17 results on '"McLean, Catriona A"'
Search Results
2. Whole-genome sequencing analysis reveals new susceptibility loci and structural variants associated with progressive supranuclear palsy
- Author
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Wang, Hui, Chang, Timothy S., Dombroski, Beth A., Cheng, Po-Liang, Patil, Vishakha, Valiente-Banuet, Leopoldo, Farrell, Kurt, Mclean, Catriona, Molina-Porcel, Laura, Rajput, Alex, De Deyn, Peter Paul, Le Bastard, Nathalie, Gearing, Marla, Kaat, Laura Donker, Van Swieten, John C., Dopper, Elise, Ghetti, Bernardino F., Newell, Kathy L., Troakes, Claire, de Yébenes, Justo G., Rábano-Gutierrez, Alberto, Meller, Tina, Oertel, Wolfgang H., Respondek, Gesine, Stamelou, Maria, Arzberger, Thomas, Roeber, Sigrun, Müller, Ulrich, Hopfner, Franziska, Pastor, Pau, Brice, Alexis, Durr, Alexandra, Le Ber, Isabelle, Beach, Thomas G., Serrano, Geidy E., Hazrati, Lili-Naz, Litvan, Irene, Rademakers, Rosa, Ross, Owen A., Galasko, Douglas, Boxer, Adam L., Miller, Bruce L., Seeley, Willian W., Van Deerlin, Vivanna M., Lee, Edward B., White, III, Charles L., Morris, Huw, de Silva, Rohan, Crary, John F., Goate, Alison M., Friedman, Jeffrey S., Leung, Yuk Yee, Coppola, Giovanni, Naj, Adam C., Wang, Li-San, Dalgard, Clifton, Dickson, Dennis W., Höglinger, Günter U., Schellenberg, Gerard D., Geschwind, Daniel H., and Lee, Wan-Ping
- Published
- 2024
- Full Text
- View/download PDF
3. Microglial ferroptotic stress causes non-cell autonomous neuronal death
- Author
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Liddell, Jeffrey R., Hilton, James B. W., Kysenius, Kai, Billings, Jessica L., Nikseresht, Sara, McInnes, Lachlan E., Hare, Dominic J., Paul, Bence, Mercer, Stephen W., Belaidi, Abdel A., Ayton, Scott, Roberts, Blaine R., Beckman, Joseph S., McLean, Catriona A., White, Anthony R., Donnelly, Paul S., Bush, Ashley I., and Crouch, Peter J.
- Published
- 2024
- Full Text
- View/download PDF
4. Common variants in breast cancer risk loci predispose to distinct tumor subtypes
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Ahearn, Thomas U., Zhang, Haoyu, Michailidou, Kyriaki, Milne, Roger L., Bolla, Manjeet K., Dennis, Joe, Dunning, Alison M., Lush, Michael, Wang, Qin, Andrulis, Irene L., Anton-Culver, Hoda, Arndt, Volker, Aronson, Kristan J., Auer, Paul L., Augustinsson, Annelie, Baten, Adinda, Becher, Heiko, Behrens, Sabine, Benitez, Javier, Bermisheva, Marina, Blomqvist, Carl, Bojesen, Stig E., Bonanni, Bernardo, Børresen-Dale, Anne-Lise, Brauch, Hiltrud, Brenner, Hermann, Brooks-Wilson, Angela, Brüning, Thomas, Burwinkel, Barbara, Buys, Saundra S., Canzian, Federico, Castelao, Jose E., Chang-Claude, Jenny, Chanock, Stephen J., Chenevix-Trench, Georgia, Clarke, Christine L., Collée, J. Margriet, Cox, Angela, Cross, Simon S., Czene, Kamila, Daly, Mary B., Devilee, Peter, Dörk, Thilo, Dwek, Miriam, Eccles, Diana M., Evans, D. Gareth, Fasching, Peter A., Figueroa, Jonine, Floris, Giuseppe, Gago-Dominguez, Manuela, Gapstur, Susan