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Vassy JL, Brunette CA, Lebo MS, MacIsaac K, Yi T, Danowski ME, Alexander NVJ, Cardellino MP, Christensen KD, Gala M, Green RC, Harris E, Jones NE, Kerman BJ, Kraft P, Kulkarni P, Lewis ACF, Lubitz SA, Natarajan P, Antwi AA. The GenoVA study: Equitable implementation of a pragmatic randomized trial of polygenic-risk scoring in primary care. Am J Hum Genet 2023; 110:1841-1852. [PMID: 37922883 PMCID: PMC10645559 DOI: 10.1016/j.ajhg.2023.10.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 10/03/2023] [Accepted: 10/03/2023] [Indexed: 11/07/2023] Open
Abstract
Polygenic risk scores (PRSs) hold promise for disease risk assessment and prevention. The Genomic Medicine at Veterans Affairs (GenoVA) Study is addressing three main challenges to the clinical implementation of PRSs in preventive care: defining and determining their clinical utility, implementing them in time-constrained primary care settings, and countering their potential to exacerbate healthcare disparities. The study processes used to test patients, report their PRS results to them and their primary care providers (PCPs), and promote the use of those results in clinical decision-making are modeled on common practices in primary care. The following diseases were chosen for their prevalence and familiarity to PCPs: coronary artery disease; type 2 diabetes; atrial fibrillation; and breast, colorectal, and prostate cancers. A randomized clinical trial (RCT) design and primary outcome of time-to-new-diagnosis of a target disease bring methodological rigor to the question of the clinical utility of PRS implementation. The study's pragmatic RCT design enhances its relevance to how PRS might reasonably be implemented in primary care. Steps the study has taken to promote health equity include the thoughtful handling of genetic ancestry in PRS construction and reporting and enhanced recruitment strategies to address underrepresentation in research participation. To date, enhanced recruitment efforts have been both necessary and successful: participants of underrepresented race and ethnicity groups have been less likely to enroll in the study than expected but ultimately achieved proportional representation through targeted efforts. The GenoVA Study experience to date offers insights for evaluating the clinical utility of equitable PRS implementation in adult primary care.
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Affiliation(s)
- Jason L Vassy
- VA Boston Healthcare System, Boston, MA, USA; Division of General Internal Medicine and Primary Care, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA; Ariadne Labs, Boston, MA, USA.
| | - Charles A Brunette
- VA Boston Healthcare System, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Matthew S Lebo
- Harvard Medical School, Boston, MA, USA; Laboratory for Molecular Medicine, Mass General Brigham, Boston, MA, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Thomas Yi
- VA Boston Healthcare System, Boston, MA, USA
| | | | - Nicholas V J Alexander
- VA Boston Healthcare System, Boston, MA, USA; Bucharest University Emergency Hospital, Bucharest, Romania; Bucharest University of Economic Studies, Bucharest, Romania
| | | | - Kurt D Christensen
- Harvard Medical School, Boston, MA, USA; Department of Population Medicine, Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - Manish Gala
- Harvard Medical School, Boston, MA, USA; Division of Gastroenterology and Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Robert C Green
- Harvard Medical School, Boston, MA, USA; Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA; Ariadne Labs, Boston, MA, USA; Department of Medicine (Genetics), Mass General Brigham, Boston, MA, USA
| | | | - Natalie E Jones
- VA Boston Healthcare System, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Benjamin J Kerman
- Division of General Internal Medicine and Primary Care, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Peter Kraft
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | | | - Anna C F Lewis
- Department of Medicine (Genetics), Mass General Brigham, Boston, MA, USA; Edmond and Lily Safra Center for Ethics, Harvard University, Boston, MA, USA
| | - Steven A Lubitz
- Demoulas Center for Cardiac Arrhythmias, Massachusetts General Hospital, Boston, MA, USA; Novartis Institutes for BioMedical Research, Novartis, Basel, Basel-Stadt, Switzerland
| | - Pradeep Natarajan
- Harvard Medical School, Boston, MA, USA; Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
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Neyaz A, Rickelt S, Yilmaz OH, Parrack PH, Lu C, Yilmaz O, Wu EY, Choi WT, Gala M, Ting DT, Odze RD, Patil DT, Deshpande V. Quantitative p53 immunostaining aids in the detection of prevalent dysplasia. J Clin Pathol 2023; 76:582-590. [PMID: 36823143 DOI: 10.1136/jcp-2022-208721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 02/02/2023] [Indexed: 02/25/2023]
Abstract
AIMS The lack of accepted scoring criteria has precluded the use of p53 in routine practice. We evaluate the utility of automated quantitative p53 analysis in risk stratifying Barrett's oesophagus (BE) patients using non-dysplastic BE (NDBE) biopsies in a multicentric cohort of BE progressor (P) and non-progressor (NP) patients. METHODS NDBE biopsies prior to the diagnosis of advanced neoplasia from 75 BE-P, and index and last surveillance biopsies from 148 BE-NP were stained for p53, and scored digitally as 1+, 2+ and 3+. A secondary cohort of 30 BE-P was evaluated. RESULTS Compared with BE-NP, BE-P was predominantly men (p=0.001), ≥55 years of age (p=0.008), with longer BE segments (71% vs 33%; p<0.001). The mean number of 3+p53 positive cells and 3+ positive glands were significantly more in BE-P versus BE-NP NDBE biopsies (175 vs 9.7, p<0.001; 9.8 vs 0.1; p<0.001, respectively). At a cut-off of ≥10 p53 (3+) positive cells, the sensitivity and specificity of the assay to identify BE-P were 39% and 93%. On multivariate analysis, scoring p53 in NDBE biopsies, age, gender and length of BE were significantly associated with neoplastic progression. 54% of patients classified as prevalent dysplasia showed an abnormal p53 immunohistochemical stain. These findings were validated in the secondary cohort. CONCLUSIONS Automated p53 analysis in NDBE biopsies serves as a promising tool for assessing BE neoplastic progression and risk stratification. Our study highlights the practical applicability of p53 assay to routine surveillance practice and its ability to detect prevalent dysplasia.
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Affiliation(s)
- Azfar Neyaz
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Steffen Rickelt
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Omer H Yilmaz
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Paige H Parrack
- Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Chenyue Lu
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts, USA
| | - Osman Yilmaz
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Elizabeth Y Wu
- Pathology, Brown University Warren Alpert Medical School, Providence, Rhode Island, USA
| | - Won-Tak Choi
- Pathology, University of California, San Francisco, California, USA
| | - Manish Gala
- Department of Medicine, Gastrointestinal Unit, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - David T Ting
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts, USA
| | - Robert D Odze
- Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Deepa T Patil
- Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Vikram Deshpande
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
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Downie JM, Riaz M, Xie J, Lee M, Chan AT, Gibbs P, Orchard SG, Mahady SE, Sebra RP, Murray AM, Macrae F, Schadt E, Woods RL, McNeil JJ, Lacaze P, Gala M. Incident Cancer Risk and Signatures Among Older MUTYH Carriers: Analysis of Population-Based and Genomic Cohorts. Cancer Prev Res (Phila) 2022; 15:509-519. [PMID: 35609203 PMCID: PMC9356994 DOI: 10.1158/1940-6207.capr-22-0080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/31/2022] [Accepted: 05/10/2022] [Indexed: 02/03/2023]
Abstract
MUTYH carriers have an increased colorectal cancer risk in case-control studies, with loss of heterozygosity (LOH) as the presumed mechanism. We evaluated cancer risk among carriers in a prospective, population-based cohort of older adults. In addition, we assessed if cancers from carriers demonstrated mutational signatures (G:C>T:A transversions) associated with early LOH. We calculated incident risk of cancer and colorectal cancer among 13,131 sequenced study participants of the ASPirin in Reducing Events in the Elderly cohort, stratified by sex and adjusting for age, smoking, alcohol use, BMI, polyp history, history of cancer, and aspirin use. MUTYH carriers were identified among 13,033 participants in The Cancer Genome Atlas and International Cancer Genome Consortium, and somatic signatures of cancers were analyzed. Male MUTYH carriers demonstrated an increased risk for overall cancer incidence [multivariable HR, 1.66; 95% confidence interval (CI), 1.03-2.68; P = 0.038] driven by increased colorectal cancer incidence (multivariable HR, 3.55; 95% CI, 1.42-8.78; P = 0.007), as opposed to extracolonic cancer incidence (multivariable HR, 1.40; 95% CI, 0.81-2.44; P = 0.229). Female carriers did not demonstrate increased risk of cancer, colorectal cancer, or extracolonic cancers. Analysis of mutation signatures from cancers of MUTYH carriers revealed no significant contribution toward early mutagenesis from widespread G:C>T:A transversions among gastrointestinal epithelial cancers. Among cancers from carriers, somatic transversions associated with base-excision repair deficiency are uncommon, suggestive of diverse mechanisms of carcinogenesis in carriers compared with those who inherit biallelic MUTYH mutations. PREVENTION RELEVANCE Despite absence of loss of heterozygosity in colorectal cancers, elderly male MUTYH carriers appeared to be at increased of colorectal cancer.
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Affiliation(s)
- Jonathan M. Downie
- Gastrointestinal Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Moeen Riaz
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC, Australia
| | - Jing Xie
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC, Australia
| | - Minyi Lee
- Gastrointestinal Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA
- MD-Ph.D. Program, Boston University School of Medicine, Boston, MA
| | - Andrew T. Chan
- Gastrointestinal Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Peter Gibbs
- Division of Personalised Oncology, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Oncology, Western Health, Melbourne, Australia
- Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Australia
| | - Suzanne G. Orchard
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC, Australia
| | - Suzanne E. Mahady
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC, Australia
- Department of Gastroenterology, Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Robert P. Sebra
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Anne M. Murray
- Berman Center for Outcomes and Clinical Research, Hennepin Healthcare Research Institute, Hennepin Healthcare, Minneapolis, MN, USA
| | - Finlay Macrae
- Department of Genomic Medicine; Family Cancer Clinic, Department of Medicine, Department of Pathology, Royal Melbourne Hospital, University of Melbourne, Parkville, VIC, Australia
| | - Eric Schadt
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Robyn L. Woods
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC, Australia
| | - John J. McNeil
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC, Australia
| | - Paul Lacaze
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC, Australia
| | - Manish Gala
- Gastrointestinal Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA
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Loomans-Kropp HA, Song Y, Gala M, Parikh AR, Van Seventer EE, Alvarez R, Hitchins MP, Shoemaker RH, Umar A. Methylated Septin9 (m SEPT9): A promising blood-based biomarker for the detection and screening of early-onset colorectal cancer. Cancer Res Commun 2022; 2:90-98. [PMID: 35992328 PMCID: PMC9387652 DOI: 10.1158/2767-9764.crc-21-0142] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/20/2021] [Accepted: 02/01/2022] [Indexed: 06/15/2023]
Abstract
Early-onset colorectal cancer (EOCRC), defined as a diagnosis under age 50, is an emerging public health burden. As many of these individuals fall outside of screening guidelines, the development of a minimally invasive, accurate screening modality for this population is warranted. We evaluated the FDA-approved blood-based biomarker methylated Septin9 (mSEPT9) test as screening tool for EOCRC. EOCRC plasma, healthy plasma, and serum-free conditioned media from cancer cell lines was collected. Cell-free DNA (cfDNA) was isolated and bisulfite converted for use in the assay. mSEPT9 and ACTB measured using Epi proColon® V2.0. EOCRC plasma was collected at Massachusetts General Hospital (2005-2019) and controls were collected at the National Institutes of Health and by ZenBio Inc. (prior to 2019). Twenty-seven EOCRC cases, 48 healthy controls <50 years old, and 39 healthy controls ≥50 years old were included in this study. mSEPT9 was detected more frequently in EOCRC cases (88.9%) compared to healthy controls age <50 (4.2%) and ≥50 (15.4%), respectively (p<0.001). The sensitivity, specificity, positive predictive value, and negative predictive values of the mSEPT9 assay to detect EOCRC was 90.8% (95% CI: 84.7-96.9%), 88.9% (95% CI: 77.0-100.0%), 96.3% (95% CI: 92.3-100.0%), and 75.0% (95% CI 60.0-90.0%), respectively, compared to all healthy controls. mSEPT9 cfDNA level was an independent predictor of survival (p=0.02). mSEPT9 is a sensitive and specific biomarker for EOCRC detection. These results suggest that mSEPT9 may be useful in the detection of EOCRC, providing a minimally invasive method for screening in this growing population of CRC patients.
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Affiliation(s)
- Holli A. Loomans-Kropp
- Cancer Prevention Fellowship Program, Division of Cancer Prevention, NCI, NIH, Rockville, Maryland
- Gastrointestinal and Other Cancers Research Group, Division of Cancer Prevention, NCI, NIH, Rockville, Maryland
| | - Yurong Song
- Cancer ImmunoPrevention Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Manish Gala
- Gastrointestinal Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Aparna R. Parikh
- Division of Hematology and Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Emily E. Van Seventer
- Division of Hematology and Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Rocio Alvarez
- Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California
| | - Megan P. Hitchins
- Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California
| | - Robert H. Shoemaker
- Chemopreventive Agent Development Research Group, Division of Cancer Prevention, NCI, NIH, Rockville, Maryland
| | - Asad Umar
- Gastrointestinal and Other Cancers Research Group, Division of Cancer Prevention, NCI, NIH, Rockville, Maryland
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5
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Huyghe JR, Harrison TA, Bien SA, Hampel H, Figueiredo JC, Schmit SL, Conti DV, Chen S, Qu C, Lin Y, Barfield R, Baron JA, Cross AJ, Diergaarde B, Duggan D, Harlid S, Imaz L, Kang HM, Levine DM, Perduca V, Perez-Cornago A, Sakoda LC, Schumacher FR, Slattery ML, Toland AE, van Duijnhoven FJB, Van Guelpen B, Agudo A, Albanes D, Alonso MH, Anderson K, Arnau-Collell C, Arndt V, Banbury BL, Bassik MC, Berndt SI, Bézieau S, Bishop DT, Boehm J, Boeing H, Boutron-Ruault MC, Brenner H, Brezina S, Buch S, Buchanan DD, Burnett-Hartman A, Caan BJ, Campbell PT, Carr PR, Castells A, Castellví-Bel S, Chan AT, Chang-Claude J, Chanock SJ, Curtis KR, de la Chapelle A, Easton DF, English DR, Feskens EJM, Gala M, Gallinger SJ, Gauderman WJ, Giles GG, Goodman PJ, Grady WM, Grove JS, Gsur A, Gunter MJ, Haile RW, Hampe J, Hoffmeister M, Hopper JL, Hsu WL, Huang WY, Hudson TJ, Jenab M, Jenkins MA, Joshi AD, Keku TO, Kooperberg C, Kühn T, Küry S, Le Marchand L, Lejbkowicz F, Li CI, Li L, Lieb W, Lindblom A, Lindor NM, Männistö S, Markowitz SD, Milne RL, Moreno L, Murphy N, Nassir R, Offit K, Ogino S, Panico S, Parfrey PS, Pearlman R, Pharoah PDP, Phipps AI, Platz EA, Potter JD, Prentice RL, Qi L, Raskin L, Rennert G, Rennert HS, Riboli E, Schafmayer C, Schoen RE, Seminara D, Song M, Su YR, Tangen CM, Thibodeau SN, Thomas DC, Trichopoulou A, Ulrich CM, Visvanathan K, Vodicka P, Vodickova L, Vymetalkova V, Weigl K, Weinstein SJ, White E, Wolk A, Woods MO, Wu AH, Abecasis GR, Nickerson DA, Scacheri PC, Kundaje A, Casey G, Gruber SB, Hsu L, Moreno V, Hayes RB, Newcomb PA, Peters U. Genetic architectures of proximal and distal colorectal cancer are partly distinct. Gut 2021; 70:1325-1334. [PMID: 33632709 PMCID: PMC8223655 DOI: 10.1136/gutjnl-2020-321534] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 11/26/2020] [Accepted: 12/18/2020] [Indexed: 01/14/2023]
Abstract
OBJECTIVE An understanding of the etiologic heterogeneity of colorectal cancer (CRC) is critical for improving precision prevention, including individualized screening recommendations and the discovery of novel drug targets and repurposable drug candidates for chemoprevention. Known differences in molecular characteristics and environmental risk factors among tumors arising in different locations of the colorectum suggest partly distinct mechanisms of carcinogenesis. The extent to which the contribution of inherited genetic risk factors for CRC differs by anatomical subsite of the primary tumor has not been examined. DESIGN To identify new anatomical subsite-specific risk loci, we performed genome-wide association study (GWAS) meta-analyses including data of 48 214 CRC cases and 64 159 controls of European ancestry. We characterised effect heterogeneity at CRC risk loci using multinomial modelling. RESULTS We identified 13 loci that reached genome-wide significance (p<5×10-8) and that were not reported by previous GWASs for overall CRC risk. Multiple lines of evidence support candidate genes at several of these loci. We detected substantial heterogeneity between anatomical subsites. Just over half (61) of 109 known and new risk variants showed no evidence for heterogeneity. In contrast, 22 variants showed association with distal CRC (including rectal cancer), but no evidence for association or an attenuated association with proximal CRC. For two loci, there was strong evidence for effects confined to proximal colon cancer. CONCLUSION Genetic architectures of proximal and distal CRC are partly distinct. Studies of risk factors and mechanisms of carcinogenesis, and precision prevention strategies should take into consideration the anatomical subsite of the tumour.
