, Cantù, Cinzia, Cao, Shaolong, Carey, Thomas E, Carlsen, Rebecca, Cataldo, Ivana, Cazzola, Mario, Cebon, Jonathan, Cerfolio, Robert, Chadwick, Dianne E, Chalmers, Don, Chan, Kin, Chan-Seng-Yue, Michelle, Chandan, Vishal S, Chang, David K, Chanock, Stephen J, Chantrill, Lorraine A, Chateigner, Aurélien, Chatterjee, Nilanjan, Chayama, Kazuaki, Chen, Hsiao-Wei, Chen, Jieming, Chen, Yiwen, Chen, Zhaohong, Cherniack, Andrew D, Chien, Jeremy, Chiew, Yoke-Eng, Chin, Suet-Feung, Cho, Juok, Cho, Sunghoon, Choi, Wan, Chomienne, Christine, Chong, Zechen, Choo, Su Pin, Chou, Angela, Christ, Angelika N, Christie, Elizabeth L, Chuah, Eric, Cibulskis, Carrie, Cibulskis, Kristian, Cingarlini, Sara, Clapham, Peter, Claviez, Alexander, Cleary, Sean, Cloonan, Nicole, Cmero, Marek, Collins, Colin C, Connor, Ashton A, Cooke, Susanna L, Cooper, Colin S, Cope, Leslie, Corbo, Vincenzo, Cordes, Matthew G, Cordner, Stephen M, Cortés-Ciriano, Isidro, Covington, Kyle, Cowin, Prue A, Craft, Brian, Craft, David, Creighton, Chad J, Cun, Yupeng, Curley, Erin, Cutcutache, Ioana, Czajka, Karolina, Czerniak, Bogdan, Dagg, Rebecca A, Danilova, Ludmila, Davi, Maria Vittoria, Davidson, Natalie R, Davies, Helen, Davis, Ian J, Davis-Dusenbery, Brandi N, Dawson, Kevin J, De La Vega, Francisco M, De Paoli-Iseppi, Ricardo, Defreitas, Timothy, Dei Tos, Angelo P, Delaneau, Olivier, Demchok, John A, Demeulemeester, Jonas, Demidov, German M, Demircioğlu, Deniz, Dennis, Nening M, Denroche, Robert E, Dentro, Stefan C, Desai, Nikita, Deshpande, Vikram, Deshwar, Amit G, Desmedt, Christine, Dhalla, Noreen, Dhani, Neesha C, Dhir, Rajiv, DiBiase, Anthony, Ding, Li, Ding, Shuai, Dinh, Huy Q, Dirix, Luc, Doddapaneni, HarshaVardhan, Donmez, Nilgun, Dow, Michelle T, Drapkin, Ronny, Drechsel, Oliver, Drews, Ruben M, Serge, Serge, Dudderidge, Tim, Dueso-Barroso, Ana, Dunford, Andrew J, Dunn, Michael, Dursi, Lewis Jonathan, Duthie, Fraser R, Dutton-Regester, Ken, Eagles, Jenna, Easton, Douglas F, Edmonds, Stuart, Edwards, Paul A, Edwards, Sandra E, Eeles, Rosalind A, Ehinger, Anna, Eils, Juergen, Eils, Roland, El-Naggar, Adel, Eldridge, Matthew, Ellrott, Kyle, Erkek, Serap, Escaramis, Georgia, Espiritu, Shadrielle MG, Estivill, Xavier, Etemadmoghadam, Dariush, Eyfjord, Jorunn E, Faltas, Bishoy M, Fan, Daiming, Fan, Yu, Faquin, William C, Farcas, Claudiu, Fassan, Matteo, Fatima, Aquila, Favero, Francesco, Fayzullaev, Nodirjon, Felau, Ina, Fereday, Sian, Ferguson, Martin L, Ferretti, Vincent, Field, Matthew A, Finocchiaro, Gaetano, Fisher, Cyril, Fittall, Matthew W, Fitzgerald, Anna, Fitzgerald, Rebecca C, Flanagan, Adrienne M, Fleshner, Neil E, Flicek, Paul, Foekens, John A, Fong, Kwun M, Foster, Christopher S, Fox, Natalie S, Fraser, Michael, Frazer, Scott, Frenkel-Morgenstern, Milana, Friedman, William, Fronick, Catrina C, Fujimoto, Akihiro, Fujita, Masashi, Fukayama, Masashi, Fulton, Lucinda A, Fulton, Robert S, Furuta, Mayuko, Futreal, P Andrew, Füllgrabe, Anja, Gabriel, Stacey B, Gallinger, Steven, Gao, Jianjiong, Gao, Shengjie, Garraway, Levi, Garred, Øystein, Garrison, Erik, Gehlenborg, Nils, Gelpi, Josep LL, George, Joshy, Gerhard, Daniela S, Gerhauser, Clarissa, Gershenwald, Jeffrey E, Gerstung, Moritz, Ghori, Mohammed, Ghossein, Ronald, Giama, Nasra H, Gibbs, Richard A, Gibson, Bob, Gill, Anthony J, Gill, Pelvender, Giri, Dilip D, Glodzik, Dominik, Gnanapragasam, Vincent J, Goebler, Maria Elisabeth, Goldman, Mary J, Gomez, Carmen, Gonzalez, Santiago, Gonzalez-Perez, Abel, Gordenin, Dmitry A, Gossage, James, Gotoh, Kunihito, Govindan, Ramaswamy, Grabau, Dorthe, Graham, Janet S, Grant, Robert C, Green, Anthony R, Green, Eric, Greger, Liliana, Grehan, Nicola, Grimaldi, Sonia, Grimmond, Sean M, Grossman, Robert L, Grundhoff, Adam, Gundem, Gunes, Gupta, Manaswi, Gupta, Shailja, Gut, Marta, Göke, Jonathan, Ha, Gavin, Haake, Andrea, Haas, Siegfried, Haase, Kerstin, Haber, James E, Habermann, Nina, Hach, Faraz, Haider, Syed, Hama, Natsuko, Hamdy, Freddie C, Hamilton, Anne, Han, Leng, Hanna, George B, Hansmann, Martin, Harismendy, Olivier, Harliwong, Ivon, Harrington, Eoghan, Hasegawa, Takanori, Haussler, David, Hawkins, Steve, Hayami, Shinya, Hayashi, Shuto, Hayes, D Neil, Hayes, Stephen J, Hayward, Nicholas K, Hazell, Steven, He, Yao, Heath, Allison P, Heath, Simon C, Hedley, David, Hegde, Apurva M, Heiman, David I, Heinold, Michael C, Heins, Zachary, Heisler, Lawrence E, Hellstrom-Lindberg, Eva, Heo, Seong Gu, Hepperla, Austin J, Heredia-Genestar, José María, Hersey, Peter, Hilmarsdottir, Holmfridur, Hinton, Jonathan, Hirano, Satoshi, Hiraoka, Nobuyoshi, Hoadley, Katherine A, Hoell, Jessica I, Hoffmann, Steve, Hofmann, Oliver, Holbrook, Andrea, Holik, Aliaksei Z, Hollingsworth, Michael A, Holmes, Oliver, Holt, Robert A, Hong, Eun Pyo, Hong, Jongwhi H, Hooijer, Gerrit K, Hosoda, Fumie, Hou, Yong, Hovestadt, Volker, Howat, William, Hoyle, Alan P, Hruban, Ralph H, Hu, Jianhong, Hu, Taobo, Hua, Xing, Huang, Kuan-lin, Huang, Mei, Huang, Mi Ni, Huang, Vincent, Huang, Yi, Huber, Wolfgang, Hudson, Thomas J, Hummel, Michael, Hung, Jillian A, Huntsman, David, Hupp, Ted R, Huse, Jason, Huska, Matthew R, Hutter, Barbara, Hutter, Carolyn