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1. Assessing the Energy Profitability of Biofuels Generated from Coffee Waste via Microwave Pyrolysis

Author

Hui Yi Lim, Brandon Han Hoe Goh, Pui Vun Chai, Chun Kit Ang, and Cheng Tung Chong

Subjects
Chemical engineering, TP155-156, Computer engineering. Computer hardware, TK7885-7895
Abstract

The potential of coffee waste to be valorised into useful bioenergy is investigated using a continuous microwave pyrolysis rig. Coffee waste of Arabica species was ground and pretreated prior to pyrolysis at elevated temperature under CO2 atmosphere. Valorisation of the coffee waste result in char, liquid, and gaseous products. Analysis shows that biochar yield is highest at 450 °C, while bio-oil recovery peaks at 550 °C. Gaseous product results in highest yield at 650 °C. Energy analysis indicates that biochar contains the highest energy density, while bio-oil's energy density decreased with temperature due to cracking of volatiles. Energy profitability was shown to be negative across all temperatures, with highest deficit at 450 °C due to the formation of non-recoverable products such as water. Higher energy profitability was achieved at 650 °C as more volatiles could be recovered in gaseous form. The study shows that microwave pyrolysis is effective in valorising coffee waste and essential to enhance the energy recovery from coffee waste.

Published
2024

2. Risk factors for disease severity among children with Covid-19: a clinical prediction model

Author

David Chun-Ern Ng, Chuin-Hen Liew, Kah Kee Tan, Ling Chin, Grace Sieng Sing Ting, Nur Fadzreena Fadzilah, Hui Yi Lim, Nur Emylia Zailanalhuddin, Shir Fong Tan, Muhamad Akmal Affan, Fatin Farihah Wan Ahmad Nasir, Thayasheri Subramaniam, Marlindawati Mohd Ali, Mohammad Faid Abd Rashid, Song-Quan Ong, and Chin Chin Ch’ng

Subjects
COVID-19, Pediatric, Nomogram, Predictor severity, Infectious and parasitic diseases, RC109-216
Abstract

Abstract Background Children account for a significant proportion of COVID-19 hospitalizations, but data on the predictors of disease severity in children are limited. We aimed to identify risk factors associated with moderate/severe COVID-19 and develop a nomogram for predicting children with moderate/severe COVID-19. Methods We identified children ≤ 12 years old hospitalized for COVID-19 across five hospitals in Negeri Sembilan, Malaysia, from 1 January 2021 to 31 December 2021 from the state’s pediatric COVID-19 case registration system. The primary outcome was the development of moderate/severe COVID-19 during hospitalization. Multivariate logistic regression was performed to identify independent risk factors for moderate/severe COVID-19. A nomogram was constructed to predict moderate/severe disease. The model performance was evaluated using the area under the curve (AUC), sensitivity, specificity, and accuracy. Results A total of 1,717 patients were included. After excluding the asymptomatic cases, 1,234 patients (1,023 mild cases and 211 moderate/severe cases) were used to develop the prediction model. Nine independent risk factors were identified, including the presence of at least one comorbidity, shortness of breath, vomiting, diarrhea, rash, seizures, temperature on arrival, chest recessions, and abnormal breath sounds. The nomogram’s sensitivity, specificity, accuracy, and AUC for predicting moderate/severe COVID-19 were 58·1%, 80·5%, 76·8%, and 0·86 (95% CI, 0·79 – 0·92) respectively. Conclusion Our nomogram, which incorporated readily available clinical parameters, would be useful to facilitate individualized clinical decisions.

Published
2023
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3. Comparison of Severe Viral Pneumonia Caused by SARS-CoV-2 and Other Respiratory Viruses Among Malaysian Children During the COVID-19 Pandemic

Author

David Chun-Ern Ng, Kah Kee Tan, Grace Sieng Sing TING, Chin Ling, Nur Fadzreena Binti Fadzilah, Shir Fong TAN, Thayasheri Subramaniam, Nur Emylia Binti Zailanalhuddin, Hui Yi LIM, Suhaila Binti Baharuddin, Yee Lean LEE, Airena Mohamad Nor, and Erwin Jiayuan Khoo

Subjects
children, COVID-19, SARS-CoV-2, severe pneumonia, viral pneumonia, Pediatrics, RJ1-570
Abstract

ObjectivesWe described the etiology of severe pneumonia in children during the height of the COVID-19 pandemic in Malaysia and compared the clinical features of severe SARS-CoV-2 to other respiratory viruses.MethodsThis retrospective study included all children aged 12 years and below hospitalized with severe pneumonia in Negeri Sembilan, Malaysia, between 1 April 2021 and 31 October 2021. We extracted demographic and clinical data and used logistic regression to examine risk factors associated with severe SARS-CoV-2 or other viral pneumonia.ResultsA total of 111 children were included. The median age was 15 months. Human rhinovirus/enterovirus, SARS-CoV-2 and respiratory syncytial virus were the most common etiology of severe pneumonia. Codetection of >1 viral pathogen was present in 14 (12.6%) patients. Children with severe COVID-19 presented early in the course of illness and had lower rates of pediatric intensive care admission. The presence of sick contact with an adult was a predictor for SARS-CoV-2, whereas adventitious breath sounds were predictive of other respiratory viruses.ConclusionsThe etiology of severe pneumonia in children evolved with the epidemic curve of COVID-19 and school closures. Children with severe pneumonia due to SARS-CoV-2 experienced a milder clinical course when compared to other respiratory viruses.

