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51. Meta-analysis of genome-wide association studies discovers multiple loci for chronic lymphocytic leukemia

Author

Sonja I. Berndt, Nicola J. Camp, Christine F. Skibola, Joseph Vijai, Zhaoming Wang, Jian Gu, Alexandra Nieters, Rachel S. Kelly, Karin E. Smedby, Alain Monnereau, Wendy Cozen, Angela Cox, Sophia S. Wang, Qing Lan, Lauren R. Teras, Moara Machado, Meredith Yeager, Angela R. Brooks-Wilson, Patricia Hartge, Mark P. Purdue, Brenda M. Birmann, Claire M. Vajdic, Pierluigi Cocco, Yawei Zhang, Graham G. Giles, Anne Zeleniuch-Jacquotte, Charles Lawrence, Rebecca Montalvan, Laurie Burdett, Amy Hutchinson, Yuanqing Ye, Timothy G. Call, Tait D. Shanafelt, Anne J. Novak, Neil E. Kay, Mark Liebow, Julie M. Cunningham, Cristine Allmer, Henrik Hjalgrim, Hans-Olov Adami, Mads Melbye, Bengt Glimelius, Ellen T. Chang, Martha Glenn, Karen Curtin, Lisa A. Cannon-Albright, W Ryan Diver, Brian K. Link, George J. Weiner, Lucia Conde, Paige M. Bracci, Jacques Riby, Donna K. Arnett, Degui Zhi, Justin M. Leach, Elizabeth A. Holly, Rebecca D. Jackson, Lesley F. Tinker, Yolanda Benavente, Núria Sala, Delphine Casabonne, Nikolaus Becker, Paolo Boffetta, Paul Brennan, Lenka Foretova, Marc Maynadie, James McKay, Anthony Staines, Kari G. Chaffee, Sara J. Achenbach, Celine M. Vachon, Lynn R. Goldin, Sara S. Strom, Jose F. Leis, J. Brice Weinberg, Neil E. Caporaso, Aaron D. Norman, Anneclaire J. De Roos, Lindsay M. Morton, Richard K. Severson, Elio Riboli, Paolo Vineis, Rudolph Kaaks, Giovanna Masala, Elisabete Weiderpass, María- Dolores Chirlaque, Roel C. H. Vermeulen, Ruth C. Travis, Melissa C. Southey, Roger L. Milne, Demetrius Albanes, Jarmo Virtamo, Stephanie Weinstein, Jacqueline Clavel, Tongzhang Zheng, Theodore R. Holford, Danylo J. Villano, Ann Maria, John J. Spinelli, Randy D. Gascoyne, Joseph M. Connors, Kimberly A. Bertrand, Edward Giovannucci, Peter Kraft, Anne Kricker, Jenny Turner, Maria Grazia Ennas, Giovanni M. Ferri, Lucia Miligi, Liming Liang, Baoshan Ma, Jinyan Huang, Simon Crouch, Ju-Hyun Park, Nilanjan Chatterjee, Kari E. North, John A. Snowden, Josh Wright, Joseph F. Fraumeni, Kenneth Offit, Xifeng Wu, Silvia de Sanjose, James R. Cerhan, Stephen J. Chanock, Nathaniel Rothman, and Susan L. Slager

Subjects
Science
Abstract

Chronic lymphocytic leukemia is a highly inheritable cancer. Here the authors conduct a metaanalysis of four genome-wide association studies and identify three novel loci located near EOMES, SERPINB6 and LPPassociated with risk of this disease.

Published
2016
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52. Sex Steroid Hormone Gene Variants, Pesticide Use and the Risk of Prostate Cancer: A Nested Case-Control Study within the Agricultural Health Study

Author

Carol H Christensen, Kathryn Hughes Barry, Gabriella Andreotti, Michael CR Alavanja, Michael B Cook, Scott P. Kelly, Laurie A. Burdette, Meredith Yeager, Laura E. Beane Freeman, Sonja I. Berndt, and Stella Koutros

Subjects
Pesticides, prostate cancer, Interaction, Single nucleotide polymorphism, sex steroid hormones, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract

Experimental and epidemiologic investigations suggest that certain pesticides may alter sex steroid hormone synthesis, metabolism or regulation and the risk of hormone-related cancers. Here we evaluated whether single nucleotide polymorphisms (SNPs) involved in hormone homeostasis alter the effect of pesticide exposure on prostate cancer risk. We evaluated pesticide–SNP interactions between 39 pesticides and SNPs with respect to prostate cancer among 776 cases and 1444 controls nested in the Agricultural Health Study cohort. In these interactions, we included candidate SNPs involved in hormone synthesis, metabolism and regulation (N=1100), as well as SNPs associated with circulating sex steroid concentrations as identified by genome-wide association studies (N=17). Unconditional logistic regression was used to estimate odds ratios (ORs) and 95% confidence intervals (CIs). Multiplicative SNP–pesticide interactions were calculated using a likelihood ratio test. We translated p-values for interaction into q-values, which reflected the false discovery rate, to account for multiple comparisons. We observed a significant interaction, which was robust to multiple comparison testing, between the herbicide dicamba and rs8192166 in the testosterone metabolizing gene SRD5A1 (p-interaction=4.0x10-5; q-value=0.03), such that men with two copies of the wild-type genotype CC had a reduced risk of prostate cancer associated with low use of dicamba (OR=0.62 95% CI: 0.41, 0.93), and high use of dicamba (OR=0.44, 95% CI: 0.29, 0.68), compared to those who reported no use of dicamba; in contrast, there was no significant association between dicamba and prostate cancer among those carrying one or two copies of the variant T allele at rs8192166. In addition, interactions between two organophosphate insecticides and SNPs related to estradiol metabolism were observed to result in an increased risk of prostate cancer. While replication is needed, these data suggest both agonistic or antagonistic effects on circulating hormones, due to the combination of exposure to pesticides and genetic susceptibility, may impact prostate cancer risk.

Published
2016
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53. The Interaction between Pesticide Use and Genetic Variants Involved in Lipid Metabolism on Prostate Cancer Risk

Author

Gabriella Andreotti, Stella Koutros, Sonja I. Berndt, Kathryn Hughes Barry, Lifang Hou, Jane A. Hoppin, Dale P. Sandler, Jay H. Lubin, Laurie A. Burdette, Jeffrey Yuenger, Meredith Yeager, Laura E. Beane Freeman, and Michael C. R. Alavanja

Subjects
Medicine
Abstract

Background. Lipid metabolism processes have been implicated in prostate carcinogenesis. Since several pesticides are lipophilic or are metabolized via lipid-related mechanisms, they may interact with variants of genes in the lipid metabolism pathway. Methods. In a nested case-control study of 776 cases and 1444 controls from the Agricultural Health Study (AHS), a prospective cohort study of pesticide applicators, we examined the interactions between 39 pesticides (none, low, and high exposure) and 220 single nucleotide polymorphisms (SNPs) in 59 genes. The false discovery rate (FDR) was used to account for multiple comparisons. Results. We found 17 interactions that displayed a significant monotonic increase in prostate cancer risk with pesticide exposure in one genotype and no significant association in the other genotype. The most noteworthy association was for ALOXE3 rs3027208 and terbufos, such that men carrying the T allele who were low users had an OR of 1.86 (95% CI = 1.16–2.99) and high users an OR of 2.00 (95% CI = 1.28–3.15) compared to those with no use of terbufos, while men carrying the CC genotype did not exhibit a significant association. Conclusion. Genetic variation in lipid metabolism genes may modify pesticide associations with prostate cancer; however our results require replication.

Published
2012
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54. Correction: Identification, Replication, and Fine-Mapping of Loci Associated with Adult Height in Individuals of African Ancestry.

Author

Amidou N'Diaye, Gary K. Chen, Cameron D. Palmer, Bing Ge, Bamidele Tayo, Rasika A. Mathias, Jingzhong Ding, Michael A. Nalls, Adebowale Adeyemo, Véronique Adoue, Christine B. Ambrosone, Larry Atwood, Elisa V. Bandera, Lewis C. Becker, Sonja I. Berndt, Leslie Bernstein, William J. Blot, Eric Boerwinkle, Angela Britton, Graham Casey, Stephen J. Chanock, Ellen Demerath, Sandra L. Deming, W. Ryan Diver, Caroline Fox, Tamara B. Harris, Dena G. Hernandez, Jennifer J. Hu, Sue A. Ingles, Esther M. John, Craig Johnson, Brendan Keating, Rick A. Kittles, Laurence N. Kolonel, Stephen B. Kritchevsky, Loic Le Marchand, Kurt Lohman, Jiankang Liu, Robert C. Millikan, Adam Murphy, Solomon Musani, Christine Neslund-Dudas, Kari E. North, Sarah Nyante, Adesola Ogunniyi, Elaine A. Ostrander, George Papanicolaou, Sanjay Patel, Curtis A. Pettaway, Michael F. Press, Susan Redline, Jorge L. Rodriguez-Gil, Charles Rotimi, Benjamin A. Rybicki, Babatunde Salako, Pamela J. Schreiner, Lisa B. Signorello, Andrew B. Singleton, Janet L. Stanford, Alex H. Stram, Daniel O. Stram, Sara S. Strom, Bhoom Suktitipat, Michael J. Thun, John S. Witte, Lisa R. Yanek, Regina G. Ziegler, Wei Zheng, Xiaofeng Zhu, Joseph M. Zmuda, Alan B. Zonderman, Michele K. Evans, Yongmei Liu, Diane M. Becker, Richard S. Cooper, Tomi Pastinen, Brian E. Henderson, Joel N. Hirschhorn, Guillaume Lettre, and Christopher A. Haiman

Subjects
Genetics, QH426-470
Published
2011
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56. Prognostic role of detailed colorectal location and tumor molecular features: analyses of 13,101 colorectal cancer patients including 2994 early-onset cases

Author

Tomotaka Ugai, Naohiko Akimoto, Koichiro Haruki, Tabitha A. Harrison, Yin Cao, Conghui Qu, Andrew T. Chan, Peter T. Campbell, Sonja I. Berndt, Daniel D. Buchanan, Amanda J. Cross, Brenda Diergaarde, Steven J. Gallinger, Marc J. Gunter, Sophia Harlid, Akihisa Hidaka, Michael Hoffmeister, Hermann Brenner, Jenny Chang-Claude, Li Hsu, Mark A. Jenkins, Yi Lin, Roger L. Milne, Victor Moreno, Polly A. Newcomb, Reiko Nishihara, Mireia Obon-Santacana, Rish K. Pai, Lori C. Sakoda, Robert E. Schoen, Martha L. Slattery, Wei Sun, Efrat L. Amitay, Elizabeth Alwers, Stephen N. Thibodeau, Amanda E. Toland, Bethany Van Guelpen, Syed H. Zaidi, John D. Potter, Jeffrey A. Meyerhardt, Marios Giannakis, Mingyang Song, Jonathan A. Nowak, Ulrike Peters, Amanda I. Phipps, and Shuji Ogino

Subjects
Gastroenterology
Abstract

BACKGROUND: The pathogenic effect of colorectal tumor molecular features may be influenced by several factors, including those related to microbiota, inflammation, metabolism, and epigenetics, which may change along colorectal segments. We hypothesized that the prognostic association of colon cancer location might differ by tumor molecular characteristics. METHODS: Utilizing a consortium dataset of 13,101 colorectal cancer cases, including 2994 early-onset cases, we conducted survival analyses of detailed tumor location stratified by statuses of microsatellite instability (MSI), CpG island methylator phenotype (CIMP), and KRAS and BRAF oncogenic mutation. RESULTS: There was a statistically significant trend for better colon cancer-specific survival in relation to tumor location from the cecum to sigmoid colon (Ptrend = 0.002), excluding the rectum. The prognostic association of colon location differed by MSI status (Pinteraction = 0.001). Non-MSI-high tumors exhibited the cecum-to-sigmoid trend for better colon cancer-specific survival [Ptrend

Published
2023

57. A pleiotropic variant in <scp> DNAJB4 </scp> is associated with multiple myeloma risk

Author

Marco Dicanio, Matteo Giaccherini, Alyssa Clay‐Gilmour, Angelica Macauda, Juan Sainz, Mitchell J. Machiela, Malwina Rybicka‐Ramos, Aaron D. Norman, Agata Tyczyńska, Stephen J. Chanock, Torben Barington, Shaji K. Kumar, Parveen Bhatti, Wendy Cozen, Elizabeth E. Brown, Anna Suska, Eva K. Haastrup, Robert Z. Orlowski, Marek Dudziński, Ramon Garcia‐Sanz, Marcin Kruszewski, Joaquin Martinez‐Lopez, Katia Beider, Elżbieta Iskierka‐Jazdzewska, Matteo Pelosini, Sonja I. Berndt, Małgorzata Raźny, Krzysztof Jamroziak, S. Vincent Rajkumar, Artur Jurczyszyn, Annette Juul Vangsted, Pilar Garrido Collado, Ulla Vogel, Jonathan N. Hofmann, Mario Petrini, Aleksandra Butrym, Susan L. Slager, Elad Ziv, Edyta Subocz, Graham G. Giles, Niels Frost Andersen, Grzegorz Mazur, Marzena Watek, Fabienne Lesueur, Michelle A. T. Hildebrandt, Daria Zawirska, Lene Hyldahl Ebbesen, Herlander Marques, Federica Gemignani, Charles Dumontet, Judit Várkonyi, Gabriele Buda, Arnon Nagler, Agnieszka Druzd‐Sitek, Xifeng Wu, Katalin Kadar, Nicola J. Camp, Norbert Grzasko, Rosalie G. Waller, Celine Vachon, Federico Canzian, and Daniele Campa

Subjects
Cancer Research, genetic susceptibility, multiple myeloma, pleiotropy, pleiotropy scan, polymorphisms, Humans, Oncogenes, Alleles, Phenotype, Polymorphism, Single Nucleotide, Genome-Wide Association Study, Genetic Predisposition to Disease, HSP40 Heat-Shock Proteins, DNA-Binding Proteins, RNA-Binding Proteins, Multiple Myeloma, Single Nucleotide, Oncology, Polymorphism
Abstract

Pleiotropy, which consists of a single gene or allelic variant affecting multiple unrelated traits, is common across cancers, with evidence for genome-wide significant loci shared across cancer and noncancer traits. This feature is particularly relevant in multiple myeloma (MM) because several susceptibility loci that have been identified to date are pleiotropic. Therefore, the aim of this study was to identify novel pleiotropic variants involved in MM risk using 28 684 independent single nucleotide polymorphisms (SNPs) from GWAS Catalog that reached a significant association (P < 5 × 10−8) with their respective trait. The selected SNPs were analyzed in 2434 MM cases and 3446 controls from the International Lymphoma Epidemiology Consortium (InterLymph). The 10 SNPs showing the strongest associations with MM risk in InterLymph were selected for replication in an independent set of 1955 MM cases and 1549 controls from the International Multiple Myeloma rESEarch (IMMEnSE) consortium and 418 MM cases and 147 282 controls from the FinnGen project. The combined analysis of the three studies identified an association between DNAJB4-rs34517439-A and an increased risk of developing MM (OR = 1.22, 95%CI 1.13-1.32, P = 4.81 × 10−7). rs34517439-A is associated with a modified expression of the FUBP1 gene, which encodes a multifunctional DNA and RNA-binding protein that it was observed to influence the regulation of various genes involved in cell cycle regulation, among which various oncogenes and oncosuppressors. In conclusion, with a pleiotropic scan approach we identified DNAJB4-rs34517439 as a potentially novel MM risk locus.