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Affiliation(s)
- Jeroen R Huyghe
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Tabitha A Harrison
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Stephanie A Bien
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Heather Hampel
- Division of Human Genetics, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, USA
| | - Jane C Figueiredo
- Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | | | - David V Conti
- Department of Preventive Medicine and USC Norris Comprehensive Cancer Center, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Sai Chen
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - Conghui Qu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Yi Lin
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Richard Barfield
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - John A Baron
- Department of Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Amanda J Cross
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
| | - Brenda Diergaarde
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- UPMC Hillman Cancer Center, Pittsburgh, Pennsylvania, USA
| | - David Duggan
- Translational Genomics Research Institute - An Affiliate of City of Hope, Phoenix, Arizona, USA
| | - Sophia Harlid
- Department of Radiation Sciences, Oncology Unit, Umeå University, Umeå, Sweden
| | - Liher Imaz
- Public Health Division of Gipuzkoa, Health Department of Basque Country, San Sebastian, Spain
| | - Hyun Min Kang
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - David M Levine
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | - Vittorio Perduca
- Laboratoire de Mathématiques Appliquées MAP5 (UMR CNRS 8145), Université Paris Descartes, Paris, France
- Centre for Research in Epidemiology and Population Health (CESP), Institut pour la Santé et la Recherche Médicale (INSERM) U1018, Université Paris-Saclay, Villejuif, France
| | - Aurora Perez-Cornago
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Lori C Sakoda
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Division of Research, Kaiser Permanente Northern California, Oakland, California, USA
| | - Fredrick R Schumacher
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Martha L Slattery
- Department of Internal Medicine, University of Utah Health, Salt Lake City, Utah, USA
| | - Amanda E Toland
- Departments of Cancer Biology and Genetics and Internal Medicine, The Ohio State University, Columbus, Ohio, USA
| | | | - Bethany Van Guelpen
- Department of Radiation Sciences, Oncology Unit, Umeå University, Umeå, Sweden
| | - Antonio Agudo
- Unit of Nutrition and Cancer, Cancer Epidemiology Research Program, Catalan Institute of Oncology - IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - M Henar Alonso
- Cancer Prevention and Control Program, Catalan Institute of Oncology - IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Kristin Anderson
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, Minnesota, USA
| | - Coral Arnau-Collell
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona, Spain
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Barbara L Banbury
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Michael C Bassik
- Department of Genetics, Stanford University, Stanford, California, USA
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Stéphane Bézieau
- Service de Génétique Médicale, Centre Hospitalier Universitaire (CHU) de Nantes, Nantes, France
| | - D Timothy Bishop
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Juergen Boehm
- Huntsman Cancer Institute and Department of Population Health Sciences, University of Utah Health, Salt Lake City, Utah, USA
| | - Heiner Boeing
- Department of Epidemiology, German Institute of Human Nutrition (DIfE), Potsdam-Rehbrücke, Germany
| | - Marie-Christine Boutron-Ruault
- Centre for Research in Epidemiology and Population Health (CESP), Institut pour la Santé et la Recherche Médicale (INSERM) U1018, Université Paris-Saclay, Villejuif, France
- Institut Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Centre (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Centre (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefanie Brezina
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Stephan Buch
- Department of Medicine I, University Hospital Dresden, Technische Universität Dresden (TU Dresden), Dresden, Germany
| | - Daniel D Buchanan
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Colorectal Oncogenomics Group, Genetic Epidemiology Laboratory, Department of Clinical Pathology, The University of Melbourne, Melbourne, Victoria, Australia
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | | | - Bette J Caan
- Division of Research, Kaiser Permanente Medical Care Program, Oakland, California, USA
| | - Peter T Campbell
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, Georgia, USA
| | - Prudence R Carr
- Division of Clinical Epidemiology, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Antoni Castells
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona, Spain
| | - Sergi Castellví-Bel
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona, Spain
| | - Andrew T Chan
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Centre (DKFZ), Heidelberg, Germany
- Cancer Epidemiology Group, University Medical Centre Hamburg-Eppendorf, University Cancer Centre Hamburg (UCCH), Hamburg, Germany
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Keith R Curtis
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Albert de la Chapelle
- Department of Cancer Biology and Genetics and the Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA
| | - Douglas F Easton
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Dallas R English
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Edith J M Feskens
- Division of Human Nutrition and Health, Wageningen University & Research, Wageningen, The Netherlands
| | - Manish Gala
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Steven J Gallinger
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - W James Gauderman
- Department of Preventive Medicine and USC Norris Comprehensive Cancer Center, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Graham G Giles
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Phyllis J Goodman
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - William M Grady
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - John S Grove
- University of Hawai'i Cancer Center, Honolulu, Hawaii, USA
| | - Andrea Gsur
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Marc J Gunter
- Nutrition and Metabolism Section, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Robert W Haile
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Jochen Hampe
- Department of Medicine I, University Hospital Dresden, Technische Universität Dresden (TU Dresden), Dresden, Germany
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Department of Epidemiology, School of Public Health and Institute of Health and Environment, Seoul National University, Seoul, South Korea
| | - Wan-Ling Hsu
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | - Wen-Yi Huang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Thomas J Hudson
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Mazda Jenab
- Nutrition and Metabolism Section, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Mark A Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Amit D Joshi
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
| | - Temitope O Keku
- Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Charles Kooperberg
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Tilman Kühn
- Division of Cancer Epidemiology, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Sébastien Küry
- Service de Génétique Médicale, Centre Hospitalier Universitaire (CHU) de Nantes, Nantes, France
| | | | - Flavio Lejbkowicz
- The Clalit Health Services, Personalized Genomic Service, Carmel Medical Center, Haifa, Israel
- Department of Community Medicine and Epidemiology, Lady Davis Carmel Medical Center, Haifa, Israel
- Clalit National Cancer Control Center, Haifa, Israel
| | - Christopher I Li
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Li Li
- Department of Family Medicine, University of Virginia, Charlottesville, Virginia, USA
| | - Wolfgang Lieb
- Institute of Epidemiology, PopGen Biobank, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Annika Lindblom
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Noralane M Lindor
- Department of Health Science Research, Mayo Clinic, Scottsdale, Arizona, USA
| | - Satu Männistö
- Department of Public Health Solutions, National Institute for Health and Welfare, Helsinki, Finland
| | - Sanford D Markowitz
- Departments of Medicine and Genetics, Case Comprehensive Cancer Center, Case Western Reserve University and University Hospitals of Cleveland, Cleveland, Ohio, USA
| | - Roger L Milne
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Lorena Moreno
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona, Spain
| | - Neil Murphy
- Nutrition and Metabolism Section, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Rami Nassir
- Department of Pathology, School of Medicine, Umm Al-Qura'a University, Mecca, Saudi Arabia
| | - Kenneth Offit
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Shuji Ogino
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Salvatore Panico
- Dipartimento di Medicina Clinica e Chirurgia, University of Naples Federico II, Naples, Italy
| | - Patrick S Parfrey
- Clinical Epidemiology Unit, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - Rachel Pearlman
- Division of Human Genetics, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, USA
| | - Paul D P Pharoah
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Amanda I Phipps
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
| | - Elizabeth A Platz
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - John D Potter
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Ross L Prentice
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Lihong Qi
- Department of Public Health Sciences, School of Medicine, University of California Davis, Davis, California, USA
| | - Leon Raskin
- Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Gad Rennert
- Department of Community Medicine and Epidemiology, Lady Davis Carmel Medical Center, Haifa, Israel
- Clalit National Cancer Control Center, Haifa, Israel
- Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Hedy S Rennert
- Department of Community Medicine and Epidemiology, Lady Davis Carmel Medical Center, Haifa, Israel
- Clalit National Cancer Control Center, Haifa, Israel
- Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Elio Riboli
- School of Public Health, Imperial College London, London, UK
| | - Clemens Schafmayer
- Department of General Surgery, University Hospital Rostock, Rostock, Germany
| | - Robert E Schoen
- Department of Medicine and Epidemiology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Daniela Seminara
- Division of Cancer Control and Population Sciences, National Cancer Institute, Bethesda, Maryland, USA
| | - Mingyang Song
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
| | - Yu-Ru Su
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Catherine M Tangen
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Stephen N Thibodeau
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, MayoClinic, Rochester, Minnesota, USA
| | - Duncan C Thomas
- Department of Preventive Medicine and USC Norris Comprehensive Cancer Center, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Antonia Trichopoulou
- Hellenic Health Foundation, Athens, Greece
- WHO Collaborating Center for Nutrition and Health, Unit of Nutritional Epidemiology and Nutrition in Public Health, Department of Hygiene, Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Cornelia M Ulrich
- Huntsman Cancer Institute and Department of Population Health Sciences, University of Utah Health, Salt Lake City, Utah, USA
| | - Kala Visvanathan
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University, Pilsen, Czech Republic
| | - Ludmila Vodickova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University, Pilsen, Czech Republic
| | - Veronika Vymetalkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University, Pilsen, Czech Republic
| | - Korbinian Weigl
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Centre (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Medical Faculty, University of Heidelberg, Heidelberg, Germany
| | - Stephanie J Weinstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Emily White
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Alicja Wolk
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Michael O Woods
- Discipline of Genetics, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - Anna H Wu
- Department of Preventive Medicine and USC Norris Comprehensive Cancer Center, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Goncalo R Abecasis
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Peter C Scacheri
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Case Comprehensive Cancer Center, Cleveland, Ohio, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, California, USA
- Department of Computer Science, Stanford University, Stanford, California, USA
| | - Graham Casey
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
| | - Stephen B Gruber
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, California, USA
- City of Hope National Medical Center, Duarte, California, USA
| | - Li Hsu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | - Victor Moreno
- Cancer Prevention and Control Program, Catalan Institute of Oncology - IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Richard B Hayes
- Division of Epidemiology, Department of Population Health, New York University School of Medicine, New York, New York, USA
| | - Polly A Newcomb
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
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6
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Li DK, Haffar S, Horibe M, Homsi HA, Zukerberg L, Murad MH, Visrodia KH, Gala M, Katzka DA, Bazerbachi F. Verrucous esophageal carcinoma is a unique indolent subtype of squamous cell carcinoma: a systematic review and individual patient regression analysis. J Gastroenterol 2021; 56:12-24. [PMID: 33079233 DOI: 10.1007/s00535-020-01736-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 09/26/2020] [Indexed: 02/04/2023]
Abstract
BACKGROUND AND AIMS Verrucous esophageal carcinoma (VEC) is a rare malignancy that presents a diagnostic challenge. We aim to characterize the clinical and genomic features, tumor behavior, and treatment outcomes of VEC to guide clinical practice. METHODS We performed a systematic review of the literature and identified additional cases from Massachusetts General Hospital records and The Cancer Genome Atlas (TCGA). We obtained individual VEC patient data and analyzed publicly available clinicogenomic data from TCGA. We performed a regression analysis comparing cases of VEC to esophageal squamous cell carcinoma (ESCC) to identify factors influencing survival. RESULTS A total of 135 patients were reported in 82 publications, and four unpublished cases from Massachusetts General Hospital (median age 65 years, 69% males, 48% smokers, 33% consumed alcohol). Symptoms were present at diagnosis in 95% of patients, most commonly dysphagia and weight loss. Median symptom onset to diagnosis time was 11.5 months with frequent misdiagnosis as Candida esophagitis. Among VEC cases with pathologic staging, lymph node metastases were rare (5%) compared to ESCC (40%). VEC was genomically characterized by enrichment of SMARCA4 missense mutations and a lack of pathogenic TP53 mutations. Despite its diagnostic elusiveness, in a multivariate regression analysis, VEC was detected at earlier stages (p = < 0.001) compared to ESCC, and advanced stage was the only significant factor affecting survival (p = 0.013). CONCLUSIONS VEC is a rare, clinically and genomically distinct subtype of ESCC. Recognition and diagnosis of this lesion may allow the pursuit of curative and less morbid treatment strategies.
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Affiliation(s)
- Darrick K Li
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Samir Haffar
- Digestive Center for Diagnosis and Treatment, Damascus, Syrian Arab Republic
| | - Masayasu Horibe
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Shinjuku, Tokyo, Japan
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Haya A Homsi
- School of Public Health, University of Waterloo, Waterloo, ON, Canada
| | - Lawrence Zukerberg
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Mohammad H Murad
- Evidence-Based Practice Center, Robert D. and Patricia E. Kern Center for the Science of Health Care Delivery, Mayo Clinic, Rochester, MN, USA
| | - Kavel H Visrodia
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Manish Gala
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA.
- Assistant in Medicine, Instructor in Medicine, Harvard Medical School, Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital, 55 Fruit Street, GRJ 825D, Boston, MA, 02114, USA.
| | - David A Katzka
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Fateh Bazerbachi
- Assistant in Medicine, Instructor in Medicine, Harvard Medical School, Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital, 55 Fruit Street, GRJ 825D, Boston, MA, 02114, USA.
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7
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Wentworth AJ, Byrne JD, Orguc S, Sands J, Maji S, Tov C, Babaee S, Huang HW, Boyce H, Chai PR, Min S, Li C, Chu JN, Som A, Becker SL, Gala M, Chandrakasan A, Traverso G. Prospective Evaluation of the Transparent, Elastomeric, Adaptable, Long-Lasting (TEAL) Respirator. ACS Pharmacol Transl Sci 2020; 3:1076-1082. [PMID: 33330837 PMCID: PMC7671102 DOI: 10.1021/acsptsci.0c00157] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Indexed: 11/28/2022]
Abstract
N95 filtering facepiece respirators (FFR) and surgical masks are essential in reducing airborne disease transmission, particularly during the COVID-19 pandemic. However, currently available FFR's and masks have major limitations, including masking facial features, waste, and integrity after decontamination. In a multi-institutional trial, we evaluated a transparent, elastomeric, adaptable, long-lasting (TEAL) respirator to evaluate success of qualitative fit test with user experience and biometric evaluation of temperature, respiratory rate, and fit of respirator using a novel sensor. There was a 100% successful fit test among participants, with feedback demonstrating excellent or good fit (90% of participants), breathability (77.5%), and filter exchange (95%). Biometric testing demonstrated significant differences between exhalation and inhalation pressures among a poorly fitting respirator, well-fitting respirator, and the occlusion of one filter of the respirator. We have designed and evaluated a transparent elastomeric respirator and a novel biometric feedback system that could be implemented in the hospital setting.
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Affiliation(s)
- Adam J. Wentworth
- Division
of Gastroenterology, Brigham and Women’s
Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- Department
of Mechanical Engineering, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
- David
H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, United States
| | - James D. Byrne
- Division
of Gastroenterology, Brigham and Women’s
Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- Department
of Mechanical Engineering, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
- David
H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, United States
- Harvard
Radiation Oncology Program, Brigham and
Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Sirma Orguc
- Microsystems
Technology Laboratories, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02139, United States
| | - Joanna Sands
- Microsystems
Technology Laboratories, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02139, United States
| | - Saurav Maji
- Microsystems
Technology Laboratories, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02139, United States
| | - Caitlynn Tov
- Division
of Gastroenterology, Brigham and Women’s
Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Sahab Babaee
- Department
of Mechanical Engineering, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
- David
H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, United States
| | - Hen-Wei Huang
- Division
of Gastroenterology, Brigham and Women’s
Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- Department
of Mechanical Engineering, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
- David
H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, United States
| | - Hannah Boyce
- Division
of Gastroenterology, Brigham and Women’s
Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Peter R. Chai
- David
H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, United States
- Division
of Medical Toxicology, Department of Emergency Medicine, Brigham and Women’s Hospital, Harvard Medical
School, Boston, Massachusetts 02115, United States
- The
Fenway Institute, Boston, Massachusetts 02215, United States
- Department
of Psychosocial Oncology and Palliative Care, Dana Farber Cancer Institute, Boston Massachusetts 02215, United States
| | - Seokkee Min
- Department
of Mechanical Engineering, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Canchen Li
- David
H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, United States
| | - Jacqueline N. Chu
- Division
of Gastroenterology, Massachusetts General
Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Avik Som
- Department
of Radiology, Massachusetts General Hospital,
Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Sarah L. Becker
- Division
of Gastroenterology, Brigham and Women’s
Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Manish Gala
- Division
of Gastroenterology, Massachusetts General
Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Anantha Chandrakasan
- Microsystems
Technology Laboratories, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02139, United States
| | - Giovanni Traverso
- Division
of Gastroenterology, Brigham and Women’s
Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- Department
of Mechanical Engineering, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
- David
H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, United States
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8
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Neumeyer S, Hua X, Seibold P, Jansen L, Benner A, Burwinkel B, Halama N, Berndt SI, Phipps AI, Sakoda LC, Schoen RE, Slattery ML, Chan AT, Gala M, Joshi AD, Ogino S, Song M, Herpel E, Bläker H, Kloor M, Scherer D, Ulrich A, Ulrich CM, Win AK, Figueiredo JC, Hopper JL, Macrae F, Milne RL, Giles GG, Buchanan DD, Peters U, Hoffmeister M, Brenner H, Newcomb PA, Chang-Claude J. Genetic Variants in the Regulatory T cell-Related Pathway and Colorectal Cancer Prognosis. Cancer Epidemiol Biomarkers Prev 2020; 29:2719-2728. [PMID: 33008876 PMCID: PMC7976673 DOI: 10.1158/1055-9965.epi-20-0714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/29/2020] [Accepted: 09/28/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND High numbers of lymphocytes in tumor tissue, including T regulatory cells (Treg), have been associated with better colorectal cancer survival. Tregs, a subset of CD4+ T lymphocytes, are mediators of immunosuppression in cancer, and therefore variants in genes related to Treg differentiation and function could be associated with colorectal cancer prognosis. METHODS In a prospective German cohort of 3,593 colorectal cancer patients, we assessed the association of 771 single-nucleotide polymorphisms (SNP) in 58 Treg-related genes with overall and colorectal cancer-specific survival using Cox regression models. Effect modification by microsatellite instability (MSI) status was also investigated because tumors with MSI show greater lymphocytic infiltration and have been associated with better prognosis. Replication of significant results was attempted in 2,047 colorectal cancer patients of the International Survival Analysis in Colorectal Cancer Consortium (ISACC). RESULTS A significant association of the TGFBR3 SNP rs7524066 with more favorable colorectal cancer-specific survival [hazard ratio (HR) per minor allele: 0.83; 95% confidence interval (CI), 0.74-0.94; P value: 0.0033] was replicated in ISACC (HR: 0.82; 95% CI, 0.68-0.98; P value: 0.03). Suggestive evidence for association was found with two IL7 SNPs, rs16906568 and rs7845577. Thirteen SNPs with differential associations with overall survival according to MSI in the discovery analysis were not confirmed. CONCLUSIONS Common genetic variation in the Treg pathway implicating genes such as TGFBR3 and IL7 was shown to be associated with prognosis of colorectal cancer patients. IMPACT The implicated genes warrant further investigation.