M, Hübschmann, Daniel, Iacobuzio-Donahue, Christine A, Imbusch, Charles David, Imielinski, Marcin, Imoto, Seiya, Isaacs, William B, Ishikawa, Shumpei, Iskar, Murat, Islam, SM Ashiqul, Ittmann, Michael, Ivkovic, Sinisa, Jacquemier, Jocelyne, Jakrot, Valerie, Jamieson, Nigel B, Jang, Gun Ho, Jang, Se Jin, Jayaseelan, Joy C, Jayasinghe, Reyka, Jefferys, Stuart R, Jegalian, Karine, Jennings, Jennifer L, Jeon, Seung-Hyup, Jerman, Lara, Ji, Yuan, Jiao, Wei, Johansson, Peter A, Johns, Amber L, Johns, Jeremy, Jolly, Clemency, Joly, Yann, Jonasson, Jon G, Jones, Corbin D, Jones, David R, Jones, David TW, Jones, Nic, Jones, Steven JM, Jonkers, Jos, Ju, Young Seok, Juhl, Hartmut, Jung, Jongsun, Juul, Sissel, Jäger, Natalie, Kabbe, Rolf, Kaiser, Vera B, Kakavand, Hojabr, Kalimuthu, Sangeetha, von Kalle, Christof, Kang, Koo Jeong, Karaszi, Katalin, Karlan, Beth, Karlić, Rosa, Karsch, Dennis, Kasaian, Katayoon, Kassahn, Karin S, Katai, Hitoshi, Kato, Mamoru, Katoh, Hiroto, Kawakami, Yoshiiku, Kay, Jonathan D, Kazakoff, Stephen H, Kazanov, Marat D, Keays, Maria, Kebebew, Electron, Kefford, Richard F, Kench, James G, Kennedy, Catherine J, Kerssemakers, Jules NA, Khoo, David, Khoo, Vincent, Khuntikeo, Narong, Kilpinen, Helena, Kim, Hark Kyun, Kim, Hyung-Lae, Kim, Hyung-Yong, Kim, Hyunghwan, Kim, Jihoon, King, Tari A, Klapper, Wolfram, Kleinheinz, Kortine, Klimczak, Leszek J, Knappskog, Stian, Kneba, Michael, Knoppers, Bartha M, Koh, Youngil, Komura, Daisuke, Komura, Mitsuhiro, Kong, Gu, Kool, Marcel, Korchina, Viktoriya, Korshunov, Andrey, Koscher, Michael, Koster, Roelof, Kote-Jarai, Zsofia, Koures, Antonios, Kovacevic, Milena, Kremeyer, Barbara, Kretzmer, Helene, Kreuz, Markus, Krishnamurthy, Savitri, Kube, Dieter, Kumar, Kiran, Kumar, Pardeep, Kumar, Yogesh, Kundra, Ritika, Kübler, Kirsten, Küppers, Ralf, Lagergren, Jesper, Lai, Phillip H, Laird, Peter W, Lakhani, Sunil R, Lalansingh, Christopher M, Lalonde, Emilie, Lamaze, Fabien C, Lambert, Adam, Lander, Eric, Landgraf, Pablo, Landoni, Luca, Langerød, Anita, Larsimont, Denis, Lathrop, Mark, Lau, Loretta MS, Lawerenz, Chris, Lawlor, Rita T, Lazar, Alexander J, Lazic, Ana Mijalkovic, Le, Xuan, Lee, Darlene, Lee, Eunjung Alice, Lee, Hee Jin, Lee, Jake June-Koo, Lee, Jeong-Yeon, Lee, Juhee, Lee, Ming Ta Michael, Lee-Six, Henry, Lehrach, Hans, Lenze, Dido, Leonard, Conrad R, Leongamornlert, Daniel A, Leshchiner, Ignaty, Letourneau, Louis, Letunic, Ivica, Levine, Douglas A, Lewis, Lora, Ley, Tim, Li, Chang, Li, Constance H, Li, Haiyan Irene, Li, Jun, Li, Lin, Li, Siliang, Li, Xiaobo, Li, Xinyue, Li, Yilong, Liang, Han, Liang, Sheng-Ben, Lichter, Peter, Lin, Pei, Linehan, WM, Lingjærde, Ole Christian, Liu, Dongbing, Liu, Fei-Fei Fei, Liu, Fenglin, Liu, Jia, Liu, Xingmin, Livingstone, Julie, Livitz, Dimitri, Livni, Naomi, Loeffler, Markus, Long, Georgina V, Lopez-Guillermo, Armando, Louis, David N, Lovat, Laurence B, Lu, Yiling, Lu, Yong-Jie, Lu, Youyong, Luchini, Claudio, Lungu, Ilinca, Luo, Xuemei, Luxton, Hayley J, Lynch, Andy G, Lype, Lisa, López, Cristina, López-Otín, Carlos, Z, Eric, Ma, Yussanne, MacGrogan, Gaetan, MacRae, Shona, Macintyre, Geoff, Maejima, Kazuhiro, Mafficini, Andrea, Maglinte, Dennis T, Maitra, Arindam, Majumder, Partha P, Malcovati, Luca, Malikic, Salem, Malleo, Giuseppe, Mann, Graham J, Mantovani-Löffler, Luisa, Marchegiani, Giovanni, Mardis, Elaine R, Margolin, Adam A, Marin, Maximillian G, Markowetz, Florian, Markowski, Julia, Marks, Jeffrey, Marques-Bonet, Tomas, Marra, Marco A, Marsden, Luke, Martens, John WM, Martin, Sancha, Martin-Subero, Jose I, Mashl, R Jay, Massie, Charlie E, Matthew, Thomas J, Matthews, Lucy, Mayer, Erik, Mayes, Simon, Mayo, Michael, Mbabaali, Faridah, McCune, Karen, McDermott, Ultan, McLellan, Michael D, McPherson, John D, McPherson, John R, McPherson, Treasa A, Meier, Samuel R, Meng, Alice, Meng, Shaowu, Menzies, Andrew, Merrett, Neil D, Merson, Sue, Meyerson, Matthew, Mieczkowski, Piotr A, Mihaiescu, George L, Mijalkovic, Sanja, Mikkelsen, Tom, Milella, Michele, Mileshkin, Linda, Miller, Christopher A, Miller, David K, Miller, Jessica K, Mills, Gordon B, Milovanovic, Ana, Minner, Sarah, Miotto, Marco, Arnau, Gisela Mir, Mirabello, Lisa, Mitchell, Chris, Mitchell, Thomas J, Miyano, Satoru, Miyoshi, Naoki, Mizuno, Shinichi, Molnár-Gábor, Fruzsina, Moore, Malcolm J, Moore, Richard A, Morganella, Sandro, Morris, Quaid D, Morrison, Carl, Mose, Lisle E, Moser, Catherine D, Mungall, Andrew J, Mungall, Karen, Musgrove, Elizabeth A, Mustonen, Ville, Mutch, David, Muyas, Francesc, Muzny, Donna M, Muñoz, Alfonso, Myers, Jerome, Myklebost, Ola, Möller, Peter, Nagae, Genta, Nagrial, Adnan M, Nahal-Bose, Hardeep K, Nakagama, Hitoshi, Nakamura, Hiromi, Nakamura, Toru, Nakano, Kaoru, Nandi, Tannistha, Nangalia, Jyoti, Nastic, Mia, Navarro, Arcadi, Navarro, Fabio CP, Neal, David E, Nettekoven, Gerd, Newell, Felicity, Newhouse, Steven J, Newton, Yulia, Ng, Alvin Wei Tian, Ng, Anthony, Nicholson, Jonathan, Nicol, David, Nie, Yongzhan, Nielsen, G Petur, Nik-Zainal, Serena, Noble, Michael S, Nones, Katia, Northcott, Paul A, Notta, Faiyaz, O’Connor, Brian