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1. A comprehensive analysis of germline predisposition to early-onset ovarian cancer

Author

Klara Horackova, Petra Zemankova, Petr Nehasil, Michal Vocka, Milena Hovhannisyan, Katerina Matejkova, Marketa Janatova, Marta Cerna, Petra Kleiblova, Sandra Jelinkova, Barbora Stastna, Pavel Just, Tatana Dolezalova, Barbora Nemcova, Marketa Urbanova, Monika Koudova, Jana Hazova, Eva Machackova, Lenka Foretova, Viktor Stranecky, Michal Zikan, Zdenek Kleibl, and Jana Soukupova

Subjects
Ovarian cancer, Early-onset, Germline whole exome sequencing, Polygenic risk score, HLA, Mutation burden, Medicine, Science
Abstract

Abstract The subset of ovarian cancer (OC) diagnosed ≤ 30yo represents a distinct subgroup exhibiting disparities from late-onset OC in many aspects, including indefinite germline cancer predisposition. We performed DNA/RNA-WES with HLA-typing, PRS assessment and survival analysis in 123 early-onset OC-patients compared to histology/stage-matched late-onset and unselected OC-patients, and population-matched controls. Only 6/123(4.9%) early-onset OC-patients carried a germline pathogenic variant (GPV) in high-penetrance OC-predisposition genes. Nevertheless, our comprehensive germline analysis of early-onset OC-patients revealed two divergent trajectories of potential germline susceptibility. Firstly, overrepresentation analysis highlighted a connection to breast cancer (BC) that was supported by the CHEK2 GPV enrichment in early-onset OC(p = 1.2 × 10–4), and the presumably BC-specific PRS313, which successfully stratified early-onset OC-patients from controls(p = 0.03). The second avenue pointed towards the impaired immune response, indicated by LY75-CD302 GPV(p = 8.3 × 10–4) and diminished HLA diversity compared with controls(p = 3 × 10–7). Furthermore, we found a significantly higher overall GPV burden in early-onset OC-patients compared to controls(p = 3.8 × 10–4). The genetic predisposition to early-onset OC appears to be a heterogeneous and complex process that goes beyond the traditional Mendelian monogenic understanding of hereditary cancer predisposition, with a significant role of the immune system. We speculate that rather a cumulative overall GPV burden than specific GPV may potentially increase OC risk, concomitantly with reduced HLA diversity.

Published
2024
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2. Respirable crystalline silica and lung cancer in community-based studies: impact of job-exposure matrix specifications on exposure–response relationships

Author

Johan Ohlander, Hans Kromhout, Roel Vermeulen, Lützen Portengen, Benjamin Kendzia, Barbara Savary, Domenico Cavallo, Andrea Cattaneo, Enrica Migliori, Lorenzo Richiardi, Nils Plato, Heinz-Erich Wichmann, Stefan Karrasch, Dario Consonni, Maria Teresa Landi, Neil E Caporaso, Jack Siemiatycki, Per Gustavsson, Karl-Heinz Jöckel, Wolfgang Ahrens, Hermann Pohlabeln, Guillermo Fernández-Tardón, David Zaridze, Jolanta Lissowska Jolanta Lissowska, Beata Swiatkowska Beata Swiatkowska, John K Field John K Field, John R McLaughlin, Paul A Demers, Tamas Pandics, Francesco Forastiere, Eleonora Fabianova, Miriam Schejbalova, Lenka Foretova, Vladimir Janout, Dana Mates, Christine Barul, Thomas Brüning, Thomas Behrens, Kurt Straif, Joachim Schüz, Ann Olsson, and Susan Peters

Subjects
case-control study, cancer, lung cancer, job-exposure matrix, general population, lung neoplasm, jem, quantitative exposure assessment, exposure–response, respirable crystalline silica, respirable quartz exposure, Public aspects of medicine, RA1-1270
Abstract

OBJECTIVES: The quantitative job-exposure matrix SYN-JEM consists of various dimensions: job-specific estimates, region-specific estimates, and prior expert ratings of jobs by the semi-quantitative DOM-JEM. We analyzed the effect of different JEM dimensions on the exposure–response relationships between occupational silica exposure and lung cancer risk to investigate how these variations influence estimates of exposure by a quantitative JEM and associated health endpoints. METHODS: Using SYN-JEM, and alternative SYN-JEM specifications with varying dimensions included, cumulative silica exposure estimates were assigned to 16 901 lung cancer cases and 20 965 controls pooled from 14 international community-based case-control studies. Exposure–response relationships based on SYN-JEM and alternative SYN-JEM specifications were analyzed using regression analyses (by quartiles and log-transformed continuous silica exposure) and generalized additive models (GAM), adjusted for age, sex, study, cigarette pack-years, time since quitting smoking, and ever employment in occupations with established lung cancer risk. RESULTS: SYN-JEM and alternative specifications generated overall elevated and similar lung cancer odds ratios ranging from 1.13 (1st quartile) to 1.50 (4th quartile). In the categorical and log-linear analyses SYN-JEM with all dimensions included yielded the best model fit, and exclusion of job-specific estimates from SYN-JEM yielded the poorest model fit. Additionally, GAM showed the poorest model fit when excluding job-specific estimates. CONCLUSION: The established exposure–response relationship between occupational silica exposure and lung cancer was marginally influenced by varying the dimensions of SYN-JEM. Optimized modelling of exposure–response relationships will be obtained when incorporating all relevant dimensions, namely prior rating, job, time, and region. Quantitative job-specific estimates appeared to be the most prominent dimension for this general population JEM.

Published
2024
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3. A comprehensive study evaluating germline FANCG variants in predisposition to breast and ovarian cancer

Author

Jana Soukupova, Barbora Stastna, Madiha Kanwal, Jan Hojny, Petra Zemankova, Marianna Borecka, Leona Cerna, Marta Cerna, Monika Cerna, Vaclava Curtisova, Tatana Dolezalova, Petra Duskova, Lenka Foretova, Ondrej Havranek, Klara Horackova, Milena Hovhannisyan, Lucie Hruskova, Stepan Chvojka, Marketa Janatova, Maria Janikova, Sandra Jelinkova, Pavel Just, Marta Kalousova, Petra Kleiblova, Marcela Kosarova, Monika Koudova, Jan Kral, Michaela Krausova, Vera Krutilkova, Eva Machackova, Katerina Matejkova, Renata Michalovska, Petr Nehasil, Barbora Nemcova, Jan Novotny, Matous Palek, Pavel Pesek, Marketa Safarikova, Ondrej Scheinost, Drahomira Springer, Lenka Stolarova, Viktor Stranecky, Ivan Subrt, Spiros Tavandzis, Eva Tureckova, Kamila Vesela, Zdenka Vlckova, Michal Vocka, Tomas Zima, Libor Macurek, Zdenek Kleibl, and the CZECANCA consortium

Subjects
breast cancer, Fanconi anemia complementation group G, functional analysis, germline genetic testing, hereditary tumors, ovarian cancer, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract

Abstract Background Monoallelic germline pathogenic variants (GPVs) in five Fanconi anemia (FA) genes (BRCA1/FANCS, BRCA2/FANCD1, PALB2/FANCN, BRIP1/FANCJ, and RAD51C/FANCO) confer an increased risk of breast (BC) and/or ovarian (OC) cancer, but the role of GPVs in 17 other FA genes remains unclear. Methods Here, we investigated the association of germline variants in FANCG/XRCC9 with BC and OC risk. Results The frequency of truncating GPVs in FANCG did not differ between BC (20/10,204; 0.20%) and OC (8/2966; 0.27%) patients compared to controls (6/3250; 0.18%). In addition, only one out of five tumor samples showed loss‐of‐heterozygosity of the wild‐type FANCG allele. Finally, none of the nine functionally tested rare recurrent missense FANCG variants impaired DNA repair activities (FANCD2 monoubiquitination and FANCD2 foci formation) upon DNA damage, in contrast to all tested FANCG truncations. Conclusion Our study suggests that heterozygous germline FANCG variants are unlikely to contribute to the development of BC or OC.

Published
2024
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4. A deep intronic recurrent CHEK2 variant c.1009-118_1009-87delinsC affects pre-mRNA splicing and contributes to hereditary breast cancer predisposition

Author

Petra Zemankova, Marta Cerna, Klara Horackova, Corinna Ernst, Jana Soukupova, Marianna Borecka, Britta Blümcke, Leona Cerna, Monika Cerna, Vaclava Curtisova, Tatana Dolezalova, Petra Duskova, Lenka Dvorakova, Lenka Foretova, Ondrej Havranek, Jan Hauke, Eric Hahnen, Miloslava Hodulova, Milena Hovhannisyan, Lucie Hruskova, Marketa Janatova, Maria Janikova, Sandra Jelinkova, Pavel Just, Marcela Kosarova, Monika Koudova, Vera Krutilkova, Eva Machackova, Katerina Matejkova, Renata Michalovska, Adela Misove, Petr Nehasil, Barbora Nemcova, Jan Novotny, Ales Panczak, Pavel Pesek, Ondrej Scheinost, Drahomira Springer, Barbora Stastna, Viktor Stranecky, Ivan Subrt, Spiros Tavandzis, Eva Tureckova, Kamila Vesela, Zdenka Vlckova, Michal Vocka, Barbara Wappenschmidt, Tomas Zima, Zdenek Kleibl, and Petra Kleiblova

Subjects
Deep intronic CHEK2 variant, Breast cancer, NGS, RNA analysis, Genetic testing, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract

Germline CHEK2 pathogenic variants confer an increased risk of female breast cancer (FBC). Here we describe a recurrent germline intronic variant c.1009-118_1009-87delinsC, which showed a splice acceptor shift in RNA analysis, introducing a premature stop codon (p.Tyr337PhefsTer37).The variant was found in 21/10,204 (0.21%) Czech FBC patients compared to 1/3250 (0.03%) controls (p = 0.04) and in 4/3639 (0.11%) FBC patients from an independent German dataset. In addition, we found this variant in 5/2966 (0.17%) Czech (but none of the 443 German) ovarian cancer patients, three of whom developed early-onset tumors.Based on these observations, we classified this variant as likely pathogenic.

Published
2024
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5. Associations of height, body mass index, and weight gain with breast cancer risk in carriers of a pathogenic variant in BRCA1 or BRCA2: the BRCA1 and BRCA2 Cohort Consortium

Author

Karin Kast, Esther M. John, John L. Hopper, Nadine Andrieu, Catherine Noguès, Emmanuelle Mouret-Fourme, Christine Lasset, Jean-Pierre Fricker, Pascaline Berthet, Véronique Mari, Lucie Salle, Marjanka K. Schmidt, Margreet G. E. M. Ausems, Encarnacion B. Gomez Garcia, Irma van de Beek, Marijke R. Wevers, D. Gareth Evans, Marc Tischkowitz, Fiona Lalloo, Jackie Cook, Louise Izatt, Vishakha Tripathi, Katie Snape, Hannah Musgrave, Saba Sharif, Jennie Murray, EMBRACE Collaborators, Sarah V. Colonna, Irene L. Andrulis, Mary B. Daly, Melissa C. Southey, Miguel de la Hoya, Ana Osorio, Lenka Foretova, Dita Berkova, Anne-Marie Gerdes, Edith Olah, Anna Jakubowska, Christian F. Singer, Yen Tan, Annelie Augustinsson, Johanna Rantala, Jacques Simard, Rita K. Schmutzler, Roger L. Milne, Kelly-Anne Phillips, Mary Beth Terry, David Goldgar, Flora E. van Leeuwen, Thea M. Mooij, Antonis C. Antoniou, Douglas F. Easton, Matti A. Rookus, and Christoph Engel

Subjects
Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract

Abstract Introduction Height, body mass index (BMI), and weight gain are associated with breast cancer risk in the general population. It is unclear whether these associations also exist for carriers of pathogenic variants in the BRCA1 or BRCA2 genes. Patients and methods An international pooled cohort of 8091 BRCA1/2 variant carriers was used for retrospective and prospective analyses separately for premenopausal and postmenopausal women. Cox regression was used to estimate breast cancer risk associations with height, BMI, and weight change. Results In the retrospective analysis, taller height was associated with risk of premenopausal breast cancer for BRCA2 variant carriers (HR 1.20 per 10 cm increase, 95% CI 1.04–1.38). Higher young-adult BMI was associated with lower premenopausal breast cancer risk for both BRCA1 (HR 0.75 per 5 kg/m2, 95% CI 0.66–0.84) and BRCA2 (HR 0.76, 95% CI 0.65–0.89) variant carriers in the retrospective analysis, with consistent, though not statistically significant, findings from the prospective analysis. In the prospective analysis, higher BMI and adult weight gain were associated with higher postmenopausal breast cancer risk for BRCA1 carriers (HR 1.20 per 5 kg/m2, 95% CI 1.02–1.42; and HR 1.10 per 5 kg weight gain, 95% CI 1.01–1.19, respectively). Conclusion Anthropometric measures are associated with breast cancer risk for BRCA1 and BRCA2 variant carriers, with relative risk estimates that are generally consistent with those for women from the general population.

Published
2023
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6. Survival and prognostic factors of early‐stage non‐small cell lung cancer in Central and Eastern Europe: A prospective cohort study

Author

Mahdi Sheikh, Shama Virani, Hilary A. Robbins, Lenka Foretova, Ivana Holcatova, Vladimir Janout, Jolanta Lissowska, Marie Navratilova, Anush Mukeriya, Miodrag Ognjanovic, Beata Swiatkowska, David Zaridze, and Paul Brennan

Subjects
alcohol, death, mortality, neoplasm, smoking, tobacco, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract

Abstract Background Although early diagnosis and surgical resection of the tumor have been shown to be the most important predictors of lung cancer survival, long‐term survival for surgically‐resected early‐stage lung cancer remains poor. Aims In this prospective study we aimed to investigate the survival and prognostic factors of surgically‐resected early‐stage non‐small cell lung cancer (NSCLC) in Central and Eastern Europe. Methods We recruited 2052 patients with stage I‐IIIA NSCLC from 9 centers in Russia, Poland, Serbia, Czech Republic, and Romania, between 2007–2016 and followed them annually through 2020. Results During follow‐up, there were 1121 deaths (including 730 cancer‐specific deaths). Median survival time was 4.9 years, and the 5‐year overall survival was 49.5%. In the multivariable model, mortality was increased among older individuals (HR for each 10‐year increase: 1.31 [95% CI: 1.21–1.42]), males (HR:1.24 [1.04–1.49]), participants with significant weight loss (HR:1.25 [1.03–1.52]), current smokers (HR:1.30 [1.04–1.62]), alcohol drinkers (HR:1.22 [1.03–1.44]), and those with higher stage tumors (HR stage IIIA vs. I: 5.54 [4.10 – 7.48]). However, education, chronic obstructive pulmonary diseases (COPD), and tumor histology were not associated with risk of death. All baseline indicators of smoking and alcohol drinking showed a dose‐dependent association with the risk of cancer‐specific mortality. This included pack‐years of cigarettes smoked (p‐trend = 0.04), quantity of smoking (p‐trend = 0.008), years of smoking (p‐trend = 0.010), gram‐days of alcohol drank (p‐trend = 0.002), frequency of drinking (p‐trend = 0.006), and years of drinking (p‐trend = 0.016). Conclusion This study shows that the 5‐year survival rate of surgically‐resected stage I‐IIIA NSCLC is still around 50% in Central and Eastern Europe. In addition to non‐modifiable prognostic factors, lifetime patterns of smoking and alcohol drinking affected the risk of death and disease progression in a dose‐dependent manner in this population.

