1,401 results on '"Defazio, A"'
Search Results
2. Outcomes and Resource Utilization Associated with Use of Routine Pre-Discharge White Blood Cell Count for Clinical Decision-Making in Children with Complicated Appendicitis: A Multicenter Hospital-Level Analysis
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Shannon L. Cramm, Dionne A. Graham, Martin L. Blakely, Nicole M. Chandler, Robert A. Cowles, Shaun M. Kunisaki, Robert T. Russell, Myron Allukian, Jennifer R. DeFazio, Cornelia L. Griggs, Matthew T. Santore, Stefan Scholz, Danielle I. Aronowitz, Brendan T. Campbell, Devon T. Collins, Sarah J. Commander, Abigail Engwall-Gill, Joseph R. Esparaz, Christina Feng, Claire Gerall, David N. Hanna, Olivia A. Keane, Abdulraouf Lamoshi, Aaron M. Lipskar, Claudia P. Orlas Bolanos, Elizabeth Pace, Maia D. Regan, Elisabeth T. Tracy, Sacha Williams, Lucy Zhang, and Shawn J. Rangel
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Pediatrics, Perinatology and Child Health ,Surgery ,General Medicine - Published
- 2023
3. <scp>3D Whole‐body</scp> skin imaging for automated melanoma detection
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M. A. Marchetti, Z. H. Nazir, J. K. Nanda, S. W. Dusza, B. M. D'Alessandro, J. DeFazio, A. C. Halpern, V. M. Rotemberg, and A. A. Marghoob
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Infectious Diseases ,Dermatology - Published
- 2023
4. CCNE1 and survival of patients with tubo-ovarian high-grade serous carcinoma
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Eun-Young, Kang, Ashley, Weir, Nicola S, Meagher, Kyo, Farrington, Gregg S, Nelson, Prafull, Ghatage, Cheng-Han, Lee, Marjorie J, Riggan, Adelyn, Bolithon, Gordana, Popovic, Betty, Leung, Katrina, Tang, Neil, Lambie, Joshua, Millstein, Jennifer, Alsop, Michael S, Anglesio, Beyhan, Ataseven, Ellen, Barlow, Matthias W, Beckmann, Jessica, Berger, Christiani, Bisinotto, Hans, Bösmüller, Jessica, Boros, Alison H, Brand, Angela, Brooks-Wilson, Sara Y, Brucker, Michael E, Carney, Yovanni, Casablanca, Alicia, Cazorla-Jiménez, Paul A, Cohen, Thomas P, Conrads, Linda S, Cook, Penny, Coulson, Madeleine, Courtney-Brooks, Daniel W, Cramer, Philip, Crowe, Julie M, Cunningham, Cezary, Cybulski, Kathleen M, Darcy, Mona A, El-Bahrawy, Esther, Elishaev, Ramona, Erber, Rhonda, Farrell, Sian, Fereday, Anna, Fischer, María J, García, Simon A, Gayther, Aleksandra, Gentry-Maharaj, C Blake, Gilks, Marcel, Grube, Paul R, Harnett, Shariska Petersen, Harrington, Philipp, Harter, Arndt, Hartmann, Jonathan L, Hecht, Sebastian, Heikaus, Alexander, Hein, Florian, Heitz, Joy, Hendley, Brenda Y, Hernandez, Susanna Hernando, Polo, Sabine, Heublein, Akira, Hirasawa, Estrid, Høgdall, Claus K, Høgdall, Hugo M, Horlings, David G, Huntsman, Tomasz, Huzarski, Andrea, Jewell, Mercedes, Jimenez-Linan, Michael E, Jones, Scott H, Kaufmann, Catherine J, Kennedy, Dineo, Khabele, Felix K F, Kommoss, Roy F P M, Kruitwagen, Diether, Lambrechts, Nhu D, Le, Marcin, Lener, Jenny, Lester, Yee, Leung, Anna, Linder, Liselore, Loverix, Jan, Lubiński, Rashna, Madan, G Larry, Maxwell, Francesmary, Modugno, Susan L, Neuhausen, Alexander, Olawaiye, Siel, Olbrecht, Sandra, Orsulic, José, Palacios, Celeste Leigh, Pearce, Malcolm C, Pike, Carmel M, Quinn, Ganendra Raj, Mohan, Cristina, Rodríguez-Antona, Matthias, Ruebner, Andy, Ryan, Stuart G, Salfinger, Naoko, Sasamoto, Joellen M, Schildkraut, Minouk J, Schoemaker, Mitul, Shah, Raghwa, Sharma, Yurii B, Shvetsov, Naveena, Singh, Gabe S, Sonke, Linda, Steele, Colin J R, Stewart, Karin, Sundfeldt, Anthony J, Swerdlow, Aline, Talhouk, Adeline, Tan, Sarah E, Taylor, Kathryn L, Terry, Aleksandra, Tołoczko, Nadia, Traficante, Koen K, Van de Vijver, Maaike A, van der Aa, Toon, Van Gorp, Els, Van Nieuwenhuysen, Lilian, van-Wagensveld, Ignace, Vergote, Robert A, Vierkant, Chen, Wang, Lynne R, Wilkens, Stacey J, Winham, Anna H, Wu, Javier, Benitez, Andrew, Berchuck, Francisco J, Candido Dos Reis, Anna, DeFazio, Peter A, Fasching, Ellen L, Goode, Marc T, Goodman, Jacek, Gronwald, Beth Y, Karlan, Stefan, Kommoss, Usha, Menon, Hans-Peter, Sinn, Annette, Staebler, James D, Brenton, David D, Bowtell, Paul D P, Pharoah, Susan J, Ramus, Martin, Köbel, MUMC+: MA Obstetrie Gynaecologie (3), MUMC+: Vrouw Moeder en Kind Centrum (3), Obstetrie & Gynaecologie, MUMC+: MA Arts Assistenten Obstetrie Gynaecologie (6), RS: GROW - R2 - Basic and Translational Cancer Biology, and AOCS Group
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Cancer Research ,ovarian cancer ,Oncology ,high-grade serous carcinoma ,Human medicine ,prognosis ,CCNE1 amplification ,cyclin E1 expression - Abstract
BACKGROUND: Cyclin E1 (CCNE1) is a potential predictive marker and therapeutic target in tubo-ovarian high-grade serous carcinoma (HGSC). Smaller studies have revealed unfavorable associations for CCNE1 amplification and CCNE1 overexpression with survival, but to date no large-scale, histotype-specific validation has been performed. The hypothesis was that high-level amplification of CCNE1 and CCNE1 overexpression, as well as a combination of the two, are linked to shorter overall survival in HGSC. METHODS: Within the Ovarian Tumor Tissue Analysis consortium, amplification status and protein level in 3029 HGSC cases and mRNA expression in 2419 samples were investigated. RESULTS: High-level amplification (>8 copies by chromogenic in situ hybridization) was found in 8.6% of HGSC and overexpression (>60% with at least 5% demonstrating strong intensity by immunohistochemistry) was found in 22.4%. CCNE1 high-level amplification and overexpression both were linked to shorter overall survival in multivariate survival analysis adjusted for age and stage, with hazard stratification by study (hazard ratio [HR], 1.26; 95% CI, 1.08-1.47, p = .034, and HR, 1.18; 95% CI, 1.05-1.32, p = .015, respectively). This was also true for cases with combined high-level amplification/overexpression (HR, 1.26; 95% CI, 1.09-1.47, p = .033). CCNE1 mRNA expression was not associated with overall survival (HR, 1.00 per 1-SD increase; 95% CI, 0.94-1.06; p = .58). CCNE1 high-level amplification is mutually exclusive with the presence of germline BRCA1/2 pathogenic variants and shows an inverse association to RB1 loss. CONCLUSION: This study provides large-scale validation that CCNE1 high-level amplification is associated with shorter survival, supporting its utility as a prognostic biomarker in HGSC. ispartof: CANCER vol:129 issue:5 pages:697-713 ispartof: location:United States status: published
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- 2023
5. Validation of a guideline to reduce variability in diagnosing cervical dystonia
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Giovanni Defazio, Daniele Belvisi, Cynthia Comella, Mark Hallett, Hyder A. Jinnah, Paola Cimino, Anna Latorre, Marcello Mario Mascia, Lorenzo Rocchi, Angelo Fabio Gigante, Tommaso Ercoli, and Alfredo Berardelli
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Neurology ,Neurology (clinical) - Abstract
Background Cervical dystonia is characterized by a variable pattern of neck muscle involvement. Due to the lack of a diagnostic test, cervical dystonia diagnosis is based on clinical examination and is therefore subjective. The present work was designed to provide practical guidance for clinicians in confirming or refuting suspected cervical dystonia. Methods Participants were video recorded according to a standardized protocol to assess 6 main clinical features possibly contributing to cervical dystonia diagnosis: presence of repetitive, patterned head/neck movements/postures inducing head/neck deviation from neutral position (item 1); sensory trick (item 2); and red flags related to conditions mimicking dystonia that should be absent in dystonia (items 3–6). Inter-/intra-rater agreement among three independent raters was assessed by k statistics. To estimate sensitivity and specificity, the gold standard was cervical dystonia diagnosis reviewed at each site by independent senior neurologists. Results The validation sample included 43 idiopathic cervical dystonia patients and 41 control subjects (12 normal subjects, 6 patients with isolated head tremor, 4 with chorea, 6 with tics, 4 with head ptosis due to myasthenia or amyotrophic lateral sclerosis, 7 with orthopedic/rheumatologic neck diseases, and 2 with ocular torticollis). The best combination of sensitivity and specificity was observed considering all the items except for an item related to capability to voluntarily suppress spasms (sensitivity: 96.1%; specificity: 81%). Conclusions An accurate diagnosis of cervical dystonia can be achieved if, in addition to the core motor features, we also consider some clinical features related to dystonia mimics that should be absent in dystonia.
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- 2023
6. Common analgesics and ovarian cancer survival: the Ovarian cancer Prognosis And Lifestyle (OPAL) Study
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Azam Majidi, Renhua Na, Susan J Jordan, Anna DeFazio, Andreas Obermair, Michael Friedlander, Peter Grant, and Penelope M Webb
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Cancer Research ,Oncology - Abstract
Background Most women with ovarian cancer (OC) are diagnosed with advanced disease. They often experience recurrence after primary treatment, and their subsequent prognosis is poor. Our goal was to evaluate the association between use of nonsteroidal antiinflammatory drugs (NSAIDs), including regular and low-dose aspirin, and 5-year cancer-specific survival after an OC diagnosis. Methods The Ovarian cancer Prognosis And Lifestyle study is a prospective population-based cohort of 958 Australian women with OC. Information was gathered through self-completed questionnaires. We classified NSAID use during the year prediagnosis and postdiagnosis as none or occasional ( Results Compared with nonusers and infrequent users, we observed better survival associated with frequent NSAID use prediagnosis (HR = 0.73, 95% CI = 0.55 to 0.97) or postdiagnosis (HR = 0.65, 95% CI = 0.45 to 0.94). Estimates were similar for aspirin and nonaspirin NSAIDs, new and continuous users and in weighted models. These differences would translate to a 2.5-month increase in mean survival by 5 years postdiagnosis. There was no association with acetaminophen. Conclusions Our findings confirm a previous study suggesting NSAID use might improve OC survival.
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- 2023
7. Profiling the immune landscape in mucinous ovarian carcinoma
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Nicola S. Meagher, Phineas Hamilton, Katy Milne, Shelby Thornton, Bronwyn Harris, Ashley Weir, Jennifer Alsop, Christiani Bisinoto, James D. Brenton, Angela Brooks-Wilson, Derek S. Chiu, Kara L. Cushing-Haugen, Sian Fereday, Dale W. Garsed, Simon A. Gayther, Aleksandra Gentry-Maharaj, Blake Gilks, Mercedes Jimenez-Linan, Catherine J. Kennedy, Nhu D. Le, Anna M. Piskorz, Marjorie J. Riggan, Mitul Shah, Naveena Singh, Aline Talhouk, Martin Widschwendter, David D.L. Bowtell, Francisco J. Candido dos Reis, Linda S. Cook, Renée T. Fortner, María J. García, Holly R. Harris, David G. Huntsman, Anthony N. Karnezis, Martin Köbel, Usha Menon, Paul D.P. Pharoah, Jennifer A. Doherty, Michael S. Anglesio, Malcolm C. Pike, Celeste Leigh Pearce, Michael L. Friedlander, Anna DeFazio, Brad H. Nelson, and Susan J. Ramus
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Ovarian Neoplasms ,Lymphocytes, Tumor-Infiltrating ,Oncology ,Tumor Microenvironment ,Humans ,Obstetrics and Gynecology ,Female ,Forkhead Transcription Factors ,Carcinoma, Ovarian Epithelial ,CD8-Positive T-Lymphocytes ,B7-H1 Antigen - Abstract
Mucinous ovarian carcinoma (MOC) is a rare histotype of ovarian cancer, with low response rates to standard chemotherapy, and very poor survival for patients diagnosed at advanced stage. There is a limited understanding of the MOC immune landscape, and consequently whether immune checkpoint inhibitors could be considered for a subset of patients.We performed multicolor immunohistochemistry (IHC) and immunofluorescence (IF) on tissue microarrays in a cohort of 126 MOC patients. Cell densities were calculated in the epithelial and stromal components for tumor-associated macrophages (CD68+/PD-L1+, CD68+/PD-L1-), T cells (CD3+/CD8-, CD3+/CD8+), putative T-regulatory cells (Tregs, FOXP3+), B cells (CD20+/CD79A+), plasma cells (CD20-/CD79a+), and PD-L1+ and PD-1+ cells, and compared these values with clinical factors. Univariate and multivariable Cox Proportional Hazards assessed overall survival. Unsupervised k-means clustering identified patient subsets with common patterns of immune cell infiltration.Mean densities of PD1+ cells, PD-L1- macrophages, CD4+ and CD8+ T cells, and FOXP3+ Tregs were higher in the stroma compared to the epithelium. Tumors from advanced (Stage III/IV) MOC had greater epithelial infiltration of PD-L1- macrophages, and fewer PD-L1+ macrophages compared with Stage I/II cancers (p = 0.004 and p = 0.014 respectively). Patients with high epithelial density of FOXP3+ cells, CD8+/FOXP3+ cells, or PD-L1- macrophages, had poorer survival, and high epithelial CD79a + plasma cells conferred better survival, all upon univariate analysis only. Clustering showed that most MOC (86%) had an immune depleted (cold) phenotype, with only a small proportion (11/76,14%) considered immune inflamed (hot) based on T cell and PD-L1 infiltrates.In summary, MOCs are mostly immunogenically 'cold', suggesting they may have limited response to current immunotherapies.