Published
2022

58. Genetically adjusted PSA levels for prostate cancer screening

Author

Linda Kachuri, Thomas J. Hoffmann, Yu Jiang, Sonja I. Berndt, John P. Shelley, Kerry Schaffer, Mitchell J. Machiela, Neal D. Freedman, Wen-Yi Huang, Shengchao A. Li, Ryder Easterlin, Phyllis J. Goodman, Cathee Till, Ian Thompson, Hans Lilja, Stephen K. Van Den Eeden, Stephen J. Chanock, Christopher A. Haiman, David V. Conti, Robert J. Klein, Jonathan D. Mosley, Rebecca E. Graff, and John S. Witte

Subjects
Male, Urologic Diseases, Aging, Biopsy, Prevention, Prostate Cancer, Immunology, Prostatic Neoplasms, Prostate-Specific Antigen, Medical and Health Sciences, Good Health and Well Being, Genetics, Humans, Neoplasm Grading, Early Detection of Cancer, Cancer
Abstract

Prostate-specific antigen (PSA) screening for prostate cancer remains controversial because it increases overdiagnosis and overtreatment of clinically insignificant tumors. Accounting for genetic determinants of constitutive, non-cancer-related PSA variation has potential to improve screening utility. We discovered 128 genome-wide significant associations (P-8) in a multi-ancestry meta-analysis of 95,768 men and developed a PSA polygenic score (PGSPSA) that explains 9.61% of constitutive PSA variation. We found that in men of European ancestry, using PGS-adjusted PSA would avoid 31% of negative prostate biopsies, but also result in 12% fewer biopsies in patients with prostate cancer, mostly with Gleason score P=6.2×10-14; AUC=0.755) than unadjusted PSA (OR=3.31,P=1.1×10-12; AUC=0.738) in 106 cases and 23,667 controls. Compared to a prostate cancer PGS alone (AUC=0.712), including genetically adjusted PSA improved detection of aggressive disease (AUC=0.786,P=7.2×10-4). Our findings highlight the potential utility of incorporating PGS for personalized biomarkers in prostate cancer screening.

Published
2023

59. Transcriptome-Wide Association Analysis Identifies Novel Candidate Susceptibility Genes for Prostate-Specific Antigen Levels in Men Without Prostate Cancer

Author

Dorothy M. Chen, Ruocheng Dong, Linda Kachuri, Thomas Hoffmann, Yu Jiang, Sonja I. Berndt, John P. Shelley, Kerry R. Schaffer, Mitchell J. Machiela, Neal D. Freedman, Wen-Yi Huang, Shengchao A. Li, Hans Lilja, Stephen K. Van Den Eeden, Stephen Chanock, Christopher A. Haiman, David V. Conti, Robert J. Klein, Jonathan D. Mosley, John S. Witte, and Rebecca E. Graff

Subjects
Article
Abstract

Deciphering the genetic basis of prostate-specific antigen (PSA) levels may improve their utility to screen for prostate cancer (PCa). We thus conducted a transcriptome-wide association study (TWAS) of PSA levels using genome-wide summary statistics from 95,768 PCa-free men, the MetaXcan framework, and gene prediction models trained in Genotype-Tissue Expression (GTEx) project data. Tissue-specific analyses identified 41 statistically significant (p < 0.05/12,192 = 4.10e-6) associations in whole blood and 39 statistically significant (p < 0.05/13,844 = 3.61e-6) associations in prostate tissue, with 18 genes associated in both tissues. Cross-tissue analyses that combined associations across 45 tissues identified 155 genes that were statistically significantly (p < 0.05/22,249 = 2.25e-6) associated with PSA levels. Based on conditional analyses that assessed whether TWAS associations were attributable to a lead GWAS variant, we found 20 novel genes (11 single-tissue, 9 cross-tissue) that were associated with PSA levels in the TWAS. Of these novel genes, five showed evidence of colocalization (colocalization probability > 0.5):EXOSC9, CCNA2, HIST1H2BN, RP11-182L21.6, andRP11-327J17.2. Six of the 20 novel genes are not known to impact PCa risk. These findings yield new hypotheses for genetic factors underlying PSA levels that should be further explored toward improving our understanding of PSA biology.

Published
2023

60. The association between genetically elevated polyunsaturated fatty acids and risk of cancer

Author

Philip C. Haycock, Maria Carolina Borges, Kimberley Burrows, Rozenn N. Lemaitre, Stephen Burgess, Nikhil K. Khankari, Konstantinos K. Tsilidis, Tom R. Gaunt, Gibran Hemani, Jie Zheng, Therese Truong, Brenda M. Birmann, Tracy OMara, Amanda B. Spurdle, Mark M. Iles, Matthew H. Law, Susan L. Slager, Fatemeh Saberi Hosnijeh, Daniela Mariosa, Michelle Cotterchio, James R. Cerhan, Ulrike Peters, Stefan Enroth, Puya Gharahkhani, Loic Le Marchand, Ann C. Williams, Robert C. Block, Christopher I. Amos, Rayjean J. Hung, Wei Zheng, Marc J. Gunter, George Davey Smith, Caroline Relton, Richard M. Martin, Nathan Tintle, Terri Rice, Iona Cheng, Mark Jenkins, Steve Gallinger, Alex J. Cornish, Amit Sud, Jayaram Vijayakrishnan, Margaret Wrensch, Mattias Johansson, Aaron D. Norman, Alison Klein, Alyssa Clay-Gilmour, Andre Franke, Andres V. Ardisson Korat, Bill Wheeler, Björn Nilsson, Caren Smith, Chew-Kiat Heng, Ci Song, David Riadi, Elizabeth B. Claus, Eva Ellinghaus, Evgenia Ostroumova, null Hosnijeh, Florent de Vathaire, Giovanni Cugliari, Giuseppe Matullo, Irene Oi-Lin Ng, Jeanette E. Passow, Jia Nee Foo, Jiali Han, Jianjun Liu, Jill Barnholtz-Sloan, Joellen M. Schildkraut, John Maris, Joseph L. Wiemels, Kari Hemminki, Keming Yang, Lambertus A. Kiemeney, Lang Wu, Laufey Amundadottir, Marc-Henri Stern, Marie-Christine Boutron, Mark Martin Iles, Mark P. Purdue, Martin Stanulla, Melissa Bondy, Mia Gaudet, Lenha Mobuchon, Nicola J. Camp, Pak Chung Sham, Pascal Guénel, Paul Brennan, Philip R. Taylor, Quinn Ostrom, Rachael Stolzenberg-Solomon, Rajkumar Dorajoo, Richard Houlston, Robert B. Jenkins, Sharon Diskin, Sonja I. Berndt, Spiridon Tsavachidis, Stephen J. Channock, Tabitha Harrison, Tessel Galesloot, Ulf Gyllensten, Vijai Joseph, Y. Shi, Wenjian Yang, Yi Lin, and Stephen K. Van Den Eeden

Subjects
Cancer och onkologi, General Practice, Delta-5 desaturase, General Medicine, General Biochemistry, Genetics and Molecular Biology, Omega 6, Allmänmedicin, Cancer risk, Omega 3, Cancer and Oncology, Mendelian randomization, Delta-6 desaturase, Polyunsaturated fatty acids, Bristol Population Health Science Institute
Abstract

BackgroundThe causal relevance of polyunsaturated fatty acids (PUFAs) for risk of site-specific cancers remains uncertain.MethodsUsing a Mendelian randomization (MR) framework, we assessed the causal relevance of PUFAs for risk of cancer in European and East Asian ancestry individuals. We defined the primary exposure as PUFA desaturase activity, proxied by rs174546 at the FADS locus. Secondary exposures were defined as omega 3 and omega 6 PUFAs that could be proxied by genetic polymorphisms outside the FADS region. Our study used summary genetic data on 10 PUFAs and 67 cancers, corresponding to 562,871 cases and 1,619,465 controls, collected by the Fatty Acids in Cancer Mendelian Randomization Collaboration. We estimated odds ratios (ORs) for cancer per standard deviation increase in genetically proxied PUFA exposures.FindingsGenetically elevated PUFA desaturase activity was associated (P < 0.0007) with higher risk (OR [95% confidence interval]) of colorectal cancer (1.09 [1.07–1.11]), esophageal squamous cell carcinoma (1.16 [1.06–1.26]), lung cancer (1.06 [1.03–1.08]) and basal cell carcinoma (1.05 [1.02–1.07]). There was little evidence for associations with reproductive cancers (OR = 1.00 [95% CI: 0.99–1.01]; Pheterogeneity = 0.25), urinary system cancers (1.03 [0.99–1.06], Pheterogeneity = 0.51), nervous system cancers (0.99 [0.95–1.03], Pheterogeneity = 0.92) or blood cancers (1.01 [0.98–1.04], Pheterogeneity = 0.09). Findings for colorectal cancer and esophageal squamous cell carcinoma remained compatible with causality in sensitivity analyses for violations of assumptions. Secondary MR analyses highlighted higher omega 6 PUFAs (arachidonic acid, gamma-linolenic acid and dihomo-gamma-linolenic acid) as potential mediators. PUFA biosynthesis is known to interact with aspirin, which increases risk of bleeding and inflammatory bowel disease. In a phenome-wide MR study of non-neoplastic diseases, we found that genetic lowering of PUFA desaturase activity, mimicking a hypothetical intervention to reduce cancer risk, was associated (P < 0.0006) with increased risk of inflammatory bowel disease but not bleeding.InterpretationThe PUFA biosynthesis pathway may be an intervention target for prevention of colorectal cancer and esophageal squamous cell carcinoma but with potential for increased risk of inflammatory bowel disease.FundingCancer Resesrch UK (C52724/A20138, C18281/A19169). UK Medical Research Council (MR/P014054/1). National Institute for Health Research (NIHR202411). UK Medical Research Council (MC_UU_00011/1, MC_UU_00011/3, MC_UU_00011/6, and MC_UU_00011/4). National Cancer Institute (R00 CA215360). National Institutes of Health (U01 CA164973, R01 CA60987, R01 CA72520, U01 CA74806, R01 CA55874, U01 CA164973 and U01 CA164973).

Published
2023

61. Supplementary Tables S1 - S5, Figures S1 - S5 from A Large Multiethnic Genome-Wide Association Study of Prostate Cancer Identifies Novel Risk Variants and Substantial Ethnic Differences

Author

John S. Witte, Neil Risch, Catherine Schaefer, Pui-Yan Kwok, Mark N. Kvale, Daniela Seminara, Brian E. Henderson, Christopher A. Haiman, Lorelei A. Mucci, Kathryn L. Penney, Matthew L. Freedman, Qiyuan Li, Stephen N. Thibodeau, Daniel J. Schaid, Amy J. French, Shannon K. McDonnell, Stephen J. Chanock, Sonja I. Berndt, Zhaoming Wang, Joseph Presti, David Aaronson, Charles P. Quesenberry, Dilrini K. Ranatunga, Jun Shan, Nirupa R. Ghai, Chun R. Chao, Nima C. Emami, Clinton L. Cario, Michael N. Passarelli, Rebecca E. Graff, Laurel A. Habel, Eric Jorgenson, Lori C. Sakoda, Stephen K. Van Den Eeden, and Thomas J. Hoffmann

Abstract

Supplementary Table S1. Descriptive factors for KP study population, broken down by study. Supplementary Table S2. Genome-wide significant SNPs found in our cohort. Supplementary Table S3. Cis-eQTL expression of rs4646284. Supplementary Table S4. Results at the 105 loci previously found to be associated with prostate cancer. Supplementary Table S5. Risk score of and variance explained by the 105 previously reported hits. Supplementary Figure S1. Manhattan and Q-Q plots of each race/ethnicity and meta-analysis. Supplementary Figure S2. Local plots of novel replicated rs4646284 and suggestive rs2659124. Supplementary Figure S3. Cis-eQTL of SLC22A1 and SLC22A3. Supplementary Figure S4. Comparison of ORs of KP to previous reports by race/ethnicity. Supplementary Figure S5. KP AUC estimates.

