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1. Associations of a Breast Cancer Polygenic Risk Score With Tumor Characteristics and Survival

Author

Lopes Cardozo, Josephine MN, Andrulis, Irene L, Bojesen, Stig E, Dörk, Thilo, Eccles, Diana M, Fasching, Peter A, Hooning, Maartje J, Keeman, Renske, Nevanlinna, Heli, Rutgers, Emiel JT, Easton, Douglas F, Hall, Per, Pharoah, Paul DP, van 't Veer, Laura J, Schmidt, Marjanka K, Ahearn, Thomas U, Anton-Culver, Hoda, Arndt, Volker, Auer, Paul L, Augustinsson, Annelie, Beane Freeman, Laura E, Becher, Heiko, Beckmann, Matthias W, Behrens, Sabine, Benitez, Javier, Bermisheva, Marina, Blomqvist, Carl, Bolla, Manjeet K, Bonanni, Bernardo, Boyle, Terry, Brenner, Hermann, Brucker, Sara Y, Brüning, Thomas, Burwinkel, Barbara, Buys, Saundra S, Camp, Nicola J, Canzian, Federico, Cardoso, Fatima, Castelao, Jose E, Cessna, Melissa H, Chan, Tsun L, Chang-Claude, Jenny, Chenevix-Trench, Georgia, Choi, Ji-Yeob, Colonna, Sarah V, Copson, Ellen, Couch, Fergus J, Cox, Angela, Cross, Simon S, Czene, Kamila, Daly, Mary B, Dennis, Joe, Devilee, Peter, Drukker, Caroline A, Dunning, Alison M, Dwek, Miriam, Eliassen, A Heather, Engel, Christoph, Evans, D Gareth, Figueroa, Jonine D, Fletcher, Olivia, Flyger, Henrik, Gago-Dominguez, Manuela, García-Closas, Montserrat, García-Sáenz, José A, Genkinger, Jeanine, Giles, Graham G, González-Neira, Anna, Guénel, Pascal, Gündert, Melanie, Hahnen, Eric, Haiman, Christopher A, Håkansson, Niclas, Hamann, Ute, Hartman, Mikael, Heemskerk-Gerritsen, Bernadette AM, Hein, Alexander, Ho, Weang-Kee, Hoppe, Reiner, Hopper, John L, Houlston, Richard S, Howell, Anthony, Hunter, David J, Ito, Hidemi, Jakubowska, Anna, Jernström, Helena, John, Esther M, Johnson, Nichola, Jones, Michael E, Joseph, Vijai, Kaaks, Rudolf, Kang, Daehee, Kim, Sung-Won, Kitahara, Cari M, Koppert, Linetta B, Kosma, Veli-Matti, Kraft, Peter, Kristensen, Vessela N, Kubelka-Sabit, Katerina, and Koutros, Stella

Subjects
Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Breast Cancer, Cancer, Good Health and Well Being, Female, Humans, Breast Neoplasms, Risk Factors, Prognosis, Proportional Hazards Models, Breast, Breast Cancer Association Consortium and MINDACT Collaborators, Clinical Sciences, Oncology & Carcinogenesis, Oncology and carcinogenesis
Abstract

PurposeA polygenic risk score (PRS) consisting of 313 common genetic variants (PRS313) is associated with risk of breast cancer and contralateral breast cancer. This study aimed to evaluate the association of the PRS313 with clinicopathologic characteristics of, and survival following, breast cancer.MethodsWomen with invasive breast cancer were included, 98,397 of European ancestry and 12,920 of Asian ancestry, from the Breast Cancer Association Consortium (BCAC), and 683 women from the European MINDACT trial. Associations between PRS313 and clinicopathologic characteristics, including the 70-gene signature for MINDACT, were evaluated using logistic regression analyses. Associations of PRS313 (continuous, per standard deviation) with overall survival (OS) and breast cancer-specific survival (BCSS) were evaluated with Cox regression, adjusted for clinicopathologic characteristics and treatment.ResultsThe PRS313 was associated with more favorable tumor characteristics. In BCAC, increasing PRS313 was associated with lower grade, hormone receptor-positive status, and smaller tumor size. In MINDACT, PRS313 was associated with a low risk 70-gene signature. In European women from BCAC, higher PRS313 was associated with better OS and BCSS: hazard ratio (HR) 0.96 (95% CI, 0.94 to 0.97) and 0.96 (95% CI, 0.94 to 0.98), but the association disappeared after adjustment for clinicopathologic characteristics (and treatment): OS HR, 1.01 (95% CI, 0.98 to 1.05) and BCSS HR, 1.02 (95% CI, 0.98 to 1.07). The results in MINDACT and Asian women from BCAC were consistent.ConclusionAn increased PRS313 is associated with favorable tumor characteristics, but is not independently associated with prognosis. Thus, PRS313 has no role in the clinical management of primary breast cancer at the time of diagnosis. Nevertheless, breast cancer mortality rates will be higher for women with higher PRS313 as increasing PRS313 is associated with an increased risk of disease. This information is crucial for modeling effective stratified screening programs.

Published
2023

2. Inherited Germline Cancer Susceptibility Gene Variants in Individuals with Non-Muscle-Invasive Bladder Cancer

Author

Pietzak, Eugene J, Whiting, Karissa, Srinivasan, Preethi, Bandlamudi, Chaitanya, Khurram, Aliya, Joseph, Vijai, Walasek, Aleksandra, Bochner, Emily, Clinton, Timothy, Almassi, Nima, Truong, Hong, de Jesus Escano, Manuel R, Wiseman, Michal, Mandelker, Diana, Kemel, Yelena, Zhang, Liying, Walsh, Michael F, Cadoo, Karen A, Coleman, Jonathan A, Al-Ahmadie, Hikmat, Rosenberg, Jonathan E, Iyer, Gopakumar V, Solit, David B, Ostrovnaya, Irina, Offit, Kenneth, Robson, Mark E, Stadler, Zsofia K, Berger, Michael F, Bajorin, Dean F, Carlo, Maria, and Bochner, Bernard H

Subjects
Prevention, Cancer, Clinical Trials and Supportive Activities, Urologic Diseases, Clinical Research, Genetics, Aetiology, 2.1 Biological and endogenous factors, Good Health and Well Being, Adjuvants, Immunologic, BCG Vaccine, Carcinoma, Transitional Cell, Germ Cells, Humans, Neoplasm Invasiveness, Urinary Bladder Neoplasms, Xeroderma Pigmentosum Group D Protein, Oncology and Carcinogenesis, Oncology & Carcinogenesis
Abstract

PurposeIdentification of inherited germline variants can guide personalized cancer screening, prevention, and treatment. Pathogenic and likely pathogenic (P/LP) germline variants in cancer predisposition genes are frequent among patients with locally advanced or metastatic urothelial carcinoma, but their prevalence and significance in patients with non-muscle-invasive bladder cancer (NMIBC), the most common form of urothelial carcinoma, is understudied.Experimental designGermline analysis was conducted on paired tumor/normal sequencing results from two distinct cohorts of patients initially diagnosed with NMIBC. Associations between clinicopathologic features and clinical outcomes with the presence of P/LP germline variants in ≥76 hereditary cancer predisposition genes were analyzed.ResultsA similar frequency of P/LP germline variants were seen in our two NMIBC cohorts [12% (12/99) vs. 8.7% (10/115), P = 0.4]. In the combined analysis, P/LP germline variants were found only in patients with high-grade NMIBC (22/163), but none of the 46 patients with low-grade NMIBC (13.5% vs. 0%, P = 0.005). Fifteen (9.2%) patients with high-grade NMIBC had P/LP variants in DNA damage response genes, most within the nucleotide excision repair (ERCC2/3) and homologous recombination repair (BRCA1, NBN, RAD50) pathways. Contrary to prior reports in patients with NMIBC not receiving Bacillus Calmette-Guerin (BCG), P/LP germline variants were not associated with worse recurrence-free or progression-free survival in patients treated with BCG or with risk of developing upper tract urothelial carcinoma.ConclusionsOur results support offering germline counseling and testing for all patients with high-grade bladder cancer, regardless of initial tumor stage. Therapeutic strategies that target impaired DNA repair may benefit patients with high-grade NMIBC.

Published
2022

3. Copy number variants as modifiers of breast cancer risk for BRCA1/BRCA2 pathogenic variant carriers

Author

Hakkaart, Christopher, Pearson, John F, Marquart, Louise, Dennis, Joe, Wiggins, George AR, Barnes, Daniel R, Robinson, Bridget A, Mace, Peter D, Aittomäki, Kristiina, Andrulis, Irene L, Arun, Banu K, Azzollini, Jacopo, Balmaña, Judith, Barkardottir, Rosa B, Belhadj, Sami, Berger, Lieke, Blok, Marinus J, Boonen, Susanne E, Borde, Julika, Bradbury, Angela R, Brunet, Joan, Buys, Saundra S, Caligo, Maria A, Campbell, Ian, Chung, Wendy K, Claes, Kathleen BM, Collonge-Rame, Marie-Agnès, Cook, Jackie, Cosgrove, Casey, Couch, Fergus J, Daly, Mary B, Dandiker, Sita, Davidson, Rosemarie, de la Hoya, Miguel, de Putter, Robin, Delnatte, Capucine, Dhawan, Mallika, Diez, Orland, Ding, Yuan Chun, Domchek, Susan M, Donaldson, Alan, Eason, Jacqueline, Easton, Douglas F, Ehrencrona, Hans, Engel, Christoph, Evans, D Gareth, Faust, Ulrike, Feliubadaló, Lidia, Fostira, Florentia, Friedman, Eitan, Frone, Megan, Frost, Debra, Garber, Judy, Gayther, Simon A, Gehrig, Andrea, Gesta, Paul, Godwin, Andrew K, Goldgar, David E, Greene, Mark H, Hahnen, Eric, Hake, Christopher R, Hamann, Ute, Hansen, Thomas VO, Hauke, Jan, Hentschel, Julia, Herold, Natalie, Honisch, Ellen, Hulick, Peter J, Imyanitov, Evgeny N, Isaacs, Claudine, Izatt, Louise, Izquierdo, Angel, Jakubowska, Anna, James, Paul A, Janavicius, Ramunas, John, Esther M, Joseph, Vijai, Karlan, Beth Y, Kemp, Zoe, Kirk, Judy, Konstantopoulou, Irene, Koudijs, Marco, Kwong, Ava, Laitman, Yael, Lalloo, Fiona, Lasset, Christine, Lautrup, Charlotte, Lazaro, Conxi, Legrand, Clémentine, Leslie, Goska, Lesueur, Fabienne, Mai, Phuong L, Manoukian, Siranoush, Mari, Véronique, Martens, John WM, McGuffog, Lesley, Mebirouk, Noura, Meindl, Alfons, Miller, Austin, and Montagna, Marco

Subjects
Human Genome, Prevention, Breast Cancer, Cancer, Genetics, Aetiology, 2.1 Biological and endogenous factors, BRCA1 Protein, BRCA2 Protein, Breast Neoplasms, DNA Copy Number Variations, Female, Genetic Predisposition to Disease, Heterozygote, Humans, RNA, Messenger, GEMO Study Collaborators, EMBRACE Collaborators, SWE-BRCA Investigators, kConFab Investigators, HEBON Investigators
Abstract

The contribution of germline copy number variants (CNVs) to risk of developing cancer in individuals with pathogenic BRCA1 or BRCA2 variants remains relatively unknown. We conducted the largest genome-wide analysis of CNVs in 15,342 BRCA1 and 10,740 BRCA2 pathogenic variant carriers. We used these results to prioritise a candidate breast cancer risk-modifier gene for laboratory analysis and biological validation. Notably, the HR for deletions in BRCA1 suggested an elevated breast cancer risk estimate (hazard ratio (HR) = 1.21), 95% confidence interval (95% CI = 1.09-1.35) compared with non-CNV pathogenic variants. In contrast, deletions overlapping SULT1A1 suggested a decreased breast cancer risk (HR = 0.73, 95% CI 0.59-0.91) in BRCA1 pathogenic variant carriers. Functional analyses of SULT1A1 showed that reduced mRNA expression in pathogenic BRCA1 variant cells was associated with reduced cellular proliferation and reduced DNA damage after treatment with DNA damaging agents. These data provide evidence that deleterious variants in BRCA1 plus SULT1A1 deletions contribute to variable breast cancer risk in BRCA1 carriers.

Published
2022

4. Nucleotide excision repair deficiency is a targetable therapeutic vulnerability in clear cell renal cell carcinoma

Author

Aurel Prosz, Haohui Duan, Viktoria Tisza, Pranshu Sahgal, Sabine Topka, Gregory T. Klus, Judit Börcsök, Zsofia Sztupinszki, Timothy Hanlon, Miklos Diossy, Laura Vizkeleti, Dag Rune Stormoen, Istvan Csabai, Helle Pappot, Joseph Vijai, Kenneth Offit, Thomas Ried, Nilay Sethi, Kent W. Mouw, Sandor Spisak, Shailja Pathania, and Zoltan Szallasi

Subjects
Medicine, Science
Abstract

Abstract Due to a demonstrated lack of DNA repair deficiencies, clear cell renal cell carcinoma (ccRCC) has not benefitted from targeted synthetic lethality-based therapies. We investigated whether nucleotide excision repair (NER) deficiency is present in an identifiable subset of ccRCC cases that would render those tumors sensitive to therapy targeting this specific DNA repair pathway aberration. We used functional assays that detect UV-induced 6–4 pyrimidine-pyrimidone photoproducts to quantify NER deficiency in ccRCC cell lines. We also measured sensitivity to irofulven, an experimental cancer therapeutic agent that specifically targets cells with inactivated transcription-coupled nucleotide excision repair (TC-NER). In order to detect NER deficiency in clinical biopsies, we assessed whole exome sequencing data for the presence of an NER deficiency associated mutational signature previously identified in ERCC2 mutant bladder cancer. Functional assays showed NER deficiency in ccRCC cells. Some cell lines showed irofulven sensitivity at a concentration that is well tolerated by patients. Prostaglandin reductase 1 (PTGR1), which activates irofulven, was also associated with this sensitivity. Next generation sequencing data of the cell lines showed NER deficiency-associated mutational signatures. A significant subset of ccRCC patients had the same signature and high PTGR1 expression. ccRCC cell line-based analysis showed that NER deficiency is likely present in this cancer type. Approximately 10% of ccRCC patients in the TCGA cohort showed mutational signatures consistent with ERCC2 inactivation associated NER deficiency and also substantial levels of PTGR1 expression. These patients may be responsive to irofulven, a previously abandoned anticancer agent that has minimal activity in NER-proficient cells.