Published
2023
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7. Application of two job indices for general occupational demands in a pooled analysis of case–control studies on lung cancer

Author

Jan Hovanec, Jack Siemiatycki, David I Conway, Ann Olsson, Pascal Guenel, Danièle Luce, Karl-Heinz Jöckel, Hermann Pohlabeln, Wolfgang Ahrens, Stefan Karrasch, Heinz-Erich Wichmann, Per Gustavsson, Dario Consonni, Franco Merletti, Lorenzo Richiardi, Simonato Lorenzo, Cristina Fortes, Marie-Élise Parent, John R McLaughlin, Paul Demers, Maria Teresa Landi, Neil Caporaso, Guillermo Fernández-Tardón, David Zaridze, Beata Świątkowska, Tamas Pándics, Jolanta Lissowska, Eleonora Fabianova, John K Field, Dana Mates, Vladimir Bencko, Lenka Foretova, Vladimir Janout, Hans Kromhout, Roel Vermeulen, Paolo Boffetta, Kurt Straif, Joachim Schüz, Swaantje Casjens, Beate Pesch, Thomas Brüning, and Thomas Behrens

Subjects
cancer, smoking, lung cancer, psychosocial, job index, case–control, tumor subtype, social prestige, occupational demand, Public aspects of medicine, RA1-1270
Abstract

OBJECTIVES: We investigated general job demands as a risk factor for lung cancer as well as their role in the association between occupational prestige and lung cancer. METHODS: In 13 case–control studies on lung cancer, as part of the international SYNERGY project, we applied indices for physical (PHI) and psychosocial (PSI) job demands – each with four categories (high to low). We estimated odds ratios (OR) and 95% confidence intervals (CI) for lung cancer by unconditional logistic regression, separately for men and women and adjusted for study centre, age, smoking behavior, and former employment in occupations with potential exposure to carcinogens. Further, we investigated, whether higher risks among men with low occupational prestige (Treiman’s Standard International Occupational Prestige Scale) were affected by adjustment for the job indices. RESULTS: In 30 355 men and 7371 women, we found increased risks (OR) for lung cancer with high relative to low job demands in both men [PHI 1.74 (95% CI 1.56–1.93), PSI 1.33 (95% CI 1.17–1.51)] and women [PHI 1.62 (95% CI 1.24–2.11), PSI 1.31 (95% CI 1.09–1.56)]. OR for lung cancer among men with low occupational prestige were slightly reduced when adjusting for PHI [low versus high prestige OR from 1.44 (95% CI 1.32–1.58) to 1.30 (95% CI 1.17–1.45)], but not PSI. CONCLUSIONS: Higher physical job demands were associated with increased risks of lung cancer, while associations for higher psychosocial demands were less strong. In contrast to physical demands, psychosocial demands did not contribute to clarify the association of occupational prestige and lung cancer.

Published
2021
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8. Occupational exposure to organic dust and risk of lymphoma subtypes in the EPILYMPH case–control study

Author

Pierluigi Cocco, Giannina Satta, Federico Meloni, Ilaria Pilia, Fahad Ahmed, Nikolaus Becker, Delphine Casabonne, Silvia de Sanjosé, Lenka Foretova, Marc Maynadié, Alexandra Nieters, Anthony Staines, Andrea ’t Mannetje, Mariagrazia Zucca, Maria Grazia Ennas, Marcello Campagna, Sara De Matteis, and Yolanda Benavente

Subjects
hodgkin lymphoma, lymphoma subtype, epilymph, textile dust, leather dust, b cell lymphoma, flour dust, epidemiology, occupational exposure, wood dust, lymphoma, organic dust, case–control study, Public aspects of medicine, RA1-1270
Abstract

OBJECTIVES: This study aimed to estimate the risk of lymphoma and its major subtypes in relation to occupational exposure to specific organic dusts. METHODS: We explored the association in 1853 cases and 1997 controls who participated in the EpiLymph case–control study, conducted in six European countries in 1998–2004. Based on expert assessment of lifetime occupational exposures, we calculated the risk of the major lymphoma subtypes associated with exposure to six specific organic dusts, namely, flour, hardwood, softwood, natural textile, synthetic textile, and leather, and two generic (any types) groups: wood and textile dusts. Risk was predicted with unconditional regression modeling, adjusted by age, gender, study center, and education. RESULTS: We observed a 2.1-fold increase in risk of follicular lymphoma associated with ever exposure to leather dust [95% confidence interval (CI) 1.01–4.20]. After excluding subjects who ever worked in a farm or had ever been exposed to solvents, risk of B-cell lymphoma was elevated in relation to ever exposure to leather dust [odd ratio (OR) 2.2, 95% CI 1.00–4.78], but it was not supported by increasing trends with the exposure metrics. Risk of Hodgkin lymphoma was elevated (OR 2.0, 95% CI 0.95–4.30) for exposure to textile dust, with consistent upward trends by cumulative exposure and three independent exposure metrics combined (P=0.023, and P=0.0068, respectively). CONCLUSIONS: Future, larger studies might provide further insights into the nature of the association we observed between exposure to textile dust and risk of Hodgkin lymphoma.

Published
2021
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9. Occupational exposure to ionizing radiation and risk of lymphoma subtypes: results of the Epilymph European case-control study

Author

Giannina Satta, Matteo Loi, Nickolaus Becker, Yolanda Benavente, Silvia De Sanjose, Lenka Foretova, Anthony Staines, Marc Maynadie, Alexandra Nieters, Federico Meloni, Ilaria Pilia, Marcello Campagna, Marco Pau, Lydia B. Zablotska, and Pierluigi Cocco

Subjects
Ionizing radiation, Lymphoma, Diffuse large B cell lymphoma, Occupational exposure, Industrial medicine. Industrial hygiene, RC963-969, Public aspects of medicine, RA1-1270
Abstract

Abstract Background Evidence linking risk of lymphoma and B-cell lymphoma subtypes to ionizing radiation is inconclusive, particularly at low exposure levels. Methods We investigated risk of lymphoma (all subtypes), B-cell lymphomas, and its major subtypes, associated with low-level occupational exposure to ionizing radiation, in 2346 lymphoma cases and 2463 controls, who participated in the multicenter EpiLymph case-control study. We developed a job-exposure matrix to estimate exposure to ionizing radiation, distinguishing between internal and external radiation, and we applied it to the lifetime occupational history of study subjects, We calculated the Odds Ratio (OR) and its 95% confidence interval (95% CI) for lymphoma (all subtypes combined), B-cell lymphoma, and its major subtypes using unconditional, polytomous logistic regression adjusting for age, gender, and education. Results We did not observe an association between exposure metrics of external and internal radiation and risk of lymphoma (all subtypes), nor with B-cell lymphoma, or its major subtypes, at the levels regularly experienced in occupational settings. An elevated risk of diffuse large B cell lymphoma was observed among the most likely exposed study subjects with relatively higher exposure intensity, which would be worth further investigation. Conclusions Further investigation is warranted on risk of B cell lymphoma subtypes associated with low-level occupational exposure to external ionizing radiation, and to clarify whether lymphoma should be included among the cancer outcomes related to ionizing radiation.

Published
2020
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10. Risk-reducing salpingo-oophorectomy, natural menopause, and breast cancer risk: an international prospective cohort of BRCA1 and BRCA2 mutation carriers

Author

Nasim Mavaddat, Antonis C. Antoniou, Thea M. Mooij, Maartje J. Hooning, Bernadette A. Heemskerk-Gerritsen, GENEPSO, Catherine Noguès, Marion Gauthier-Villars, Olivier Caron, Paul Gesta, Pascal Pujol, Alain Lortholary, EMBRACE, Daniel Barrowdale, Debra Frost, D. Gareth Evans, Louise Izatt, Julian Adlard, Ros Eeles, Carole Brewer, Marc Tischkowitz, Alex Henderson, Jackie Cook, Diana Eccles, HEBON, Klaartje van Engelen, Marian J. E. Mourits, Margreet G. E. M. Ausems, Linetta B. Koppert, John L. Hopper, Esther M. John, Wendy K. Chung, Irene L. Andrulis, Mary B. Daly, Saundra S. Buys, kConFab Investigators, Javier Benitez, Trinidad Caldes, Anna Jakubowska, Jacques Simard, Christian F. Singer, Yen Tan, Edith Olah, Marie Navratilova, Lenka Foretova, Anne-Marie Gerdes, Marie-José Roos-Blom, Flora E. Van Leeuwen, Brita Arver, Håkan Olsson, Rita K. Schmutzler, Christoph Engel, Karin Kast, Kelly-Anne Phillips, Mary Beth Terry, Roger L. Milne, David E. Goldgar, Matti A. Rookus, Nadine Andrieu, Douglas F. Easton, on behalf of IBCCS, kConFab, and BCFR

Subjects
Breast cancer, BRCA1, BRCA2, Mutation, Risk-reducing salpingo-oophorectomy, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract

Abstract Background The effect of risk-reducing salpingo-oophorectomy (RRSO) on breast cancer risk for BRCA1 and BRCA2 mutation carriers is uncertain. Retrospective analyses have suggested a protective effect but may be substantially biased. Prospective studies have had limited power, particularly for BRCA2 mutation carriers. Further, previous studies have not considered the effect of RRSO in the context of natural menopause. Methods A multi-centre prospective cohort of 2272 BRCA1 and 1605 BRCA2 mutation carriers was followed for a mean of 5.4 and 4.9 years, respectively; 426 women developed incident breast cancer. RRSO was modelled as a time-dependent covariate in Cox regression, and its effect assessed in premenopausal and postmenopausal women. Results There was no association between RRSO and breast cancer for BRCA1 (HR = 1.23; 95% CI 0.94–1.61) or BRCA2 (HR = 0.88; 95% CI 0.62–1.24) mutation carriers. For BRCA2 mutation carriers, HRs were 0.68 (95% CI 0.40–1.15) and 1.07 (95% CI 0.69–1.64) for RRSO carried out before or after age 45 years, respectively. The HR for BRCA2 mutation carriers decreased with increasing time since RRSO (HR = 0.51; 95% CI 0.26–0.99 for 5 years or longer after RRSO). Estimates for premenopausal women were similar. Conclusion We found no evidence that RRSO reduces breast cancer risk for BRCA1 mutation carriers. A potentially beneficial effect for BRCA2 mutation carriers was observed, particularly after 5 years following RRSO. These results may inform counselling and management of carriers with respect to RRSO.

Published
2020
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11. Correction to: Risk-reducing salpingo-oophorectomy, natural menopause, and breast cancer risk: an international prospective cohort of BRCA1 and BRCA2 mutation carriers

Author

Nasim Mavaddat, Antonis C. Antoniou, Thea M. Mooij, Maartje J. Hooning, Bernadette A. Heemskerk-Gerritsen, GENEPSO, Catherine Noguès, Marion Gauthier-Villars, Olivier Caron, Paul Gesta, Pascal Pujol, Alain Lortholary, EMBRACE, Daniel Barrowdale, Debra Frost, D. Gareth Evans, Louise Izatt, Julian Adlard, Ros Eeles, Carole Brewer, Marc Tischkowitz, Alex Henderson, Jackie Cook, Diana Eccles, HEBON, Klaartje van Engelen, Marian J. E. Mourits, Margreet G. E. M. Ausems, Linetta B. Koppert, John L. Hopper, Esther M. John, Wendy K. Chung, Irene L. Andrulis, Mary B. Daly, Saundra S. Buys, kConFab Investigators, Javier Benitez, Trinidad Caldes, Anna Jakubowska, Jacques Simard, Christian F. Singer, Yen Tan, Edith Olah, Marie Navratilova, Lenka Foretova, Anne-Marie Gerdes, Marie-José Roos-Blom, Flora E. Van Leeuwen, Brita Arver, Håkan Olsson, Rita K. Schmutzler, Christoph Engel, Karin Kast, Kelly-Anne Phillips, Mary Beth Terry, Roger L. Milne, David E. Goldgar, Matti A. Rookus, Nadine Andrieu, Douglas F. Easton, and on behalf of IBCCS, kConFab and BCFR

Subjects
Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract

After publication of the original article [1], we were notified that columns in Table 2 were erroneously displayed.

Published
2020
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12. Circulating tumour-derived KRAS mutations in pancreatic cancer cases are predominantly carried by very short fragments of cell-free DNA

Author

Maria Zvereva, Gabriel Roberti, Geoffroy Durand, Catherine Voegele, Minh Dao Nguyen, Tiffany M. Delhomme, Priscilia Chopard, Eleonora Fabianova, Zora Adamcakova, Ivana Holcatova, Lenka Foretova, Vladimir Janout, Paul Brennan, Matthieu Foll, Graham B. Byrnes, James D. McKay, Ghislaine Scelo, and Florence Le Calvez-Kelm

Subjects
Cell-free DNA, KRAS mutations, Plasma, Pancreatic cancer detection, Medicine, Medicine (General), R5-920
Abstract

Background: The DNA released into the bloodstream by malignant tumours· called circulating tumour DNA (ctDNA), is often a small fraction of total cell-free DNA shed predominantly by hematopoietic cells and is therefore challenging to detect. Understanding the biological properties of ctDNA is key to the investigation of its clinical relevance as a non-invasive marker for cancer detection and monitoring. Methods: We selected 40 plasma DNA samples of pancreatic cancer cases previously reported to carry a KRAS mutation at the ‘hotspot’ codon 12 and re-screened the cell-free DNA using a 4-size amplicons strategy (57 bp, 79 bp, 167 bp and 218 bp) combined with ultra-deep sequencing in order to investigate whether amplicon lengths could impact on the capacity of detection of ctDNA, which in turn could provide inference of ctDNA and non-malignant cell-free DNA size distribution. Findings: Higher KRAS amplicon size (167 bp and 218 bp) was associated with lower detectable cell-free DNA mutant allelic fractions (p

Published
2020
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13. Association of ionizing radiation dose from common medical diagnostic procedures and lymphoma risk in the Epilymph case-control study.