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- 2023
8. Lifestyle and personal factors associated with having macroscopic residual disease after ovarian cancer primary cytoreductive surgery
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Minh Tung Phung, Penelope M. Webb, Anna DeFazio, Sian Fereday, Alice W. Lee, David D.L. Bowtell, Peter A. Fasching, Ellen L. Goode, Marc T. Goodman, Beth Y. Karlan, Jenny Lester, Keitaro Matsuo, Francesmary Modugno, James D. Brenton, Toon Van Gorp, Paul D.P. Pharoah, Joellen M. Schildkraut, Karen McLean, Rafael Meza, Bhramar Mukherjee, Jean Richardson, Bronwyn Grout, Anne Chase, Cindy McKinnon Deurloo, Kathryn L. Terry, Gillian E. Hanley, Malcolm C. Pike, Andrew Berchuck, Susan J. Ramus, and Celeste Leigh Pearce
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Oncology ,Obstetrics and Gynecology - Abstract
The presence of macroscopic residual disease after primary cytoreductive surgery (PCS) is an important factor influencing survival for patients with high-grade serous ovarian cancer (HGSC). More research is needed to identify factors associated with having macroscopic residual disease. We analyzed 12 lifestyle and personal exposures known to be related to ovarian cancer risk or inflammation to identify those associated with having residual disease after surgery.This analysis used data on 2054 patients with advanced stage HGSC from the Ovarian Cancer Association Consortium. The exposures were body mass index, breastfeeding, oral contraceptive use, depot-medroxyprogesterone acetate use, endometriosis, first-degree family history of ovarian cancer, incomplete pregnancy, menopausal hormone therapy use, menopausal status, parity, smoking, and tubal ligation. Logistic regression models were fit to assess the association between these exposures and having residual disease following PCS.Menopausal estrogen-only therapy (ET) use was associated with 33% lower odds of having macroscopic residual disease compared to never use (OR = 0.67, 95%CI 0.46-0.97, p = 0.033). Compared to nulliparous women, parous women who did not breastfeed had 36% lower odds of having residual disease (OR = 0.64, 95%CI 0.43-0.94, p = 0.022), while there was no association among parous women who breastfed (OR = 0.90, 95%CI 0.65-1.25, p = 0.53).The association between ET and having no macroscopic residual disease is plausible given a strong underlying biologic hypothesis between this exposure and diagnosis with HGSC. If this or the parity finding is replicated, these factors could be included in risk stratification models to determine whether HGSC patients should receive PCS or neoadjuvant chemotherapy.
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- 2023
9. The genomic and immune landscape of long-term survivors of high-grade serous ovarian cancer
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Garsed, Dale W, Pandey, Ahwan, Fereday, Sian, Kennedy, Catherine J, Takahashi, Kazuaki, Alsop, Kathryn, Hamilton, Phineas T, Hendley, Joy, Chiew, Yoke-Eng, Traficante, Nadia, Provan, Pamela, Ariyaratne, Dinuka, Au-Yeung, George, Bateman, Nicholas W, Bowes, Leanne, Brand, Alison, Christie, Elizabeth L, Cunningham, Julie M, Friedlander, Michael, Grout, Bronwyn, Harnett, Paul, Hung, Jillian, McCauley, Bryan, McNally, Orla, Piskorz, Anna M, Saner, Flurina A M, Vierkant, Robert A, Wang, Chen, Winham, Stacey J, Pharoah, Paul D P, Brenton, James D, Conrads, Thomas P, Maxwell, George L, Ramus, Susan J, Pearce, Celeste Leigh, Pike, Malcolm C, Nelson, Brad H, Goode, Ellen L, DeFazio, Anna, and Bowtell, David D L
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Ovarian Neoplasms ,Genetics ,Humans ,Female ,Genomics ,Survivors ,610 Medizin und Gesundheit - Abstract
Fewer than half of all patients with advanced-stage high-grade serous ovarian cancers (HGSCs) survive more than five years after diagnosis, but those who have an exceptionally long survival could provide insights into tumor biology and therapeutic approaches. We analyzed 60 patients with advanced-stage HGSC who survived more than 10 years after diagnosis using whole-genome sequencing, transcriptome and methylome profiling of their primary tumor samples, comparing this data to 66 short- or moderate-term survivors. Tumors of long-term survivors were more likely to have multiple alterations in genes associated with DNA repair and more frequent somatic variants resulting in an increased predicted neoantigen load. Patients clustered into survival groups based on genomic and immune cell signatures, including three subsets of patients with BRCA1 alterations with distinctly different outcomes. Specific combinations of germline and somatic gene alterations, tumor cell phenotypes and differential immune responses appear to contribute to long-term survival in HGSC.
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- 2022
10. A comparison of <scp>DNA</scp> sequencing and gene expression profiling to assist tissue of origin diagnosis in cancer of unknown primary
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Atara Posner, Owen WJ Prall, Tharani Sivakumaran, Dariush Etemadamoghadam, Niko Thio, Andrew Pattison, Shiva Balachander, Krista Fisher, Samantha Webb, Colin Wood, Anna DeFazio, Nicholas Wilcken, Bo Gao, Christos S Karapetis, Madhu Singh, Ian M Collins, Gary Richardson, Christopher Steer, Mark Warren, Narayan Karanth, Gavin Wright, Scott Williams, Joshy George, Rodney J Hicks, Alex Boussioutas, Anthony J Gill, Benjamin J Solomon, Huiling Xu, Andrew Fellowes, Stephen B Fox, Penelope Schofield, David Bowtell, Linda Mileshkin, and Richard W Tothill
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Pathology and Forensic Medicine - Abstract
Cancer of unknown primary (CUP) is a syndrome defined by clinical absence of a primary cancer after standardised investigations. Gene expression profiling (GEP) and DNA sequencing have been used to predict primary tissue of origin (TOO) in CUP and find molecularly guided treatments; however, a detailed comparison of the diagnostic yield from these two tests has not been described. Here, we compared the diagnostic utility of RNA and DNA tests in 215 CUP patients (82% received both tests) in a prospective Australian study. Based on retrospective assessment of clinicopathological data, 77% (166/215) of CUPs had insufficient evidence to support TOO diagnosis (clinicopathology unresolved). The remainder had either a latent primary diagnosis (10%) or clinicopathological evidence to support a likely TOO diagnosis (13%) (clinicopathology resolved). We applied a microarray (CUPGuide) or custom NanoString 18-class GEP test to 191 CUPs with an accuracy of 91.5% in known metastatic cancers for high-medium confidence predictions. Classification performance was similar in clinicopathology-resolved CUPs - 80% had high-medium predictions and 94% were concordant with pathology. Notably, only 56% of the clinicopathology-unresolved CUPs had high-medium confidence GEP predictions. Diagnostic DNA features were interrogated in 201 CUP tumours guided by the cancer type specificity of mutations observed across 22 cancer types from the AACR Project GENIE database (77,058 tumours) as well as mutational signatures (e.g. smoking). Among the clinicopathology-unresolved CUPs, mutations and mutational signatures provided additional diagnostic evidence in 31% of cases. GEP classification was useful in only 13% of cases and oncoviral detection in 4%. Among CUPs where genomics informed TOO, lung and biliary cancers were the most frequently identified types, while kidney tumours were another identifiable subset. In conclusion, DNA and RNA profiling supported an unconfirmed TOO diagnosis in one-third of CUPs otherwise unresolved by clinicopathology assessment alone. DNA mutation profiling was the more diagnostically informative assay. © 2022 The Authors. The Journal of Pathology published by John WileySons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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- 2022
11. Increased FOXJ1 protein expression is associated with improved overall survival in high-grade serous ovarian carcinoma: an Ovarian Tumor Tissue Analysis Consortium Study
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Ashley, Weir, Eun-Young, Kang, Nicola S, Meagher, Gregg S, Nelson, Prafull, Ghatage, Cheng-Han, Lee, Marjorie J, Riggan, Aleksandra, Gentry-Maharaj, Andy, Ryan, Naveena, Singh, Martin, Widschwendter, Jennifer, Alsop, Michael S, Anglesio, Matthias W, Beckmann, Jessica, Berger, Christiani, Bisinotto, Jessica, Boros, Alison H, Brand, James D, Brenton, Angela, Brooks-Wilson, Michael E, Carney, Julie M, Cunningham, Kara L, Cushing-Haugen, Cezary, Cybulski, Esther, Elishaev, Ramona, Erber, Sian, Fereday, Anna, Fischer, Luis, Paz-Ares, Javier, Gayarre, Blake C, Gilks, Marcel, Grube, Paul R, Harnett, Holly R, Harris, Arndt, Hartmann, Alexander, Hein, Joy, Hendley, Brenda Y, Hernandez, Sabine, Heublein, Yajue, Huang, Tomasz, Huzarski, Anna, Jakubowska, Mercedes, Jimenez-Linan, Catherine J, Kennedy, Felix K F, Kommoss, Jennifer M, Koziak, Bernhard, Kraemer, Nhu D, Le, Jaime, Lesnock, Jenny, Lester, Jan, Lubiński, Janusz, Menkiszak, Britta, Ney, Alexander, Olawaiye, Sandra, Orsulic, Ana, Osorio, Luis, Robles-Díaz, Matthias, Ruebner, Mitul, Shah, Raghwa, Sharma, Yurii B, Shvetsov, Helen, Steed, Aline, Talhouk, Sarah E, Taylor, Nadia, Traficante, Robert A, Vierkant, Chen, Wang, Lynne R, Wilkens, Stacey J, Winham, Javier, Benitez, Andrew, Berchuck, David D, Bowtell, Francisco J, Candido Dos Reis, Linda S, Cook, Anna, DeFazio, Jennifer A, Doherty, Peter A, Fasching, María J, García, Ellen L, Goode, Marc T, Goodman, Jacek, Gronwald, David G, Huntsman, Beth Y, Karlan, Stefan, Kommoss, Francesmary, Modugno, Joellen M, Schildkraut, Hans-Peter, Sinn, Annette, Staebler, Linda E, Kelemen, Caroline E, Ford, Usha, Menon, Paul D P, Pharoah, Martin, Köbel, and R, Sharma
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Cancer Research ,Oncology - Abstract
Background Recently, we showed a >60% difference in 5-year survival for patients with tubo-ovarian high-grade serous carcinoma (HGSC) when stratified by a 101-gene mRNA expression prognostic signature. Given the varied patient outcomes, this study aimed to translate prognostic mRNA markers into protein expression assays by immunohistochemistry and validate their survival association in HGSC. Methods Two prognostic genes, FOXJ1 and GMNN, were selected based on high-quality antibodies, correlation with protein expression and variation in immunohistochemical scores in a preliminary cohort (n = 134 and n = 80, respectively). Six thousand four hundred and thirty-four (FOXJ1) and 5470 (GMNN) formalin-fixed, paraffin-embedded ovarian neoplasms (4634 and 4185 HGSC, respectively) represented on tissue microarrays from the Ovarian Tumor Tissue Analysis consortium underwent immunohistochemical staining and scoring, then univariate and multivariate survival analysis. Results Consistent with mRNA, FOXJ1 protein expression exhibited a linear, increasing association with improved overall survival in HGSC patients. Women with >50% expression had the most favourable outcomes (HR = 0.78, 95% CI 0.67–0.91, p 35% GMNN expression showed a trend for better outcomes, though this was not significant. Conclusion We provide foundational evidence for the prognostic value of FOXJ1 in HGSC, validating the prior mRNA-based prognostic association by immunohistochemistry.
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- 2022
12. Motor and psychiatric features in idiopathic blepharospasm: A data-driven cluster analysis
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Giovanni Defazio, Angelo F. Gigante, Mark Hallett, Alfredo Berardelli, Joel S. Perlmutter, Brian D. Berman, Joseph Jankovic, Tobias Bäumer, Cynthia Comella, Tommaso Ercoli, Gina Ferrazzano, Susan H. Fox, Han-Joon Kim, Emile Sami Moukheiber, Sarah Pirio Richardson, Anne Weissbach, and Hyder A. Jinnah
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Spasm ,Neurology ,Dystonic Disorders ,Blepharospasm ,Humans ,Cluster Analysis ,Neurology (clinical) ,Anxiety ,Geriatrics and Gerontology - Abstract
Idiopathic blepharospasm is a clinically heterogeneous dystonia also characterized by non motor symptoms.We used a k-means cluster analysis to assess 188 patients with idiopathic blepharospasm in order to identify relatively homogeneous subpopulations of patients, using a set of motor and psychiatric variables to generate the cluster solution.Blepharospasm patients reached higher scores on scales assessing depressive- and anxiety-related disorders than healthy/disease controls. Cluster analysis suggested the existence of three groups of patients that differed by type of spasms, overall motor severity, and presence/severity of psychiatric problems. The greater severity of motor symptoms was observed in Group 1, the least severity in Group 3, while the severity of blepharospasm in Group 2 was between that observed in Groups 1 and 3. The three motor subtypes also differed by psychiatric features: the lowest severity of psychiatric symptoms was observed in the group with least severe motor symptoms (group 3), while the highest psychiatric severity scores were observed in group 2 that carried intermediate motor severity rather than in the group with more severe motor symptoms (group 1). The three groups did not differ by disease duration, age of onset, sex or other clinical features.The present study suggests that blepharospasm patients may be classified in different subtypes according to the type of spasms, overall motor severity and presence/severity of depressive symptoms and anxiety.