Published
2022
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4. Supplementary Grant Support from Genome-Wide Meta-Analyses of Breast, Ovarian, and Prostate Cancer Association Studies Identify Multiple New Susceptibility Loci Shared by at Least Two Cancer Types

Author

Diether Lambrechts, Paul D.P. Pharoah, Rosalind Eeles, Georgia Chenevix-Trench, Douglas F. Easton, Simon A. Gayther, Per Hall, Fergus J. Couch, Stephen J. Chanock, Peter Kraft, Brian E. Henderson, David J. Hunter, Thomas A. Sellers, Amanda Spurdle, Christopher A. Haiman, Jacques Simard, Alison M. Dunning, Andrew Berchuck, Matthew L. Freedman, Fredrick Schumacher, Yu-Tang Gao, Xiao-Ou Shu, Wojciech Kluzniak, William J. Blot, Weiva Sieh, Wei Zheng, Walther Vogel, Volker Arndt, Vessela Kristensen, Veronica Wendy Setiawan, Veli-Matti Kosma, Vanio Mitev, Ute Hamann, Usha Menon, Todd L. Edwards, Tim J. Key, Tiina Wahlfors, Thomas Brüning, Thilo Dörk, Teuvo L.J. Tammela, Tanja Pejovic, Susanne Krüger Kjær, Susan M. Gapstur, Stig E. Bojesen, Stephen N. Thibodeau, Soo-Hwang Teo, Soo Chin Lee, Sonja Berndt, Sofia Maia, Shelley S. Tworoger, Shannon K. McDonnell, Sara H. Olson, Sara Benlloch, Ruth C. Travis, Roger L. Milne, Roberta Ness, Robert Winqvist, Robert N. Hoover, Robert J. MacInnis, Robert A. Stephenson, Rita K. Schmutzler, Reidun Kristin Kopperud, Ralf Butzow, Radka Kaneva, Qiyuan Li, Qiuyin Cai, Qin Wang, Peter Devilee, Peter A. Fasching, Per Broberg, Penelope M. Webb, Paula Paulo, Paul Brennan, Pascal Guénel, Paolo Peterlongo, Nora Pashayan, Nicolas Wentzensen, Nick Orr, Nhu D. Le, Nazneen Rahman, Natalia Bogdanova, Montserrat Garcia-Closas, Minouk J. Schoemaker, Ming-Feng Hou, Michelle A.T. Hildebrandt, Michael Lush, Michael Jones, Melissa C. Southey, Maureen Sanderson, Matthieu Moisse, Matthias W. Beckmann, Mary Anne Rossing, Markus Aly, Marjorie Riggan, Marjanka K. Schmidt, Marc T. Goodman, Manuel R. Teixeira, Manuel Luedeke, Manjeet K. Bolla, Malcolm C. Pike, Maartje J. Hooning, Lisa Cannon-Albright, Linda S. Cook, Liesel M. Fitzgerald, Leon F.A.G. Massuger, Lambertus A. Kiemeney, Kunle Odunsi, Kristiina Aittomäki, Kirsten B. Moysich, Kexin Chen, Kenneth Offitt, Kenneth Muir, Keitaro Matsuo, Kay-Tee Khaw, Kathleen Herkommer, Karen H. Lu, Kamila Czene, Jyotsna Batra, Julio Pow-Sang, Julie M. Cunningham, Julian Peto, Julia A. Knight, Judith A. Clements, Jonine Figueroa, Jong Y. Park, Jolanta Kupryjanczyk, John L. Hopper, Johanna Schleutker, Joellen M. Schildkraut, Joe Dennis, Jenny L. Donovan, Jenny Chang-Claude, Jennifer B. Permuth, Jennifer A. Doherty, Javier Benítez, Janet L. Stanford, Jan Lubiński, Jacek Gronwald, Ignace Vergote, Ian Campbell, Iain McNeish, Hui-Yi Lim, Honglin Song, Hoda Anton-Culver, Hiltrud Brauch, Hermann Brenner, Henrik Gronberg, Heli Nevanlinna, Helga B. Salvesen, Hatef Darabi, Harvey A. Risch, Hardev Pandha, Hans-Ulrich Ulmer, Hans Wildiers, Håkan Olsson, Graham G. Giles, Fredrik Wiklund, Freddie C. Hamdy, Francesmary Modugno, Florian Heitz, Fiona Bruinsma, Fengju Song, Estrid Høgdall, Elza Khusnutdinova, Ellen L. Goode, Elizabeth M. Poole, Elisa V. Bandera, Elinor J. Sawyer, Drakoulis Yannoukakos, Douglas A. Levine, Dominika Wokozorczyk, Digna R. Velez Edwards, Dieter Flesch-Janys, Diana Eccles, David E. Neal, Daniel W. Cramer, Daniel O. Stram, Daniel J. Schaid, Daniel C. Tessier, Daehee Kang, Craig C. Teerlink, Claus K. Høgdall, Christine B. Ambrosone, Christiane Maier, Christa Stegmaier, Chavdar Slavov, Cezary Cybulski, Celine Vachon, Celeste Leigh Pearce, Catriona McLean, Catherine Phelan, Carl Blomqvist, Børge G. Nordestgaard, Beth Y. Karlan, Barbara Burwinkel, Arif B. Ekici, Argyrios Ziogas, Anthony Swerdlow, Annika Lindblom, Anna H. Wu, Anna Gonzalez-Neira, Anja Rudolph, Angela Cox, Andrzej Kierzek, Ana Peixoto, Alvaro Monteiro, Alicja Wolk, Alice S. Whittemore, Aleksandra Gentry-Maharaj, Aida K. Dieffenbach, Agnieszka Michael, Agnieszka Dansonka-Mieszkowska, Adam S. Kibel, Deborah J. Thompson, Susan J. Ramus, Sara Lindstrom, Kate Lawrenson, ZSofia Kote-Jarai, Jonathan Tyrer, Kyriaki Michailidou, Ali Amin Al Olama, Jonathan Beesley, and Siddhartha P. Kar

Abstract

Supplementary Grant Support

Published
2023
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5. Supplementary Methods, Figures S1 - S3 from Genome-Wide Meta-Analyses of Breast, Ovarian, and Prostate Cancer Association Studies Identify Multiple New Susceptibility Loci Shared by at Least Two Cancer Types