Author

Elisa Pasqual, Michelle C Turner, Esther Gracia-Lavedan, Delphine Casabonne, Yolanda Benavente, Isabelle Thierry Chef, Marc Maynadié, Pierluigi Cocco, Anthony Staines, Lenka Foretova, Alexandra Nieters, Paolo Boffetta, Paul Brennan, Elisabeth Cardis, and Silvia de Sanjose

Subjects
Medicine, Science
Abstract

Medical diagnostic X-rays are an important source of ionizing radiation (IR) exposure in the general population; however, it is unclear if the resulting low patient doses increase lymphoma risk. We examined the association between lifetime medical diagnostic X-ray dose and lymphoma risk, taking into account potential confounding factors, including medical history. The international Epilymph study (conducted in the Czech-Republic, France, Germany, Ireland, Italy, and Spain) collected self-reported information on common diagnostic X-ray procedures from 2,362 lymphoma cases and 2,465 frequency-matched (age, sex, country) controls. Individual lifetime cumulative bone marrow (BM) dose was estimated using time period-based dose estimates for different procedures and body parts. The association between categories of BM dose and lymphoma risk was examined using unconditional logistic regression models adjusting for matching factors, socioeconomic variables, and the presence of underlying medical conditions (atopic, autoimmune, infectious diseases, osteoarthritis, having had a sick childhood, and family history of lymphoma) as potential confounders of the association. Cumulative BM dose was low (median 2.25 mGy) and was not positively associated with lymphoma risk. Odds ratios (ORs) were consistently less than 1.0 in all dose categories compared to the reference category (less than 1 mGy). Results were similar after adjustment for potential confounding factors, when using different exposure scenarios, and in analyses by lymphoma subtype and by type of control (hospital-, population-based). Overall no increased risk of lymphoma was observed. The reduced ORs may be related to unmeasured confounding or other sources of systematic bias.We found little evidence that chronic medical conditions confound lymphoma risk and medical radiation associations.

Published
2020
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14. Correction: Association of ionizing radiation dose from common medical diagnostic procedures and lymphoma risk in the Epilymph case-control study.

Author

Elisa Pasqual, Michelle C Turner, Esther Gracia-Lavedan, Delphine Casabonne, Yolanda Benavente, Isabelle Thierry-Chef, Marc Maynadié, Pierluigi Cocco, Anthony Staines, Lenka Foretova, Alexandra Nieters, Paolo Boffetta, Paul Brennan, Elisabeth Cardis, and Silvia de Sanjose

Subjects
Medicine, Science
Abstract

[This corrects the article DOI: 10.1371/journal.pone.0235658.].

Published
2020
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15. Genetically Determined Height and Risk of Non-hodgkin Lymphoma

Author

Amy Moore, Eleanor Kane, Zhaoming Wang, Orestis A. Panagiotou, Lauren R. Teras, Alain Monnereau, Nicole Wong Doo, Mitchell J. Machiela, Christine F. Skibola, Susan L. Slager, Gilles Salles, Nicola J. Camp, Paige M. Bracci, Alexandra Nieters, Roel C. H. Vermeulen, Joseph Vijai, Karin E. Smedby, Yawei Zhang, Claire M. Vajdic, Wendy Cozen, John J. Spinelli, Henrik Hjalgrim, Graham G. Giles, Brian K. Link, Jacqueline Clavel, Alan A. Arslan, Mark P. Purdue, Lesley F. Tinker, Demetrius Albanes, Giovanni M. Ferri, Thomas M. Habermann, Hans-Olov Adami, Nikolaus Becker, Yolanda Benavente, Simonetta Bisanzi, Paolo Boffetta, Paul Brennan, Angela R. Brooks-Wilson, Federico Canzian, Lucia Conde, David G. Cox, Karen Curtin, Lenka Foretova, Susan M. Gapstur, Hervé Ghesquières, Martha Glenn, Bengt Glimelius, Rebecca D. Jackson, Qing Lan, Mark Liebow, Marc Maynadie, James McKay, Mads Melbye, Lucia Miligi, Roger L. Milne, Thierry J. Molina, Lindsay M. Morton, Kari E. North, Kenneth Offit, Marina Padoan, Alpa V. Patel, Sara Piro, Vignesh Ravichandran, Elio Riboli, Silvia de Sanjose, Richard K. Severson, Melissa C. Southey, Anthony Staines, Carolyn Stewart, Ruth C. Travis, Elisabete Weiderpass, Stephanie Weinstein, Tongzhang Zheng, Stephen J. Chanock, Nilanjan Chatterjee, Nathaniel Rothman, Brenda M. Birmann, James R. Cerhan, and Sonja I. Berndt

Subjects
non-Hodgkin lymphoma, height, genetics, chronic lymphocytic leukemia, diffuse large B-cell lymphoma, follicular lymphoma, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract

Although the evidence is not consistent, epidemiologic studies have suggested that taller adult height may be associated with an increased risk of some non-Hodgkin lymphoma (NHL) subtypes. Height is largely determined by genetic factors, but how these genetic factors may contribute to NHL risk is unknown. We investigated the relationship between genetic determinants of height and NHL risk using data from eight genome-wide association studies (GWAS) comprising 10,629 NHL cases, including 3,857 diffuse large B-cell lymphoma (DLBCL), 2,847 follicular lymphoma (FL), 3,100 chronic lymphocytic leukemia (CLL), and 825 marginal zone lymphoma (MZL) cases, and 9,505 controls of European ancestry. We evaluated genetically predicted height by constructing polygenic risk scores using 833 height-associated SNPs. We used logistic regression to estimate odds ratios (OR) and 95% confidence intervals (CI) for association between genetically determined height and the risk of four NHL subtypes in each GWAS and then used fixed-effect meta-analysis to combine subtype results across studies. We found suggestive evidence between taller genetically determined height and increased CLL risk (OR = 1.08, 95% CI = 1.00–1.17, p = 0.049), which was slightly stronger among women (OR = 1.15, 95% CI: 1.01–1.31, p = 0.036). No significant associations were observed with DLBCL, FL, or MZL. Our findings suggest that there may be some shared genetic factors between CLL and height, but other endogenous or environmental factors may underlie reported epidemiologic height associations with other subtypes.

Published
2020
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16. Two high-risk susceptibility loci at 6p25.3 and 14q32.13 for Waldenström macroglobulinemia

Author

Mary L. McMaster, Sonja I. Berndt, Jianqing Zhang, Susan L. Slager, Shengchao Alfred Li, Claire M. Vajdic, Karin E. Smedby, Huihuang Yan, Brenda M. Birmann, Elizabeth E. Brown, Alex Smith, Geffen Kleinstern, Mervin M. Fansler, Christine Mayr, Bin Zhu, Charles C. Chung, Ju-Hyun Park, Laurie Burdette, Belynda D. Hicks, Amy Hutchinson, Lauren R. Teras, Hans-Olov Adami, Paige M. Bracci, James McKay, Alain Monnereau, Brian K. Link, Roel C. H. Vermeulen, Stephen M. Ansell, Ann Maria, W. Ryan Diver, Mads Melbye, Akinyemi I. Ojesina, Peter Kraft, Paolo Boffetta, Jacqueline Clavel, Edward Giovannucci, Caroline M. Besson, Federico Canzian, Ruth C. Travis, Paolo Vineis, Elisabete Weiderpass, Rebecca Montalvan, Zhaoming Wang, Meredith Yeager, Nikolaus Becker, Yolanda Benavente, Paul Brennan, Lenka Foretova, Marc Maynadie, Alexandra Nieters, Silvia de Sanjose, Anthony Staines, Lucia Conde, Jacques Riby, Bengt Glimelius, Henrik Hjalgrim, Nisha Pradhan, Andrew L. Feldman, Anne J. Novak, Charles Lawrence, Bryan A. Bassig, Qing Lan, Tongzhang Zheng, Kari E. North, Lesley F. Tinker, Wendy Cozen, Richard K. Severson, Jonathan N. Hofmann, Yawei Zhang, Rebecca D. Jackson, Lindsay M. Morton, Mark P. Purdue, Nilanjan Chatterjee, Kenneth Offit, James R. Cerhan, Stephen J. Chanock, Nathaniel Rothman, Joseph Vijai, Lynn R. Goldin, Christine F. Skibola, and Neil E. Caporaso

Subjects
Science
Abstract

Waldenström macroglobulinemia (WM)/lymphoplasmacytic lymphoma (LPL) is a non-Hodgkin-type B cell lymphoma. Here, the authors identify two risk loci for WM/LPL in a two-stage GWAS involving a family-oversampling approach and provide evidence for a functional role of the non-coding SNP rs116446171.

Published
2018
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17. Genome-wide meta-analysis identifies five new susceptibility loci for pancreatic cancer

Author

Alison P. Klein, Brian M. Wolpin, Harvey A. Risch, Rachael Z. Stolzenberg-Solomon, Evelina Mocci, Mingfeng Zhang, Federico Canzian, Erica J. Childs, Jason W. Hoskins, Ashley Jermusyk, Jun Zhong, Fei Chen, Demetrius Albanes, Gabriella Andreotti, Alan A. Arslan, Ana Babic, William R. Bamlet, Laura Beane-Freeman, Sonja I. Berndt, Amanda Blackford, Michael Borges, Ayelet Borgida, Paige M. Bracci, Lauren Brais, Paul Brennan, Hermann Brenner, Bas Bueno-de-Mesquita, Julie Buring, Daniele Campa, Gabriele Capurso, Giulia Martina Cavestro, Kari G. Chaffee, Charles C. Chung, Sean Cleary, Michelle Cotterchio, Frederike Dijk, Eric J. Duell, Lenka Foretova, Charles Fuchs, Niccola Funel, Steven Gallinger, J. Michael M. Gaziano, Maria Gazouli, Graham G. Giles, Edward Giovannucci, Michael Goggins, Gary E. Goodman, Phyllis J. Goodman, Thilo Hackert, Christopher Haiman, Patricia Hartge, Manal Hasan, Peter Hegyi, Kathy J. Helzlsouer, Joseph Herman, Ivana Holcatova, Elizabeth A. Holly, Robert Hoover, Rayjean J. Hung, Eric J. Jacobs, Krzysztof Jamroziak, Vladimir Janout, Rudolf Kaaks, Kay-Tee Khaw, Eric A. Klein, Manolis Kogevinas, Charles Kooperberg, Matthew H. Kulke, Juozas Kupcinskas, Robert J. Kurtz, Daniel Laheru, Stefano Landi, Rita T. Lawlor, I.-Min Lee, Loic LeMarchand, Lingeng Lu, Núria Malats, Andrea Mambrini, Satu Mannisto, Roger L. Milne, Beatrice Mohelníková-Duchoňová, Rachel E. Neale, John P. Neoptolemos, Ann L. Oberg, Sara H. Olson, Irene Orlow, Claudio Pasquali, Alpa V. Patel, Ulrike Peters, Raffaele Pezzilli, Miquel Porta, Francisco X. Real, Nathaniel Rothman, Ghislaine Scelo, Howard D. Sesso, Gianluca Severi, Xiao-Ou Shu, Debra Silverman, Jill P. Smith, Pavel Soucek, Malin Sund, Renata Talar-Wojnarowska, Francesca Tavano, Mark D. Thornquist, Geoffrey S. Tobias, Stephen K. Van Den Eeden, Yogesh Vashist, Kala Visvanathan, Pavel Vodicka, Jean Wactawski-Wende, Zhaoming Wang, Nicolas Wentzensen, Emily White, Herbert Yu, Kai Yu, Anne Zeleniuch-Jacquotte, Wei Zheng, Peter Kraft, Donghui Li, Stephen Chanock, Ofure Obazee, Gloria M. Petersen, and Laufey T. Amundadottir

Subjects
Science
Abstract

Genetic variants associated with susceptibility to pancreatic cancer have been identified using genome wide association studies (GWAS). Here, the authors combine data from over 9000 patients and perform a meta-analysis to identify five novel loci linked to pancreatic cancer.

Published
2018
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18. Genome-wide association study identifies multiple risk loci for renal cell carcinoma

Author

Ghislaine Scelo, Mark P. Purdue, Kevin M. Brown, Mattias Johansson, Zhaoming Wang, Jeanette E. Eckel-Passow, Yuanqing Ye, Jonathan N. Hofmann, Jiyeon Choi, Matthieu Foll, Valerie Gaborieau, Mitchell J. Machiela, Leandro M. Colli, Peng Li, Joshua N. Sampson, Behnoush Abedi-Ardekani, Celine Besse, Helene Blanche, Anne Boland, Laurie Burdette, Amelie Chabrier, Geoffroy Durand, Florence Le Calvez-Kelm, Egor Prokhortchouk, Nivonirina Robinot, Konstantin G. Skryabin, Magdalena B. Wozniak, Meredith Yeager, Gordana Basta-Jovanovic, Zoran Dzamic, Lenka Foretova, Ivana Holcatova, Vladimir Janout, Dana Mates, Anush Mukeriya, Stefan Rascu, David Zaridze, Vladimir Bencko, Cezary Cybulski, Eleonora Fabianova, Viorel Jinga, Jolanta Lissowska, Jan Lubinski, Marie Navratilova, Peter Rudnai, Neonila Szeszenia-Dabrowska, Simone Benhamou, Geraldine Cancel-Tassin, Olivier Cussenot, Laura Baglietto, Heiner Boeing, Kay-Tee Khaw, Elisabete Weiderpass, Borje Ljungberg, Raviprakash T. Sitaram, Fiona Bruinsma, Susan J. Jordan, Gianluca Severi, Ingrid Winship, Kristian Hveem, Lars J. Vatten, Tony Fletcher, Kvetoslava Koppova, Susanna C. Larsson, Alicja Wolk, Rosamonde E. Banks, Peter J. Selby, Douglas F. Easton, Paul Pharoah, Gabriella Andreotti, Laura E. Beane Freeman, Stella Koutros, Demetrius Albanes, Satu Männistö, Stephanie Weinstein, Peter E. Clark, Todd L. Edwards, Loren Lipworth, Susan M. Gapstur, Victoria L. Stevens, Hallie Carol, Matthew L. Freedman, Mark M. Pomerantz, Eunyoung Cho, Peter Kraft, Mark A. Preston, Kathryn M. Wilson, J. Michael Gaziano, Howard D. Sesso, Amanda Black, Neal D. Freedman, Wen-Yi Huang, John G. Anema, Richard J. Kahnoski, Brian R. Lane, Sabrina L. Noyes, David Petillo, Bin Tean Teh, Ulrike Peters, Emily White, Garnet L. Anderson, Lisa Johnson, Juhua Luo, Julie Buring, I-Min Lee, Wong-Ho Chow, Lee E. Moore, Christopher Wood, Timothy Eisen, Marc Henrion, James Larkin, Poulami Barman, Bradley C. Leibovich, Toni K. Choueiri, G. Mark Lathrop, Nathaniel Rothman, Jean-Francois Deleuze, James D. McKay, Alexander S. Parker, Xifeng Wu, Richard S. Houlston, Paul Brennan, and Stephen J. Chanock

Subjects
Science
Abstract

Risk for renal cell carcinoma (RCC) is higher when there are first-degree family members with the disease. Here, Scelo and colleagues perform a genome-wide association meta-analysis and new genome-wide scan to identify seven new loci with significant RCC association.

Published
2017
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19. The influence of obesity-related factors in the etiology of renal cell carcinoma-A mendelian randomization study.