M., García-Sáenz, José A., Gaudet, Mia M., Giles, Graham G., Goldberg, Mark S., González-Neira, Anna, Alnæs, Grethe I. Grenaker, Grip, Mervi, Guénel, Pascal, Haiman, Christopher A., Hall, Per, Hamann, Ute, Harkness, Elaine F., Heemskerk-Gerritsen, Bernadette A. M., Holleczek, Bernd, Hollestelle, Antoinette, Hooning, Maartje J., Hoover, Robert N., Hopper, John L., Howell, Anthony, Jakimovska, Milena, Jakubowska, Anna, John, Esther M., Jones, Michael E., Jung, Audrey, Kaaks, Rudolf, Kauppila, Saila, Keeman, Renske, Khusnutdinova, Elza, Kitahara, Cari M., Ko, Yon-Dschun, Koutros, Stella, Kristensen, Vessela N., Krüger, Ute, Kubelka-Sabit, Katerina, Kurian, Allison W., Kyriacou, Kyriacos, Lambrechts, Diether, Lee, Derrick G., Lindblom, Annika, Linet, Martha, Lissowska, Jolanta, Llaneza, Ana, Lo, Wing-Yee, MacInnis, Robert J., Mannermaa, Arto, Manoochehri, Mehdi, Margolin, Sara, Martinez, Maria Elena, McLean, Catriona, Meindl, Alfons, Menon, Usha, Nevanlinna, Heli, Newman, William G., Nodora, Jesse, Offit, Kenneth, Olsson, Håkan, Orr, Nick, Park-Simon, Tjoung-Won, Patel, Alpa V., Peto, Julian, Pita, Guillermo, Plaseska-Karanfilska, Dijana, Prentice, Ross, Punie, Kevin, Pylkäs, Katri, Radice, Paolo, Rennert, Gad, Romero, Atocha, Rüdiger, Thomas, Saloustros, Emmanouil, Sampson, Sarah, Sandler, Dale P., Sawyer, Elinor J., Schmutzler, Rita K., Schoemaker, Minouk J., Schöttker, Ben, Sherman, Mark E., Shu, Xiao-Ou, Smichkoska, Snezhana, Southey, Melissa C., Spinelli, John J., Swerdlow, Anthony J., Tamimi, Rulla M., Tapper, William J., Taylor, Jack A., Teras, Lauren R., Terry, Mary Beth, Torres, Diana, Troester, Melissa A., Vachon, Celine M., van Deurzen, Carolien H. M., van Veen, Elke M., Wagner, Philippe, Weinberg, Clarice R., Wendt, Camilla, Wesseling, Jelle, Winqvist, Robert, Wolk, Alicja, Yang, Xiaohong R., Zheng, Wei, Couch, Fergus J., Simard, Jacques, Kraft, Peter, Easton, Douglas F., Pharoah, Paul D. P., Schmidt, Marjanka K., García-Closas, Montserrat, and Chatterjee, Nilanjan
- Published
- 2022
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- View/download PDF
5. Evaluation of FGFR targeting in breast cancer through interrogation of patient-derived models
- Author
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Chew, Nicole J., Lim Kam Sian, Terry C. C., Nguyen, Elizabeth V., Shin, Sung-Young, Yang, Jessica, Hui, Mun N., Deng, Niantao, McLean, Catriona A., Welm, Alana L., Lim, Elgene, Gregory, Peter, Nottle, Tim, Lang, Tali, Vereker, Melissa, Richardson, Gary, Kerr, Genevieve, Micati, Diana, Jardé, Thierry, Abud, Helen E., Lee, Rachel S., Swarbrick, Alex, and Daly, Roger J.
- Published
- 2021
- Full Text
- View/download PDF
6. Association of variably methylated tumour DNA regions with overall survival for invasive lobular breast cancer
- Author
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Suman, Medha, Dugué, Pierre-Antoine, Wong, Ee Ming, Joo, JiHoon Eric, Hopper, John L., Nguyen-Dumont, Tu, Giles, Graham G., Milne, Roger L., McLean, Catriona, and Southey, Melissa C.