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- 2022
13. Writing tremor in Parkinson’s disease: frequency and associated clinical features
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Marcello Mario Mascia, Gianni Orofino, Paola Cimino, Gianluca Cadeddu, Tommaso Ercoli, and Giovanni Defazio
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Psychiatry and Mental health ,Neurology ,Neurology (clinical) ,Biological Psychiatry - Published
- 2022
14. Gene-Expression Profiling of Mucinous Ovarian Tumors and Comparison with Upper and Lower Gastrointestinal Tumors Identifies Markers Associated with Adverse Outcomes
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Nicola S, Meagher, Kylie L, Gorringe, Matthew, Wakefield, Adelyn, Bolithon, Chi Nam Ignatius, Pang, Derek S, Chiu, Michael S, Anglesio, Kylie-Ann, Mallitt, Jennifer A, Doherty, Holly R, Harris, Joellen M, Schildkraut, Andrew, Berchuck, Kara L, Cushing-Haugen, Ksenia, Chezar, Angela, Chou, Adeline, Tan, Jennifer, Alsop, Ellen, Barlow, Matthias W, Beckmann, Jessica, Boros, David D L, Bowtell, Alison H, Brand, James D, Brenton, Ian, Campbell, Dane, Cheasley, Joshua, Cohen, Cezary, Cybulski, Esther, Elishaev, Ramona, Erber, Rhonda, Farrell, Anna, Fischer, Zhuxuan, Fu, Blake, Gilks, Anthony J, Gill, Charlie, Gourley, Marcel, Grube, Paul R, Harnett, Arndt, Hartmann, Anusha, Hettiaratchi, Claus K, Høgdall, Tomasz, Huzarski, Anna, Jakubowska, Mercedes, Jimenez-Linan, Catherine J, Kennedy, Byoung-Gie, Kim, Jae-Weon, Kim, Jae-Hoon, Kim, Kayla, Klett, Jennifer M, Koziak, Tiffany, Lai, Angela, Laslavic, Jenny, Lester, Yee, Leung, Na, Li, Winston, Liauw, Belle W X, Lim, Anna, Linder, Jan, Lubiński, Sakshi, Mahale, Constantina, Mateoiu, Simone, McInerny, Janusz, Menkiszak, Parham, Minoo, Suzana, Mittelstadt, David, Morris, Sandra, Orsulic, Sang-Yoon, Park, Celeste Leigh, Pearce, John V, Pearson, Malcolm C, Pike, Carmel M, Quinn, Ganendra Raj, Mohan, Jianyu, Rao, Marjorie J, Riggan, Matthias, Ruebner, Stuart, Salfinger, Clare L, Scott, Mitul, Shah, Helen, Steed, Colin J R, Stewart, Deepak, Subramanian, Soseul, Sung, Katrina, Tang, Paul, Timpson, Robyn L, Ward, Rebekka, Wiedenhoefer, Heather, Thorne, Paul A, Cohen, Philip, Crowe, Peter A, Fasching, Jacek, Gronwald, Nicholas J, Hawkins, Estrid, Høgdall, David G, Huntsman, Paul A, James, Beth Y, Karlan, Linda E, Kelemen, Stefan, Kommoss, Gottfried E, Konecny, Francesmary, Modugno, Sue K, Park, Annette, Staebler, Karin, Sundfeldt, Anna H, Wu, Aline, Talhouk, Paul D P, Pharoah, Lyndal, Anderson, Anna, DeFazio, Martin, Köbel, Michael L, Friedlander, and Susan J, Ramus
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Ovarian Neoplasms ,Cancer Research ,BORDERLINE TUMORS ,CARCINOMA ,ADENOCARCINOMA ,TRANSGELIN ,Carcinoma, Ovarian Epithelial ,EXPANSILE ,Prognosis ,INTESTINAL-TYPE ,CANCER ,Adenocarcinoma, Mucinous ,PATTERN ,RARE ,Oncology ,POOR-PROGNOSIS ,Humans ,Female ,Neoplasm Staging ,Gastrointestinal Neoplasms - Abstract
Purpose: Advanced-stage mucinous ovarian carcinoma (MOC) has poor chemotherapy response and prognosis and lacks biomarkers to aid stage I adjuvant treatment. Differentiating primary MOC from gastrointestinal (GI) metastases to the ovary is also challenging due to phenotypic similarities. Clinicopathologic and gene-expression data were analyzed to identify prognostic and diagnostic features. Experimental Design: Discovery analyses selected 19 genes with prognostic/diagnostic potential. Validation was performed through the Ovarian Tumor Tissue Analysis consortium and GI cancer biobanks comprising 604 patients with MOC (n = 333), mucinous borderline ovarian tumors (MBOT, n = 151), and upper GI (n = 65) and lower GI tumors (n = 55). Results: Infiltrative pattern of invasion was associated with decreased overall survival (OS) within 2 years from diagnosis, compared with expansile pattern in stage I MOC [hazard ratio (HR), 2.77; 95% confidence interval (CI), 1.04–7.41, P = 0.042]. Increased expression of THBS2 and TAGLN was associated with shorter OS in MOC patients (HR, 1.25; 95% CI, 1.04–1.51, P = 0.016) and (HR, 1.21; 95% CI, 1.01–1.45, P = 0.043), respectively. ERBB2 (HER2) amplification or high mRNA expression was evident in 64 of 243 (26%) of MOCs, but only 8 of 243 (3%) were also infiltrative (4/39, 10%) or stage III/IV (4/31, 13%). Conclusions: An infiltrative growth pattern infers poor prognosis within 2 years from diagnosis and may help select stage I patients for adjuvant therapy. High expression of THBS2 and TAGLN in MOC confers an adverse prognosis and is upregulated in the infiltrative subtype, which warrants further investigation. Anti-HER2 therapy should be investigated in a subset of patients. MOC samples clustered with upper GI, yet markers to differentiate these entities remain elusive, suggesting similar underlying biology and shared treatment strategies.
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- 2022
15. Epithelial-to-Mesenchymal Transition Supports Ovarian Carcinosarcoma Tumorigenesis and Confers Sensitivity to Microtubule Targeting with Eribulin
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Gwo Yaw, Ho, Elizabeth L, Kyran, Justin, Bedo, Matthew J, Wakefield, Darren P, Ennis, Hasan B, Mirza, Cassandra J, Vandenberg, Elizabeth, Lieschke, Andrew, Farrell, Anthony, Hadla, Ratana, Lim, Genevieve, Dall, James E, Vince, Ngee Kiat, Chua, Olga, Kondrashova, Rosanna, Upstill-Goddard, Ulla-Maja, Bailey, Suzanne, Dowson, Patricia, Roxburgh, Rosalind M, Glasspool, Gareth, Bryson, Andrew V, Biankin, Susanna L, Cooke, Gayanie, Ratnayake, Orla, McNally, Nadia, Traficante, Anna, DeFazio, S John, Weroha, David D, Bowtell, Iain A, McNeish, Anthony T, Papenfuss, Clare L, Scott, and Holly E, Barker
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Ovarian Neoplasms ,Cancer Research ,Epithelial-Mesenchymal Transition ,Cell Transformation, Neoplastic ,Carcinosarcoma ,Oncology ,Carcinoma ,Humans ,Female ,Antineoplastic Agents ,Microtubules - Abstract
Ovarian carcinosarcoma (OCS) is an aggressive and rare tumor type with limited treatment options. OCS is hypothesized to develop via the combination theory, with a single progenitor resulting in carcinomatous and sarcomatous components, or alternatively via the conversion theory, with the sarcomatous component developing from the carcinomatous component through epithelial-to-mesenchymal transition (EMT). In this study, we analyzed DNA variants from isolated carcinoma and sarcoma components to show that OCS from 18 women is monoclonal. RNA sequencing indicated that the carcinoma components were more mesenchymal when compared with pure epithelial ovarian carcinomas, supporting the conversion theory and suggesting that EMT is important in the formation of these tumors. Preclinical OCS models were used to test the efficacy of microtubule-targeting drugs, including eribulin, which has previously been shown to reverse EMT characteristics in breast cancers and induce differentiation in sarcomas. Vinorelbine and eribulin more effectively inhibited OCS growth than standard-of-care platinum-based chemotherapy, and treatment with eribulin reduced mesenchymal characteristics and N-MYC expression in OCS patient-derived xenografts. Eribulin treatment resulted in an accumulation of intracellular cholesterol in OCS cells, which triggered a downregulation of the mevalonate pathway and prevented further cholesterol biosynthesis. Finally, eribulin increased expression of genes related to immune activation and increased the intratumoral accumulation of CD8+ T cells, supporting exploration of immunotherapy combinations in the clinic. Together, these data indicate that EMT plays a key role in OCS tumorigenesis and support the conversion theory for OCS histogenesis. Targeting EMT using eribulin could help improve OCS patient outcomes. Significance: Genomic analyses and preclinical models of ovarian carcinosarcoma support the conversion theory for disease development and indicate that microtubule inhibitors could be used to suppress EMT and stimulate antitumor immunity.
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- 2022
16. Case Report: Modulation of Effective Connectivity in Brain Networks after Prosthodontic Tooth Loss Repair
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Antonella Muroni, Daniel Barbar, Matteo Fraschini, Marco Monticone, Giovanni Defazio, and Francesco Marrosu
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INTRODUCTION. Recent neuroimaging studies suggest that dental loss replacements induce changes in neuroplasticity as well as in correlated connectivity between brain networks. However, as the typical temporal delay in detecting brain activity by neuroimaging cannot account for the influence one neural system exerts over another in a context of real activation (“effective” connectivity), it seems of interest to approach this dynamic aspect of brain networking in the time frame of milliseconds by exploiting electroencephalographic (EEG) data. MATERIAL AND METHODS. The present study describes one subject who received a new prosthodontic provisional implant in substitution for previous dental repairs. Two EEG sessions led with a portable device were recorded before and after positioning the new dental implant. By following MATLAB-EEGLAB processing supported by the plugins FIELDTRIP and SIFT, the independent component analysis (ICA) derived from EEG raw signals was rendered as current density fields and interpolated with the dipoles generated by each electrode for a dynamic study of the effective connectivity. One more recording session was undertaken six months after the placement of the final implant. RESULTS. Compared to the baseline, the new prosthodontic implant induced a novel modulation of the neuroplasticity in sensory-motor areas which was maintained following the definitive implant after six months, as revealed by changes in the effective connectivity from the basal strong enslavement of a single brain area over the others, to an equilibrate inter-related connectivity evenly distributed along the frontotemporal regions of both hemispheres. CONCLUSIONS. The rapid shift of the effective connectivity after positioning the new prosthodontic implant and its substantial stability after six months suggest the possibility that synaptic modifications, induced by novel sensory motor conditions, modulate the neuroplasticity and reshape the final dynamic frame of the interarea connectivity. Moreover, given the viability of the EEG practice, this approach could be of some interest in assessing the association between oral pathophysiology and neuronal networking.
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- 2022
17. Prodigy: An Expeditiously Adaptive Parameter-Free Learner
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Mishchenko, Konstantin and Defazio, Aaron
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FOS: Computer and information sciences ,Computer Science - Machine Learning ,Artificial Intelligence (cs.AI) ,Optimization and Control (math.OC) ,Computer Science - Artificial Intelligence ,Statistics - Machine Learning ,FOS: Mathematics ,Machine Learning (stat.ML) ,Mathematics - Optimization and Control ,Machine Learning (cs.LG) - Abstract
We consider the problem of estimating the learning rate in adaptive methods, such as Adagrad and Adam. We describe two techniques, Prodigy and Resetting, to provably estimate the distance to the solution $D$, which is needed to set the learning rate optimally. Our techniques are modifications of the D-Adaptation method for learning-rate-free learning. Our methods improve upon the convergence rate of D-Adaptation by a factor of $O(\sqrt{\log(D/d_0)})$, where $d_0$ is the initial estimate of $D$. We test our methods on 12 common logistic-regression benchmark datasets, VGG11 and ResNet-50 training on CIFAR10, ViT training on Imagenet, LSTM training on IWSLT14, DLRM training on Criteo dataset, VarNet on Knee MRI dataset, as well as RoBERTa and GPT transformer training on BookWiki. Our experimental results show that our approaches consistently outperform D-Adaptation and reach test accuracy values close to that of hand-tuned Adam.
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- 2023
18. Association of Gangrenous, Suppurative, and Exudative Findings With Outcomes and Resource Utilization in Children With Nonperforated Appendicitis
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Shannon L, Cramm, Aaron M, Lipskar, Dionne A, Graham, Shaun M, Kunisaki, Cornelia L, Griggs, Myron, Allukian, Robert T, Russell, Nicole M, Chandler, Matthew T, Santore, Danielle I, Aronowitz, Martin L, Blakely, Brendan, Campbell, Devon T, Collins, Sarah J, Commander, Robert A, Cowles, Jennifer R, DeFazio, Justice C, Echols, Joseph R, Esparaz, Christina, Feng, Richard A, Guyer, David N, Hanna, Katherine, He, Anastasia M, Kahan, Olivia A, Keane, Abdulraouf, Lamoshi, Carla M, Lopez, Sean E, McLean, Elizabeth, Pace, Maia D, Regan, Stefan, Scholz, Elisabeth T, Tracy, Sasha A, Williams, Lucy, Zhang, Shawn J, Rangel, and Goeto, Dantes
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Suppuration ,Appendix ,Length of Stay ,Infections ,Appendicitis ,Cohort Studies ,Gangrene ,Treatment Outcome ,Acute Disease ,Appendectomy ,Humans ,Surgical Wound Infection ,Surgery ,Child ,Original Investigation ,Retrospective Studies - Abstract
IMPORTANCE: The clinical significance of gangrenous, suppurative, or exudative (GSE) findings is poorly characterized in children with nonperforated appendicitis. OBJECTIVE: To evaluate whether GSE findings in children with nonperforated appendicitis are associated with increased risk of surgical site infections and resource utilization. DESIGN, SETTING, AND PARTICIPANTS: This multicenter cohort study used data from the Appendectomy Targeted Database of the American College of Surgeons Pediatric National Surgical Quality Improvement Program, which were augmented with operative report data obtained by supplemental medical record review. Data were obtained from 15 hospitals participating in the Eastern Pediatric Surgery Network (EPSN) research consortium. The study cohort comprised children (aged ≤18 years) with nonperforated appendicitis who underwent appendectomy from July 1, 2015, to June 30, 2020. EXPOSURES: The presence of GSE findings was established through standardized, keyword-based audits of operative reports by EPSN surgeons. Interrater agreement for the presence or absence of GSE findings was evaluated in a random sample of 900 operative reports. MAIN OUTCOMES AND MEASURES: The primary outcome was 30-day postoperative surgical site infections (incisional and organ space infections). Secondary outcomes included rates of hospital revisits, postoperative abdominal imaging, and postoperative length of stay. Multivariable mixed-effects regression was used to adjust measures of association for patient characteristics and clustering within hospitals. RESULTS: Among 6133 children with nonperforated appendicitis, 867 (14.1%) had GSE findings identified from operative report review (hospital range, 4.2%-30.2%; P
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- 2023
19. The Pain in Dystonia Scale (PIDS)—Development and Validation in Cervical Dystonia
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Veronica Bruno, Beatrice Achen, Francesca Morgante, Roberto Erro, Susan H. Fox, Mark J. Edwards, Anette Schrag, Maria Stamelou, Silke Appel‐Cresswell, Giovanni Defazio, K. Ray Chaudhuri, Sarah Pirio Richardson, Hyder A. Jinnah, and Davide Martino
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Neurology ,Neurology (clinical) - Published