Author

Mattias Johansson, Robert Carreras-Torres, Ghislaine Scelo, Mark P Purdue, Daniela Mariosa, David C Muller, Nicolas J Timpson, Philip C Haycock, Kevin M Brown, Zhaoming Wang, Yuanqing Ye, Jonathan N Hofmann, Matthieu Foll, Valerie Gaborieau, Mitchell J Machiela, Leandro M Colli, Peng Li, Jean-Guillaume Garnier, Helene Blanche, Anne Boland, Laurie Burdette, Egor Prokhortchouk, Konstantin G Skryabin, Meredith Yeager, Sanja Radojevic-Skodric, Simona Ognjanovic, Lenka Foretova, Ivana Holcatova, Vladimir Janout, Dana Mates, Anush Mukeriya, Stefan Rascu, David Zaridze, Vladimir Bencko, Cezary Cybulski, Eleonora Fabianova, Viorel Jinga, Jolanta Lissowska, Jan Lubinski, Marie Navratilova, Peter Rudnai, Simone Benhamou, Geraldine Cancel-Tassin, Olivier Cussenot, Elisabete Weiderpass, Börje Ljungberg, Raviprakash Tumkur Sitaram, Christel Häggström, Fiona Bruinsma, Susan J Jordan, Gianluca Severi, Ingrid Winship, Kristian Hveem, Lars J Vatten, Tony Fletcher, Susanna C Larsson, Alicja Wolk, Rosamonde E Banks, Peter J Selby, Douglas F Easton, Gabriella Andreotti, Laura E Beane Freeman, Stella Koutros, Satu Männistö, Stephanie Weinstein, Peter E Clark, Todd L Edwards, Loren Lipworth, Susan M Gapstur, Victoria L Stevens, Hallie Carol, Matthew L Freedman, Mark M Pomerantz, Eunyoung Cho, Kathryn M Wilson, J Michael Gaziano, Howard D Sesso, Neal D Freedman, Alexander S Parker, Jeanette E Eckel-Passow, Wen-Yi Huang, Richard J Kahnoski, Brian R Lane, Sabrina L Noyes, David Petillo, Bin Tean Teh, Ulrike Peters, Emily White, Garnet L Anderson, Lisa Johnson, Juhua Luo, Julie Buring, I-Min Lee, Wong-Ho Chow, Lee E Moore, Timothy Eisen, Marc Henrion, James Larkin, Poulami Barman, Bradley C Leibovich, Toni K Choueiri, G Mark Lathrop, Jean-Francois Deleuze, Marc Gunter, James D McKay, Xifeng Wu, Richard S Houlston, Stephen J Chanock, Caroline Relton, J Brent Richards, Richard M Martin, George Davey Smith, and Paul Brennan

Subjects
Medicine
Abstract

BackgroundSeveral obesity-related factors have been associated with renal cell carcinoma (RCC), but it is unclear which individual factors directly influence risk. We addressed this question using genetic markers as proxies for putative risk factors and evaluated their relation to RCC risk in a mendelian randomization (MR) framework. This methodology limits bias due to confounding and is not affected by reverse causation.Methods and findingsGenetic markers associated with obesity measures, blood pressure, lipids, type 2 diabetes, insulin, and glucose were initially identified as instrumental variables, and their association with RCC risk was subsequently evaluated in a genome-wide association study (GWAS) of 10,784 RCC patients and 20,406 control participants in a 2-sample MR framework. The effect on RCC risk was estimated by calculating odds ratios (ORSD) for a standard deviation (SD) increment in each risk factor. The MR analysis indicated that higher body mass index increases the risk of RCC (ORSD: 1.56, 95% confidence interval [CI] 1.44-1.70), with comparable results for waist-to-hip ratio (ORSD: 1.63, 95% CI 1.40-1.90) and body fat percentage (ORSD: 1.66, 95% CI 1.44-1.90). This analysis further indicated that higher fasting insulin (ORSD: 1.82, 95% CI 1.30-2.55) and diastolic blood pressure (DBP; ORSD: 1.28, 95% CI 1.11-1.47), but not systolic blood pressure (ORSD: 0.98, 95% CI 0.84-1.14), increase the risk for RCC. No association with RCC risk was seen for lipids, overall type 2 diabetes, or fasting glucose.ConclusionsThis study provides novel evidence for an etiological role of insulin in RCC, as well as confirmatory evidence that obesity and DBP influence RCC risk.

Published
2019
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20. Germline multigene panel testing of patients with endometrial cancer

Author

Jan Kral, Sandra Jelinkova, Petra Zemankova, Michal Vocka, Marianna Borecka, Leona Cerna, Marta Cerna, Lukas Dostalek, Petra Duskova, Lenka Foretova, Ondrej Havranek, Klara Horackova, Milena Hovhannisyan, Stepan Chvojka, Marta Kalousova, Marcela Kosarova, Monika Koudova, Vera Krutilkova, Eva Machackova, Petr Nehasil, Jan Novotny, Barbora Otahalova, Alena Puchmajerova, Marketa Safarikova, Jiri Slama, Viktor Stranecky, Ivan Subrt, Spiros Tavandzis, Michal Zikan, Tomas Zima, Jana Soukupova, Petra Kleiblova, Zdenek Kleibl, and Marketa Janatova

Subjects
Cancer Research, Oncology
Published
2023

21. Figure S3 from Application of Genomic Sequencing to Refine Patient Stratification for Adjuvant Therapy in Renal Cell Carcinoma

Author

Rosamonde E. Banks, Yasser Riazalhosseini, Mark Lathrop, Paul Brennan, Jörg Tost, Alvis Brazma, Guillaume Bourque, Anne Cambon-Thomsen, Bozidar Kovacevic, Ljiljana Bogdanovic, Viorel Jinga, Dana Mates, Marie Navratilova, Lenka Foretova, Oxana Shangina, Anush Moukeria, David Zaridze, Estelle Chanudet, Vladimir Janout, Antonin Brisuda, Ivana Holcatova, Magdalena B. Wozniak, Poulam M. Patel, Adebanji Adeyoju, Naeem Soomro, Jon Cartledge, Michael Kimuli, Sebastian Trainor, Peter J. Selby, Anne Y. Warren, Behnoush Abedi-Ardekani, Sharon M. Jackson, Edgars Celms, Juris Viksna, Lars Egevad, Antoine Paccard, Madeleine Arseneault, Nazanin Nourbehesht, Robert Eveleigh, Louis Letourneau, Michelle Wilson, Kate I. Glennon, Ghislaine Scelo, and Naveen S. Vasudev

Abstract

DFS by tumor stage stratified by genomic classifier

Published
2023

22. Supplementary Methods S1 from Application of Genomic Sequencing to Refine Patient Stratification for Adjuvant Therapy in Renal Cell Carcinoma

Author

Rosamonde E. Banks, Yasser Riazalhosseini, Mark Lathrop, Paul Brennan, Jörg Tost, Alvis Brazma, Guillaume Bourque, Anne Cambon-Thomsen, Bozidar Kovacevic, Ljiljana Bogdanovic, Viorel Jinga, Dana Mates, Marie Navratilova, Lenka Foretova, Oxana Shangina, Anush Moukeria, David Zaridze, Estelle Chanudet, Vladimir Janout, Antonin Brisuda, Ivana Holcatova, Magdalena B. Wozniak, Poulam M. Patel, Adebanji Adeyoju, Naeem Soomro, Jon Cartledge, Michael Kimuli, Sebastian Trainor, Peter J. Selby, Anne Y. Warren, Behnoush Abedi-Ardekani, Sharon M. Jackson, Edgars Celms, Juris Viksna, Lars Egevad, Antoine Paccard, Madeleine Arseneault, Nazanin Nourbehesht, Robert Eveleigh, Louis Letourneau, Michelle Wilson, Kate I. Glennon, Ghislaine Scelo, and Naveen S. Vasudev

Abstract

Supplementary Methods

Published
2023

23. Supplementary Table S1 from Application of Genomic Sequencing to Refine Patient Stratification for Adjuvant Therapy in Renal Cell Carcinoma

Author

Rosamonde E. Banks, Yasser Riazalhosseini, Mark Lathrop, Paul Brennan, Jörg Tost, Alvis Brazma, Guillaume Bourque, Anne Cambon-Thomsen, Bozidar Kovacevic, Ljiljana Bogdanovic, Viorel Jinga, Dana Mates, Marie Navratilova, Lenka Foretova, Oxana Shangina, Anush Moukeria, David Zaridze, Estelle Chanudet, Vladimir Janout, Antonin Brisuda, Ivana Holcatova, Magdalena B. Wozniak, Poulam M. Patel, Adebanji Adeyoju, Naeem Soomro, Jon Cartledge, Michael Kimuli, Sebastian Trainor, Peter J. Selby, Anne Y. Warren, Behnoush Abedi-Ardekani, Sharon M. Jackson, Edgars Celms, Juris Viksna, Lars Egevad, Antoine Paccard, Madeleine Arseneault, Nazanin Nourbehesht, Robert Eveleigh, Louis Letourneau, Michelle Wilson, Kate I. Glennon, Ghislaine Scelo, and Naveen S. Vasudev

Abstract

Clinical information and 12 gene mutation status for cohorts C1-C3

Published
2023

24. Supplementary Tables S3-S13 from Application of Genomic Sequencing to Refine Patient Stratification for Adjuvant Therapy in Renal Cell Carcinoma

Author

Rosamonde E. Banks, Yasser Riazalhosseini, Mark Lathrop, Paul Brennan, Jörg Tost, Alvis Brazma, Guillaume Bourque, Anne Cambon-Thomsen, Bozidar Kovacevic, Ljiljana Bogdanovic, Viorel Jinga, Dana Mates, Marie Navratilova, Lenka Foretova, Oxana Shangina, Anush Moukeria, David Zaridze, Estelle Chanudet, Vladimir Janout, Antonin Brisuda, Ivana Holcatova, Magdalena B. Wozniak, Poulam M. Patel, Adebanji Adeyoju, Naeem Soomro, Jon Cartledge, Michael Kimuli, Sebastian Trainor, Peter J. Selby, Anne Y. Warren, Behnoush Abedi-Ardekani, Sharon M. Jackson, Edgars Celms, Juris Viksna, Lars Egevad, Antoine Paccard, Madeleine Arseneault, Nazanin Nourbehesht, Robert Eveleigh, Louis Letourneau, Michelle Wilson, Kate I. Glennon, Ghislaine Scelo, and Naveen S. Vasudev

Abstract

Supplementary Tables S3-S13

Published
2023

25. Data from Application of Genomic Sequencing to Refine Patient Stratification for Adjuvant Therapy in Renal Cell Carcinoma

Author

Rosamonde E. Banks, Yasser Riazalhosseini, Mark Lathrop, Paul Brennan, Jörg Tost, Alvis Brazma, Guillaume Bourque, Anne Cambon-Thomsen, Bozidar Kovacevic, Ljiljana Bogdanovic, Viorel Jinga, Dana Mates, Marie Navratilova, Lenka Foretova, Oxana Shangina, Anush Moukeria, David Zaridze, Estelle Chanudet, Vladimir Janout, Antonin Brisuda, Ivana Holcatova, Magdalena B. Wozniak, Poulam M. Patel, Adebanji Adeyoju, Naeem Soomro, Jon Cartledge, Michael Kimuli, Sebastian Trainor, Peter J. Selby, Anne Y. Warren, Behnoush Abedi-Ardekani, Sharon M. Jackson, Edgars Celms, Juris Viksna, Lars Egevad, Antoine Paccard, Madeleine Arseneault, Nazanin Nourbehesht, Robert Eveleigh, Louis Letourneau, Michelle Wilson, Kate I. Glennon, Ghislaine Scelo, and Naveen S. Vasudev

Abstract

Purpose:Patients with resected localized clear-cell renal cell carcinoma (ccRCC) remain at variable risk of recurrence. Incorporation of biomarkers may refine risk prediction and inform adjuvant treatment decisions. We explored the role of tumor genomics in this setting, leveraging the largest cohort to date of localized ccRCC tissues subjected to targeted gene sequencing.Experimental Design:The somatic mutation status of 12 genes was determined in 943 ccRCC cases from a multinational cohort of patients, and associations to outcomes were examined in a Discovery (n = 469) and Validation (n = 474) framework.Results:Tumors containing a von-Hippel Lindau (VHL) mutation alone were associated with significantly improved outcomes in comparison with tumors containing a VHL plus additional mutations. Within the Discovery cohort, those with VHL+0, VHL+1, VHL+2, and VHL+≥3 tumors had disease-free survival (DFS) rates of 90.8%, 80.1%, 68.2%, and 50.7% respectively, at 5 years. This trend was replicated in the Validation cohort. Notably, these genomically defined groups were independent of tumor mutational burden. Amongst patients eligible for adjuvant therapy, those with a VHL+0 tumor (29%) had a 5-year DFS rate of 79.3% and could, therefore, potentially be spared further treatment. Conversely, patients with VHL+2 and VHL+≥3 tumors (32%) had equivalent DFS rates of 45.6% and 35.3%, respectively, and should be prioritized for adjuvant therapy.Conclusions:Genomic characterization of ccRCC identified biologically distinct groups of patients with divergent relapse rates. These groups account for the ∼80% of cases with VHL mutations and could be used to personalize adjuvant treatment discussions with patients as well as inform future adjuvant trial design.

Published
2023

26. Supplementary Tables 1-3 from A Sex-Specific Association between a 15q25 Variant and Upper Aerodigestive Tract Cancers

Author

James D. McKay, Paul Brennan, Paolo Boffetta, Richard B. Hayes, Mia Hashibe, Stefania Boccia, Leticia Fernandez, José Eluf-Neto, Victor Wünsch-Filho, Ana Menezes, Sergio Koifman, Maria Paula Curado, Vladimir Janout, Lenka Foretova, Vladimir Bencko, Alexandru Bucur, Eleonora Fabianova, Jolanta Lissowska, Neonila Szeszenia-Dabrowska, David Zaridze, Wolfgang Ahrens, Claire M. Healy, Ariana Znaor, David I. Conway, Nalin S. Thakker, Cristina Canova, Luigi Barzan, Tatiana V. Macfarlane, Xavier Castellsagué, Antonio Agudo, Kristina Kjaerheim, Lorenzo Richiardi, Ivana Holcátová, Pagona Lagiou, Simone Benhamou, Chu Chen, Stephen M. Schwartz, Renyi Wang, Shen-Chih Chang, Zuo-Feng Zhang, Erich M. Sturgis, Qingyi Wei, Philip Lazarus, Joshua E. Muscat, Marcin Lener, Joanna Trubicka, Jan Lubiński, Wilbert H. M. Peters, Johannes J. Manni, Martin Lacko, Michael D. McClean, Brock Christensen, Karl T. Kelsey, Renato Talamini, Rolando Herrero, Silvia Franceschi, Tomoko Nukui, Shama Buch, Marjorie Romkes, Jingchun Luo, Mark C. Weissler, Andrew F. Olshan, Shu-chun Chuang, Amelie Chabrier, Graham Byrnes, Valerie Gaborieau, Therese Truong, and Dan Chen

Abstract

Supplementary Tables 1-3 from A Sex-Specific Association between a 15q25 Variant and Upper Aerodigestive Tract Cancers

Published
2023

27. Supplementary Tables S1-S6 from Effect of Occupational Exposures on Lung Cancer Susceptibility: A Study of Gene–Environment Interaction Analysis

Author

Paolo Boffetta, Vladimir Janout, Lenka Foretova, Isabelle Stücker, Valerie Gaborieau, Vladimir Bencko, Dana Mates, Eleonora Fabianova, Jolanta Lissowska, Peter Rudnai, Beata Świątkowska, Neonila Szeszenia-Dabrowska, David Zaridze, Paul Brennan, Samantha Sartori, and Jyoti Malhotra

Abstract

Supplementary Tables S1-S6. Table S1. Number and percentage of cases and control with exposure to each occupational agent. Table S2. SNP-level significant occupational exposure interactions for known occupational lung carcinogens. Table S3. SNP-level significant occupational exposure interactions for occupational exposures with increased risk for lung cancer not clear. Table S4. Gene-level significant occupational exposure interactions for occupational exposures with increased risk for lung cancer not clear. Table S5. Significant genomic regions for occupational exposure interactions and the significant genes identified in these regions. Table S6. Main categories of proteins coded by the significant genes identified by the gene-occupational interaction analyses.