Published
2023
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5. The predictive ability of the 313 variant-based polygenic risk score for contralateral breast cancer risk prediction in women of European ancestry with a heterozygous BRCA1 or BRCA2 pathogenic variant.

Author

Lakeman, Inge MM, van den Broek, Alexandra J, Vos, Juliën AM, Barnes, Daniel R, Adlard, Julian, Andrulis, Irene L, Arason, Adalgeir, Arnold, Norbert, Arun, Banu K, Balmaña, Judith, Barrowdale, Daniel, Benitez, Javier, Borg, Ake, Caldés, Trinidad, Caligo, Maria A, Chung, Wendy K, Claes, Kathleen BM, GEMO Study Collaborators, EMBRACE Collaborators, Collée, J Margriet, Couch, Fergus J, Daly, Mary B, Dennis, Joe, Dhawan, Mallika, Domchek, Susan M, Eeles, Ros, Engel, Christoph, Evans, D Gareth, Feliubadaló, Lidia, Foretova, Lenka, Friedman, Eitan, Frost, Debra, Ganz, Patricia A, Garber, Judy, Gayther, Simon A, Gerdes, Anne-Marie, Godwin, Andrew K, Goldgar, David E, Hahnen, Eric, Hake, Christopher R, Hamann, Ute, Hogervorst, Frans BL, Hooning, Maartje J, Hopper, John L, Hulick, Peter J, Imyanitov, Evgeny N, OCGN Investigators, HEBON Investigators, KconFab Investigators, Isaacs, Claudine, Izatt, Louise, Jakubowska, Anna, James, Paul A, Janavicius, Ramunas, Jensen, Uffe Birk, Jiao, Yue, John, Esther M, Joseph, Vijai, Karlan, Beth Y, Kets, Carolien M, Konstantopoulou, Irene, Kwong, Ava, Legrand, Clémentine, Leslie, Goska, Lesueur, Fabienne, Loud, Jennifer T, Lubiński, Jan, Manoukian, Siranoush, McGuffog, Lesley, Miller, Austin, Gomes, Denise Molina, Montagna, Marco, Mouret-Fourme, Emmanuelle, Nathanson, Katherine L, Neuhausen, Susan L, Nevanlinna, Heli, Yie, Joanne Ngeow Yuen, Olah, Edith, Olopade, Olufunmilayo I, Park, Sue K, Parsons, Michael T, Peterlongo, Paolo, Piedmonte, Marion, Radice, Paolo, Rantala, Johanna, Rennert, Gad, Risch, Harvey A, Schmutzler, Rita K, Sharma, Priyanka, Simard, Jacques, Singer, Christian F, Stadler, Zsofia, Stoppa-Lyonnet, Dominique, Sutter, Christian, Tan, Yen Yen, Teixeira, Manuel R, Teo, Soo Hwang, Teulé, Alex, Thomassen, Mads, and Thull, Darcy L

Subjects
GEMO Study Collaborators, EMBRACE Collaborators, OCGN Investigators, HEBON Investigators, KconFab Investigators, Humans, Breast Neoplasms, Genetic Predisposition to Disease, BRCA1 Protein, BRCA2 Protein, Risk Factors, Retrospective Studies, Heterozygote, Mutation, Adult, Female, Prevention, Cancer, Aging, Breast Cancer, 2.1 Biological and endogenous factors, Genetics & Heredity, Genetics, Clinical Sciences
Abstract

PurposeTo evaluate the association between a previously published 313 variant-based breast cancer (BC) polygenic risk score (PRS313) and contralateral breast cancer (CBC) risk, in BRCA1 and BRCA2 pathogenic variant heterozygotes.MethodsWe included women of European ancestry with a prevalent first primary invasive BC (BRCA1 = 6,591 with 1,402 prevalent CBC cases; BRCA2 = 4,208 with 647 prevalent CBC cases) from the Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA), a large international retrospective series. Cox regression analysis was performed to assess the association between overall and ER-specific PRS313 and CBC risk.ResultsFor BRCA1 heterozygotes the estrogen receptor (ER)-negative PRS313 showed the largest association with CBC risk, hazard ratio (HR) per SD = 1.12, 95% confidence interval (CI) (1.06-1.18), C-index = 0.53; for BRCA2 heterozygotes, this was the ER-positive PRS313, HR = 1.15, 95% CI (1.07-1.25), C-index = 0.57. Adjusting for family history, age at diagnosis, treatment, or pathological characteristics for the first BC did not change association effect sizes. For women developing first BC

Published
2021

6. Functional annotation of the 2q35 breast cancer risk locus implicates a structural variant in influencing activity of a long-range enhancer element

Author

Baxter, Joseph S, Johnson, Nichola, Tomczyk, Katarzyna, Gillespie, Andrea, Maguire, Sarah, Brough, Rachel, Fachal, Laura, Michailidou, Kyriaki, Bolla, Manjeet K, Wang, Qin, Dennis, Joe, Ahearn, Thomas U, Andrulis, Irene L, Anton-Culver, Hoda, Antonenkova, Natalia N, Arndt, Volker, Aronson, Kristan J, Augustinsson, Annelie, Becher, Heiko, Beckmann, Matthias W, Behrens, Sabine, Benitez, Javier, Bermisheva, Marina, Bogdanova, Natalia V, Bojesen, Stig E, Brenner, Hermann, Brucker, Sara Y, Cai, Qiuyin, Campa, Daniele, Canzian, Federico, Castelao, Jose E, Chan, Tsun L, Chang-Claude, Jenny, Chanock, Stephen J, Chenevix-Trench, Georgia, Choi, Ji-Yeob, Clarke, Christine L, Collaborators, NBCS, Colonna, Sarah, Conroy, Don M, Couch, Fergus J, Cox, Angela, Cross, Simon S, Czene, Kamila, Daly, Mary B, Devilee, Peter, Dörk, Thilo, Dossus, Laure, Dwek, Miriam, Eccles, Diana M, Ekici, Arif B, Eliassen, A Heather, Engel, Christoph, Fasching, Peter A, Figueroa, Jonine, Flyger, Henrik, Gago-Dominguez, Manuela, Gao, Chi, García-Closas, Montserrat, García-Sáenz, José A, Ghoussaini, Maya, Giles, Graham G, Goldberg, Mark S, González-Neira, Anna, Guénel, Pascal, Gündert, Melanie, Haeberle, Lothar, Hahnen, Eric, Haiman, Christopher A, Hall, Per, Hamann, Ute, Hartman, Mikael, Hatse, Sigrid, Hauke, Jan, Hollestelle, Antoinette, Hoppe, Reiner, Hopper, John L, Hou, Ming-Feng, Investigators, kConFab, Investigators, ABCTB, Ito, Hidemi, Iwasaki, Motoki, Jager, Agnes, Jakubowska, Anna, Janni, Wolfgang, John, Esther M, Joseph, Vijai, Jung, Audrey, Kaaks, Rudolf, Kang, Daehee, Keeman, Renske, Khusnutdinova, Elza, Kim, Sung-Won, Kosma, Veli-Matti, Kraft, Peter, Kristensen, Vessela N, Kubelka-Sabit, Katerina, Kurian, Allison W, Kwong, Ava, and Lacey, James V

Subjects
Human Genome, Genetics, Cancer, Estrogen, Prevention, Breast Cancer, 2.1 Biological and endogenous factors, Aetiology, Breast Neoplasms, CRISPR-Cas Systems, Cell Line, Chromosome Mapping, Chromosomes, Human, Pair 2, Female, Genetic Association Studies, Genetic Variation, Humans, Insulin-Like Growth Factor Binding Protein 5, Molecular Sequence Annotation, Promoter Regions, Genetic, Risk Factors, Sequence Deletion, NBCS Collaborators, kConFab Investigators, ABCTB Investigators, breast cancer risk, functional annotation, risk locus, Biological Sciences, Medical and Health Sciences, Genetics & Heredity
Abstract

A combination of genetic and functional approaches has identified three independent breast cancer risk loci at 2q35. A recent fine-scale mapping analysis to refine these associations resulted in 1 (signal 1), 5 (signal 2), and 42 (signal 3) credible causal variants at these loci. We used publicly available in silico DNase I and ChIP-seq data with in vitro reporter gene and CRISPR assays to annotate signals 2 and 3. We identified putative regulatory elements that enhanced cell-type-specific transcription from the IGFBP5 promoter at both signals (30- to 40-fold increased expression by the putative regulatory element at signal 2, 2- to 3-fold by the putative regulatory element at signal 3). We further identified one of the five credible causal variants at signal 2, a 1.4 kb deletion (esv3594306), as the likely causal variant; the deletion allele of this variant was associated with an average additional increase in IGFBP5 expression of 1.3-fold (MCF-7) and 2.2-fold (T-47D). We propose a model in which the deletion allele of esv3594306 juxtaposes two transcription factor binding regions (annotated by estrogen receptor alpha ChIP-seq peaks) to generate a single extended regulatory element. This regulatory element increases cell-type-specific expression of the tumor suppressor gene IGFBP5 and, thereby, reduces risk of estrogen receptor-positive breast cancer (odds ratio = 0.77, 95% CI 0.74-0.81, p = 3.1 × 10-31).

Published
2021

7. Genome-wide Association Study of Bladder Cancer Reveals New Biological and Translational Insights

Author

Koutros, Stella, Kiemeney, Lambertus A., Pal Choudhury, Parichoy, Milne, Roger L., Lopez de Maturana, Evangelina, Ye, Yuanqing, Joseph, Vijai, Florez-Vargas, Oscar, Dyrskjøt, Lars, Figueroa, Jonine, Dutta, Diptavo, Giles, Graham G., Hildebrandt, Michelle A.T., Offit, Kenneth, Kogevinas, Manolis, Weiderpass, Elisabete, McCullough, Marjorie L., Freedman, Neal D., Albanes, Demetrius, Kooperberg, Charles, Cortessis, Victoria K., Karagas, Margaret R., Johnson, Alison, Schwenn, Molly R., Baris, Dalsu, Furberg, Helena, Bajorin, Dean F., Cussenot, Olivier, Cancel-Tassin, Geraldine, Benhamou, Simone, Kraft, Peter, Porru, Stefano, Carta, Angela, Bishop, Timothy, Southey, Melissa C., Matullo, Giuseppe, Fletcher, Tony, Kumar, Rajiv, Taylor, Jack A., Lamy, Philippe, Prip, Frederik, Kalisz, Mark, Weinstein, Stephanie J., Hengstler, Jan G., Selinski, Silvia, Harland, Mark, Teo, Mark, Kiltie, Anne E., Tardón, Adonina, Serra, Consol, Carrato, Alfredo, García-Closas, Reina, Lloreta, Josep, Schned, Alan, Lenz, Petra, Riboli, Elio, Brennan, Paul, Tjønneland, Anne, Otto, Thomas, Ovsiannikov, Daniel, Volkert, Frank, Vermeulen, Sita H., Aben, Katja K., Galesloot, Tessel E., Turman, Constance, De Vivo, Immaculata, Giovannucci, Edward, Hunter, David J., Hohensee, Chancellor, Hunt, Rebecca, Patel, Alpa V., Huang, Wen-Yi, Thorleifsson, Gudmar, Gago-Dominguez, Manuela, Amiano, Pilar, Golka, Klaus, Stern, Mariana C., Yan, Wusheng, Liu, Jia, Li, Shengchao Alfred, Katta, Shilpa, Hutchinson, Amy, Hicks, Belynda, Wheeler, William A., Purdue, Mark P., McGlynn, Katherine A., Kitahara, Cari M., Haiman, Christopher A., Greene, Mark H., Rafnar, Thorunn, Chatterjee, Nilanjan, Chanock, Stephen J., Wu, Xifeng, Real, Francisco X., Silverman, Debra T., Garcia-Closas, Montserrat, Stefansson, Kari, Prokunina-Olsson, Ludmila, Malats, Núria, and Rothman, Nathaniel

Published
2023
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8. The association between genetically elevated polyunsaturated fatty acids and risk of cancer

Author

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

Published
2023
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9. Polygenic risk scores and breast and epithelial ovarian cancer risks for carriers of BRCA1 and BRCA2 pathogenic variants