- 2023
20. p53 and ovarian carcinoma survival: an Ovarian Tumor Tissue Analysis consortium study
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Köbel, Martin, Kang, Eun-Young, Weir, Ashley, Rambau, Peter F, Lee, Cheng-Han, Nelson, Gregg S, Ghatage, Prafull, Meagher, Nicola S, Riggan, Marjorie J, Alsop, Jennifer, Anglesio, Michael S, Beckmann, Matthias W, Bisinotto, Christiani, Boisen, Michelle, Boros, Jessica, Brand, Alison H, Brooks-Wilson, Angela, Carney, Michael E, Coulson, Penny, Courtney-Brooks, Madeleine, Cushing-Haugen, Kara L, Cybulski, Cezary, Deen, Suha, El-Bahrawy, Mona A, Elishaev, Esther, Erber, Ramona, Fereday, Sian, AOCS Group, Fischer, Anna, Gayther, Simon A, Barquin-Garcia, Arantzazu, Gentry-Maharaj, Aleksandra, Gilks, C Blake, Gronwald, Helena, Grube, Marcel, Harnett, Paul R, Harris, Holly R, Hartkopf, Andreas D, Hartmann, Arndt, Hein, Alexander, Hendley, Joy, Hernandez, Brenda Y, Huang, Yajue, Jakubowska, Anna, Jimenez-Linan, Mercedes, Jones, Michael E, Kennedy, Catherine J, Kluz, Tomasz, Koziak, Jennifer M, Lesnock, Jaime, Lester, Jenny, Lubiński, Jan, Longacre, Teri A, Lycke, Maria, Mateoiu, Constantina, McCauley, Bryan M, McGuire, Valerie, Ney, Britta, Olawaiye, Alexander, Orsulic, Sandra, Osorio, Ana, Paz-Ares, Luis, Ramón Y Cajal, Teresa, Rothstein, Joseph H, Ruebner, Matthias, Schoemaker, Minouk J, Shah, Mitul, Sharma, Raghwa, Sherman, Mark E, Shvetsov, Yurii B, Singh, Naveena, Steed, Helen, Storr, Sarah J, Talhouk, Aline, Traficante, Nadia, Wang, Chen, Whittemore, Alice S, Widschwendter, Martin, Wilkens, Lynne R, Winham, Stacey J, Benitez, Javier, Berchuck, Andrew, Bowtell, David D, Candido Dos Reis, Francisco J, Campbell, Ian, Cook, Linda S, DeFazio, Anna, Doherty, Jennifer A, Fasching, Peter A, Fortner, Renée T, García, María J, Goodman, Marc T, Goode, Ellen L, Gronwald, Jacek, Huntsman, David G, Karlan, Beth Y, Kelemen, Linda E, Kommoss, Stefan, Le, Nhu D, Martin, Stewart G, Menon, Usha, Modugno, Francesmary, Pharoah, Paul Dp, Schildkraut, Joellen M, Sieh, Weiva, Staebler, Annette, Sundfeldt, Karin, Swerdlow, Anthony J, Ramus, Susan J, Brenton, James D, Köbel, Martin [0000-0002-6615-2037], Weir, Ashley [0000-0002-3072-2616], Anglesio, Michael S [0000-0003-1639-5003], Erber, Ramona [0000-0003-0315-1229], Gilks, C Blake [0000-0001-7889-8250], Shvetsov, Yurii B [0000-0001-5131-9618], Campbell, Ian [0000-0002-7773-4155], Huntsman, David G [0000-0003-4934-3322], and Apollo - University of Cambridge Repository
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clear cell ,p53 ,Ovarian Neoplasms ,ovarian cancer ,high-grade serous carcinoma ,Humans ,Female ,TP53 ,prognosis ,Tumor Suppressor Protein p53 ,Carcinoma, Ovarian Epithelial ,endometrioid ,Carcinoma, Endometrioid - Abstract
Funder: Biomedical Research Centre, Funder: European Regional Development Fund, Funder: Mayo Foundation for Medical Education and Research, Funder: Pomeranian Medical University, Funder: Pomorski Uniwersytet Medyczny W Szczecinie, Funder: Cancer Council NSW, Funder: Cancer Institute NSW, Funder: Deutsches Krebsforschungszentrum, Funder: The BC Cancer Foundation, Funder: University College London Hospitals Biomedical Research Centre, Funder: Breast Cancer Now, Funder: Cancer Council Tasmania, Funder: Clinical Academic Reserve, Funder: ELAN Funds of the University of Erlangen-Nuremberg, Funder: Fondo Europeo de Desarrollo Regional, Funder: National Institute for Health Research (NIHR), Funder: National Institute for Health and Care Research, Funder: Ovarian Cancer Australia, Funder: Queensland Cancer Fund, Funder: Cancer Council New South Wales, Funder: Fred C. and Katherine B. Andersen Foundation, Funder: German Cancer Research Center, Funder: Institute of Cancer Research, Funder: Mayo Foundation, Funder: Minnesota Ovarian Cancer Alliance, Funder: Peter MacCallum Foundation, Funder: University of Cambridge, Funder: Cancer Foundation of Western Australia, Funder: VGH and UBC Hospital Foundation, Funder: Cancer Council Victoria, Funder: NHS, Funder: UK National Institute for Health Research, Funder: Cancer Council South Australia, Funder: Oak Foundation, Funder: Sydney West Translational Cancer Research Centre, Our objective was to test whether p53 expression status is associated with survival for women diagnosed with the most common ovarian carcinoma histotypes (high-grade serous carcinoma [HGSC], endometrioid carcinoma [EC], and clear cell carcinoma [CCC]) using a large multi-institutional cohort from the Ovarian Tumor Tissue Analysis (OTTA) consortium. p53 expression was assessed on 6,678 cases represented on tissue microarrays from 25 participating OTTA study sites using a previously validated immunohistochemical (IHC) assay as a surrogate for the presence and functional effect of TP53 mutations. Three abnormal expression patterns (overexpression, complete absence, and cytoplasmic) and the normal (wild type) pattern were recorded. Survival analyses were performed by histotype. The frequency of abnormal p53 expression was 93.4% (4,630/4,957) in HGSC compared to 11.9% (116/973) in EC and 11.5% (86/748) in CCC. In HGSC, there were no differences in overall survival across the abnormal p53 expression patterns. However, in EC and CCC, abnormal p53 expression was associated with an increased risk of death for women diagnosed with EC in multivariate analysis compared to normal p53 as the reference (hazard ratio [HR] = 2.18, 95% confidence interval [CI] 1.36-3.47, p = 0.0011) and with CCC (HR = 1.57, 95% CI 1.11-2.22, p = 0.012). Abnormal p53 was also associated with shorter overall survival in The International Federation of Gynecology and Obstetrics stage I/II EC and CCC. Our study provides further evidence that functional groups of TP53 mutations assessed by abnormal surrogate p53 IHC patterns are not associated with survival in HGSC. In contrast, we validate that abnormal p53 IHC is a strong independent prognostic marker for EC and demonstrate for the first time an independent prognostic association of abnormal p53 IHC with overall survival in patients with CCC.
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- 2023
21. Increased FOXJ1 protein expression is associated with improved overall survival in high-grade serous ovarian carcinoma: an Ovarian Tumor Tissue Analysis Consortium Study
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Weir, Ashley, Kang, Eun-Young, Meagher, Nicola S, Nelson, Gregg S, Ghatage, Prafull, Lee, Cheng-Han, Riggan, Marjorie J, Gentry-Maharaj, Aleksandra, Ryan, Andy, Singh, Naveena, Widschwendter, Martin, Alsop, Jennifer, Anglesio, Michael S, Beckmann, Matthias W, Berger, Jessica, Bisinotto, Christiani, Boros, Jessica, Brand, Alison H, Brenton, James D, Brooks-Wilson, Angela, Carney, Michael E, Cunningham, Julie M, Cushing-Haugen, Kara L, Cybulski, Cezary, Elishaev, Esther, Erber, Ramona, Fereday, Sian, Fischer, Anna, Paz-Ares, Luis, Gayarre, Javier, Gilks, Blake C, Grube, Marcel, Harnett, Paul R, Harris, Holly R, Hartmann, Arndt, Hein, Alexander, Hendley, Joy, Hernandez, Brenda Y, Heublein, Sabine, Huang, Yajue, Huzarski, Tomasz, Jakubowska, Anna, Jimenez-Linan, Mercedes, Kennedy, Catherine J, Kommoss, Felix KF, Koziak, Jennifer M, Kraemer, Bernhard, Le, Nhu D, Lesnock, Jaime, Lester, Jenny, Lubiński, Jan, Menkiszak, Janusz, Ney, Britta, Olawaiye, Alexander, Orsulic, Sandra, Osorio, Ana, Robles-Díaz, Luis, Ruebner, Matthias, Shah, Mitul, Sharma, Raghwa, Shvetsov, Yurii B, Steed, Helen, Talhouk, Aline, Taylor, Sarah E, Traficante, Nadia, Vierkant, Robert A, Wang, Chen, Wilkens, Lynne R, Winham, Stacey J, Benitez, Javier, Berchuck, Andrew, Bowtell, David D, Candido Dos Reis, Francisco J, Cook, Linda S, DeFazio, Anna, AOCs Group, Doherty, Jennifer A, Fasching, Peter A, García, María J, Goode, Ellen L, Goodman, Marc T, Gronwald, Jacek, Huntsman, David G, Karlan, Beth Y, Kommoss, Stefan, Modugno, Francesmary, Schildkraut, Joellen M, Sinn, Hans-Peter, Staebler, Annette, Kelemen, Linda E, Ford, Caroline E, Menon, Usha, Pharoah, Paul DP, Köbel, Martin, Ramus, Susan J, Meagher, Nicola S [0000-0001-9134-2118], Ghatage, Prafull [0000-0002-2371-0844], Riggan, Marjorie J [0000-0002-3701-8031], Widschwendter, Martin [0000-0002-7778-8380], Brenton, James D [0000-0002-5738-6683], Cunningham, Julie M [0000-0002-8159-3025], Hein, Alexander [0000-0003-2601-3398], Jakubowska, Anna [0000-0002-5650-0501], Kennedy, Catherine J [0000-0002-4465-5784], Kommoss, Felix KF [0000-0003-0876-9087], Osorio, Ana [0000-0001-8124-3984], Vierkant, Robert A [0000-0001-6242-5221], Winham, Stacey J [0000-0002-8492-9102], Bowtell, David D [0000-0001-9089-7525], Candido Dos Reis, Francisco J [0000-0001-5758-5917], DeFazio, Anna [0000-0003-0057-4744], Doherty, Jennifer A [0000-0002-1454-8187], Fasching, Peter A [0000-0003-4885-8471], García, María J [0000-0002-2236-9912], Karlan, Beth Y [0000-0002-9451-2933], Sinn, Hans-Peter [0000-0003-2836-6699], Ford, Caroline E [0000-0002-4438-2309], Menon, Usha [0000-0003-3708-1732], Pharoah, Paul DP [0000-0001-8494-732X], Ramus, Susan J [0000-0003-0005-7798], and Apollo - University of Cambridge Repository
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Ovarian Neoplasms ,Biomarkers, Tumor ,Humans ,Female ,Forkhead Transcription Factors ,RNA, Messenger ,Prognosis ,Survival Analysis ,Cystadenocarcinoma, Serous - Abstract
Funder: Funder: Calgary Laboratory Services (research support fund) Grant reference number: RS19-612, Funder: Funder: National Cancer Institute: National Institutes of Health Grant reference number: R01CA172404, BACKGROUND: Recently, we showed a >60% difference in 5-year survival for patients with tubo-ovarian high-grade serous carcinoma (HGSC) when stratified by a 101-gene mRNA expression prognostic signature. Given the varied patient outcomes, this study aimed to translate prognostic mRNA markers into protein expression assays by immunohistochemistry and validate their survival association in HGSC. METHODS: Two prognostic genes, FOXJ1 and GMNN, were selected based on high-quality antibodies, correlation with protein expression and variation in immunohistochemical scores in a preliminary cohort (n = 134 and n = 80, respectively). Six thousand four hundred and thirty-four (FOXJ1) and 5470 (GMNN) formalin-fixed, paraffin-embedded ovarian neoplasms (4634 and 4185 HGSC, respectively) represented on tissue microarrays from the Ovarian Tumor Tissue Analysis consortium underwent immunohistochemical staining and scoring, then univariate and multivariate survival analysis. RESULTS: Consistent with mRNA, FOXJ1 protein expression exhibited a linear, increasing association with improved overall survival in HGSC patients. Women with >50% expression had the most favourable outcomes (HR = 0.78, 95% CI 0.67-0.91, p < 0.0001). GMNN protein expression was not significantly associated with overall HSGC patient survival. However, HGSCs with >35% GMNN expression showed a trend for better outcomes, though this was not significant. CONCLUSION: We provide foundational evidence for the prognostic value of FOXJ1 in HGSC, validating the prior mRNA-based prognostic association by immunohistochemistry.
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- 2023
22. Uncertainty and the unmet informational needs of patients with cancer of unknown primary (CUP): a cross-sectional multi-site study
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Lisa Guccione, Krista Fisher, Linda Mileshkin, Richard Tothill, David Bowtell, Stephen Quinn, Anna DeFazio, Chris S. Karapetis, Nicholas Wilcken, Madhu Singh, Christopher Steer, Bo Gao, Mark Warren, Ian M. Collins, Narayan Karanth, Cindy Bryant, and Penelope Schofield
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Health Services Needs and Demand ,Cross-Sectional Studies ,Oncology ,Surveys and Questionnaires ,Quality of Life ,Uncertainty ,Humans ,Neoplasms, Unknown Primary - Abstract
Objective This study aimed to determine the healthcare experiences, quality of life, and psychosocial needs of patients with cancer of unknown primary (CUP) early after diagnosis; comparing their experiences to patients with advanced cancer of a known primary (non-CUP control patients) and published general population reference data where available. Methods This study was a cross-sectional, multi-site study comparing CUP patients (n = 139) compared to non-CUP controls (n = 45). Demographic, clinical information and patient-reported outcome questionnaire data were collected at baseline. Results Differences in healthcare experienced were found between CUP and non-CUP controls with CUP patients reporting higher scores for unmet medical communication/information needs compared with non-CUP control patients (p = 0.013) as well as greater uncertainty in illness (p = 0.042). Whilst no differences were found between CUP and non-CUP controls on the EORTC and PROMIS measures, of those that ‘received written information about your cancer…’ and asked ‘…how useful was it?’ fewer CUP patients reported finding the information useful 40% vs 61%, and more were likely to not have received written information at all 59% vs 32%; (p = 0.002). Additionally, of those that found information about their cancer online, fewer patients with CUP reported finding it useful 32% vs 48% control patients (p = 0.005). Conclusions CUP patients have unmet medical communication/information needs and greater uncertainty in illness but do not differ in health-related quality of life domains compared to patients with advanced cancer of a known primary.
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- 2022
23. Neurological phenomenology of the IRF2BPL mutation syndrome: Analysis of a new case and systematic review of the literature
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S. Pisano, M. Melis, M. Figorilli, L. Polizzi, L. Rocchi, S. Giglio, G. Defazio, and A. Muroni
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Epilepsy ,Neurology ,Dystonic Disorders ,Mutation ,Humans ,Nuclear Proteins ,Syndrome ,Neurology (clinical) ,General Medicine ,Carrier Proteins - Abstract
IRF2BPL is an intronless gene that was mapped to 14q24.3 chromosome in 2000 and codes for the interferon regulatory factor 2 binding like protein.To analyses the clinical characteristics of the patients reported in the literature and of an additional patient we observed in order to better delineate the phenomenological spectrum of the disease and provide indications to improve clinical recognition and facilitate diagnosis.We reported on 28 patients carrying the IRF2BPL mutation who were identified in 10 papers (n.27), using PUBMED as the search engine, and in our hospital (n. 1).All patients shared developmental delay/regression. Additional neurological symptoms were present in a large proportion of patients and reflected the involvement of five main neurological domains, i.e. epilepsy, dystonia, ataxia, spasticity, and ocular disturbances. Correlation analysis suggested a significant positive correlation between the number of affected neurological domains and the presence of MRI abnormalities (rho = 0.45, p = 0.02), while no significant correlation emerged between the number of affected clinical domains and age at disease onset (rho = 0.18, p = 0.35) or variant type (rho = 0.30, p = 0.12).Our analysis highlights that the IRF2BPL mutation syndrome is highly specific to the central nervous system. Diagnostic work-up should consider the clinical picture of the IRF2BPL mutation syndrome herein delineated and the existence of conditions that share developmental delay/regression and result from acquired/genetic or unidentifiable underlying etiology.