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Affiliation(s)
- Sonja Neumeyer
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Xinwei Hua
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
- School of Public Health, University of Washington, Seattle, Washington
| | - Petra Seibold
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lina Jansen
- Division of Clinical Epidemiology and Aging Research, DKFZ, Heidelberg, Germany
| | - Axel Benner
- Division of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Barbara Burwinkel
- Division of Molecular Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Gynecology and Obstetrics, Molecular Biology of Breast Cancer, University of Heidelberg, Heidelberg, Germany
| | - Niels Halama
- Department of Medical Oncology, National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany
- Tissue Imaging and Analysis Center, National Center for Tumor Diseases, BIOQUANT, University of Heidelberg, Heidelberg, Germany
- Institute for Immunology, University Hospital Heidelberg, Heidelberg, Germany
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, Maryland
| | - Amanda I Phipps
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
- Epidemiology Department, University of Washington, Seattle, Washington
| | - Lori C Sakoda
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
- Division of Research, Kaiser Permanente Northern California, Oakland, California
| | - Robert E Schoen
- Department of Medicine and Epidemiology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Martha L Slattery
- Department of Internal Medicine, University of Utah, Salt Lake City, Utah
| | - Andrew T Chan
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Manish Gala
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Amit D Joshi
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts
| | - Shuji Ogino
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Mingyang Song
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts
| | - Esther Herpel
- NCT Tissue Bank, National Center for Tumor Diseases (NCT), Heidelberg, Germany
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Hendrik Bläker
- Institute of Pathology, Charité University Medicine, Berlin, Germany
| | - Matthias Kloor
- Department of Applied Tumor Biology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Dominique Scherer
- Institute of Medical Biometry and Informatics, University Hospital Heidelberg, Heidelberg, Germany
| | - Alexis Ulrich
- Department of General, Visceral and Transplantation Surgery, University Hospital Heidelberg, University of Heidelberg, Germany
| | - Cornelia M Ulrich
- Huntsman Cancer Institute, Population Sciences, Salt Lake City, Utah
- Department of Population Health Sciences, University of Utah, Salt Lake City, Utah
| | - Aung K Win
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, Melbourne, Australia
| | - Jane C Figueiredo
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles California
| | - John L Hopper
- Colorectal Medicine and Genetics, The Royal Melbourne Hospital, Victoria, Australia
| | - Finlay Macrae
- Colorectal Medicine and Genetics, The Royal Melbourne Hospital, Victoria, Australia
| | - Roger L Milne
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, Melbourne, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Graham G Giles
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, Melbourne, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Daniel D Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Victoria, Australia
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
- Department of Epidemiology, University of Washington, Seattle, Washington
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, DKFZ, Heidelberg, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, DKFZ, Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Polly A Newcomb
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Cancer Epidemiology Group, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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9
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Pardini B, Corrado A, Paolicchi E, Cugliari G, Berndt SI, Bezieau S, Bien SA, Brenner H, Caan BJ, Campbell PT, Casey G, Chan AT, Chang-Claude J, Cotterchio M, Gala M, Gallinger SJ, Haile RW, Harrison TA, Hayes RB, Hoffmeister M, Hopper JL, Hsu L, Huyghe J, Jenkins MA, Le Marchand L, Lin Y, Lindor NM, Nan H, Newcomb PA, Ogino S, Potter JD, Schoen RE, Slattery ML, White E, Vodickova L, Vymetalkova V, Vodicka P, Gemignani F, Peters U, Naccarati A, Landi S. DNA repair and cancer in colon and rectum: Novel players in genetic susceptibility. Int J Cancer 2020; 146:363-372. [PMID: 31209889 PMCID: PMC7301215 DOI: 10.1002/ijc.32516] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 05/27/2019] [Indexed: 01/07/2023]
Abstract
Interindividual differences in DNA repair systems may play a role in modulating the individual risk of developing colorectal cancer. To better ascertain the role of DNA repair gene polymorphisms on colon and rectal cancer risk individually, we evaluated 15,419 single nucleotide polymorphisms (SNPs) within 185 DNA repair genes using GWAS data from the Colon Cancer Family Registry (CCFR) and the Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO), which included 8,178 colon cancer, 2,936 rectum cancer cases and 14,659 controls. Rs1800734 (in MLH1 gene) was associated with colon cancer risk (p-value = 3.5 × 10-6 ) and rs2189517 (in RAD51B) with rectal cancer risk (p-value = 5.7 × 10-6 ). The results had statistical significance close to the Bonferroni corrected p-value of 5.8 × 10-6 . Ninety-four SNPs were significantly associated with colorectal cancer risk after Binomial Sequential Goodness of Fit (BSGoF) procedure and confirmed the relevance of DNA mismatch repair (MMR) and homologous recombination pathways for colon and rectum cancer, respectively. Defects in MMR genes are known to be crucial for familial form of colorectal cancer but our findings suggest that specific genetic variations in MLH1 are important also in the individual predisposition to sporadic colon cancer. Other SNPs associated with the risk of colon cancer (e.g., rs16906252 in MGMT) were found to affect mRNA expression levels in colon transverse and therefore working as possible cis-eQTL suggesting possible mechanisms of carcinogenesis.
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Affiliation(s)
- Barbara Pardini
- Italian Institute for Genomic Medicine (IIGM), Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Alda Corrado
- Department of Biology, University of Pisa, Pisa, Italy
| | | | - Giovanni Cugliari
- Italian Institute for Genomic Medicine (IIGM), Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Sonja I. Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD. USA
| | - Stephane Bezieau
- Service de Génétique Médicale, Centre Hospitalier Universitaire (CHU) Nantes, France
| | - Stephanie A. Bien
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- School of Public Health, University of Washington, Seattle, WA, USA
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ) Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Bette J. Caan
- Kaiser Permanente Medical Care Program of Northern California, Oakland, CA, USA
| | - Peter T. Campbell
- Epidemiology Research Program, American Cancer Society, Atlanta, GA, USA
| | - Graham Casey
- Public Health Sciences, University of Virginia, VA, USA
| | - Andrew T. Chan
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ) Heidelberg, Germany
| | | | - Manish Gala
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
| | | | | | - Tabitha A. Harrison
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Richard B. Hayes
- Division of Epidemiology, Department of Population Health, New York University School of Medicine, New York, NY, USA
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ) Heidelberg, Germany
| | - John L. Hopper
- Melborne School of Population Health, The University of Melborne, Melborne, Australia
| | - Li Hsu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jeroen Huyghe
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Mark A. Jenkins
- Melborne School of Population Health, The University of Melborne, Melborne, Australia
| | - Loic Le Marchand
- Epidemiology Program, Research Cancer Center of Hawaii, University of Hawaii, Honolulu, HI, USA
| | - Yi Lin
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Noralane M. Lindor
- Department of Health Sciences Research, Mayo Clinic Arizona, Scottsdale, AZ, USA
| | - Hongmei Nan
- Department of Epidemiology, Richard M. Fairbanks School of Public Health, Indiana University, Indianapolis, IN, USA
| | - Polly A. Newcomb
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Shuji Ogino
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women’s Hospital, and Harvard Medical School
- Department of Oncologic Pathology, Dana-Farber Cancer Institute
- Department of Epidemiology, Harvard T.H. Chan School of Public Health; all in, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - John D. Potter
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Robert E. Schoen
- Department of Medicine and Epidemiology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Martha L. Slattery
- Department of Internal Medicine, University of Utah Health Sciences Center, Salt Lake City, UT, USA
| | - Emily White
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Ludmila Vodickova
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University, Pilsen, Czech Republic
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, The Czech Academy of Sciences, Prague, Czech Republic
| | - Veronika Vymetalkova
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University, Pilsen, Czech Republic
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, The Czech Academy of Sciences, Prague, Czech Republic
| | - Pavel Vodicka
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University, Pilsen, Czech Republic
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, The Czech Academy of Sciences, Prague, Czech Republic
| | | | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Alessio Naccarati
- Italian Institute for Genomic Medicine (IIGM), Turin, Italy
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, The Czech Academy of Sciences, Prague, Czech Republic
| | - Stefano Landi
- Department of Biology, University of Pisa, Pisa, Italy
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10
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Schmit SL, Edlund CK, Schumacher FR, Gong J, Harrison TA, Huyghe JR, Qu C, Melas M, Van Den Berg DJ, Wang H, Tring S, Plummer SJ, Albanes D, Alonso MH, Amos CI, Anton K, Aragaki AK, Arndt V, Barry EL, Berndt SI, Bezieau S, Bien S, Bloomer A, Boehm J, Boutron-Ruault MC, Brenner H, Brezina S, Buchanan DD, Butterbach K, Caan BJ, Campbell PT, Carlson CS, Castelao JE, Chan AT, Chang-Claude J, Chanock SJ, Cheng I, Cheng YW, Chin LS, Church JM, Church T, Coetzee GA, Cotterchio M, Cruz Correa M, Curtis KR, Duggan D, Easton DF, English D, Feskens EJM, Fischer R, FitzGerald LM, Fortini BK, Fritsche LG, Fuchs CS, Gago-Dominguez M, Gala M, Gallinger SJ, Gauderman WJ, Giles GG, Giovannucci EL, Gogarten SM, Gonzalez-Villalpando C, Gonzalez-Villalpando EM, Grady WM, Greenson JK, Gsur A, Gunter M, Haiman CA, Hampe J, Harlid S, Harju JF, Hayes RB, Hofer P, Hoffmeister M, Hopper JL, Huang SC, Huerta JM, Hudson TJ, Hunter DJ, Idos GE, Iwasaki M, Jackson RD, Jacobs EJ, Jee SH, Jenkins MA, Jia WH, Jiao S, Joshi AD, Kolonel LN, Kono S, Kooperberg C, Krogh V, Kuehn T, Küry S, LaCroix A, Laurie CA, Lejbkowicz F, Lemire M, Lenz HJ, Levine D, Li CI, Li L, Lieb W, Lin Y, Lindor NM, Liu YR, Loupakis F, Lu Y, Luh F, Ma J, Mancao C, Manion FJ, Markowitz SD, Martin V, Matsuda K, Matsuo K, McDonnell KJ, McNeil CE, Milne R, Molina AJ, Mukherjee B, Murphy N, Newcomb PA, Offit K, Omichessan H, Palli D, Cotoré JPP, Pérez-Mayoral J, Pharoah PD, Potter JD, Qu C, Raskin L, Rennert G, Rennert HS, Riggs BM, Schafmayer C, Schoen RE, Sellers TA, Seminara D, Severi G, Shi W, Shibata D, Shu XO, Siegel EM, Slattery ML, Southey M, Stadler ZK, Stern MC, Stintzing S, Taverna D, Thibodeau SN, Thomas DC, Trichopoulou A, Tsugane S, Ulrich CM, van Duijnhoven FJB, van Guelpan B, Vijai J, Virtamo J, Weinstein SJ, White E, Win AK, Wolk A, Woods M, Wu AH, Wu K, Xiang YB, Yen Y, Zanke BW, Zeng YX, Zhang B, Zubair N, Kweon SS, Figueiredo JC, Zheng W, Marchand LL, Lindblom A, Moreno V, Peters U, Casey G, Hsu L, Conti DV, Gruber SB. Novel Common Genetic Susceptibility Loci for Colorectal Cancer. J Natl Cancer Inst 2019; 111:146-157. [PMID: 29917119 PMCID: PMC6555904 DOI: 10.1093/jnci/djy099] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 03/09/2018] [Accepted: 04/27/2018] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Previous genome-wide association studies (GWAS) have identified 42 loci (P < 5 × 10-8) associated with risk of colorectal cancer (CRC). Expanded consortium efforts facilitating the discovery of additional susceptibility loci may capture unexplained familial risk. METHODS We conducted a GWAS in European descent CRC cases and control subjects using a discovery-replication design, followed by examination of novel findings in a multiethnic sample (cumulative n = 163 315). In the discovery stage (36 948 case subjects/30 864 control subjects), we identified genetic variants with a minor allele frequency of 1% or greater associated with risk of CRC using logistic regression followed by a fixed-effects inverse variance weighted meta-analysis. All novel independent variants reaching genome-wide statistical significance (two-sided P < 5 × 10-8) were tested for replication in separate European ancestry samples (12 952 case subjects/48 383 control subjects). Next, we examined the generalizability of discovered variants in East Asians, African Americans, and Hispanics (12 085 case subjects/22 083 control subjects). Finally, we examined the contributions of novel risk variants to familial relative risk and examined the prediction capabilities of a polygenic risk score. All statistical tests were two-sided. RESULTS The discovery GWAS identified 11 variants associated with CRC at P < 5 × 10-8, of which nine (at 4q22.2/5p15.33/5p13.1/6p21.31/6p12.1/10q11.23/12q24.21/16q24.1/20q13.13) independently replicated at a P value of less than .05. Multiethnic follow-up supported the generalizability of discovery findings. These results demonstrated a 14.7% increase in familial relative risk explained by common risk alleles from 10.3% (95% confidence interval [CI] = 7.9% to 13.7%; known variants) to 11.9% (95% CI = 9.2% to 15.5%; known and novel variants). A polygenic risk score identified 4.3% of the population at an odds ratio for developing CRC of at least 2.0. CONCLUSIONS This study provides insight into the architecture of common genetic variation contributing to CRC etiology and improves risk prediction for individualized screening.
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Affiliation(s)
- Stephanie L Schmit
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center
| | | | | | | | | | | | - Chenxu Qu
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center
- Public Health Sciences Division
| | - Marilena Melas
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center
| | | | - Hansong Wang
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI
| | - Stephanie Tring
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center
- National Cancer Center, Tokyo, Japan
- Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Sarah J Plummer
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | - M Henar Alonso
- Catalan Institute of Oncology, Bellvitge Biomedical Research Institute
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- University of Barcelona, Barcelona, Spain
| | | | | | | | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research
| | - Elizabeth L Barry
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Hanover, NH
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | | | - Stephanie Bien
- Centre Hospitalier Universitaire Hotel-Dieu, Nantes, France
| | - Amanda Bloomer
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL
| | - Juergen Boehm
- Huntsman Cancer Institute and Department of Population Health Sciences, University of Utah, Salt Lake City, UT
| | - Marie-Christine Boutron-Ruault
- CESP (U1018 INSERM), Facultés de Médecine Université Paris-Sud, UVSQ, Université Paris-Saclay, Villejuif, France
- Gustave Roussy, Villejuif, France
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research
- German Cancer Consortium
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Stefanie Brezina
- Service de Génétique Médicale, Centre Hospitalier Universitaire (CHU), Nantes, France
| | - Daniel D Buchanan
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
- Colorectal Oncogenomics Group, Department of Pathology (DDB) and Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Melbourne, Victoria, Australia
- Genetic Medicine and Familial Cancer Centre, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | | | - Bette J Caan
- Division of Research, Kaiser Permanente Medical Care Program of Northern California, Oakland, CA
| | - Peter T Campbell
- Epidemiology Research Program, American Cancer Society, Atlanta, GA
| | | | - Jose E Castelao
- Genetic Oncology Unit, Instituto de Investigación Sanitaria Galicia Sur (IISGS), Complejo Hospitalario Universitario de Vigo (CHUVI), SERGAS, Vigo (Pontevedra) Spain
| | - Andrew T Chan
- Division of Gastroenterology
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA
| | - Jenny Chang-Claude
- Unit of Genetic Epidemiology, Division of Cancer Epidemiology
- Harvard Medical School, Boston, MA
- University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | - Iona Cheng
- Cancer Prevention Institute of California, Fremont, CA
| | - Ya-Wen Cheng
- Ph.D. Program of Cancer Research and Drug Discovery
| | - Lee Soo Chin
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - James M Church
- Department of Colorectal Surgery, Cleveland Clinic, Cleveland, OH
| | - Timothy Church
- Division of Environmental Health Sciences, University of Minnesota, Minneapolis, MN
| | | | | | | | | | - David Duggan
- Genetic Basis of Human Disease Division, Translational Genomics Research Institute, Phoenix, AZ
| | | | - Dallas English
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Edith J M Feskens
- Division of Human Nutrition, Wageningen University and Research, Wageningen, the Netherlands
| | - Rocky Fischer
- University of Michigan Comprehensive Cancer Center, Ann Arbor, MI
| | - Liesel M FitzGerald
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Victoria, Australia
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | | | - Lars G Fritsche
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Norwegian University of Science and Technology, Trondheim, Sør-Trøndelag, Norway
| | - Charles S Fuchs
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brookline, MA
- Department of Medicine, Brigham and Women’s Institute, Brookline, MA
| | - Manuela Gago-Dominguez
- Genomic Medicine Group, Galician Foundation of Genomic Medicine, Complejo Hospitalario Universitario de Santiago, Servicio Galego de Saude (SERGAS), Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago De Compostela, Spain
- Moores Cancer Center, University of California San Diego, La Jolla, CA
| | | | - Steven J Gallinger
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - W James Gauderman
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center
| | - Graham G Giles
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Edward L Giovannucci
- Harvard Medical School, Boston, MA
- Channing Division of Network Medicine, Brigham and Women’s Institute, Brookline, MA
| | | | - Clicerio Gonzalez-Villalpando
- Unidad de Investigacion en Diabetes y Riesgo Cardiovascular, Centro de Investigacion en Salud Poblacional, Instituto Nacional de Salud Publica, Cuernavaca, Morelos, Mexico
| | | | - William M Grady
- Department of Medicine, Division of Gastroenterology, School of Medicine
| | - Joel K Greenson
- Department of Pathology, University of Michigan, Ann Arbor, MI
| | - Andrea Gsur
- Medical University of Vienna, Department of Medicine I, Institute of Cancer Research, Vienna, Austria
| | - Marc Gunter
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA
| | | | - Jochen Hampe
- Medical Department 1, University Hospital Dresden, TU Dresden, Dresden, Germany
| | - Sophia Harlid
- Department of Radiation Sciences, Oncology, Umea University, Umea, Sweden
| | - John F Harju
- University of Michigan Comprehensive Cancer Center, Ann Arbor, MI
| | - Richard B Hayes
- Division of Epidemiology, Department of Population Health, New York University School of Medicine, New York, NY
| | - Philipp Hofer
- Medical University of Vienna, Department of Medicine I, Institute of Cancer Research, Vienna, Austria
| | | | - John L Hopper
- Centre for MEGA Epidemiology, The University of Melbourne, Carlton, Victoria, Australia
| | - Shu-Chen Huang
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center
| | - Jose Maria Huerta
- Department of Epidemiology, Murcia Regional Health Council, IMIB-Arrixaca, Murcia, Spain
| | - Thomas J Hudson
- AbbVie, Redwood City, CA
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - David J Hunter
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology, Harvard School of Public Health, Boston, MA
| | - Gregory E Idos
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center
| | - Motoki Iwasaki
- Division of Epidemiology, Center for Public Health Sciences
| | | | - Eric J Jacobs
- Epidemiology Research Program, American Cancer Society, Atlanta, GA
| | - Sun Ha Jee
- Department of Epidemiology and Health Promotion, Graduate School of Public Health, Yonsei University, Seoul, South Korea
| | - Mark A Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Wei-Hua Jia
- State Key Laboratory of Oncology in South China, Cancer Center, Sun Yatsen University, Guangzhou, China
| | | | - Amit D Joshi
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology, Harvard School of Public Health, Boston, MA
| | - Laurence N Kolonel
- Office of Public Health Studies, University of Hawaii Manoa, Honolulu, HI
| | - Suminori Kono
- Service de Génétique Médicale, Centre Hospitalier Universitaire (CHU), Nantes, France
| | | | - Vittorio Krogh
- Epidemiology and Prevention Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | | | - Sébastien Küry
- Department of Preventive Medicine, Kyushu University, Fukuoka, Japan
| | | | | | - Flavio Lejbkowicz
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL
- School of Medicine, Taipei Medical University, Taipei, Taiwan