- Published
- 2021
- Full Text
- View/download PDF
7. Distribution of Parkinson’s disease associated RAB39B in mouse brain tissue
- Author
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Gao, Yujing, Wilson, Gabrielle R., Stephenson, Sarah E. M., Oulad-Abdelghani, Mustapha, Charlet-Berguerand, Nicolas, Bozaoglu, Kiymet, McLean, Catriona A., Thomas, Paul Q., Finkelstein, David I., and Lockhart, Paul J.
- Published
- 2020
- Full Text
- View/download PDF
8. Comparison of amyloid PET measured in Centiloid units with neuropathological findings in Alzheimer’s disease
- Author
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Amadoru, Sanka, Doré, Vincent, McLean, Catriona A., Hinton, Fairlie, Shepherd, Claire E., Halliday, Glenda M., Leyton, Cristian E., Yates, Paul A., Hodges, John R., Masters, Colin L., Villemagne, Victor L., and Rowe, Christopher C.
- Published
- 2020
- Full Text
- View/download PDF
9. Gastric adenocarcinoma causing biliary obstruction without ductal dilatation: a case report
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Vaz, Karl, Luber, Raphael P., McLean, Catriona, Gerstenmaier, Jan Frank, and Roberts, Stuart K.
- Published
- 2019
- Full Text
- View/download PDF
10. Reversal of end-stage heart failure in juvenile hemochromatosis with iron chelation therapy: a case report.
- Author
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Cooray, Shamil D., Heerasing, Neel M., Selkrig, Laura A., Subramaniam, V. Nathan, Hamblin, P. Shane, McDonald, Cameron J., McLean, Catriona A., McNamara, Elissa, Leet, Angeline S., and Roberts, Stuart K.
- Subjects
HEART failure ,HEMOCHROMATOSIS ,EXTRACORPOREAL membrane oxygenation ,CHELATION therapy ,MUSCLE cells - Abstract
Background: Juvenile hemochromatosis is the most severe form of iron overloading phenotype. Although rare, it should be suspected in patients who present with hypogonadotropic hypogonadism, diabetes mellitus, or cardiomyopathy without a clear cause.Case Presentation: A young Serbian male presenting with end-stage heart failure was referred for extracorporeal membrane oxygenation. An endomyocardial biopsy revealed cytoplasmic iron deposits in myocytes. His condition was stabilized with biventricular assist devices and he was listed for heart transplantation. Iron chelation therapy was commenced and resulted in rapid removal of iron burden. Serial outpatient echocardiograms demonstrated myocardial recovery such that a successful biventricular assist device explant occurred 131 days after initial implant. Targeted gene sequencing revealed a loss-of-function mutation within the HJV gene, which is consistent with juvenile hemochromatosis.Conclusions: This rare case of a patient with juvenile hemochromatosis associated with a HJV mutation provides histologic evidence documenting the reversal of associated end-stage heart failure, requiring emergent mechanical circulatory support, with iron chelation therapy. [ABSTRACT FROM AUTHOR]- Published
- 2018
- Full Text
- View/download PDF
11. Iatrogenic Creutzfeldt-Jakob disease with Amyloid-β pathology: an international study.
- Author
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Cali, Ignazio, Cohen, Mark L., Haїk, Stéphane, Parchi, Piero, Giaccone, Giorgio, Collins, Steven J., Kofskey, Diane, Wang, Han, McLean, Catriona A., Brandel, Jean-Philippe, Privat, Nicolas, Sazdovitch, Véronique, Duyckaerts, Charles, Kitamoto, Tetsuyuki, Belay, Ermias D., Maddox, Ryan A., Tagliavini, Fabrizio, Pocchiari, Maurizio, Leschek, Ellen, and Appleby, Brian S.