D, O’Donnell, Peter, O’Donovan, Maria, O’Meara, Sarah, O’Neill, Brian Patrick, O’Neill, J Robert, Ocana, David, Ochoa, Angelica, Oesper, Layla, Ogden, Christopher, Ohdan, Hideki, Ohi, Kazuhiro, Ohno-Machado, Lucila, Oien, Karin A, Ojesina, Akinyemi I, Ojima, Hidenori, Okusaka, Takuji, Omberg, Larsson, Ong, Choon Kiat, Ossowski, Stephan, Ott, German, Ouellette, BF Francis, P’ng, Christine, Paiella, Salvatore, Pairojkul, Chawalit, Pajic, Marina, Pan-Hammarström, Qiang, Papaemmanuil, Elli, Papatheodorou, Irene, Paramasivam, Nagarajan, Park, Ji Wan, Park, Joong-Won, Park, Peter J, Parker, Joel S, Parsons, Simon L, Pass, Harvey, Pasternack, Danielle, Pastore, Alessandro, Patch, Ann-Marie, Pauporté, Iris, Pea, Antonio, Pearson, John V, Pedamallu, Chandra Sekhar, Pederzoli, Paolo, Peifer, Martin, Pennell, Nathan A, Perou, Charles M, Perry, Marc D, Petersen, Gloria M, Peto, Myron, Petrelli, Nicholas, Petryszak, Robert, Pfister, Stefan M, Phillips, Mark, Pich, Oriol, Pickett, Hilda A, Pihl, Todd D, Pillay, Nischalan, Pinder, Sarah, Pinese, Mark, Pinho, Andreia V, Pitkänen, Esa, Pivot, Xavier, Piñeiro-Yáñez, Elena, Planko, Laura, Plass, Christoph, Polak, Paz, Popescu, Irinel, Potapova, Olga, Prasad, Aparna, Preston, Shaun R, Prinz, Manuel, Pritchard, Antonia L, Prokopec, Stephenie D, Provenzano, Elena, Puente, Xose S, Puig, Sonia, Puiggròs, Montserrat, Pupo, Gulietta M, Purdie, Colin A, Quinn, Michael C, Rabionet, Raquel, Rader, Janet S, Radlwimmer, Bernhard, Radovic, Petar, Raeder, Benjamin, Raine, Keiran M, Ramakrishna, Manasa, Ramakrishnan, Kamna, Ramalingam, Suresh, Rathmell, W Kimryn, Rausch, Tobias, Reifenberger, Guido, Reis-Filho, Jorge, Reuter, Victor, Reynolds, Sheila M, Riazalhosseini, Yasser, Richardson, Andrea L, Richter, Julia, Ringel, Matthew, Ringnér, Markus, Rino, Yasushi, Rippe, Karsten, Roach, Jeffrey, Roberts, Lewis R, Roberts, Nicola D, Roberts, Steven A, Robertson, A Gordon, Robertson, Alan J, Rodriguez, Javier Bartolomé, Rodriguez-Martin, Bernardo, Rodríguez-González, F Germán, Roehrl, Michael HA, Rohde, Marius, Rokutan, Hirofumi, Romieu, Gilles, Rooman, Ilse, Roques, Tom, Rosebrock, Daniel, Rosenberg, Mara, Rosenstiel, Philip C, Rosenwald, Andreas, Rowe, Edward W, Royo, Romina, Rozen, Steven G, Rubanova, Yulia, Rudneva, Vasilisa A, Rusev, Borislav C, Ruzzenente, Andrea, Rätsch, Gunnar, Sabarinathan, Radhakrishnan, Sabelnykova, Veronica Y, Sadeghi, Sara, Saini, Natalie, Saito-Adachi, Mihoko, Salcedo, Adriana, Salgado, Roberto, Sallari, Richard, Saller, Charles, Salvia, Roberto, Sam, Michelle, Samra, Jaswinder S, Sanchez-Vega, Francisco, Sanders, Grant, Sarin, Rajiv, Sarrafi, Iman, Sasaki-Oku, Aya, Sauer, Torill, Sauter, Guido, Saw, Robyn PM, Scardoni, Maria, Scarlett, Christopher J, Scarpa, Aldo, Scelo, Ghislaine, Schadendorf, Dirk, Schein, Jacqueline E, Schilhabel, Markus B, Schlesner, Matthias, Schlomm, Thorsten, Schmidt, Heather K, Schramm, Sarah-Jane, Schreiber, Stefan, Schultz, Nikolaus, Schwarz, Roland F, Scolyer, Richard A, Scott, David, Scully, Ralph, Seethala, Raja, Segre, Ayellet V, Selander, Iris, Semple, Colin A, Senbabaoglu, Yasin, Sengupta, Subhajit, Sereni, Elisabetta, Serra, Stefano, Sgroi, Dennis C, Shah, Nimish C, Shahabi, Sagedeh, Shang, Catherine A, Shang, Ping, Shelton, Troy, Shen, Hui, Shepherd, Rebecca, Shi, Ruian, Shi, Yan, Shiah, Yu-Jia, Shibata, Tatsuhiro, Shih, Juliann, Shimizu, Eigo, Shimizu, Kiyo, Shin, Seung Jun, Shiraishi, Yuichi, Shmaya, Tal, Shmulevich, Ilya, Shorser, Solomon I, Short, Charles, Shringarpure, Suyash S, Shriver, Craig, Siebert, Reiner, Sieuwerts, Anieta M, Signoretti, Sabina, Sikora, Katarzyna O, Simbolo, Michele, Simon, Ronald, Simons, Janae V, Simpson, Jared T, Simpson, Peter T, Singer, Samuel, Sipahimalani, Payal, Skelly, Tara J, Smid, Marcel, Smith, Jaclyn, Smith-McCune, Karen, Socci, Nicholas D, Sofia, Heidi J, Soloway, Matthew G, Song, Lei, Sood, Anil K, Sothi, Sharmila, Sotiriou, Christos, Soulette, Cameron M, Span, Paul N, Spellman, Paul T, Sperandio, Nicola, Spillane, Andrew J, Spiro, Oliver, Spring, Jonathan, Staaf, Johan, Stadler, Peter F, Staib, Peter, Stark, Stefan G, Stebbings, Lucy, Stefánsson, Ólafur Andri, Stegle, Oliver, Stenhouse, Alasdair, Stewart, Chip, Stilgenbauer, Stephan, Stobbe, Miranda D, Stratton, Michael R, Stretch, Jonathan R, Struck, Adam J, Stunnenberg, Henk G, Su, Hong, Su, Xiaoping, Sun, Ren X, Sungalee, Stephanie, Susak, Hana, Suzuki, Akihiro, Sweep, Fred, Szczepanowski, Monika, Sültmann, Holger, Yugawa, Takashi, Tam, Angela, Tan, Benita Kiat Tee, Tan, Donghui, Tan, Patrick, Tanaka, Hiroko, Taniguchi, Hirokazu, Tanskanen, Tomas J, Tarabichi, Maxime, Tarnuzzer, Roy, Tarpey, Patrick, Taschuk, Morgan L, Tatsuno, Kenji, Tavaré, Simon, Taylor, Darrin F, Taylor-Weiner, Amaro, Teague, Jon W, Teh, Bin Tean, Tembe, Varsha, Temes, Javier, Thai, Kevin, Thayer, Sarah P, Thiessen, Nina, Thomas, Gilles, Thomas, Sarah, Thompson, Alan, Thompson, Alastair M, Thompson, John FF, Thompson, R Houston, Thorne, Heather, Thorne, Leigh B, Thorogood, Adrian, Tijanic, Nebojsa, Timms, Lee E, Tirabosco, Roberto, Tojo, Marta, Tommasi, Stefania, Toon, Christopher W, Toprak, Umut