Author

Barnes, Daniel R, Rookus, Matti A, McGuffog, Lesley, Leslie, Goska, Mooij, Thea M, Dennis, Joe, Mavaddat, Nasim, Adlard, Julian, Ahmed, Munaza, Aittomäki, Kristiina, Andrieu, Nadine, Andrulis, Irene L, Arnold, Norbert, Arun, Banu K, Azzollini, Jacopo, Balmaña, Judith, Barkardottir, Rosa B, Barrowdale, Daniel, Benitez, Javier, Berthet, Pascaline, Białkowska, Katarzyna, Blanco, Amie M, Blok, Marinus J, Bonanni, Bernardo, Boonen, Susanne E, Borg, Åke, Bozsik, Aniko, Bradbury, Angela R, Brennan, Paul, Brewer, Carole, Brunet, Joan, Buys, Saundra S, Caldés, Trinidad, Caligo, Maria A, Campbell, Ian, Christensen, Lise Lotte, Chung, Wendy K, Claes, Kathleen BM, Colas, Chrystelle, Collonge-Rame, Marie-Agnès, Cook, Jackie, Daly, Mary B, Davidson, Rosemarie, de la Hoya, Miguel, de Putter, Robin, Delnatte, Capucine, Devilee, Peter, Diez, Orland, Ding, Yuan Chun, Domchek, Susan M, Dorfling, Cecilia M, Dumont, Martine, Eeles, Ros, Ejlertsen, Bent, Engel, Christoph, Evans, D Gareth, Faivre, Laurence, Foretova, Lenka, Fostira, Florentia, Friedlander, Michael, Friedman, Eitan, Frost, Debra, Ganz, Patricia A, Garber, Judy, Gehrig, Andrea, Gerdes, Anne-Marie, Gesta, Paul, Giraud, Sophie, Glendon, Gord, Godwin, Andrew K, Goldgar, David E, González-Neira, Anna, Greene, Mark H, Gschwantler-Kaulich, Daphne, Hahnen, Eric, Hamann, Ute, Hanson, Helen, Hentschel, Julia, Hogervorst, Frans BL, Hooning, Maartje J, Horvath, Judit, Hu, Chunling, Hulick, Peter J, Imyanitov, Evgeny N, Isaacs, Claudine, Izatt, Louise, Izquierdo, Angel, Jakubowska, Anna, James, Paul A, Janavicius, Ramunas, John, Esther M, Joseph, Vijai, Karlan, Beth Y, Kast, Karin, Koudijs, Marco, Kruse, Torben A, Kwong, Ava, Laitman, Yael, Lasset, Christine, and Lazaro, Conxi

Subjects
Clinical Research, Cancer, Ovarian Cancer, Prevention, Rare Diseases, Breast Cancer, 2.1 Biological and endogenous factors, Aetiology, BRCA1 Protein, BRCA2 Protein, Breast Neoplasms, Carcinoma, Ovarian Epithelial, Female, Genetic Predisposition to Disease, Heterozygote, Humans, Mutation, Ovarian Neoplasms, Prospective Studies, Retrospective Studies, Risk Factors, BRCA1, 2, breast cancer, ovarian cancer, PRS, genetics, GEMO Study Collaborators, EMBRACE Collaborators, kConFab Investigators, HEBON Investigators, GENEPSO Investigators, Consortium of Investigators of Modifiers of BRCA and BRCA2, BRCA1/2, Genetics, Clinical Sciences, Genetics & Heredity
Abstract

PurposeWe assessed the associations between population-based polygenic risk scores (PRS) for breast (BC) or epithelial ovarian cancer (EOC) with cancer risks for BRCA1 and BRCA2 pathogenic variant carriers.MethodsRetrospective cohort data on 18,935 BRCA1 and 12,339 BRCA2 female pathogenic variant carriers of European ancestry were available. Three versions of a 313 single-nucleotide polymorphism (SNP) BC PRS were evaluated based on whether they predict overall, estrogen receptor (ER)-negative, or ER-positive BC, and two PRS for overall or high-grade serous EOC. Associations were validated in a prospective cohort.ResultsThe ER-negative PRS showed the strongest association with BC risk for BRCA1 carriers (hazard ratio [HR] per standard deviation = 1.29 [95% CI 1.25-1.33], P = 3×10-72). For BRCA2, the strongest association was with overall BC PRS (HR = 1.31 [95% CI 1.27-1.36], P = 7×10-50). HR estimates decreased significantly with age and there was evidence for differences in associations by predicted variant effects on protein expression. The HR estimates were smaller than general population estimates. The high-grade serous PRS yielded the strongest associations with EOC risk for BRCA1 (HR = 1.32 [95% CI 1.25-1.40], P = 3×10-22) and BRCA2 (HR = 1.44 [95% CI 1.30-1.60], P = 4×10-12) carriers. The associations in the prospective cohort were similar.ConclusionPopulation-based PRS are strongly associated with BC and EOC risks for BRCA1/2 carriers and predict substantial absolute risk differences for women at PRS distribution extremes.

Published
2020

10. Aggregation tests identify new gene associations with breast cancer in populations with diverse ancestry

Author

Stefanie H. Mueller, Alvina G. Lai, Maria Valkovskaya, Kyriaki Michailidou, Manjeet K. Bolla, Qin Wang, Joe Dennis, Michael Lush, Zomoruda Abu-Ful, Thomas U. Ahearn, Irene L. Andrulis, Hoda Anton-Culver, Natalia N. Antonenkova, Volker Arndt, Kristan J. Aronson, Annelie Augustinsson, Thais Baert, Laura E. Beane Freeman, Matthias W. Beckmann, Sabine Behrens, Javier Benitez, Marina Bermisheva, Carl Blomqvist, Natalia V. Bogdanova, Stig E. Bojesen, Bernardo Bonanni, Hermann Brenner, Sara Y. Brucker, Saundra S. Buys, Jose E. Castelao, Tsun L. Chan, Jenny Chang-Claude, Stephen J. Chanock, Ji-Yeob Choi, Wendy K. Chung, NBCS Collaborators, Sarah V. Colonna, CTS Consortium, Sten Cornelissen, Fergus J. Couch, Kamila Czene, Mary B. Daly, Peter Devilee, Thilo Dörk, Laure Dossus, Miriam Dwek, Diana M. Eccles, Arif B. Ekici, A. Heather Eliassen, Christoph Engel, D. Gareth Evans, Peter A. Fasching, Olivia Fletcher, Henrik Flyger, Manuela Gago-Dominguez, Yu-Tang Gao, Montserrat García-Closas, José A. García-Sáenz, Jeanine Genkinger, Aleksandra Gentry-Maharaj, Felix Grassmann, Pascal Guénel, Melanie Gündert, Lothar Haeberle, Eric Hahnen, Christopher A. Haiman, Niclas Håkansson, Per Hall, Elaine F. Harkness, Patricia A. Harrington, Jaana M. Hartikainen, Mikael Hartman, Alexander Hein, Weang-Kee Ho, Maartje J. Hooning, Reiner Hoppe, John L. Hopper, Richard S. Houlston, Anthony Howell, David J. Hunter, Dezheng Huo, ABCTB Investigators, Hidemi Ito, Motoki Iwasaki, Anna Jakubowska, Wolfgang Janni, Esther M. John, Michael E. Jones, Audrey Jung, Rudolf Kaaks, Daehee Kang, Elza K. Khusnutdinova, Sung-Won Kim, Cari M. Kitahara, Stella Koutros, Peter Kraft, Vessela N. Kristensen, Katerina Kubelka-Sabit, Allison W. Kurian, Ava Kwong, James V. Lacey, Diether Lambrechts, Loic Le Marchand, Jingmei Li, Martha Linet, Wing-Yee Lo, Jirong Long, Artitaya Lophatananon, Arto Mannermaa, Mehdi Manoochehri, Sara Margolin, Keitaro Matsuo, Dimitrios Mavroudis, Usha Menon, Kenneth Muir, Rachel A. Murphy, Heli Nevanlinna, William G. Newman, Dieter Niederacher, Katie M. O’Brien, Nadia Obi, Kenneth Offit, Olufunmilayo I. Olopade, Andrew F. Olshan, Håkan Olsson, Sue K. Park, Alpa V. Patel, Achal Patel, Charles M. Perou, Julian Peto, Paul D. P. Pharoah, Dijana Plaseska-Karanfilska, Nadege Presneau, Brigitte Rack, Paolo Radice, Dhanya Ramachandran, Muhammad U. Rashid, Gad Rennert, Atocha Romero, Kathryn J. Ruddy, Matthias Ruebner, Emmanouil Saloustros, Dale P. Sandler, Elinor J. Sawyer, Marjanka K. Schmidt, Rita K. Schmutzler, Michael O. Schneider, Christopher Scott, Mitul Shah, Priyanka Sharma, Chen-Yang Shen, Xiao-Ou Shu, Jacques Simard, Harald Surowy, Rulla M. Tamimi, William J. Tapper, Jack A. Taylor, Soo Hwang Teo, Lauren R. Teras, Amanda E. Toland, Rob A. E. M. Tollenaar, Diana Torres, Gabriela Torres-Mejía, Melissa A. Troester, Thérèse Truong, Celine M. Vachon, Joseph Vijai, Clarice R. Weinberg, Camilla Wendt, Robert Winqvist, Alicja Wolk, Anna H. Wu, Taiki Yamaji, Xiaohong R. Yang, Jyh-Cherng Yu, Wei Zheng, Argyrios Ziogas, Elad Ziv, Alison M. Dunning, Douglas F. Easton, Harry Hemingway, Ute Hamann, and Karoline B. Kuchenbaecker

Subjects
Breast cancer susceptibility, Diverse ancestry, Rare variants, Gene regulation, Genome-wide association study, Medicine, Genetics, QH426-470
Abstract

Abstract Background Low-frequency variants play an important role in breast cancer (BC) susceptibility. Gene-based methods can increase power by combining multiple variants in the same gene and help identify target genes. Methods We evaluated the potential of gene-based aggregation in the Breast Cancer Association Consortium cohorts including 83,471 cases and 59,199 controls. Low-frequency variants were aggregated for individual genes’ coding and regulatory regions. Association results in European ancestry samples were compared to single-marker association results in the same cohort. Gene-based associations were also combined in meta-analysis across individuals with European, Asian, African, and Latin American and Hispanic ancestry. Results In European ancestry samples, 14 genes were significantly associated (q

Published
2023
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11. Gene-based Confirmatory Germline Testing Following Tumor-only Sequencing of Prostate Cancer

Author

Truong, Hong, Breen, Kelsey, Nandakumar, Subhiksha, Sjoberg, Daniel D., Kemel, Yelena, Mehta, Nikita, Lenis, Andrew T., Reisz, Peter A., Carruthers, Jessica, Benfante, Nicole, Joseph, Vijai, Khurram, Aliya, Gopalan, Anuradha, Fine, Samson W., Reuter, Victor E., Vickers, Andrew J., Birsoy, Ozge, Liu, Ying, Walsh, Michael, Latham, Alicia, Mandelker, Diana, Stadler, Zsofia K., Pietzak, Eugene, Ehdaie, Behfar, Touijer, Karim A., Laudone, Vincent P., Slovin, Susan F., Autio, Karen A., Danila, Daniel C., Rathkopf, Dana E., Eastham, James A., Chen, Yu, Morris, Michael J., Offit, Kenneth, Solit, David B., Scher, Howard I., Abida, Wassim, Robson, Mark E., and Carlo, Maria I.

Published
2023
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12. Characterising the contribution of rare protein-coding germline variants to prostate cancer risk and severity in 37,184 cases

Author

Mitchell, Jonathan, primary, Camacho, Niedzica, additional, Shea, Patrick, additional, Stopsack, Konrad, additional, Joseph, Vijai, additional, Burren, Oliver Simon, additional, Dhindsa, Ryan, additional, Nag, Abhishek, additional, Berchuck, Jacob, additional, O'Neill, Amanda, additional, Abbasi, Ali, additional, Zoghbi, Anthony, additional, Alegre-Diaz, Jesus, additional, Kuri-Morales, Pablo, additional, Berumen, Jaime, additional, Tapia-Conyer, Roberto, additional, Emberson, Jonathan, additional, Torres, Jason, additional, Collins, Rory, additional, Wang, Quanli, additional, Goldstein, David, additional, Matakidou, Athena, additional, Haefliger, Carolina, additional, Anderson-Dring, Lauren, additional, March, Ruth, additional, Jobanputra, Vaidehi, additional, Dougherty, Brian, additional, Carss, Keren, additional, Petrovski, Slave, additional, Kantoff, Philip, additional, Offit, Kenneth, additional, Mucci, Lorelei, additional, Pomerantz, Mark, additional, and Fabre, Margarete, additional

Published
2024
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13. P063: Prospective longitudinal validation of a breast cancer risk prediction model in a cohort of 130,058 individuals

Author

Brent Mabey, Elisha Hughes, Braden Probst, Holly Pederson, Timothy Simmons, Brian Morris, Brooke Hullinger, Susan Domchek, Charis Eng, Monique Gary, Jennifer Klemp, Semanti Mukherjee, Joseph Vijai, Kenneth Offit, Olufunmilayo Olopade, Sandhya Pruthi, Allison Kurian, Mark Robson, Pat Whitworth, Susanne Wagner, Jerry Lanchbury, Thomas Slavin, and Alexander Gutin

Subjects
Genetics, QH426-470, Medicine
Published
2023
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14. Germline Variants Identified in Patients with Early-onset Renal Cell Carcinoma Referred for Germline Genetic Testing

Author

Truong, Hong, Sheikh, Rania, Kotecha, Ritesh, Kemel, Yelena, Reisz, Peter A., Lenis, Andrew T., Mehta, Nikita N., Khurram, Aliya, Joseph, Vijai, Mandelker, Diana, Latham, Alicia, Ceyhan-Birsoy, Ozge, Ladanyi, Marc, Shah, Neil J., Walsh, Michael F., Voss, Martin H., Lee, Chung-Han, Russo, Paul, Coleman, Jonathan A., Hakimi, A. Ari, Feldman, Darren R., Stadler, Zsofia K., Robson, Mark E., Motzer, Robert J., Offit, Kenneth, Patil, Sujata, and Carlo, Maria I.

Published
2021
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15. Association of breast cancer risk in BRCA1 and BRCA2 mutation carriers with genetic variants showing differential allelic expression: identification of a modifier of breast cancer risk at locus 11q22.3.