- Subjects
CREUTZFELDT-Jakob disease ,CEREBRAL amyloid angiopathy ,AMYLOID - Abstract
The presence of pathology related to the deposition of amyloid-β (Aβ) has been recently reported in iatrogenic Creutzfeldt-Jakob disease (iCJD) acquired from inoculation of growth hormone (GH) extracted from human cadaveric pituitary gland or use of cadaveric dura mater (DM) grafts. To investigate this phenomenon further, a cohort of 27 iCJD cases - 21 with adequate number of histopathological sections -originating from Australia, France, Italy and the Unites States, were examined by immunohistochemistry, amyloid staining and Western blot analysis of the scrapie prion protein (PrPSc) and compared with age-group matched cases of sporadic CJD (sCJD), Alzheimer disease (AD) or free of neurodegenerative diseases (non-ND). Cases of iCJD and sCJD shared similar profiles of proteinase K-resistant PrPSc with the exception of iCJD harboring the "MMi" phenotype. Cerebral amyloid angiopathy (CAA), either associated with, or free of, Thioflavin S-positive amyloid core plaques (CP), was observed in 52% of 21 cases of iCJD, which comprised 37.5% and 61.5% of the cases of GH and DM-iCJD, respectively. If only cases younger than 54 years were considered, Aβ pathology affected 41%, 2% and 0% of iCJD, sCJD and non-ND, respectively. Despite the patient's younger age CAA was more severe in iCJD than sCJD, while Aβ diffuse plaques, in absence of Aβ CP, populated one third of sCJD. Aβ pathology was by far most severe in AD. Tau pathology was scanty in iCJD and sCJD. In conclusion, (i) despite the divergences in the use of cadaveric GH and DM products, our cases combined with previous studies showed remarkably similar iCJD and Aβ phenotypes indicating that the occurrence of Aβ pathology in iCJD is a widespread phenomenon, (ii) CAA emerges as the hallmark of the Aβ phenotype in iCJD since it is observed in nearly 90% of all iCJD with Aβ pathology reported to date including ours and it is shared by GH and DM-iCJD, (iii) although the contributions to Aβ pathology of other factors, including GH deficiency, cannot be discounted, our findings increase the mounting evidence that this pathology is acquired by a mechanism resembling that of prion diseases. [ABSTRACT FROM AUTHOR]
- Published
- 2018
- Full Text
- View/download PDF
12. Mammographic density and risk of breast cancer by tumor characteristics: a case-control study.
- Author
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Krishnan, Kavitha, Baglietto, Laura, Stone, Jennifer, McLean, Catriona, Southey, Melissa C., English, Dallas R., Giles, Graham G., and Hopper, John L.
- Subjects
BREAST cancer diagnosis ,MAMMOGRAMS ,BODY mass index ,EARLY detection of cancer ,CASE-control method ,BREAST ,BREAST tumors ,LONGITUDINAL method ,RESEARCH funding ,ACQUISITION of data - Abstract
Background: In a previous paper, we had assumed that the risk of screen-detected breast cancer mostly reflects inherent risk, and the risk of whether a breast cancer is interval versus screen-detected mostly reflects risk of masking. We found that inherent risk was predicted by body mass index (BMI) and dense area (DA) or percent dense area (PDA), but not by non-dense area (NDA). Masking, however, was best predicted by PDA but not BMI. In this study, we aimed to investigate if these associations vary by tumor characteristics and mode of detection.Methods: We conducted a case-control study nested within the Melbourne Collaborative Cohort Study of 244 screen-detected cases matched to 700 controls and 148 interval cases matched to 446 controls. DA, NDA and PDA were measured using the Cumulus software. Tumor characteristics included size, grade, lymph node involvement, and ER, PR, and HER2 status. Conditional and unconditional logistic regression were applied as appropriate to estimate the Odds per Adjusted Standard Deviation (OPERA) adjusted for age and BMI, allowing the association with BMI to be a function of age at diagnosis.Results: For screen-detected cancer, both DA and PDA were associated to an increased risk of tumors of large size (OPERA ~ 1.6) and positive lymph node involvement (OPERA ~ 1.8); no association was observed for BMI and NDA. For risk of interval versus screen-detected breast cancer, the association with risk for any of the three mammographic measures did not vary by tumor characteristics; an association was observed for BMI for positive lymph nodes (OPERA ~ 0.6). No associations were observed for tumor grade and ER, PR and HER2 status of tumor.Conclusions: Both DA and PDA were predictors of inherent risk of larger breast tumors and positive nodal status, whereas for each of the three mammographic density measures the association with risk of masking did not vary by tumor characteristics. This might raise the hypothesis that the risk of breast tumours with poorer prognosis, such as larger and node positive tumours, is intrinsically associated with increased mammographic density and not through delay of diagnosis due to masking. [ABSTRACT FROM AUTHOR]- Published