H, Torrents, David, Tortora, Giampaolo, Tost, Jörg, Totoki, Yasushi, Townend, David, Traficante, Nadia, Treilleux, Isabelle, Trotta, Jean-Rémi, Trümper, Lorenz HP, Tsao, Ming, MC Tubio, Jose, Tucker, Olga, Turkington, Richard, Turner, Daniel J, Tutt, Andrew, Ueno, Masaki, Ueno, Naoto T, Umbricht, Christopher, Underwood, Timothy J, Urban, Lara, Urushidate, Tomoko, Ushiku, Tetsuo, Van Den Berg, David J, Van Laere, Steven, Van Loo, Peter, Van Meir, Erwin G, Van den Eynden, Gert G, Van der Kwast, Theodorus, Vasudev, Naveen, Vedururu, Ravikiran, Veluvolu, Umadevi, Vembu, Shankar, Vermeulen, Peter, Verrill, Clare, Viari, Alain, Vicente, David, Vicentini, Caterina, VijayRaghavan, K, Viksna, Juris, Vilain, Ricardo E, Villasante, Izar, 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Human Biology & Physiology ,Ecology,Evolution & Ethology ,Tumour Biology ,Genetics & Genomics ,Structural Biology & Biophysics ,Computational & Systems Biology - Abstract
The catalog of cancer driver mutations in protein-coding genes has greatly expanded in the past decade. However, non-coding cancer driver mutations are less well-characterized and only a handful of recurrent non-coding mutations, most notably TERT promoter mutations, have been reported. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancer across 38 tumor types, we perform multi-faceted pathway and network analyses of non-coding mutations across 2583 whole cancer genomes from 27 tumor types compiled by the ICGC/TCGA PCAWG project that was motivated by the success of pathway and network analyses in prioritizing rare mutations in protein-coding genes. While few non-coding genomic elements are recurrently mutated in this cohort, we identify 93 genes harboring non-coding mutations that cluster into several modules of interacting proteins. Among these are promoter mutations associated with reduced mRNA expression in TP53, TLE4, and TCF4. We find that biological processes had variable proportions of coding and non-coding mutations, with chromatin remodeling and proliferation pathways altered primarily by coding mutations, while developmental pathways, including Wnt and Notch, altered by both coding and non-coding mutations. RNA splicing is primarily altered by non-coding mutations in this cohort, and samples containing non-coding mutations in well-known RNA splicing factors exhibit similar gene expression signatures as samples with coding mutations in these genes. These analyses contribute a new repertoire of possible cancer genes and mechanisms that are altered by non-coding mutations and offer insights into additional cancer vulnerabilities that can be investigated for potential therapeutic treatments.
- Published
- 2023
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38. Divergent mutational processes distinguish hypoxic and normoxic tumours
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Bhandari, Vinayak, Li, Constance H, Bristow, Robert G, Boutros, Paul C, Aaltonen, Lauri A, Abascal, Federico, Abeshouse, Adam, Aburatani, Hiroyuki, Adams, David J, Agrawal, Nishant, Ahn, Keun Soo, Ahn, Sung-Min, Aikata, Hiroshi, Akbani, Rehan, Akdemir, Kadir C, Al-Ahmadie, Hikmat, Al-Sedairy, Sultan T, Al-Shahrour, Fatima, Alawi, Malik, Albert, Monique, Aldape, Kenneth, Alexandrov, Ludmil B, Ally, Adrian, Alsop, Kathryn, Alvarez, Eva G, Amary, Fernanda, Amin, Samirkumar B, Aminou, Brice, Ammerpohl, Ole, Anderson, Matthew J, Ang, Yeng, Antonello, Davide, Anur, Pavana, Aparicio, Samuel, Appelbaum, Elizabeth L, Arai, Yasuhito, Aretz, Axel, Arihiro, Koji, Ariizumi, Shun-ichi, Armenia, Joshua, Arnould, Laurent, Asa, Sylvia, Assenov, Yassen, Atwal, Gurnit, Aukema, Sietse, Auman, J Todd, Aure, Miriam RR, Awadalla, Philip, Aymerich, Marta, Bader, Gary D, Baez-Ortega, Adrian, Bailey, Matthew H, Bailey, Peter J, Balasundaram, Miruna, Balu, Saianand, Bandopadhayay, Pratiti, Banks, Rosamonde E, 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Human Biology & Physiology ,Ecology,Evolution & Ethology ,Tumour Biology ,Genetics & Genomics ,Structural Biology & Biophysics ,Computational & Systems Biology - Abstract
Many primary tumours have low levels of molecular oxygen (hypoxia), and hypoxic tumours respond poorly to therapy. Pan-cancer molecular hallmarks of tumour hypoxia remain poorly understood, with limited comprehension of its associations with specific mutational processes, non-coding driver genes and evolutionary features. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumour types, we quantify hypoxia in 1188 tumours spanning 27 cancer types. Elevated hypoxia associates with increased mutational load across cancer types, irrespective of underlying mutational class. The proportion of mutations attributed to several mutational signatures of unknown aetiology directly associates with the level of hypoxia, suggesting underlying mutational processes for these signatures. At the gene level, driver mutations in TP53, MYC and PTEN are enriched in hypoxic tumours, and mutations in PTEN interact with hypoxia to direct tumour evolutionary trajectories. Overall, hypoxia plays a critical role in shaping the genomic and evolutionary landscapes of cancer.