Author

Hamdi, Yosr, Soucy, Penny, Kuchenbaeker, Karoline B, Pastinen, Tomi, Droit, Arnaud, Lemaçon, Audrey, Adlard, Julian, Aittomäki, Kristiina, Andrulis, Irene L, Arason, Adalgeir, Arnold, Norbert, Arun, Banu K, Azzollini, Jacopo, Bane, Anita, Barjhoux, Laure, Barrowdale, Daniel, Benitez, Javier, Berthet, Pascaline, Blok, Marinus J, Bobolis, Kristie, Bonadona, Valérie, Bonanni, Bernardo, Bradbury, Angela R, Brewer, Carole, Buecher, Bruno, Buys, Saundra S, Caligo, Maria A, Chiquette, Jocelyne, Chung, Wendy K, Claes, Kathleen BM, Daly, Mary B, Damiola, Francesca, Davidson, Rosemarie, De la Hoya, Miguel, De Leeneer, Kim, Diez, Orland, Ding, Yuan Chun, Dolcetti, Riccardo, Domchek, Susan M, Dorfling, Cecilia M, Eccles, Diana, Eeles, Ros, Einbeigi, Zakaria, Ejlertsen, Bent, EMBRACE, Engel, Christoph, Gareth Evans, D, Feliubadalo, Lidia, Foretova, Lenka, Fostira, Florentia, Foulkes, William D, Fountzilas, George, Friedman, Eitan, Frost, Debra, Ganschow, Pamela, Ganz, Patricia A, Garber, Judy, Gayther, Simon A, GEMO Study Collaborators, Gerdes, Anne-Marie, Glendon, Gord, Godwin, Andrew K, Goldgar, David E, Greene, Mark H, Gronwald, Jacek, Hahnen, Eric, Hamann, Ute, Hansen, Thomas VO, Hart, Steven, Hays, John L, HEBON, Hogervorst, Frans BL, Hulick, Peter J, Imyanitov, Evgeny N, Isaacs, Claudine, Izatt, Louise, Jakubowska, Anna, James, Paul, Janavicius, Ramunas, Jensen, Uffe Birk, John, Esther M, Joseph, Vijai, Just, Walter, Kaczmarek, Katarzyna, Karlan, Beth Y, KConFab Investigators, Kets, Carolien M, Kirk, Judy, Kriege, Mieke, Laitman, Yael, Laurent, Maïté, Lazaro, Conxi, Leslie, Goska, Lester, Jenny, Lesueur, Fabienne, Liljegren, Annelie, Loman, Niklas, Loud, Jennifer T, Manoukian, Siranoush, and Mariani, Milena

Subjects
EMBRACE, GEMO Study Collaborators, HEBON, KConFab Investigators, Chromosomes, Human, Pair 11, Humans, Breast Neoplasms, Genetic Predisposition to Disease, Risk, Gene Expression, Heterozygote, Mutation, Alleles, Genes, BRCA1, Genes, BRCA2, Quantitative Trait Loci, Female, Genetic Variation, Biomarkers, Tumor, BRCA1 and BRCA2 mutation carriers, Breast cancer, Cis-regulatory variants, Differential allelic expression, Genetic modifiers, Genetic susceptibility, Chromosomes, Human, Pair 11, Genes, BRCA1, BRCA2, Biomarkers, Tumor, Oncology & Carcinogenesis, Oncology and Carcinogenesis, Clinical Sciences
Abstract

PurposeCis-acting regulatory SNPs resulting in differential allelic expression (DAE) may, in part, explain the underlying phenotypic variation associated with many complex diseases. To investigate whether common variants associated with DAE were involved in breast cancer susceptibility among BRCA1 and BRCA2 mutation carriers, a list of 175 genes was developed based of their involvement in cancer-related pathways.MethodsUsing data from a genome-wide map of SNPs associated with allelic expression, we assessed the association of ~320 SNPs located in the vicinity of these genes with breast and ovarian cancer risks in 15,252 BRCA1 and 8211 BRCA2 mutation carriers ascertained from 54 studies participating in the Consortium of Investigators of Modifiers of BRCA1/2.ResultsWe identified a region on 11q22.3 that is significantly associated with breast cancer risk in BRCA1 mutation carriers (most significant SNP rs228595 p = 7 × 10-6). This association was absent in BRCA2 carriers (p = 0.57). The 11q22.3 region notably encompasses genes such as ACAT1, NPAT, and ATM. Expression quantitative trait loci associations were observed in both normal breast and tumors across this region, namely for ACAT1, ATM, and other genes. In silico analysis revealed some overlap between top risk-associated SNPs and relevant biological features in mammary cell data, which suggests potential functional significance.ConclusionWe identified 11q22.3 as a new modifier locus in BRCA1 carriers. Replication in larger studies using estrogen receptor (ER)-negative or triple-negative (i.e., ER-, progesterone receptor-, and HER2-negative) cases could therefore be helpful to confirm the association of this locus with breast cancer risk.

Published
2017

16. A case-only study to identify genetic modifiers of breast cancer risk for BRCA1/BRCA2 mutation carriers

Author

Juliette Coignard, Michael Lush, Jonathan Beesley, Tracy A. O’Mara, Joe Dennis, Jonathan P. Tyrer, Daniel R. Barnes, Lesley McGuffog, Goska Leslie, Manjeet K. Bolla, Muriel A. Adank, Simona Agata, Thomas Ahearn, Kristiina Aittomäki, Irene L. Andrulis, Hoda Anton-Culver, Volker Arndt, Norbert Arnold, Kristan J. Aronson, Banu K. Arun, Annelie Augustinsson, Jacopo Azzollini, Daniel Barrowdale, Caroline Baynes, Heko Becher, Marina Bermisheva, Leslie Bernstein, Katarzyna Białkowska, Carl Blomqvist, Stig E. Bojesen, Bernardo Bonanni, Ake Borg, Hiltrud Brauch, Hermann Brenner, Barbara Burwinkel, Saundra S. Buys, Trinidad Caldés, Maria A. Caligo, Daniele Campa, Brian D. Carter, Jose E. Castelao, Jenny Chang-Claude, Stephen J. Chanock, Wendy K. Chung, Kathleen B. M. Claes, Christine L. Clarke, GEMO Study Collaborators, EMBRACE Collaborators, J. Margriet Collée, Don M. Conroy, Kamila Czene, Mary B. Daly, Peter Devilee, Orland Diez, Yuan Chun Ding, Susan M. Domchek, Thilo Dörk, Isabel dos-Santos-Silva, Alison M. Dunning, Miriam Dwek, Diana M. Eccles, A. Heather Eliassen, Christoph Engel, Mikael Eriksson, D. Gareth Evans, Peter A. Fasching, Henrik Flyger, Florentia Fostira, Eitan Friedman, Lin Fritschi, Debra Frost, Manuela Gago-Dominguez, Susan M. Gapstur, Judy Garber, Vanesa Garcia-Barberan, Montserrat García-Closas, José A. García-Sáenz, Mia M. Gaudet, Simon A. Gayther, Andrea Gehrig, Vassilios Georgoulias, Graham G. Giles, Andrew K. Godwin, Mark S. Goldberg, David E. Goldgar, Anna González-Neira, Mark H. Greene, Pascal Guénel, Lothar Haeberle, Eric Hahnen, Christopher A. Haiman, Niclas Håkansson, Per Hall, Ute Hamann, Patricia A. Harrington, Steven N. Hart, Wei He, Frans B. L. Hogervorst, Antoinette Hollestelle, John L. Hopper, Darling J. Horcasitas, Peter J. Hulick, David J. Hunter, Evgeny N. Imyanitov, KConFab Investigators, HEBON Investigators, ABCTB Investigators, Agnes Jager, Anna Jakubowska, Paul A. James, Uffe Birk Jensen, Esther M. John, Michael E. Jones, Rudolf Kaaks, Pooja Middha Kapoor, Beth Y. Karlan, Renske Keeman, Elza Khusnutdinova, Johanna I. Kiiski, Yon-Dschun Ko, Veli-Matti Kosma, Peter Kraft, Allison W. Kurian, Yael Laitman, Diether Lambrechts, Loic Le Marchand, Jenny Lester, Fabienne Lesueur, Tricia Lindstrom, Adria Lopez-Fernández, Jennifer T. Loud, Craig Luccarini, Arto Mannermaa, Siranoush Manoukian, Sara Margolin, John W. M. Martens, Noura Mebirouk, Alfons Meindl, Austin Miller, Roger L. Milne, Marco Montagna, Katherine L. Nathanson, Susan L. Neuhausen, Heli Nevanlinna, Finn C. Nielsen, Katie M. O’Brien, Olufunmilayo I. Olopade, Janet E. Olson, Håkan Olsson, Ana Osorio, Laura Ottini, Tjoung-Won Park-Simon, Michael T. Parsons, Inge Sokilde Pedersen, Beth Peshkin, Paolo Peterlongo, Julian Peto, Paul D. P. Pharoah, Kelly-Anne Phillips, Eric C. Polley, Bruce Poppe, Nadege Presneau, Miquel Angel Pujana, Kevin Punie, Paolo Radice, Johanna Rantala, Muhammad U. Rashid, Gad Rennert, Hedy S. Rennert, Mark Robson, Atocha Romero, Maria Rossing, Emmanouil Saloustros, Dale P. Sandler, Regina Santella, Maren T. Scheuner, Marjanka K. Schmidt, Gunnar Schmidt, Christopher Scott, Priyanka Sharma, Penny Soucy, Melissa C. Southey, John J. Spinelli, Zoe Steinsnyder, Jennifer Stone, Dominique Stoppa-Lyonnet, Anthony Swerdlow, Rulla M. Tamimi, William J. Tapper, Jack A. Taylor, Mary Beth Terry, Alex Teulé, Darcy L. Thull, Marc Tischkowitz, Amanda E. Toland, Diana Torres, Alison H. Trainer, Thérèse Truong, Nadine Tung, Celine M. Vachon, Ana Vega, Joseph Vijai, Qin Wang, Barbara Wappenschmidt, Clarice R. Weinberg, Jeffrey N. Weitzel, Camilla Wendt, Alicja Wolk, Siddhartha Yadav, Xiaohong R. Yang, Drakoulis Yannoukakos, Wei Zheng, Argyrios Ziogas, Kristin K. Zorn, Sue K. Park, Mads Thomassen, Kenneth Offit, Rita K. Schmutzler, Fergus J. Couch, Jacques Simard, Georgia Chenevix-Trench, Douglas F. Easton, Nadine Andrieu, and Antonis C. Antoniou

Subjects
Science
Abstract

Breast cancer risk for BRCA1/BRCA2 mutation carriers varies depending on other genetic factors. Here, the authors perform a case-only genome-wide association study and highlight novel loci associated with breast cancer risk for BRCA1/BRCA2 mutation carriers.

Published
2021
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17. Clonal hematopoiesis is associated with risk of severe Covid-19

Author

Bolton, Kelly L., Koh, Youngil, Foote, Michael B., Im, Hogune, Jee, Justin, Sun, Choong Hyun, Safonov, Anton, Ptashkin, Ryan, Moon, Joon Ho, Lee, Ji Yeon, Jung, Jongtak, Kang, Chang Kyung, Song, Kyoung-Ho, Choe, Pyoeng Gyun, Park, Wan Beom, Kim, Hong Bin, Oh, Myoung-don, Song, Han, Kim, Sugyeong, Patel, Minal, Derkach, Andriy, Gedvilaite, Erika, Tkachuk, Kaitlyn A., Wiley, Brian J., Chan, Ireaneus C., Braunstein, Lior Z., Gao, Teng, Papaemmanuil, Elli, Esther Babady, N., Pessin, Melissa S., Kamboj, Mini, Diaz, Jr, Luis A., Ladanyi, Marc, Rauh, Michael J., Natarajan, Pradeep, Machiela, Mitchell J., Awadalla, Philip, Joseph, Vijai, Offit, Kenneth, Norton, Larry, Berger, Michael F., Levine, Ross L., Kim, Eu Suk, Kim, Nam Joong, and Zehir, Ahmet

Published
2021
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19. Genome-wide association study identifies multiple risk loci for chronic lymphocytic leukemia

Author

Berndt, Sonja I, Skibola, Christine F, Joseph, Vijai, Camp, Nicola J, Nieters, Alexandra, Wang, Zhaoming, Cozen, Wendy, Monnereau, Alain, Wang, Sophia S, Kelly, Rachel S, Lan, Qing, Teras, Lauren R, Chatterjee, Nilanjan, Chung, Charles C, Yeager, Meredith, Brooks-Wilson, Angela R, Hartge, Patricia, Purdue, Mark P, Birmann, Brenda M, Armstrong, Bruce K, Cocco, Pierluigi, Zhang, Yawei, Severi, Gianluca, Zeleniuch-Jacquotte, Anne, Lawrence, Charles, Burdette, Laurie, Yuenger, Jeffrey, Hutchinson, Amy, Jacobs, Kevin B, Call, Timothy G, Shanafelt, Tait D, Novak, Anne J, Kay, Neil E, Liebow, Mark, Wang, Alice H, Smedby, Karin E, Adami, Hans-Olov, Melbye, Mads, Glimelius, Bengt, Chang, Ellen T, Glenn, Martha, Curtin, Karen, Cannon-Albright, Lisa A, Jones, Brandt, Diver, W Ryan, Link, Brian K, Weiner, George J, Conde, Lucia, Bracci, Paige M, Riby, Jacques, Holly, Elizabeth A, Smith, Martyn T, Jackson, Rebecca D, Tinker, Lesley F, Benavente, Yolanda, Becker, Nikolaus, Boffetta, Paolo, Brennan, Paul, Foretova, Lenka, Maynadie, Marc, McKay, James, Staines, Anthony, Rabe, Kari G, Achenbach, Sara J, Vachon, Celine M, Goldin, Lynn R, Strom, Sara S, Lanasa, Mark C, Spector, Logan G, Leis, Jose F, Cunningham, Julie M, Weinberg, J Brice, Morrison, Vicki A, Caporaso, Neil E, Norman, Aaron D, Linet, Martha S, De Roos, Anneclaire J, Morton, Lindsay M, Severson, Richard K, Riboli, Elio, Vineis, Paolo, Kaaks, Rudolph, Trichopoulos, Dimitrios, Masala, Giovanna, Weiderpass, Elisabete, Chirlaque, María-Dolores, Vermeulen, Roel CH, Travis, Ruth C, Giles, Graham G, Albanes, Demetrius, Virtamo, Jarmo, Weinstein, Stephanie, Clavel, Jacqueline, Zheng, Tongzhang, Holford, Theodore R, Offit, Kenneth, Zelenetz, Andrew, Klein, Robert J, Spinelli, John J, and Bertrand, Kimberly A