- 2017
- Full Text
- View/download PDF
13. Rubidium and potassium levels are altered in Alzheimer's disease brain and blood but not in cerebrospinal fluid.
- Author
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Roberts, Blaine R., Doecke, James D., Rembach, Alan, Yévenes, L. Fernanda, Fowler, Christopher J., McLean, Catriona A., Lind, Monica, Volitakis, Irene, Masters, Colin L., Bush, Ashley I., and Hare, Dominic J.
- Subjects
ALZHEIMER'S disease ,POTASSIUM in the body ,RUBIDIUM - Abstract
Loss of intracellular compartmentalization of potassium is a biochemical feature of Alzheimer's disease indicating a loss of membrane integrity and mitochondrial dysfunction. We examined potassium and rubidium (a biological proxy for potassium) in brain tissue, blood fractions and cerebrospinal fluid from Alzheimer's disease and healthy control subjects to investigate the diagnostic potential of these two metal ions. We found that both potassium and rubidium levels were significantly decreased across all intracellular compartments in the Alzheimer's disease brain. Serum from over 1000 participants in the Australian Imaging, Biomarkers and Lifestyle Flagship Study of Ageing (AIBL), showed minor changes according to disease state. Potassium and rubidium levels in erythrocytes and cerebrospinal fluid were not significantly different according to disease state, and rubidium was slightly decreased in Alzheimer's disease patients compared to healthy controls. Our data provides evidence that contrasts the hypothesized disruption of the blood-brain barrier in Alzheimer's disease, with the systemic decrease in cortical potassium and rubidium levels suggesting influx of ions from the blood is minimal and that the observed changes are more likely indicative of an internal energy crisis within the brain. These findings may be the basis for potential diagnostic imaging studies using radioactive potassium and rubidium tracers. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
- View/download PDF
14. Tools for translational epigenetic studies involving formalin-fixed paraffin-embedded human tissue: applying the Infinium HumanMethyation450 Beadchip assay to large population-based studies.
- Author
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Ee Ming Wong, Joo, JiHoon E., McLean, Catriona A., Baglietto, Laura, English, Dallas R., Severi, Gianluca, Hopper, John L., Milne, Roger L., FitzGerald, Liesel M., Giles, Graham G., and Southey, Melissa C.