Author

Diether Lambrechts, Paul D.P. Pharoah, Rosalind Eeles, Georgia Chenevix-Trench, Douglas F. Easton, Simon A. Gayther, Per Hall, Fergus J. Couch, Stephen J. Chanock, Peter Kraft, Brian E. Henderson, David J. Hunter, Thomas A. Sellers, Amanda Spurdle, Christopher A. Haiman, Jacques Simard, Alison M. Dunning, Andrew Berchuck, Matthew L. Freedman, Fredrick Schumacher, Yu-Tang Gao, Xiao-Ou Shu, Wojciech Kluzniak, William J. Blot, Weiva Sieh, Wei Zheng, Walther Vogel, Volker Arndt, Vessela Kristensen, Veronica Wendy Setiawan, Veli-Matti Kosma, Vanio Mitev, Ute Hamann, Usha Menon, Todd L. Edwards, Tim J. Key, Tiina Wahlfors, Thomas Brüning, Thilo Dörk, Teuvo L.J. Tammela, Tanja Pejovic, Susanne Krüger Kjær, Susan M. Gapstur, Stig E. Bojesen, Stephen N. Thibodeau, Soo-Hwang Teo, Soo Chin Lee, Sonja Berndt, Sofia Maia, Shelley S. Tworoger, Shannon K. McDonnell, Sara H. Olson, Sara Benlloch, Ruth C. Travis, Roger L. Milne, Roberta Ness, Robert Winqvist, Robert N. Hoover, Robert J. MacInnis, Robert A. Stephenson, Rita K. Schmutzler, Reidun Kristin Kopperud, Ralf Butzow, Radka Kaneva, Qiyuan Li, Qiuyin Cai, Qin Wang, Peter Devilee, Peter A. Fasching, Per Broberg, Penelope M. Webb, Paula Paulo, Paul Brennan, Pascal Guénel, Paolo Peterlongo, Nora Pashayan, Nicolas Wentzensen, Nick Orr, Nhu D. Le, Nazneen Rahman, Natalia Bogdanova, Montserrat Garcia-Closas, Minouk J. Schoemaker, Ming-Feng Hou, Michelle A.T. Hildebrandt, Michael Lush, Michael Jones, Melissa C. Southey, Maureen Sanderson, Matthieu Moisse, Matthias W. Beckmann, Mary Anne Rossing, Markus Aly, Marjorie Riggan, Marjanka K. Schmidt, Marc T. Goodman, Manuel R. Teixeira, Manuel Luedeke, Manjeet K. Bolla, Malcolm C. Pike, Maartje J. Hooning, Lisa Cannon-Albright, Linda S. Cook, Liesel M. Fitzgerald, Leon F.A.G. Massuger, Lambertus A. Kiemeney, Kunle Odunsi, Kristiina Aittomäki, Kirsten B. Moysich, Kexin Chen, Kenneth Offitt, Kenneth Muir, Keitaro Matsuo, Kay-Tee Khaw, Kathleen Herkommer, Karen H. Lu, Kamila Czene, Jyotsna Batra, Julio Pow-Sang, Julie M. Cunningham, Julian Peto, Julia A. Knight, Judith A. Clements, Jonine Figueroa, Jong Y. Park, Jolanta Kupryjanczyk, John L. Hopper, Johanna Schleutker, Joellen M. Schildkraut, Joe Dennis, Jenny L. Donovan, Jenny Chang-Claude, Jennifer B. Permuth, Jennifer A. Doherty, Javier Benítez, Janet L. Stanford, Jan Lubiński, Jacek Gronwald, Ignace Vergote, Ian Campbell, Iain McNeish, Hui-Yi Lim, Honglin Song, Hoda Anton-Culver, Hiltrud Brauch, Hermann Brenner, Henrik Gronberg, Heli Nevanlinna, Helga B. Salvesen, Hatef Darabi, Harvey A. Risch, Hardev Pandha, Hans-Ulrich Ulmer, Hans Wildiers, Håkan Olsson, Graham G. Giles, Fredrik Wiklund, Freddie C. Hamdy, Francesmary Modugno, Florian Heitz, Fiona Bruinsma, Fengju Song, Estrid Høgdall, Elza Khusnutdinova, Ellen L. Goode, Elizabeth M. Poole, Elisa V. Bandera, Elinor J. Sawyer, Drakoulis Yannoukakos, Douglas A. Levine, Dominika Wokozorczyk, Digna R. Velez Edwards, Dieter Flesch-Janys, Diana Eccles, David E. Neal, Daniel W. Cramer, Daniel O. Stram, Daniel J. Schaid, Daniel C. Tessier, Daehee Kang, Craig C. Teerlink, Claus K. Høgdall, Christine B. Ambrosone, Christiane Maier, Christa Stegmaier, Chavdar Slavov, Cezary Cybulski, Celine Vachon, Celeste Leigh Pearce, Catriona McLean, Catherine Phelan, Carl Blomqvist, Børge G. Nordestgaard, Beth Y. Karlan, Barbara Burwinkel, Arif B. Ekici, Argyrios Ziogas, Anthony Swerdlow, Annika Lindblom, Anna H. Wu, Anna Gonzalez-Neira, Anja Rudolph, Angela Cox, Andrzej Kierzek, Ana Peixoto, Alvaro Monteiro, Alicja Wolk, Alice S. Whittemore, Aleksandra Gentry-Maharaj, Aida K. Dieffenbach, Agnieszka Michael, Agnieszka Dansonka-Mieszkowska, Adam S. Kibel, Deborah J. Thompson, Susan J. Ramus, Sara Lindstrom, Kate Lawrenson, ZSofia Kote-Jarai, Jonathan Tyrer, Kyriaki Michailidou, Ali Amin Al Olama, Jonathan Beesley, and Siddhartha P. Kar

Abstract

Supplementary Figure S1. LocusZoom regional association plots for the seven new cross-cancer loci that were > 1 Mb from known index SNPs. Supplementary Figure S2A-B. Box plots showing eQTL associations between (A) rs9375701 and L3MBTL3 in normal breast and prostate tissues and (B) rs8037137 and RCCD1 in normal breast and ovarian tissues. Supplementary Figure S3. Interactions between BCL2L11 and the 32 Biocarta "Death Pathway" genes. Interactions were identified using the GeneMania server. Circles contain gene names, lines represent interactions, and the color of the line indicates a specific type of interaction as listed in the legend.