- Sino-American Cancer Foundation, Temple City, CA
| | - Mathieu Lemire
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Heinz-Josef Lenz
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center
- Department of Medicine, University of Southern California, Los Angeles, CA
| | | | - Christopher I Li
- Translational Research Program, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Li Li
- Department of Family Medicine and Community Health, Mary Ann Swetland Center for Environmental Health, Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH
| | - Wolfgang Lieb
- Institute of Epidemiology, PopGen Biobank, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Yi Lin
- Public Health Sciences Division
| | - Noralane M Lindor
- Department of Health Science Research, Mayo Clinic, Scottsdale, AZ
- Unit of Oncology, Department of Clinical and Experimental Oncology, Instituto Oncologico Veneto, IRCCS Padua, Italy
| | | | | | - Yingchang Lu
- Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, TN
| | - Frank Luh
- Clalit Health Services National Israeli Cancer Control Center, Haifa, Israel
| | - Jing Ma
- Harvard School of Public Health, Boston, MA
| | | | - Frank J Manion
- University of Michigan Comprehensive Cancer Center, Ann Arbor, MI
| | - Sanford D Markowitz
- Departments of Medicine and Genetics, Case Comprehensive Cancer Center, Case Western Reserve University, and University Hospitals of Cleveland, Cleveland, OH
| | - Vicente Martin
- Biomedicine Institute (IBIOMED), University of León, León, Spain
| | - Koichi Matsuda
- Laboratory of Genome Technology, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN
| | - Keitaro Matsuo
- Department of Epidemiology, Nagoya University Graduate School of Medicine, Showa-ku, Nagoya, Japan
- Division of Molecular and Clinical Epidemiology, Aichi Cancer Center Research Institute, Chikusa-Ku Nagoya, Japan
| | - Kevin J McDonnell
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center
| | - Caroline E McNeil
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center
| | - Roger Milne
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Antonio J Molina
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Research Group on Gene-Environment Interactions and Health, University of León, León, Spain
| | | | - Neil Murphy
- Nutrition and Metabolism Section, IARC, Lyon, CEDEX 08, France
| | | | - Kenneth Offit
- Clinical Genetics Service (KO), Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Hanane Omichessan
- CESP (U1018 INSERM), Facultés de Médecine Université Paris-Sud, UVSQ, Université Paris-Saclay, Villejuif, France
- Gustave Roussy, Villejuif, France
| | - Domenico Palli
- Cancer Risk Factors and Life-Style Epidemiology Unit, Cancer Research and Prevention Institute-ISPO, Florence, Italy
| | - Jesus P Paredes Cotoré
- Department of Surgery, Complejo Hospitalario Universitario de Santiago (CHUS), Servicio Galego de Saúde (SERGAS), Santiago De Compostela, Spain
| | | | - Paul D Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | | | - Conghui Qu
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center
- Public Health Sciences Division
| | - Leon Raskin
- Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, TN
- Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN
| | - Gad Rennert
- Clalit Health Services National Israeli Cancer Control Center, Haifa, Israel
- Department of Community Medicine and Epidemiology, Carmel Medical Center, Haifa, Israel
- Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Hedy S Rennert
- Clalit Health Services National Israeli Cancer Control Center, Haifa, Israel
- Department of Community Medicine and Epidemiology, Carmel Medical Center, Haifa, Israel
| | - Bridget M Riggs
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL
| | - Clemens Schafmayer
- Department of Visceral and Thoracic Surgery, University Hospital Schleswig-Holstein, Kiel Campus, Kiel, Germany
| | - Robert E Schoen
- Department of Medicine and Epidemiology, University of Pittsburgh Medical Center, Pittsburgh, PA
| | - Thomas A Sellers
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL
| | - Daniela Seminara
- Epidemiology and Genomics Research Program, Division of Cancer Control and Population Sciences, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Gianluca Severi
- CESP (U1018 INSERM), Facultés de Médecine Université Paris-Sud, UVSQ, Université Paris-Saclay, Villejuif, France
- Human Genetics Foundation (HuGeF), Torino, Italy
| | - Wei Shi
- Department of Surgery, Children’s Hospital Los Angeles, Los Angeles, CA
| | - David Shibata
- Department of Surgery, University of Tennessee Health Science Center, Memphis, TN
| | - Xiao-Ou Shu
- Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, TN
- Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN
| | - Erin M Siegel
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL
| | - Martha L Slattery
- Department of Internal Medicine, University of Utah Health Sciences Center, Salt Lake City, UT
| | - Melissa Southey
- Colorectal Oncogenomics Group, Department of Pathology (DDB) and Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Melbourne, Victoria, Australia
| | - Zsofia K Stadler
- Clinical Genetics Service (KO), Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Weill Cornell Medical Center, New York, NY
| | - Mariana C Stern
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center
| | - Sebastian Stintzing
- Department of Hematology and Oncology University of Munich (LMU), Munich, Germany
| | | | | | - Duncan C Thomas
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center
| | | | - Shoichiro Tsugane
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center
- National Cancer Center, Tokyo, Japan
- Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Cornelia M Ulrich
- Huntsman Cancer Institute and Department of Population Health Sciences, University of Utah, Salt Lake City, UT
| | | | | | - Joseph Vijai
- Clinical Genetics Service (KO), Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jarmo Virtamo
- Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland
| | - Stephanie J Weinstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | | | - Aung Ko Win
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | | | - Michael Woods
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Anna H Wu
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center
| | - Kana Wu
- Department of Nutrition, Harvard School of Public Health, Boston, MA
| | - Yong-Bing Xiang
- State Key Laboratory of Oncogene and Related Genes and Department of Epidemiology, Shanghai Cancer Institute, Shanghai, China
| | - Yun Yen
- Ph.D. Program of Cancer Research and Drug Discovery
- Department of Medical Oncology and Therapeutic Research, City of Hope National Medical Center, Duarte, CA
| | - Brent W Zanke
- Clinical Epidemiology Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
- The University of Ottawa, Ottawa, Ontario, Canada
| | - Yi-Xin Zeng
- State Key Laboratory of Oncology in South China, Cancer Center, Sun Yatsen University, Guangzhou, China
| | - Ben Zhang
- Division of Noncommunicable Disease Epidemiology and Southwest Hospital Clinical Research Center, Third Military Medical University, Chongqing, China
| | | | - Sun-Seog Kweon
- Department of Preventive Medicine, Chonnam National University Medical School, Gwangju, South Korea
- South Korea Jeonnam Regional Cancer Center, Chonnam National University Hwasun Hospital, Hwasun, South Korea
| | - Jane C Figueiredo
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Wei Zheng
- Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, TN
- Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI
| | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institutet Solna, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Victor Moreno
- Catalan Institute of Oncology, Bellvitge Biomedical Research Institute
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- University of Barcelona, Barcelona, Spain
| | - Ulrike Peters
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA
| | - Graham Casey
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA
| | - Li Hsu
- Public Health Sciences Division
| | - David V Conti
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center
| | - Stephen B Gruber
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center
- Department of Medicine, University of Southern California, Los Angeles, CA
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11
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Huyghe JR, Bien SA, Harrison TA, Kang HM, Chen S, Schmit SL, Conti DV, Qu C, Jeon J, Edlund CK, Greenside P, Wainberg M, Schumacher FR, Smith JD, Levine DM, Nelson SC, Sinnott-Armstrong NA, Albanes D, Alonso MH, Anderson K, Arnau-Collell C, Arndt V, Bamia C, Banbury BL, Baron JA, Berndt SI, Bézieau S, Bishop DT, Boehm J, Boeing H, Brenner H, Brezina S, Buch S, Buchanan DD, Burnett-Hartman A, Butterbach K, Caan BJ, Campbell PT, Carlson CS, Castellví-Bel S, Chan AT, Chang-Claude J, Chanock SJ, Chirlaque MD, Cho SH, Connolly CM, Cross AJ, Cuk K, Curtis KR, de la Chapelle A, Doheny KF, Duggan D, Easton DF, Elias SG, Elliott F, English DR, Feskens EJM, Figueiredo JC, Fischer R, FitzGerald LM, Forman D, Gala M, Gallinger S, Gauderman WJ, Giles GG, Gillanders E, Gong J, Goodman PJ, Grady WM, Grove JS, Gsur A, Gunter MJ, Haile RW, Hampe J, Hampel H, Harlid S, Hayes RB, Hofer P, Hoffmeister M, Hopper JL, Hsu WL, Huang WY, Hudson TJ, Hunter DJ, Ibañez-Sanz G, Idos GE, Ingersoll R, Jackson RD, Jacobs EJ, Jenkins MA, Joshi AD, Joshu CE, Keku TO, Key TJ, Kim HR, Kobayashi E, Kolonel LN, Kooperberg C, Kühn T, Küry S, Kweon SS, Larsson SC, Laurie CA, Le Marchand L, Leal SM, Lee SC, Lejbkowicz F, Lemire M, Li CI, Li L, Lieb W, Lin Y, Lindblom A, Lindor NM, Ling H, Louie TL, Männistö S, Markowitz SD, Martín V, Masala G, McNeil CE, Melas M, Milne RL, Moreno L, Murphy N, Myte R, Naccarati A, Newcomb PA, Offit K, Ogino S, Onland-Moret NC, Pardini B, Parfrey PS, Pearlman R, Perduca V, Pharoah PDP, Pinchev M, Platz EA, Prentice RL, Pugh E, Raskin L, Rennert G, Rennert HS, Riboli E, Rodríguez-Barranco M, Romm J, Sakoda LC, Schafmayer C, Schoen RE, Seminara D, Shah M, Shelford T, Shin MH, Shulman K, Sieri S, Slattery ML, Southey MC, Stadler ZK, Stegmaier C, Su YR, Tangen CM, Thibodeau SN, Thomas DC, Thomas SS, Toland AE, Trichopoulou A, Ulrich CM, Van Den Berg DJ, van Duijnhoven FJB, Van Guelpen B, van Kranen H, Vijai J, Visvanathan K, Vodicka P, Vodickova L, Vymetalkova V, Weigl K, Weinstein SJ, White E, Win AK, Wolf CR, Wolk A, Woods MO, Wu AH, Zaidi SH, Zanke BW, Zhang Q, Zheng W, Scacheri PC, Potter JD, Bassik MC, Kundaje A, Casey G, Moreno V, Abecasis GR, Nickerson DA, Gruber SB, Hsu L, Peters U. Discovery of common and rare genetic risk variants for colorectal cancer. Nat Genet 2019; 51:76-87. [PMID: 30510241 PMCID: PMC6358437 DOI: 10.1038/s41588-018-0286-6] [Citation(s) in RCA: 293] [Impact Index Per Article: 58.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 10/22/2018] [Indexed: 12/17/2022]
Abstract
To further dissect the genetic architecture of colorectal cancer (CRC), we performed whole-genome sequencing of 1,439 cases and 720 controls, imputed discovered sequence variants and Haplotype Reference Consortium panel variants into genome-wide association study data, and tested for association in 34,869 cases and 29,051 controls. Findings were followed up in an additional 23,262 cases and 38,296 controls. We discovered a strongly protective 0.3% frequency variant signal at CHD1. In a combined meta-analysis of 125,478 individuals, we identified 40 new independent signals at P < 5 × 10-8, bringing the number of known independent signals for CRC to ~100. New signals implicate lower-frequency variants, Krüppel-like factors, Hedgehog signaling, Hippo-YAP signaling, long noncoding RNAs and somatic drivers, and support a role for immune function. Heritability analyses suggest that CRC risk is highly polygenic, and larger, more comprehensive studies enabling rare variant analysis will improve understanding of biology underlying this risk and influence personalized screening strategies and drug development.
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Affiliation(s)
- Jeroen R Huyghe
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Stephanie A Bien
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Tabitha A Harrison
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Hyun Min Kang
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Sai Chen
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Stephanie L Schmit
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - David V Conti
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Conghui Qu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jihyoun Jeon
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Christopher K Edlund
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Peyton Greenside
- Biomedical Informatics Program, Stanford University, Stanford, CA, USA
| | - Michael Wainberg
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Fredrick R Schumacher
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Joshua D Smith
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - David M Levine
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Sarah C Nelson
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | | | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - M Henar Alonso
- Cancer Prevention and Control Program, Catalan Institute of Oncology-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
- CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Kristin Anderson
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, MN, USA
| | - Coral Arnau-Collell
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona, Spain
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christina Bamia
- Hellenic Health Foundation, Athens, Greece
- WHO Collaborating Center for Nutrition and Health, Unit of Nutritional Epidemiology and Nutrition in Public Health, Department of Hygiene, Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Barbara L Banbury
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - John A Baron
- Department of Medicine, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Stéphane Bézieau
- Service de Génétique Médicale, Centre Hospitalier Universitaire (CHU) Nantes, Nantes, France
| | - D Timothy Bishop
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Juergen Boehm
- Huntsman Cancer Institute and Department of Population Health Sciences, University of Utah, Salt Lake City, UT, USA
| | - Heiner Boeing
- Department of Epidemiology, German Institute of Human Nutrition (DIfE), Potsdam-Rehbrücke, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefanie Brezina
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Stephan Buch
- Department of Medicine I, University Hospital Dresden, Technische Universität Dresden (TU Dresden), Dresden, Germany
| | - Daniel D Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Victoria, Australia
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | | | - Katja Butterbach
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Bette J Caan
- Division of Research, Kaiser Permanente Medical Care Program, Oakland, CA, USA
| | - Peter T Campbell
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, GA, USA
| | - Christopher S Carlson
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Sergi Castellví-Bel
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona, Spain
| | - Andrew T Chan
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Cancer Epidemiology Group, University Medical Centre Hamburg-Eppendorf, University Cancer Centre Hamburg (UCCH), Hamburg, Germany
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Maria-Dolores Chirlaque
- CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Department of Epidemiology, Regional Health Council, IMIB-Arrixaca, Murcia University, Murcia, Spain
| | - Sang Hee Cho
- Department of Hematology-Oncology, Chonnam National University Hospital, Hwasun, South Korea
| | - Charles M Connolly
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Amanda J Cross
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Katarina Cuk
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Keith R Curtis
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Albert de la Chapelle
- Department of Cancer Biology and Genetics and the Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Kimberly F Doheny
- Center for Inherited Disease Research (CIDR), Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - David Duggan
- Translational Genomics Research Institute - An Affiliate of City of Hope, Phoenix, AZ, USA
| | - Douglas F Easton
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Sjoerd G Elias
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Faye Elliott
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Dallas R English
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Edith J M Feskens
- Division of Human Nutrition and Health, Wageningen University and Research, Wageningen, The Netherlands
| | - Jane C Figueiredo
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Rocky Fischer
- University of Michigan Comprehensive Cancer Center, Ann Arbor, MI, USA
| | - Liesel M FitzGerald
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - David Forman
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Manish Gala
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Steven Gallinger
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - W James Gauderman
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Graham G Giles
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Elizabeth Gillanders
- Division of Cancer Control and Population Sciences, National Cancer Institute, Bethesda, MD, USA
| | - Jian Gong
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Phyllis J Goodman
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - William M Grady
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - John S Grove
- University of Hawaii Cancer Research Center, Honolulu, HI, USA
| | - Andrea Gsur
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Marc J Gunter
- Nutrition and Metabolism Section, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Robert W Haile
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Jochen Hampe
- Department of Medicine I, University Hospital Dresden, Technische Universität Dresden (TU Dresden), Dresden, Germany
| | - Heather Hampel
- Division of Human Genetics, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Sophia Harlid
- Department of Radiation Sciences, Oncology Unit, Umeå University, Umeå, Sweden
| | - Richard B Hayes
- Division of Epidemiology, Department of Population Health, New York University School of Medicine, New York, NY, USA
| | - Philipp Hofer
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Department of Epidemiology, School of Public Health and Institute of Health and Environment, Seoul National University, Seoul, South Korea
| | - Wan-Ling Hsu
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Wen-Yi Huang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Thomas J Hudson
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - David J Hunter
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Gemma Ibañez-Sanz
- Cancer Prevention and Control Program, Catalan Institute of Oncology-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
- Gastroenterology Department, Bellvitge University Hospital, L'Hospitalet de Llobregat, Barcelona, Spain
- Colorectal Cancer Group, ONCOBELL Program, Bellvitge Biomedical Research Institute-IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Gregory E Idos
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Roxann Ingersoll
- Center for Inherited Disease Research (CIDR), Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Rebecca D Jackson
- Department of Medicine, Division of Endocrinology, Diabetes and Metabolism, The Ohio State University, Columbus, OH, USA
| | - Eric J Jacobs
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, GA, USA
| | - Mark A Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Amit D Joshi
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Corinne E Joshu
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Temitope O Keku
- Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, NC, USA
| | - Timothy J Key
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Hyeong Rok Kim
- Department of Surgery, Chonnam National University Hwasun Hospital and Medical School, Hwasun, Korea
| | - Emiko Kobayashi
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Laurence N Kolonel
- Office of Public Health Studies, University of Hawaii Manoa, Honolulu, HI, USA
| | - Charles Kooperberg
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Tilman Kühn
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sébastien Küry
- Service de Génétique Médicale, Centre Hospitalier Universitaire (CHU) Nantes, Nantes, France
| | - Sun-Seog Kweon
- Department of Preventive Medicine, Chonnam National University Medical School, Gwangju, Korea
- Jeonnam Regional Cancer Center, Chonnam National University Hwasun Hospital, Hwasun, Korea
| | - Susanna C Larsson
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Cecelia A Laurie
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | | | - Suzanne M Leal
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Soo Chin Lee
- Department of Haematology-Oncology, National University Cancer Institute, Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Flavio Lejbkowicz
- The Clalit Health Services, Personalized Genomic Service, Carmel, Haifa, Israel
- Department of Community Medicine and Epidemiology, Lady Davis Carmel Medical Center, Haifa, Israel
- Clalit National Cancer Control Center, Haifa, Israel
| | - Mathieu Lemire
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Christopher I Li
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Li Li
- Center for Community Health Integration and Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
| | - Wolfgang Lieb
- Institute of Epidemiology, PopGen Biobank, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Yi Lin
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Annika Lindblom
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Noralane M Lindor
- Department of Health Science Research, Mayo Clinic, Scottsdale, AZ, USA
| | - Hua Ling
- Center for Inherited Disease Research (CIDR), Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Tin L Louie
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Satu Männistö
- Department of Public Health Solutions, National Institute for Health and Welfare, Helsinki, Finland
| | - Sanford D Markowitz