Published
2023

62. Supplementary Tables and Figure from DNA Methylation Levels at Chromosome 8q24 in Peripheral Blood Are Associated with 8q24 Cancer Susceptibility Loci

Author

Sonja I. Berndt, Laufey Amundadottir, Meredith Yeager, Zhaoming Wang, Charles C. Chung, Andrew J. Oler, Ann Meyer, Liying Yan, Joshua Sampson, Lee E. Moore, and Kathryn Hughes Barry

Abstract

Supplementary Tables and Figure. Supplementary Table S1. Cancer susceptibility SNPs at chromosome 8q24, sorted by coordinate. Supplementary Table S2. DNA methylation levels and QC results for the 60 CpG sites with a CV less than 25. Supplementary Figure S1. Boxplots displaying percent DNA methylation by genotype for the CpG site - SNP correlations (panels A-J) meeting a False Discovery Rate less than 0.05.

Published
2023

63. Does a Multiple Myeloma Polygenic Risk Score Predict Overall Survival of Patients with Myeloma?

Author

Angelica Macauda, Alyssa Clay-Gilmour, Thomas Hielscher, Michelle A.T. Hildebrandt, Marcin Kruszewski, Robert Z. Orlowski, Shaji K. Kumar, Elad Ziv, Enrico Orciuolo, Elizabeth E. Brown, Asta Försti, Rosalie G. Waller, Mitchell J. Machiela, Stephen J. Chanock, Nicola J. Camp, Marcin Rymko, Małgorzata Raźny, Wendy Cozen, Judit Várkonyi, Chiara Piredda, Matteo Pelosini, Alem A. Belachew, Edyta Subocz, Kari Hemminki, Malwina Rybicka-Ramos, Graham G. Giles, Roger L. Milne, Jonathan N. Hofmann, Jan Maciej Zaucha, Annette Juul Vangsted, Hartmut Goldschmidt, S. Vincent Rajkumar, Waldemar Tomczak, Juan Sainz, Aleksandra Butrym, Marzena Watek, Elżbieta Iskierka-Jazdzewska, Gabriele Buda, Dennis P. Robinson, Artur Jurczyszyn, Marek Dudziński, Joaquin Martinez-Lopez, Jason P. Sinnwell, Susan L. Slager, Krzysztof Jamroziak, Rui Manuel Vieira Reis, Niels Weinhold, Parveen Bhatti, Luis G. Carvajal-Carmona, Daria Zawirska, Aaron D. Norman, Grzegorz Mazur, Sonja I. Berndt, Daniele Campa, Celine M. Vachon, and Federico Canzian

Subjects
Oncology, Risk Factors, Epidemiology, Humans, Genetic Predisposition to Disease, Multiple Myeloma, Polymorphism, Single Nucleotide, Genome-Wide Association Study
Abstract

Background: Genome-wide association studies (GWAS) of multiple myeloma in populations of European ancestry (EA) identified and confirmed 24 susceptibility loci. For other cancers (e.g., colorectum and melanoma), risk loci have also been associated with patient survival. Methods: We explored the possible association of all the known risk variants and their polygenic risk score (PRS) with multiple myeloma overall survival (OS) in multiple populations of EA [the International Multiple Myeloma rESEarch (IMMEnSE) consortium, the International Lymphoma Epidemiology consortium, CoMMpass, and the German GWAS] for a total of 3,748 multiple myeloma cases. Cox proportional hazards regression was used to assess the association between each risk SNP with OS under the allelic and codominant models of inheritance. All analyses were adjusted for age, sex, country of origin (for IMMEnSE) or principal components (for the others) and disease stage (ISS). SNP associations were meta-analyzed. Results: SNP associations were meta-analyzed. From the meta-analysis, two multiple myeloma risk SNPs were associated with OS (P < 0.05), specifically POT1-AS1-rs2170352 [HR = 1.37; 95% confidence interval (CI) = 1.09–1.73; P = 0.007] and TNFRSF13B-rs4273077 (HR = 1.19; 95% CI = 1.01–1.41; P = 0.04). The association between the combined 24 SNP MM-PRS and OS, however, was not significant. Conclusions: Overall, our results did not support an association between the majority of multiple myeloma risk SNPs and OS. Impact: This is the first study to investigate the association between multiple myeloma PRS and OS in multiple myeloma.

Published
2022

64. Supplementary Data from Smoking Modifies Pancreatic Cancer Risk Loci on 2q21.3

Author

Rachael Stolzenberg-Solomon, Alison P. Klein, Nilanjan Chatterjee, Peter Kraft, Harvey A. Risch, Brian M. Wolpin, Gloria M. Petersen, Eric J. Jacobs, Donghui Li, Laufey T. Amundadottir, Anne Zeleniuch-Jacquotte, Fangcheng Yuan, Herbert Yu, Lynne R. Wilkens, Nicolas Wentzensen, Jean Wactawski-Wende, Stephen K. Van Den Eeden, Antonia Trichopoulou, Anne Tjonneland, Ian M. Thompson, Oliver Strobel, Victoria L. Stevens, Debra T. Silverman, Howard D. Sesso, Ghislaine Scelo, Nathaniel Rothman, Elio Riboli, Kari G. Rabe, Miquel Porta, Ulrike Peters, Salvatore Panico, Ann L. Oberg, Kimmie Ng, Roger L. Milne, Núria Malats, I-Min Lee, Robert C. Kurtz, Rayjean J. Hung, Robert N. Hoover, Elizabeth A. Holly, Manal M. Hassan, Patricia Hartge, Michael G. Goggins, Edward L. Giovannucci, J. Michael Gaziano, Charles S. Fuchs, Eric J. Duell, Erica J. Childs, Stephen J. Chanock, Daniele Campa, Julie E. Buring, Bas Bueno-de-Mesquita, Amanda L. Blackford, Sonja I. Berndt, William R. Bamlet, Ana Babic, Gabriella Andreotti, Demetrius Albanes, Wei Zheng, Emily White, Kala Visvanathan, Xiao-Ou Shu, Rachel E. Neale, Loic Le Marchand, Charles Kooperberg, Phyllis J. Goodman, Graham G. Giles, Steven Gallinger, Mengmeng Du, Federico Canzian, Paul Brennan, Paige M. Bracci, Laura E. Beane-Freeman, Alan A. Arslan, William Wheeler, Prosenjit Kundu, and Evelina Mocci

Abstract

Supplemental figures 1 and 2. Supplemental tables 1-7.

Published
2023

65. Data from Refining the Prostate Cancer Genetic Association within the JAZF1 Gene on Chromosome 7p15.2

Author

Meredith Yeager, Stephen J. Chanock, Nilanjan Chatterjee, Gilles Thomas, David J. Hunter, Joseph F. Fraumeni, Robert N. Hoover, Margaret Tucker, Merethe Kumle, Kristian Hveem, Lars J. Vatten, Jianfeng Xu, Fredrik Wiklund, Henrik Grönberg, Sarah D. Isaacs, William B. Isaacs, Rudolf Kaaks, Ruth Travis, Elio Riboli, Afshan Siddiq, Loic Le Marchand, Laurence Kolonel, Brian E. Henderson, Christopher A. Haiman, E. David Crawford, Gerald L. Andriole, Antoine Valeri, Olivier Cussenot, Geraldine Cancel-Tassin, Fredrick R. Schumacher, Stephanie Weinstein, Jarmo Virtamo, Demetrius Albanes, W. Ryan Diver, Michael J. Thun, Heather Spencer Feigelson, Amy Hutchinson, Kai Yu, Sholom Wacholder, Sonja I. Berndt, Peter Kraft, Richard B. Hayes, Kevin B. Jacobs, Wei Tang, Yi-Ping Fu, and Ludmila Prokunina-Olsson

Abstract

Background: Genome-wide association studies have identified multiple genetic variants associated with susceptibility to prostate cancer (PrCa). In the two-stage Cancer Genetic Markers of Susceptibility prostate cancer scan, a single-nucleotide polymorphism (SNP), rs10486567, located within intron 2 of JAZF1 gene on chromosome 7p15.2, showed a promising association with PrCa overall (P = 2.14 × 10−6), with a suggestion of stronger association with aggressive disease (P = 1.2 × 10−7).Methods: In the third stage of genome-wide association studies, we genotyped 106 JAZF1 SNPs in 10,286 PrCa cases and 9,135 controls of European ancestry.Results: The strongest association was observed with the initial marker rs10486567, which now achieves genome-wide significance [P = 7.79 × 10−11; ORHET, 1.19 (95% confidence interval, 1.12-1.27); ORHOM, 1.37 (95% confidence interval, 1.20-1.56)]. We did not confirm a previous suggestion of a stronger association of rs10486567 with aggressive disease (P = 1.60 × 10−4 for aggressive cancer, n = 4,597; P = 3.25 × 10−8 for nonaggressive cancer, n = 4,514). Based on a multilocus model with adjustment for rs10486567, no additional independent signals were observed at chromosome 7p15.2. There was no association between PrCa risk and SNPs in JAZF1 previously associated with height (rs849140; P = 0.587), body stature (rs849141, tagged by rs849136; P = 0.171), and risk of type 2 diabetes and systemic lupus erythematosus (rs864745, tagged by rs849142; P = 0.657).Conclusion: rs10486567 remains the most significant marker for PrCa risk within JAZF1 in individuals of European ancestry.Impact: Future studies should identify all variants in high linkage disequilibrium with rs10486567 and evaluate their functional significance for PrCa. Cancer Epidemiol Biomarkers Prev; 19(5); 1349–55. ©2010 AACR.

Published
2023

66. Supplementary Methods from CYP19A1 Genetic Variation in Relation to Prostate Cancer Risk and Circulating Sex Hormone Concentrations in Men from the Breast and Prostate Cancer Cohort Consortium

Author

David J. Hunter, Loïc Le Marchand, Jarmo Virtamo, Paolo Vineis, Dimitrios Trichopoulos, Anne Tjønneland, Michael J. Thun, Daniel O. Stram, Meir Stampfer, Elio Riboli, Laudina Rodriguez, Jing Ma, Laurence N. Kolonel, Rudolf Kaaks, Brian E. Henderson, Christopher A. Haiman, Edward Giovannucci, J. Michael Gaziano, Heather Spencer Feigelson, Richard Hayes, Alison M. Dunning, Stephen Chanock, Eugenia E. Calle, H. Bas Bueno-de-Mesquita, Heiner Boeing, Sonja I. Berndt, Goran Berglund, Demetrius Albanes, Naomi E. Allen, Peter Kraft, Joel N. Hirschhorn, Fredrick Schumacher, and Ruth C. Travis

Abstract

Supplementary Methods from CYP19A1 Genetic Variation in Relation to Prostate Cancer Risk and Circulating Sex Hormone Concentrations in Men from the Breast and Prostate Cancer Cohort Consortium

Published
2023

67. Data from CYP19A1 Genetic Variation in Relation to Prostate Cancer Risk and Circulating Sex Hormone Concentrations in Men from the Breast and Prostate Cancer Cohort Consortium

Author

David J. Hunter, Loïc Le Marchand, Jarmo Virtamo, Paolo Vineis, Dimitrios Trichopoulos, Anne Tjønneland, Michael J. Thun, Daniel O. Stram, Meir Stampfer, Elio Riboli, Laudina Rodriguez, Jing Ma, Laurence N. Kolonel, Rudolf Kaaks, Brian E. Henderson, Christopher A. Haiman, Edward Giovannucci, J. Michael Gaziano, Heather Spencer Feigelson, Richard Hayes, Alison M. Dunning, Stephen Chanock, Eugenia E. Calle, H. Bas Bueno-de-Mesquita, Heiner Boeing, Sonja I. Berndt, Goran Berglund, Demetrius Albanes, Naomi E. Allen, Peter Kraft, Joel N. Hirschhorn, Fredrick Schumacher, and Ruth C. Travis

Abstract

Sex hormones, particularly the androgens, are important for the growth of the prostate gland and have been implicated in prostate cancer carcinogenesis, yet the determinants of endogenous steroid hormone levels remain poorly understood. Twin studies suggest a heritable component for circulating concentrations of sex hormones, although epidemiologic evidence linking steroid hormone gene variants to prostate cancer is limited. Here we report on findings from a comprehensive study of genetic variation at the CYP19A1 locus in relation to prostate cancer risk and to circulating steroid hormone concentrations in men by the Breast and Prostate Cancer Cohort Consortium (BPC3), a large collaborative prospective study. The BPC3 systematically characterized variation in CYP19A1 by targeted resequencing and dense genotyping; selected haplotype-tagging single nucleotide polymorphisms (htSNP) that efficiently predict common variants in U.S. and European whites, Latinos, Japanese Americans, and Native Hawaiians; and genotyped these htSNPs in 8,166 prostate cancer cases and 9,079 study-, age-, and ethnicity-matched controls. CYP19A1 htSNPs, two common missense variants and common haplotypes were not significantly associated with risk of prostate cancer. However, several htSNPs in linkage disequilibrium blocks 3 and 4 were significantly associated with a 5% to 10% difference in estradiol concentrations in men [association per copy of the two-SNP haplotype rs749292-rs727479 (A-A) versus noncarriers; P = 1 × 10-5], and with inverse, although less marked changes, in free testosterone concentrations. These results suggest that although germline variation in CYP19A1 characterized by the htSNPs produces measurable differences in sex hormone concentrations in men, they do not substantially influence risk of prostate cancer. (Cancer Epidemiol Biomarkers Prev 2009;18(10):2734–44)