Published
2023
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6. Supplementary Tables S1 - S10 from Genome-Wide Meta-Analyses of Breast, Ovarian, and Prostate Cancer Association Studies Identify Multiple New Susceptibility Loci Shared by at Least Two Cancer Types

Author

Diether Lambrechts, Paul D.P. Pharoah, Rosalind Eeles, Georgia Chenevix-Trench, Douglas F. Easton, Simon A. Gayther, Per Hall, Fergus J. Couch, Stephen J. Chanock, Peter Kraft, Brian E. Henderson, David J. Hunter, Thomas A. Sellers, Amanda Spurdle, Christopher A. Haiman, Jacques Simard, Alison M. Dunning, Andrew Berchuck, Matthew L. Freedman, Fredrick Schumacher, Yu-Tang Gao, Xiao-Ou Shu, Wojciech Kluzniak, William J. Blot, Weiva Sieh, Wei Zheng, Walther Vogel, Volker Arndt, Vessela Kristensen, Veronica Wendy Setiawan, Veli-Matti Kosma, Vanio Mitev, Ute Hamann, Usha Menon, Todd L. Edwards, Tim J. Key, Tiina Wahlfors, Thomas Brüning, Thilo Dörk, Teuvo L.J. Tammela, Tanja Pejovic, Susanne Krüger Kjær, Susan M. Gapstur, Stig E. Bojesen, Stephen N. Thibodeau, Soo-Hwang Teo, Soo Chin Lee, Sonja Berndt, Sofia Maia, Shelley S. Tworoger, Shannon K. McDonnell, Sara H. Olson, Sara Benlloch, Ruth C. Travis, Roger L. Milne, Roberta Ness, Robert Winqvist, Robert N. Hoover, Robert J. MacInnis, Robert A. Stephenson, Rita K. Schmutzler, Reidun Kristin Kopperud, Ralf Butzow, Radka Kaneva, Qiyuan Li, Qiuyin Cai, Qin Wang, Peter Devilee, Peter A. Fasching, Per Broberg, Penelope M. Webb, Paula Paulo, Paul Brennan, Pascal Guénel, Paolo Peterlongo, Nora Pashayan, Nicolas Wentzensen, Nick Orr, Nhu D. Le, Nazneen Rahman, Natalia Bogdanova, Montserrat Garcia-Closas, Minouk J. Schoemaker, Ming-Feng Hou, Michelle A.T. Hildebrandt, Michael Lush, Michael Jones, Melissa C. Southey, Maureen Sanderson, Matthieu Moisse, Matthias W. Beckmann, Mary Anne Rossing, Markus Aly, Marjorie Riggan, Marjanka K. Schmidt, Marc T. Goodman, Manuel R. Teixeira, Manuel Luedeke, Manjeet K. Bolla, Malcolm C. Pike, Maartje J. Hooning, Lisa Cannon-Albright, Linda S. Cook, Liesel M. Fitzgerald, Leon F.A.G. Massuger, Lambertus A. Kiemeney, Kunle Odunsi, Kristiina Aittomäki, Kirsten B. Moysich, Kexin Chen, Kenneth Offitt, Kenneth Muir, Keitaro Matsuo, Kay-Tee Khaw, Kathleen Herkommer, Karen H. Lu, Kamila Czene, Jyotsna Batra, Julio Pow-Sang, Julie M. Cunningham, Julian Peto, Julia A. Knight, Judith A. Clements, Jonine Figueroa, Jong Y. Park, Jolanta Kupryjanczyk, John L. Hopper, Johanna Schleutker, Joellen M. Schildkraut, Joe Dennis, Jenny L. Donovan, Jenny Chang-Claude, Jennifer B. Permuth, Jennifer A. Doherty, Javier Benítez, Janet L. Stanford, Jan Lubiński, Jacek Gronwald, Ignace Vergote, Ian Campbell, Iain McNeish, Hui-Yi Lim, Honglin Song, Hoda Anton-Culver, Hiltrud Brauch, Hermann Brenner, Henrik Gronberg, Heli Nevanlinna, Helga B. Salvesen, Hatef Darabi, Harvey A. Risch, Hardev Pandha, Hans-Ulrich Ulmer, Hans Wildiers, Håkan Olsson, Graham G. Giles, Fredrik Wiklund, Freddie C. Hamdy, Francesmary Modugno, Florian Heitz, Fiona Bruinsma, Fengju Song, Estrid Høgdall, Elza Khusnutdinova, Ellen L. Goode, Elizabeth M. Poole, Elisa V. Bandera, Elinor J. Sawyer, Drakoulis Yannoukakos, Douglas A. Levine, Dominika Wokozorczyk, Digna R. Velez Edwards, Dieter Flesch-Janys, Diana Eccles, David E. Neal, Daniel W. Cramer, Daniel O. Stram, Daniel J. Schaid, Daniel C. Tessier, Daehee Kang, Craig C. Teerlink, Claus K. Høgdall, Christine B. Ambrosone, Christiane Maier, Christa Stegmaier, Chavdar Slavov, Cezary Cybulski, Celine Vachon, Celeste Leigh Pearce, Catriona McLean, Catherine Phelan, Carl Blomqvist, Børge G. Nordestgaard, Beth Y. Karlan, Barbara Burwinkel, Arif B. Ekici, Argyrios Ziogas, Anthony Swerdlow, Annika Lindblom, Anna H. Wu, Anna Gonzalez-Neira, Anja Rudolph, Angela Cox, Andrzej Kierzek, Ana Peixoto, Alvaro Monteiro, Alicja Wolk, Alice S. Whittemore, Aleksandra Gentry-Maharaj, Aida K. Dieffenbach, Agnieszka Michael, Agnieszka Dansonka-Mieszkowska, Adam S. Kibel, Deborah J. Thompson, Susan J. Ramus, Sara Lindstrom, Kate Lawrenson, ZSofia Kote-Jarai, Jonathan Tyrer, Kyriaki Michailidou, Ali Amin Al Olama, Jonathan Beesley, and Siddhartha P. Kar