Published
2023

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

Author

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

Abstract

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

Published
2023

29. Data from Effect of Occupational Exposures on Lung Cancer Susceptibility: A Study of Gene–Environment Interaction Analysis

Author

Paolo Boffetta, Vladimir Janout, Lenka Foretova, Isabelle Stücker, Valerie Gaborieau, Vladimir Bencko, Dana Mates, Eleonora Fabianova, Jolanta Lissowska, Peter Rudnai, Beata Świątkowska, Neonila Szeszenia-Dabrowska, David Zaridze, Paul Brennan, Samantha Sartori, and Jyoti Malhotra

Abstract

Background: Occupational exposures are known risk factors for lung cancer. Role of genetically determined host factors in occupational exposure–related lung cancer is unclear.Methods: We used genome-wide association (GWA) data from a case–control study conducted in 6 European countries from 1998 to 2002 to identify gene–occupation interactions and related pathways for lung cancer risk. GWA analysis was performed for each exposure using logistic regression and interaction term for genotypes, and exposure was included in this model. Both SNP-based and gene-based interaction P values were calculated. Pathway analysis was performed using three complementary methods, and analyses were adjusted for multiple comparisons. We analyzed 312,605 SNPs and occupational exposure to 70 agents from 1,802 lung cancer cases and 1,725 cancer-free controls.Results: Mean age of study participants was 60.1 ± 9.1 years and 75% were male. Largest number of significant associations (P ≤ 1 × 10−5) at SNP level was demonstrated for nickel, brick dust, concrete dust, and cement dust, and for brick dust and cement dust at the gene-level (P ≤ 1 × 10−4). Approximately 14 occupational exposures showed significant gene–occupation interactions with pathways related to response to environmental information processing via signal transduction (P < 0.001 and FDR < 0.05). Other pathways that showed significant enrichment were related to immune processes and xenobiotic metabolism.Conclusion: Our findings suggest that pathways related to signal transduction, immune process, and xenobiotic metabolism may be involved in occupational exposure–related lung carcinogenesis.Impact: Our study exemplifies an integrative approach using pathway-based analysis to demonstrate the role of genetic variants in occupational exposure–related lung cancer susceptibility. Cancer Epidemiol Biomarkers Prev; 24(3); 570–9. ©2015 AACR.

Published
2023

30. Supplementary Tables S1- S6 and Supplementary Figure S1 from A Novel Risk Locus at 6p21.3 for Epstein–Barr Virus-Positive Hodgkin Lymphoma

Author

James D. McKay, Ruth F. Jarrett, Henrik Hjalgrim, Anke van den Berg, Arjan Diepstra, Paul Brennan, Mads Melbye, Mark Lathrop, Silvia de Sanjosé, Eve Roman, Lambertus Kiemeney, Eric J. Duell, Lars J. Vatten, Pilar Galan, Pierluigi Cocco, Tracy Lightfoot, Ingrid Glimelius, Karin Ekstrom Smedby, Anthony Staines, Marc Maynadié, Lenka Foretova, Nikolaus Becker, Alexandra Nieters, Yolanda Benavente, Amelie Chabrier, Matthieu Foll, Rianne Veenstra, Valérie Gaborieau, Kevin Y. Urayama, and Manon Delahaye-Sourdeix

Abstract

Supplementary Table S1. Summary of results for rs6457715 in total classical Hodgkin lymphoma and subgroups. Supplementary Table S2. Regression analysis of EBV-positive cHL risk and rs6457715 genotype. Supplementary Table S3. Association between risk score comprising rs2734986, rs6904029, and rs6457715 and EBV+ Hodgkin lymphoma in the GWAS population. Supplementary Table S4. HLA-DPB1 significant eQTLs and their effect on EBV-positive cHL risk. Supplementary Table S5. Subjects included in the genome-wide association imputation analysis and independent replication of classical Hodgkin lymphoma. Supplementary Table S6. Concordance rates between HLA imputed and directly genotyped data across 334 UK and 284 Dutch individuals. Supplementary Figure S1. Association between genetic variants and HL and Epstein-Barr virus (EBV)-negative HL within an approximately 6.5 Mb region of the extended major histocompatibility complex located at 6p21.

Published
2023

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

Author

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

Abstract

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

Published
2023

32. Data from Can Lactase Persistence Genotype Be Used to Reassess the Relationship between Renal Cell Carcinoma and Milk Drinking? Potentials and Problems in the Application of Mendelian Randomization

Author

George Davey Smith, Roger M. Harbord, Paolo Boffetta, Nathaniel Rothman, Wong-Ho Chow, Vladimir Janout, Lenka Foretova, Vladimir Bencko, Dana Mates, Jolanta Lissowska, Neonilia Szeszenia-Dabrowska, Vsevolod Matveev, David Zaridze, Lee Moore, Valérie Gaborieau, Paul Brennan, and Nicholas J. Timpson

Abstract

Background: Increased risk of renal cell carcinoma (RCC) with milk consumption has been reported from observational studies. Whether this represents a causal association or is a result of confounding or bias is unclear. We assessed the potential for using genetic variation in lactase persistence as a tool for the study of this relationship.Methods: Using a large, hospital-based case-control study, we used observational, phenotypic, and genetic data to determine whether the MCM6 −13910 C/T(rs4988235) variant may be used as a nonconfounded and unbiased marker for milk consumption.Results: Consumption of milk during adulthood was associated with increased risk of RCC [odds ratio (OR), 1.35; 95% confidence interval (95% CI), 1.03-1.76; P = 0.03]. Among controls, consumption of milk was associated with the lactase persistence genotype at rs4988235 (OR, 2.39; 95% CI, 1.81-3.15; P = 6.9 × 10−10); however, the same genotype was not associated with RCC (OR, 1.01; 95% CI, 0.83-1.22; P = 0.9). In controls, milk consumption was associated with confounding factors, including smoking and educational attainment, whereas genotypes at rs4988235 showed negligible association with confounding factors.Conclusion: The absence of an association between the MCM6 genotype and RCC suggests that observational associations between milk consumption and RCC may be due to confounding or bias.Impact: Although these data suggest that associations between milk consumption and RCC may be spurious, if the association between genotype and behavioral exposure is weak, then the power of this test may be low. The nature of intermediate risk factor instrumentation is an important consideration in the undertaking and interpretation of this type of causal analysis experiment. Cancer Epidemiol Biomarkers Prev; 19(5); 1341–8. ©2010 AACR.

Published
2023

33. Supplementary Figures from BRCA2 Hypomorphic Missense Variants Confer Moderate Risks of Breast Cancer

Author

Fergus J. Couch, Maaike P.G. Vreeswijk, Aura Carreira, David E. Goldgar, Alvaro N.A. Monteiro, Harry Vrieling, Peter Devilee, Amanda Spurdle, Douglas F. Easton, Setareh Moghadasi, Liliana Varesco, Kathleen B.M. Claes, Florentia Fostira, Lenka Foretova, Logan Walker, Jennifer Leary, Ying Zheng, Wei Zheng, Jyh-Cherng Yu, Anna H. Wu, Robert Winqvist, Qin Wang, Lizet E. van der Kolk, Christi J. van Asperen, Thérèse Truong, Diana Torres, Ian Tomlinson, Soo H. Teo, Anthony Swerdlow, Daniel O. Stram, Melissa C. Southey, Susan Slager, Xiao-Ou Shu, Martha Shrubsole, Chen-Yang Shen, Mitul Shah, Caroline Seynaeve, Minouk J. Schoemaker, Marjanka K. Schmidt, Elinor J. Sawyer, Suleeporn Sangrajrang, Anja Rudolph, Valerie Rhenius, Muhammad Usman Rashid, Paolo Radice, Katri Pylkäs, Paul D.P. Pharoah, Julian Peto, Paolo Peterlongo, Ana Osorio, Jan J.C. Oosterwijk, Curtis Olswold, Janet E. Olson, Heli Nevanlinna, Susan L. Neuhausen, Kenneth Muir, Roger L. Milne, Kyriaki Michailidou, Hui Miao, Keitaro Matsuo, Frederik Marme, Sara Margolin, Arto Mannermaa, Eva Machackova, Jan Lubinski, Artitaya Lophatananon, Annika Lindblom, Jingmei Li, Loic Le Marchand, Diether Lambrechts, Kah-Nyin Lai, Vessela Kristensen, Veli-Matti Kosma, Daehee Kang, Anna Jakubowska, Hidemi Ito, John L. Hopper, Antoinette Hollestelle, Frans B. Hogervorst, Mikael Hartman, Ute Hamann, Per Hall, Christopher A. Haiman, Pascal Guénel, Gord Glendon, Graham G. Giles, Montserrat García-Closas, Henrik Flyger, Jonine Figueroa, Peter A. Fasching, Alison M. Dunning, Isabel dos-Santos-Silva, Thilo Dörk, Joe Dennis, Hatef Darabi, Kamila Czene, Simon S. Cross, Angela Cox, J. Margriet Collée, Ji-Yeob Choi, Ching-Yu Cheng, Georgia Chenevix-Trench, Jenny Chang-Claude, Barbara Burwinkel, Thomas Brüning, Barbara Brouwers, Annegien Broeks, Hermann Brenner, Paul Brennan, Hiltrud Brauch, Anne-Lise Borresen-Dale, Manjeet K. Bolla, Stig E. Bojesen, Natalia V. Bogdanova, Javier Benitez, Matthias W. Beckmann, Volker Arndt, Hoda Anton-Culver, Irene Andrulis, Kristiina Aittomäki, Cora M. Aalfs, Chunling Hu, Jenna Lilyquist, Jamie Hinton, Emily Hallberg, Huong Meeks, Fabienne M.G.R. Calléja, Charlotte Martin, Lucia Guidugli, Asa Ehlen, Catharina Von Nicolai, Romy L.S. Mesman, and Hermela Shimelis

Abstract

Figure S1: BCRA2 p.Y3035S Pedigrees. Figure S2: Western blot of ectopically expressed full-length wildtype and mutant hBRCA2 protein in VC8 DR-GFP cells subjected to HDR assay. Figure S3: Purification of wildtype and mutant BRCA2 from human cells. Figure S4: Position of BRCA2 DNA binding domain (DBD) variants on a ribbon diagram of the murine DBD crystal structure.

Published
2023

34. Supplementary Tables and References from BRCA2 Hypomorphic Missense Variants Confer Moderate Risks of Breast Cancer

Author

Fergus J. Couch, Maaike P.G. Vreeswijk, Aura Carreira, David E. Goldgar, Alvaro N.A. Monteiro, Harry Vrieling, Peter Devilee, Amanda Spurdle, Douglas F. Easton, Setareh Moghadasi, Liliana Varesco, Kathleen B.M. Claes, Florentia Fostira, Lenka Foretova, Logan Walker, Jennifer Leary, Ying Zheng, Wei Zheng, Jyh-Cherng Yu, Anna H. Wu, Robert Winqvist, Qin Wang, Lizet E. van der Kolk, Christi J. van Asperen, Thérèse Truong, Diana Torres, Ian Tomlinson, Soo H. Teo, Anthony Swerdlow, Daniel O. Stram, Melissa C. Southey, Susan Slager, Xiao-Ou Shu, Martha Shrubsole, Chen-Yang Shen, Mitul Shah, Caroline Seynaeve, Minouk J. Schoemaker, Marjanka K. Schmidt, Elinor J. Sawyer, Suleeporn Sangrajrang, Anja Rudolph, Valerie Rhenius, Muhammad Usman Rashid, Paolo Radice, Katri Pylkäs, Paul D.P. Pharoah, Julian Peto, Paolo Peterlongo, Ana Osorio, Jan J.C. Oosterwijk, Curtis Olswold, Janet E. Olson, Heli Nevanlinna, Susan L. Neuhausen, Kenneth Muir, Roger L. Milne, Kyriaki Michailidou, Hui Miao, Keitaro Matsuo, Frederik Marme, Sara Margolin, Arto Mannermaa, Eva Machackova, Jan Lubinski, Artitaya Lophatananon, Annika Lindblom, Jingmei Li, Loic Le Marchand, Diether Lambrechts, Kah-Nyin Lai, Vessela Kristensen, Veli-Matti Kosma, Daehee Kang, Anna Jakubowska, Hidemi Ito, John L. Hopper, Antoinette Hollestelle, Frans B. Hogervorst, Mikael Hartman, Ute Hamann, Per Hall, Christopher A. Haiman, Pascal Guénel, Gord Glendon, Graham G. Giles, Montserrat García-Closas, Henrik Flyger, Jonine Figueroa, Peter A. Fasching, Alison M. Dunning, Isabel dos-Santos-Silva, Thilo Dörk, Joe Dennis, Hatef Darabi, Kamila Czene, Simon S. Cross, Angela Cox, J. Margriet Collée, Ji-Yeob Choi, Ching-Yu Cheng, Georgia Chenevix-Trench, Jenny Chang-Claude, Barbara Burwinkel, Thomas Brüning, Barbara Brouwers, Annegien Broeks, Hermann Brenner, Paul Brennan, Hiltrud Brauch, Anne-Lise Borresen-Dale, Manjeet K. Bolla, Stig E. Bojesen, Natalia V. Bogdanova, Javier Benitez, Matthias W. Beckmann, Volker Arndt, Hoda Anton-Culver, Irene Andrulis, Kristiina Aittomäki, Cora M. Aalfs, Chunling Hu, Jenna Lilyquist, Jamie Hinton, Emily Hallberg, Huong Meeks, Fabienne M.G.R. Calléja, Charlotte Martin, Lucia Guidugli, Asa Ehlen, Catharina Von Nicolai, Romy L.S. Mesman, and Hermela Shimelis

Abstract

Table S1: Description of the BCAC studies contributing to COGS. Table S2: Predicted effects of BRCA1 and BRCA2 variants included in the iCOGS array on protein function. Table S3: Frequency of BRCA1 and BRCA2 variants from iCOGS in breast cancer cases and controls. Table S4: Family studies of Y3035S showing scores for each family by constant relative risk and 75% penetrance. Supplementary References.