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- 2022
24. Functional movement disorder gender, age and phenotype study
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Lidstone, Sarah C, Costa-Parke, Michael, Robinson, Emily J, Ercoli, Tommaso, Stone, Jon, Collaborators Omar Ahmad, Sepideh, Akbaripanahi, Albanese, Alberto, Selma, Aybek, José Fidel Baizabal- Carvallo, Beek, Peter J., Bhatia, Kailash P., Verónica, Cabreira, Carson, Alan J., Castagna, Anna, Dale, Russell C., Carlo, Dallocchio, Giovanni, Defazio, Bertrand, Degos, Benedetta, Demartini, Günther, Deuschl, Galina, Diukova, Duque, Kevin R., Edwards, Mark J., Epstein, Steven A., Espay, Alberto J., Factor, Stewart A., Beatrice, Garcin, Geroin, Christian, Muriel, Hagenaars, Mark, Hallett, Thomas, Hassa, Anhar, Hassan, Herbert, Lorena D., Holden, Samantha K., Joseph, Jankovic, Kanaan, Richard A., Lianne, Kempe, Maja, Kojovic, Katie, Kompoliti, Kostić, Vladimir S., Kevin, Kyle, Kathrin, Lafaver, Lang, Anthony E., Lindsey, Macgillivray, Davide, Martino, João, Massano, Maurer, Carine W., Laura, Mcwhirter, Raja, Mehanna, Francine, Mesrati, Morris, John C., Glenn, Nielsen, Anastasia, Obukhova, Sanjay, Pandey, Perez, David L., Igor, Petrović, Pullman, Seth L., Angelo, Quartarone, Karin, Roelofs, Anette, Schrag, Yury, Seliverstov, Tereza, Serranová, Ulf, Søgaard, Petr, Sojka, Maria, Stamelou, Stephen, Christopher D., Stins, John F., Tinazzi, Michele, Aleksandra, Tomić, Anabela, Valadas, Valerie, Voon, Waugh, Jeff L., and Allan, D. Wu.
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Movement Disorders ,230 Affective Neuroscience ,systematic reviews ,meta-analysis ,Experimental Psychopathology and Treatment ,Psychiatry and Mental health ,Dystonia ,Phenotype ,Conversion Disorder ,SDG 3 - Good Health and Well-being ,functional neurological disorder ,Tremor ,Humans ,Surgery ,Female ,Neurology (clinical) - Abstract
Contains fulltext : 289359.pdf (Publisher’s version ) (Closed access) Functional movement disorder (FMD) is a common manifestation of functional neurological disorder presenting with diverse phenotypes such as tremor, weakness and gait disorder. Our current understanding of the basic epidemiological features of this condition is unclear. We aimed to describe and examine the relationship between age at onset, phenotype and gender in FMD in a large meta-analysis of published and unpublished individual patient cases. An electronic search of PubMed was conducted for studies from 1968 to 2019 according to Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. Individual patient data were collected through a research network. We described the distribution of age of onset and how this varied by gender and motor phenotype. A one-stage meta-analysis was performed using multilevel mixed-effects linear regression, including random intercepts for country and data source. A total of 4905 individual cases were analysed (72.6% woman). The mean age at onset was 39.6 years (SD 16.1). Women had a significantly earlier age of onset than men (39.1 years vs 41.0 years). Mixed FMD (23.1%), tremor (21.6%) and weakness (18.1%) were the most common phenotypes. Compared with tremor (40.7 years), the mean ages at onset of dystonia (34.5 years) and weakness (36.4 years) were significantly younger, while gait disorders (43.2 years) had a significantly later age at onset. The interaction between gender and phenotype was not significant. FMD peaks in midlife with varying effects of gender on age at onset and phenotype. The data gives some support to ‘lumping’ FMD as a unitary disorder but also highlights the value in ‘splitting’ into individual phenotypes where relevant.Data are available upon reasonable request. 8 p.
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- 2022
25. A scaling calculus for the design and initialization of ReLU networks
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Aaron Defazio and Léon Bottou
- Subjects
Artificial Intelligence ,Software - Abstract
We propose a system for calculating a “scaling constant” for layers and weights of neural networks. We relate this scaling constant to two important quantities that relate to the optimizability of neural networks, and argue that a network that is “preconditioned” via scaling, in the sense that all weights have the same scaling constant, will be easier to train. This scaling calculus results in a number of consequences, among them the fact that the geometric mean of the fan-in and fan-out, rather than the fan-in, fan-out, or arithmetic mean, should be used for the initialization of the variance of weights in a neural network. Our system allows for the off-line design & engineering of ReLU (Rectified Linear Unit) neural networks, potentially replacing blind experimentation. We verify the effectiveness of our approach on a set of benchmark problems.
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- 2022
26. Data from Mutation of ERBB2 Provides a Novel Alternative Mechanism for the Ubiquitous Activation of RAS-MAPK in Ovarian Serous Low Malignant Potential Tumors
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David D.L. Bowtell, Georgia Chenevix-Trench, Anna deFazio, Michael J. Birrer, Raghwa Sharma, Peter Russell, Nadia Traficante, Sian Fereday, Bianca Locandro, Lisa Simms, Nic Waddell, Richard Tothill, Anna V. Tinker, Joshy George, Jeremy M. Arnold, and Michael S. Anglesio
- Abstract
Approximately, 10% to 15% of serous ovarian tumors fall into the category designated as tumors of low malignant potential (LMP). Like their invasive counterparts, LMP tumors may be associated with extraovarian disease, for example, in the peritoneal cavity and regional lymph nodes. However, unlike typical invasive carcinomas, patients generally have a favorable prognosis. The mutational profile also differs markedly from that seen in most serous carcinomas. Typically, LMP tumors are associated with KRAS and BRAF mutations. Interrogation of expression profiles in serous LMP tumors suggested overall redundancy of RAS-MAPK pathway mutations and a distinct mechanism of oncogenesis compared with high-grade ovarian carcinomas. Our findings indicate that activating mutation of the RAS-MAPK pathway in serous LMP may be present in >70% of cases compared with ∼12.5% in serous ovarian carcinomas. In addition to mutations of KRAS (18%) and BRAF (48%) mutations, ERBB2 mutations (6%), but not EGFR, are prevalent among serous LMP tumors. Based on the expression profile signature observed throughout our serous LMP cohort, we propose that RAS-MAPK pathway activation is a requirement of serous LMP tumor development and that other activators of this pathway are yet to be defined. Importantly, as few nonsurgical options exist for treatment of recurrent LMP tumors, therapeutic targeting of this pathway may prove beneficial, especially in younger patients where maintaining fertility is important. (Mol Cancer Res 2008;6(11):1678–90)
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- 2023
27. Supplementary Tables 1 - 4 from Large-Scale Evaluation of Common Variation in Regulatory T Cell–Related Genes and Ovarian Cancer Outcome
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Ellen L. Goode, Keith L. Knutson, Lara E. Sucheston, Kunle Odunsi, Roberta B. Ness, Simon A. Gayther, Paul D.P. Pharoah, Georgia Chenevix-Trench, Mary Anne Rossing, Daniel W. Cramer, Celeste Leigh Pearce, Joellen M. Schildkraut, Usha Menon, Susanne K. Kjaer, Douglas A. Levine, Jacek Gronwald, Hoda Anton Culver, Alice S. Whittemore, Beth Y. Karlan, Diether Lambrechts, Nicolas Wentzensen, Jolanta Kupryjanczyk, Jenny Chang-Claude, Elisa V. Bandera, Estrid Hogdall, Florian Heitz, Stanley B. Kaye, Gottfried Konecny, Peter A. Fasching, Ian Campbell, Marc T. Goodman, Tanja Pejovic, Yukie T. Bean, Laura E. Hays, Galina Lurie, Diana Eccles, Alexander Hein, Matthias W. Beckmann, Arif B. Ekici, James Paul, Robert Brown, James M. Flanagan, Philipp Harter, Andreas du Bois, Ira Schwaab, Claus K. Hogdall, Sara H. Olson, Lene Lundvall, Irene Orlow, Lisa E. Paddock, Anja Rudolph, Petra Seibold, Agnieszka Dansonka-Mieszkowska, Iwona K. Rzepecka, Beata Spiewankiewicz, Louise A. Brinton, Hannah Yang, Montserrat Garcia-Closas, Evelyn Despierre, Sandrina Lambrechts, Ignace Vergote, Christine Walsh, Jenny Lester, Weiva Sieh, Valerie McGuire, Joseph H. Rothstein, Argyrios Ziogas, Jan Lubiński, Cezary Cybulski, Janusz Menkiszak, Allan Jensen, Howard Shen, Brenda Diergaarde, Susan J. Ramus, Aleksandra Gentry-Maharaj, Andrew Berchuck, Anna H. Wu, Malcolm C. Pike, David Van Den Berg, Kathryn L. Terry, Allison F. Vitonis, Starr M. Ramirez, Thomas A. Sellers, Catherine M. Phelan, Jennifer A. Doherty, Sharon E. Johnatty, Anna deFazio, Honglin Song, Jonathan Tyrer, Chen Wang, Kate Lawrenson, Lynn C. Hartmann, Claudia Preston, David N. Rider, Julie M. Cunningham, Brooke L. Fridley, Krista M. Goergen, Matthew J. Maurer, Matthew S. Block, Zachary C. Fogarty, Robert A. Vierkant, Ann L. Oberg, Kimberly R. Kalli, Kirsten B. Moysich, and Bridget Charbonneau
- Abstract
PDF file - 157K, Supplemental Table 1. Regulatory T cell genes included in this study (N=25). Supplemental Table 2. Regulatory T cell SNPs included in this study. Supplemental Table 3. Participating invasive epithelial ovarian cancer studies. Supplemental Table 4. Association between clinical variables and overall survival.
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- 2023
28. Data from Large-Scale Evaluation of Common Variation in Regulatory T Cell–Related Genes and Ovarian Cancer Outcome
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Ellen L. Goode, Keith L. Knutson, Lara E. Sucheston, Kunle Odunsi, Roberta B. Ness, Simon A. Gayther, Paul D.P. Pharoah, Georgia Chenevix-Trench, Mary Anne Rossing, Daniel W. Cramer, Celeste Leigh Pearce, Joellen M. Schildkraut, Usha Menon, Susanne K. Kjaer, Douglas A. Levine, Jacek Gronwald, Hoda Anton Culver, Alice S. Whittemore, Beth Y. Karlan, Diether Lambrechts, Nicolas Wentzensen, Jolanta Kupryjanczyk, Jenny Chang-Claude, Elisa V. Bandera, Estrid Hogdall, Florian Heitz, Stanley B. Kaye, Gottfried Konecny, Peter A. Fasching, Ian Campbell, Marc T. Goodman, Tanja Pejovic, Yukie T. Bean, Laura E. Hays, Galina Lurie, Diana Eccles, Alexander Hein, Matthias W. Beckmann, Arif B. Ekici, James Paul, Robert Brown, James M. Flanagan, Philipp Harter, Andreas du Bois, Ira Schwaab, Claus K. Hogdall, Sara H. Olson, Lene Lundvall, Irene Orlow, Lisa E. Paddock, Anja Rudolph, Petra Seibold, Agnieszka Dansonka-Mieszkowska, Iwona K. Rzepecka, Beata Spiewankiewicz, Louise A. Brinton, Hannah Yang, Montserrat Garcia-Closas, Evelyn Despierre, Sandrina Lambrechts, Ignace Vergote, Christine Walsh, Jenny Lester, Weiva Sieh, Valerie McGuire, Joseph H. Rothstein, Argyrios Ziogas, Jan Lubiński, Cezary Cybulski, Janusz Menkiszak, Allan Jensen, Howard Shen, Brenda Diergaarde, Susan J. Ramus, Aleksandra Gentry-Maharaj, Andrew Berchuck, Anna H. Wu, Malcolm C. Pike, David Van Den Berg, Kathryn L. Terry, Allison F. Vitonis, Starr M. Ramirez, Thomas A. Sellers, Catherine M. Phelan, Jennifer A. Doherty, Sharon E. Johnatty, Anna deFazio, Honglin Song, Jonathan Tyrer, Chen Wang, Kate Lawrenson, Lynn C. Hartmann, Claudia Preston, David N. Rider, Julie M. Cunningham, Brooke L. Fridley, Krista M. Goergen, Matthew J. Maurer, Matthew S. Block, Zachary C. Fogarty, Robert A. Vierkant, Ann L. Oberg, Kimberly R. Kalli, Kirsten B. Moysich, and Bridget Charbonneau
- Abstract
The presence of regulatory T cells (Treg) in solid tumors is known to play a role in patient survival in ovarian cancer and other malignancies. We assessed inherited genetic variations via 749 tag single-nucleotide polymorphisms (SNP) in 25 Treg-associated genes (CD28, CTLA4, FOXP3, IDO1, IL10, IL10RA, IL15, 1L17RA, IL23A, IL23R, IL2RA, IL6, IL6R, IL8, LGALS1, LGALS9, MAP3K8, STAT5A, STAT5B, TGFB1, TGFB2, TGFB3, TGFBR1, TGRBR2, and TGFBR3) in relation to ovarian cancer survival. We analyzed genotype and overall survival in 10,084 women with invasive epithelial ovarian cancer, including 5,248 high-grade serous, 1,452 endometrioid, 795 clear cell, and 661 mucinous carcinoma cases of European descent across 28 studies from the Ovarian Cancer Association Consortium (OCAC). The strongest associations were found for endometrioid carcinoma and IL2RA SNPs rs11256497 [HR, 1.42; 95% confidence interval (CI), 1.22–1.64; P = 5.7 × 10−6], rs791587 (HR, 1.36; 95% CI, 1.17–1.57; P = 6.2 × 10−5), rs2476491 (HR, = 1.40; 95% CI, 1.19–1.64; P = 5.6 × 10−5), and rs10795763 (HR, 1.35; 95% CI, 1.17–1.57; P = 7.9 × 10−5), and for clear cell carcinoma and CTLA4 SNP rs231775 (HR, 0.67; 95% CI, 0.54–0.82; P = 9.3 × 10−5) after adjustment for age, study site, population stratification, stage, grade, and oral contraceptive use. The rs231775 allele associated with improved survival in our study also results in an amino acid change in CTLA4 and previously has been reported to be associated with autoimmune conditions. Thus, we found evidence that SNPs in genes related to Tregs seem to play a role in ovarian cancer survival, particularly in patients with clear cell and endometrioid epithelial ovarian cancer. Cancer Immunol Res; 2(4); 332–40. ©2014 AACR.