- Subjects
EPIGENETICS ,TISSUE physiology ,METHYLATION ,IMMUNOASSAY ,IMMUNOENZYME technique - Abstract
Background: Large population-based translational epigenetic studies are emerging due to recent technological advances that have made molecular analyses possible. For example, the Infinium HumanMethylation450 Beadchip (HM450K) has enabled studies of genome-wide methylation on a scale not previously possible. However, application of the HM450K to DNA extracted from formalin-fixed paraffin-embedded (FFPE) tumour material has been more challenging than application to high quality DNA extracted from blood. To facilitate the application of this assay consistently across a large number of FFPE tumour-enriched DNA samples we have devised a modification to the HM450K protocol for FFPE that includes an additional quality control (QC) checkpoint. Results: QC checkpoint 3 was designed to assess the presence of DNA after bisulfite conversion and restoration, just prior to application of the HM450K assay. DNA was extracted from 474 archival FFPE breast tumour material. Five samples did not have a detectable amount of DNA with an additional 42 failing to progress past QC checkpoint 3. Genome-wide methylation was measured for the remaining 428 tumour-enriched DNA. Of these, only 4 samples failed our stringent HM450K data criteria thus representing a 99 % success rate. Using prior knowledge about methylation marks associated with breast cancer we further explored the quality of the data. Twenty probes in the BRCA1 promoter region showed increased methylation in triple-negative breast cancers compared to Luminal A, Luminal B and HER2-positive breast cancer subtypes. Validation of this observation in published data from The Cancer Genome Atlas (TCGA) Network (obtained from DNA extracted from fresh frozen tumour samples) confirms the quality of the data obtained from the improved protocol. Conclusions: The modified protocol is suitable for the analysis of FFPE tumour-enriched DNA and can be systematically applied to hundreds of samples. This protocol will have utility in population-based translational epigenetic studies and is applicable to a wide variety of translated studies interested in analysis of methylation and its role in the predisposition to disease and disease progression. [ABSTRACT FROM AUTHOR]
- Published
- 2015
- Full Text
- View/download PDF
15. Assessing THK523 selectivity for tau deposits in Alzheimer's disease and non Alzheimer's disease tauopathies.
- Author
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Fodero-Tavoletti, Michelle T., Shozo Furumoto, Taylor, Leanne, McLean, Catriona A., Mulligan, Rachel S., Birchall, Ian, Ryuichi Harada, Masters, Colin L., Kazuhiko Yanai, Yukitsuka Kudo, Rowe, Christopher C., Nobuyuki Okamura, and Villemagne, Victor L.
- Subjects
TAU proteins ,ALZHEIMER'S disease ,AUDITORY evoked response ,PROGRESSIVE supranuclear palsy ,PRESENILE dementia ,NEURODEGENERATION - Abstract
Introduction The introduction of tau imaging agents such as
18 F-THK523, offers new hope for the in vivo assessment of tau deposition in tauopathies such as Alzheimer's disease (AD), where preliminary18 F-THK523-PET studies demonstrated significantly higher cortical retention of18 F-THK523 in AD compared to age-matched healthy individuals. In addition to AD, tau imaging with PET may also be of value to assess non-AD tauopathies, such as corticobasal degeneration (CBD), progressive supranuclear palsy (PSP) and Pick's disease (PiD). Methods To further investigate the ability of THK523 to recognize tau lesions, we undertook immunohistochemical and fluorescent studies in serial brain sections from AD (n = 3), CBD (n = 2), PSP (n = 1), PiD (n = 2) and Parkinson's disease (PD, n = 2). In addition to the neuropathological analysis, one PSP patient had undergone a 18F-THK523 PET scan five months before death. Results While THK523 labeled tau-containing lesions such as neurofibrillary tangles and neuropil threads in the hippocampus and frontal regions of AD brains, it failed to label tau-containing lesions in non-AD tauopathies. Furthermore, while THK523 faintly labeled dense cored amyloid-beta plaques in the AD frontal cortex, it failed to label a-synuclein containing Lewy bodies in PD brain sections. Conclusion This study suggests that 18F-THK523 selectively binds to paired helical filament-tau in AD brains but does not bind to tau lesions in non-AD tauopathies, nor to a-synuclein in PD brains. [ABSTRACT FROM AUTHOR]- Published
- 2014
- Full Text
- View/download PDF
16. Common germline polymorphisms associated with breast cancer-specific survival
- Author