Published
2023

35. Data from BRCA2 Hypomorphic Missense Variants Confer Moderate Risks of Breast Cancer

Author

Fergus J. Couch, Maaike P.G. Vreeswijk, Aura Carreira, David E. Goldgar, Alvaro N.A. Monteiro, Harry Vrieling, Peter Devilee, Amanda Spurdle, Douglas F. Easton, Setareh Moghadasi, Liliana Varesco, Kathleen B.M. Claes, Florentia Fostira, Lenka Foretova, Logan Walker, Jennifer Leary, Ying Zheng, Wei Zheng, Jyh-Cherng Yu, Anna H. Wu, Robert Winqvist, Qin Wang, Lizet E. van der Kolk, Christi J. van Asperen, Thérèse Truong, Diana Torres, Ian Tomlinson, Soo H. Teo, Anthony Swerdlow, Daniel O. Stram, Melissa C. Southey, Susan Slager, Xiao-Ou Shu, Martha Shrubsole, Chen-Yang Shen, Mitul Shah, Caroline Seynaeve, Minouk J. Schoemaker, Marjanka K. Schmidt, Elinor J. Sawyer, Suleeporn Sangrajrang, Anja Rudolph, Valerie Rhenius, Muhammad Usman Rashid, Paolo Radice, Katri Pylkäs, Paul D.P. Pharoah, Julian Peto, Paolo Peterlongo, Ana Osorio, Jan J.C. Oosterwijk, Curtis Olswold, Janet E. Olson, Heli Nevanlinna, Susan L. Neuhausen, Kenneth Muir, Roger L. Milne, Kyriaki Michailidou, Hui Miao, Keitaro Matsuo, Frederik Marme, Sara Margolin, Arto Mannermaa, Eva Machackova, Jan Lubinski, Artitaya Lophatananon, Annika Lindblom, Jingmei Li, Loic Le Marchand, Diether Lambrechts, Kah-Nyin Lai, Vessela Kristensen, Veli-Matti Kosma, Daehee Kang, Anna Jakubowska, Hidemi Ito, John L. Hopper, Antoinette Hollestelle, Frans B. Hogervorst, Mikael Hartman, Ute Hamann, Per Hall, Christopher A. Haiman, Pascal Guénel, Gord Glendon, Graham G. Giles, Montserrat García-Closas, Henrik Flyger, Jonine Figueroa, Peter A. Fasching, Alison M. Dunning, Isabel dos-Santos-Silva, Thilo Dörk, Joe Dennis, Hatef Darabi, Kamila Czene, Simon S. Cross, Angela Cox, J. Margriet Collée, Ji-Yeob Choi, Ching-Yu Cheng, Georgia Chenevix-Trench, Jenny Chang-Claude, Barbara Burwinkel, Thomas Brüning, Barbara Brouwers, Annegien Broeks, Hermann Brenner, Paul Brennan, Hiltrud Brauch, Anne-Lise Borresen-Dale, Manjeet K. Bolla, Stig E. Bojesen, Natalia V. Bogdanova, Javier Benitez, Matthias W. Beckmann, Volker Arndt, Hoda Anton-Culver, Irene Andrulis, Kristiina Aittomäki, Cora M. Aalfs, Chunling Hu, Jenna Lilyquist, Jamie Hinton, Emily Hallberg, Huong Meeks, Fabienne M.G.R. Calléja, Charlotte Martin, Lucia Guidugli, Asa Ehlen, Catharina Von Nicolai, Romy L.S. Mesman, and Hermela Shimelis

Abstract

Breast cancer risks conferred by many germline missense variants in the BRCA1 and BRCA2 genes, often referred to as variants of uncertain significance (VUS), have not been established. In this study, associations between 19 BRCA1 and 33 BRCA2 missense substitution variants and breast cancer risk were investigated through a breast cancer case–control study using genotyping data from 38 studies of predominantly European ancestry (41,890 cases and 41,607 controls) and nine studies of Asian ancestry (6,269 cases and 6,624 controls). The BRCA2 c.9104A>C, p.Tyr3035Ser (OR = 2.52; P = 0.04), and BRCA1 c.5096G>A, p.Arg1699Gln (OR = 4.29; P = 0.009) variant were associated with moderately increased risks of breast cancer among Europeans, whereas BRCA2 c.7522G>A, p.Gly2508Ser (OR = 2.68; P = 0.004), and c.8187G>T, p.Lys2729Asn (OR = 1.4; P = 0.004) were associated with moderate and low risks of breast cancer among Asians. Functional characterization of the BRCA2 variants using four quantitative assays showed reduced BRCA2 activity for p.Tyr3035Ser compared with wild-type. Overall, our results show how BRCA2 missense variants that influence protein function can confer clinically relevant, moderately increased risks of breast cancer, with potential implications for risk management guidelines in women with these specific variants. Cancer Res; 77(11); 2789–99. ©2017 AACR.

Published
2023

36. Supplementary Table 1 from Can Lactase Persistence Genotype Be Used to Reassess the Relationship between Renal Cell Carcinoma and Milk Drinking? Potentials and Problems in the Application of Mendelian Randomization

Author

George Davey Smith, Roger M. Harbord, Paolo Boffetta, Nathaniel Rothman, Wong-Ho Chow, Vladimir Janout, Lenka Foretova, Vladimir Bencko, Dana Mates, Jolanta Lissowska, Neonilia Szeszenia-Dabrowska, Vsevolod Matveev, David Zaridze, Lee Moore, Valérie Gaborieau, Paul Brennan, and Nicholas J. Timpson

Abstract

Supplementary Table 1 from Can Lactase Persistence Genotype Be Used to Reassess the Relationship between Renal Cell Carcinoma and Milk Drinking? Potentials and Problems in the Application of Mendelian Randomization

Published
2023

37. Data from A Novel Risk Locus at 6p21.3 for Epstein–Barr Virus-Positive Hodgkin Lymphoma

Author

James D. McKay, Ruth F. Jarrett, Henrik Hjalgrim, Anke van den Berg, Arjan Diepstra, Paul Brennan, Mads Melbye, Mark Lathrop, Silvia de Sanjosé, Eve Roman, Lambertus Kiemeney, Eric J. Duell, Lars J. Vatten, Pilar Galan, Pierluigi Cocco, Tracy Lightfoot, Ingrid Glimelius, Karin Ekstrom Smedby, Anthony Staines, Marc Maynadié, Lenka Foretova, Nikolaus Becker, Alexandra Nieters, Yolanda Benavente, Amelie Chabrier, Matthieu Foll, Rianne Veenstra, Valérie Gaborieau, Kevin Y. Urayama, and Manon Delahaye-Sourdeix

Abstract

Background: A proportion of the genetic variants involved in susceptibility to Hodgkin lymphoma differ by the tumor's Epstein–Barr virus (EBV) status, particularly within the MHC region.Methods: We have conducted an SNP imputation study of the MHC region, considering tumor EBV status in 1,200 classical Hodgkin lymphoma (cHL) cases and 5,726 control subjects of European origin. Notable findings were genotyped in an independent study population of 468 cHL cases and 551 controls.Results: We identified and subsequently replicated a novel association between a common genetic variant rs6457715 and cHL. Although strongly associated with EBV-positive cHL [OR, 2.33; 95% confidence interval (CI), 1.83–2.97; P = 7 × 10–12], there was little evidence for association between rs6457715 and the EBV-negative subgroup of cHL (OR, 1.06; 95% CI, 0.92–1.21), indicating that this association was specific to the EBV-positive subgroup (Phet < P = 10−8). Furthermore, the association was limited to EBV-positive cHL subgroups within mixed cell (MCHL) and nodular sclerosis subtypes (NSHL), suggesting that the association is independent of histologic subtype of cHL.Conclusions: rs6457715, located near the HLA-DPB1 gene, is associated with EBV-positive cHL and suggests this region as a novel susceptibility locus for cHL.Impact: This expands the number of genetic variants that are associated with cHL and provides additional evidence for a critical and specific role of EBV in the etiology of this disease. Cancer Epidemiol Biomarkers Prev; 24(12); 1838–43. ©2015 AACR.

Published
2023

38. Data from A Sex-Specific Association between a 15q25 Variant and Upper Aerodigestive Tract Cancers

Author

James D. McKay, Paul Brennan, Paolo Boffetta, Richard B. Hayes, Mia Hashibe, Stefania Boccia, Leticia Fernandez, José Eluf-Neto, Victor Wünsch-Filho, Ana Menezes, Sergio Koifman, Maria Paula Curado, Vladimir Janout, Lenka Foretova, Vladimir Bencko, Alexandru Bucur, Eleonora Fabianova, Jolanta Lissowska, Neonila Szeszenia-Dabrowska, David Zaridze, Wolfgang Ahrens, Claire M. Healy, Ariana Znaor, David I. Conway, Nalin S. Thakker, Cristina Canova, Luigi Barzan, Tatiana V. Macfarlane, Xavier Castellsagué, Antonio Agudo, Kristina Kjaerheim, Lorenzo Richiardi, Ivana Holcátová, Pagona Lagiou, Simone Benhamou, Chu Chen, Stephen M. Schwartz, Renyi Wang, Shen-Chih Chang, Zuo-Feng Zhang, Erich M. Sturgis, Qingyi Wei, Philip Lazarus, Joshua E. Muscat, Marcin Lener, Joanna Trubicka, Jan Lubiński, Wilbert H. M. Peters, Johannes J. Manni, Martin Lacko, Michael D. McClean, Brock Christensen, Karl T. Kelsey, Renato Talamini, Rolando Herrero, Silvia Franceschi, Tomoko Nukui, Shama Buch, Marjorie Romkes, Jingchun Luo, Mark C. Weissler, Andrew F. Olshan, Shu-chun Chuang, Amelie Chabrier, Graham Byrnes, Valerie Gaborieau, Therese Truong, and Dan Chen

Abstract

Background: Sequence variants located at 15q25 have been associated with lung cancer and propensity to smoke. We recently reported an association between rs16969968 and risk of upper aerodigestive tract (UADT) cancers (oral cavity, oropharynx, hypopharynx, larynx, and esophagus) in women (OR = 1.24, P = 0.003) with little effect in men (OR = 1.04, P = 0.35).Methods: In a coordinated genotyping study within the International Head and Neck Cancer Epidemiology (INHANCE) consortium, we have sought to replicate these findings in an additional 4,604 cases and 6,239 controls from 10 independent UADT cancer case–control studies.Results: rs16969968 was again associated with UADT cancers in women (OR = 1.21, 95% CI = 1.08–1.36, P = 0.001) and a similar lack of observed effect in men [OR = 1.02, 95% CI = 0.95–1.09, P = 0.66; P-heterogeneity (Phet) = 0.01]. In a pooled analysis of the original and current studies, totaling 8,572 UADT cancer cases and 11,558 controls, the association was observed among females (OR = 1.22, 95% CI = 1.12–1.34, P = 7 × 10−6) but not males (OR = 1.02, 95% CI = 0.97–1.08, P = 0.35; Phet = 6 × 10−4). There was little evidence for a sexdifference in the association between this variant and cigarettes smoked per day, with male and female rs16969968 variant carriers smoking approximately the same amount more in the 11,991 ever smokers in the pooled analysis of the 14 studies (Phet = 0.86).Conclusions: This study has confirmed a sex difference in the association between the 15q25 variant rs16969968 and UADT cancers.Impact: Further research is warranted to elucidate the mechanisms underlying these observations. Cancer Epidemiol Biomarkers Prev; 20(4); 658–64. ©2011 AACR.

Published
2023

39. Supplementary Table 2 from No Causal Association Identified for Human Papillomavirus Infections in Lung Cancer

Author

Paul Brennan, Massimo Tommasino, Ghislaine Scelo, Michael Pawlita, Mattias Johansson, Elisabete Weiderpass, Françoise Clavel-Chapelon, Anastasia Kotanidou, H. Bas Bueno-de-Mesquita, Vittorio Krogh, Mikael Johansson, J. Ramón Quirós, Heiner Boeing, Ruth C. Travis, Anne Tjønneland, Eleonora Fabianova, Peter Rudnai, Vladimir Bencko, Lenka Foretova, Vladimir Janout, Dana Mates, Jolanta Lissowska, Neonila Szeszenia-Dabrowska, Anush Mukeria, David Zaridze, Sandrine McKay-Chopin, Behnoush Abedi-Ardekani, Christine Carreira, Gordana Halec, Tim Waterboer, Tarik Gheit, and Devasena Anantharaman

Abstract

PDF file - 67KB, Antibodies to type-specific HPV proteins and the risk of lung cancer.

Published
2023

40. Data from No Causal Association Identified for Human Papillomavirus Infections in Lung Cancer

Author

Paul Brennan, Massimo Tommasino, Ghislaine Scelo, Michael Pawlita, Mattias Johansson, Elisabete Weiderpass, Françoise Clavel-Chapelon, Anastasia Kotanidou, H. Bas Bueno-de-Mesquita, Vittorio Krogh, Mikael Johansson, J. Ramón Quirós, Heiner Boeing, Ruth C. Travis, Anne Tjønneland, Eleonora Fabianova, Peter Rudnai, Vladimir Bencko, Lenka Foretova, Vladimir Janout, Dana Mates, Jolanta Lissowska, Neonila Szeszenia-Dabrowska, Anush Mukeria, David Zaridze, Sandrine McKay-Chopin, Behnoush Abedi-Ardekani, Christine Carreira, Gordana Halec, Tim Waterboer, Tarik Gheit, and Devasena Anantharaman

Abstract

Human papillomavirus (HPV) infections have been implicated in lung carcinogenesis, but causal associations remain uncertain. We evaluated a potential causal role for HPV infections in lung cancer through an analysis involving serology, tumor DNA, RNA, and p16 protein expression. Association between type-specific HPV antibodies and risk of lung cancer was examined among 3,083 cases and 4,328 controls in two case–control studies (retrospective) and one nested case–control study (prospective design). Three hundred and thirty-four available tumors were subjected to pathologic evaluation and subsequent HPV genotyping following stringent conditions to detect all high-risk and two low-risk HPV types. All HPV DNA-positive tumors were further tested for the expression of p16 protein and type-specific HPV mRNA. On the basis of the consistency of the results, although HPV11 and HPV31 E6 antibodies were associated with lung cancer risk in the retrospective study, no association was observed in the prospective design. Presence of type-specific antibodies correlated poorly with the presence of the corresponding HPV DNA in the tumor. Although nearly 10% of the lung tumors were positive for any HPV DNA (7% for HPV16 DNA), none expressed the viral oncogenes. No association was observed between HPV antibodies or DNA and lung cancer survival. In conclusion, we found no supportive evidence for the hypothesized causal association between HPV infections and lung cancer. Cancer Res; 74(13); 3525–34. ©2014 AACR.

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2023

41. Supplementary Table 1 from No Causal Association Identified for Human Papillomavirus Infections in Lung Cancer

Author

Paul Brennan, Massimo Tommasino, Ghislaine Scelo, Michael Pawlita, Mattias Johansson, Elisabete Weiderpass, Françoise Clavel-Chapelon, Anastasia Kotanidou, H. Bas Bueno-de-Mesquita, Vittorio Krogh, Mikael Johansson, J. Ramón Quirós, Heiner Boeing, Ruth C. Travis, Anne Tjønneland, Eleonora Fabianova, Peter Rudnai, Vladimir Bencko, Lenka Foretova, Vladimir Janout, Dana Mates, Jolanta Lissowska, Neonila Szeszenia-Dabrowska, Anush Mukeria, David Zaridze, Sandrine McKay-Chopin, Behnoush Abedi-Ardekani, Christine Carreira, Gordana Halec, Tim Waterboer, Tarik Gheit, and Devasena Anantharaman

Abstract

PDF file - 55KB, Association between type-specific HPV antibodies and risk of lung cancer by seropositivity threshold.