- Published
- 2023
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39. Genomic footprints of activated telomere maintenance mechanisms in cancer
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Michael, Koster, Roelof, Kote-Jarai, Zsofia, Koures, Antonios, Kovacevic, Milena, Kremeyer, Barbara, Kretzmer, Helene, Kreuz, Markus, Krishnamurthy, Savitri, Kube, Dieter, Kumar, Pardeep, Kumar, Sushant, Kumar, Yogesh, Kundra, Ritika, Kübler, Kirsten, Küppers, Ralf, Lagergren, Jesper, Lai, Phillip H, Laird, Peter W, Lakhani, Sunil R, Lalansingh, Christopher M, Lalonde, Emilie, Lamaze, Fabien C, Lambert, Adam, Lander, Eric, Landgraf, Pablo, Landoni, Luca, Langerød, Anita, Lanzós, Andrés, Larsimont, Denis, Larsson, Erik, Lathrop, Mark, Lau, Loretta MS, Lawerenz, Chris, Lawlor, Rita T, Lawrence, Michael S, Lazar, Alexander J, Lazic, Ana Mijalkovic, Le, Xuan, Lee, Darlene, Lee, Donghoon, Lee, Hee Jin, Lee, Jeong-Yeon, Lee, Juhee, Lee, Ming Ta Michael, Lee-Six, Henry, Lehmann, Kjong-Van, Lehrach, Hans, Lenze, Dido, Leonard, Conrad R, Leongamornlert, Daniel A, Leshchiner, Ignaty, Letourneau, Louis, Letunic, Ivica, Levine, Douglas A, Lewis, Lora, Ley, Tim, Li, Chang, Li, Constance H, Li, Haiyan Irene, Li, Jun, Li, Lin, Li, Shantao, Li, Siliang, Li, Xiaobo, Li, Xiaotong, Li, Xinyue, Liang, Han, Liang, Sheng-Ben, Lichter, Peter, Lin, Pei, Lin, Ziao, Linehan, WM, Lingjærde, Ole Christian, Liu, Dongbing, Liu, Eric Minwei, Liu, Fei-Fei Fei, Liu, Fenglin, Liu, Jia, Liu, Xingmin, Livingstone, Julie, Livitz, Dimitri, Livni, Naomi, Lochovsky, Lucas, Loeffler, Markus, Long, Georgina V, Lopez-Guillermo, Armando, Lou, Shaoke, Louis, David N, Lovat, Laurence B, Lu, Yiling, Lu, Yong-Jie, Lu, Youyong, Luchini, Claudio, Lungu, Ilinca, Luo, Xuemei, Luxton, Hayley J, Lype, Lisa, López, Cristina, López-Otín, Carlos, Z, Eric, Ma, Yussanne, MacGrogan, Gaetan, MacRae, Shona, Madsen, Tobias, Maejima, Kazuhiro, Mafficini, Andrea, Maglinte, Dennis T, Maitra, Arindam, Majumder, Partha P, Malcovati, Luca, Malikic, Salem, Malleo, Giuseppe, Mann, Graham J, Mantovani-Löffler, Luisa, Marchal, Kathleen, Marchegiani, Giovanni, Mardis, Elaine R, Margolin, Adam A, Marin, Maximillian G, Markowski, Julia, Marks, Jeffrey, Marques-Bonet, Tomas, Marra, Marco A, Marsden, Luke, Martens, John WM, Martin, Sancha, Martin-Subero, Jose I, Maruvka, Yosef E, Mashl, R Jay, Massie, Charlie E, Matthew, Thomas J, Matthews, Lucy, Mayer, Erik, Mayes, Simon, Mayo, Michael, Mbabaali, Faridah, McCune, Karen, McDermott, Ultan, McGillivray, Patrick D, McLellan, Michael D, McPherson, John D, McPherson, John R, McPherson, Treasa A, Meier, Samuel R, Meng, Alice, Meng, Shaowu, Menzies, Andrew, Merrett, Neil D, Merson, Sue, Meyerson, William, Mieczkowski, Piotr A, Mihaiescu, George L, Mijalkovic, Sanja, Mikkelsen, Tom, Milella, Michele, Mileshkin, Linda, Miller, Christopher A, Miller, David K, Miller, Jessica K, Mills, Gordon B, Milovanovic, Ana, Minner, Sarah, Miotto, Marco, Arnau, Gisela Mir, Mirabello, Lisa, Mitchell, Chris, Mitchell, Thomas J, Miyoshi, Naoki, Mizuno, Shinichi, Molnár-Gábor, Fruzsina, Moore, Malcolm J, Moore, Richard A, Morganella, Sandro, Morris, Quaid D, Morrison, Carl, Mose, Lisle E, Moser, Catherine D, Muiños, Ferran, Mularoni, Loris, Mungall, Andrew J, Mungall, Karen, Musgrove, Elizabeth A, Mustonen, Ville, Mutch, David, Muyas, Francesc, Muzny, Donna M, Muñoz, Alfonso, Myers, Jerome, Myklebost, Ola, Möller, Peter, Nagae, Genta, Nagrial, Adnan M, Nahal-Bose, Hardeep K, Nakagama, Hitoshi, Nakamura, Hiromi, Nakamura, Toru, Nakano, Kaoru, Nandi, Tannistha, Nangalia, Jyoti, Nastic, Mia, Navarro, Arcadi, Neal, David E, Nettekoven, Gerd, Newell, Felicity, Newhouse, Steven J, Newton, Yulia, Ng, Alvin Wei Tian, Ng, Anthony, Nicholson, Jonathan, Nicol, David, Nie, Yongzhan, Nielsen, G Petur, Nielsen, Morten Muhlig, Nik-Zainal, Serena, Noble, Michael S, Nones, Katia, Northcott, Paul A, Notta, Faiyaz, O’Connor, Brian D, O’Donnell, Peter, O’Donovan, Maria, O’Meara, Sarah, O’Neill, Brian Patrick, O’Neill, J Robert, Ocana, David, Ochoa, Angelica, Oesper, Layla, Ogden, Christopher, Ohdan, Hideki, Ohi, Kazuhiro, Ohno-Machado, Lucila, Oien, Karin A, Ojesina, Akinyemi I, Ojima, Hidenori, Okusaka, Takuji, Omberg, Larsson, Ong, Choon Kiat, Ott, German, Ouellette, BF Francis, P’ng, Christine, Paczkowska, Marta, Paiella, Salvatore, Pairojkul, Chawalit, Pajic, Marina, Pan-Hammarström, Qiang, Papaemmanuil, Elli, Papatheodorou, Irene, Paramasivam, Nagarajan, Park, Ji Wan, Park, Joong-Won, Park, Keunchil, Park, Kiejung, Parker, Joel S, Parsons, Simon L, Pass, Harvey, Pasternack, Danielle, Pastore, Alessandro, Patch, Ann-Marie, Pauporté, Iris, Pea, Antonio, Pedamallu, Chandra Sekhar, Pedersen, Jakob Skou, Pederzoli, Paolo, Peifer, Martin, Pennell, Nathan A, Perou, Charles M, Perry, Marc D, Petersen, Gloria M, Peto, Myron, Petrelli, Nicholas, Petryszak, Robert, Pfister, Stefan M, Phillips, Mark, Pich, Oriol, Pickett, Hilda A, Pihl, Todd D, Pillay, Nischalan, Pinder, Sarah, Pinese, Mark, Pinho, Andreia V, Pitkänen, Esa, Pivot, Xavier, Piñeiro-Yáñez, Elena, Planko, Laura, Plass, Christoph, Polak, Paz, Pons, Tirso, Popescu, Irinel, Potapova, Olga, Prasad, Aparna, Preston, Shaun R, Prinz, Manuel, Pritchard, Antonia L, Prokopec, Stephenie D, Provenzano, Elena, Puente, Xose S, Puig, Sonia, Pulido-Tamayo, Sergio, Pupo, Gulietta M, Purdie, Colin A, Quinn, Michael C, Rabionet, Raquel, Rader, Janet S, Radlwimmer, Bernhard, Radovic, Petar, Raeder, Benjamin, Raine, Keiran M, Ramakrishna, Manasa, Ramakrishnan, Kamna, Ramalingam, Suresh, Raphael, Benjamin J, Rathmell, W Kimryn, Rausch, Tobias, Reifenberger, Guido, Reimand, Jüri, Reis-Filho, Jorge, Reuter, Victor, Reyes-Salazar, Iker, Reyna, Matthew A, Reynolds, Sheila