Abstract

Supplementary Table S1. Known risk loci for each cancer. Supplementary Table S2. Regions where known index SNPs for at least two of the three cancers lie within 1 Mb of each other. Supplementary Table S3. Full results from the meta-analysis of breast, ovarian, and prostate cancer showing the 18 independent loci associated at P < 10-8 with the same direction of effect across all three cancers. Supplementary Table S4. Conditional analysis of the rs1469713 (breast-ovarian-prostate cancer) signal, conditioning on the rs4808801 (breast cancer-specific) signal that was < 1 Mb away using GCTA software. Supplementary Table S5. Most significantly-associated genotyped SNP at new loci where index SNPs were imputed. Supplementary Table S6. Expression QTL analysis results from the GTEx Portal for the new cross-cancer risk loci listed in main Table 2. Supplementary Table S7. SNPs with P < 10-8 at the new cross-cancer risk loci listed in main Table 2 that overlap predicted enhancers in at least two cell types. Supplementary Table S8. HaploReg and non-coding RNA annotation of variants with P < 10-8 at the new cross-cancer risk loci listed in main Table 2. Supplementary Table S9. Eight of the 32 genes involved in induction of apoptosis through DR3 and DR4/5 Death Receptors (MSigDB: Biocarta "Death Pathway") a that were < 1 Mb away from an independent P < 10-5 index SNP in the 3-cancer meta-analysis. Supplementary Table S10. INRICH pathway analysis results for pathways with empirical P < 0.05. Apoptosis-related pathways containing BCL2L11 are shaded.

Published
2023
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7. Supplementary notes from Genome-Wide Association Study of Prostate Cancer–Specific Survival

Author

Fredrik Wiklund, Sara Lindström, Johanna Schleutker, Lovise Maehle, David G. Cox, Anne Tjønneland, Bas H. Bueno-de-Mesquita, Antonia Trichopoulou, Stephanie J. Weinstein, Victoria L. Stevens, Meir J. Stampfer, Kathryn L. Penney, Alison M. Mondul, Jing Ma, Loic Le Marchand, Peter Kraft, David J. Hunter, Edward L. Giovannucci, Susan M. Gapstur, Stephen Chanock, Sonja I. Berndt, Gerald L. Andriole, Demetrius Albanes, Judith A. Clements, Jyotsna Batra, Andrzej Kierzek, Agnieszka Michael, Hardev Pandha, Sofia Maia, Paula Paulo, Manuel R. Teixeira, Amanda Spurdle, Vanio I. Mitev, Radka P. Kaneva, Chavdar Slavov, Hui-Yi Lim, Thomas A. Sellers, Jong Y. Park, Bernd Holleczek, Volker Herrmann, Hermann Brenner, Lisa Cannon-Albright, Wojciech Kluźniak, Jan Lubiński, Cezary Cybulski, Adam S. Kibel, Kathleen Herkommer, Manuel Luedeke, Walther Vogel, Christiane Maier, Daniel J. Schaid, Shannon K. McDonnell, Stephen N. Thibodeau, Janet L. Stanford, Kay-Tee Khaw, Nora Pashayan, Paul D.P. Pharoah, Freddie C. Hamdy, Jenny L. Donovan, David E. Neal, Ruth C. Travis, Timothy J. Key, Børge G. Nordestgaard, Teuvo L.J. Tammela, Csilla Sipeky, Christopher A. Haiman, Fredrick R. Schumacher, Brian E. Henderson, Liesel M. FitzGerald, Melissa C. Southey, Graham G. Giles, Kenneth Muir, Sara Benlloch, Ali Amin Al Olama, Zsofia Kote-Jarai, Douglas F. Easton, Rosalind A. Eeles, Henrik Gronberg, Markus Aly, Thomas Whitington, Robert Karlsson, and Robert Szulkin

Abstract

Supplementary acknowledgments.

Published
2023
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8. Data from Genome-Wide Association Study of Prostate Cancer–Specific Survival

Author

Fredrik Wiklund, Sara Lindström, Johanna Schleutker, Lovise Maehle, David G. Cox, Anne Tjønneland, Bas H. Bueno-de-Mesquita, Antonia Trichopoulou, Stephanie J. Weinstein, Victoria L. Stevens, Meir J. Stampfer, Kathryn L. Penney, Alison M. Mondul, Jing Ma, Loic Le Marchand, Peter Kraft, David J. Hunter, Edward L. Giovannucci, Susan M. Gapstur, Stephen Chanock, Sonja I. Berndt, Gerald L. Andriole, Demetrius Albanes, Judith A. Clements, Jyotsna Batra, Andrzej Kierzek, Agnieszka Michael, Hardev Pandha, Sofia Maia, Paula Paulo, Manuel R. Teixeira, Amanda Spurdle, Vanio I. Mitev, Radka P. Kaneva, Chavdar Slavov, Hui-Yi Lim, Thomas A. Sellers, Jong Y. Park, Bernd Holleczek, Volker Herrmann, Hermann Brenner, Lisa Cannon-Albright, Wojciech Kluźniak, Jan Lubiński, Cezary Cybulski, Adam S. Kibel, Kathleen Herkommer, Manuel Luedeke, Walther Vogel, Christiane Maier, Daniel J. Schaid, Shannon K. McDonnell, Stephen N. Thibodeau, Janet L. Stanford, Kay-Tee Khaw, Nora Pashayan, Paul D.P. Pharoah, Freddie C. Hamdy, Jenny L. Donovan, David E. Neal, Ruth C. Travis, Timothy J. Key, Børge G. Nordestgaard, Teuvo L.J. Tammela, Csilla Sipeky, Christopher A. Haiman, Fredrick R. Schumacher, Brian E. Henderson, Liesel M. FitzGerald, Melissa C. Southey, Graham G. Giles, Kenneth Muir, Sara Benlloch, Ali Amin Al Olama, Zsofia Kote-Jarai, Douglas F. Easton, Rosalind A. Eeles, Henrik Gronberg, Markus Aly, Thomas Whitington, Robert Karlsson, and Robert Szulkin