- Departments of Medicine and Genetics, Case Comprehensive Cancer Center, Case Western Reserve University, and University Hospitals of Cleveland, Cleveland, OH, USA
| | - Vicente Martín
- CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Biomedicine Institute (IBIOMED), University of León, León, Spain
| | - Giovanna Masala
- Cancer Risk Factors and Life-Style Epidemiology Unit, Institute of Cancer Research, Prevention and Clinical Network - ISPRO, Florence, Italy
| | - Caroline E McNeil
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Marilena Melas
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Roger L Milne
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Lorena Moreno
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona, Spain
| | - Neil Murphy
- Nutrition and Metabolism Section, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Robin Myte
- Department of Radiation Sciences, Oncology Unit, Umeå University, Umeå, Sweden
| | - Alessio Naccarati
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Italian Institute for Genomic Medicine (IIGM), Turin, Italy
| | - Polly A Newcomb
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Kenneth Offit
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Shuji Ogino
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - N Charlotte Onland-Moret
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Barbara Pardini
- Italian Institute for Genomic Medicine (IIGM), Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Patrick S Parfrey
- The Clinical Epidemiology Unit, Memorial University Medical School, Newfoundland, Canada
| | - Rachel Pearlman
- Division of Human Genetics, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Vittorio Perduca
- Laboratoire de Mathématiques Appliquées MAP5 (UMR CNRS 8145), Université Paris Descartes, Paris, France
- CESP (Inserm U1018), Facultés de Medicine Université Paris-Sud, UVSQ, Université Paris-Saclay, Gustave Roussy, Villejuif, France
| | - Paul D P Pharoah
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Mila Pinchev
- Department of Community Medicine and Epidemiology, Lady Davis Carmel Medical Center, Haifa, Israel
| | - Elizabeth A Platz
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Ross L Prentice
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Elizabeth Pugh
- Center for Inherited Disease Research (CIDR), Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Leon Raskin
- Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Gad Rennert
- Department of Community Medicine and Epidemiology, Lady Davis Carmel Medical Center, Haifa, Israel
- Clalit National Cancer Control Center, Haifa, Israel
- Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Hedy S Rennert
- Department of Community Medicine and Epidemiology, Lady Davis Carmel Medical Center, Haifa, Israel
- Clalit National Cancer Control Center, Haifa, Israel
- Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Elio Riboli
- School of Public Health, Imperial College London, London, UK
| | - Miguel Rodríguez-Barranco
- CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Escuela Andaluza de Salud Pública. Instituto de Investigación Biosanitaria ibs.GRANADA, Hospitales Universitarios de Granada, Universidad de Granada, Granada, Spain
| | - Jane Romm
- Center for Inherited Disease Research (CIDR), Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Lori C Sakoda
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Clemens Schafmayer
- Department of General and Thoracic Surgery, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Robert E Schoen
- Department of Medicine and Epidemiology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Daniela Seminara
- Division of Cancer Control and Population Sciences, National Cancer Institute, Bethesda, MD, USA
| | - Mitul Shah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Tameka Shelford
- Center for Inherited Disease Research (CIDR), Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Min-Ho Shin
- Department of Preventive Medicine, Chonnam National University Medical School, Gwangju, Korea
| | | | - Sabina Sieri
- Epidemiology and Prevention Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Martha L Slattery
- Department of Internal Medicine, University of Utah, Salt Lake City, UT, USA
| | - Melissa C Southey
- Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Melbourne, Australia
| | - Zsofia K Stadler
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Yu-Ru Su
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Catherine M Tangen
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Stephen N Thibodeau
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Duncan C Thomas
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Sushma S Thomas
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Amanda E Toland
- Departments of Cancer Biology and Genetics and Internal Medicine, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Antonia Trichopoulou
- Hellenic Health Foundation, Athens, Greece
- WHO Collaborating Center for Nutrition and Health, Unit of Nutritional Epidemiology and Nutrition in Public Health, Department of Hygiene, Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Cornelia M Ulrich
- Huntsman Cancer Institute and Department of Population Health Sciences, University of Utah, Salt Lake City, UT, USA
| | - David J Van Den Berg
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | - Bethany Van Guelpen
- Department of Radiation Sciences, Oncology Unit, Umeå University, Umeå, Sweden
| | - Henk van Kranen
- National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Joseph Vijai
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kala Visvanathan
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University, Pilsen, Czech Republic
| | - Ludmila Vodickova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University, Pilsen, Czech Republic
| | - Veronika Vymetalkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University, Pilsen, Czech Republic
| | - Korbinian Weigl
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Medical Faculty, University of Heidelberg, Heidelberg, Germany
| | - Stephanie J Weinstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Emily White
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Aung Ko Win
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - C Roland Wolf
- School of Medicine, University of Dundee, Dundee, Scotland, UK
| | - Alicja Wolk
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Michael O Woods
- Memorial University of Newfoundland, Discipline of Genetics, St. John's, Newfoundland, Canada
| | - Anna H Wu
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Syed H Zaidi
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Brent W Zanke
- Division of Hematology, University of Toronto, Toronto, Ontario, Canada
| | - Qing Zhang
- Genomics Shared Resource, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Peter C Scacheri
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Case Comprehensive Cancer Center, Cleveland, OH, USA
| | - John D Potter
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Anshul Kundaje
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Graham Casey
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Victor Moreno
- Cancer Prevention and Control Program, Catalan Institute of Oncology-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
- CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
- Colorectal Cancer Group, ONCOBELL Program, Bellvitge Biomedical Research Institute-IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Goncalo R Abecasis
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | | | - Stephen B Gruber
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Li Hsu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
- Department of Epidemiology, University of Washington, Seattle, WA, USA.
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12
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Su YR, Di C, Bien S, Huang L, Dong X, Abecasis G, Berndt S, Bezieau S, Brenner H, Caan B, Casey G, Chang-Claude J, Chanock S, Chen S, Connolly C, Curtis K, Figueiredo J, Gala M, Gallinger S, Harrison T, Hoffmeister M, Hopper J, Huyghe JR, Jenkins M, Joshi A, Le Marchand L, Newcomb P, Nickerson D, Potter J, Schoen R, Slattery M, White E, Zanke B, Peters U, Hsu L. A Mixed-Effects Model for Powerful Association Tests in Integrative Functional Genomics. Am J Hum Genet 2018; 102:904-919. [PMID: 29727690 PMCID: PMC5986723 DOI: 10.1016/j.ajhg.2018.03.019] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 03/15/2018] [Indexed: 01/05/2023] Open
Abstract
Genome-wide association studies (GWASs) have successfully identified thousands of genetic variants for many complex diseases; however, these variants explain only a small fraction of the heritability. Recently, genetic association studies that leverage external transcriptome data have received much attention and shown promise for discovering novel variants. One such approach, PrediXcan, is to use predicted gene expression through genetic regulation. However, there are limitations in this approach. The predicted gene expression may be biased, resulting from regularized regression applied to moderately sample-sized reference studies. Further, some variants can individually influence disease risk through alternative functional mechanisms besides expression. Thus, testing only the association of predicted gene expression as proposed in PrediXcan will potentially lose power. To tackle these challenges, we consider a unified mixed effects model that formulates the association of intermediate phenotypes such as imputed gene expression through fixed effects, while allowing residual effects of individual variants to be random. We consider a set-based score testing framework, MiST (mixed effects score test), and propose two data-driven combination approaches to jointly test for the fixed and random effects. We establish the asymptotic distributions, which enable rapid calculation of p values for genome-wide analyses, and provide p values for fixed and random effects separately to enhance interpretability over GWASs. Extensive simulations demonstrate that our approaches are more powerful than existing ones. We apply our approach to a large-scale GWAS of colorectal cancer and identify two genes, POU5F1B and ATF1, which would have otherwise been missed by PrediXcan, after adjusting for all known loci.
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Affiliation(s)
- Yu-Ru Su
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
| | - Chongzhi Di
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Stephanie Bien
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Licai Huang
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Xinyuan Dong
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Goncalo Abecasis
- Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sonja Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA
| | - Stephane Bezieau
- Service de Génétique Médicale Centre Hospitalier Universitaire (CHU) Nantes, Nantes 44093, France
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Bette Caan
- Division of Research, Kaiser Permanente Medical Care Program of Northern California, Oakland, CA 94612, USA
| | - Graham Casey
- Public Health Sciences Division, University of Virginia, Charlottesville, VA 22908, USA
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center, Heidelberg 69009, Germany
| | - Stephen Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA
| | - Sai Chen
- Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Charles Connolly
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Keith Curtis
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Jane Figueiredo
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Manish Gala
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Steven Gallinger
- Department of Surgery, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Tabitha Harrison
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - John Hopper
- Melborne School of Population Health, The University of Melborne, Carlton, VIC 3010, Australia
| | - Jeroen R Huyghe
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Mark Jenkins
- Melborne School of Population Health, The University of Melborne, Carlton, VIC 3010, Australia
| | - Amit Joshi
- Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI 96813, USA
| | - Polly Newcomb
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Epidemiology, University of Washington School of Public Health, Seattle, WA 98109, USA
| | | | - John Potter
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Epidemiology, University of Washington School of Public Health, Seattle, WA 98109, USA
| | - Robert Schoen
- Department of Medicine and Epidemiology, University of Pittsburgh Medical Center, Pittsburgh, PA 15213, USA
| | - Martha Slattery
- Department of Internal Medicine, University of Utah Health Sciences Center, Salt Lake City, UT 84132, USA
| | - Emily White
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Epidemiology, University of Washington School of Public Health, Seattle, WA 98109, USA
| | - Brent Zanke
- Division of Hematology, Faculty of Medicine, The University of Ottawa, Ottawa, ON K1Y 4E9, USA
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Epidemiology, University of Washington School of Public Health, Seattle, WA 98109, USA
| | - Li Hsu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Biostatistics, University of Washington, Seattle, WA 98195, USA.
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13
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Luther J, Gala M, Patel SJ, Dave M, Borren N, Xavier RJ, Ananthakrishnan AN. Loss of Response to Anti-Tumor Necrosis Factor Alpha Therapy in Crohn's Disease Is Not Associated with Emergence of Novel Inflammatory Pathways. Dig Dis Sci 2018; 63:738-745. [PMID: 29372477 PMCID: PMC6152907 DOI: 10.1007/s10620-018-4932-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 01/13/2018] [Indexed: 12/19/2022]
Abstract
BACKGROUND While monoclonal antibodies against tumor necrosis factor-α (TNFα) are effective in treating Crohn's disease (CD), approximately one-third of patients lose response. The mechanisms underlying this loss of response remain elusive. AIM We sought to determine if novel biological pathways, including TNFα-independent inflammatory pathways, emerge in those with loss of response to anti-TNFα. METHODS Using RNA microarray technology in 28 patients with CD, we examined the colonic gene expression differences between those with active inflammation in the setting of loss of response to TNFα-antagonist therapy ("loss of responders") compared to anti-TNFα naïve patients with active inflammation and those on anti-TNF therapy in disease remission. Pathway enrichment analyses were performed. RESULTS We found that colonic expression of chemokines known to drive inflammation (CXCL20, CXCL9, and CXCL10) was elevated in those with loss of response compared to those in remission. Expression of genes critical to modulating oxidative stress burden (DUOX2, DUOXA2, and NOS2) was also elevated. Additionally, MMP3, MMP1, and MMP12 were elevated in those with continued inflammation. Gene enrichment analysis revealed that loss of responders exhibited dysregulation in the cysteine and methionine metabolism pathway, suggesting alteration in oxidative stress burden. There were no differences in genes or pathways between loss of responders and those who were TNFα-naïve. However, loss of response occurred despite the ability of anti-TNFα therapy to normalize APO gene expression. CONCLUSION Our analyses suggest that loss of response to anti-TNFα is not driven by the emergence of pathways that bypass the action or induce resistance to anti-TNFα therapy.
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Affiliation(s)
- Jay Luther
- Gastrointestinal Unit, Massachusetts General Hospital, Harvard Medical School
| | - Manish Gala
- Gastrointestinal Unit, Massachusetts General Hospital, Harvard Medical School
| | - Suraj J. Patel
- Gastrointestinal Unit, Massachusetts General Hospital, Harvard Medical School
| | - Maneesh Dave
- Department of Medicine, Case Western Reserve University
| | - Nynke Borren
- Gastrointestinal Unit, Massachusetts General Hospital, Harvard Medical School
| | - Ramnik J. Xavier
- Gastrointestinal Unit, Massachusetts General Hospital, Harvard Medical School
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14
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Kedrin D, Gandhi SCC, Wolf M, Roper J, Yilmaz O, Corey K, Khalili H, Stanford FC, Gala M. Bariatric Surgery Prior to Index Screening Colonoscopy Is Associated With a Decreased Rate of Colorectal Adenomas in Obese Individuals. Clin Transl Gastroenterol 2017; 8:e73. [PMID: 28181993 PMCID: PMC5387748 DOI: 10.1038/ctg.2017.1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 12/13/2016] [Indexed: 12/20/2022] Open
Abstract
Objectives: Obesity is an important risk factor for the development of colorectal cancer (CRC). Although the impact of bariatric surgery on CRC is conflicting, its impact on precursor lesions is unknown. The aim of this study was to determine whether bariatric surgery before index screening colonoscopy is associated with decreased development of colorectal adenomas. Methods: We performed a retrospective cohort study of bariatric surgery patients who had undergone index, screening colonoscopy at an academic center from 2001 to 2014. Patients who had bariatric surgery at least 1 year before index colonoscopy were compared with those who had surgery after colonoscopy, using multivariable logistic regression to control for presurgical body mass index, sex, gender, race, type of surgery, aspirin use, metformin use, smoking, and age at colonoscopy. Results: One hundred and twenty-five obese individuals who had bariatric surgery before colonoscopy were compared with 223 individuals who had colonoscopy after surgery. Adenomatous polyps were found in 16.8% of individuals who had surgery first vs. 35.5% who had colonoscopy before bariatric surgery (unadjusted odds ratio (OR) 0.37, 95% confidence interval (CI): 0.21–0.64, P=0.0003). After multivariable adjustment, bariatric surgery before index screening colonoscopy was associated with a decreased risk of adenomas at index colonoscopy (adjusted OR 0.37, 95% CI: 0.19–0.69, P=0.002). Conclusions: Bariatric surgery is associated with a decreased risk of colorectal adenomas in obese individuals without a family history of CRC.
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Affiliation(s)
- Dmitriy Kedrin
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Koch Institute for Integrative Cancer Research, MIT, Cambridge, Massachusetts, USA
| | - Shaan-Chirag Chandrahas Gandhi
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Department of Internal Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Molly Wolf
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Department of Internal Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Jatin Roper
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, Massachusetts, USA.,Division of Gastroenterology, Tufts Medical Center, Boston Massachusetts, USA
| | - Omer Yilmaz
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, Massachusetts, USA
| | - Kathleen Corey
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.,The Massachusetts General Weight Center, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Hamed Khalili
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Fatima Cody Stanford
- The Massachusetts General Weight Center, Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Pediatrics, Division of Endocrinology, Boston, Massachusetts, USA
| | - Manish Gala
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
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15
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Karami S, Han Y, Pande M, Cheng I, Rudd J, Pierce BL, Nutter EL, Schumacher FR, Kote-Jarai Z, Lindstrom S, Witte JS, Fang S, Han J, Kraft P, Hunter DJ, Song F, Hung RJ, McKay J, Gruber SB, Chanock SJ, Risch A, Shen H, Haiman CA, Boardman L, Ulrich CM, Casey G, Peters U, Amin Al Olama A, Berchuck A, Berndt SI, Bezieau S, Brennan P, Brenner H, Brinton L, Caporaso N, Chan AT, Chang-Claude J, Christiani DC, Cunningham JM, Easton D, Eeles RA, Eisen T, Gala M, Gallinger SJ, Gayther SA, Goode EL, Grönberg H, Henderson BE, Houlston R, Joshi AD, Küry S, Landi MT, Le Marchand L, Muir K, Newcomb PA, Permuth-Wey J, Pharoah P, Phelan C, Potter JD, Ramus SJ, Risch H, Schildkraut J, Slattery ML, Song H, Wentzensen N, White E, Wiklund F, Zanke BW, Sellers TA, Zheng W, Chatterjee N, Amos CI, Doherty JA. Telomere structure and maintenance gene variants and risk of five cancer types. Int J Cancer 2016; 139:2655-2670. [PMID: 27459707 PMCID: PMC5198774 DOI: 10.1002/ijc.30288] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 06/21/2016] [Indexed: 01/20/2023]
Abstract
Telomeres cap chromosome ends, protecting them from degradation, double-strand breaks, and end-to-end fusions. Telomeres are maintained by telomerase, a reverse transcriptase encoded by TERT, and an RNA template encoded by TERC. Loci in the TERT and adjoining CLPTM1L region are associated with risk of multiple cancers. We therefore investigated associations between variants in 22 telomere structure and maintenance gene regions and colorectal, breast, prostate, ovarian, and lung cancer risk. We performed subset-based meta-analyses of 204,993 directly-measured and imputed SNPs among 61,851 cancer cases and 74,457 controls of European descent. Independent associations for SNP minor alleles were identified using sequential conditional analysis (with gene-level p value cutoffs ≤3.08 × 10-5 ). Of the thirteen independent SNPs observed to be associated with cancer risk, novel findings were observed for seven loci. Across the DCLRE1B region, rs974494 and rs12144215 were inversely associated with prostate and lung cancers, and colorectal, breast, and prostate cancers, respectively. Across the TERC region, rs75316749 was positively associated with colorectal, breast, ovarian, and lung cancers. Across the DCLRE1B region, rs974404 and rs12144215 were inversely associated with prostate and lung cancers, and colorectal, breast, and prostate cancers, respectively. Near POT1, rs116895242 was inversely associated with colorectal, ovarian, and lung cancers, and RTEL1 rs34978822 was inversely associated with prostate and lung cancers. The complex association patterns in telomere-related genes across cancer types may provide insight into mechanisms through which telomere dysfunction in different tissues influences cancer risk.