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Pirie, Ailith, Guo, Qi, Kraft, Peter, Canisius, Sander, Eccles, Diana M, Rahman, Nazneen, Nevanlinna, Heli, Chen, Constance, Khan, Sofia, Tyrer, Jonathan, Bolla, Manjeet K, Wang, Qin, Dennis, Joe, Michailidou, Kyriaki, Lush, Michael, Dunning, Alison M, Shah, Mitul, Czene, Kamila, Darabi, Hatef, Eriksson, Mikael, Lambrechts, Dieter, Weltens, Caroline, Leunen, Karin, van Ongeval, Chantal, Nordestgaard, Børge G, Nielsen, Sune F, Flyger, Henrik, Rudolph, Anja, Seibold, Petra, Flesch-Janys, Dieter, Blomqvist, Carl, Aittomäki, Kristiina, Fagerholm, Rainer, Muranen, Taru A, Olsen, Janet E, Hallberg, Emily, Vachon, Celine, Knight, Julia A, Glendon, Gord, Mulligan, Anna Marie, Broeks, Annegien, Cornelissen, Sten, Haiman, Christopher A, Henderson, Brian E, Schumacher, Frederick, Le Marchand, Loic, Hopper, John L, Tsimiklis, Helen, Apicella, Carmel, Southey, Melissa C, Cross, Simon S, Reed, Malcolm WR, Giles, Graham G, Milne, Roger L, McLean, Catriona, Winqvist, Robert, Pylkäs, Katri, Jukkola-Vuorinen, Arja, Grip, Mervi, Hooning, Maartje J, Hollestelle, Antoinette, Martens, John WM, van den Ouweland, Ans MW, Marme, Federick, Schneeweiss, Andreas, Yang, Rongxi, Burwinkel, Barbara, Figueroa, Jonine, Chanock, Stephen J, Lissowska, Jolanta, Sawyer, Elinor J, Tomlinson, Ian, Kerin, Michael J, Miller, Nicola, Brenner, Hermann, Butterbach, Katja, Holleczek, Bernd, Kataja, Vesa, Kosma, Veli-Matti, Hartikainen, Jaana M, Li, Jingmei, Brand, Judith S, Humphreys, Keith, Devilee, Peter, Tollenaar, Robert AEM, Seynaeve, Caroline, Radice, Paolo, Peterlongo, Paolo, Manoukian, Siranoush, Ficarazzi, Filomena, Beckmann, Matthias W, Hein, Alexander, Ekici, Arif B, Balleine, Rosemary, Phillips, Kelly-Anne, Benitez, Javier, Zamora, M Pilar, Perez, Jose Ignacio Arias, Menéndez, Primitiva, Jakubowska, Anna, Lubinski, Jan, Gronwald, Jacek, Durda, Katarzyna, Hamann, Ute, Kabisch, Maria, Ulmer, Hans Ulrich, Rüdiger, Thomas, Margolin, Sara, Kristensen, Vessela, Nord, Siljie, Evans, D Gareth, Abraham, Jean, Earl, Helena, Poole, Christopher J, Hiller, Louise, Dunn, Janet A, Bowden, Sarah, Yang, Rose, Campa, Daniele, Diver, W Ryan, Gapstur, Susan M, Gaudet, Mia M, Hankinson, Susan, Hoover, Robert N, Hüsing, Anika, Kaaks, Rudolf, Machiela, Mitchell J, Willett, Walter, Barrdahl, Myrto, Canzian, Federico, Chin, Suet-Feung, Caldas, Carlos, Hunter, David J, Lindstrom, Sara, Garcia-Closas, Montserrat, Couch, Fergus J, Chenevix-Trench, Georgia, Mannermaa, Arto, Andrulis, Irene L, Hall, Per, Chang-Claude, Jenny, Easton, Douglas F, Bojesen, Stig E, Cox, Angela, Fasching, Peter A, Pharoah, Paul DP, and Schmidt, Marjanka K
- Abstract
Introduction: Previous studies have identified common germline variants nominally associated with breast cancer survival. These associations have not been widely replicated in further studies. The purpose of this study was to evaluate the association of previously reported SNPs with breast cancer-specific survival using data from a pooled analysis of eight breast cancer survival genome-wide association studies (GWAS) from the Breast Cancer Association Consortium. Methods: A literature review was conducted of all previously published associations between common germline variants and three survival outcomes: breast cancer-specific survival, overall survival and disease-free survival. All associations that reached the nominal significance level of P value <0.05 were included. Single nucleotide polymorphisms that had been previously reported as nominally associated with at least one survival outcome were evaluated in the pooled analysis of over 37,000 breast cancer cases for association with breast cancer-specific survival. Previous associations were evaluated using a one-sided test based on the reported direction of effect. Results: Fifty-six variants from 45 previous publications were evaluated in the meta-analysis. Fifty-four of these were evaluated in the full set of 37,954 breast cancer cases with 2,900 events and the two additional variants were evaluated in a reduced sample size of 30,000 samples in order to ensure independence from the previously published studies. Five variants reached nominal significance (P <0.05) in the pooled GWAS data compared to 2.8 expected under the null hypothesis. Seven additional variants were associated (P <0.05) with ER-positive disease. Conclusions: Although no variants reached genome-wide significance (P <5 x 10−8), these results suggest that there is some evidence of association between candidate common germline variants and breast cancer prognosis. Larger studies from multinational collaborations are necessary to increase the power to detect associations, between common variants and prognosis, at more stringent significance levels. Electronic supplementary material The online version of this article (doi:10.1186/s13058-015-0570-7) contains supplementary material, which is available to authorized users.