Published
2023

68. Supplementary Table 1 from CYP19A1 Genetic Variation in Relation to Prostate Cancer Risk and Circulating Sex Hormone Concentrations in Men from the Breast and Prostate Cancer Cohort Consortium

Author

David J. Hunter, Loïc Le Marchand, Jarmo Virtamo, Paolo Vineis, Dimitrios Trichopoulos, Anne Tjønneland, Michael J. Thun, Daniel O. Stram, Meir Stampfer, Elio Riboli, Laudina Rodriguez, Jing Ma, Laurence N. Kolonel, Rudolf Kaaks, Brian E. Henderson, Christopher A. Haiman, Edward Giovannucci, J. Michael Gaziano, Heather Spencer Feigelson, Richard Hayes, Alison M. Dunning, Stephen Chanock, Eugenia E. Calle, H. Bas Bueno-de-Mesquita, Heiner Boeing, Sonja I. Berndt, Goran Berglund, Demetrius Albanes, Naomi E. Allen, Peter Kraft, Joel N. Hirschhorn, Fredrick Schumacher, and Ruth C. Travis

Abstract

Supplementary Table 1 from CYP19A1 Genetic Variation in Relation to Prostate Cancer Risk and Circulating Sex Hormone Concentrations in Men from the Breast and Prostate Cancer Cohort Consortium

Published
2023

69. Supplemental Table from HLA Class I and II Diversity Contributes to the Etiologic Heterogeneity of Non-Hodgkin Lymphoma Subtypes

Author

Christine F. Skibola, Patricia Hartge, Nathaniel Rothman, Stephen J. Chanock, Peter Kraft, Yawei Zhang, Anne Kricker, Eve Roman, Martyn T. Smith, Angela Brooks-Wilson, Qing Lan, Richard K. Severson, Scott Davis, Anthony Staines, Lenka Foretova, Paulo Bofetta, Gilles Salles, Hervé Ghesquières, David G. Cox, Alain Monnereau, Jacqueline Clavel, Karen Curtin, Martha Glenn, Nicola J. Camp, Lucia Conde, Bengt Glimelius, Mads Melbye, Hans-Olov Adami, Mark P. Purdue, Alan A. Arslan, Jacob Musinsky, Kenneth Offit, Roger L. Milne, Melissa C. Southey, Graham G. Giles, Nicole Wong Doo, Andrew L. Feldman, Giancarlo Latte, Maria Grazia Ennas, Corrado Magnani, Brian K. Link, Marie-Hélène Delfau-Larue, James McKay, Paul Brennan, Yolanda Benavente, Elio Riboli, Rudolph Kaaks, Ruth C. Travis, Stephanie J. Lax, W. Ryan Diver, Lauren R. Teras, Stephanie J. Weinstein, Demetrius Albanes, Pierluigi Cocco, Marc Maynadie, Dennis Weisenburger, Eleanor Kane, Elizabeth A. Holly, Nikolaus Becker, Christopher R. Flowers, Brenda M. Birmann, Tongzhang Zheng, John J. Spinelli, Jennifer Turner, Elizabeth E. Brown, Wendy Cozen, Silvia de Sanjose, Alexandra Nieters, Martha S. Linet, Claire M. Vajdic, Ora Paltiel, Roel Vermeulen, Lindsay M. Morton, Joseph Vijai, Henrik Hjalgrim, Karin E. Smedby, James R. Cerhan, Jenna Voutsinas, Paige M. Bracci, Susan L. Slager, Sonja I. Berndt, Mary Carrington, and Sophia S. Wang

Abstract

SUPPLEMENTAL TABLE: Effect of homozygosity at the three HLA class I loci -A, -B and -C and five HLA class I loci -DRB1, DQA1, DQB1, DPA1, and DPB1 on susceptibility to four NHL subtypes (DLBCL, FL, CLL/SLL, and MZL) stratified by GWAS platform (analyses adjusted for sex, age, and ancestry/principal components)

Published
2023

70. Supplementary Table S2 from Intake of Dietary Fruit, Vegetables, and Fiber and Risk of Colorectal Cancer According to Molecular Subtypes: A Pooled Analysis of 9 Studies

Author

Ulrike Peters, Peter T. Campbell, Daniel D. Buchanan, Li Hsu, Wei Sun, Michael Hoffmeister, Stephen N. Thibodeau, Bethany Van Guelpen, Michael O. Woods, Xiaoliang Wang, Caroline Y. Um, Robert S. Steinfelder, Martha L. Slattery, John D. Potter, Patrick S. Parfrey, Mireia Obón-Santacana, Shuji Ogino, Reiko Nishihara, Polly A. Newcomb, Victor Moreno, Yi Lin, Mark A. Jenkins, Heather Hampel, Sophia Harlid, Mark A. Guinter, Marc J. Gunter, Steven Gallinger, Andrew T. Chan, Ivan Borozan, Sonja I. Berndt, Efrat L. Amitay, Amanda E. Toland, Syed H. Zaidi, Jane C. Figueiredo, Amanda I. Phipps, Mingyang Song, Marios Giannakis, Richard Barfield, Lori C. Sakoda, Yin Cao, Tabitha A. Harrison, and Akihisa Hidaka

Abstract

Supplementary Table S2

Published
2023

71. 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

72. Data from Genetic Predictors of Circulating 25-Hydroxyvitamin D and Risk of Colorectal Cancer

Author

Andrew T. Chan, Ulrike Peters, Peter Kraft, Brent W. Zanke, Kana Wu, Emily White, Jean Wactawski-Wende, Martha L. Slattery, Daniela Seminara, Fredrick R. Schumacher, Robert E. Schoen, John D. Potter, Kimmie Ng, Polly A. Newcomb, Hongmei Nan, JoAnn E. Manson, Jing Ma, Mathieu Lemire, Loic Le Marchand, Sébastien Küry, Mark A. Jenkins, Thomas J. Hudson, John L. Hopper, Michael Hoffmeister, Brian Henderson, Aditi Hazra, Richard B. Hayes, Tabitha A. Harrison, Edward L. Giovannucci, Steven Gallinger, Charles S. Fuchs, David Duggan, David V. Conti, Stephen J. Chanock, Jenny Chang-Claude, Graham Casey, Bette J. Caan, Hermann Brenner, Stéphane Bézieau, Sonja I. Berndt, John A. Baron, Carolyn M. Hutter, Conghui Qu, and Linda T. Hiraki

Abstract

Background: Experimental evidence has demonstrated an antineoplastic role for vitamin D in the colon, and higher circulating 25-hydroxyvitamin D [25(OH)D] levels are consistently associated with a lower risk of colorectal cancer. Genome-wide association studies have identified loci associated with levels of circulating 25(OH)D. The identified single-nucleotide polymorphisms (SNPs) from four gene regions collectively explain approximately 5% of the variance in circulating 25(OH)D.Methods: We investigated whether five polymorphisms in GC, CYP2R1, CYP24A1, and DHCR7/NADSYN1, genes previously shown to be associated with circulating 25(OH)D levels, were associated with colorectal cancer risk in 10,061 cases and 12,768 controls drawn from 13 studies included in the Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO) and Colon Cancer Family Registry (CCFR). We conducted a meta-analysis of crude and multivariate-adjusted logistic regression models to calculate odds ratios and associated confidence intervals for SNPs individually, SNPs simultaneously, and for a vitamin D additive genetic risk score (GRS).Results: We did not observe a statistically significant association between the 25(OH)D-associated SNPs and colorectal cancer marginally, conditionally, or as a GRS, or for colon or rectal cancer separately.Conclusions: Our findings do not support an association between SNPs associated with circulating 25(OH)D and risk of colorectal cancer. Additional work is warranted to investigate the complex relationship between 25(OH)D and colorectal cancer risk.Impact: There was no association observed between genetic markers of circulating 25(OH)D and colorectal cancer. These genetic markers account for a small proportion of the variance in 25(OH)D. Cancer Epidemiol Biomarkers Prev; 22(11); 2037–46. ©2013 AACR.

Published
2023

73. Supplementary Table 2 and Supplemental Figures from Cross-Cancer Genome-Wide Analysis of Lung, Ovary, Breast, Prostate, and Colorectal Cancer Reveals Novel Pleiotropic Associations

Author

Rayjean J. Hung, Brian E. Henderson, Christopher A. Haiman, David J. Hunter, Douglas F. Easton, Thomas A. Sellers, Christopher I. Amos, Stephen B. Gruber, Ulrike Peters, Jian Gong, Stephen J. Chanock, Daniela Seminara, Qiyuan Li, Matthew L. Freedman, Wim Timens, David Nickle, Ma'en Obeidat, Yohan Bossé, Atsushi Takahashi, Kouya Shiraishi, Xiao-Ou Shu, Zhibin Hu, Hongbing Shen, Yongyue Wei, David C. Christiani, Jonathan P. Tyrer, Y. Ann Chen, Patrick Sulem, Kari Stefansson, Simon N. Stacey, Julius Gudmundsson, Thorunn Rafnar, Michael O. Woods, Stephen N. Thibodeau, Stephanie L. Schmit, Noralene M. Lindor, Li Li, Loïc Le Marchand, Mark Jenkins, Robert W. Haile, Steven Gallinger, Christopher K. Edlund, David V. Conti, Graham Casey, Daniel D. Buchanan, Wei Zheng, Xiaohong R. Yang, Alice S. Whittemore, Zhaoming Wang, Andre G. Uitterlinden, Clare Turnbull, Ruth C. Travis, Rulla Tamimi, Melissa C. Southey, Rita K. Schmutzler, Daniel F. Schmidt, Maria Jose Sanchez, Nazneen Rahman, Ross L. Prentice, Julian Peto, Petra H. Peeters, Heli Nevanlinna, Taru A. Muranen, Bertram Müller-Myhsok, Alfons Meindl, Enes Makalic, Eiliv Lund, Jianjun Liu, Peter Lichtner, Muhammad G. Kibriya, Rudolf Kaaks, Mattias Johansson, Astrid Irwanto, John L. Hopper, Albert Hofman, Rebecca Hein, Aditi Hazra, Per Hall, Nichola Johnson, Mia M. Gaudet, Montserrat Garcia-Closas, Olivia Fletcher, Dieter Flesch-Janys, Jonine D. Figueroa, A. Heather Eliassen, Isabel dos-Santos-Silva, Kamila Czene, Federico Canzian, Carl Blomquist, Laura Baglietto, Kristiina Aittomäki, Habibul Ahsan, Muriel A. Adank, Emily White, Martha L. Slattery, Robert E. Schoen, Polly A. Newcomb, Jonathan K. Kocarnik, Thomas J. Hudson, Jenny Chang-Claude, Andrew T. Chan, Hermann Brenner, Stephane Bezieau, Brett M. Reid, Harvey A. Risch, Jennifer B. Permuth, Ellen L. Goode, Walter C. Willett, Fredrik Wiklund, Victoria L. Stevens, Meir J. Stampfer, Kenneth Muir, Jing Ma, Zsofia Kote-Jarai, Henrik Grönberg, Edward L. Giovannucci, Sonja I. Berndt, Ali Amin Al Olama, Angela Risch, Neil Caporaso, Maria Teresa Landi, Richard S. Houlston, Heike Bickeböller, Paul Brennan, Sara Lindström, Joellen M. Schildkraut, Fredrick R. Schumacher, Nilanjan Chatterjee, Rosalind A. Eeles, Paul D. Pharoah, Peter Kraft, and Gordon Fehringer

Abstract

Table S2: Odds ratio and 95% confidence limits for cancers associated with variants with pleiotropic associations. Figure S1: Flowchart showing analysis steps. Figure S2. Manhattan plots by chromosome for individual cancer sites. Figure S3. Results for rs11571833. Figure S4: Conditional QQ-plots.

Published
2023

74. Data from HLA Class I and II Diversity Contributes to the Etiologic Heterogeneity of Non-Hodgkin Lymphoma Subtypes

Author

Christine F. Skibola, Patricia Hartge, Nathaniel Rothman, Stephen J. Chanock, Peter Kraft, Yawei Zhang, Anne Kricker, Eve Roman, Martyn T. Smith, Angela Brooks-Wilson, Qing Lan, Richard K. Severson, Scott Davis, Anthony Staines, Lenka Foretova, Paulo Bofetta, Gilles Salles, Hervé Ghesquières, David G. Cox, Alain Monnereau, Jacqueline Clavel, Karen Curtin, Martha Glenn, Nicola J. Camp, Lucia Conde, Bengt Glimelius, Mads Melbye, Hans-Olov Adami, Mark P. Purdue, Alan A. Arslan, Jacob Musinsky, Kenneth Offit, Roger L. Milne, Melissa C. Southey, Graham G. Giles, Nicole Wong Doo, Andrew L. Feldman, Giancarlo Latte, Maria Grazia Ennas, Corrado Magnani, Brian K. Link, Marie-Hélène Delfau-Larue, James McKay, Paul Brennan, Yolanda Benavente, Elio Riboli, Rudolph Kaaks, Ruth C. Travis, Stephanie J. Lax, W. Ryan Diver, Lauren R. Teras, Stephanie J. Weinstein, Demetrius Albanes, Pierluigi Cocco, Marc Maynadie, Dennis Weisenburger, Eleanor Kane, Elizabeth A. Holly, Nikolaus Becker, Christopher R. Flowers, Brenda M. Birmann, Tongzhang Zheng, John J. Spinelli, Jennifer Turner, Elizabeth E. Brown, Wendy Cozen, Silvia de Sanjose, Alexandra Nieters, Martha S. Linet, Claire M. Vajdic, Ora Paltiel, Roel Vermeulen, Lindsay M. Morton, Joseph Vijai, Henrik Hjalgrim, Karin E. Smedby, James R. Cerhan, Jenna Voutsinas, Paige M. Bracci, Susan L. Slager, Sonja I. Berndt, Mary Carrington, and Sophia S. Wang

Abstract

A growing number of loci within the human leukocyte antigen (HLA) region have been implicated in non-Hodgkin lymphoma (NHL) etiology. Here, we test a complementary hypothesis of “heterozygote advantage” regarding the role of HLA and NHL, whereby HLA diversity is beneficial and homozygous HLA loci are associated with increased disease risk. HLA alleles at class I and II loci were imputed from genome-wide association studies (GWAS) using SNP2HLA for 3,617 diffuse large B-cell lymphomas (DLBCL), 2,686 follicular lymphomas (FL), 2,878 chronic lymphocytic leukemia/small lymphocytic lymphomas (CLL/SLL), 741 marginal zone lymphomas (MZL), and 8,753 controls of European descent. Both DLBCL and MZL risk were elevated with homozygosity at class I HLA-B and -C loci (OR DLBCL = 1.31, 95% CI = 1.06–1.60; OR MZL = 1.45, 95% CI = 1.12–1.89) and class II HLA-DRB1 locus (OR DLBCL = 2.10, 95% CI = 1.24–3.55; OR MZL = 2.10, 95% CI = 0.99–4.45). Increased FL risk was observed with the overall increase in number of homozygous HLA class II loci (P trend < 0.0001, FDR = 0.0005). These results support a role for HLA zygosity in NHL etiology and suggests that distinct immune pathways may underly the etiology of the different NHL subtypes.Significance: HLA gene diversity reduces risk for non-Hodgkin lymphoma. Cancer Res; 78(14); 4086–96. ©2018 AACR.