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Affiliation(s)
- Sara Karami
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH
| | - Younghun Han
- The Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Lebanon, NH
| | - Mala Pande
- Department of Gastroenterology, Hepatology and Nutrition, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Iona Cheng
- Cancer Prevention Institute of California, Fremont, CA; Stanford Cancer Institute, Stanford, CA
| | - James Rudd
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH
| | - Brandon L Pierce
- Departments of Public Health Sciences and Human Genetics and Comprehensive Cancer Center, The University of Chicago, Chicago, IL
| | - Ellen L Nutter
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH
| | - Fredrick R Schumacher
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Zsofia Kote-Jarai
- Oncogenetics Team, The Institute of Cancer Research and Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Sara Lindstrom
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. School of Public Health, Boston, MA
| | - John S Witte
- Division of Genetic and Cancer Epidemiology, Department of Epidemiology and Biostatistics and Institute of Human Genetics, University of California, San Francisco, CA
| | - Shenying Fang
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jiali Han
- Department of Epidemiology, Fairbanks School of Public Health, Simon Cancer Center, Indiana University, Indianapolis, IN
| | - Peter Kraft
- Department of Epidemiology and Biostatistics, Harvard School of Public Health, Boston, MA
| | - David J Hunter
- Department of Epidemiology and Biostatistics, Harvard School of Public Health, Boston, MA
| | - Fengju Song
- Department of Epidemiology and Biostatistics, Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Centre of Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, People's Republic of China
| | - Rayjean J Hung
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, University of Toronto, Toronto, ON, Canada
| | - James McKay
- Genetic Cancer Susceptibility Group, Genetic Epidemiology Group International Agency for Research on Cancer (IARC), Lyon, France
| | - Stephen B Gruber
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD
| | - Angela Risch
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany; Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
| | - Hongbing Shen
- Department of Epidemiology and Biostatistics, Collaborative Innovation Center for Cancer Medicine, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China
| | - Christopher A Haiman
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | | | - Cornelia M Ulrich
- Huntsman Cancer Institute, Salt Lake City, UT
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Graham Casey
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Ali Amin Al Olama
- Department of Public Health and Primary Care, Center for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Andrew Berchuck
- Department of Obstetrics and Gynecology, Duke University, Durham, NC
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD
| | | | - Paul Brennan
- Genetic Cancer Susceptibility Group, Genetic Epidemiology Group International Agency for Research on Cancer (IARC), Lyon, France
| | - Hermann Brenner
- Klinische Epidemiologie und Alternsforschung, Deutsches Krebsforschungszentrum, Heidelberg, Germany
| | - Louise Brinton
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD
| | - Neil Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD
| | - Andrew T Chan
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David C Christiani
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. School of Public Health, Boston, MA
| | | | - Douglas Easton
- Department of Public Health and Primary Care, Center for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
- Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Rosalind A Eeles
- Oncogenetics Team, The Institute of Cancer Research and Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Timothy Eisen
- Addenbrooke's Hospital, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Manish Gala
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA
| | - Steven J Gallinger
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, University of Toronto, Toronto, ON, Canada
| | - Simon A Gayther
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | | | - Henrik Grönberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Brian E Henderson
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | | | - Amit D Joshi
- Department of Epidemiology and Biostatistics, Harvard School of Public Health, Boston, MA
| | - Sébastien Küry
- Service de Génétique Médicale, CHU Nantes, Nantes, France
| | - Mari T Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD
| | - Loic Le Marchand
- Division of Epidemiology, University of Hawaii Cancer Center, Honolulu, HI
| | - Kenneth Muir
- Warwick Medical School, University of Warwick, Coventry, United Kingdom
- Institute of Population Health, University of Manchester, Manchester, United Kingdom
| | - Polly A Newcomb
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | | | - Paul Pharoah
- Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | | | - John D Potter
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Susan J Ramus
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | | | | | | | - Honglin Song
- Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD
| | - Emily White
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Fredrik Wiklund
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Brent W Zanke
- Division of Hematology, The University of Ottawa, Ottawa Hospital Research Institute, Ottawa, ON
| | | | - Wei Zheng
- Vanderbilt Epidemiology Center and Division of Epidemiology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN
| | - Nilanjan Chatterjee
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD
| | - Christopher I Amos
- The Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Lebanon, NH
| | - Jennifer A Doherty
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH.
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16
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Joshi AD, Andersson C, Buch S, Stender S, Noordam R, Weng LC, Weeke PE, Auer PL, Boehm B, Chen C, Choi H, Curhan G, Denny JC, De Vivo I, Eicher JD, Ellinghaus D, Folsom AR, Fuchs C, Gala M, Haessler J, Hofman A, Hu F, Hunter DJ, Janssen HL, Kang JH, Kooperberg C, Kraft P, Kratzer W, Lieb W, Lutsey PL, Murad SD, Nordestgaard BG, Pasquale LR, Reiner AP, Ridker PM, Rimm E, Rose LM, Shaffer CM, Schafmayer C, Tamimi RM, Uitterlinden AG, Völker U, Völzke H, Wakabayashi Y, Wiggs JL, Zhu J, Roden DM, Stricker BH, Tang W, Teumer A, Hampe J, Tybjærg-Hansen A, Chasman DI, Chan AT, Johnson AD. Four Susceptibility Loci for Gallstone Disease Identified in a Meta-analysis of Genome-Wide Association Studies. Gastroenterology 2016; 151:351-363.e28. [PMID: 27094239 PMCID: PMC4959966 DOI: 10.1053/j.gastro.2016.04.007] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 04/06/2016] [Accepted: 04/07/2016] [Indexed: 01/01/2023]
Abstract
BACKGROUND & AIMS A genome-wide association study (GWAS) of 280 cases identified the hepatic cholesterol transporter ABCG8 as a locus associated with risk for gallstone disease, but findings have not been reported from any other GWAS of this phenotype. We performed a large-scale, meta-analysis of GWASs of individuals of European ancestry with available prior genotype data, to identify additional genetic risk factors for gallstone disease. METHODS We obtained per-allele odds ratio (OR) and standard error estimates using age- and sex-adjusted logistic regression models within each of the 10 discovery studies (8720 cases and 55,152 controls). We performed an inverse variance weighted, fixed-effects meta-analysis of study-specific estimates to identify single-nucleotide polymorphisms that were associated independently with gallstone disease. Associations were replicated in 6489 cases and 62,797 controls. RESULTS We observed independent associations for 2 single-nucleotide polymorphisms at the ABCG8 locus: rs11887534 (OR, 1.69; 95% confidence interval [CI], 1.54-1.86; P = 2.44 × 10(-60)) and rs4245791 (OR, 1.27; P = 1.90 × 10(-34)). We also identified and/or replicated associations for rs9843304 in TM4SF4 (OR, 1.12; 95% CI, 1.08-1.16; P = 6.09 × 10(-11)), rs2547231 in SULT2A1 (encodes a sulfoconjugation enzyme that acts on hydroxysteroids and cholesterol-derived sterol bile acids) (OR, 1.17; 95% CI, 1.12-1.21; P = 2.24 × 10(-10)), rs1260326 in glucokinase regulatory protein (OR, 1.12; 95% CI, 1.07-1.17; P = 2.55 × 10(-10)), and rs6471717 near CYP7A1 (encodes an enzyme that catalyzes conversion of cholesterol to primary bile acids) (OR, 1.11; 95% CI, 1.08-1.15; P = 8.84 × 10(-9)). Among individuals of African American and Hispanic American ancestry, rs11887534 and rs4245791 were associated positively with gallstone disease risk, whereas the association for the rs1260326 variant was inverse. CONCLUSIONS In this large-scale GWAS of gallstone disease, we identified 4 loci in genes that have putative functions in cholesterol metabolism and transport, and sulfonylation of bile acids or hydroxysteroids.
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Affiliation(s)
- Amit D. Joshi
- Program in Genetic Epidemiology and Statistical Genetics, Harvard School of Public Health, Boston, MA,Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA,Clinical and Translational Epidemiology Unit, Massachusetts General Hospital Boston, MA,To whom correspondence should be addressed: Amit D. Joshi, MBBS, PhD, Clinical and Translational Epidemiology Unit, Division of Gastroenterology, Massachusetts General Hospital, 55 Fruit Street, Boston, Massachusetts 02114, USA. Tel: +1 617 724 7558; Charlotte Andersson, MD, PhD, The Framingham Heart Study, 73 Mt Wayte Avenue, Framingham, Massachusetts 01702, USA. , Andrew T. Chan, MD, MPH, Massachusetts General Hospital and Harvard Medical School, Clinical and Translational Epidemiology Unit, Division of Gastroenterology, GRJ-825C, Boston, Massachusetts 02114, USA. Tel:+1 617 724 0283; Fax: +1 617 726 3673; , Andrew D. Johnson, PhD, Division of Intramural Research, National Heart, Lung and Blood Institute, Cardiovascular Epidemiology and Human Genomics Branch, The Framingham Heart Study, 73 Mt. Wayte Ave., Suite #2, Framingham, MA, 01702, USA. Tel: +1 508 663 4082; Fax: +1 508 626 1262;
| | - Charlotte Andersson
- The National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, Massachusetts.
| | - Stephan Buch
- Medical Department 1, University Hospital Dresden, TU Dresden, Dresden Germany
| | - Stefan Stender
- Department of Clinical Biochemistry, Rigshospitalet, Copenhagen, Denmark
| | - Raymond Noordam
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands,Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Lu-Chen Weng
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, MN
| | - Peter E. Weeke
- Department of Medicine, Vanderbilt University, Nashville, TN,Department of Cardiology, The Heart Centre, Rigshospitalet, Copenhagen University Hospital, Denmark
| | - Paul L. Auer
- Joseph J. Zilber School of Public Health, University of Wisconsin, Milwaukee,Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Bernhard Boehm
- Department of Internal Medicine I, Ulm University Hospital, Ulm, Germany
| | - Constance Chen
- Program in Genetic Epidemiology and Statistical Genetics, Harvard School of Public Health, Boston, MA
| | - Hyon Choi
- Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital, Boston, MA
| | - Gary Curhan
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA,Renal Division, Department of Medicine, Brigham and Women’s Hospital, Boston, MA
| | - Joshua C. Denny
- Department of Medicine, Vanderbilt University, Nashville, TN,Department of Biomedical Informatics, Vanderbilt University, Nashville, TN
| | - Immaculata De Vivo
- Program in Genetic Epidemiology and Statistical Genetics, Harvard School of Public Health, Boston, MA,Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA,Department of Epidemiology, Harvard School of Public Health, Boston, MA
| | - John D. Eicher
- The National Heart, Lung, and Blood Institute’s Framingham Heart Study, Framingham, MA,Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Framingham, MA
| | - David Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Aaron R. Folsom
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, MN
| | - Charles Fuchs
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA
| | - Manish Gala
- Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Jeffrey Haessler
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Albert Hofman
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Frank Hu
- Department of Epidemiology, Harvard School of Public Health, Boston, MA,Department of Nutrition, Harvard School of Public Health, Boston, MA
| | - David J. Hunter
- Program in Genetic Epidemiology and Statistical Genetics, Harvard School of Public Health, Boston, MA,Department of Epidemiology, Harvard School of Public Health, Boston, MA
| | - Harry L.A. Janssen
- Department of Gastroenterology and Hepatology, Erasmus MC, Rotterdam, the Netherlands,Toronto Centre for Liver Disease, Toronto Western and General Hospital, University Health Network, Toronto, Canada
| | - Jae H. Kang
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Peter Kraft
- Program in Genetic Epidemiology and Statistical Genetics, Harvard School of Public Health, Boston, MA,Department of Epidemiology, Harvard School of Public Health, Boston, MA
| | - Wolfgang Kratzer
- Department of Internal Medicine I, Ulm University Hospital, Ulm, Germany
| | - Wolfgang Lieb
- Institute of Epidemiology, Christian Albrechts Universität Kiel, Niemannsweg 11, Kiel, Germany
| | - Pamela L. Lutsey
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, MN
| | - Sarwa Darwish Murad
- Department of Gastroenterology and Hepatology, Erasmus MC, Rotterdam, the Netherlands
| | - Børge G. Nordestgaard
- The Copenhagen General Population Study and,Department of Clinical Biochemistry, Herlev Hospital, Herlev Denmark,Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Louis R. Pasquale
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA,Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, MA
| | - Alex P. Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Paul M Ridker
- Division of Preventive Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Eric Rimm
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA,Department of Epidemiology, Harvard School of Public Health, Boston, MA,Department of Nutrition, Harvard School of Public Health, Boston, MA
| | - Lynda M. Rose
- Division of Preventive Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | | | - Clemens Schafmayer
- Department of General, Abdominal, Thoracic and Transplantation Surgery, University of Kiel, Kiel, Germany
| | - Rulla M. Tamimi
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA,Department of Epidemiology, Harvard School of Public Health, Boston, MA
| | - André G Uitterlinden
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands,Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Uwe Völker
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Germany
| | - Henry Völzke
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany,German Center for Cardiovascular Research, Partner Site Greifswald,German Center for Diabetes Research, Site Greifswald
| | - Yoshiyuki Wakabayashi
- The National Heart, Lung, and Blood Institute, DNA Sequencing Core Laboratory, Bethesda, MD
| | - Janey L. Wiggs
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, MA
| | - Jun Zhu
- The National Heart, Lung, and Blood Institute, DNA Sequencing Core Laboratory, Bethesda, MD
| | - Dan M. Roden
- Department of Medicine, Vanderbilt University, Nashville, TN
| | - Bruno H. Stricker
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands,Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Weihong Tang
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, MN
| | - Alexander Teumer
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Jochen Hampe
- Medical Department 1, University Hospital Dresden, TU Dresden, Dresden Germany
| | - Anne Tybjærg-Hansen
- Department of Clinical Biochemistry, Rigshospitalet, Copenhagen, Denmark,Department of Clinical Biochemistry, Herlev Hospital, Herlev Denmark
| | - Daniel I. Chasman
- Division of Preventive Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Andrew T. Chan
- Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA,Clinical and Translational Epidemiology Unit, Massachusetts General Hospital Boston, MA,Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA,To whom correspondence should be addressed: Amit D. Joshi, MBBS, PhD, Clinical and Translational Epidemiology Unit, Division of Gastroenterology, Massachusetts General Hospital, 55 Fruit Street, Boston, Massachusetts 02114, USA. Tel: +1 617 724 7558; Charlotte Andersson, MD, PhD, The Framingham Heart Study, 73 Mt Wayte Avenue, Framingham, Massachusetts 01702, USA. , Andrew T. Chan, MD, MPH, Massachusetts General Hospital and Harvard Medical School, Clinical and Translational Epidemiology Unit, Division of Gastroenterology, GRJ-825C, Boston, Massachusetts 02114, USA. Tel:+1 617 724 0283; Fax: +1 617 726 3673; , Andrew D. Johnson, PhD, Division of Intramural Research, National Heart, Lung and Blood Institute, Cardiovascular Epidemiology and Human Genomics Branch, The Framingham Heart Study, 73 Mt. Wayte Ave., Suite #2, Framingham, MA, 01702, USA. Tel: +1 508 663 4082; Fax: +1 508 626 1262;
| | - Andrew D. Johnson
- The National Heart, Lung, and Blood Institute’s Framingham Heart Study, Framingham, MA,Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Framingham, MA,To whom correspondence should be addressed: Amit D. Joshi, MBBS, PhD, Clinical and Translational Epidemiology Unit, Division of Gastroenterology, Massachusetts General Hospital, 55 Fruit Street, Boston, Massachusetts 02114, USA. Tel: +1 617 724 7558; Charlotte Andersson, MD, PhD, The Framingham Heart Study, 73 Mt Wayte Avenue, Framingham, Massachusetts 01702, USA. , Andrew T. Chan, MD, MPH, Massachusetts General Hospital and Harvard Medical School, Clinical and Translational Epidemiology Unit, Division of Gastroenterology, GRJ-825C, Boston, Massachusetts 02114, USA. Tel:+1 617 724 0283; Fax: +1 617 726 3673; , Andrew D. Johnson, PhD, Division of Intramural Research, National Heart, Lung and Blood Institute, Cardiovascular Epidemiology and Human Genomics Branch, The Framingham Heart Study, 73 Mt. Wayte Ave., Suite #2, Framingham, MA, 01702, USA. Tel: +1 508 663 4082; Fax: +1 508 626 1262;
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17
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Du M, Jiao S, Bien SA, Gala M, Abecasis G, Bezieau S, Brenner H, Butterbach K, Caan BJ, Carlson CS, Casey G, Chang-Claude J, Conti DV, Curtis KR, Duggan D, Gallinger S, Haile RW, Harrison TA, Hayes RB, Hoffmeister M, Hopper JL, Hudson TJ, Jenkins MA, Küry S, Le Marchand L, Leal SM, Newcomb PA, Nickerson DA, Potter JD, Schoen RE, Schumacher FR, Seminara D, Slattery ML, Hsu L, Chan AT, White E, Berndt SI, Peters U. Fine-Mapping of Common Genetic Variants Associated with Colorectal Tumor Risk Identified Potential Functional Variants. PLoS One 2016; 11:e0157521. [PMID: 27379672 PMCID: PMC4933364 DOI: 10.1371/journal.pone.0157521] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 06/01/2016] [Indexed: 01/27/2023] Open
Abstract
Genome-wide association studies (GWAS) have identified many common single nucleotide polymorphisms (SNPs) associated with colorectal cancer risk. These SNPs may tag correlated variants with biological importance. Fine-mapping around GWAS loci can facilitate detection of functional candidates and additional independent risk variants. We analyzed 11,900 cases and 14,311 controls in the Genetics and Epidemiology of Colorectal Cancer Consortium and the Colon Cancer Family Registry. To fine-map genomic regions containing all known common risk variants, we imputed high-density genetic data from the 1000 Genomes Project. We tested single-variant associations with colorectal tumor risk for all variants spanning genomic regions 250-kb upstream or downstream of 31 GWAS-identified SNPs (index SNPs). We queried the University of California, Santa Cruz Genome Browser to examine evidence for biological function. Index SNPs did not show the strongest association signals with colorectal tumor risk in their respective genomic regions. Bioinformatics analysis of SNPs showing smaller P-values in each region revealed 21 functional candidates in 12 loci (5q31.1, 8q24, 11q13.4, 11q23, 12p13.32, 12q24.21, 14q22.2, 15q13, 18q21, 19q13.1, 20p12.3, and 20q13.33). We did not observe evidence of additional independent association signals in GWAS-identified regions. Our results support the utility of integrating data from comprehensive fine-mapping with expanding publicly available genomic databases to help clarify GWAS associations and identify functional candidates that warrant more onerous laboratory follow-up. Such efforts may aid the eventual discovery of disease-causing variant(s).