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- 2023
29. Supplementary Data from Mutation of ERBB2 Provides a Novel Alternative Mechanism for the Ubiquitous Activation of RAS-MAPK in Ovarian Serous Low Malignant Potential Tumors
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David D.L. Bowtell, Georgia Chenevix-Trench, Anna deFazio, Michael J. Birrer, Raghwa Sharma, Peter Russell, Nadia Traficante, Sian Fereday, Bianca Locandro, Lisa Simms, Nic Waddell, Richard Tothill, Anna V. Tinker, Joshy George, Jeremy M. Arnold, and Michael S. Anglesio
- Abstract
Supplementary Data from Mutation of ERBB2 Provides a Novel Alternative Mechanism for the Ubiquitous Activation of RAS-MAPK in Ovarian Serous Low Malignant Potential Tumors
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- 2023
30. Supplementary Methods 1 from Gene-Expression Profiling of Mucinous Ovarian Tumors and Comparison with Upper and Lower Gastrointestinal Tumors Identifies Markers Associated with Adverse Outcomes
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Susan J. Ramus, Michael L. Friedlander, Martin Köbel, Anna DeFazio, Lyndal Anderson, Paul D.P. Pharoah, Aline Talhouk, Anna H. Wu, Karin Sundfeldt, Annette Staebler, Sue K. Park, Francesmary Modugno, Gottfried E. Konecny, Stefan Kommoss, Linda E. Kelemen, Beth Y. Karlan, Paul A. James, David G. Huntsman, Estrid Høgdall, Nicholas J. Hawkins, Jacek Gronwald, Peter A. Fasching, Philip Crowe, Paul A. Cohen, Heather Thorne, Rebekka Wiedenhoefer, Robyn L. Ward, Paul Timpson, Katrina Tang, Soseul Sung, Deepak Subramanian, Colin J.R. Stewart, Helen Steed, Mitul Shah, Clare L. Scott, Stuart Salfinger, Matthias Ruebner, Marjorie J. Riggan, Jianyu Rao, Ganendra Raj Mohan, Carmel M. Quinn, Malcolm C. Pike, John V. Pearson, Celeste Leigh Pearce, Sang-Yoon Park, Sandra Orsulic, David Morris, Suzana Mittelstadt, Parham Minoo, Janusz Menkiszak, Simone McInerny, Constantina Mateoiu, Sakshi Mahale, Jan Lubiński, Anna Linder, Belle W.X. Lim, Winston Liauw, Na Li, Yee Leung, Jenny Lester, Angela Laslavic, Tiffany Lai, Jennifer M. Koziak, Kayla Klett, Jae-Hoon Kim, Jae-Weon Kim, Byoung-Gie Kim, Catherine J. Kennedy, Mercedes Jimenez-Linan, Anna Jakubowska, Tomasz Huzarski, Claus K. Høgdall, Anusha Hettiaratchi, Arndt Hartmann, Paul R. Harnett, Marcel Grube, Charlie Gourley, Anthony J. Gill, Blake Gilks, Zhuxuan Fu, Anna Fischer, Rhonda Farrell, Ramona Erber, Esther Elishaev, Cezary Cybulski, Joshua Cohen, Dane Cheasley, Ian Campbell, James D. Brenton, Alison H. Brand, David D.L. Bowtell, Jessica Boros, Matthias W. Beckmann, Ellen Barlow, Jennifer Alsop, Adeline Tan, Angela Chou, Ksenia Chezar, Kara L. Cushing-Haugen, Andrew Berchuck, Joellen M. Schildkraut, Holly R. Harris, Jennifer A. Doherty, Kylie-Ann Mallitt, Michael S. Anglesio, Derek S. Chiu, Chi Nam Ignatius Pang, Adelyn Bolithon, Matthew Wakefield, Kylie L. Gorringe, and Nicola S. Meagher
- Abstract
Supplementary Methods
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- 2023
31. Data from Molecular Subclasses of Clear Cell Ovarian Carcinoma and Their Impact on Disease Behavior and Outcomes
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Elli Papaemmanuil, Ellen L. Goode, Kate Lawrenson, Francesmary Modugno, Jason Konner, Simon Gayther, David Huntsman, Michael S. Anglesio, Britta Weigelt, James D. Brenton, Beth Karlan, Anna DeFazio, Charlie Gourley, Michael Churchman, Ronny Drapkin, Kevin M. Elias, Paul Pharoah, Yoke-Eng Chiew, Alison H. Brand, Magdalena Sekowska, Anna Piskorz, Catherine J. Kennedy, Angela Laslavic, Esther Elishaev, Jenny Lester, Sebastian M. Armasu, Stacey J. Winham, Lea A. Moukarzel, Brian J. Wiley, Irenaeus C.C. Chan, Julie M. Cunningham, Yanis Tazi, Martin Köbel, Rajmohan Murali, Zhuxuan Fu, Rosario Corona de la Fuente, Denise Chen, and Kelly L. Bolton
- Abstract
Purpose:To identify molecular subclasses of clear cell ovarian carcinoma (CCOC) and assess their impact on clinical presentation and outcomes.Experimental Design:We profiled 421 primary CCOCs that passed quality control using a targeted deep sequencing panel of 163 putative CCOC driver genes and whole transcriptome sequencing of 211 of these tumors. Molecularly defined subgroups were identified and tested for association with clinical characteristics and overall survival.Results:We detected a putative somatic driver mutation in at least one candidate gene in 95% (401/421) of CCOC tumors including ARID1A (in 49% of tumors), PIK3CA (49%), TERT (20%), and TP53 (16%). Clustering of cancer driver mutations and RNA expression converged upon two distinct subclasses of CCOC. The first was dominated by ARID1A-mutated tumors with enriched expression of canonical CCOC genes and markers of platinum resistance; the second was largely comprised of tumors with TP53 mutations and enriched for the expression of genes involved in extracellular matrix organization and mesenchymal differentiation. Compared with the ARID1A-mutated group, women with TP53-mutated tumors were more likely to have advanced-stage disease, no antecedent history of endometriosis, and poorer survival, driven by their advanced stage at presentation. In women with ARID1A-mutated tumors, there was a trend toward a lower rate of response to first-line platinum-based therapy.Conclusions:Our study suggests that CCOC consists of two distinct molecular subclasses with distinct clinical presentation and outcomes, with potential relevance to both traditional and experimental therapy responsiveness.See related commentary by Lheureux, p. 4838
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- 2023
32. Supplementary Data from Molecular Subclasses of Clear Cell Ovarian Carcinoma and Their Impact on Disease Behavior and Outcomes
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Elli Papaemmanuil, Ellen L. Goode, Kate Lawrenson, Francesmary Modugno, Jason Konner, Simon Gayther, David Huntsman, Michael S. Anglesio, Britta Weigelt, James D. Brenton, Beth Karlan, Anna DeFazio, Charlie Gourley, Michael Churchman, Ronny Drapkin, Kevin M. Elias, Paul Pharoah, Yoke-Eng Chiew, Alison H. Brand, Magdalena Sekowska, Anna Piskorz, Catherine J. Kennedy, Angela Laslavic, Esther Elishaev, Jenny Lester, Sebastian M. Armasu, Stacey J. Winham, Lea A. Moukarzel, Brian J. Wiley, Irenaeus C.C. Chan, Julie M. Cunningham, Yanis Tazi, Martin Köbel, Rajmohan Murali, Zhuxuan Fu, Rosario Corona de la Fuente, Denise Chen, and Kelly L. Bolton
- Abstract
Supplementary Data from Molecular Subclasses of Clear Cell Ovarian Carcinoma and Their Impact on Disease Behavior and Outcomes
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- 2023
33. Supplementary Figures S1-S13 from Gene-Expression Profiling of Mucinous Ovarian Tumors and Comparison with Upper and Lower Gastrointestinal Tumors Identifies Markers Associated with Adverse Outcomes
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Susan J. Ramus, Michael L. Friedlander, Martin Köbel, Anna DeFazio, Lyndal Anderson, Paul D.P. Pharoah, Aline Talhouk, Anna H. Wu, Karin Sundfeldt, Annette Staebler, Sue K. Park, Francesmary Modugno, Gottfried E. Konecny, Stefan Kommoss, Linda E. Kelemen, Beth Y. Karlan, Paul A. James, David G. Huntsman, Estrid Høgdall, Nicholas J. Hawkins, Jacek Gronwald, Peter A. Fasching, Philip Crowe, Paul A. Cohen, Heather Thorne, Rebekka Wiedenhoefer, Robyn L. Ward, Paul Timpson, Katrina Tang, Soseul Sung, Deepak Subramanian, Colin J.R. Stewart, Helen Steed, Mitul Shah, Clare L. Scott, Stuart Salfinger, Matthias Ruebner, Marjorie J. Riggan, Jianyu Rao, Ganendra Raj Mohan, Carmel M. Quinn, Malcolm C. Pike, John V. Pearson, Celeste Leigh Pearce, Sang-Yoon Park, Sandra Orsulic, David Morris, Suzana Mittelstadt, Parham Minoo, Janusz Menkiszak, Simone McInerny, Constantina Mateoiu, Sakshi Mahale, Jan Lubiński, Anna Linder, Belle W.X. Lim, Winston Liauw, Na Li, Yee Leung, Jenny Lester, Angela Laslavic, Tiffany Lai, Jennifer M. Koziak, Kayla Klett, Jae-Hoon Kim, Jae-Weon Kim, Byoung-Gie Kim, Catherine J. Kennedy, Mercedes Jimenez-Linan, Anna Jakubowska, Tomasz Huzarski, Claus K. Høgdall, Anusha Hettiaratchi, Arndt Hartmann, Paul R. Harnett, Marcel Grube, Charlie Gourley, Anthony J. Gill, Blake Gilks, Zhuxuan Fu, Anna Fischer, Rhonda Farrell, Ramona Erber, Esther Elishaev, Cezary Cybulski, Joshua Cohen, Dane Cheasley, Ian Campbell, James D. Brenton, Alison H. Brand, David D.L. Bowtell, Jessica Boros, Matthias W. Beckmann, Ellen Barlow, Jennifer Alsop, Adeline Tan, Angela Chou, Ksenia Chezar, Kara L. Cushing-Haugen, Andrew Berchuck, Joellen M. Schildkraut, Holly R. Harris, Jennifer A. Doherty, Kylie-Ann Mallitt, Michael S. Anglesio, Derek S. Chiu, Chi Nam Ignatius Pang, Adelyn Bolithon, Matthew Wakefield, Kylie L. Gorringe, and Nicola S. Meagher
- Abstract
Supplementary Figures S1-S13
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- 2023
34. Data from Gene-Expression Profiling of Mucinous Ovarian Tumors and Comparison with Upper and Lower Gastrointestinal Tumors Identifies Markers Associated with Adverse Outcomes
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Susan J. Ramus, Michael L. Friedlander, Martin Köbel, Anna DeFazio, Lyndal Anderson, Paul D.P. Pharoah, Aline Talhouk, Anna H. Wu, Karin Sundfeldt, Annette Staebler, Sue K. Park, Francesmary Modugno, Gottfried E. Konecny, Stefan Kommoss, Linda E. Kelemen, Beth Y. Karlan, Paul A. James, David G. Huntsman, Estrid Høgdall, Nicholas J. Hawkins, Jacek Gronwald, Peter A. Fasching, Philip Crowe, Paul A. Cohen, Heather Thorne, Rebekka Wiedenhoefer, Robyn L. Ward, Paul Timpson, Katrina Tang, Soseul Sung, Deepak Subramanian, Colin J.R. Stewart, Helen Steed, Mitul Shah, Clare L. Scott, Stuart Salfinger, Matthias Ruebner, Marjorie J. Riggan, Jianyu Rao, Ganendra Raj Mohan, Carmel M. Quinn, Malcolm C. Pike, John V. Pearson, Celeste Leigh Pearce, Sang-Yoon Park, Sandra Orsulic, David Morris, Suzana Mittelstadt, Parham Minoo, Janusz Menkiszak, Simone McInerny, Constantina Mateoiu, Sakshi Mahale, Jan Lubiński, Anna Linder, Belle W.X. Lim, Winston Liauw, Na Li, Yee Leung, Jenny Lester, Angela Laslavic, Tiffany Lai, Jennifer M. Koziak, Kayla Klett, Jae-Hoon Kim, Jae-Weon Kim, Byoung-Gie Kim, Catherine J. Kennedy, Mercedes Jimenez-Linan, Anna Jakubowska, Tomasz Huzarski, Claus K. Høgdall, Anusha Hettiaratchi, Arndt Hartmann, Paul R. Harnett, Marcel Grube, Charlie Gourley, Anthony J. Gill, Blake Gilks, Zhuxuan Fu, Anna Fischer, Rhonda Farrell, Ramona Erber, Esther Elishaev, Cezary Cybulski, Joshua Cohen, Dane Cheasley, Ian Campbell, James D. Brenton, Alison H. Brand, David D.L. Bowtell, Jessica Boros, Matthias W. Beckmann, Ellen Barlow, Jennifer Alsop, Adeline Tan, Angela Chou, Ksenia Chezar, Kara L. Cushing-Haugen, Andrew Berchuck, Joellen M. Schildkraut, Holly R. Harris, Jennifer A. Doherty, Kylie-Ann Mallitt, Michael S. Anglesio, Derek S. Chiu, Chi Nam Ignatius Pang, Adelyn Bolithon, Matthew Wakefield, Kylie L. Gorringe, and Nicola S. Meagher
- Abstract
Purpose:Advanced-stage mucinous ovarian carcinoma (MOC) has poor chemotherapy response and prognosis and lacks biomarkers to aid stage I adjuvant treatment. Differentiating primary MOC from gastrointestinal (GI) metastases to the ovary is also challenging due to phenotypic similarities. Clinicopathologic and gene-expression data were analyzed to identify prognostic and diagnostic features.Experimental Design:Discovery analyses selected 19 genes with prognostic/diagnostic potential. Validation was performed through the Ovarian Tumor Tissue Analysis consortium and GI cancer biobanks comprising 604 patients with MOC (n = 333), mucinous borderline ovarian tumors (MBOT, n = 151), and upper GI (n = 65) and lower GI tumors (n = 55).Results:Infiltrative pattern of invasion was associated with decreased overall survival (OS) within 2 years from diagnosis, compared with expansile pattern in stage I MOC [hazard ratio (HR), 2.77; 95% confidence interval (CI), 1.04–7.41, P = 0.042]. Increased expression of THBS2 and TAGLN was associated with shorter OS in MOC patients (HR, 1.25; 95% CI, 1.04–1.51, P = 0.016) and (HR, 1.21; 95% CI, 1.01–1.45, P = 0.043), respectively. ERBB2 (HER2) amplification or high mRNA expression was evident in 64 of 243 (26%) of MOCs, but only 8 of 243 (3%) were also infiltrative (4/39, 10%) or stage III/IV (4/31, 13%).Conclusions:An infiltrative growth pattern infers poor prognosis within 2 years from diagnosis and may help select stage I patients for adjuvant therapy. High expression of THBS2 and TAGLN in MOC confers an adverse prognosis and is upregulated in the infiltrative subtype, which warrants further investigation. Anti-HER2 therapy should be investigated in a subset of patients. MOC samples clustered with upper GI, yet markers to differentiate these entities remain elusive, suggesting similar underlying biology and shared treatment strategies.