Subjects
Cancer, Case-Control Studies, Chromosomes, Human, Pair 2, Genetic Loci, Genetic Predisposition to Disease, Genome-Wide Association Study, Humans, Leukemia, Lymphocytic, Chronic, B-Cell, Linkage Disequilibrium, Polymorphism, Single Nucleotide, Recombination, Genetic, Risk, Biological Sciences, Medical and Health Sciences, Developmental Biology
Abstract

Genome-wide association studies (GWAS) have previously identified 13 loci associated with risk of chronic lymphocytic leukemia or small lymphocytic lymphoma (CLL). To identify additional CLL susceptibility loci, we conducted the largest meta-analysis for CLL thus far, including four GWAS with a total of 3,100 individuals with CLL (cases) and 7,667 controls. In the meta-analysis, we identified ten independent associated SNPs in nine new loci at 10q23.31 (ACTA2 or FAS (ACTA2/FAS), P=1.22×10(-14)), 18q21.33 (BCL2, P=7.76×10(-11)), 11p15.5 (C11orf21, P=2.15×10(-10)), 4q25 (LEF1, P=4.24×10(-10)), 2q33.1 (CASP10 or CASP8 (CASP10/CASP8), P=2.50×10(-9)), 9p21.3 (CDKN2B-AS1, P=1.27×10(-8)), 18q21.32 (PMAIP1, P=2.51×10(-8)), 15q15.1 (BMF, P=2.71×10(-10)) and 2p22.2 (QPCT, P=1.68×10(-8)), as well as an independent signal at an established locus (2q13, ACOXL, P=2.08×10(-18)). We also found evidence for two additional promising loci below genome-wide significance at 8q22.3 (ODF1, P=5.40×10(-8)) and 5p15.33 (TERT, P=1.92×10(-7)). Although further studies are required, the proximity of several of these loci to genes involved in apoptosis suggests a plausible underlying biological mechanism.

Published
2013

21. Author Correction: A case-only study to identify genetic modifiers of breast cancer risk for BRCA1/BRCA2 mutation carriers

Author

Juliette Coignard, Michael Lush, Jonathan Beesley, Tracy A. O’Mara, Joe Dennis, Jonathan P. Tyrer, Daniel R. Barnes, Lesley McGuffog, Goska Leslie, Manjeet K. Bolla, Muriel A. Adank, Simona Agata, Thomas Ahearn, Kristiina Aittomäki, Irene L. Andrulis, Hoda Anton-Culver, Volker Arndt, Norbert Arnold, Kristan J. Aronson, Banu K. Arun, Annelie Augustinsson, Jacopo Azzollini, Daniel Barrowdale, Caroline Baynes, Heko Becher, Marina Bermisheva, Leslie Bernstein, Katarzyna Białkowska, Carl Blomqvist, Stig E. Bojesen, Bernardo Bonanni, Ake Borg, Hiltrud Brauch, Hermann Brenner, Barbara Burwinkel, Saundra S. Buys, Trinidad Caldés, Maria A. Caligo, Daniele Campa, Brian D. Carter, Jose E. Castelao, Jenny Chang-Claude, Stephen J. Chanock, Wendy K. Chung, Kathleen B. M. Claes, Christine L. Clarke, GEMO Study Collaborators, EMBRACE Collaborators, J. Margriet Collée, Don M. Conroy, Kamila Czene, Mary B. Daly, Peter Devilee, Orland Diez, Yuan Chun Ding, Susan M. Domchek, Thilo Dörk, Isabel dos-Santos-Silva, Alison M. Dunning, Miriam Dwek, Diana M. Eccles, A. Heather Eliassen, Christoph Engel, Mikael Eriksson, D. Gareth Evans, Peter A. Fasching, Henrik Flyger, Florentia Fostira, Eitan Friedman, Lin Fritschi, Debra Frost, Manuela Gago-Dominguez, Susan M. Gapstur, Judy Garber, Vanesa Garcia-Barberan, Montserrat García-Closas, José A. García-Sáenz, Mia M. Gaudet, Simon A. Gayther, Andrea Gehrig, Vassilios Georgoulias, Graham G. Giles, Andrew K. Godwin, Mark S. Goldberg, David E. Goldgar, Anna González-Neira, Mark H. Greene, Pascal Guénel, Lothar Haeberle, Eric Hahnen, Christopher A. Haiman, Niclas Håkansson, Per Hall, Ute Hamann, Patricia A. Harrington, Steven N. Hart, Wei He, Frans B. L. Hogervorst, Antoinette Hollestelle, John L. Hopper, Darling J. Horcasitas, Peter J. Hulick, David J. Hunter, Evgeny N. Imyanitov, KConFab Investigators, HEBON Investigators, ABCTB Investigators, Agnes Jager, Anna Jakubowska, Paul A. James, Uffe Birk Jensen, Esther M. John, Michael E. Jones, Rudolf Kaaks, Pooja Middha Kapoor, Beth Y. Karlan, Renske Keeman, Elza Khusnutdinova, Johanna I. Kiiski, Yon-Dschun Ko, Veli-Matti Kosma, Peter Kraft, Allison W. Kurian, Yael Laitman, Diether Lambrechts, Loic Le Marchand, Jenny Lester, Fabienne Lesueur, Tricia Lindstrom, Adria Lopez-Fernández, Jennifer T. Loud, Craig Luccarini, Arto Mannermaa, Siranoush Manoukian, Sara Margolin, John W. M. Martens, Noura Mebirouk, Alfons Meindl, Austin Miller, Roger L. Milne, Marco Montagna, Katherine L. Nathanson, Susan L. Neuhausen, Heli Nevanlinna, Finn C. Nielsen, Katie M. O’Brien, Olufunmilayo I. Olopade, Janet E. Olson, Håkan Olsson, Ana Osorio, Laura Ottini, Tjoung-Won Park-Simon, Michael T. Parsons, Inge Sokilde Pedersen, Beth Peshkin, Paolo Peterlongo, Julian Peto, Paul D. P. Pharoah, Kelly-Anne Phillips, Eric C. Polley, Bruce Poppe, Nadege Presneau, Miquel Angel Pujana, Kevin Punie, Paolo Radice, Johanna Rantala, Muhammad U. Rashid, Gad Rennert, Hedy S. Rennert, Mark Robson, Atocha Romero, Maria Rossing, Emmanouil Saloustros, Dale P. Sandler, Regina Santella, Maren T. Scheuner, Marjanka K. Schmidt, Gunnar Schmidt, Christopher Scott, Priyanka Sharma, Penny Soucy, Melissa C. Southey, John J. Spinelli, Zoe Steinsnyder, Jennifer Stone, Dominique Stoppa-Lyonnet, Anthony Swerdlow, Rulla M. Tamimi, William J. Tapper, Jack A. Taylor, Mary Beth Terry, Alex Teulé, Darcy L. Thull, Marc Tischkowitz, Amanda E. Toland, Diana Torres, Alison H. Trainer, Thérèse Truong, Nadine Tung, Celine M. Vachon, Ana Vega, Joseph Vijai, Qin Wang, Barbara Wappenschmidt, Clarice R. Weinberg, Jeffrey N. Weitzel, Camilla Wendt, Alicja Wolk, Siddhartha Yadav, Xiaohong R. Yang, Drakoulis Yannoukakos, Wei Zheng, Argyrios Ziogas, Kristin K. Zorn, Sue K. Park, Mads Thomassen, Kenneth Offit, Rita K. Schmutzler, Fergus J. Couch, Jacques Simard, Georgia Chenevix-Trench, Douglas F. Easton, Nadine Andrieu, and Antonis C. Antoniou

Subjects
Science
Abstract

A Correction to this paper has been published: https://doi.org/10.1038/s41467-021-23162-4

Published
2021
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22. Common variants at 12p11, 12q24, 9p21, 9q31.2 and in ZNF365 are associated with breast cancer risk for BRCA1 and/or BRCA2 mutation carriers

Author

Antoniou, Antonis C, Kuchenbaecker, Karoline B, Soucy, Penny, Beesley, Jonathan, Chen, Xiaoqing, McGuffog, Lesley, Lee, Andrew, Barrowdale, Daniel, Healey, Sue, Sinilnikova, Olga M, Caligo, Maria A, Loman, Niklas, Harbst, Katja, Lindblom, Annika, Arver, Brita, Rosenquist, Richard, Karlsson, Per, Nathanson, Kate, Domchek, Susan, Rebbeck, Tim, Jakubowska, Anna, Lubinski, Jan, Jaworska, Katarzyna, Durda, Katarzyna, Złowowcka-Perłowska, Elżbieta, Osorio, Ana, Durán, Mercedes, Andrés, Raquel, Benítez, Javier, Hamann, Ute, Hogervorst, Frans B, van Os, Theo A, Verhoef, Senno, Meijers-Heijboer, Hanne EJ, Wijnen, Juul, Gómez Garcia, Encarna B, Ligtenberg, Marjolijn J, Kriege, Mieke, Collée, J Margriet, Ausems, Margreet GEM, Oosterwijk, Jan C, Peock, Susan, Frost, Debra, Ellis, Steve D, Platte, Radka, Fineberg, Elena, Evans, D Gareth, Lalloo, Fiona, Jacobs, Chris, Eeles, Ros, Adlard, Julian, Davidson, Rosemarie, Cole, Trevor, Cook, Jackie, Paterson, Joan, Douglas, Fiona, Brewer, Carole, Hodgson, Shirley, Morrison, Patrick J, Walker, Lisa, Rogers, Mark T, Donaldson, Alan, Dorkins, Huw, Godwin, Andrew K, Bove, Betsy, Stoppa-Lyonnet, Dominique, Houdayer, Claude, Buecher, Bruno, de Pauw, Antoine, Mazoyer, Sylvie, Calender, Alain, Léoné, Mélanie, Bressac- de Paillerets, Brigitte, Caron, Olivier, Sobol, Hagay, Frenay, Marc, Prieur, Fabienne, Ferrer, Sandra, Mortemousque, Isabelle, Buys, Saundra, Daly, Mary, Miron, Alexander, Terry, Mary, Hopper, John L, John, Esther M, Southey, Melissa, Goldgar, David, Singer, Christian F, Fink-Retter, Anneliese, Tea, Muy-Kheng, Kaulich, Daphne, Hansen, Thomas VO, Nielsen, Finn C, Barkardottir, Rosa B, Gaudet, Mia, Kirchhoff, Tomas, Joseph, Vijai, Dutra-Clarke, Ana, Offit, Kenneth, and Piedmonte, Marion

Abstract

AbstractIntroductionSeveral common alleles have been shown to be associated with breast and/or ovarian cancer risk for BRCA1 and BRCA2 mutation carriers. Recent genome-wide association studies of breast cancer have identified eight additional breast cancer susceptibility loci: rs1011970 (9p21, CDKN2A/B), rs10995190 (ZNF365), rs704010 (ZMIZ1), rs2380205 (10p15), rs614367 (11q13), rs1292011 (12q24), rs10771399 (12p11 near PTHLH) and rs865686 (9q31.2). MethodsTo evaluate whether these single nucleotide polymorphisms (SNPs) are associated with breast cancer risk for BRCA1 and BRCA2 carriers, we genotyped these SNPs in 12599 BRCA1 and 7132 BRCA2 mutation carriers and analysed the associations with breast cancer risk within a retrospective likelihood framework. ResultsOnly SNP rs10771399 near PTHLH was associated with breast cancer risk for BRCA1 mutation carriers (per-allele Hazard Ratio (HR)= 0.87, 95%CI:0.81-0.94, P-trend=3x10^-4). The association was restricted to mutations proven or predicted to lead to absence of protein expression (HR=0.82, 95%CI:0.74-0.90, P-trend=3.1x10^-5, P-difference=0.03). Four SNPs were associated with the risk of breast cancer for BRCA2 mutation carriers: rs10995190, P-trend=0.015; rs1011970, P-trend=0.048; rs865686, 2df-P=0.007; rs1292011 2df-P=0.03. rs10771399 (PTHLH) was predominantly associated with estrogen receptor (ER)-negative breast cancer for BRCA1 mutation carriers (HR=0.81, 95%CI: 0.74-0.90, P-trend=4x10^-5) and there was marginal evidence of association with ER-negative breast cancer for BRCA2 mutation carriers (HR=0.78, 95%CI:0.62-1.00, P-trend=0.049). ConclusionsThe present findings, in combination with previously identified modifiers of risk, will ultimately lead to more accurate risk prediction and an improved understanding of the disease etiology in BRCA1 and BRCA2 mutation carriers.