Published
2023

75. Data from Common Genetic Variants in Prostate Cancer Risk Prediction—Results from the NCI Breast and Prostate Cancer Cohort Consortium (BPC3)

Author

Peter Kraft, Stephen J. Chanock, Christopher A. Haiman, Gianluca Severi, Richard B. Hayes, Meredith Yeager, Walter C. Willett, Stephanie J. Weinstein, Jarmo Virtamo, Dimitrios Trichopoulos, Anne Tjonneland, Michael J. Thun, Daniel O. Stram, Meir Stampfer, Valeria Pala, Loïc Le Marchand, Jing Ma, Laurence N. Kolonel, Mattias Johansson, David J. Hunter, Brian Henderson, Carlos A. Gonzalez, Edward Giovannucci, Graham G. Giles, J. Michael Gaziano, W. Ryan Diver, E. David Crawford, H. Bas Bueno-de-Mesquita, Heiner Boeing, Sonja I. Berndt, Gerald Andriole, Naomi E. Allen, Demetrius Albanes, Ruth C. Travis, David Cox, Fredrick R. Schumacher, and Sara Lindström

Abstract

Background: One of the goals of personalized medicine is to generate individual risk profiles that could identify individuals in the population that exhibit high risk. The discovery of more than two-dozen independent single-nucleotide polymorphism markers in prostate cancer has raised the possibility for such risk stratification. In this study, we evaluated the discriminative and predictive ability for prostate cancer risk models incorporating 25 common prostate cancer genetic markers, family history of prostate cancer, and age.Methods: We fit a series of risk models and estimated their performance in 7,509 prostate cancer cases and 7,652 controls within the National Cancer Institute Breast and Prostate Cancer Cohort Consortium (BPC3). We also calculated absolute risks based on SEER incidence data.Results: The best risk model (C-statistic = 0.642) included individual genetic markers and family history of prostate cancer. We observed a decreasing trend in discriminative ability with advancing age (P = 0.009), with highest accuracy in men younger than 60 years (C-statistic = 0.679). The absolute ten-year risk for 50-year-old men with a family history ranged from 1.6% (10th percentile of genetic risk) to 6.7% (90th percentile of genetic risk). For men without family history, the risk ranged from 0.8% (10th percentile) to 3.4% (90th percentile).Conclusions: Our results indicate that incorporating genetic information and family history in prostate cancer risk models can be particularly useful for identifying younger men that might benefit from prostate-specific antigen screening.Impact: Although adding genetic risk markers improves model performance, the clinical utility of these genetic risk models is limited. Cancer Epidemiol Biomarkers Prev; 21(3); 437–44. ©2012 AACR.

Published
2023

76. Supplementary Tables S1-3 from Mendelian Randomization Study of Body Mass Index and Colorectal Cancer Risk

Author

Peter T. Campbell, Li Hsu, Emily White, Hermann Brenner, Michael Hoffmeister, Polly A. Newcomb, John D. Potter, Cornelia M. Ulrich, John L. Hopper, Mark A. Jenkins, Aung Ko Win, Michelle Cotterchio, Stephen N. Thibodeau, Kana Wu, Mingyang Song, Daniela Seminara, Noralane M. Lindor, Loïc Le Marchand, David J. Duggan, Mark Thornquist, Tabitha A. Harrison, Mengmeng Du, Robert W. Haile, Graham Casey, Stephen J. Chanock, Sonja I. Berndt, Shuji Ogino, Bette J. Caan, John A. Baron, Richard B. Hayes, Steven Gallinger, Tune H. Pers, Anne E. Justice, Bratati Kahali, Adam E. Locke, Andrew T. Chan, Martha L. Slattery, Anja Rudolph, Jenny Chang-Claude, Ulrike Peters, Jian Gong, and Aaron P. Thrift

Abstract

Supplementary Tables S1-3. Supplementary Table S1 Description of the characteristics by study. Supplementary Table S2 Associations between confounders and body mass index and the weighted genetic risk score among controls. Supplementary Table S3 Odds ratios (OR) and 95% confidence intervals (CI) for the association between a 1-unit increase in the weighted genetic risk score (the instrumental variable [IV]) and risk of colorectal cancer.

Published
2023

77. Supplementary Tables 1-8 from Common Genetic Variants in Prostate Cancer Risk Prediction—Results from the NCI Breast and Prostate Cancer Cohort Consortium (BPC3)

Author

Peter Kraft, Stephen J. Chanock, Christopher A. Haiman, Gianluca Severi, Richard B. Hayes, Meredith Yeager, Walter C. Willett, Stephanie J. Weinstein, Jarmo Virtamo, Dimitrios Trichopoulos, Anne Tjonneland, Michael J. Thun, Daniel O. Stram, Meir Stampfer, Valeria Pala, Loïc Le Marchand, Jing Ma, Laurence N. Kolonel, Mattias Johansson, David J. Hunter, Brian Henderson, Carlos A. Gonzalez, Edward Giovannucci, Graham G. Giles, J. Michael Gaziano, W. Ryan Diver, E. David Crawford, H. Bas Bueno-de-Mesquita, Heiner Boeing, Sonja I. Berndt, Gerald Andriole, Naomi E. Allen, Demetrius Albanes, Ruth C. Travis, David Cox, Fredrick R. Schumacher, and Sara Lindström

Abstract

PDF file - 169K

Published
2023

79. Supplementary Figure 1 from Common Genetic Variants in Prostate Cancer Risk Prediction—Results from the NCI Breast and Prostate Cancer Cohort Consortium (BPC3)

Author

Peter Kraft, Stephen J. Chanock, Christopher A. Haiman, Gianluca Severi, Richard B. Hayes, Meredith Yeager, Walter C. Willett, Stephanie J. Weinstein, Jarmo Virtamo, Dimitrios Trichopoulos, Anne Tjonneland, Michael J. Thun, Daniel O. Stram, Meir Stampfer, Valeria Pala, Loïc Le Marchand, Jing Ma, Laurence N. Kolonel, Mattias Johansson, David J. Hunter, Brian Henderson, Carlos A. Gonzalez, Edward Giovannucci, Graham G. Giles, J. Michael Gaziano, W. Ryan Diver, E. David Crawford, H. Bas Bueno-de-Mesquita, Heiner Boeing, Sonja I. Berndt, Gerald Andriole, Naomi E. Allen, Demetrius Albanes, Ruth C. Travis, David Cox, Fredrick R. Schumacher, and Sara Lindström

Abstract

PDF file - 71K

Published
2023

80. Data from Genome-Wide Association Study Data Reveal Genetic Susceptibility to Chronic Inflammatory Intestinal Diseases and Pancreatic Ductal Adenocarcinoma Risk

Author

Rachael Stolzenberg-Solomon, Alison P. Klein, Kai Yu, Harvey A. Risch, Brian M. Wolpin, Gloria M. Petersen, Donghui Li, Laufey T. Amundadottir, Eric J. Duell, Jianxin Shi, Anne Zeleniuch-Jacquotte, Herbert Yu, Lynne R. Wilkens, Nicolas Wentzensen, Xiaoliang Wang, Jean Wactawski-Wende, Ian M. Thompson, Debra T. Silverman, Howard D. Sesso, Nathaniel Rothman, Francisco X. Real, Kari G. Rabe, Miquel Porta, Ann L. Oberg, Kimmie Ng, Neil Murphy, Roger L. Milne, Nuria Malats, I-Min Lee, Robert C. Kurtz, Holger Kirsten, Verena Katzke, Robert N. Hoover, Elizabeth A. Holly, Manal M. Hassan, Patricia Hartge, Thilo Hackert, Michael G. Goggins, J. Michael Gaziano, Charles S. Fuchs, Stephen J. Chanock, Peter T. Campbell, Julie E. Buring, Bas Bueno-de-Mesquita, Paul Brennan, Sonja I. Berndt, William R. Bamlet, Ana Babic, Gabriella Andreotti, Pilar Amiano, Demetrius Albanes, Wei Zheng, Emily White, Kala Visvanathan, Xiao-Ou Shu, Ghislaine Scelo, Jonas Rosendahl, Rachel E. Neale, Loic Le Marchand, Charles Kooperberg, Phyllis J. Goodman, Graham G. Giles, Steven Gallinger, Mengmeng Du, Federico Canzian, Paige Bracci, Laura E. Beane Freeman, Alan A. Arslan, Lei Song, William Wheeler, Elizabeth A. Platz, Han Zhang, Naomi Walsh, Rayjean J. Hung, and Fangcheng Yuan

Abstract

Registry-based epidemiologic studies suggest associations between chronic inflammatory intestinal diseases and pancreatic ductal adenocarcinoma (PDAC). As genetic susceptibility contributes to a large proportion of chronic inflammatory intestinal diseases, we hypothesize that the genomic regions surrounding established genome-wide associated variants for these chronic inflammatory diseases are associated with PDAC. We examined the association between PDAC and genomic regions (±500 kb) surrounding established common susceptibility variants for ulcerative colitis, Crohn's disease, inflammatory bowel disease, celiac disease, chronic pancreatitis, and primary sclerosing cholangitis. We analyzed summary statistics from genome-wide association studies data for 8,384 cases and 11,955 controls of European descent from two large consortium studies using the summary data-based adaptive rank truncated product method to examine the overall association of combined genomic regions for each inflammatory disease group. Combined genomic susceptibility regions for ulcerative colitis, Crohn disease, inflammatory bowel disease, and chronic pancreatitis were associated with PDAC at P values < 0.05 (0.0040, 0.0057, 0.011, and 3.4 × 10−6, respectively). After excluding the 20 PDAC susceptibility regions (±500 kb) previously identified by GWAS, the genomic regions for ulcerative colitis, Crohn disease, and inflammatory bowel disease remained associated with PDAC (P = 0.0029, 0.0057, and 0.0098, respectively). Genomic regions for celiac disease (P = 0.22) and primary sclerosing cholangitis (P = 0.078) were not associated with PDAC. Our results support the hypothesis that genomic regions surrounding variants associated with inflammatory intestinal diseases, particularly, ulcerative colitis, Crohn disease, inflammatory bowel disease, and chronic pancreatitis are associated with PDAC.Significance:The joint effects of common variants in genomic regions containing susceptibility loci for inflammatory bowel disease and chronic pancreatitis are associated with PDAC and may provide insights to understanding pancreatic cancer etiology.

Published
2023

81. Data from Eighteen Insulin-like Growth Factor Pathway Genes, Circulating Levels of IGF-I and Its Binding Protein, and Risk of Prostate and Breast Cancer

Author

Peter Kraft, Regina G. Ziegler, Elio Riboli, Rudolf Kaaks, Shumin M. Zhang, Meredith Yeager, Walter C. Willett, Stephanie J. Weinstein, Jarmo Virtamo, Rosario Tumino, Dimitrios Trichopoulos, Anne Tjønneland, Michael J. Thun, Gilles Thomas, Daniel O. Stram, Pär Stattin, Meir J. Stampfer, Maria-José Sánchez, Carlotta Sacerdote, Laudina Rodriguez, Kim Overvad, N. Charlotte Onland-Moret, Jing Ma, Eiliv Lund, Loic LeMarchand, I-Min Lee, Pagona Lagiou, Laurence N. Kolonel, Kay-Tee Khaw, Timothy J. Key, Mattias Johansson, Robert N. Hoover, David J. Hunter, Brian E. Henderson, Richard B. Hayes, Susan E. Hankinson, Christopher A. Haiman, Edward L. Giovannucci, J. Michael Gaziano, Vanessa Dumeaux, Françoise Clavel-Chapelon, Stephen J. Chanock, Nathalie Chabbert-Buffet, Julie E. Buring, H. Bas Bueno-de-Mesquita, Heiner Boeing, Sonja I. Berndt, Christine D. Berg, Demetrius Albanes, Naomi E. Allen, Federico Canzian, Fredrick R. Schumacher, and Fangyi Gu

Abstract

Background: Circulating levels of insulin-like growth factor I (IGF-I) and its main binding protein, IGF binding protein 3 (IGFBP-3), have been associated with risk of several types of cancer. Heritable factors explain up to 60% of the variation in IGF-I and IGFBP-3 in studies of adult twins.Methods: We systematically examined common genetic variation in 18 genes in the IGF signaling pathway for associations with circulating levels of IGF-I and IGFBP-3. A total of 302 single nucleotide polymorphisms (SNP) were genotyped in >5,500 Caucasian men and 5,500 Caucasian women from the Breast and Prostate Cancer Cohort Consortium.Results: After adjusting for multiple testing, SNPs in the IGF1 and SSTR5 genes were significantly associated with circulating IGF-I (P < 2.1 × 10−4); SNPs in the IGFBP3 and IGFALS genes were significantly associated with circulating IGFBP-3. Multi-SNP models explained R2 = 0.62% of the variation in circulating IGF-I and 3.9% of the variation in circulating IGFBP-3. We saw no significant association between these multi-SNP predictors of circulating IGF-I or IGFBP-3 and risk of prostate or breast cancers.Conclusion: Common genetic variation in the IGF1 and SSTR5 genes seems to influence circulating IGF-I levels, and variation in IGFBP3 and IGFALS seems to influence circulating IGFBP-3. However, these variants explain only a small percentage of the variation in circulating IGF-I and IGFBP-3 in Caucasian men and women.Impact: Further studies are needed to explore contributions from other genetic factors such as rare variants in these genes and variation outside of these genes. Cancer Epidemiol Biomarkers Prev; 19(11); 2877–87. ©2010 AACR.