Published
2023

42. Supplementary Table 3 from No Causal Association Identified for Human Papillomavirus Infections in Lung Cancer

Author

Paul Brennan, Massimo Tommasino, Ghislaine Scelo, Michael Pawlita, Mattias Johansson, Elisabete Weiderpass, Françoise Clavel-Chapelon, Anastasia Kotanidou, H. Bas Bueno-de-Mesquita, Vittorio Krogh, Mikael Johansson, J. Ramón Quirós, Heiner Boeing, Ruth C. Travis, Anne Tjønneland, Eleonora Fabianova, Peter Rudnai, Vladimir Bencko, Lenka Foretova, Vladimir Janout, Dana Mates, Jolanta Lissowska, Neonila Szeszenia-Dabrowska, Anush Mukeria, David Zaridze, Sandrine McKay-Chopin, Behnoush Abedi-Ardekani, Christine Carreira, Gordana Halec, Tim Waterboer, Tarik Gheit, and Devasena Anantharaman

Abstract

PDF file - 52KB, Comparison of HPV16 DNA positivity by sex, smoking status and lung histology.

Published
2023

43. Supplementary Methods, Tables 1-3, Figure 1 from Common Breast Cancer Susceptibility Alleles and the Risk of Breast Cancer for BRCA1 and BRCA2 Mutation Carriers: Implications for Risk Prediction

Author

Douglas F. Easton, Georgia Chenevix-Trench, Radka Platte, Xiaoqing Chen, Helene Holland, Amanda B. Spurdle, Jacques Simard, Heli Nevanlinna, Kristiina Aittomäki, Miguel de la Hoya, Trinidad Caldes, Ines Schönbuchner, Karin Kast, Sabine Preisler-Adams, Dorothea Gadzicki, Helmut Deissler, Christian Sutter, Dieter Niederacher, Raymonda Varon-Mateeva, Simone Heidemann, Norbert Arnold, Magdalena Lochmann, Alfons Meindl, Christoph Engel, Barbara Wappenschmidt, Rita Schmutzler, Jenny Gross, Beth Y. Karlan, Lara Sucheston, Susan J. Ramus, Conxi Lazaro, Ignacio Blanco, Laima Tihomirova, Evgeny Imyanitov, Cinzia Casella, Marco Montagna, Amanda Ewart Toland, Stephanie V. Blank, Peter E. Schwartz, Jack Basil, John F. Boggess, Katie Wakeley, Gustavo C. Rodriguez, Marion Piedmonte, Ana Dutra-Clarke, Vincent Devlin, Kenneth Offit, Tomas Kirchhoff, Bjarni A. Agnarsson, Lars Jønson, Thomas V.O. Hansen, Georg Pfeiler, Daphne Gschwantler-Kaulich, Anne Catharina Dressler, Christian F. Singer, David Goldgar, Alexander Miron, Yosuf Yassin, Saundra S. Buys, Esther M. John, Mary B. Terry, Mary B. Daly, John L. Hopper, Laurence Vénat-Bouvet, Marc Frénay, Catherine Nogues, Etienne Rouleau, Hagay Sobol, Tetsuro Noguchi, Catherine Loustalot, Laurence Faivre, Pascaline Berthet, Agnès Hardouin, Dominique Leroux, Hélène Dreyfus, Christine Lasset, Valérie Bonadona, Sylvie Mazoyer, Antoine de Pauw, Dominique Stoppa-Lyonnet, Andrew K. Godwin, Susan Peock, Huw Dorkins, M. John Kennedy, Lisa Walker, Mary E. Porteous, Patrick J. Morrison, Shirley Hodgson, Joan Paterson, Jackie Cook, Trevor Cole, Rosemarie Davidson, Gabriella Pichert, Fiona Lalloo, D. Gareth Evans, Don Conroy, Debra Frost, Clare Oliver, Margaret Cook, Matti Rookus, Frans Hogervorst, Cora M. Aalfs, Marinus J. Blok, E.J. Meijers-Heijboer, Peter Devilee, Christi J. van Asperen, Rob B. van der Luijt, Nicoline Hoogerbrugge, Mieke Kriege, Ute Hamann, Javier Benitez, Javier Godino, Maria-Isabel Tejada, Mercedes Durán, Adriana Lasa, Ana Osorio, Tomasz Huzarski, Jan Lubinski, Ania Jakubowska, Susan Domchek, Kate Nathanson, Beatrice Melin, Marie Stenmark-Askmalm, Johanna Rantala, Annika Lindblom, Helena Jernström, Ake Borg, Shimrit Cohen, Maya Dubrovsky, Roni Milgrom, Yael Laitman, Bella Kaufman, Eitan Friedman, Maria Caligo, Uffe Birk Jensen, Dorthe Cruger, Lone Sunde, Anne-Marie Gerdes, Mads Thomassen, Irene L. Andrulis, Hilmi Ozcelik, Gord Glendon, Flavio Lejbkowicz, Gad Rennert, Mark H. Greene, Phuong L. Mai, Lenka Foretova, Bruce Poppe, Kathleen Claes, Michal Zikan, Csilla I. Szabo, Paolo Peterlongo, Valentina Dall'Olio, Anna Allavena, Alessandra Viel, Monica Barile, Daniela Zaffaroni, Bernard Peissel, Siranoush Manoukian, Paolo Radice, Vernon S. Pankratz, Noralane M. Lindor, Xianshu Wang, Fergus J. Couch, Olufunmilayo I. Olopade, Gail Tomlinson, Patricia A. Ganz, Claudine Isaacs, Henry T. Lynch, Jeffrey N. Weitzel, Timothy R. Rebbeck, Yuan Chun Ding, Susan L. Neuhausen, Sue Healey, Olga M. Sinilnikova, Lesley McGuffog, Jonathan Beesley, and Antonis C. Antoniou

Abstract

Supplementary Methods, Tables 1-3, Figure 1 from Common Breast Cancer Susceptibility Alleles and the Risk of Breast Cancer for BRCA1 and BRCA2 Mutation Carriers: Implications for Risk Prediction

Published
2023

44. Functional mechanisms underlying pleiotropic risk alleles at the 19p13.1 breast–ovarian cancer susceptibility locus

Author

Kate Lawrenson, Siddhartha Kar, Karen McCue, Karoline Kuchenbaeker, Kyriaki Michailidou, Jonathan Tyrer, Jonathan Beesley, Susan J. Ramus, Qiyuan Li, Melissa K. Delgado, Janet M. Lee, Kristiina Aittomäki, Irene L. Andrulis, Hoda Anton-Culver, Volker Arndt, Banu K. Arun, Brita Arver, Elisa V. Bandera, Monica Barile, Rosa B. Barkardottir, Daniel Barrowdale, Matthias W. Beckmann, Javier Benitez, Andrew Berchuck, Maria Bisogna, Line Bjorge, Carl Blomqvist, William Blot, Natalia Bogdanova, Anders Bojesen, Stig E. Bojesen, Manjeet K. Bolla, Bernardo Bonanni, Anne-Lise Børresen-Dale, Hiltrud Brauch, Paul Brennan, Hermann Brenner, Fiona Bruinsma, Joan Brunet, Shaik Ahmad Buhari, Barbara Burwinkel, Ralf Butzow, Saundra S. Buys, Qiuyin Cai, Trinidad Caldes, Ian Campbell, Rikki Canniotto, Jenny Chang-Claude, Jocelyne Chiquette, Ji-Yeob Choi, Kathleen B. M. Claes, GEMO Study Collaborators, Linda S. Cook, Angela Cox, Daniel W. Cramer, Simon S. Cross, Cezary Cybulski, Kamila Czene, Mary B. Daly, Francesca Damiola, Agnieszka Dansonka-Mieszkowska, Hatef Darabi, Joe Dennis, Peter Devilee, Orland Diez, Jennifer A. Doherty, Susan M. Domchek, Cecilia M. Dorfling, Thilo Dörk, Martine Dumont, Hans Ehrencrona, Bent Ejlertsen, Steve Ellis, EMBRACE, Christoph Engel, Eunjung Lee, D. Gareth Evans, Peter A. Fasching, Lidia Feliubadalo, Jonine Figueroa, Dieter Flesch-Janys, Olivia Fletcher, Henrik Flyger, Lenka Foretova, Florentia Fostira, William D. Foulkes, Brooke L. Fridley, Eitan Friedman, Debra Frost, Gaetana Gambino, Patricia A. Ganz, Judy Garber, Montserrat García-Closas, Aleksandra Gentry-Maharaj, Maya Ghoussaini, Graham G. Giles, Rosalind Glasspool, Andrew K. Godwin, Mark S. Goldberg, David E. Goldgar, Anna González-Neira, Ellen L. Goode, Marc T. Goodman, Mark H. Greene, Jacek Gronwald, Pascal Guénel, Christopher A. Haiman, Per Hall, Emily Hallberg, Ute Hamann, Thomas V. O. Hansen, Patricia A. Harrington, Mikael Hartman, Norhashimah Hassan, Sue Healey, The Hereditary Breast and Ovarian Cancer Research Group Netherlands (HEBON), Florian Heitz, Josef Herzog, Estrid Høgdall, Claus K. Høgdall, Frans B. L. Hogervorst, Antoinette Hollestelle, John L. Hopper, Peter J. Hulick, Tomasz Huzarski, Evgeny N. Imyanitov, KConFab Investigators, Australian Ovarian Cancer Study Group, Claudine Isaacs, Hidemi Ito, Anna Jakubowska, Ramunas Janavicius, Allan Jensen, Esther M. John, Nichola Johnson, Maria Kabisch, Daehee Kang, Miroslav Kapuscinski, Beth Y. Karlan, Sofia Khan, Lambertus A. Kiemeney, Susanne Kruger Kjaer, Julia A. Knight, Irene Konstantopoulou, Veli-Matti Kosma, Vessela Kristensen, Jolanta Kupryjanczyk, Ava Kwong, Miguel de la Hoya, Yael Laitman, Diether Lambrechts, Nhu Le, Kim De Leeneer, Jenny Lester, Douglas A. Levine, Jingmei Li, Annika Lindblom, Jirong Long, Artitaya Lophatananon, Jennifer T. Loud, Karen Lu, Jan Lubinski, Arto Mannermaa, Siranoush Manoukian, Loic Le Marchand, Sara Margolin, Frederik Marme, Leon F. A. G. Massuger, Keitaro Matsuo, Sylvie Mazoyer, Lesley McGuffog, Catriona McLean, Iain McNeish, Alfons Meindl, Usha Menon, Arjen R. Mensenkamp, Roger L. Milne, Marco Montagna, Kirsten B. Moysich, Kenneth Muir, Anna Marie Mulligan, Katherine L. Nathanson, Roberta B. Ness, Susan L. Neuhausen, Heli Nevanlinna, Silje Nord, Robert L. Nussbaum, Kunle Odunsi, Kenneth Offit, Edith Olah, Olufunmilayo I. Olopade, Janet E. Olson, Curtis Olswold, David O’Malley, Irene Orlow, Nick Orr, Ana Osorio, Sue Kyung Park, Celeste L. Pearce, Tanja Pejovic, Paolo Peterlongo, Georg Pfeiler, Catherine M. Phelan, Elizabeth M. Poole, Katri Pylkäs, Paolo Radice, Johanna Rantala, Muhammad Usman Rashid, Gad Rennert, Valerie Rhenius, Kerstin Rhiem, Harvey A. Risch, Gus Rodriguez, Mary Anne Rossing, Anja Rudolph, Helga B. Salvesen, Suleeporn Sangrajrang, Elinor J. Sawyer, Joellen M. Schildkraut, Marjanka K. Schmidt, Rita K. Schmutzler, Thomas A. Sellers, Caroline Seynaeve, Mitul Shah, Chen-Yang Shen, Xiao-Ou Shu, Weiva Sieh, Christian F. Singer, Olga M. Sinilnikova, Susan Slager, Honglin Song, Penny Soucy, Melissa C. Southey, Marie Stenmark-Askmalm, Dominique Stoppa-Lyonnet, Christian Sutter, Anthony Swerdlow, Sandrine Tchatchou, Manuel R. Teixeira, Soo H. Teo, Kathryn L. Terry, Mary Beth Terry, Mads Thomassen, Maria Grazia Tibiletti, Laima Tihomirova, Silvia Tognazzo, Amanda Ewart Toland, Ian Tomlinson, Diana Torres, Thérèse Truong, Chiu-chen Tseng, Nadine Tung, Shelley S. Tworoger, Celine Vachon, Ans M. W. van den Ouweland, Helena C. van Doorn, Elizabeth J. van Rensburg, Laura J. Van't Veer, Adriaan Vanderstichele, Ignace Vergote, Joseph Vijai, Qin Wang, Shan Wang-Gohrke, Jeffrey N. Weitzel, Nicolas Wentzensen, Alice S. Whittemore, Hans Wildiers, Robert Winqvist, Anna H. Wu, Drakoulis Yannoukakos, Sook-Yee Yoon, Jyh-Cherng Yu, Wei Zheng, Ying Zheng, Kum Kum Khanna, Jacques Simard, Alvaro N. Monteiro, Juliet D. French, Fergus J. Couch, Matthew L. Freedman, Douglas F. Easton, Alison M. Dunning, Paul D. Pharoah, Stacey L. Edwards, Georgia Chenevix-Trench, Antonis C. Antoniou, and Simon A. Gayther

Subjects
Science
Abstract

A region on chromosome 19p13 is associated with the risk of developing ovarian and breast cancer. Here, the authors genotyped SNPs in this region in thousands of breast and ovarian cancer patients and identified SNPs associated with three genes, which were analysed with functional studies.

Published
2016
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45. Meta-analysis of genome-wide association studies discovers multiple loci for chronic lymphocytic leukemia

Author

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

Subjects
Science
Abstract

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

Published
2016
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46. Identification of Germline Mutations in Melanoma Patients with Early Onset, Double Primary Tumors, or Family Cancer History by NGS Analysis of 217 Genes

Author

Lenka Stolarova, Sandra Jelinkova, Radka Storchova, Eva Machackova, Petra Zemankova, Michal Vocka, Ondrej Kodet, Jan Kral, Marta Cerna, Zuzana Volkova, Marketa Janatova, Jana Soukupova, Viktor Stranecky, Pavel Dundr, Lenka Foretova, Libor Macurek, Petra Kleiblova, and Zdenek Kleibl

Subjects
melanoma, familial melanoma, hereditary cancer predisposition, germline mutations, panel sequencing, NGS, Biology (General), QH301-705.5
Abstract

Cutaneous melanoma is the deadliest skin malignity with a rising prevalence worldwide. Patients carrying germline mutations in melanoma-susceptibility genes face an increased risk of melanoma and other cancers. To assess the spectrum of germline variants, we analyzed 264 Czech melanoma patients indicated for testing due to early melanoma (at POT1 and CHEK2 variants were characterized by functional assays. Mutations in clinically relevant genes were significantly more frequent in melanoma patients than in controls (31/264; 11.7% vs. 58/1479; 3.9%; p = 2.0 × 10−6). A total of 9 patients (3.4%) carried mutations in high-to-moderate melanoma risk genes (CDKN2A, POT1, ACD) and 22 (8.3%) patients in other cancer syndrome genes (NBN, BRCA1/2, CHEK2, ATM, WRN, RB1). Mutations in high-to-moderate melanoma risk genes (OR = 52.2; 95%CI 6.6–413.1; p = 3.2 × 10−7) and in other cancer syndrome genes (OR = 2.3; 95%CI 1.4–3.8; p = 0.003) were significantly associated with melanoma risk. We found an increased potential to carry these mutations (OR = 2.9; 95%CI 1.2–6.8) in patients with double primary melanoma, melanoma and other primary cancer, but not in patients with early age at onset. The analysis revealed affected genes in Czech melanoma patients and identified individuals who may benefit from genetic testing and future surveillance management of mutation carriers.