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Affiliation(s)
- Mengmeng Du
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, United States of America
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
- * E-mail: (MD); (UP)
| | - Shuo Jiao
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Stephanie A. Bien
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
- School of Public Health, University of Washington, Seattle, WA, United States of America
| | - Manish Gala
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States of America
| | - Goncalo Abecasis
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, United States of America
| | | | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Katja Butterbach
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Bette J. Caan
- Division of Research, Kaiser Permanente Medical Care Program of Northern California, Oakland, CA, United States of America
| | - Christopher S. Carlson
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Graham Casey
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States of America
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David V. Conti
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States of America
| | - Keith R. Curtis
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - David Duggan
- Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Steven Gallinger
- Department of Surgery, Mount Sinai Hospital, Toronto, ON, Canada
| | - Robert W. Haile
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States of America
| | - Tabitha A. Harrison
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Richard B. Hayes
- Division of Epidemiology, Department of Population Health, New York University School of Medicine, New York, NY, United States of America
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - John L. Hopper
- Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Thomas J. Hudson
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Departments of Medical Biophysics and Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Mark A. Jenkins
- Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Sébastien Küry
- Service de Génétique Médicale, CHU Nantes, Nantes, France
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, United States of America
| | - Suzanne M. Leal
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States of America
| | - Polly A. Newcomb
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
- School of Public Health, University of Washington, Seattle, WA, United States of America
| | - Deborah A. Nickerson
- Genome Sciences, University of Washington, Seattle, WA, United States of America
| | - John D. Potter
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
- School of Public Health, University of Washington, Seattle, WA, United States of America
- Centre for Public Health Research, Massey University, Wellington, New Zealand
| | - Robert E. Schoen
- Department of Medicine and Epidemiology, University of Pittsburgh Medical Center, Pittsburgh, PA, United States of America
| | - Fredrick R. Schumacher
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States of America
| | - Daniela Seminara
- Division of Cancer Control and Population Sciences, National Cancer Institute, Bethesda, MD, United States of America
| | - Martha L. Slattery
- Department of Internal Medicine, University of Utah Health Sciences Center, Salt Lake City, UT, United States of America
| | - Li Hsu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Andrew T. Chan
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States of America
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States of America
| | - Emily White
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
- School of Public Health, University of Washington, Seattle, WA, United States of America
| | - Sonja I. Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, United States of America
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
- School of Public Health, University of Washington, Seattle, WA, United States of America
- * E-mail: (MD); (UP)
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18
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Phipps AI, Passarelli MN, Chan AT, Harrison TA, Jeon J, Hutter CM, Berndt SI, Brenner H, Caan BJ, Campbell PT, Chang-Claude J, Chanock SJ, Cheadle JP, Curtis KR, Duggan D, Fisher D, Fuchs CS, Gala M, Giovannucci EL, Hayes RB, Hoffmeister M, Hsu L, Jacobs EJ, Jansen L, Kaplan R, Kap EJ, Maughan TS, Potter JD, Schoen RE, Seminara D, Slattery ML, West H, White E, Peters U, Newcomb PA. Common genetic variation and survival after colorectal cancer diagnosis: a genome-wide analysis. Carcinogenesis 2015; 37:87-95. [PMID: 26586795 DOI: 10.1093/carcin/bgv161] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 11/13/2015] [Indexed: 12/14/2022] Open
Abstract
Genome-wide association studies have identified several germline single nucleotide polymorphisms (SNPs) significantly associated with colorectal cancer (CRC) incidence. Common germline genetic variation may also be related to CRC survival. We used a discovery-based approach to identify SNPs related to survival outcomes after CRC diagnosis. Genome-wide genotyping arrays were conducted for 3494 individuals with invasive CRC enrolled in six prospective cohort studies (median study-specific follow-up = 4.2-8.1 years). In pooled analyses, we used Cox regression to assess SNP-specific associations with CRC-specific and overall survival, with additional analyses stratified by stage at diagnosis. Top findings were followed-up in independent studies. A P value threshold of P < 5×10(-8) in analyses combining discovery and follow-up studies was required for genome-wide significance. Among individuals with distant-metastatic CRC, several SNPs at 6p12.1, nearest the ELOVL5 gene, were statistically significantly associated with poorer survival, with the strongest associations noted for rs209489 [hazard ratio (HR) = 1.8, P = 7.6×10(-10) and HR = 1.8, P = 3.7×10(-9) for CRC-specific and overall survival, respectively). No SNPs were statistically significantly associated with survival among all cases combined or in cases without distant-metastases. SNPs in 6p12.1/ELOVL5 were associated with survival outcomes in individuals with distant-metastatic CRC, and merit further follow-up for functional significance. Findings from this genome-wide association study highlight the potential importance of genetic variation in CRC prognosis and provide clues to genomic regions of potential interest.
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Affiliation(s)
- Amanda I Phipps
- Epidemiology Department, University of Washington, Seattle, WA 98195, USA.,Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Michael N Passarelli
- Epidemiology Department, University of Washington, Seattle, WA 98195, USA.,Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Andrew T Chan
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.,Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Tabitha A Harrison
- Public Health Sciences Division , Fred Hutchinson Cancer Research Center , Seattle , WA 98109 , USA
| | - Jihyoun Jeon
- Public Health Sciences Division , Fred Hutchinson Cancer Research Center , Seattle , WA 98109 , USA
| | - Carolyn M Hutter
- Public Health Sciences Division , Fred Hutchinson Cancer Research Center , Seattle , WA 98109 , USA
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics , National Cancer Institute , National Institutes of Health , Bethesda , MD 20892 , USA
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany.,German Cancer Consortium (DKTK), Heidelberg 69120, Germany
| | - Bette J Caan
- Division of Research , Kaiser Permanente Medical Care Program of Northern California , Oakland , CA 94612 , USA
| | - Peter T Campbell
- Epidemiology Research Program , American Cancer Society , Atlanta , GA 30303 , USA
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology , Unit of Genetic Epidemiology , German Cancer Research Center (DKFZ) , Heidelberg 69120 , Germany
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics , National Cancer Institute , National Institutes of Health , Bethesda , MD 20892 , USA
| | - Jeremy P Cheadle
- Institute of Cancer and Genetics , School of Medicine , Cardiff University , Cardiff CF14 4XN , UK
| | - Keith R Curtis
- Public Health Sciences Division , Fred Hutchinson Cancer Research Center , Seattle , WA 98109 , USA
| | - David Duggan
- Translational Genomics Research Institute , Phoenix , AZ 85004 , USA
| | - David Fisher
- MRC Clinical Trials Unit , University College London , Aviation House , London WC2B 6NH , UK
| | - Charles S Fuchs
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA.,Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA 02215, USA
| | - Manish Gala
- Harvard School of Public Health , Boston , MA 02115 , USA
| | - Edward L Giovannucci
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA.,Harvard School of Public Health, Boston, MA 02115, USA
| | - Richard B Hayes
- Division of Epidemiology , Department of Population Health , New York University School of Medicine , New York , NY 10016 , USA
| | | | - Li Hsu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,Biostatistics Department, University of Washington, Seattle, WA 98195, USA
| | - Eric J Jacobs
- Division of Cancer Epidemiology , Unit of Genetic Epidemiology , German Cancer Research Center (DKFZ) , Heidelberg 69120 , Germany
| | - Lina Jansen
- Division of Clinical Epidemiology and Aging Research , German Cancer Research Center (DKFZ) , Heidelberg 69120 , Germany
| | - Richard Kaplan
- MRC Clinical Trials Unit , University College London , Aviation House , London WC2B 6NH , UK
| | - Elisabeth J Kap
- Division of Cancer Epidemiology , Unit of Genetic Epidemiology , German Cancer Research Center (DKFZ) , Heidelberg 69120 , Germany
| | - Timothy S Maughan
- Gray Institute for Radiation Oncology and Biology , University of Oxford , Oxford OX3 7DQ , UK
| | - John D Potter
- Epidemiology Department, University of Washington, Seattle, WA 98195, USA.,Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,Centre for Public Health Research, Massey University, Wellington 6140, New Zealand
| | - Robert E Schoen
- Department of Medicine and Epidemiology , University of Pittsburgh Medical Center , Pittsburgh , PA 15213 , USA
| | - Daniela Seminara
- Division of Cancer Control and Population Sciences , National Cancer Institute , National Institutes of Health , Bethesda , MD 20892 , USA , and
| | - Martha L Slattery
- Department of Internal Medicine , University of Utah Health Sciences Center , Salt Lake City , UT 84132 , USA
| | - Hannah West
- Institute of Cancer and Genetics , School of Medicine , Cardiff University , Cardiff CF14 4XN , UK
| | - Emily White
- Epidemiology Department, University of Washington, Seattle, WA 98195, USA.,Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Ulrike Peters
- Epidemiology Department, University of Washington, Seattle, WA 98195, USA.,Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Polly A Newcomb
- Epidemiology Department, University of Washington, Seattle, WA 98195, USA.,Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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19
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Khalili H, Gong J, Brenner H, Austin TR, Hutter CM, Baba Y, Baron JA, Berndt SI, Bézieau S, Caan B, Campbell PT, Chang-Claude J, Chanock SJ, Chen C, Hsu L, Jiao S, Conti DV, Duggan D, Fuchs CS, Gala M, Gallinger S, Haile RW, Harrison TA, Hayes R, Hazra A, Henderson B, Haiman C, Hoffmeister M, Hopper JL, Jenkins MA, Kolonel LN, Küry S, LaCroix A, Marchand LL, Lemire M, Lindor NM, Ma J, Manson JE, Morikawa T, Nan H, Ng K, Newcomb PA, Nishihara R, Potter JD, Qu C, Schoen RE, Schumacher FR, Seminara D, Taverna D, Thibodeau S, Wactawski-Wende J, White E, Wu K, Zanke BW, Casey G, Hudson TJ, Kraft P, Peters U, Slattery ML, Ogino S, Chan AT. Identification of a common variant with potential pleiotropic effect on risk of inflammatory bowel disease and colorectal cancer. Carcinogenesis 2015; 36:999-1007. [PMID: 26071399 DOI: 10.1093/carcin/bgv086] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2015] [Accepted: 06/06/2015] [Indexed: 12/12/2022] Open
Abstract
Although genome-wide association studies (GWAS) have separately identified many genetic susceptibility loci for ulcerative colitis (UC), Crohn's disease (CD) and colorectal cancer (CRC), there has been no large-scale examination for pleiotropy, or shared genetic susceptibility, for these conditions. We used logistic regression modeling to examine the associations of 181 UC and CD susceptibility variants previously identified by GWAS with risk of CRC using data from the Genetics and Epidemiology of Colorectal Cancer Consortium and the Colon Cancer Family Registry. We also examined associations of significant variants with clinical and molecular characteristics in a subset of the studies. Among 11794 CRC cases and 14190 controls, rs11676348, the susceptibility single nucleotide polymorphism (SNP) for UC, was significantly associated with reduced risk of CRC (P = 7E-05). The multivariate-adjusted odds ratio of CRC with each copy of the T allele was 0.93 (95% CI 0.89-0.96). The association of the SNP with risk of CRC differed according to mucinous histological features (P heterogeneity = 0.008). In addition, the (T) allele was associated with lower risk of tumors with Crohn's-like reaction but not tumors without such immune infiltrate (P heterogeneity = 0.02) and microsatellite instability-high (MSI-high) but not microsatellite stable or MSI-low tumors (P heterogeneity = 0.03). The minor allele (T) in SNP rs11676348, located downstream from CXCR2 that has been implicated in CRC progression, is associated with a lower risk of CRC, particularly tumors with a mucinous component, Crohn's-like reaction and MSI-high. Our findings offer the promise of risk stratification of inflammatory bowel disease patients for complications such as CRC.
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Affiliation(s)
- Hamed Khalili
- Gastrointestinal Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Jian Gong
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany, German Cancer Cosortium (DKTK), Heidelberg, Germany
| | | | - Carolyn M Hutter
- Division of Cancer Control and Population Sciences, National Cancer Institute, Bethesda, MD, USA
| | - Yoshifumi Baba
- Department of Gastroenterological Surgery, Kumamoto University, Kumamoto, Japan
| | - John A Baron
- Department of Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | | | - Bette Caan
- Division of Hematology, Faculty of Medicine, The University of Ottawa, Ottawa, ON, Canada
| | - Peter T Campbell
- Epidemiology Research Program, American Cancer Society, Atlanta, GA, USA
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Constance Chen
- Program in Molecular and Genetic Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Li Hsu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Shuo Jiao
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - David V Conti
- Keck School of Medicine, University of Southern California, Los Angles, CA, USA
| | - David Duggan
- Systems Imagination, Computational Biology, Pheonix, AZ, USA
| | - Charles S Fuchs
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA, Department of Epidemiology, Indiana University School of Public Health, Indianapolis, IN, USA
| | - Manish Gala
- Gastrointestinal Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Steven Gallinger
- Department of Surgery, University Health Network Toronto General Hospital, Toronto, ON, Canada
| | | | - Tabitha A Harrison
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Richard Hayes
- Division of Epidemiology, New York University School of Medicine, New York, NY, USA
| | - Aditi Hazra
- Department of Epidemiology, Indiana University School of Public Health, Indianapolis, IN, USA
| | - Brian Henderson
- Keck School of Medicine, University of Southern California, Los Angles, CA, USA
| | - Chris Haiman
- Keck School of Medicine, University of Southern California, Los Angles, CA, USA
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany
| | - John L Hopper
- Melbourne School of Population Health, The University of Melbourne, Melbourne, Australia
| | - Mark A Jenkins
- Division of Epidemiology, New York University School of Medicine, New York, NY, USA
| | - Laurence N Kolonel
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Sébastien Küry
- CHU Nantes, Service de Génétique Médicale, Nantes, France
| | - Andrea LaCroix
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Mathieu Lemire
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Noralane M Lindor
- Department of Health Science Services, Mayo Clinic, Scottsdale, AZ, USA
| | - Jing Ma
- Department of Epidemiology, Indiana University School of Public Health, Indianapolis, IN, USA
| | - JoAnn E Manson
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Teppei Morikawa
- Department of Pathology, The University of Tokyo Hospital, Tokyo, Japan
| | - Hongmei Nan
- Department of Epidemiology, Indiana University School of Public Health, Indianapolis, IN, USA
| | - Kimmie Ng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Polly A Newcomb
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Reiko Nishihara
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA, Department of Nutrition, Harvard School of Public Health, Boston, MA, USA
| | - John D Potter
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA, Department of Epidemiology, University of Washington, Seattle, WA, USA, Center for Public Health Research, Massey University, Wellington, New Zealand
| | - Conghui Qu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Robert E Schoen
- Department of Medicine and Epidemiology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | | | - Daniela Seminara
- Division of Cancer Control and Population Sciences, National Cancer Institute, Bethesda, MD, USA
| | - Darin Taverna
- Systems Imagination, Computational Biology, Pheonix, AZ, USA
| | - Stephen Thibodeau
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Jean Wactawski-Wende
- Department of Social and Preventive Medicine, University of Buffalo, Buffalo, NY, USA
| | - Emily White
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Kana Wu
- Department of Nutrition, Harvard School of Public Health, Boston, MA, USA
| | - Brent W Zanke
- Clinical Epidemiology Program, Ottawa Hospital Research Institute, Ottawa, ON, USA
| | - Graham Casey
- Keck School of Medicine, University of Southern California, Los Angles, CA, USA
| | - Thomas J Hudson
- Ontario Institute for Cancer Research, Toronto, ON, Canada, Department of Medical Biophysics, University of Toronto, Toronto, ON, USA
| | - Peter Kraft
- Program in Molecular and Genetic Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA, Department of Epidemiology, Indiana University School of Public Health, Indianapolis, IN, USA
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Martha L Slattery
- Department of Internal Medicine, University of Utah Health Sciences Center, Salt Lake City, UT, USA
| | - Shuji Ogino
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA, Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Andrew T Chan
- Gastrointestinal Unit, Massachusetts General Hospital, Boston, MA, USA, Department of Epidemiology, Indiana University School of Public Health, Indianapolis, IN, USA,
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20
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Kocarnik JM, Passarelli MN, Phipps AI, Chan AT, Gala M, Joshi A, Campbell PT, Slattery ML, Potter J, White E, Berndt S, Peters U, Newcomb PA. Abstract 2187: Colorectal cancer survival is not associated with genetic variants related to risk of other cancers: The GECCO study. Cancer Res 2014. [DOI: 10.1158/1538-7445.am2014-2187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background:
Colorectal cancer (CRC) is a major cause of morbidity and mortality. Previous genome-wide association studies (GWAS) have identified a large number of single nucleotide polymorphisms (SNPs) associated with CRC, at least one of which has also been found to be associated with CRC survival. Furthermore, some SNPs have demonstrated risk associations with multiple cancers (i.e. pleiotropy), including CRC. Together, this raises the possibility that SNPs associated with risk of other cancers may also be associated with survival after a diagnosis of CRC. To investigate this question, we evaluated 526 SNPs reported as strongly associated with risk of any type of cancer in the National Human Genome Research Institute GWAS catalog (as of 11/13/2013) for an association with CRC-specific and overall survival. This study utilized data available from multiple studies in the Genetic Epidemiology of Colorectal Cancer Consortium (GECCO).
Methods:
We evaluated 526 SNPs associated with risk of cancers other than CRC in six studies participating in GECCO: the Health Professionals Follow-up Study; the Nurses' Health Study; the Physicians' Health Study; the Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial; the VITamins And Lifestyle Study; and the Women's Health Initiative. A total of 3,494 colorectal cancer cases were evaluated, of whom 1,223 (35%) died (830 from CRC, 24%) during follow-up (average median follow-up time of 6.8 years). Cox proportional hazards regression was used to calculate the per-allele hazard ratio (HR) and 95% confidence interval (95% CI) for the association between each SNP and CRC-specific or overall survival, adjusting for age at diagnosis, sex, study sample, and the first three principal components of genetic ancestry.
Results:
After Bonferroni correction for multiple comparisons (P = 0.05/526 = 9.51e-5), no SNPs were statistically significantly associated with either CRC-specific or overall survival. For CRC-specific survival, 35 SNPs showed a nominal association (p<0.05), the strongest being breast cancer SNP rs6504950 in STXBP4 (HR = 1.19, 95% CI = 1.06-1.31, p = 0.0018). For overall survival, 38 SNPs showed a nominal association, the strongest being melanoma SNP rs1393350 in TYR (HR = 1.15, 95% CI = 1.06-1.26, p = 0.0012). More SNPs showed a nominal association with survival than expected by chance (0.05*526 = 26 SNPs).
Conclusion:
These preliminary results broadly suggest that CRC-specific and overall survival do not appear to be strongly associated with genetic variants related to incidence for other cancers. However, some suggestive evidence of nominal associations with survival supports further investigation. Planned future steps include the incorporation of two additional studies (Cancer Prevention Study II; Diet, Activity, and Lifestyle Study), as well as analyses stratified by factors such as cancer site, stage at diagnosis, and sex.