M, Rheinbay, Esther, Riazalhosseini, Yasser, Richardson, Andrea L, Richter, Julia, Ringel, Matthew, Ringnér, Markus, Rino, Yasushi, Roach, Jeffrey, Roberts, Lewis R, Robertson, A Gordon, Robertson, Alan J, Rodriguez, Javier Bartolomé, Rodríguez-González, F Germán, Roehrl, Michael HA, Rohde, Marius, Rokutan, Hirofumi, Romieu, Gilles, Rooman, Ilse, Roques, Tom, Rosebrock, Daniel, Rosenberg, Mara, Rosenstiel, Philip C, Rosenwald, Andreas, Rowe, Edward W, Royo, Romina, Rozen, Steven G, Rubanova, Yulia, Rubin, Mark A, Rubio-Perez, Carlota, Rudneva, Vasilisa A, Rusev, Borislav C, Ruzzenente, Andrea, Rätsch, Gunnar, Sabarinathan, Radhakrishnan, Sabelnykova, Veronica Y, Sadeghi, Sara, Sahinalp, S Cenk, Saini, Natalie, Saito-Adachi, Mihoko, Saksena, Gordon, Salcedo, Adriana, Salgado, Roberto, Salichos, Leonidas, Sallari, Richard, Saller, Charles, Salvia, Roberto, Sam, Michelle, Samra, Jaswinder S, Sanchez-Vega, Francisco, Sander, Chris, Sanders, Grant, Sarin, Rajiv, Sarrafi, Iman, Sasaki-Oku, Aya, Sauer, Torill, Sauter, Guido, Saw, Robyn PM, Scardoni, Maria, Scarlett, Christopher J, Scarpa, Aldo, Scelo, Ghislaine, Schadendorf, Dirk, Schein, Jacqueline E, Schilhabel, Markus B, Schlomm, Thorsten, Schmidt, Heather K, Schramm, Sarah-Jane, Schreiber, Stefan, Schultz, Nikolaus, Schwarz, Roland F, Scolyer, Richard A, Scott, David, Seethala, Raja, Segre, Ayellet V, Selander, Iris, Semple, Colin A, Senbabaoglu, Yasin, Sengupta, Subhajit, Sereni, Elisabetta, Serra, Stefano, Sgroi, Dennis C, Shah, Nimish C, Shahabi, Sagedeh, Shang, Catherine A, Shang, Ping, Shapira, Ofer, Shelton, Troy, Shen, Ciyue, Shen, Hui, Shepherd, Rebecca, Shi, Ruian, Shi, Yan, Shiah, Yu-Jia, Shibata, Tatsuhiro, Shih, Juliann, Shimizu, Eigo, Shimizu, Kiyo, Shin, Seung Jun, Shiraishi, Yuichi, Shmaya, Tal, Shmulevich, Ilya, Shorser, Solomon I, Short, Charles, Shrestha, Raunak, Shringarpure, Suyash S, Shriver, Craig, Shuai, Shimin, Siebert, Reiner, Sieuwerts, Anieta M, Signoretti, Sabina, Sikora, Katarzyna O, Simbolo, Michele, Simon, Ronald, Simons, Janae V, Simpson, Jared T, Simpson, Peter T, Singer, Samuel, Sinnott-Armstrong, Nasa, Sipahimalani, Payal, Skelly, Tara J, Smid, Marcel, Smith, Jaclyn, Smith-McCune, Karen, Socci, Nicholas D, Sofia, Heidi J, Soloway, Matthew G, Song, Lei, Sood, Anil K, Sothi, Sharmila, Sotiriou, Christos, Soulette, Cameron M, Span, Paul N, Spellman, Paul T, Sperandio, Nicola, Spillane, Andrew J, Spiro, Oliver, Spring, Jonathan, Staaf, Johan, Stadler, Peter F, Staib, Peter, Stark, Stefan G, Stebbings, Lucy, Stefánsson, Ólafur Andri, Stegle, Oliver, Stein, Lincoln D, Stenhouse, Alasdair, Stilgenbauer, Stephan, Stobbe, Miranda D, Stratton, Michael R, Stretch, Jonathan R, Struck, Adam J, Stuart, Joshua M, Stunnenberg, Henk G, Su, Hong, Su, Xiaoping, Sun, Ren X, Sungalee, Stephanie, Susak, Hana, Suzuki, Akihiro, Sweep, Fred, Szczepanowski, Monika, Sültmann, Holger, Yugawa, Takashi, Tam, Angela, Tamborero, David, Tan, Benita Kiat Tee, Tan, Donghui, Tan, Patrick, Tanaka, Hiroko, Taniguchi, Hirokazu, Tanskanen, Tomas J, Tarabichi, Maxime, Tarnuzzer, Roy, Tarpey, Patrick, Taschuk, Morgan L, Tatsuno, Kenji, Tavaré, Simon, Taylor, Darrin F, Taylor-Weiner, Amaro, Teague, Jon W, Teh, Bin Tean, Tembe, Varsha, Temes, Javier, Thai, Kevin, Thayer, Sarah P, Thiessen, Nina, Thomas, Gilles, Thomas, Sarah, Thompson, Alan, Thompson, Alastair M, Thompson, John FF, Thompson, R Houston, Thorne, Heather, Thorne, Leigh B, Thorogood, Adrian, Tiao, Grace, Tijanic, Nebojsa, Timms, Lee E, Tirabosco, Roberto, Tojo, Marta, Tommasi, Stefania, Toon, Christopher W, Toprak, Umut H, Tortora, Giampaolo, Tost, Jörg, Totoki, Yasushi, Townend, David, Traficante, Nadia, Treilleux, Isabelle, Trotta, Jean-Rémi, Trümper, Lorenz HP, Tsao, Ming, Tsunoda, Tatsuhiko, Tucker, Olga, Turkington, Richard, Turner, Daniel J, Tutt, Andrew, Ueno, Masaki, Ueno, Naoto T, Umbricht, Christopher, Umer, Husen M, Underwood, Timothy J, Urban, Lara, Urushidate, Tomoko, Ushiku, Tetsuo, Uusküla-Reimand, Liis, Valencia, Alfonso, Van Den Berg, David J, Van Laere, Steven, Van Loo, Peter, Van Meir, Erwin G, Van den Eynden, Gert G, Van der Kwast, Theodorus, Vasudev, Naveen, Vazquez, Miguel, Vedururu, Ravikiran, Veluvolu, Umadevi, Vembu, Shankar, Verbeke, Lieven PC, Vermeulen, Peter, Verrill, Clare, Viari, Alain, Vicente, David, Vicentini, Caterina, VijayRaghavan, K, Viksna, Juris, Vilain, Ricardo E, Vincent-Salomon, Anne, Visakorpi, Tapio, Voet, Douglas, Vyas, Paresh, Vázquez-García, Ignacio, Waddell, Nick M, Wadelius, Claes, Wadi, Lina, Wagener, Rabea, Wang, Jian, Wang, Jiayin, Wang, Linghua, Wang, Qi, Wang, Wenyi, Wang, Yumeng, Wang, Zhining, Waring, Paul M, Warnatz, Hans-Jörg, Warrell, Jonathan, Warren, Anne Y, Waszak, Sebastian M, Wedge, David C, Weichenhan, Dieter, Weinberger, Paul, Weinstein, John N, Weisenberger, Daniel J, Welch, Ian, Wendl, Michael C, Werner, Johannes, Whalley, Justin P, Wheeler, David A, Whitaker, Hayley C, Wigle, Dennis, Wilkerson, Matthew D, Williams, Ashley, Wilmott, James S, Wilson, Gavin W, Wilson, Julie M, Wilson, Richard K, Winterhoff, Boris, Wintersinger, Jeffrey A, Wiznerowicz, Maciej, Wolf, Stephan, Wong, Bernice H, Wong, Tina, Wong, Winghing, Woo, Youngchoon, Wood, Scott, Wouters, Bradly G, Wright, Adam J, Wright, Derek W, Wright, Mark H, Wu, Chin-Lee, Wu, Dai-Ying, Wu, Guanming, Wu, Jianmin, Wu, Kui, Wu, Yang, Wu, Zhenggang, Xi, Liu, Xia, Tian, Xiang, Qian, Xiao, Xiao, Xing, Rui, Xiong, Heng, Xu, Qinying, Xu, Yanxun, Xue, Hong, Yachida, Shinichi, Yakneen, Sergei, Yamaguchi, Rui, Yamaguchi, Takafumi N, Yamamoto, Masakazu, Yamamoto, Shogo, Yamaue, Hiroki, Yang, Fan, Yang, Huanming, Yang, Jean Y, Yang, Liming, Yang, Shanlin, Yang, Tsun-Po, Yang, Yang, Yaspo, Marie-Laure, Yates, Lucy, Yau, Christina, Ye, Chen, Ye, Kai, Yellapantula, Venkata D, Yoon, Christopher J, Yousif, Fouad, Yu, Jun, Yu, Kaixian, Yu, Willie, Yu, Yingyan, Yuan, Ke, Yuan, Yuan, Yuen, Denis, Yung, Christina K, Zaikova, Olga, Zapatka, Marc, Zenklusen, Jean C, Zenz, Thorsten, Zeps, Nikolajs, Zhang, Fan, Zhang, Hailei, Zhang, Hongwei, Zhang, Hongxin, Zhang, Jiashan, Zhang, Jing, Zhang, Junjun, Zhang, Xiuqing, Zhang, Xuanping, Zhang, Yan, Zhang, Zemin, Zhao, Zhongming, Zheng, Liangtao, Zheng, Xiuqing, Zhou, Wanding, Zhou, Yong, Zhu, Bin, Zhu, Hongtu, Zhu, Jingchun, Zhu, Shida, Zou, Lihua, Zou, Xueqing, deFazio, Anna, van As, Nicholas, van Deurzen, Carolien HM, van de Vijver, Marc J, Veer, L van’t, and von Mering, Christian