Published
2012

23. NBN Pathogenic Germline Variants are Associated with Pan-Cancer Susceptibility and In Vitro DNA Damage Response Defects

Author

Sami Belhadj, Aliya Khurram, Chaitanya Bandlamudi, Guillermo Palou-Márquez, Vignesh Ravichandran, Zoe Steinsnyder, Temima Wildman, Amanda Catchings, Yelena Kemel, Semanti Mukherjee, Benjamin Fesko, Kanika Arora, Miika Mehine, Sita Dandiker, Aalin Izhar, John Petrini, Susan Domchek, Katherine L. Nathanson, Jamie Brower, Fergus Couch, Zsofia Stadler, Mark Robson, Michael Walsh, Joseph Vijai, Michael Berger, Fran Supek, Rachid Karam, Sabine Topka, and Kenneth Offit

Subjects
Cancer Research, Oncology
Abstract

Purpose: To explore the role of NBN as a pan-cancer susceptibility gene. Experimental Design: Matched germline and somatic DNA samples from 34,046 patients were sequenced using Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets and presumed pathogenic germline variants (PGV) identified. Allele-specific and gene-centered analysis of enrichment was conducted and a validation cohort of 26,407 pan-cancer patients was analyzed. Functional studies utilized cellular models with analysis of protein expression, MRN complex formation/localization, and viability assessment following treatment with γ-irradiation. Results: We identified 83 carriers of 32 NBN PGVs (0.25% of the studied series), 40% of which (33/83) carried the Slavic founder p.K219fs. The frequency of PGVs varied across cancer types. Patients harboring NBN PGVs demonstrated increased loss of the wild-type allele in their tumors [OR = 2.7; confidence interval (CI): 1.4–5.5; P = 0.0024; pan-cancer], including lung and pancreatic tumors compared with breast and colorectal cancers. p.K219fs was enriched across all tumor types (OR = 2.22; CI: 1.3–3.6; P = 0.0018). Gene-centered analysis revealed enrichment of PGVs in cases compared with controls in the European population (OR = 1.9; CI: 1.3–2.7; P = 0.0004), a finding confirmed in the replication cohort (OR = 1.8; CI: 1.2–2.6; P = 0.003). Two novel truncating variants, p.L19* and p.N71fs, produced a 45 kDa fragment generated by alternative translation initiation that maintained binding to MRE11. Cells expressing these fragments showed higher sensitivity to γ-irradiation and lower levels of radiation-induced KAP1 phosphorylation. Conclusions: Burden analyses, biallelic inactivation, and functional evidence support the role of NBN as contributing to a broad cancer spectrum. Further studies in large pan-cancer series and the assessment of epistatic and environmental interactions are warranted to further define these associations.

Published
2022

24. 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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25. 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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26. Genetic Ancestry Correlates with Somatic Differences in a Real-World Clinical Cancer Sequencing Cohort

Author

Kanika Arora, Thinh N. Tran, Yelena Kemel, Miika Mehine, Ying L. Liu, Subhiksha Nandakumar, Shaleigh A. Smith, A. Rose Brannon, Irina Ostrovnaya, Konrad H. Stopsack, Pedram Razavi, Anton Safonov, Hira A. Rizvi, Matthew D. Hellmann, Joseph Vijai, Thomas C. Reynolds, James A. Fagin, Jian Carrot-Zhang, Kenneth Offit, David B. Solit, Marc Ladanyi, Nikolaus Schultz, Ahmet Zehir, Carol L. Brown, Zsofia K. Stadler, Debyani Chakravarty, Chaitanya Bandlamudi, and Michael F. Berger

Subjects
Genetics, Population, Oncology, Neoplasms, Humans, Precision Medicine, Polymorphism, Single Nucleotide, White People, Article
Abstract

Accurate ancestry inference is critical for identifying genetic contributors of cancer disparities among populations. Although methods to infer genetic ancestry have historically relied upon genome-wide markers, the adaptation to targeted clinical sequencing panels presents an opportunity to incorporate ancestry inference into routine diagnostic workflows. We show that global ancestral contributions and admixture of continental populations can be quantitatively inferred using markers captured by the MSK-IMPACT clinical panel. In a pan-cancer cohort of 45,157 patients, we observed differences by ancestry in the frequency of somatic alterations, recapitulating known associations and revealing novel associations. Despite the comparable overall prevalence of driver alterations by ancestry group, the proportion of patients with clinically actionable alterations was lower for African (30%) compared with European (33%) ancestry. Although this result is largely explained by population-specific cancer subtype differences, it reveals an inequity in the degree to which different populations are served by existing precision oncology interventions. Significance: We performed a comprehensive analysis of ancestral associations with somatic mutations in a real-world pan-cancer cohort, including >5,000 non-European individuals. Using an FDA-authorized tumor sequencing panel and an FDA-recognized oncology knowledge base, we detected differences in the prevalence of clinically actionable alterations, potentially contributing to health care disparities affecting underrepresented populations. This article is highlighted in the In This Issue feature, p. 2483

Published
2022

27. Integrative clinical genomics of metastatic cancer.

Author

Dan R. Robinson, Yi-Mi Wu, Robert J. Lonigro, Pankaj Vats, Erin Cobain, Jessica Everett, Xuhong Cao, Erica Rabban, Chandan Kumar-Sinha, Victoria Raymond, Scott Schuetze, Ajjai Alva, Javed Siddiqui, Rashmi Chugh, Francis Worden, Mark M. Zalupski, Jeffrey W. Innis, Rajen J. Mody, Scott A. Tomlins, David Lucas, Laurence H. Baker, Nithya Ramnath, Ann F. Schott, Daniel F. Hayes, Joseph Vijai, Kenneth Offit, Elena M. Stoffel, J. Scott Roberts, David C. Smith, Lakshmi P. Kunju, Moshe Talpaz, Marcin Cieslik, and Arul M. Chinnaiyan

Published
2017
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29. The contribution of pathogenic variants in breast cancer susceptibility genes to familial breast cancer risk

Author

Thomas P. Slavin, Kara N. Maxwell, Jenna Lilyquist, Joseph Vijai, Susan L. Neuhausen, Steven N. Hart, Vignesh Ravichandran, Tinu Thomas, Ann Maria, Danylo Villano, Kasmintan A. Schrader, Raymond Moore, Chunling Hu, Bradley Wubbenhorst, Brandon M. Wenz, Kurt D’Andrea, Mark E. Robson, Paolo Peterlongo, Bernardo Bonanni, James M. Ford, Judy E. Garber, Susan M. Domchek, Csilla Szabo, Kenneth Offit, Katherine L. Nathanson, Jeffrey N. Weitzel, and Fergus J. Couch

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

Familial breast cancer: Pinning down susceptibility genes beyond BRCA Women with the heritable form of breast cancer often harbor mutations in cancer-linked genes other than the usual suspects, BRCA1 and BRCA2. Slavin, Maxwell, Lilyquist, Joseph, and colleagues from major national and international cancer centers studied 2134 women with familial breast cancer who tested negative for BRCA1/2 gene mutations. The researchers sequenced 26 known or proposed breast cancer susceptibility genes and found mutations in approximately 1 in every 12 of the study subjects. They then further broke down the susceptibility genes into those that confer high-, moderate- or low-risk—although not all the proposed breast cancer genes reached statistical significance and, as such, their clinical importance remains unclear. The results support adding some of the high- and moderate-risk genes to multi-panel diagnostic tests that aim to determine the likelihood of a women developing heritable breast cancer.

Published
2017
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30. Supplementary Data from Inherited Germline Cancer Susceptibility Gene Variants in Individuals with Non–Muscle-Invasive Bladder Cancer

Author

Pietzak, Eugene J., primary, Whiting, Karissa, primary, Srinivasan, Preethi, primary, Bandlamudi, Chaitanya, primary, Khurram, Aliya, primary, Joseph, Vijai, primary, Walasek, Aleksandra, primary, Bochner, Emily, primary, Clinton, Timothy, primary, Almassi, Nima, primary, Truong, Hong, primary, de Jesus Escano, Manuel R., primary, Wiseman, Michal, primary, Mandelker, Diana, primary, Kemel, Yelena, primary, Zhang, Liying, primary, Walsh, Michael F., primary, Cadoo, Karen A., primary, Coleman, Jonathan A., primary, Al-Ahmadie, Hikmat, primary, Rosenberg, Jonathan E., primary, Iyer, Gopakumar V., primary, Solit, David B., primary, Ostrovnaya, Irina, primary, Offit, Kenneth, primary, Robson, Mark E., primary, Stadler, Zsofia K., primary, Berger, Michael F., primary, Bajorin, Dean F., primary, Carlo, Maria, primary, and Bochner, Bernard H., primary

Published
2023
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31. Supplementary Table S1 from Germline Lysine-Specific Demethylase 1 (LSD1/KDM1A) Mutations Confer Susceptibility to Multiple Myeloma

Author

Wei, Xiaomu, primary, Calvo-Vidal, M. Nieves, primary, Chen, Siwei, primary, Wu, Gang, primary, Revuelta, Maria V., primary, Sun, Jian, primary, Zhang, Jinghui, primary, Walsh, Michael F., primary, Nichols, Kim E., primary, Joseph, Vijai, primary, Snyder, Carrie, primary, Vachon, Celine M., primary, McKay, James D., primary, Wang, Shu-Ping, primary, Jayabalan, David S., primary, Jacobs, Lauren M., primary, Becirovic, Dina, primary, Waller, Rosalie G., primary, Artomov, Mykyta, primary, Viale, Agnes, primary, Patel, Jayeshkumar, primary, Phillip, Jude, primary, Chen-Kiang, Selina, primary, Curtin, Karen, primary, Salama, Mohamed, primary, Atanackovic, Djordje, primary, Niesvizky, Ruben, primary, Landgren, Ola, primary, Slager, Susan L., primary, Godley, Lucy A., primary, Churpek, Jane, primary, Garber, Judy E., primary, Anderson, Kenneth C., primary, Daly, Mark J., primary, Roeder, Robert G., primary, Dumontet, Charles, primary, Lynch, Henry T., primary, Mullighan, Charles G., primary, Camp, Nicola J., primary, Offit, Kenneth, primary, Klein, Robert J., primary, Yu, Haiyuan, primary, Cerchietti, Leandro, primary, and Lipkin, Steven M., primary

Published
2023
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32. Data from A Rare TP53 Mutation Predominant in Ashkenazi Jews Confers Risk of Multiple Cancers

Author

Powers, Jacquelyn, primary, Pinto, Emilia M., primary, Barnoud, Thibaut, primary, Leung, Jessica C., primary, Martynyuk, Tetyana, primary, Kossenkov, Andrew V., primary, Philips, Aaron H., primary, Desai, Heena, primary, Hausler, Ryan, primary, Kelly, Gregory, primary, Le, Anh N., primary, Li, Marilyn M., primary, MacFarland, Suzanne P., primary, Pyle, Louise C., primary, Zelley, Kristin, primary, Nathanson, Katherine L., primary, Domchek, Susan M., primary, Slavin, Thomas P., primary, Weitzel, Jeffrey N., primary, Stopfer, Jill E., primary, Garber, Judy E., primary, Joseph, Vijai, primary, Offit, Kenneth, primary, Dolinsky, Jill S., primary, Gutierrez, Stephanie, primary, McGoldrick, Kelly, primary, Couch, Fergus J., primary, Levin, Brooke, primary, Edelman, Morris C., primary, Levy, Carolyn Fein, primary, Spunt, Sheri L., primary, Kriwacki, Richard W., primary, Zambetti, Gerard P., primary, Ribeiro, Raul C., primary, Murphy, Maureen E., primary, and Maxwell, Kara N., primary

Published
2023
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33. Supplementary Data from Germline Lysine-Specific Demethylase 1 (LSD1/KDM1A) Mutations Confer Susceptibility to Multiple Myeloma

Author

Wei, Xiaomu, primary, Calvo-Vidal, M. Nieves, primary, Chen, Siwei, primary, Wu, Gang, primary, Revuelta, Maria V., primary, Sun, Jian, primary, Zhang, Jinghui, primary, Walsh, Michael F., primary, Nichols, Kim E., primary, Joseph, Vijai, primary, Snyder, Carrie, primary, Vachon, Celine M., primary, McKay, James D., primary, Wang, Shu-Ping, primary, Jayabalan, David S., primary, Jacobs, Lauren M., primary, Becirovic, Dina, primary, Waller, Rosalie G., primary, Artomov, Mykyta, primary, Viale, Agnes, primary, Patel, Jayeshkumar, primary, Phillip, Jude, primary, Chen-Kiang, Selina, primary, Curtin, Karen, primary, Salama, Mohamed, primary, Atanackovic, Djordje, primary, Niesvizky, Ruben, primary, Landgren, Ola, primary, Slager, Susan L., primary, Godley, Lucy A., primary, Churpek, Jane, primary, Garber, Judy E., primary, Anderson, Kenneth C., primary, Daly, Mark J., primary, Roeder, Robert G., primary, Dumontet, Charles, primary, Lynch, Henry T., primary, Mullighan, Charles G., primary, Camp, Nicola J., primary, Offit, Kenneth, primary, Klein, Robert J., primary, Yu, Haiyuan, primary, Cerchietti, Leandro, primary, and Lipkin, Steven M., primary

Published
2023
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34. Supplementary Table 2 from Candidate Genetic Modifiers for Breast and Ovarian Cancer Risk in BRCA1 and BRCA2 Mutation Carriers