Citation Format: Jonathan M. Kocarnik, Michael N. Passarelli, Amanda I. Phipps, Andrew T. Chan, Manish Gala, Amit Joshi, Peter T. Campbell, Martha L. Slattery, John Potter, Emily White, Sonja Berndt, Ulrike Peters, Polly A. Newcomb. Colorectal cancer survival is not associated with genetic variants related to risk of other cancers: The GECCO study. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 2187. doi:10.1158/1538-7445.AM2014-2187
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Affiliation(s)
| | | | | | | | | | | | | | | | - John Potter
- 1Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Emily White
- 1Fred Hutchinson Cancer Research Center, Seattle, WA
| | | | - Ulrike Peters
- 1Fred Hutchinson Cancer Research Center, Seattle, WA
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21
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Visnovcova Z, Mestanik M, Javorka M, Mokra D, Gala M, Jurko A, Calkovska A, Tonhajzerova I. Complexity and time asymmetry of heart rate variability are altered in acute mental stress. Physiol Meas 2014; 35:1319-34. [PMID: 24854052 DOI: 10.1088/0967-3334/35/7/1319] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We aimed to study the complexity and time asymmetry of short-term heart rate variability (HRV) as an index of complex neurocardiac control in response to stress using symbolic dynamics and time irreversibility methods. ECG was recorded at rest and during and after two stressors (Stroop, arithmetic test) in 70 healthy students. Symbolic dynamics parameters (NUPI, NCI, 0V%, 1V%, 2LV%, 2UV%), and time irreversibility indices (P%, G%, E) were evaluated. Additionally, HRV magnitude was quantified by linear parameters: spectral powers in low (LF) and high frequency (HF) bands. Our results showed a reduction of HRV complexity in stress (lower NUPI with both stressors, lower NCI with Stroop). Pattern classification analysis revealed significantly higher 0V% and lower 2LV% with both stressors, indicating a shift in sympathovagal balance, and significantly higher 1V% and lower 2UV% with Stroop. An unexpected result was found in time irreversibility: significantly lower G% and E with both stressors, P% index significantly declined only with arithmetic test. Linear HRV analysis confirmed vagal withdrawal (lower HF) with both stressors; LF significantly increased with Stroop and decreased with arithmetic test. Correlation analysis revealed no significant associations between symbolic dynamics and time irreversibility. Concluding, symbolic dynamics and time irreversibility could provide independent information related to alterations of neurocardiac control integrity in stress-related disease.
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Affiliation(s)
- Z Visnovcova
- Department of Physiology, Jessenius Faculty of Medicine, Comenius University, Martin, Slovak Republic
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22
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Wang L, Gala M, Yamamoto M, Pino MS, Kikuchi H, Shue DS, Shirasawa S, Austin TR, Lynch MP, Rueda BR, Zukerberg LR, Chung DC. Adrenomedullin is a therapeutic target in colorectal cancer. Int J Cancer 2013; 134:2041-50. [PMID: 24519534 DOI: 10.1002/ijc.28542] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 09/27/2013] [Indexed: 12/17/2022]
Abstract
The KRAS oncogene influences angiogenesis, metastasis and chemoresistance in colorectal cancers (CRCs), and these processes are all enhanced in hypoxic conditions. To define functional activities of mutant KRAS in a hypoxic microenvironment, we first performed cDNA microarray experiments in isogenic DKs5 and DKO3 colon cancer cell lines that differ only by their expression of mutant KRAS (K-ras(D13)). Adrenomedullin (ADM) was identified as one of the most significantly upregulated genes in DKs5 cells that express the KRAS oncogene in hypoxia (3.2-fold, p = 1.47 × 10(-5)). Ectopic expression of mutant KRAS (K-ras(V12)) in Caco-2 cells (K-ras(WT)) induced ADM, whereas selective knockdown of mutant KRAS alleles (K-ras(D13) or K-ras(V12)) in HCT116, DLD1 and SW480 colon cancer cells suppressed the expression of ADM in hypoxia. Knockdown of ADM in colon tumor xenografts blocked angiogenesis and stimulated apoptosis, resulting in tumor suppression. Furthermore, ADM also regulated colon cancer cell invasion in vitro. Among 56 patients with CRC, significantly higher expression levels of ADM were observed in samples harboring a KRAS mutation. Collectively, ADM is a new target of oncogenic KRAS in the setting of hypoxia. This observation suggests that therapeutic targets may differ depending upon the specific tumor microenvironment.
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Affiliation(s)
- Liangjing Wang
- Gastrointestinal Unit Massachusetts General Hospital, Harvard Medical School, Boston, MA; Department of Gastroenterology Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
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23
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Duerr EM, Mizukami Y, Moriichi K, Gala M, Jo WS, Kikuchi H, Xavier RJ, Chung DC. Oncogenic KRAS regulates BMP4 expression in colon cancer cell lines. Am J Physiol Gastrointest Liver Physiol 2012; 302:G1223-30. [PMID: 22383492 PMCID: PMC3362092 DOI: 10.1152/ajpgi.00047.2011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Activating mutations in the KRAS oncogene are common in colorectal cancer. However, the complete spectrum of KRAS targets that mediate its tumorigenic effect has not yet been fully delineated. We identified bone morphogenetic protein 4 (Bmp4), a transforming growth factor-β family member that regulates development and tissue homeostasis, as a new target of KRAS. In SW480, Hela, and 293 cells, oncogenic KRAS(V12) downregulated BMP4 RNA levels, a BMP4 promoter luciferase construct, and Bmp4 protein levels. The MEK inhibitor PD98059 but not the phosphatidylinositol 3-kinase inhibitor LY294002 blocked this downregulation of BMP4. To identify the region of the BMP4 promoter that mediated this regulation by KRAS, serial 5'-deletions of the promoter were generated. An inhibitory region was identified between -3,285 and -3,258 bp in the Bmp4 promoter. In summary, oncogenic KRAS can downregulate Bmp4 through a transcriptional pathway that depends on ERK. These findings point to a unique link between two pathways that are frequently altered in colon cancer.
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Affiliation(s)
- Eva-Maria Duerr
- 1Gastrointestinal Unit, ,3Department of Gastroenterology, Klinikum Grosshadern, Ludwig-Maximilians-University of Munich, Munich, Germany; and
| | - Yusuke Mizukami
- 1Gastrointestinal Unit, ,4Center for Clinical and Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Japan
| | | | | | | | | | - Ramnik J. Xavier
- 1Gastrointestinal Unit, ,2Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts;
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Abstract
Colon cancer is associated with a family history in up to 25% of cases. As many as 5% are associated with an established hereditary syndrome, demonstrating the profound influence of inheritable genetic mechanisms in the development of this disease. These syndromes confer a diverse spectrum of risk, age of presentation, endoscopic and histological findings, extracolonic manifestations, and modes of inheritance. As the molecular characteristics of these disorders become better described, enhanced genotype-phenotype correlations may offer a more targeted approach to diagnosis, screening, and surveillance. While the strategies for diagnosis and management of familial adenomatous polyposis (FAP) and Lynch syndrome are more established, the approach to newly recognized syndromes such as MUTYH-associated polyposis (MAP) and hyperplastic polyposis syndromes continues to evolve. Effective cancer prevention in affected individuals and at-risk family members first requires timely recognition of these hereditary colon cancer syndromes followed by integration of genetic testing and clinical examinations.
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Affiliation(s)
- Manish Gala
- Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
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Maurea N, Tocchetti CG, Coppola C, Ragone G, Barbieri A, Rea D, Palma G, Gala M, Luciano A, Arra C, De Lorenzo C, Iaffaioli RV. The ErbB2-antibody 2C4 and cardiac dysfunction in mice. J Clin Oncol 2011. [DOI: 10.1200/jco.2011.29.15_suppl.e11040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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26
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Iaffaioli RV, Tocchetti CG, Coppola C, Ragone G, Barbieri A, Rea D, Palma G, Gala M, Luciano A, Arra C, Maurea N. Early detection of cardiac dysfunction induced by the mTOR inhibitor temsirolimus. J Clin Oncol 2011. [DOI: 10.1200/jco.2011.29.15_suppl.e13612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Bifulco K, Longanesi-Cattani I, Gala M, DI Carluccio G, Masucci MT, Pavone V, Lista L, Arra C, Stoppelli MP, Carriero MV. The soluble form of urokinase receptor promotes angiogenesis through its Ser⁸⁸-Arg-Ser-Arg-Tyr⁹² chemotactic sequence. J Thromb Haemost 2010; 8:2789-99. [PMID: 20880257 DOI: 10.1111/j.1538-7836.2010.04075.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
BACKGROUND The urokinase plasminogen activator receptor (u-PAR) focuses the proteolytic activity of the urokinase plasminogen activator (u-PA) on the endothelial cell surface, thus promoting angiogenesis in a protease-dependent manner. The u-PAR may exist in a glycophosphatidylinositol-anchored and in a soluble form (soluble u-PAR [Su-PAR]), both including the chemotactic Ser⁸⁸ -Arg-Ser-Arg-Tyr⁹² internal sequence. OBJECTIVE To investigate whether Su-PAR may trigger endothelial cell signaling leading to new vessel formation through its chemotactic Ser⁸⁸ -Arg-Ser-Arg-Tyr⁹² sequence. METHODS AND RESULTS In this study, the formation of vascular-like structures by human umbilical vein endothelial cells was assessed by using a matrigel basement membrane preparation. First, we found that Su-PAR protein promotes the formation of cord-like structures, and that this ability is retained by the isolated Ser(88) -Arg-Ser-Arg-Tyr⁹² chemotactic sequence, the maximal effect being reached at 10 nmol L⁻¹ SRSRY peptide (SRSRY). This effect is mediated by the α(v) β₃ vitronectin receptor, is independent of u-PA proteolytic activity, and involves the internalization of the G-protein-coupled formyl-peptide receptor in endothelial cells. Furthermore, exposure of human saphenous vein rings to Su-PAR or SRSRY leads to a remarkable degree of sprouting. Finally, we show that Su-PAR and SRSRY promote a marked response in angioreactors implanted into the dorsal flank of nude mice, retaining 91% and 66%, respectively, of the angiogenic response generated by a mixture of vascular endothelial growth factor and fibroblast growth factor type 2. CONCLUSIONS Our results show a new protease-independent activity of Su-PAR that stimulates in vivo angiogenesis through its Ser⁸⁸ -Arg-Ser-Arg-Tyr⁹² chemotactic sequence.
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Affiliation(s)
- K Bifulco
- Department of Experimental Oncology, National Cancer Institute of Naples, Naples, Italy
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Mizukami Y, Fujiki K, Duerr EM, Gala M, Jo WS, Zhang X, Chung DC. Hypoxic regulation of vascular endothelial growth factor through the induction of phosphatidylinositol 3-kinase/Rho/ROCK and c-Myc. J Biol Chem 2006; 281:13957-63. [PMID: 16543245 DOI: 10.1074/jbc.m511763200] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The induction of vascular endothelial growth factor (VEGF) is an essential feature of tumor angiogenesis. Hypoxia is a potent stimulator of VEGF expression, and hypoxia-inducible factor-1 (HIF-1) is considered to be critical for this induction. However, we have previously demonstrated that induction of VEGF by hypoxia was preserved when HIF-1alpha was silenced. We sought to better define the molecular basis of this HIF-1-independent regulation. In colon cancer cells, hypoxia stimulated multiple K-ras effector pathways including phosphatidylinositol 3-kinase. VEGF promoter deletion studies identified a novel promoter region between -418 and -223 bp that was responsive to hypoxia in a PI3K/Rho/ROCK-dependent manner. Electrophoretic mobility shift assays identified a fragment between -300 and -251 bp that demonstrated a unique shift only in hypoxic conditions. Inhibition of PI3K or ROCK blocked the formation of this complex. A binding site for c-Myc, a target of ROCK, was identified at -271 bp. A role for c-Myc in the hypoxic induction of VEGF was demonstrated by site-directed mutagenesis of the VEGF promoter and silencing of c-Myc by small interfering RNA. Collectively, these findings suggest an alternative mechanism for the hypoxic induction of VEGF in colon cancer that does not depend upon HIF-1alpha but instead requires the activation of PI3K/Rho/ROCK and c-Myc.
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Affiliation(s)
- Yusuke Mizukami
- Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA
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Mizukami Y, Jo WS, Duerr EM, Gala M, Li J, Zhang X, Zimmer MA, Iliopoulos O, Zukerberg LR, Kohgo Y, Lynch MP, Rueda BR, Chung DC. Induction of interleukin-8 preserves the angiogenic response in HIF-1α–deficient colon cancer cells. Nat Med 2005; 11:992-7. [PMID: 16127434 DOI: 10.1038/nm1294] [Citation(s) in RCA: 357] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2005] [Accepted: 08/02/2005] [Indexed: 01/10/2023]
Abstract
Hypoxia inducible factor-1 (HIF-1) is considered a crucial mediator of the cellular response to hypoxia through its regulation of genes that control angiogenesis. It represents an attractive therapeutic target in colon cancer, one of the few tumor types that shows a clinical response to antiangiogenic therapy. But it is unclear whether inhibition of HIF-1 alone is sufficient to block tumor angiogenesis. In HIF-1alpha knockdown DLD-1 colon cancer cells (DLD-1(HIF-kd)), the hypoxic induction of vascular endothelial growth factor (VEGF) was only partially blocked. Xenografts remained highly vascularized with microvessel densities identical to DLD-1 tumors that had wild-type HIF-1alpha (DLD-1(HIF-wt)). In addition to the preserved expression of VEGF, the proangiogenic cytokine interleukin (IL)-8 was induced by hypoxia in DLD-1(HIF-kd) but not DLD-1(HIF-wt) cells. This induction was mediated by the production of hydrogen peroxide and subsequent activation of NF-kappaB. Furthermore, the KRAS oncogene, which is commonly mutated in colon cancer, enhanced the hypoxic induction of IL-8. A neutralizing antibody to IL-8 substantially inhibited angiogenesis and tumor growth in DLD-1(HIF-kd) but not DLD-1(HIF-wt) xenografts, verifying the functional significance of this IL-8 response. Thus, compensatory pathways can be activated to preserve the tumor angiogenic response, and strategies that inhibit HIF-1alpha may be most effective when IL-8 is simultaneously targeted.
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Affiliation(s)
- Yusuke Mizukami
- Gastrointestinal Unit, Massachusetts General Hospital and Harvard Medical School, 50 Blossom Street, Boston, Massachusetts 02114, USA
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Abstract
Non-steroidal anti-inflammatory drugs (NSAIDs) have been shown to reduce the risk of colorectal cancer (CRC). They are also known to induce the regression of colorectal adenomas, which are precursors to CRC. Despite these evidences, the exact mechanism by which NSAIDs exerts its anti-oncogenic effect is not completely understood. Using a focus formation assay, here we show that sulindac sulfide, a NSAID, specifically inhibits cell transformation mediated by oncogenic Ha-Ras, but not by other established oncogene products such as v-Src, Galpha12, and Galpha13. Our results suggest that the ability of sulindac sulfide to suppress transformation is confined to specific oncogenic pathways. Further studies of the sulindac-resistant oncogenic pathways may lead to identification of novel therapeutic agents that are effective in the prevention or treatment of CRC.
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Affiliation(s)
- Manish Gala
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ronggai Sun
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Vincent W. Yang
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Johns Hopkins Oncology Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Corresponding author. Department of Medicine, 2101 Woodruff Memorial Building, Emory University School of Medicine, Atlanta, GA 30322, USA. Tel.: +1-404-727-5638; fax: +1-404-727-5767., E-mail address: (V.W. Yang)
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Mahieu P, Bonduelle Y, Bernard A, De Cabooter A, Gala M, Hassoun A, Koenig J, Lauwerys R. Acute diquat intoxication. Interest of its repeated determination in urine and the evaluation of renal proximal tubule integrity. J Toxicol Clin Toxicol 1984; 22:363-9. [PMID: 6527399 DOI: 10.3109/15563658408992567] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
A 33-year old farmer ingested approximately 300 ml of a 20% solution of diquat along with about 80 mg flunitrazepam. The patient presented neurological (coma grade I), digestive (oro-pharyngeal erosions, ileus), hepatic (cytolysis), hematological (thrombopenia) and renal (tubular dysfunction) signs. Plasma creatinine did not exceed 1.22 mg/dl (upper normal value), but retinol binding protein level in urine (a marker of renal tubular dysfunction) reached a value of 337 mg/d (normal values less than 300 micrograms/d). Its level returned to normal value 18 days after the ingestion. Four hours after the poisoning, diquat level in blood amounted to 10.4 mg/l, but its level was below the detection limit (0.2 mg/l) 6 hours later. In urine, however, diquat was detected until day 13. The following therapy was applied: ventilation (FiO2:0.21), gastro-intestinal lavage, hemoperfusion, anti-oxidants and prolonged forced diuresis. The patient made an uneventful recovery. intestinal washout must be applied with caution since an ileus is a classical complication of diquat poisoning. Hemoperfusion was found to be of little value. The interest of prolonged application of forced diuresis is suggested by the detection of diquat in urine for about 2 weeks along with the presence of biological signs of renal tubular dysfunction.
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Abstract
The extent of growth suppression and recovery following exposure to 4,5',8-trimethylpsoralen (TMP) plus UV-A irradiation was studied in 3 diploid human fibroblast strains. Inhibition of cellular proliferation was dose-dependent within the concentration range of TMP that was tested (1-4 X 10(-7) M), using a constant level of UV-A (0.24 J/cm2). The population generation (doubling) times for all cell strains were progressively lengthened under these conditions while maximal cell densities were reduced. At 2-4 X 10(-7) M TMP in the presence of UV-A, there was a triphasic pattern of growth which consisted of (1) proliferative activity during the first 24-36 hr, followed by; (2) complete growth inhibition for variable periods of time and; (3) a recovery period of log phase proliferation that was not as vigorous as measured for untreated cells. There were also declines in the percentage of cells labeled with 3H-Tdr at various times after TMP-UV-A treatment. These measurements were essentially identical for the three fibroblast strains evaluated. In that the cells employed for these investigations were derived from embryonic pulmonary tissue, neonatal foreskin and the buttock skin of an adult male, it seems unlikely that donor age and tissue source were important variables in determining growth response patterns after TMP-UV-A exposure. Because proliferative recovery was attenuated after this photochemical injury, we conclude that the biologic effect(s) of TMP-UV-A extend beyond the known period of psoralen-DNA cross-link removal.
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