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- 2023
35. Supplementary Tables S1-S11 from Gene-Expression Profiling of Mucinous Ovarian Tumors and Comparison with Upper and Lower Gastrointestinal Tumors Identifies Markers Associated with Adverse Outcomes
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Susan J. Ramus, Michael L. Friedlander, Martin Köbel, Anna DeFazio, Lyndal Anderson, Paul D.P. Pharoah, Aline Talhouk, Anna H. Wu, Karin Sundfeldt, Annette Staebler, Sue K. Park, Francesmary Modugno, Gottfried E. Konecny, Stefan Kommoss, Linda E. Kelemen, Beth Y. Karlan, Paul A. James, David G. Huntsman, Estrid Høgdall, Nicholas J. Hawkins, Jacek Gronwald, Peter A. Fasching, Philip Crowe, Paul A. Cohen, Heather Thorne, Rebekka Wiedenhoefer, Robyn L. Ward, Paul Timpson, Katrina Tang, Soseul Sung, Deepak Subramanian, Colin J.R. Stewart, Helen Steed, Mitul Shah, Clare L. Scott, Stuart Salfinger, Matthias Ruebner, Marjorie J. Riggan, Jianyu Rao, Ganendra Raj Mohan, Carmel M. Quinn, Malcolm C. Pike, John V. Pearson, Celeste Leigh Pearce, Sang-Yoon Park, Sandra Orsulic, David Morris, Suzana Mittelstadt, Parham Minoo, Janusz Menkiszak, Simone McInerny, Constantina Mateoiu, Sakshi Mahale, Jan Lubiński, Anna Linder, Belle W.X. Lim, Winston Liauw, Na Li, Yee Leung, Jenny Lester, Angela Laslavic, Tiffany Lai, Jennifer M. Koziak, Kayla Klett, Jae-Hoon Kim, Jae-Weon Kim, Byoung-Gie Kim, Catherine J. Kennedy, Mercedes Jimenez-Linan, Anna Jakubowska, Tomasz Huzarski, Claus K. Høgdall, Anusha Hettiaratchi, Arndt Hartmann, Paul R. Harnett, Marcel Grube, Charlie Gourley, Anthony J. Gill, Blake Gilks, Zhuxuan Fu, Anna Fischer, Rhonda Farrell, Ramona Erber, Esther Elishaev, Cezary Cybulski, Joshua Cohen, Dane Cheasley, Ian Campbell, James D. Brenton, Alison H. Brand, David D.L. Bowtell, Jessica Boros, Matthias W. Beckmann, Ellen Barlow, Jennifer Alsop, Adeline Tan, Angela Chou, Ksenia Chezar, Kara L. Cushing-Haugen, Andrew Berchuck, Joellen M. Schildkraut, Holly R. Harris, Jennifer A. Doherty, Kylie-Ann Mallitt, Michael S. Anglesio, Derek S. Chiu, Chi Nam Ignatius Pang, Adelyn Bolithon, Matthew Wakefield, Kylie L. Gorringe, and Nicola S. Meagher
- Abstract
Supplementary Tables S1-S11
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- 2023
36. Table S8 from A Transcriptome-Wide Association Study Among 97,898 Women to Identify Candidate Susceptibility Genes for Epithelial Ovarian Cancer Risk
- Author
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Jirong Long, Wei Zheng, Paul D.P. Pharoah, Thomas A. Sellers, Georgia Chenevix-Trench, Ellen L. Goode, Andrew Berchuck, Antonis C. Antoniou, Simon A. Gayther, Kristin K. Zorn, Drakoulis Yannoukakos, Anna H. Wu, Alicja Wolk, Emily White, Nicolas Wentzensen, Jeffrey N. Weitzel, Penelope M. Webb, Digna Velez Edwards, Ana Vega, Adriaan Vanderstichele, Elizabeth J. van Rensburg, Shelley S. Tworoger, Nadine Tung, Antonia Trichopoulou, Amanda E. Toland, Marc Tischkowitz, Mads Thomassen, Soo H. Teo, Manuel R. Teixeira, Anthony J. Swerdlow, Rebecca Sutphen, Amanda B. Spurdle, Melissa C. Southey, Honglin Song, Christian F. Singer, Jacques Simard, Weiva Sieh, Priyanka Sharma, Veronica W. Setiawan, Rita K. Schmutzler, Dale P. Sandler, Iwona K. Rzepecka, Mary Anne Rossing, Matti A. Rookus, Isabelle Romieu, Cristina Rodríguez-Antona, Gustavo C. Rodriguez, Harvey Risch, Gad Rennert, Susan J. Ramus, Miquel Angel Pujana, Catherine M. Phelan, Paolo Peterlongo, Tanja Pejovic, Petra H.M. Peeters, Michael T. Parsons, Sue K. Park, Ana Osorio, Håkan Olsson, Sara H. Olson, Olufunmilayo I. Olopade, Edith Olah, Kenneth Offit, Robert L. Nussbaum, Liene Nikitina-Zake, Finn C. Nielsen, Heli Nevanlinna, Susan L. Neuhausen, Marco Montagna, Francesmary Modugno, Melissa A. Merritt, Iain A. McNeish, Lesley McGuffog, Taymaa May, Amalia Mattiello, Douglas A. Levine, Fabienne Lesueur, Goska Leslie, Nhu D. Le, Ava Kwong, Susanne K. Kjaer, Lambertus A. Kiemeney, Linda E. Kelemen, Beth Y. Karlan, Paul James, Anna Jakubowska, Claudine Isaacs, Evgeny N. Imyanitov, David G. Huntsman, Peter J. Hulick, Antoinette Hollestelle, Claus K. Høgdall, Michelle A.T. Hildebrandt, Florian Heitz, Ute Hamann, Jacek Gronwald, Mark H. Greene, Marc T. Goodman, David E. Goldgar, Andrew K. Godwin, Graham G. Giles, Judy Garber, Patricia A. Ganz, Eitan Friedman, George Fountzilas, Renée T. Fortner, Peter A. Fasching, Diana M. Eccles, Douglas F. Easton, Thilo Dörk, Susan M. Domchek, Orland Diez, Joe Dennis, Anna deFazio, Mary B. Daly, Daniel W. Cramer, Fergus J. Couch, Kathleen B.M. Claes, Jenny Chang-Claude, Ian Campbell, Maria A. Caligo, Trinidad Caldes, Ralf Butzow, James Brenton, Line Bjorge, Javier Benitez, Daniel R. Barnes, Rosa B. Barkardottir, Elisa V. Bandera, Banu K. Arun, Hoda Anton-Culver, Irene L. Andrulis, Kirsten B. Moysich, Jamie K. Teer, Brett M. Reid, Jennifer B. Permuth, Yian A. Chen, Hae Kyung Im, Joellen M. Schildkraut, Bingshan Li, Xingyi Guo, Lang Wu, Alicia Beeghly-Fadiel, and Yingchang Lu
- Abstract
Association results between minor alleles of 467 variants incorportated in cross tissue gene expression prediction model for the gene of CRHR1.
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- 2023
37. Supplementary Table 16 from Nonequivalent Gene Expression and Copy Number Alterations in High-Grade Serous Ovarian Cancers with BRCA1 and BRCA2 Mutations
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David D. Bowtell, Gillian Mitchell, Douglas A. Levine, Gordon K. Smyth, Anna deFazio, Alexander Dobrovic, Thomas Mikeska, Heather Hondow, Dariush Etemadmoghadam, Kathryn Alsop, and Joshy George
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PDF file - 28K
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- 2023
38. Supplementary Tables 4 - 8 from Profiles of Genomic Instability in High-Grade Serous Ovarian Cancer Predict Treatment Outcome
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Ursula A. Matulonis, David D.L. Bowtell, J. Dirk Iglehart, Ross S. Berkowitz, John Quackenbush, Anna DeFazio, Gillian Mitchell, Helga B. Salvesen, Alexander Miron, Dariush Etemadmoghadam, Joyce Liu, Huiying Piao, Kathryn E. Daniels, Kathryn Alsop, Matthew Schwede, Ruiyang Tian, Aquila Fatima, Ronny Drapkin, Aedín C. Culhane, Nicolai Juul Birkbak, and Zhigang C. Wang
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PDF file, 80K, Supplementary Tables 4-8: 4. LOH patterns in three cohorts, 5A&B. FLOH and chemotherapy resistance in three cohorts, 6. BRCA mutations in the AOCS, 7. Univariate and multivariate analysis of platinum resistantce, 8. PFS in LOH subclusters and patients with BRCA mutations.
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- 2023
39. Figure S3 from Investigation of Exomic Variants Associated with Overall Survival in Ovarian Cancer
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Ellen L. Goode, Thomas A. Sellers, Brooke L. Fridley, Paul D.P. Pharoah, Catherine M. Phelan, Jennifer Permuth-Wey, Joellen M. Schildkraut, Andrew Berchuck, Argyrios Ziogas, Hannah Yang, Anna H. Wu, Lynne R. Wilkens, Christine Walsh, Allison F. Vitonis, Robert A. Vierkant, David J. van den Berg, Jonathan P. Tyrer, Pamela J. Thompson, Kathryn L. Terry, Honglin Song, Susan J. Ramus, Malcolm C. Pike, Irene Orlow, Kirsten B. Moysich, Francesmary Modugno, Janusz Menkiszak, Jan Lubinski, Jolanta Lissowska, Hui-Yi Lin, Jenny Lester, Sharon E. Johnatty, Allan Jensen, Edwin S. Iversen, Martin Gore, Aleksandra Gentry-Maharaj, Simon A. Gayther, Robert P. Edwards, Ed M. Dicks, Anna deFazio, Cezary Cybulski, Julie M. Cunningham, Michael E. Carney, Louise A. Brinton, Maria Bisogna, Yukie T. Bean, Nicolas Wentzensen, Mary Anne Rossing, Tanja Pejovic, Celeste L. Pearce, Roberta B. Ness, Usha Menon, Douglas A. Levine, Susanne K. Kjaer, Beth Y. Karlan, Jacek Gronwald, Marc T. Goodman, Jennifer A. Doherty, Daniel Cramer, Elisa V. Bandera, Hoda Anton-Culver, Madalene A. Earp, Zachary C. Fogarty, Melissa C. Larson, Yian Ann Chen, Ailith Pirie, and Stacey J. Winham
- Abstract
Supplemental Figure S 3
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- 2023
40. Table S5 from Homologous Recombination DNA Repair Pathway Disruption and Retinoblastoma Protein Loss Are Associated with Exceptional Survival in High-Grade Serous Ovarian Cancer
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Anna deFazio, David D. L. Bowtell, Brad H. Nelson, Paul Harnett, Martin Köbel, Alexander Dobrovic, Alison Brand, Michael Friedlander, Penny Blomfield, Philip Beale, Robert M. Rome, Yee C. Leung, Paul A. Cohen, Marisa Grossi, Sumitra Ananda, Anne Hamilton, Linda Mileshkin, Orla McNally, Peter F. Rambau, Prue E. Allan, Raghwa Sharma, Colin J.R. Stewart, Jillian Hung, Nicola Waddell, John V. Pearson, Sean M. Grimmond, Kaushalya Amarasinghe, Giada V. Zapparoli, Thomas Mikeska, Joy Hendley, Yoke-Eng Chiew, Sreeja R. Gadipally, Timothy Semple, Gisela Mir Arnau, Jason Li, Ann-Marie Patch, Joshy George, Katy Milne, Maartje C.A. Wouters, Elizabeth L. Christie, Valérie Garès, Val Gebski, Bo Gao, Dariush Etemadmoghadam, Catherine J. Kennedy, Catherine Emmanuel, Sian Fereday, Kathryn Alsop, and Dale W. Garsed
- Abstract
HR pathway mutations
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- 2023
41. Supplementary Tables 1 - 3 from Profiles of Genomic Instability in High-Grade Serous Ovarian Cancer Predict Treatment Outcome
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Ursula A. Matulonis, David D.L. Bowtell, J. Dirk Iglehart, Ross S. Berkowitz, John Quackenbush, Anna DeFazio, Gillian Mitchell, Helga B. Salvesen, Alexander Miron, Dariush Etemadmoghadam, Joyce Liu, Huiying Piao, Kathryn E. Daniels, Kathryn Alsop, Matthew Schwede, Ruiyang Tian, Aquila Fatima, Ronny Drapkin, Aedín C. Culhane, Nicolai Juul Birkbak, and Zhigang C. Wang
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XLS file, 509K, supplementary Tables 1-3: 1. Information from the Boston cohort, 2. Information from AOCS cohort, 3. Information from TCGA.
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- 2023
42. Data from Integrated Genome-Wide DNA Copy Number and Expression Analysis Identifies Distinct Mechanisms of Primary Chemoresistance in Ovarian Carcinomas
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David Bowtell, Matthew Meyerson, Helga B. Salvesen, Mitsuyoshi Urashima, William Sellers, Stephen Fox, Daryl Johnson, Sian Fereday, Nadia Traficante, Yoke-Eng Chiew, Kathryn Alsop, Bianca Locandro, Anna V. Tinker, Lars A. Akslen, Stephen Lade, Paul Harnett, Maria B. Raeder, Aikou Okamoto, Richard Tothill, Gad Getz, Joshy George, Craig Mermel, Rameen Beroukhim, Anna deFazio, and Dariush Etemadmoghadam
- Abstract
Purpose: A significant number of women with serous ovarian cancer are intrinsically refractory to platinum-based treatment. We analyzed somatic DNA copy number variation and gene expression data to identify key mechanisms associated with primary resistance in advanced-stage serous cancers.Experimental Design: Genome-wide copy number variation was measured in 118 ovarian tumors using high-resolution oligonucleotide microarrays. A well-defined subset of 85 advanced-stage serous tumors was then used to relate copy number variation to primary resistance to treatment. The discovery-based approach was complemented by quantitative-PCR copy number analysis of 12 candidate genes as independent validation of previously reported associations with clinical outcome. Likely copy number variation targets and tumor molecular subtypes were further characterized by gene expression profiling.Results: Amplification of 19q12, containing cyclin E (CCNE1), and 20q11.22-q13.12, mapping immediately adjacent to the steroid receptor coactivator NCOA3, was significantly associated with poor response to primary treatment. Other genes previously associated with copy number variation and clinical outcome in ovarian cancer were not associated with primary treatment resistance. Chemoresistant tumors with high CCNE1 copy number and protein expression were associated with increased cellular proliferation but so too was a subset of treatment-responsive patients, suggesting a cell-cycle independent role for CCNE1 in modulating chemoresponse. Patients with a poor clinical outcome without CCNE1 amplification overexpressed genes involved in extracellular matrix deposition.Conclusions: We have identified two distinct mechanisms of primary treatment failure in serous ovarian cancer, involving CCNE1 amplification and enhanced extracellular matrix deposition. CCNE1 copy number is validated as a dominant marker of patient outcome in ovarian cancer.