Author

Peterlongo, Paolo, primary, Chang-Claude, Jenny, primary, Moysich, Kirsten B., primary, Rudolph, Anja, primary, Schmutzler, Rita K., primary, Simard, Jacques, primary, Soucy, Penny, primary, Eeles, Rosalind A., primary, Easton, Douglas F., primary, Hamann, Ute, primary, Wilkening, Stefan, primary, Chen, Bowang, primary, Rookus, Matti A., primary, Schmidt, Marjanka K., primary, van der Baan, Frederieke H., primary, Spurdle, Amanda B., primary, Walker, Logan C., primary, Lose, Felicity, primary, Maia, Ana-Teresa, primary, Montagna, Marco, primary, Matricardi, Laura, primary, Lubinski, Jan, primary, Jakubowska, Anna, primary, Gómez Garcia, Encarna B., primary, Olopade, Olufunmilayo I., primary, Nussbaum, Robert L., primary, Nathanson, Katherine L., primary, Domchek, Susan M., primary, Rebbeck, Timothy R., primary, Arun, Banu K., primary, Karlan, Beth Y., primary, Orsulic, Sandra, primary, Lester, Jenny, primary, Chung, Wendy K., primary, Miron, Alex, primary, Southey, Melissa C., primary, Goldgar, David E., primary, Buys, Saundra S., primary, Janavicius, Ramunas, primary, Dorfling, Cecilia M., primary, van Rensburg, Elizabeth J., primary, Ding, Yuan Chun, primary, Neuhausen, Susan L., primary, Hansen, Thomas V.O., primary, Gerdes, Anne-Marie, primary, Ejlertsen, Bent, primary, Jønson, Lars, primary, Osorio, Ana, primary, Martínez-Bouzas, Cristina, primary, Benitez, Javier, primary, Conway, Edye E., primary, Blazer, Kathleen R., primary, Weitzel, Jeffrey N., primary, Manoukian, Siranoush, primary, Peissel, Bernard, primary, Zaffaroni, Daniela, primary, Scuvera, Giulietta, primary, Barile, Monica, primary, Ficarazzi, Filomena, primary, Mariette, Frederique, primary, Fortuzzi, Stefano, primary, Viel, Alessandra, primary, Giannini, Giuseppe, primary, Papi, Laura, primary, Martayan, Aline, primary, Tibiletti, Maria Grazia, primary, Radice, Paolo, primary, Vratimos, Athanassios, primary, Fostira, Florentia, primary, Garber, Judy E., primary, Donaldson, Alan, primary, Brewer, Carole, primary, Foo, Claire, primary, Evans, D. Gareth R., primary, Frost, Debra, primary, Eccles, Diana, primary, Brady, Angela, primary, Cook, Jackie, primary, Tischkowitz, Marc, primary, Adlard, Julian, primary, Barwell, Julian, primary, Walker, Lisa, primary, Izatt, Louise, primary, Side, Lucy E., primary, Kennedy, M. John, primary, Rogers, Mark T., primary, Porteous, Mary E., primary, Morrison, Patrick J., primary, Platte, Radka, primary, Davidson, Rosemarie, primary, Hodgson, Shirley V., primary, Ellis, Steve, primary, Cole, Trevor, primary, Godwin, Andrew K., primary, Claes, Kathleen, primary, Van Maerken, Tom, primary, Meindl, Alfons, primary, Gehrig, Andrea, primary, Sutter, Christian, primary, Engel, Christoph, primary, Niederacher, Dieter, primary, Steinemann, Doris, primary, Plendl, Hansjoerg, primary, Kast, Karin, primary, Rhiem, Kerstin, primary, Ditsch, Nina, primary, Arnold, Norbert, primary, Varon-Mateeva, Raymonda, primary, Wappenschmidt, Barbara, primary, Wang-Gohrke, Shan, primary, Bressac-de Paillerets, Brigitte, primary, Buecher, Bruno, primary, Delnatte, Capucine, primary, Houdayer, Claude, primary, Stoppa-Lyonnet, Dominique, primary, Damiola, Francesca, primary, Coupier, Isabelle, primary, Barjhoux, Laure, primary, Venat-Bouvet, Laurence, primary, Golmard, Lisa, primary, Boutry-Kryza, Nadia, primary, Sinilnikova, Olga M., primary, Caron, Olivier, primary, Pujol, Pascal, primary, Mazoyer, Sylvie, primary, Belotti, Muriel, primary, Piedmonte, Marion, primary, Friedlander, Michael L., primary, Rodriguez, Gustavo C., primary, Copeland, Larry J., primary, de la Hoya, Miguel, primary, Segura, Pedro Perez, primary, Nevanlinna, Heli, primary, Aittomäki, Kristiina, primary, van Os, Theo A.M., primary, Meijers-Heijboer, Hanne E.J., primary, van der Hout, Annemarie H., primary, Vreeswijk, Maaike P.G., primary, Hoogerbrugge, Nicoline, primary, Ausems, Margreet G.E.M., primary, van Doorn, Helena C., primary, Collée, J. Margriet, primary, Olah, Edith, primary, Diez, Orland, primary, Blanco, Ignacio, primary, Lazaro, Conxi, primary, Brunet, Joan, primary, Feliubadalo, Lidia, primary, Cybulski, Cezary, primary, Gronwald, Jacek, primary, Durda, Katarzyna, primary, Jaworska-Bieniek, Katarzyna, primary, Sukiennicki, Grzegorz, primary, Arason, Adalgeir, primary, Chiquette, Jocelyne, primary, Teixeira, Manuel R., primary, Olswold, Curtis, primary, Couch, Fergus J., primary, Lindor, Noralane M., primary, Wang, Xianshu, primary, Szabo, Csilla I., primary, Offit, Kenneth, primary, Corines, Marina, primary, Jacobs, Lauren, primary, Robson, Mark E., primary, Zhang, Liying, primary, Joseph, Vijai, primary, Berger, Andreas, primary, Singer, Christian F., primary, Rappaport, Christine, primary, Kaulich, Daphne Geschwantler, primary, Pfeiler, Georg, primary, Tea, Muy-Kheng M., primary, Phelan, Catherine M., primary, Greene, Mark H., primary, Mai, Phuong L., primary, Rennert, Gad, primary, Mulligan, Anna Marie, primary, Glendon, Gord, primary, Tchatchou, Sandrine, primary, Andrulis, Irene L., primary, Toland, Amanda Ewart, primary, Bojesen, Anders, primary, Pedersen, Inge Sokilde, primary, Thomassen, Mads, primary, Jensen, Uffe Birk, primary, Laitman, Yael, primary, Rantala, Johanna, primary, von Wachenfeldt, Anna, primary, Ehrencrona, Hans, primary, Askmalm, Marie Stenmark, primary, Borg, Åke, primary, Kuchenbaecker, Karoline B., primary, McGuffog, Lesley, primary, Barrowdale, Daniel, primary, Healey, Sue, primary, Lee, Andrew, primary, Pharoah, Paul D.P., primary, Chenevix-Trench, Georgia, primary, Antoniou, Antonis C., primary, and Friedman, Eitan, primary

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2023
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35. Supplementary Figure S1 from Germline Lysine-Specific Demethylase 1 (LSD1/KDM1A) Mutations Confer Susceptibility to Multiple Myeloma

Author

Wei, Xiaomu, primary, Calvo-Vidal, M. Nieves, primary, Chen, Siwei, primary, Wu, Gang, primary, Revuelta, Maria V., primary, Sun, Jian, primary, Zhang, Jinghui, primary, Walsh, Michael F., primary, Nichols, Kim E., primary, Joseph, Vijai, primary, Snyder, Carrie, primary, Vachon, Celine M., primary, McKay, James D., primary, Wang, Shu-Ping, primary, Jayabalan, David S., primary, Jacobs, Lauren M., primary, Becirovic, Dina, primary, Waller, Rosalie G., primary, Artomov, Mykyta, primary, Viale, Agnes, primary, Patel, Jayeshkumar, primary, Phillip, Jude, primary, Chen-Kiang, Selina, primary, Curtin, Karen, primary, Salama, Mohamed, primary, Atanackovic, Djordje, primary, Niesvizky, Ruben, primary, Landgren, Ola, primary, Slager, Susan L., primary, Godley, Lucy A., primary, Churpek, Jane, primary, Garber, Judy E., primary, Anderson, Kenneth C., primary, Daly, Mark J., primary, Roeder, Robert G., primary, Dumontet, Charles, primary, Lynch, Henry T., primary, Mullighan, Charles G., primary, Camp, Nicola J., primary, Offit, Kenneth, primary, Klein, Robert J., primary, Yu, Haiyuan, primary, Cerchietti, Leandro, primary, and Lipkin, Steven M., primary

Published
2023
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36. Data from Germline Lysine-Specific Demethylase 1 (LSD1/KDM1A) Mutations Confer Susceptibility to Multiple Myeloma

Author

Wei, Xiaomu, primary, Calvo-Vidal, M. Nieves, primary, Chen, Siwei, primary, Wu, Gang, primary, Revuelta, Maria V., primary, Sun, Jian, primary, Zhang, Jinghui, primary, Walsh, Michael F., primary, Nichols, Kim E., primary, Joseph, Vijai, primary, Snyder, Carrie, primary, Vachon, Celine M., primary, McKay, James D., primary, Wang, Shu-Ping, primary, Jayabalan, David S., primary, Jacobs, Lauren M., primary, Becirovic, Dina, primary, Waller, Rosalie G., primary, Artomov, Mykyta, primary, Viale, Agnes, primary, Patel, Jayeshkumar, primary, Phillip, Jude, primary, Chen-Kiang, Selina, primary, Curtin, Karen, primary, Salama, Mohamed, primary, Atanackovic, Djordje, primary, Niesvizky, Ruben, primary, Landgren, Ola, primary, Slager, Susan L., primary, Godley, Lucy A., primary, Churpek, Jane, primary, Garber, Judy E., primary, Anderson, Kenneth C., primary, Daly, Mark J., primary, Roeder, Robert G., primary, Dumontet, Charles, primary, Lynch, Henry T., primary, Mullighan, Charles G., primary, Camp, Nicola J., primary, Offit, Kenneth, primary, Klein, Robert J., primary, Yu, Haiyuan, primary, Cerchietti, Leandro, primary, and Lipkin, Steven M., primary

Published
2023
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37. Supplementary Data from A Rare TP53 Mutation Predominant in Ashkenazi Jews Confers Risk of Multiple Cancers

Author

Powers, Jacquelyn, primary, Pinto, Emilia M., primary, Barnoud, Thibaut, primary, Leung, Jessica C., primary, Martynyuk, Tetyana, primary, Kossenkov, Andrew V., primary, Philips, Aaron H., primary, Desai, Heena, primary, Hausler, Ryan, primary, Kelly, Gregory, primary, Le, Anh N., primary, Li, Marilyn M., primary, MacFarland, Suzanne P., primary, Pyle, Louise C., primary, Zelley, Kristin, primary, Nathanson, Katherine L., primary, Domchek, Susan M., primary, Slavin, Thomas P., primary, Weitzel, Jeffrey N., primary, Stopfer, Jill E., primary, Garber, Judy E., primary, Joseph, Vijai, primary, Offit, Kenneth, primary, Dolinsky, Jill S., primary, Gutierrez, Stephanie, primary, McGoldrick, Kelly, primary, Couch, Fergus J., primary, Levin, Brooke, primary, Edelman, Morris C., primary, Levy, Carolyn Fein, primary, Spunt, Sheri L., primary, Kriwacki, Richard W., primary, Zambetti, Gerard P., primary, Ribeiro, Raul C., primary, Murphy, Maureen E., primary, and Maxwell, Kara N., primary

Published
2023
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38. Supplementary Table 3 from Candidate Genetic Modifiers for Breast and Ovarian Cancer Risk in BRCA1 and BRCA2 Mutation Carriers