Published
2020
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47. Lung cancer and socioeconomic status in a pooled analysis of case-control studies.

Author

Jan Hovanec, Jack Siemiatycki, David I Conway, Ann Olsson, Isabelle Stücker, Florence Guida, Karl-Heinz Jöckel, Hermann Pohlabeln, Wolfgang Ahrens, Irene Brüske, Heinz-Erich Wichmann, Per Gustavsson, Dario Consonni, Franco Merletti, Lorenzo Richiardi, Lorenzo Simonato, Cristina Fortes, Marie-Elise Parent, John McLaughlin, Paul Demers, Maria Teresa Landi, Neil Caporaso, Adonina Tardón, David Zaridze, Neonila Szeszenia-Dabrowska, Peter Rudnai, Jolanta Lissowska, Eleonora Fabianova, John Field, Rodica Stanescu Dumitru, Vladimir Bencko, Lenka Foretova, Vladimir Janout, Hans Kromhout, Roel Vermeulen, Paolo Boffetta, Kurt Straif, Joachim Schüz, Benjamin Kendzia, Beate Pesch, Thomas Brüning, and Thomas Behrens

Subjects
Medicine, Science
Abstract

An association between low socioeconomic status (SES) and lung cancer has been observed in several studies, but often without adequate control for smoking behavior. We studied the association between lung cancer and occupationally derived SES, using data from the international pooled SYNERGY study.Twelve case-control studies from Europe and Canada were included in the analysis. Based on occupational histories of study participants we measured SES using the International Socio-Economic Index of Occupational Status (ISEI) and the European Socio-economic Classification (ESeC). We divided the ISEI range into categories, using various criteria. Stratifying by gender, we calculated odds ratios (OR) and 95% confidence intervals (CI) by unconditional logistic regression, adjusting for age, study, and smoking behavior. We conducted analyses by histological subtypes of lung cancer and subgroup analyses by study region, birth cohort, education and occupational exposure to known lung carcinogens.The analysis dataset included 17,021 cases and 20,885 controls. There was a strong elevated OR between lung cancer and low SES, which was attenuated substantially after adjustment for smoking, however a social gradient persisted. SES differences in lung cancer risk were higher among men (lowest vs. highest SES category: ISEI OR 1.84 (95% CI 1.61-2.09); ESeC OR 1.53 (95% CI 1.44-1.63)), than among women (lowest vs. highest SES category: ISEI OR 1.54 (95% CI 1.20-1.98); ESeC OR 1.34 (95% CI 1.19-1.52)).SES remained a risk factor for lung cancer after adjustment for smoking behavior.

Published
2018
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48. Validation of CZECANCA (CZEch CAncer paNel for Clinical Application) for targeted NGS-based analysis of hereditary cancer syndromes.

Author

Jana Soukupova, Petra Zemankova, Klara Lhotova, Marketa Janatova, Marianna Borecka, Lenka Stolarova, Filip Lhota, Lenka Foretova, Eva Machackova, Viktor Stranecky, Spiros Tavandzis, Petra Kleiblova, Michal Vocka, Hana Hartmannova, Katerina Hodanova, Stanislav Kmoch, and Zdenek Kleibl

Subjects
Medicine, Science
Abstract

Carriers of mutations in hereditary cancer predisposition genes represent a small but clinically important subgroup of oncology patients. The identification of causal germline mutations determines follow-up management, treatment options and genetic counselling in patients' families. Targeted next-generation sequencing-based analyses using cancer-specific panels in high-risk individuals have been rapidly adopted by diagnostic laboratories. While the use of diagnosis-specific panels is straightforward in typical cases, individuals with unusual phenotypes from families with overlapping criteria require multiple panel testing. Moreover, narrow gene panels are limited by our currently incomplete knowledge about possible genetic dispositions.We have designed a multi-gene panel called CZECANCA (CZEch CAncer paNel for Clinical Application) for a sequencing analysis of 219 cancer-susceptibility and candidate predisposition genes associated with frequent hereditary cancers.The bioanalytical and bioinformatics pipeline was validated on a set of internal and commercially available DNA controls showing high coverage uniformity, sensitivity, specificity and accuracy. The panel demonstrates a reliable detection of both single nucleotide and copy number variants. Inter-laboratory, intra- and inter-run replicates confirmed the robustness of our approach.The objective of CZECANCA is a nationwide consolidation of cancer-predisposition genetic testing across various clinical indications with savings in costs, human labor and turnaround time. Moreover, the unified diagnostics will enable the integration and analysis of genotypes with associated phenotypes in a national database improving the clinical interpretation of variants.

Published
2018
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49. Lung cancer among coal miners, ore miners and quarrymen: smoking-adjusted risk estimates from the synergy pooled analysis of case–control studies

Author

Dirk Taeger, Beate Pesch, Benjamin Kendzia, Thomas Behrens, Karl-Heinz Jöckel, Dirk Dahmann, Jack Siemiatycki, Hans Kromhout, Roel Vermeulen, Susan Peters, Ann Olsson, Irene Brüske, Heinz-Erich Wichmann, Isabelle Stücker, Florence Guida, Adonina Tardón, Franco Merletti, Dario Mirabelli, Lorenzo Richiardi, Hermann Pohlabeln, Wolfgang Ahrens, Maria Teresa Landi, Neil Caporaso, Angela Cecilia Pesatori, Anush Mukeriya, Neonila Szeszenia-Dabrowska, Jolanta Lissowska, Per Gustavsson, John Field, Michael W Marcus, Eleonora Fabianova, Andrea ’t Mannetje, Neil Pearce, Peter Rudnai, Vladimir Bencko, Vladimir Janout, ­Rodica Stanescu Dumitru, Lenka Foretova, Francesco Forastiere, John McLaughlin, Paul Demers Paul Demers, Bas Bueno-de-Mesquita, Joachim Schüz, Kurt Straif, and Thomas Brüning

Subjects
coal mining, histological subtype, ore mining, ore miner, cancer, smoking, lung cancer, mining, risk estimate, population-based study, coal miner, case–control study, pooled analysis, quarrymen, Public aspects of medicine, RA1-1270
Abstract

OBJECTIVES: Working in mines and quarries has been associated with an elevated lung cancer risk but with inconsistent results for coal miners. This study aimed to estimate the smoking-adjusted lung cancer risk among coal miners and compare the risk pattern with lung cancer risks among ore miners and quarrymen. METHODS: We estimated lung cancer risks of coal and ore miners and quarrymen among 14 251 lung cancer cases and 17 267 controls from the SYNERGY pooled case–control study, controlling for smoking and employment in other at-risk occupations. RESULTS: Ever working as miner or quarryman (690 cases, 436 controls) was associated with an elevated odds ratio (OR) of 1.55 [95% confidence interval (95% CI) 1.34–1.79] for lung cancer. Ore miners (53 cases, 24 controls) had a higher OR (2.34, 95% CI 1.36-4.03) than quarrymen (67 cases, 39 controls; OR 1.92, 95% CI 1.21–3.05) and coal miners (442 cases, 297 controls; OR 1.40, 95% CI 1.18–1.67), but CI overlapped. We did not observe trends by duration of exposure or time since last exposure. CONCLUSIONS: This pooled analysis of population-based studies demonstrated an excess lung cancer risk among miners and quarrymen that remained increased after adjustment for detailed smoking history and working in other at-risk occupations. The increase in risk among coal miners were less pronounced than for ore miners or quarrymen.

Published
2015
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50. Polygenic Risk Modelling for Prediction of Epithelial Ovarian Cancer Risk

Author

V. Wendy Setiawan, Ana Osorio, Liv Cecilie Vestrheim Thomsen, Francesca Gensini, Harsha Pathak, Barbara Wappenschmidt, Ingo B. Runnebaum, Javier Benitez, Rita K. Schmutzler, Jeffrey N. Weitzel, Yin Ling Woo, Kenneth Offit, Anthony N. Karnezis, Eitan Friedman, Jacques Simard, James M. Flanagan, Pedro Pérez-Segura, Siranoush Manoukian, Melissa C. Southey, Ramunas Janavicius, Finn Cilius Nielsen, Graham G. Giles, Usha Menon, Ava Kwong, Anna H. Wu, Thomas Hansen, Cristina Rodríguez-Antona, Maria A. Caligo, Argyrios Ziogas, Allison DePersia, Anna P. Sokolenko, Clarice R. Weinberg, Hoda Anton-Culver, Digna R. Velez Edwards, Jennifer B. Permuth, Patricia A. Ganz, Ana Vega, Keitaro Matsuo, Heli Nevanlinna, Frances Wang, Natalia Antonenkova, Claudine Isaacs, Conxi Lázaro, Melissa C. Larson, Henriette Roed Nielsen, Byoung-Gie Kim, Andreas du Bois, Dale P. Sandler, Anna Jakubowska, Paul D.P. Pharoah, Jenny Lester, Paolo Radice, Natalia Bogdanova, Lambertus A. Kiemeney, Mary Anne Rossing, Thilo Dörk, Ruea-Yea Huang, Judy Garber, Taymaa May, Diana Eccles, Mary Beth Terry, Jenny Chang-Claude, Jeffrey R. Marks, Dominique Stoppa-Lyonnet, Heather Eliassen, Douglas A. Levine, Phuong L. Mai, Gerasimos Aravantinos, Hui Cai, Britton Trabert, Amanda Black, Noura Mebirouk, Robin de Putter, Rayna K. Matsuno, Ralf Bützow, Joanne Ngeow Yuen Yie, James D. Brenton, Nadine Tung, Drakoulis Yannoukakos, Jonathan Tyrer, L Yan, Yen Y. Tan, Ian Komenaka, Simona Agata, Honglin Song, Tanja Pejovic, Marjorie J. Riggan, Antonis C. Antoniou, Katja K.H. Aben, Goska Leslie, Eric A. Ross, Estrid Høgdall, Kang Shan, Holly R. Harris, Eleanor Davies, Liene Nikitina-Zake, Florian Heitz, Stephen J. Chanock, Matthew Jones, Beth Y. Karlan, Matthias W. Beckmann, Penelope M. Webb, John L. Hopper, Peter A. Fasching, Jacek Gronwald, kConFab Investigators, Ana Peixoto, Joellen M. Schildkraut, Renée T. Fortner, Susan L. Neuhausen, Daehee Kang, Anthony J. Swerdlow, Lesley McGuffog, Marco Montagna, Paolo Peterlongo, Daniel R. Barnes, Marina Bermisheva, Alicja Wolk, Yuan Chun Ding, Marc Tischkowitz, Gord Glendon, Elza Khusnutdinova, Julie M. Cunningham, Saundra S. Buys, Albina N. Minlikeeva, Jennifer A. Doherty, Annemieke H. van der Hout, Austin Miller, Fergus J. Couch, Fabienne Lesueur, Peter Devilee, Kristin K. Zorn, Daniel Barrowdale, Christian F. Singer, Line Bjørge, Åke Borg, Diether Lambrechts, Shelley S. Tworoger, Allan Jensen, Ute Hamann, Douglas F. Easton, Bernardo Bonanni, Alvaro N.A. Monteiro, Johanna Rantala, Marc T. Goodman, Ellen Valen, Wei Zheng, Thomas A. Sellers, Marcus Q. Bernardini, Alice S. Whittemore, Kunle Odunsi, Inge Søkilde Pedersen, Laura Papi, Mads Thomassen, Allison W. Kurian, Emily White, Penny Soucy, D. Gareth Evans, Lenka Foretova, Kathryn L. Terry, Ruth C. Travis, Claus Høgdall, Hebon Investigators, Darya Prokofyeva, Stacey J. Winham, Yoke-Eng Chiew, Eileen Dareng, Jan Lubinski, Elizabeth Munro, Oskar T. 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Kjaer, Mark H. Greene, Katia M. Zavaglia, Jolanta Kupryjanczyk, Nicolas Wentzensen, Karen H. Lu, Hayley Cassingham, Christopher A. Haiman, Eric Hahnen, Els Van Nieuwenhuysen, Katherine L. Nathanson, Anna deFazio, Ian G. Campbell, Paul A. James, Sara H. Olson, Eva Machackova, Anne M. van Altena, Irene L. Andrulis, Linda S. Cook, Matthias Dürst, Mary B. Daly, John R. McLaughlin, Niclas Håkansson, Jingmei Li, Diana Torres, Iain A. McNeish, Jennifer T. Loud, Roger L. Milne, Marta Santamariña, Annelie Augustinsson, Nhu D. Le, Kate Lawrenson, Kirsten B. 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Subjects
Oncology, medicine.medical_specialty, 45/61, 45/43, Single-nucleotide polymorphism, Logistic regression, 631/208/2489, 03 medical and health sciences, 0302 clinical medicine, Lasso (statistics), Internal medicine, Genotype, medicine, SNP, 030304 developmental biology, 0303 health sciences, business.industry, Hazard ratio, article, Odds ratio, 631/208/721, medicine.disease, 3. Good health, 030220 oncology & carcinogenesis, business, Ovarian cancer, 692/499
Abstract

Funder: Funding details are provided in the Supplementary Material, Polygenic risk scores (PRS) for epithelial ovarian cancer (EOC) have the potential to improve risk stratification. Joint estimation of Single Nucleotide Polymorphism (SNP) effects in models could improve predictive performance over standard approaches of PRS construction. Here, we implemented computationally-efficient, penalized, logistic regression models (lasso, elastic net, stepwise) to individual level genotype data and a Bayesian framework with continuous shrinkage, ���select and shrink for summary statistics��� (S4), to summary level data for epithelial non-mucinous ovarian cancer risk prediction. We developed the models in a dataset consisting of 23,564 non-mucinous EOC cases and 40,138 controls participating in the Ovarian Cancer Association Consortium (OCAC) and validated the best models in three populations of different ancestries: prospective data from 198,101 women of European ancestry; 7,669 women of East Asian ancestry; 1,072 women of African ancestry, and in 18,915 BRCA1 and 12,337 BRCA2 pathogenic variant carriers of European ancestry. In the external validation data, the model with the strongest association for non-mucinous EOC risk derived from the OCAC model development data was the S4 model (27,240 SNPs) with odds ratios (OR) of 1.38(95%CI:1.28���1.48,AUC:0.588) per unit standard deviation, in women of European ancestry; 1.14(95%CI:1.08���1.19,AUC:0.538) in women of East Asian ancestry; 1.38(95%CI:1.21-1.58,AUC:0.593) in women of African ancestry; hazard ratios of 1.37(95%CI:1.30���1.44,AUC:0.592) in BRCA1 pathogenic variant carriers and 1.51(95%CI:1.36-1.67,AUC:0.624) in BRCA2 pathogenic variant carriers. Incorporation of the S4 PRS in risk prediction models for ovarian cancer may have clinical utility in ovarian cancer prevention programs.

Published
2022
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