Abstract

Background: Unnecessary intervention and overtreatment of indolent disease are common challenges in clinical management of prostate cancer. Improved tools to distinguish lethal from indolent disease are critical.Methods: We performed a genome-wide survival analysis of cause-specific death in 24,023 prostate cancer patients (3,513 disease-specific deaths) from the PRACTICAL and BPC3 consortia. Top findings were assessed for replication in a Norwegian cohort (CONOR).Results: We observed no significant association between genetic variants and prostate cancer survival.Conclusions: Common genetic variants with large impact on prostate cancer survival were not observed in this study.Impact: Future studies should be designed for identification of rare variants with large effect sizes or common variants with small effect sizes. Cancer Epidemiol Biomarkers Prev; 24(11); 1796–800. ©2015 AACR.

Published
2023
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9. Genome-Wide Meta-Analyses of Breast, Ovarian, and Prostate Cancer Association Studies Identify Multiple New Susceptibility Loci Shared by at Least Two Cancer Types

Author

Agnieszka Dansonka-Mieszkowska, Usha Menon, Melissa C. Southey, Diana Eccles, Robert Winqvist, Keitaro Matsuo, Matthias W. Beckmann, Robert A. Stephenson, Paul D.P. Pharoah, Lambertus A. Kiemeney, Elizabeth M. Poole, Paul Brennan, Wojciech Kluzniak, Liesel M. FitzGerald, Alice S. Whittemore, Kunle Odunsi, Mary Anne Rossing, Craig C. Teerlink, Javier Benitez, Arif B. Ekici, Thilo Dörk, Per Hall, C. Slavov, Matthieu Moisse, Jennifer B. Permuth, Hermann Brenner, Apcb BioResource, Julia A. Knight, Teuvo L.J. Tammela, Douglas A. Levine, Alicja Wolk, Sofia Maia, Kamila Czene, Vessela N. Kristensen, Radka Kaneva, Hoda Anton-Culver, Jonathan Tyrer, Manjeet K. Bolla, Maureen Sanderson, Fengju Song, Veli-Matti Kosma, Dieter Flesch-Janys, Douglas F. Easton, John L. Hopper, Marjanka K. Schmidt, Jolanta Kupryjanczyk, Amanda B. Spurdle, Nicolas Wentzensen, kConFab Investigators, Peter A. Fasching, Leon F.A.G. Massuger, Jonathan Beesley, Qin Wang, Pascal Guénel, Penelope M. Webb, Paolo Peterlongo, Daniel C. Tessier, Peter Kraft, Jennifer A. Doherty, Daehee Kang, Christine B. Ambrosone, Weiva Sieh, Anja Rudolph, Ignace Vergote, Hiltrud Brauch, Celeste Leigh Pearce, Robert N. Hoover, Paula Paulo, Nbcs Investigators, Rosalind A. Eeles, Honglin Song, Fergus J. Couch, Brian E. Henderson, Lisa A. Cannon-Albright, William J. Blot, Soo-Chin Lee, Abctb Investigators, Ute Hamann, Angela Cox, Peter Devilee, Andrzej M. Kierzek, Qiuyin Cai, Elinor J. Sawyer, Jacek Gronwald, Janet L. Stanford, Soo-Hwang Teo, Fredrick R. Schumacher, Montserrat Garcia-Closas, Susanne K. Kjaer, Christa Stegmaier, Thomas Brüning, Graham G. Giles, Catriona McLean, Thomas A. Sellers, Georgia Chenevix-Trench, Ellen L. Goode, Maartje J. Hooning, Kathleen Herkommer, Jenny L Donovan, Fiona Bruinsma, Minouk J. Schoemaker, Marc T. Goodman, Volker Arndt, Estrid Høgdall, Yu-Tang Gao, Ruth C. Travis, Claus Høgdall, Celine M. Vachon, Jan Lubinski, Qiyuan Li, Vanio Mitev, Argyrios Ziogas, Julie M. Cunningham, Ming-Feng Hou, Marjorie J. Riggan, David J. Hunter, T. Wahlfors, Michael Jones, Diether Lambrechts, Hui-Yi Lim, Stephen N. Thibodeau, Kenneth Offitt, Stig E. Bojesen, Kexin Chen, Harvey A. Risch, Fredrik Wiklund, Hans-Ulrich Ulmer, Natalia Bogdanova, Joellen M. Schildkraut, Kristiina Aittomäki, Helga B. Salvesen, Markus Aly, Hatef Darabi, Christopher A. Haiman, Shelley S. Tworoger, Zsofia Kote-Jarai, Judith A. Clements, Andrew Berchuck, Francesmary Modugno, Drakoulis Yannoukakos, Catherine M. Phelan, Julian Peto, Børge G. Nordestgaard, Simon A. Gayther, Barbara Burwinkel, Nazneen Rahman, Todd L. Edwards, Wei Zheng, Ralf Bützow, Siddhartha Kar, Manuel R. Teixeira, Anna H. Wu, Stephen J. Chanock, Kirsten B. Moysich, Per Broberg, Ana Peixoto, Sara Lindström, Daniel J. Schaid, Sonja I. Berndt, Dominika Wokozorczyk, Jonine D. Figueroa, Aida Karina Dieffenbach, Anna González-Neira, Reidun K. Kopperud, Jacques Simard, Alvaro N.A. Monteiro, David E. Neal, Tanja Pejovic, Florian Heitz, Beth Y. Karlan, Elza Khusnutdinova, Anthony J. Swerdlow, Joe Dennis, Veronica Wendy Setiawan, Heli Nevanlinna, Christiane Maier, Walther Vogel, Henrik Grönberg, Aleksandra Gentry-Maharaj, Kay-Tee Khaw, Jenny Chang-Claude, Carl Blomqvist, Susan M. Gapstur, Adam S. Kibel, Daniel W. Cramer, Manuel Luedeke, Robert J. MacInnis, Agnieszka Michael, Daniel O. Stram, Michelle A.T. Hildebrandt, Xiao-Ou Shu, Roberta B. Ness, Ian G. Campbell, Nora Pashayan, Timothy J. Key, Julio M. Pow-Sang, Hardev Pandha, Karen Lu, Elisa V. Bandera, Freddie C. Hamdy, Håkan Olsson, Sara H. Olson, Ali Amin Al Olama, Iain A. McNeish, Alison M. Dunning, Matthew L. Freedman, Kenneth Muir, Nhu D. Le, Linda S. Cook, Annika Lindblom, Sara Benlloch, Roger L. Milne, Kate Lawrenson, Digna R. Velez Edwards, Michael Lush, Hans Wildiers, Deborah J. Thompson, Susan J. Ramus, Kyriaki Michailidou, Rita K. Schmutzler, Nick Orr, Jyotsna Batra, Malcolm C. Pike, Cezary Cybulski, Shannon K. McDonnell, Jong Y. Park, Johanna Schleutker, Medical Oncology, Clinical Genetics, Amin Al Olama, Ali [0000-0002-7178-3431], Tyrer, Jonathan [0000-0003-3724-4757], Thompson, Deborah [0000-0003-1465-5799], Song, Honglin [0000-0001-5076-7371], Dennis, Joe [0000-0003-4591-1214], Khaw, Kay-Tee [0000-0002-8802-2903], Dunning, Alison [0000-0001-6651-7166], Easton, Douglas [0000-0003-2444-3247], Pharoah, Paul [0000-0001-8494-732X], and Apollo - University of Cambridge Repository