Published
2023

82. Data from Associations between Genes in the One-Carbon Metabolism Pathway and Advanced Colorectal Adenoma Risk in Individuals with Low Folate Intake

Author

Regina G. Ziegler, Philip S. Rosenberg, Laurie A. Burdette, Jacob Selhub, Sonja I. Berndt, Laura Y. Sue, and Summer S. Han

Abstract

Background: Folate is essential for one-carbon metabolism, a pathway required by DNA synthesis, methylation, and repair. Low dietary and circulating folate and polymorphic variation in this pathway are associated with increased risk of colorectal adenoma and cancer.Methods: We genotyped 882 single nucleotide polymorphisms (SNP) in 82 one-carbon metabolism genes for 1,331 cases of advanced colorectal adenoma, identified by sigmoidoscopy at baseline, and 1,501 controls from the Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial (PLCO). We evaluated associations between one-carbon genes and adenoma risk in all subjects and stratified by folate intake. We applied the Adaptive Rank Truncated Product (ARTP) method to assess statistical significance at the gene and pathway levels.Results: Folate intake was inversely associated with advanced colorectal adenoma risk [odds ratio (OR) by quartile = 0.85, P = 1.9 × 10−5]. We found no statistically significant associations between one-carbon genes and adenoma risk in all subjects. As hypothesized, we observed a statistically significant pathway-level association (P = 0.038) in the lowest quartile of folate; no significant associations were found in higher quartiles. Several genes including adenosine deaminase (ADA) and cysteine dioxygenase (CDO1) contributed to this signal (gene-level P = 0.001 and 0.0073, respectively). The most statistically significant SNP was rs244072 in ADA (P = 2.37 × 10−5).Conclusions and Impact: Stratification by dietary folate and application of the ARTP method revealed statistically significant pathway- and gene-level associations between one-carbon metabolism genes and risk of advanced colorectal adenoma, which were not apparent in analysis of the entire population. Folate intake may interact with associations between common variants in one-carbon metabolism genes and colorectal adenoma risk. Cancer Epidemiol Biomarkers Prev; 21(3); 417–27. ©2012 AACR.

Published
2023

83. Data from Mendelian Randomization Study of Body Mass Index and Colorectal Cancer Risk

Author

Peter T. Campbell, Li Hsu, Emily White, Hermann Brenner, Michael Hoffmeister, Polly A. Newcomb, John D. Potter, Cornelia M. Ulrich, John L. Hopper, Mark A. Jenkins, Aung Ko Win, Michelle Cotterchio, Stephen N. Thibodeau, Kana Wu, Mingyang Song, Daniela Seminara, Noralane M. Lindor, Loïc Le Marchand, David J. Duggan, Mark Thornquist, Tabitha A. Harrison, Mengmeng Du, Robert W. Haile, Graham Casey, Stephen J. Chanock, Sonja I. Berndt, Shuji Ogino, Bette J. Caan, John A. Baron, Richard B. Hayes, Steven Gallinger, Tune H. Pers, Anne E. Justice, Bratati Kahali, Adam E. Locke, Andrew T. Chan, Martha L. Slattery, Anja Rudolph, Jenny Chang-Claude, Ulrike Peters, Jian Gong, and Aaron P. Thrift

Abstract

Background: High body mass index (BMI) is consistently linked to increased risk of colorectal cancer for men, whereas the association is less clear for women. As risk estimates from observational studies may be biased and/or confounded, we conducted a Mendelian randomization study to estimate the causal association between BMI and colorectal cancer.Methods: We used data from 10,226 colorectal cancer cases and 10,286 controls of European ancestry. The Mendelian randomization analysis used a weighted genetic risk score, derived from 77 genome-wide association study–identified variants associated with higher BMI, as an instrumental variable (IV). We compared the IV odds ratio (IV-OR) with the OR obtained using a conventional covariate-adjusted analysis.Results: Individuals carrying greater numbers of BMI-increasing alleles had higher colorectal cancer risk [per weighted allele OR, 1.31; 95% confidence interval (CI), 1.10–1.57]. Our IV estimation results support the hypothesis that genetically influenced BMI is directly associated with risk for colorectal cancer (IV-OR per 5 kg/m2, 1.50; 95% CI, 1.13–2.01). In the sex-specific IV analyses higher BMI was associated with higher risk of colorectal cancer among women (IV-OR per 5 kg/m2, 1.82; 95% CI, 1.26–2.61). For men, genetically influenced BMI was not associated with colorectal cancer (IV-OR per 5 kg/m2, 1.18; 95% CI, 0.73–1.92).Conclusions: High BMI was associated with increased colorectal cancer risk for women. Whether abdominal obesity, rather than overall obesity, is a more important risk factor for men requires further investigation.Impact: Overall, conventional epidemiologic and Mendelian randomization studies suggest a strong association between obesity and the risk of colorectal cancer. Cancer Epidemiol Biomarkers Prev; 24(7); 1024–31. ©2015 AACR.

Published
2023

84. Supplementary Table 3 from Refining the Prostate Cancer Genetic Association within the JAZF1 Gene on Chromosome 7p15.2

Author

Meredith Yeager, Stephen J. Chanock, Nilanjan Chatterjee, Gilles Thomas, David J. Hunter, Joseph F. Fraumeni, Robert N. Hoover, Margaret Tucker, Merethe Kumle, Kristian Hveem, Lars J. Vatten, Jianfeng Xu, Fredrik Wiklund, Henrik Grönberg, Sarah D. Isaacs, William B. Isaacs, Rudolf Kaaks, Ruth Travis, Elio Riboli, Afshan Siddiq, Loic Le Marchand, Laurence Kolonel, Brian E. Henderson, Christopher A. Haiman, E. David Crawford, Gerald L. Andriole, Antoine Valeri, Olivier Cussenot, Geraldine Cancel-Tassin, Fredrick R. Schumacher, Stephanie Weinstein, Jarmo Virtamo, Demetrius Albanes, W. Ryan Diver, Michael J. Thun, Heather Spencer Feigelson, Amy Hutchinson, Kai Yu, Sholom Wacholder, Sonja I. Berndt, Peter Kraft, Richard B. Hayes, Kevin B. Jacobs, Wei Tang, Yi-Ping Fu, and Ludmila Prokunina-Olsson

Abstract

Supplementary Table 3 from Refining the Prostate Cancer Genetic Association within the JAZF1 Gene on Chromosome 7p15.2

Published
2023

85. Supplementary Table 1 from Refining the Prostate Cancer Genetic Association within the JAZF1 Gene on Chromosome 7p15.2

Author

Meredith Yeager, Stephen J. Chanock, Nilanjan Chatterjee, Gilles Thomas, David J. Hunter, Joseph F. Fraumeni, Robert N. Hoover, Margaret Tucker, Merethe Kumle, Kristian Hveem, Lars J. Vatten, Jianfeng Xu, Fredrik Wiklund, Henrik Grönberg, Sarah D. Isaacs, William B. Isaacs, Rudolf Kaaks, Ruth Travis, Elio Riboli, Afshan Siddiq, Loic Le Marchand, Laurence Kolonel, Brian E. Henderson, Christopher A. Haiman, E. David Crawford, Gerald L. Andriole, Antoine Valeri, Olivier Cussenot, Geraldine Cancel-Tassin, Fredrick R. Schumacher, Stephanie Weinstein, Jarmo Virtamo, Demetrius Albanes, W. Ryan Diver, Michael J. Thun, Heather Spencer Feigelson, Amy Hutchinson, Kai Yu, Sholom Wacholder, Sonja I. Berndt, Peter Kraft, Richard B. Hayes, Kevin B. Jacobs, Wei Tang, Yi-Ping Fu, and Ludmila Prokunina-Olsson

Abstract

Supplementary Table 1 from Refining the Prostate Cancer Genetic Association within the JAZF1 Gene on Chromosome 7p15.2

Published
2023

86. Data from Cross-Cancer Genome-Wide Analysis of Lung, Ovary, Breast, Prostate, and Colorectal Cancer Reveals Novel Pleiotropic Associations

Author

Rayjean J. Hung, Brian E. Henderson, Christopher A. Haiman, David J. Hunter, Douglas F. Easton, Thomas A. Sellers, Christopher I. Amos, Stephen B. Gruber, Ulrike Peters, Jian Gong, Stephen J. Chanock, Daniela Seminara, Qiyuan Li, Matthew L. Freedman, Wim Timens, David Nickle, Ma'en Obeidat, Yohan Bossé, Atsushi Takahashi, Kouya Shiraishi, Xiao-Ou Shu, Zhibin Hu, Hongbing Shen, Yongyue Wei, David C. Christiani, Jonathan P. Tyrer, Y. Ann Chen, Patrick Sulem, Kari Stefansson, Simon N. Stacey, Julius Gudmundsson, Thorunn Rafnar, Michael O. Woods, Stephen N. Thibodeau, Stephanie L. Schmit, Noralene M. Lindor, Li Li, Loïc Le Marchand, Mark Jenkins, Robert W. Haile, Steven Gallinger, Christopher K. Edlund, David V. Conti, Graham Casey, Daniel D. Buchanan, Wei Zheng, Xiaohong R. Yang, Alice S. Whittemore, Zhaoming Wang, Andre G. Uitterlinden, Clare Turnbull, Ruth C. Travis, Rulla Tamimi, Melissa C. Southey, Rita K. Schmutzler, Daniel F. Schmidt, Maria Jose Sanchez, Nazneen Rahman, Ross L. Prentice, Julian Peto, Petra H. Peeters, Heli Nevanlinna, Taru A. Muranen, Bertram Müller-Myhsok, Alfons Meindl, Enes Makalic, Eiliv Lund, Jianjun Liu, Peter Lichtner, Muhammad G. Kibriya, Rudolf Kaaks, Mattias Johansson, Astrid Irwanto, John L. Hopper, Albert Hofman, Rebecca Hein, Aditi Hazra, Per Hall, Nichola Johnson, Mia M. Gaudet, Montserrat Garcia-Closas, Olivia Fletcher, Dieter Flesch-Janys, Jonine D. Figueroa, A. Heather Eliassen, Isabel dos-Santos-Silva, Kamila Czene, Federico Canzian, Carl Blomquist, Laura Baglietto, Kristiina Aittomäki, Habibul Ahsan, Muriel A. Adank, Emily White, Martha L. Slattery, Robert E. Schoen, Polly A. Newcomb, Jonathan K. Kocarnik, Thomas J. Hudson, Jenny Chang-Claude, Andrew T. Chan, Hermann Brenner, Stephane Bezieau, Brett M. Reid, Harvey A. Risch, Jennifer B. Permuth, Ellen L. Goode, Walter C. Willett, Fredrik Wiklund, Victoria L. Stevens, Meir J. Stampfer, Kenneth Muir, Jing Ma, Zsofia Kote-Jarai, Henrik Grönberg, Edward L. Giovannucci, Sonja I. Berndt, Ali Amin Al Olama, Angela Risch, Neil Caporaso, Maria Teresa Landi, Richard S. Houlston, Heike Bickeböller, Paul Brennan, Sara Lindström, Joellen M. Schildkraut, Fredrick R. Schumacher, Nilanjan Chatterjee, Rosalind A. Eeles, Paul D. Pharoah, Peter Kraft, and Gordon Fehringer

Abstract

Identifying genetic variants with pleiotropic associations can uncover common pathways influencing multiple cancers. We took a two-stage approach to conduct genome-wide association studies for lung, ovary, breast, prostate, and colorectal cancer from the GAME-ON/GECCO Network (61,851 cases, 61,820 controls) to identify pleiotropic loci. Findings were replicated in independent association studies (55,789 cases, 330,490 controls). We identified a novel pleiotropic association at 1q22 involving breast and lung squamous cell carcinoma, with eQTL analysis showing an association with ADAM15/THBS3 gene expression in lung. We also identified a known breast cancer locus CASP8/ALS2CR12 associated with prostate cancer, a known cancer locus at CDKN2B-AS1 with different variants associated with lung adenocarcinoma and prostate cancer, and confirmed the associations of a breast BRCA2 locus with lung and serous ovarian cancer. This is the largest study to date examining pleiotropy across multiple cancer-associated loci, identifying common mechanisms of cancer development and progression. Cancer Res; 76(17); 5103–14. ©2016 AACR.