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Human Biology & Physiology ,Ecology,Evolution & Ethology ,Tumour Biology ,Genetics & Genomics ,Structural Biology & Biophysics ,Computational & Systems Biology - Abstract
Cancers require telomere maintenance mechanisms for unlimited replicative potential. They achieve this through TERT activation or alternative telomere lengthening associated with ATRX or DAXX loss. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, we dissect whole-genome sequencing data of over 2500 matched tumor-control samples from 36 different tumor types aggregated within the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium to characterize the genomic footprints of these mechanisms. While the telomere content of tumors with ATRX or DAXX mutations (ATRX/DAXXtrunc) is increased, tumors with TERT modifications show a moderate decrease of telomere content. One quarter of all tumor samples contain somatic integrations of telomeric sequences into non-telomeric DNA. This fraction is increased to 80% prevalence in ATRX/DAXXtrunc tumors, which carry an aberrant telomere variant repeat (TVR) distribution as another genomic marker. The latter feature includes enrichment or depletion of the previously undescribed singleton TVRs TTCGGG and TTTGGG, respectively. Our systematic analysis provides new insight into the recurrent genomic alterations associated with telomere maintenance mechanisms in cancer.
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- 2023
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40. Safety and Efficacy of Isolated Limb Infusion Chemotherapy for Advanced Locoregional Melanoma in Elderly Patients: An Australian Multicenter Study
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Kroon, Hidde M., Coventry, Brendon J., Giles, Mitchell H., Henderson, Michael A., Speakman, David, Wall, Mark, Barbour, Andrew, Serpell, Jonathan, Paddle, Paul, Smithers, Bernard M., and Thompson, John F.
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- 2017
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41. Comparative Genomics Provides Etiologic and Biological Insight into Melanoma Subtypes
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Newell, Felicity, primary, Johansson, Peter A., additional, Wilmott, James S., additional, Nones, Katia, additional, Lakis, Vanessa, additional, Pritchard, Antonia L., additional, Lo, Serigne N., additional, Rawson, Robert V., additional, Kazakoff, Stephen H., additional, Colebatch, Andrew J., additional, Koufariotis, Lambros T., additional, Ferguson, Peter M., additional, Wood, Scott, additional, Leonard, Conrad, additional, Law, Matthew H., additional, Brooks, Kelly M., additional, Broit, Natasa, additional, Palmer, Jane M., additional, Couts, Kasey L., additional, Vergara, Ismael A., additional, Long, Georgina V., additional, Barbour, Andrew P., additional, Nieweg, Omgo E., additional, Shivalingam, Brindha, additional, Robinson, William A., additional, Stretch, Jonathan R., additional, Spillane, Andrew J., additional, Saw, Robyn P.M., additional, Shannon, Kerwin F., additional, Thompson, John F., additional, Mann, Graham J., additional, Pearson, John V., additional, Scolyer, Richard A., additional, Waddell, Nicola, additional, and Hayward, Nicholas K., additional
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- 2022
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42. 280. MULTI-OMIC FEATURES OF OESOPHAGEAL ADENOCARCINOMA PATIENTS PRE-TREATED WITH PREOPERATIVE NEOADJUVANT THERAPY
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Naeini, Marjan, primary, Newell, Felicity, additional, Aoude, Lauren G, additional, Bonazzi, Vanessa F, additional, Patel, Kalpana, additional, Lampe, Guy, additional, Koufariotis, Lambros T, additional, Lakis, Vanessa, additional, Addala, Venkateswar, additional, Kondrashova, Olga, additional, Johnston, Rebecca L, additional, Sharma, Sowmya, additional, Brosda, Sandra, additional, Holmes, Oliver, additional, Leonard, Conrad, additional, Wood, Scott, additional, Xu, Qinying, additional, Thomas, Janine, additional, Walpole, Euan, additional, Mai, G Tao, additional, Ackland, Stephen P, additional, Martin, Jarad, additional, Burge, Matthew, additional, Finch, Robert, additional, Karapetis, Christos S, additional, Shannon, Jenny, additional, Nott, Louise, additional, Bohmer, Robert, additional, Wilson, Kate, additional, Barnes, Elizabeth, additional, Zalcberg, John R, additional, Smithers, B Mark, additional, Simes, John, additional, Price, Timothy, additional, Gebski, Val, additional, Nones, Katia, additional, Watson, David I, additional, Pearson, John V, additional, Barbour, Andrew P, additional, and Waddell, Nicola, additional
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- 2022
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43. Breaking bad conduits: ‘resleeving’ the intrathoracic gastric conduit post oesophagectomy
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Evennett, Nicholas J. and Barbour, Andrew P.