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- 2023
43. Figure S6A from Investigation of Exomic Variants Associated with Overall Survival in Ovarian Cancer
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Ellen L. Goode, Thomas A. Sellers, Brooke L. Fridley, Paul D.P. Pharoah, Catherine M. Phelan, Jennifer Permuth-Wey, Joellen M. Schildkraut, Andrew Berchuck, Argyrios Ziogas, Hannah Yang, Anna H. Wu, Lynne R. Wilkens, Christine Walsh, Allison F. Vitonis, Robert A. Vierkant, David J. van den Berg, Jonathan P. Tyrer, Pamela J. Thompson, Kathryn L. Terry, Honglin Song, Susan J. Ramus, Malcolm C. Pike, Irene Orlow, Kirsten B. Moysich, Francesmary Modugno, Janusz Menkiszak, Jan Lubinski, Jolanta Lissowska, Hui-Yi Lin, Jenny Lester, Sharon E. Johnatty, Allan Jensen, Edwin S. Iversen, Martin Gore, Aleksandra Gentry-Maharaj, Simon A. Gayther, Robert P. Edwards, Ed M. Dicks, Anna deFazio, Cezary Cybulski, Julie M. Cunningham, Michael E. Carney, Louise A. Brinton, Maria Bisogna, Yukie T. Bean, Nicolas Wentzensen, Mary Anne Rossing, Tanja Pejovic, Celeste L. Pearce, Roberta B. Ness, Usha Menon, Douglas A. Levine, Susanne K. Kjaer, Beth Y. Karlan, Jacek Gronwald, Marc T. Goodman, Jennifer A. Doherty, Daniel Cramer, Elisa V. Bandera, Hoda Anton-Culver, Madalene A. Earp, Zachary C. Fogarty, Melissa C. Larson, Yian Ann Chen, Ailith Pirie, and Stacey J. Winham
- Abstract
Supplemental Figure S 6B
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- 2023
44. Data from Acquired RAD51C Promoter Methylation Loss Causes PARP Inhibitor Resistance in High-Grade Serous Ovarian Carcinoma
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Clare L. Scott, Matthew J. Wakefield, Alexander Dobrovic, Scott H. Kaufmann, Nicola Waddell, Katia Nones, S. John Weroha, Elizabeth M. Swisher, David D.L. Bowtell, Anna DeFazio, Australian Ovarian Cancer Study, Nadia Traficante, Orla McNally, Inger Olesen, Damien Kee, Maria I. Harrell, Mohammad Reza Eftekhariyan Ghamsari, Zi Qing Chai, Ashan Musafer, Marc Radke, Kristy Shield-Artin, Nirashaa Bound, Genevieve Dall, Elizabeth Lieschke, Gwo-Yaw Ho, Cassandra J. Vandenberg, Cordelia D. McGehee, Rachel M. Hurley, Olga Kondrashova, and Ksenija Nesic
- Abstract
In high-grade serous ovarian carcinoma (HGSC), deleterious mutations in DNA repair gene RAD51C are established drivers of defective homologous recombination and are emerging biomarkers of PARP inhibitor (PARPi) sensitivity. RAD51C promoter methylation (meRAD51C) is detected at similar frequencies to mutations, yet its effects on PARPi responses remain unresolved.In this study, three HGSC patient-derived xenograft (PDX) models with methylation at most or all examined CpG sites in the RAD51C promoter show responses to PARPi. Both complete and heterogeneous methylation patterns were associated with RAD51C gene silencing and homologous recombination deficiency (HRD). PDX models lost meRAD51C following treatment with PARPi rucaparib or niraparib, where a single unmethylated copy of RAD51C was sufficient to drive PARPi resistance. Genomic copy number profiling of one of the PDX models using SNP arrays revealed that this resistance was acquired independently in two genetically distinct lineages.In a cohort of 12 patients with RAD51C-methylated HGSC, various patterns of meRAD51C were associated with genomic “scarring,” indicative of HRD history, but exhibited no clear correlations with clinical outcome. Differences in methylation stability under treatment pressure were also observed between patients, where one HGSC was found to maintain meRAD51C after six lines of therapy (four platinum-based), whereas another HGSC sample was found to have heterozygous meRAD51C and elevated RAD51C gene expression (relative to homozygous meRAD51C controls) after only neoadjuvant chemotherapy.As meRAD51C loss in a single gene copy was sufficient to cause PARPi resistance in PDX, methylation zygosity should be carefully assessed in previously treated patients when considering PARPi therapy.Significance:Homozygous RAD51C methylation is a positive predictive biomarker for sensitivity to PARP inhibitors, whereas a single unmethylated gene copy is sufficient to confer resistance.
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- 2023
45. Supplementary Figures 1 - 9 from Profiles of Genomic Instability in High-Grade Serous Ovarian Cancer Predict Treatment Outcome
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Ursula A. Matulonis, David D.L. Bowtell, J. Dirk Iglehart, Ross S. Berkowitz, John Quackenbush, Anna DeFazio, Gillian Mitchell, Helga B. Salvesen, Alexander Miron, Dariush Etemadmoghadam, Joyce Liu, Huiying Piao, Kathryn E. Daniels, Kathryn Alsop, Matthew Schwede, Ruiyang Tian, Aquila Fatima, Ronny Drapkin, Aedín C. Culhane, Nicolai Juul Birkbak, and Zhigang C. Wang
- Abstract
PDF file, 366K, Supplementary Figures 1-9: 1. LOH patterns on different array platforms, 2. Allelic imbalance in LOH clusters, 3. LOH clustering breast cancer, 4. LOH and copy number prevalence in breast cancer, 5. Chemotherapy resistance and FLOH in three cohorts, 6. Chemotherapy resistance and FLOH with or without BRCA mutations, 7. PFS regardless of stage and residual disease, 8. PFS with or without BRCA mutations, 9. BRCA1 expression and FLOH.
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- 2023
46. Supplementary Figures 1-3 from Platinum Sensitivity–Related Germline Polymorphism Discovered via a Cell-Based Approach and Analysis of Its Association with Outcome in Ovarian Cancer Patients
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M. Eileen Dolan, Georgia Chenevix-Trench, Anna deFazio, Beth Y. Karlan, Jenny Gross, Ignace Vergote, Evelyn Despierre, Diether Lambrechts, Jim Paul, Robert Brown, Kunle Odunsi, Matthew Grasela, Kirsten B. Moysich, Allan Jensen, Susanne K. Kjaer, Estrid Hogdall, Brooke L. Fridley, Robert A. Vierkant, Ellen L. Goode, Stuart MacGregor, Yi Lu, Nancy J. Cox, Soma Das, Yarden S. Fraiman, Peter H. O'Donnell, Shuangli Mi, Jonathan Beesley, Peixian Chen, Emily O. Kistner, Wei Zhang, Shiwei Duan, Dana Ziliak, Hae Kyung Im, Eric R. Gamazon, Sharon E. Johnatty, and R. Stephanie Huang
- Abstract
PDF file - 263K
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- 2023
47. Supplementary Figures 1-5, Tables 1-6 from Copy Number Aberrations in Benign Serous Ovarian Tumors: A Case for Reclassification?
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Ian G. Campbell, Kylie L. Gorringe, David G. Huntsman, Teri A. Longacre, Anna deFazio, Yoke-Eng Chiew, Nataliya Melnyk, C. Blake Gilks, Raghwa Sharma, Michael S. Anglesio, and Sally M. Hunter
- Abstract
PDF file - 409K
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- 2023
48. Table S4 from A Transcriptome-Wide Association Study Among 97,898 Women to Identify Candidate Susceptibility Genes for Epithelial Ovarian Cancer Risk
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Jirong Long, Wei Zheng, Paul D.P. Pharoah, Thomas A. Sellers, Georgia Chenevix-Trench, Ellen L. Goode, Andrew Berchuck, Antonis C. Antoniou, Simon A. Gayther, Kristin K. Zorn, Drakoulis Yannoukakos, Anna H. Wu, Alicja Wolk, Emily White, Nicolas Wentzensen, Jeffrey N. Weitzel, Penelope M. Webb, Digna Velez Edwards, Ana Vega, Adriaan Vanderstichele, Elizabeth J. van Rensburg, Shelley S. Tworoger, Nadine Tung, Antonia Trichopoulou, Amanda E. Toland, Marc Tischkowitz, Mads Thomassen, Soo H. Teo, Manuel R. Teixeira, Anthony J. Swerdlow, Rebecca Sutphen, Amanda B. Spurdle, Melissa C. Southey, Honglin Song, Christian F. Singer, Jacques Simard, Weiva Sieh, Priyanka Sharma, Veronica W. Setiawan, Rita K. Schmutzler, Dale P. Sandler, Iwona K. Rzepecka, Mary Anne Rossing, Matti A. Rookus, Isabelle Romieu, Cristina Rodríguez-Antona, Gustavo C. Rodriguez, Harvey Risch, Gad Rennert, Susan J. Ramus, Miquel Angel Pujana, Catherine M. Phelan, Paolo Peterlongo, Tanja Pejovic, Petra H.M. Peeters, Michael T. Parsons, Sue K. Park, Ana Osorio, Håkan Olsson, Sara H. Olson, Olufunmilayo I. Olopade, Edith Olah, Kenneth Offit, Robert L. Nussbaum, Liene Nikitina-Zake, Finn C. Nielsen, Heli Nevanlinna, Susan L. Neuhausen, Marco Montagna, Francesmary Modugno, Melissa A. Merritt, Iain A. McNeish, Lesley McGuffog, Taymaa May, Amalia Mattiello, Douglas A. Levine, Fabienne Lesueur, Goska Leslie, Nhu D. Le, Ava Kwong, Susanne K. Kjaer, Lambertus A. Kiemeney, Linda E. Kelemen, Beth Y. Karlan, Paul James, Anna Jakubowska, Claudine Isaacs, Evgeny N. Imyanitov, David G. Huntsman, Peter J. Hulick, Antoinette Hollestelle, Claus K. Høgdall, Michelle A.T. Hildebrandt, Florian Heitz, Ute Hamann, Jacek Gronwald, Mark H. Greene, Marc T. Goodman, David E. Goldgar, Andrew K. Godwin, Graham G. Giles, Judy Garber, Patricia A. Ganz, Eitan Friedman, George Fountzilas, Renée T. Fortner, Peter A. Fasching, Diana M. Eccles, Douglas F. Easton, Thilo Dörk, Susan M. Domchek, Orland Diez, Joe Dennis, Anna deFazio, Mary B. Daly, Daniel W. Cramer, Fergus J. Couch, Kathleen B.M. Claes, Jenny Chang-Claude, Ian Campbell, Maria A. Caligo, Trinidad Caldes, Ralf Butzow, James Brenton, Line Bjorge, Javier Benitez, Daniel R. Barnes, Rosa B. Barkardottir, Elisa V. Bandera, Banu K. Arun, Hoda Anton-Culver, Irene L. Andrulis, Kirsten B. Moysich, Jamie K. Teer, Brett M. Reid, Jennifer B. Permuth, Yian A. Chen, Hae Kyung Im, Joellen M. Schildkraut, Bingshan Li, Xingyi Guo, Lang Wu, Alicia Beeghly-Fadiel, and Yingchang Lu
- Abstract
Association results after the adjustment for nearby GWAS index SNPs for genes with predicted gene expression levels associated with ovarian cancer risk at P < 2.21E-6.
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- 2023
49. Table S4 from Homologous Recombination DNA Repair Pathway Disruption and Retinoblastoma Protein Loss Are Associated with Exceptional Survival in High-Grade Serous Ovarian Cancer
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Anna deFazio, David D. L. Bowtell, Brad H. Nelson, Paul Harnett, Martin Köbel, Alexander Dobrovic, Alison Brand, Michael Friedlander, Penny Blomfield, Philip Beale, Robert M. Rome, Yee C. Leung, Paul A. Cohen, Marisa Grossi, Sumitra Ananda, Anne Hamilton, Linda Mileshkin, Orla McNally, Peter F. Rambau, Prue E. Allan, Raghwa Sharma, Colin J.R. Stewart, Jillian Hung, Nicola Waddell, John V. Pearson, Sean M. Grimmond, Kaushalya Amarasinghe, Giada V. Zapparoli, Thomas Mikeska, Joy Hendley, Yoke-Eng Chiew, Sreeja R. Gadipally, Timothy Semple, Gisela Mir Arnau, Jason Li, Ann-Marie Patch, Joshy George, Katy Milne, Maartje C.A. Wouters, Elizabeth L. Christie, Valérie Garès, Val Gebski, Bo Gao, Dariush Etemadmoghadam, Catherine J. Kennedy, Catherine Emmanuel, Sian Fereday, Kathryn Alsop, and Dale W. Garsed
- Abstract
TP53 mutations
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- 2023
50. Supplementary Figures 1-5, Tables 1-8 from Genome-wide Analysis Identifies Novel Loci Associated with Ovarian Cancer Outcomes: Findings from the Ovarian Cancer Association Consortium
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Georgia Chenevix-Trench, Penelope M. Webb, Anna deFazio, Ellen L. Goode, Paul D.P. Pharoah, Stuart MacGregor, Andrew Berchuck, Yoke-Eng Chiew, Catherine Kennedy, Thomas Sellers, Rosalind Glasspool, Nadeem Siddiqui, Karen Carty, James Paul, Ian McNeish, Lene Lundvall, Claus Høgdall, Yukie Bean, Tanja Pejovic, Irene Orlow, Elisa V. Bandera, Daniel W. Cramer, Kathryn L. Terry, Edwin S. Iversen, Joellen M. Schildkraut, Robert A. Vierkant, Julie M. Cunningham, Brooke L. Fridley, Susanne Kruger Kjaer, Allan Jensen, Estrid Høgdall, Zachary C. Fogarty, Melissa C. Larson, Madalene Earp, Stacey J. Winham, Sandra Orsulic, Jenny Lester, Christine Walsh, Beth Y. Karlan, Peter Hillemanns, Jacobus Pisterer, Philipp Harter, Ira Schwaab, Andreas du Bois, Florian Heitz, Pamela J. Thompson, Michael E. Carney, Lynne R. Wilkens, Marc T. Goodman, Beata Spiewankiewicz, Iwona K. Rzepecka, Agnieszka Dansonka-Mieszkowska, Jolanta Kupryjanczyk, Anna H. Wu, Daniel O. Stram, Malcolm C. Pike, Celeste L. Pearce, Susan J. Ramus, Usha Menon, Aleksandra Gentry-Maharaj, Simon A. Gayther, Argyrios Ziogas, Hoda Anton-Culver, Rebecca Sutphen, Joseph H. Rothstein, Valerie McGuire, Alice S. Whittemore, Weiva Sieh, Diana Eccles, Ian Campbell, Valerie Rhenius, Honglin Song, Nicolas Wentzensen, Jolanta Lissowska, Louise Brinton, Cezary Cybulski, Anna Jakubowska, Jan Lubiński, Jacek Gronwald, Leon F.A.G. Massuger, Lambertus A. Kiemeney, Douglas A. Levine, Kirsten B. Moysich, Roberta B. Ness, Francesmary Modugno, Jenny Chang-Claude, Jennifer A. Doherty, Mary Anne Rossing, Sandrina Lambrechts, Ignace Vergote, Els Van Nieuwenhuysen, Diether Lambrechts, Matthias W. Beckmann, Arif B. Ekici, Alexander Hein, Peter A. Fasching, Bo Gao, Yi Lu, Jonathan Beesley, Siddhartha Kar, Jonathan P. Tyrer, and Sharon E. Johnatty
- Abstract
Supplementary Figures 1-5, Tables 1-8. Supplementary Figure 1: Overview of the analytic approach. Supplementary Figure 2: QQ plots of SNPs with MAF ≥0.02 and imputation r2 ≥0.9 associated with Overall Survival in A. Supplementary Figure 3: ‘All OCAC’ histology-adjusted analysis. Supplementary Figure 4: Forest plots of promising SNPs. Supplementary Figure 5: KM-Plotter graphs of significant associations with outcome. Supplementary Table 1: All studies (OCAC & TCGA) eligible for analyses according to first-line chemotherapy. Supplementary Table 2: Description of individual OCAC studies included in the secondary 'all OCAC' analysis. Supplementary Table 3a: Overall Survival estimates for selected SNPs (MAF ≥0.02) comparing iCOGS imputed (r2 ≥0.3) and iPLEX genotyped samples. Supplementary Table 3b: Progression-free Survival estimates for selected SNPs (MAF ≥0.02) comparing iCOGS imputed (r2 ≥0.3) and iPLEX genotyped samples. Supplementary Table 4: SNPs with imputation r2 ≥0.9, EAF ≥0.02 and p ≤ 1E-05 for at least one of four outcomes analyzed in cases selected according to first-line chemotherapy. Supplementary Table 5: Meta-analysis of largest possible sample (TCGA, non-overlapping iCOGS and iplex genotyped) for selected promising SNPs analyzed in cases selected according to first-line chemotherapy. Supplementary Table 6: Significant association between protein-coding genes within 1Mb of promising SNPs and ovarian cancer outcomes. Supplementary Table 7: SNPs with imputation r-sq≥0.9 and p ≤ 1E-05 for Overall Survival in histology-adj 'all OCAC' analysis. Supplementary Table 8: iCOGS estimates for SNPs previously identified to be associated with response to chemotherapy as reported in the aNHGRI GWAS catalog.
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- 2023
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