Published
2023

87. Supplementary Data and Supplementary Tables 1 and 2 from Genetic Predictors of Circulating 25-Hydroxyvitamin D and Risk of Colorectal Cancer

Author

Andrew T. Chan, Ulrike Peters, Peter Kraft, Brent W. Zanke, Kana Wu, Emily White, Jean Wactawski-Wende, Martha L. Slattery, Daniela Seminara, Fredrick R. Schumacher, Robert E. Schoen, John D. Potter, Kimmie Ng, Polly A. Newcomb, Hongmei Nan, JoAnn E. Manson, Jing Ma, Mathieu Lemire, Loic Le Marchand, Sébastien Küry, Mark A. Jenkins, Thomas J. Hudson, John L. Hopper, Michael Hoffmeister, Brian Henderson, Aditi Hazra, Richard B. Hayes, Tabitha A. Harrison, Edward L. Giovannucci, Steven Gallinger, Charles S. Fuchs, David Duggan, David V. Conti, Stephen J. Chanock, Jenny Chang-Claude, Graham Casey, Bette J. Caan, Hermann Brenner, Stéphane Bézieau, Sonja I. Berndt, John A. Baron, Carolyn M. Hutter, Conghui Qu, and Linda T. Hiraki

Abstract

Contains more detailed information on the individual cohorts contributing to the study and their genotyping results; Supplemental Tables 1 and 2

Published
2023

88. Supplementary Table 1 from Eighteen Insulin-like Growth Factor Pathway Genes, Circulating Levels of IGF-I and Its Binding Protein, and Risk of Prostate and Breast Cancer

Author

Peter Kraft, Regina G. Ziegler, Elio Riboli, Rudolf Kaaks, Shumin M. Zhang, Meredith Yeager, Walter C. Willett, Stephanie J. Weinstein, Jarmo Virtamo, Rosario Tumino, Dimitrios Trichopoulos, Anne Tjønneland, Michael J. Thun, Gilles Thomas, Daniel O. Stram, Pär Stattin, Meir J. Stampfer, Maria-José Sánchez, Carlotta Sacerdote, Laudina Rodriguez, Kim Overvad, N. Charlotte Onland-Moret, Jing Ma, Eiliv Lund, Loic LeMarchand, I-Min Lee, Pagona Lagiou, Laurence N. Kolonel, Kay-Tee Khaw, Timothy J. Key, Mattias Johansson, Robert N. Hoover, David J. Hunter, Brian E. Henderson, Richard B. Hayes, Susan E. Hankinson, Christopher A. Haiman, Edward L. Giovannucci, J. Michael Gaziano, Vanessa Dumeaux, Françoise Clavel-Chapelon, Stephen J. Chanock, Nathalie Chabbert-Buffet, Julie E. Buring, H. Bas Bueno-de-Mesquita, Heiner Boeing, Sonja I. Berndt, Christine D. Berg, Demetrius Albanes, Naomi E. Allen, Federico Canzian, Fredrick R. Schumacher, and Fangyi Gu

Abstract

Supplementary Table 1 from Eighteen Insulin-like Growth Factor Pathway Genes, Circulating Levels of IGF-I and Its Binding Protein, and Risk of Prostate and Breast Cancer

Published
2023

89. Data from Intake of Dietary Fruit, Vegetables, and Fiber and Risk of Colorectal Cancer According to Molecular Subtypes: A Pooled Analysis of 9 Studies

Author

Ulrike Peters, Peter T. Campbell, Daniel D. Buchanan, Li Hsu, Wei Sun, Michael Hoffmeister, Stephen N. Thibodeau, Bethany Van Guelpen, Michael O. Woods, Xiaoliang Wang, Caroline Y. Um, Robert S. Steinfelder, Martha L. Slattery, John D. Potter, Patrick S. Parfrey, Mireia Obón-Santacana, Shuji Ogino, Reiko Nishihara, Polly A. Newcomb, Victor Moreno, Yi Lin, Mark A. Jenkins, Heather Hampel, Sophia Harlid, Mark A. Guinter, Marc J. Gunter, Steven Gallinger, Andrew T. Chan, Ivan Borozan, Sonja I. Berndt, Efrat L. Amitay, Amanda E. Toland, Syed H. Zaidi, Jane C. Figueiredo, Amanda I. Phipps, Mingyang Song, Marios Giannakis, Richard Barfield, Lori C. Sakoda, Yin Cao, Tabitha A. Harrison, and Akihisa Hidaka

Abstract

Protective associations of fruits, vegetables, and fiber intake with colorectal cancer risk have been shown in many, but not all epidemiologic studies. One possible reason for study heterogeneity is that dietary factors may have distinct effects by colorectal cancer molecular subtypes. Here, we investigate the association of fruit, vegetables, and fiber intake with four well-established colorectal cancer molecular subtypes separately and in combination. Nine observational studies including 9,592 cases with molecular subtypes for microsatellite instability (MSI), CpG island methylator phenotype (CIMP), and somatic mutations in BRAF and KRAS genes, and 7,869 controls were analyzed. Both case-only logistic regression analyses and polytomous logistic regression analyses (with one control set and multiple case groups) were used. Higher fruit intake was associated with a trend toward decreased risk of BRAF-mutated tumors [OR 4th vs. 1st quartile = 0.82 (95% confidence interval, 0.65–1.04)] but not BRAF-wildtype tumors [1.09 (0.97–1.22); P difference as shown in case-only analysis = 0.02]. This difference was observed in case–control studies and not in cohort studies. Compared with controls, higher fiber intake showed negative association with colorectal cancer risk for cases with microsatellite stable/MSI-low, CIMP-negative, BRAF-wildtype, and KRAS-wildtype tumors (Ptrend range from 0.03 to 3.4e-03), which is consistent with the traditional adenoma-colorectal cancer pathway. These negative associations were stronger compared with MSI-high, CIMP-positive, BRAF-mutated, or KRAS-mutated tumors, but the differences were not statistically significant. These inverse associations for fruit and fiber intake may explain, in part, inconsistent findings between fruit or fiber intake and colorectal cancer risk that have previously been reported.Significance:These analyses by colorectal cancer molecular subtypes potentially explain the inconsistent findings between dietary fruit or fiber intake and overall colorectal cancer risk that have previously been reported.

Published
2023

90. Data Supplement from Gene–Environment Interaction Involving Recently Identified Colorectal Cancer Susceptibility Loci

Author

Emily White, Li Hsu, Ulrike Peters, Brent W. Zanke, Greg S. Warnick, Cornelia M. Ulrich, Mark Thornquist, Fridtjof Thomas, Deanna L. Stelling, Martha L. Slattery, Daniela Seminara, Robert E. Schoen, Anja Rudolph, John D. Potter, Bethann M. Pflugeisen, Heather M. Ochs-Balcom, Polly A. Newcomb, Jing Ma, Mathieu Lemire, Loic Le Marchand, Laurence N. Kolonel, Shuo Jiao, Mark A. Jenkins, John L. Hopper, Michael Hoffmeister, Brian E. Henderson, Richard B. Hayes, Tabitha A. Harrison, Jian Gong, Edward L. Giovannucci, Charles S. Fuchs, David Duggan, Mengmeng Du, Michelle Cotterchio, Stephen J. Chanock, Jenny Chang-Claude, Andrew T. Chan, Graham Casey, Christopher S. Carlson, Peter T. Campbell, Bette J. Caan, Hermann Brenner, Sonja I. Berndt, Jessica Minnier, Carolyn M. Hutter, and Elizabeth D. Kantor

Abstract

Supplemental Table 3. Environmental Factors and colorectal cancer: associations by study design

Published
2023

91. Supplementary Table 2 from CYP19A1 Genetic Variation in Relation to Prostate Cancer Risk and Circulating Sex Hormone Concentrations in Men from the Breast and Prostate Cancer Cohort Consortium

Author

David J. Hunter, Loïc Le Marchand, Jarmo Virtamo, Paolo Vineis, Dimitrios Trichopoulos, Anne Tjønneland, Michael J. Thun, Daniel O. Stram, Meir Stampfer, Elio Riboli, Laudina Rodriguez, Jing Ma, Laurence N. Kolonel, Rudolf Kaaks, Brian E. Henderson, Christopher A. Haiman, Edward Giovannucci, J. Michael Gaziano, Heather Spencer Feigelson, Richard Hayes, Alison M. Dunning, Stephen Chanock, Eugenia E. Calle, H. Bas Bueno-de-Mesquita, Heiner Boeing, Sonja I. Berndt, Goran Berglund, Demetrius Albanes, Naomi E. Allen, Peter Kraft, Joel N. Hirschhorn, Fredrick Schumacher, and Ruth C. Travis

Abstract

Supplementary Table 2 from CYP19A1 Genetic Variation in Relation to Prostate Cancer Risk and Circulating Sex Hormone Concentrations in Men from the Breast and Prostate Cancer Cohort Consortium

Published
2023

92. Supplementary Table Legends from Refining the Prostate Cancer Genetic Association within the JAZF1 Gene on Chromosome 7p15.2

Author

Meredith Yeager, Stephen J. Chanock, Nilanjan Chatterjee, Gilles Thomas, David J. Hunter, Joseph F. Fraumeni, Robert N. Hoover, Margaret Tucker, Merethe Kumle, Kristian Hveem, Lars J. Vatten, Jianfeng Xu, Fredrik Wiklund, Henrik Grönberg, Sarah D. Isaacs, William B. Isaacs, Rudolf Kaaks, Ruth Travis, Elio Riboli, Afshan Siddiq, Loic Le Marchand, Laurence Kolonel, Brian E. Henderson, Christopher A. Haiman, E. David Crawford, Gerald L. Andriole, Antoine Valeri, Olivier Cussenot, Geraldine Cancel-Tassin, Fredrick R. Schumacher, Stephanie Weinstein, Jarmo Virtamo, Demetrius Albanes, W. Ryan Diver, Michael J. Thun, Heather Spencer Feigelson, Amy Hutchinson, Kai Yu, Sholom Wacholder, Sonja I. Berndt, Peter Kraft, Richard B. Hayes, Kevin B. Jacobs, Wei Tang, Yi-Ping Fu, and Ludmila Prokunina-Olsson

Abstract

Supplementary Table Legends from Refining the Prostate Cancer Genetic Association within the JAZF1 Gene on Chromosome 7p15.2

Published
2023

93. Data from Gene–Environment Interaction Involving Recently Identified Colorectal Cancer Susceptibility Loci

Author

Emily White, Li Hsu, Ulrike Peters, Brent W. Zanke, Greg S. Warnick, Cornelia M. Ulrich, Mark Thornquist, Fridtjof Thomas, Deanna L. Stelling, Martha L. Slattery, Daniela Seminara, Robert E. Schoen, Anja Rudolph, John D. Potter, Bethann M. Pflugeisen, Heather M. Ochs-Balcom, Polly A. Newcomb, Jing Ma, Mathieu Lemire, Loic Le Marchand, Laurence N. Kolonel, Shuo Jiao, Mark A. Jenkins, John L. Hopper, Michael Hoffmeister, Brian E. Henderson, Richard B. Hayes, Tabitha A. Harrison, Jian Gong, Edward L. Giovannucci, Charles S. Fuchs, David Duggan, Mengmeng Du, Michelle Cotterchio, Stephen J. Chanock, Jenny Chang-Claude, Andrew T. Chan, Graham Casey, Christopher S. Carlson, Peter T. Campbell, Bette J. Caan, Hermann Brenner, Sonja I. Berndt, Jessica Minnier, Carolyn M. Hutter, and Elizabeth D. Kantor

Abstract

Background: Genome-wide association studies have identified several single nucleotide polymorphisms (SNPs) that are associated with risk of colorectal cancer. Prior research has evaluated the presence of gene–environment interaction involving the first 10 identified susceptibility loci, but little work has been conducted on interaction involving SNPs at recently identified susceptibility loci, including: rs10911251, rs6691170, rs6687758, rs11903757, rs10936599, rs647161, rs1321311, rs719725, rs1665650, rs3824999, rs7136702, rs11169552, rs59336, rs3217810, rs4925386, and rs2423279.Methods: Data on 9,160 cases and 9,280 controls from the Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO) and Colon Cancer Family Registry (CCFR) were used to evaluate the presence of interaction involving the above-listed SNPs and sex, body mass index (BMI), alcohol consumption, smoking, aspirin use, postmenopausal hormone (PMH) use, as well as intake of dietary calcium, dietary fiber, dietary folate, red meat, processed meat, fruit, and vegetables. Interaction was evaluated using a fixed effects meta-analysis of an efficient Empirical Bayes estimator, and permutation was used to account for multiple comparisons.Results: None of the permutation-adjusted P values reached statistical significance.Conclusions: The associations between recently identified genetic susceptibility loci and colorectal cancer are not strongly modified by sex, BMI, alcohol, smoking, aspirin, PMH use, and various dietary factors.Impact: Results suggest no evidence of strong gene–environment interactions involving the recently identified 16 susceptibility loci for colorectal cancer taken one at a time. Cancer Epidemiol Biomarkers Prev; 23(9); 1824–33. ©2014 AACR.