- Published
- 2015
- Full Text
- View/download PDF
17. Tools for translational epigenetic studies involving formalin-fixed paraffin-embedded human tissue: applying the Infinium HumanMethyation450 Beadchip assay to large population-based studies.
- Author
-
Wong EM, Joo JE, McLean CA, Baglietto L, English DR, Severi G, Hopper JL, Milne RL, FitzGerald LM, Giles GG, and Southey MC
- Subjects
- Adult, Aged, BRCA1 Protein genetics, Cohort Studies, DNA Methylation, DNA, Neoplasm genetics, Female, Fixatives, Formaldehyde, Gene Expression, Humans, Middle Aged, Oligonucleotide Array Sequence Analysis instrumentation, Paraffin Embedding, Tissue Fixation, Triple Negative Breast Neoplasms genetics, Triple Negative Breast Neoplasms metabolism, BRCA1 Protein metabolism, DNA, Neoplasm metabolism, Epigenesis, Genetic, Genome, Human, Oligonucleotide Array Sequence Analysis methods, Triple Negative Breast Neoplasms diagnosis
- Abstract
Background: Large population-based translational epigenetic studies are emerging due to recent technological advances that have made molecular analyses possible. For example, the Infinium HumanMethylation450 Beadchip (HM450K) has enabled studies of genome-wide methylation on a scale not previously possible. However, application of the HM450K to DNA extracted from formalin-fixed paraffin-embedded (FFPE) tumour material has been more challenging than application to high quality DNA extracted from blood. To facilitate the application of this assay consistently across a large number of FFPE tumour-enriched DNA samples we have devised a modification to the HM450K protocol for FFPE that includes an additional quality control (QC) checkpoint., Results: QC checkpoint 3 was designed to assess the presence of DNA after bisulfite conversion and restoration, just prior to application of the HM450K assay. DNA was extracted from 474 archival FFPE breast tumour material. Five samples did not have a detectable amount of DNA with an additional 42 failing to progress past QC checkpoint 3. Genome-wide methylation was measured for the remaining 428 tumour-enriched DNA. Of these, only 4 samples failed our stringent HM450K data criteria thus representing a 99% success rate. Using prior knowledge about methylation marks associated with breast cancer we further explored the quality of the data. Twenty probes in the BRCA1 promoter region showed increased methylation in triple-negative breast cancers compared to Luminal A, Luminal B and HER2-positive breast cancer subtypes. Validation of this observation in published data from The Cancer Genome Atlas (TCGA) Network (obtained from DNA extracted from fresh frozen tumour samples) confirms the quality of the data obtained from the improved protocol., Conclusions: The modified protocol is suitable for the analysis of FFPE tumour-enriched DNA and can be systematically applied to hundreds of samples. This protocol will have utility in population-based translational epigenetic studies and is applicable to a wide variety of translated studies interested in analysis of methylation and its role in the predisposition to disease and disease progression.
- Published
- 2015
- Full Text
- View/download PDF
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