Subjects
Male, 0301 basic medicine, Datasets as Topic, Genome-wide association study, Prostate cancer, Gene Regulatory Networks, Ovarian Neoplasms, Genetics, education.field_of_study, Women's cancers Radboud Institute for Molecular Life Sciences [Radboudumc 17], Chromosome Mapping, prostate cancer, 3. Good health, Enhancer Elements, Genetic, ovarian cancer, Oncology, Organ Specificity, Centre for Surgical Research, Urological cancers Radboud Institute for Health Sciences [Radboudumc 15], Female, Signal Transduction, Quantitative Trait Loci, Population, Breast Neoplasms, Quantitative trait locus, Biology, Polymorphism, Single Nucleotide, Article, 03 medical and health sciences, Breast cancer, breast cancer, Meta-Analysis as Topic, SDG 3 - Good Health and Well-being, pleiotropy, medicine, Humans, Genetic Predisposition to Disease, education, Genetic association, Prostatic Neoplasms, Cancer, medicine.disease, 030104 developmental biology, Genetic Loci, Case-Control Studies, Expression quantitative trait loci, genome-wide association studies, Genome-Wide Association Study
Abstract

Breast, ovarian, and prostate cancers are hormone-related and may have a shared genetic basis, but this has not been investigated systematically by genome-wide association (GWA) studies. Meta-analyses combining the largest GWA meta-analysis data sets for these cancers totaling 112,349 cases and 116,421 controls of European ancestry, all together and in pairs, identified at P < 10−8 seven new cross-cancer loci: three associated with susceptibility to all three cancers (rs17041869/2q13/BCL2L11; rs7937840/11q12/INCENP; rs1469713/19p13/GATAD2A), two breast and ovarian cancer risk loci (rs200182588/9q31/SMC2; rs8037137/15q26/RCCD1), and two breast and prostate cancer risk loci (rs5013329/1p34/NSUN4; rs9375701/6q23/L3MBTL3). Index variants in five additional regions previously associated with only one cancer also showed clear association with a second cancer type. Cell-type–specific expression quantitative trait locus and enhancer–gene interaction annotations suggested target genes with potential cross-cancer roles at the new loci. Pathway analysis revealed significant enrichment of death receptor signaling genes near loci with P < 10−5 in the three-cancer meta-analysis. Significance: We demonstrate that combining large-scale GWA meta-analysis findings across cancer types can identify completely new risk loci common to breast, ovarian, and prostate cancers. We show that the identification of such cross-cancer risk loci has the potential to shed new light on the shared biology underlying these hormone-related cancers. Cancer Discov; 6(9); 1052–67. ©2016 AACR. This article is highlighted in the In This Issue feature, p. 932

Published
2016
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10. Prediction of Individual Genetic Risk to Prostate Cancer Using a Polygenic Score