Published
2023

94. Data from Smoking Modifies Pancreatic Cancer Risk Loci on 2q21.3

Author

Rachael Stolzenberg-Solomon, Alison P. Klein, Nilanjan Chatterjee, Peter Kraft, Harvey A. Risch, Brian M. Wolpin, Gloria M. Petersen, Eric J. Jacobs, Donghui Li, Laufey T. Amundadottir, Anne Zeleniuch-Jacquotte, Fangcheng Yuan, Herbert Yu, Lynne R. Wilkens, Nicolas Wentzensen, Jean Wactawski-Wende, Stephen K. Van Den Eeden, Antonia Trichopoulou, Anne Tjonneland, Ian M. Thompson, Oliver Strobel, Victoria L. Stevens, Debra T. Silverman, Howard D. Sesso, Ghislaine Scelo, Nathaniel Rothman, Elio Riboli, Kari G. Rabe, Miquel Porta, Ulrike Peters, Salvatore Panico, Ann L. Oberg, Kimmie Ng, Roger L. Milne, Núria Malats, I-Min Lee, Robert C. Kurtz, Rayjean J. Hung, Robert N. Hoover, Elizabeth A. Holly, Manal M. Hassan, Patricia Hartge, Michael G. Goggins, Edward L. Giovannucci, J. Michael Gaziano, Charles S. Fuchs, Eric J. Duell, Erica J. Childs, Stephen J. Chanock, Daniele Campa, Julie E. Buring, Bas Bueno-de-Mesquita, Amanda L. Blackford, Sonja I. Berndt, William R. Bamlet, Ana Babic, Gabriella Andreotti, Demetrius Albanes, Wei Zheng, Emily White, Kala Visvanathan, Xiao-Ou Shu, Rachel E. Neale, Loic Le Marchand, Charles Kooperberg, Phyllis J. Goodman, Graham G. Giles, Steven Gallinger, Mengmeng Du, Federico Canzian, Paul Brennan, Paige M. Bracci, Laura E. Beane-Freeman, Alan A. Arslan, William Wheeler, Prosenjit Kundu, and Evelina Mocci

Abstract

Germline variation and smoking are independently associated with pancreatic ductal adenocarcinoma (PDAC). We conducted genome-wide smoking interaction analysis of PDAC using genotype data from four previous genome-wide association studies in individuals of European ancestry (7,937 cases and 11,774 controls). Examination of expression quantitative trait loci data from the Genotype-Tissue Expression Project followed by colocalization analysis was conducted to determine whether there was support for common SNP(s) underlying the observed associations. Statistical tests were two sided and P < 5 × 10–8 was considered statistically significant. Genome-wide significant evidence of qualitative interaction was identified on chr2q21.3 in intron 5 of the transmembrane protein 163 (TMEM163) and upstream of the cyclin T2 (CCNT2). The most significant SNP using the Empirical Bayes method, in this region that included 45 significantly associated SNPs, was rs1818613 [per allele OR in never smokers 0.87, 95% confidence interval (CI), 0.82–0.93; former smokers 1.00, 95% CI, 0.91–1.07; current smokers 1.25, 95% CI 1.12–1.40, Pinteraction = 3.08 × 10–9). Examination of the Genotype-Tissue Expression Project data demonstrated an expression quantitative trait locus in this region for TMEM163 and CCNT2 in several tissue types. Colocalization analysis supported a shared SNP, rs842357, in high linkage disequilibrium with rs1818613 (r2 = 0. 94) driving both the observed interaction and the expression quantitative trait loci signals. Future studies are needed to confirm and understand the differential biologic mechanisms by smoking status that contribute to our PDAC findings.Significance:This large genome-wide interaction study identifies a susceptibility locus on 2q21.3 that significantly modified PDAC risk by smoking status, providing insight into smoking-associated PDAC, with implications for prevention.

Published
2023

95. Supplementary table 8 from Smoking Modifies Pancreatic Cancer Risk Loci on 2q21.3

Author

Rachael Stolzenberg-Solomon, Alison P. Klein, Nilanjan Chatterjee, Peter Kraft, Harvey A. Risch, Brian M. Wolpin, Gloria M. Petersen, Eric J. Jacobs, Donghui Li, Laufey T. Amundadottir, Anne Zeleniuch-Jacquotte, Fangcheng Yuan, Herbert Yu, Lynne R. Wilkens, Nicolas Wentzensen, Jean Wactawski-Wende, Stephen K. Van Den Eeden, Antonia Trichopoulou, Anne Tjonneland, Ian M. Thompson, Oliver Strobel, Victoria L. Stevens, Debra T. Silverman, Howard D. Sesso, Ghislaine Scelo, Nathaniel Rothman, Elio Riboli, Kari G. Rabe, Miquel Porta, Ulrike Peters, Salvatore Panico, Ann L. Oberg, Kimmie Ng, Roger L. Milne, Núria Malats, I-Min Lee, Robert C. Kurtz, Rayjean J. Hung, Robert N. Hoover, Elizabeth A. Holly, Manal M. Hassan, Patricia Hartge, Michael G. Goggins, Edward L. Giovannucci, J. Michael Gaziano, Charles S. Fuchs, Eric J. Duell, Erica J. Childs, Stephen J. Chanock, Daniele Campa, Julie E. Buring, Bas Bueno-de-Mesquita, Amanda L. Blackford, Sonja I. Berndt, William R. Bamlet, Ana Babic, Gabriella Andreotti, Demetrius Albanes, Wei Zheng, Emily White, Kala Visvanathan, Xiao-Ou Shu, Rachel E. Neale, Loic Le Marchand, Charles Kooperberg, Phyllis J. Goodman, Graham G. Giles, Steven Gallinger, Mengmeng Du, Federico Canzian, Paul Brennan, Paige M. Bracci, Laura E. Beane-Freeman, Alan A. Arslan, William Wheeler, Prosenjit Kundu, and Evelina Mocci

Abstract

Supplemental Table 8. Enrichment in regulatory regions for rs842357 and related SNPs

Published
2023

96. 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

97. Supplementary Table 1 from Cross-Cancer Genome-Wide Analysis of Lung, Ovary, Breast, Prostate, and Colorectal Cancer Reveals Novel Pleiotropic Associations

Author

Rayjean J. Hung, Brian E. Henderson, Christopher A. Haiman, David J. Hunter, Douglas F. Easton, Thomas A. Sellers, Christopher I. Amos, Stephen B. Gruber, Ulrike Peters, Jian Gong, Stephen J. Chanock, Daniela Seminara, Qiyuan Li, Matthew L. Freedman, Wim Timens, David Nickle, Ma'en Obeidat, Yohan Bossé, Atsushi Takahashi, Kouya Shiraishi, Xiao-Ou Shu, Zhibin Hu, Hongbing Shen, Yongyue Wei, David C. Christiani, Jonathan P. Tyrer, Y. Ann Chen, Patrick Sulem, Kari Stefansson, Simon N. Stacey, Julius Gudmundsson, Thorunn Rafnar, Michael O. Woods, Stephen N. Thibodeau, Stephanie L. Schmit, Noralene M. Lindor, Li Li, Loïc Le Marchand, Mark Jenkins, Robert W. Haile, Steven Gallinger, Christopher K. Edlund, David V. Conti, Graham Casey, Daniel D. Buchanan, Wei Zheng, Xiaohong R. Yang, Alice S. Whittemore, Zhaoming Wang, Andre G. Uitterlinden, Clare Turnbull, Ruth C. Travis, Rulla Tamimi, Melissa C. Southey, Rita K. Schmutzler, Daniel F. Schmidt, Maria Jose Sanchez, Nazneen Rahman, Ross L. Prentice, Julian Peto, Petra H. Peeters, Heli Nevanlinna, Taru A. Muranen, Bertram Müller-Myhsok, Alfons Meindl, Enes Makalic, Eiliv Lund, Jianjun Liu, Peter Lichtner, Muhammad G. Kibriya, Rudolf Kaaks, Mattias Johansson, Astrid Irwanto, John L. Hopper, Albert Hofman, Rebecca Hein, Aditi Hazra, Per Hall, Nichola Johnson, Mia M. Gaudet, Montserrat Garcia-Closas, Olivia Fletcher, Dieter Flesch-Janys, Jonine D. Figueroa, A. Heather Eliassen, Isabel dos-Santos-Silva, Kamila Czene, Federico Canzian, Carl Blomquist, Laura Baglietto, Kristiina Aittomäki, Habibul Ahsan, Muriel A. Adank, Emily White, Martha L. Slattery, Robert E. Schoen, Polly A. Newcomb, Jonathan K. Kocarnik, Thomas J. Hudson, Jenny Chang-Claude, Andrew T. Chan, Hermann Brenner, Stephane Bezieau, Brett M. Reid, Harvey A. Risch, Jennifer B. Permuth, Ellen L. Goode, Walter C. Willett, Fredrik Wiklund, Victoria L. Stevens, Meir J. Stampfer, Kenneth Muir, Jing Ma, Zsofia Kote-Jarai, Henrik Grönberg, Edward L. Giovannucci, Sonja I. Berndt, Ali Amin Al Olama, Angela Risch, Neil Caporaso, Maria Teresa Landi, Richard S. Houlston, Heike Bickeböller, Paul Brennan, Sara Lindström, Joellen M. Schildkraut, Fredrick R. Schumacher, Nilanjan Chatterjee, Rosalind A. Eeles, Paul D. Pharoah, Peter Kraft, and Gordon Fehringer

Abstract

Variants selected for replication

Published
2023

98. Supplementary Material: Funding, Acknowledgements, Consortia, and Bioinformatics Tools Funding sources from Cross-Cancer Genome-Wide Analysis of Lung, Ovary, Breast, Prostate, and Colorectal Cancer Reveals Novel Pleiotropic Associations

Author

Rayjean J. Hung, Brian E. Henderson, Christopher A. Haiman, David J. Hunter, Douglas F. Easton, Thomas A. Sellers, Christopher I. Amos, Stephen B. Gruber, Ulrike Peters, Jian Gong, Stephen J. Chanock, Daniela Seminara, Qiyuan Li, Matthew L. Freedman, Wim Timens, David Nickle, Ma'en Obeidat, Yohan Bossé, Atsushi Takahashi, Kouya Shiraishi, Xiao-Ou Shu, Zhibin Hu, Hongbing Shen, Yongyue Wei, David C. Christiani, Jonathan P. Tyrer, Y. Ann Chen, Patrick Sulem, Kari Stefansson, Simon N. Stacey, Julius Gudmundsson, Thorunn Rafnar, Michael O. Woods, Stephen N. Thibodeau, Stephanie L. Schmit, Noralene M. Lindor, Li Li, Loïc Le Marchand, Mark Jenkins, Robert W. Haile, Steven Gallinger, Christopher K. Edlund, David V. Conti, Graham Casey, Daniel D. Buchanan, Wei Zheng, Xiaohong R. Yang, Alice S. Whittemore, Zhaoming Wang, Andre G. Uitterlinden, Clare Turnbull, Ruth C. Travis, Rulla Tamimi, Melissa C. Southey, Rita K. Schmutzler, Daniel F. Schmidt, Maria Jose Sanchez, Nazneen Rahman, Ross L. Prentice, Julian Peto, Petra H. Peeters, Heli Nevanlinna, Taru A. Muranen, Bertram Müller-Myhsok, Alfons Meindl, Enes Makalic, Eiliv Lund, Jianjun Liu, Peter Lichtner, Muhammad G. Kibriya, Rudolf Kaaks, Mattias Johansson, Astrid Irwanto, John L. Hopper, Albert Hofman, Rebecca Hein, Aditi Hazra, Per Hall, Nichola Johnson, Mia M. Gaudet, Montserrat Garcia-Closas, Olivia Fletcher, Dieter Flesch-Janys, Jonine D. Figueroa, A. Heather Eliassen, Isabel dos-Santos-Silva, Kamila Czene, Federico Canzian, Carl Blomquist, Laura Baglietto, Kristiina Aittomäki, Habibul Ahsan, Muriel A. Adank, Emily White, Martha L. Slattery, Robert E. Schoen, Polly A. Newcomb, Jonathan K. Kocarnik, Thomas J. Hudson, Jenny Chang-Claude, Andrew T. Chan, Hermann Brenner, Stephane Bezieau, Brett M. Reid, Harvey A. Risch, Jennifer B. Permuth, Ellen L. Goode, Walter C. Willett, Fredrik Wiklund, Victoria L. Stevens, Meir J. Stampfer, Kenneth Muir, Jing Ma, Zsofia Kote-Jarai, Henrik Grönberg, Edward L. Giovannucci, Sonja I. Berndt, Ali Amin Al Olama, Angela Risch, Neil Caporaso, Maria Teresa Landi, Richard S. Houlston, Heike Bickeböller, Paul Brennan, Sara Lindström, Joellen M. Schildkraut, Fredrick R. Schumacher, Nilanjan Chatterjee, Rosalind A. Eeles, Paul D. Pharoah, Peter Kraft, and Gordon Fehringer

Abstract

Funding sources, acknowledgements, consortia involved in study and bioinformatics tools used

Published
2023

99. Supplementary Table 3 from Pesticide Use Modifies the Association Between Genetic Variants on Chromosome 8q24 and Prostate Cancer

Author

Michael C.R. Alavanja, Meredith Yeager, Jeffrey Yuenger, Laura A. Burdette, Qizhai Li, Kai Yu, Jane A. Hoppin, Dale P. Sandler, Jay H. Lubin, Gabriella Andreotti, Sonja I. Berndt, Laura E. Beane Freeman, and Stella Koutros

Abstract

Supplementary Table 3 from Pesticide Use Modifies the Association Between Genetic Variants on Chromosome 8q24 and Prostate Cancer

Published
2023

100. Supplementary Table 1 from Pesticide Use Modifies the Association Between Genetic Variants on Chromosome 8q24 and Prostate Cancer

Author

Michael C.R. Alavanja, Meredith Yeager, Jeffrey Yuenger, Laura A. Burdette, Qizhai Li, Kai Yu, Jane A. Hoppin, Dale P. Sandler, Jay H. Lubin, Gabriella Andreotti, Sonja I. Berndt, Laura E. Beane Freeman, and Stella Koutros

Abstract

Supplementary Table 1 from Pesticide Use Modifies the Association Between Genetic Variants on Chromosome 8q24 and Prostate Cancer

Published
2023

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