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- 2018
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44. Let's Get Fiscal
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Barbour, Andrew
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With the US economy continuing its weak recovery, it's tempting to think that IT budgets in higher education might begin to rebound especially in light of the increased focus on online learning. Nice thought, but no. Education costs are rising even faster than those for healthcare, and the public outcry over the cost of higher education is--deservedly--growing louder. Efficiency remains the name of the game, and IT is being tasked with finding many of those efficiencies--on top of its usual role. Unfortunately, IT's elevation to efficiency expert has not been accompanied, in most cases, by a fatter budget. To find out how schools are coping with more responsibility and anemic budgets, the journal staff talked with three IT leaders from a range of higher ed organizations.
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- 2013
45. Identification of unique neoantigen qualities in long-term survivors of pancreatic cancer
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Balachandran, Vinod P., Łuksza, Marta, Zhao, Julia N., Makarov, Vladimir, Moral, John Alec, Remark, Romain, Herbst, Brian, Askan, Gokce, Bhanot, Umesh, Senbabaoglu, Yasin, Wells, Daniel K., Ormsby Cary, Charles Ian, Grbovic-Huezo, Olivera, Attiyeh, Marc, Medina, Benjamin, Zhang, Jennifer, Loo, Jennifer, Saglimbeni, Joseph, Abu-Akeel, Mohsen, Zappasodi, Roberta, Riaz, Nadeem, Smoragiewicz, Martin, Kelley, Larkin Z., Basturk, Olca, Johns, Amber L., Mead, Scott R., Gill, Anthony J., Chang, David K., McKay, Skye H., Chantrill, Lorraine A., Chin, Venessa T., Chou, Angela, Humphris, Jeremy L., Pajic, Marina, Steinmann, Angela, Arshi, Mehreen, Drury, Ali, Froio, Danielle, Morgan, Ashleigh, Timpson, Paul, Hermann, David, Vennin, Claire, Warren, Sean, Pinese, Mark, Wu, Jianmin, Pinho, Andreia V., Tucker, Katherine, Andrews, Lesley, Samra, Jaswinder S., Arena, Jennifer, Pavlakis, Nick, High, Hilda A., Mittal, Anubhav, Biankin, Andrew V., Bailey, Peter, Martin, Sancha, Musgrove, Elizabeth A., Jones, Marc D., Nourse, Craig, Jamieson, Nigel B., Stoita, Alina, Williams, David, Spigelman, Allan, Waddell, Nicola, Pearson, John V., Patch, Ann-Marie, Nones, Katia, Newell, Felicity, Mukhopadhyay, Pamela, Addala, Venkateswar, Kazakoff, Stephen, Holmes, Oliver, Leonard, Conrad, Wood, Scott, Xu, Christina, Grimmond, Sean M., Hofmann, Oliver, Wilson, Peter J., Christ, Angelika, Bruxner, Tim, Asghari, Ray, Merrett, Neil D., Pavey, Darren, Das, Amitabha, Goodwin, Annabel, Cosman, Peter H., Ismail, Kasim, O’Connor, Chelsie, Cooper, Caroline L., Grimison, Peter, Kench, James G., Sandroussi, Charbel, Lam, Vincent W., McLeod, Duncan, Nagrial, Adnan M., Kirk, Judy, James, Virginia, Texler, Michael, Forest, Cindy, Epari, Krishna P., Ballal, Mo, Fletcher, David R., Mukhedkar, Sanjay, Zeps, Nikolajs, Beilin, Maria, Feeney, Kynan, Nguyen, Nan Q., Ruszkiewicz, Andrew R., Worthley, Chris, Chen, John, Brooke-Smith, Mark E., Papangelis, Virginia, Clouston, Andrew D., Martin, Patrick, 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., Hodgin, Mary, Scarpa, Aldo, Lawlor, Rita T., Beghelli, Stefania, Corbo, Vincenzo, Scardoni, Maria, Bassi, Claudio, Gönen, Mithat, Levine, Arnold J., Allen, Peter J., Fearon, Douglas T., Merad, Miriam, Gnjatic, Sacha, Iacobuzio-Donahue, Christine A., Wolchok, Jedd D., DeMatteo, Ronald P., Chan, Timothy A., Greenbaum, Benjamin D., Merghoub, Taha, and Leach, Steven D.
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- 2017
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46. Australian Multicenter Study of Isolated Limb Infusion for Melanoma
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Kroon, Hidde M., Coventry, Brendon J., Giles, Mitchell H., Henderson, Michael A., Speakman, David, Wall, Mark, Barbour, Andrew, Serpell, Jonathan, Paddle, Paul, Coventry, Alexander G. J., Sullivan, Thomas, Smithers, Bernard Mark, and Thompson, John F.
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- 2016
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47. Genomic analyses identify molecular subtypes of pancreatic cancer
- Author
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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
- Full Text
- View/download PDF
48. Patterns of Recurrence in Patients with Stage IIIB/C Cutaneous Melanoma of the Head and Neck Following Surgery With and Without Adjuvant Radiation Therapy: Is Isolated Regional Recurrence Salvageable?
- Author
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Barbour, Samantha, Mark Smithers, B., Allan, Chris, Bayley, Gerard, Thomas, Janine, Foote, Matthew, Burmeister, Bryan, and Barbour, Andrew P.
- Published
- 2015
- Full Text
- View/download PDF
49. Exploring Some Ethical Dilemmas and Obligations of the Ethnographer
- Author
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Barbour, Andrew
- Abstract
This paper focuses on the ethical position of the ethnographer when encountering unethical activities. Ethnography affords a rich insight into cultures, often behind previously secure doors but it is also a demanding science. Our gatekeepers control our access and our relationships with them can determine our destiny. This paper offers an exchange with ethics and the conditions experienced during an ethnography that challenged and disturbed this researcher's understanding of its rules and expectations. By drawing on data and experiences from a classroom ethnography it aims to consider the limits of ethics and the generic ritual that regardless of cost we must do no harm to others.
- Published
- 2010
- Full Text
- View/download PDF
50. Management of loco-regionally recurrent melanoma
- Author
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Geere, Simone L and Barbour, Andrew P
- Published
- 2012
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