Author

Robert, Szulkin, Thomas, Whitington, Martin, Eklund, Markus, Aly, Rosalind A, Eeles, Douglas, Easton, Z Sofia, Kote-Jarai, Ali, Amin Al Olama, Sara, Benlloch, Kenneth, Muir, Graham G, Giles, Melissa C, Southey, Liesel M, Fitzgerald, Brian E, Henderson, Fredrick, Schumacher, Christopher A, Haiman, Johanna, Schleutker, Tiina, Wahlfors, Teuvo L J, Tammela, Børge G, Nordestgaard, Tim J, Key, Ruth C, Travis, David E, Neal, Jenny L, Donovan, Freddie C, Hamdy, Paul, Pharoah, Nora, Pashayan, Kay-Tee, Khaw, Janet L, Stanford, Stephen N, Thibodeau, Shannon K, McDonnell, Daniel J, Schaid, Christiane, Maier, Walther, Vogel, Manuel, Luedeke, Kathleen, Herkommer, Adam S, Kibel, Cezary, Cybulski, Jan, Lubiński, Wojciech, Kluźniak, Lisa, Cannon-Albright, Hermann, Brenner, Katja, Butterbach, Christa, Stegmaier, Jong Y, Park, Thomas, Sellers, Hui-Yi, Lin, Hui-Yi, Lim, Chavdar, Slavov, Radka, Kaneva, Vanio, Mitev, Jyotsna, Batra, Judith A, Clements, Amanda, Spurdle, Manuel R, Teixeira, Paula, Paulo, Sofia, Maia, Hardev, Pandha, Agnieszka, Michael, Andrzej, Kierzek, Henrik, Gronberg, and Danielle M, Karyadi

Subjects
Genetic Markers, Male, Risk Factors, Genetic Variation, Humans, Prostatic Neoplasms, Genetic Predisposition to Disease, Linkage Disequilibrium, Article
Abstract

BACKGROUND. Polygenic risk scores comprising established susceptibility variants have shown to be informative classifiers for several complex diseases including prostate cancer. For prostate cancer it is unknown if inclusion of genetic markers that have so far not been associated with prostate cancer risk at a genome-wide significant level will improve disease prediction. METHODS. We built polygenic risk scores in a large training set comprising over 25,000 individuals. Initially 65 established prostate cancer susceptibility variants were selected. After LD pruning additional variants were prioritized based on their association with prostate cancer. Six-fold cross validation was performed to assess genetic risk scores and optimize the number of additional variants to be included. The final model was evaluated in an independent study population including 1,370 cases and 1,239 controls. RESULTS. The polygenic risk score with 65 established susceptibility variants provided an area under the curve (AUC) of 0.67. Adding an additional 68 novel variants significantly increased the AUC to 0.68 (P = 0.0012) and the net reclassification index with 0.21 (P = 8.5 E-08). All novel variants were located in genomic regions established as associated with prostate cancer risk. CONCLUSIONS. Inclusion of additional genetic variants from established prostate cancer susceptibility regions improves disease prediction.

Published
2015

11. Genome-wide association study of prostate cancer-specific survival

Author

David E. Neal, Jing Ma, Kenneth Muir, Sara Benlloch, David J. Hunter, Graham G. Giles, Fredrick R. Schumacher, Judith A. Clements, Douglas F. Easton, Andrzej M. Kierzek, Cezary Cybulski, Demetrius Albanes, Ruth C. Travis, Jong Y. Park, Stephen N. Thibodeau, Fredrik Wiklund, Johanna Schleutker, Brian E. Henderson, Gerald L. Andriole, Christiane Maier, David G. Cox, Daniel J. Schaid, Melissa C. Southey, Amanda B. Spurdle, Thomas A. Sellers, Nora Pashayan, Timothy J. Key, Peter Kraft, Rosalind A. Eeles, Volker Herrmann, Hardev Pandha, Sofia Maia, Wojciech Kluźniak, Børge G. Nordestgaard, Stephen J. Chanock, Paul D.P. Pharoah, Meir J. Stampfer, Sonja I. Berndt, Agnieszka Michael, Adam S. Kibel, Robert Szulkin, Jyotsna Batra, Liesel M. FitzGerald, Kay-Tee Khaw, Janet L. Stanford, Alison M. Mondul, Stephanie J. Weinstein, Hermann Brenner, C. Slavov, Csilla Sipeky, Teuvo L.J. Tammela, Paula Paulo, Freddie C. Hamdy, Susan M. Gapstur, Kathleen Herkommer, Jenny L Donovan, Vanio Mitev, Edward Giovannucci, Walther Vogel, Anne Tjønneland, Bas Bueno-de-Mesquita, Henrik Grönberg, Markus Aly, Manuel Luedeke, Kathryn L. Penney, Antonia Trichopoulou, Robert Karlsson, Hui-Yi Lim, Manuel R. Teixeira, Shannon K. McDonnell, Sara Lindström, Zsofia Kote-Jarai, Bernd Holleczek, Lisa A. Cannon-Albright, Lovise Maehle, Christopher A. Haiman, Loic Le Marchand, Tom Whitington, Radka Kaneva, Jan Lubinski, Ali Amin Al Olama, and Victoria L. Stevens

Subjects
Oncology, Male, Pathology, medicine.medical_specialty, Epidemiology, business.industry, Cancer, Prostatic Neoplasms, Genome-wide association study, Disease, medicine.disease, Polymorphism, Single Nucleotide, Survival Analysis, Article, Management of prostate cancer, Prostate cancer, Polymorphism (computer science), Internal medicine, Cohort, medicine, Humans, business, Survival analysis, Genome-Wide Association Study
Abstract

Background: Unnecessary intervention and overtreatment of indolent disease are common challenges in clinical management of prostate cancer. Improved tools to distinguish lethal from indolent disease are critical. Methods: We performed a genome-wide survival analysis of cause-specific death in 24,023 prostate cancer patients (3,513 disease-specific deaths) from the PRACTICAL and BPC3 consortia. Top findings were assessed for replication in a Norwegian cohort (CONOR). Results: We observed no significant association between genetic variants and prostate cancer survival. Conclusions: Common genetic variants with large impact on prostate cancer survival were not observed in this study. Impact: Future studies should be designed for identification of rare variants with large effect sizes or common variants with small effect sizes. Cancer Epidemiol Biomarkers Prev; 24(11); 1796–800. ©2015 AACR.

Published
2015

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