Author

Peterlongo, Paolo, primary, Chang-Claude, Jenny, primary, Moysich, Kirsten B., primary, Rudolph, Anja, primary, Schmutzler, Rita K., primary, Simard, Jacques, primary, Soucy, Penny, primary, Eeles, Rosalind A., primary, Easton, Douglas F., primary, Hamann, Ute, primary, Wilkening, Stefan, primary, Chen, Bowang, primary, Rookus, Matti A., primary, Schmidt, Marjanka K., primary, van der Baan, Frederieke H., primary, Spurdle, Amanda B., primary, Walker, Logan C., primary, Lose, Felicity, primary, Maia, Ana-Teresa, primary, Montagna, Marco, primary, Matricardi, Laura, primary, Lubinski, Jan, primary, Jakubowska, Anna, primary, Gómez Garcia, Encarna B., primary, Olopade, Olufunmilayo I., primary, Nussbaum, Robert L., primary, Nathanson, Katherine L., primary, Domchek, Susan M., primary, Rebbeck, Timothy R., primary, Arun, Banu K., primary, Karlan, Beth Y., primary, Orsulic, Sandra, primary, Lester, Jenny, primary, Chung, Wendy K., primary, Miron, Alex, primary, Southey, Melissa C., primary, Goldgar, David E., primary, Buys, Saundra S., primary, Janavicius, Ramunas, primary, Dorfling, Cecilia M., primary, van Rensburg, Elizabeth J., primary, Ding, Yuan Chun, primary, Neuhausen, Susan L., primary, Hansen, Thomas V.O., primary, Gerdes, Anne-Marie, primary, Ejlertsen, Bent, primary, Jønson, Lars, primary, Osorio, Ana, primary, Martínez-Bouzas, Cristina, primary, Benitez, Javier, primary, Conway, Edye E., primary, Blazer, Kathleen R., primary, Weitzel, Jeffrey N., primary, Manoukian, Siranoush, primary, Peissel, Bernard, primary, Zaffaroni, Daniela, primary, Scuvera, Giulietta, primary, Barile, Monica, primary, Ficarazzi, Filomena, primary, Mariette, Frederique, primary, Fortuzzi, Stefano, primary, Viel, Alessandra, primary, Giannini, Giuseppe, primary, Papi, Laura, primary, Martayan, Aline, primary, Tibiletti, Maria Grazia, primary, Radice, Paolo, primary, Vratimos, Athanassios, primary, Fostira, Florentia, primary, Garber, Judy E., primary, Donaldson, Alan, primary, Brewer, Carole, primary, Foo, Claire, primary, Evans, D. Gareth R., primary, Frost, Debra, primary, Eccles, Diana, primary, Brady, Angela, primary, Cook, Jackie, primary, Tischkowitz, Marc, primary, Adlard, Julian, primary, Barwell, Julian, primary, Walker, Lisa, primary, Izatt, Louise, primary, Side, Lucy E., primary, Kennedy, M. John, primary, Rogers, Mark T., primary, Porteous, Mary E., primary, Morrison, Patrick J., primary, Platte, Radka, primary, Davidson, Rosemarie, primary, Hodgson, Shirley V., primary, Ellis, Steve, primary, Cole, Trevor, primary, Godwin, Andrew K., primary, Claes, Kathleen, primary, Van Maerken, Tom, primary, Meindl, Alfons, primary, Gehrig, Andrea, primary, Sutter, Christian, primary, Engel, Christoph, primary, Niederacher, Dieter, primary, Steinemann, Doris, primary, Plendl, Hansjoerg, primary, Kast, Karin, primary, Rhiem, Kerstin, primary, Ditsch, Nina, primary, Arnold, Norbert, primary, Varon-Mateeva, Raymonda, primary, Wappenschmidt, Barbara, primary, Wang-Gohrke, Shan, primary, Bressac-de Paillerets, Brigitte, primary, Buecher, Bruno, primary, Delnatte, Capucine, primary, Houdayer, Claude, primary, Stoppa-Lyonnet, Dominique, primary, Damiola, Francesca, primary, Coupier, Isabelle, primary, Barjhoux, Laure, primary, Venat-Bouvet, Laurence, primary, Golmard, Lisa, primary, Boutry-Kryza, Nadia, primary, Sinilnikova, Olga M., primary, Caron, Olivier, primary, Pujol, Pascal, primary, Mazoyer, Sylvie, primary, Belotti, Muriel, primary, Piedmonte, Marion, primary, Friedlander, Michael L., primary, Rodriguez, Gustavo C., primary, Copeland, Larry J., primary, de la Hoya, Miguel, primary, Segura, Pedro Perez, primary, Nevanlinna, Heli, primary, Aittomäki, Kristiina, primary, van Os, Theo A.M., primary, Meijers-Heijboer, Hanne E.J., primary, van der Hout, Annemarie H., primary, Vreeswijk, Maaike P.G., primary, Hoogerbrugge, Nicoline, primary, Ausems, Margreet G.E.M., primary, van Doorn, Helena C., primary, Collée, J. Margriet, primary, Olah, Edith, primary, Diez, Orland, primary, Blanco, Ignacio, primary, Lazaro, Conxi, primary, Brunet, Joan, primary, Feliubadalo, Lidia, primary, Cybulski, Cezary, primary, Gronwald, Jacek, primary, Durda, Katarzyna, primary, Jaworska-Bieniek, Katarzyna, primary, Sukiennicki, Grzegorz, primary, Arason, Adalgeir, primary, Chiquette, Jocelyne, primary, Teixeira, Manuel R., primary, Olswold, Curtis, primary, Couch, Fergus J., primary, Lindor, Noralane M., primary, Wang, Xianshu, primary, Szabo, Csilla I., primary, Offit, Kenneth, primary, Corines, Marina, primary, Jacobs, Lauren, primary, Robson, Mark E., primary, Zhang, Liying, primary, Joseph, Vijai, primary, Berger, Andreas, primary, Singer, Christian F., primary, Rappaport, Christine, primary, Kaulich, Daphne Geschwantler, primary, Pfeiler, Georg, primary, Tea, Muy-Kheng M., primary, Phelan, Catherine M., primary, Greene, Mark H., primary, Mai, Phuong L., primary, Rennert, Gad, primary, Mulligan, Anna Marie, primary, Glendon, Gord, primary, Tchatchou, Sandrine, primary, Andrulis, Irene L., primary, Toland, Amanda Ewart, primary, Bojesen, Anders, primary, Pedersen, Inge Sokilde, primary, Thomassen, Mads, primary, Jensen, Uffe Birk, primary, Laitman, Yael, primary, Rantala, Johanna, primary, von Wachenfeldt, Anna, primary, Ehrencrona, Hans, primary, Askmalm, Marie Stenmark, primary, Borg, Åke, primary, Kuchenbaecker, Karoline B., primary, McGuffog, Lesley, primary, Barrowdale, Daniel, primary, Healey, Sue, primary, Lee, Andrew, primary, Pharoah, Paul D.P., primary, Chenevix-Trench, Georgia, primary, Antoniou, Antonis C., primary, and Friedman, Eitan, primary

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2023
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39. Abstract PD14-05: PD14-05 Prospective longitudinal validation of a breast cancer risk prediction model in a cohort of 130,058 women

Author

Mabey, Brent, primary, Hughes, Elisha, additional, Probst, Braden, additional, Pederson, Holly J., additional, Simmons, Timothy, additional, Morris, Brian, additional, Hullinger, Brooke, additional, Domchek, Susan, additional, Eng, Charis, additional, Gary, Monique, additional, Klemp, Jennifer, additional, Mukherjee, Semanti, additional, Joseph, Vijai, additional, Offit, Kenneth, additional, Olopade, Olufunmilayo I., additional, Pruthi, Sandhya, additional, Kurian, Allison W., additional, Robson, Mark E., additional, Whitworth, Pat, additional, Wagner, Susanne, additional, Lanchbury, Jerry, additional, Slavin, Thomas, additional, and Gutin, Alexander, additional

Published
2023
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40. Supplementary Figure from Genetic Ancestry Correlates with Somatic Differences in a Real-World Clinical Cancer Sequencing Cohort

Author

Michael F. Berger, Chaitanya Bandlamudi, Debyani Chakravarty, Zsofia K. Stadler, Carol L. Brown, Ahmet Zehir, Nikolaus Schultz, Marc Ladanyi, David B. Solit, Kenneth Offit, Jian Carrot-Zhang, James A. Fagin, Thomas C. Reynolds, Joseph Vijai, Matthew D. Hellmann, Hira A. Rizvi, Anton Safonov, Pedram Razavi, Konrad H. Stopsack, Irina Ostrovnaya, A. Rose Brannon, Shaleigh A. Smith, Subhiksha Nandakumar, Ying L. Liu, Miika Mehine, Yelena Kemel, Thinh N. Tran, and Kanika Arora

Abstract

Supplementary Figure from Genetic Ancestry Correlates with Somatic Differences in a Real-World Clinical Cancer Sequencing Cohort

Published
2023

41. Data from Genetic Ancestry Correlates with Somatic Differences in a Real-World Clinical Cancer Sequencing Cohort

Author

Michael F. Berger, Chaitanya Bandlamudi, Debyani Chakravarty, Zsofia K. Stadler, Carol L. Brown, Ahmet Zehir, Nikolaus Schultz, Marc Ladanyi, David B. Solit, Kenneth Offit, Jian Carrot-Zhang, James A. Fagin, Thomas C. Reynolds, Joseph Vijai, Matthew D. Hellmann, Hira A. Rizvi, Anton Safonov, Pedram Razavi, Konrad H. Stopsack, Irina Ostrovnaya, A. Rose Brannon, Shaleigh A. Smith, Subhiksha Nandakumar, Ying L. Liu, Miika Mehine, Yelena Kemel, Thinh N. Tran, and Kanika Arora

Abstract

Accurate ancestry inference is critical for identifying genetic contributors of cancer disparities among populations. Although methods to infer genetic ancestry have historically relied upon genome-wide markers, the adaptation to targeted clinical sequencing panels presents an opportunity to incorporate ancestry inference into routine diagnostic workflows. We show that global ancestral contributions and admixture of continental populations can be quantitatively inferred using markers captured by the MSK-IMPACT clinical panel. In a pan-cancer cohort of 45,157 patients, we observed differences by ancestry in the frequency of somatic alterations, recapitulating known associations and revealing novel associations. Despite the comparable overall prevalence of driver alterations by ancestry group, the proportion of patients with clinically actionable alterations was lower for African (30%) compared with European (33%) ancestry. Although this result is largely explained by population-specific cancer subtype differences, it reveals an inequity in the degree to which different populations are served by existing precision oncology interventions.Significance:We performed a comprehensive analysis of ancestral associations with somatic mutations in a real-world pan-cancer cohort, including >5,000 non-European individuals. Using an FDA-authorized tumor sequencing panel and an FDA-recognized oncology knowledge base, we detected differences in the prevalence of clinically actionable alterations, potentially contributing to health care disparities affecting underrepresented populations.This article is highlighted in the In This Issue feature, p. 2483

Published
2023

42. Supplementary Data from Genetic Ancestry Correlates with Somatic Differences in a Real-World Clinical Cancer Sequencing Cohort

Author

Michael F. Berger, Chaitanya Bandlamudi, Debyani Chakravarty, Zsofia K. Stadler, Carol L. Brown, Ahmet Zehir, Nikolaus Schultz, Marc Ladanyi, David B. Solit, Kenneth Offit, Jian Carrot-Zhang, James A. Fagin, Thomas C. Reynolds, Joseph Vijai, Matthew D. Hellmann, Hira A. Rizvi, Anton Safonov, Pedram Razavi, Konrad H. Stopsack, Irina Ostrovnaya, A. Rose Brannon, Shaleigh A. Smith, Subhiksha Nandakumar, Ying L. Liu, Miika Mehine, Yelena Kemel, Thinh N. Tran, and Kanika Arora

Abstract

Supplementary Data from Genetic Ancestry Correlates with Somatic Differences in a Real-World Clinical Cancer Sequencing Cohort

Published
2023

43. Supplementary Figures 1 - 6, Tables 1 - 2 from A Recurrent ERCC3 Truncating Mutation Confers Moderate Risk for Breast Cancer

Author

Kenneth Offit, Gad Rennert, Larry Norton, Katherine L. Nathanson, Fergus J. Couch, Mark J. Daly, Jeffrey N. Weitzel, Mark Robson, Zsofia K. Stadler, Hedy Rennert, Flavio Lejbkowicz, Liying Zhang, Michael F. Walsh, Susan L. Neuhausen, Steve M. Lipkin, Steven N. Hart, Kasmintan A. Schrader, Shai Carmi, Brandon Wenz, Sarah Kazzaz, Anne Lincoln, Pragna Gaddam, Tinu Thomas, Ann Maria, Kara N. Maxwell, Vignesh Ravichandran, Danylo Villano, Sabine Topka, and Joseph Vijai

Abstract

Supplementary Figure 1. Electropherogram. Supplementary Figure 2. Ramachandran plot. Supplementary Figure 3. Modeling ERCC3 R109X via CRISPR/Cas9 genome editing. Supplementary Figure 4. Haplotype analyses from the TAGC heterozygote carriers. Supplementary Figure 5. ERCC3 mutations present in the cBioPortal (MSKCC) datasets. Supplementary Figure 6. ERCC3 transcript levels in patient derived whole blood. Supplementary Table 1. Family history and pathology information on R109X carriers. Supplementary Table 2. Identity of mutations in HMLE cell lines generated by CRISPR/Cas9.

Published
2023

44. Figure S1 from NBN Pathogenic Germline Variants are Associated with Pan-Cancer Susceptibility and In Vitro DNA Damage Response Defects

Author

Kenneth Offit, Sabine Topka, Rachid Karam, Fran Supek, Michael Berger, Joseph Vijai, Michael Walsh, Mark Robson, Zsofia Stadler, Fergus Couch, Jamie Brower, Katherine L. Nathanson, Susan Domchek, John Petrini, Aalin Izhar, Sita Dandiker, Miika Mehine, Kanika Arora, Benjamin Fesko, Semanti Mukherjee, Yelena Kemel, Amanda Catchings, Temima Wildman, Zoe Steinsnyder, Vignesh Ravichandran, Guillermo Palou-Márquez, Chaitanya Bandlamudi, Aliya Khurram, and Sami Belhadj

Abstract

Supplementary Figure S1. Germline and somatic data from The Cancer Genome Atlas (TCGA) project, representing 10,268 cancer patients with whole exome sequencing data.

Published
2023

45. Data from NBN Pathogenic Germline Variants are Associated with Pan-Cancer Susceptibility and In Vitro DNA Damage Response Defects

Author

Kenneth Offit, Sabine Topka, Rachid Karam, Fran Supek, Michael Berger, Joseph Vijai, Michael Walsh, Mark Robson, Zsofia Stadler, Fergus Couch, Jamie Brower, Katherine L. Nathanson, Susan Domchek, John Petrini, Aalin Izhar, Sita Dandiker, Miika Mehine, Kanika Arora, Benjamin Fesko, Semanti Mukherjee, Yelena Kemel, Amanda Catchings, Temima Wildman, Zoe Steinsnyder, Vignesh Ravichandran, Guillermo Palou-Márquez, Chaitanya Bandlamudi, Aliya Khurram, and Sami Belhadj

Abstract

Purpose:To explore the role of NBN as a pan-cancer susceptibility gene.Experimental Design:Matched germline and somatic DNA samples from 34,046 patients were sequenced using Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets and presumed pathogenic germline variants (PGV) identified. Allele-specific and gene-centered analysis of enrichment was conducted and a validation cohort of 26,407 pan-cancer patients was analyzed. Functional studies utilized cellular models with analysis of protein expression, MRN complex formation/localization, and viability assessment following treatment with γ-irradiation.Results:We identified 83 carriers of 32 NBN PGVs (0.25% of the studied series), 40% of which (33/83) carried the Slavic founder p.K219fs. The frequency of PGVs varied across cancer types. Patients harboring NBN PGVs demonstrated increased loss of the wild-type allele in their tumors [OR = 2.7; confidence interval (CI): 1.4–5.5; P = 0.0024; pan-cancer], including lung and pancreatic tumors compared with breast and colorectal cancers. p.K219fs was enriched across all tumor types (OR = 2.22; CI: 1.3–3.6; P = 0.0018). Gene-centered analysis revealed enrichment of PGVs in cases compared with controls in the European population (OR = 1.9; CI: 1.3–2.7; P = 0.0004), a finding confirmed in the replication cohort (OR = 1.8; CI: 1.2–2.6; P = 0.003). Two novel truncating variants, p.L19* and p.N71fs, produced a 45 kDa fragment generated by alternative translation initiation that maintained binding to MRE11. Cells expressing these fragments showed higher sensitivity to γ-irradiation and lower levels of radiation-induced KAP1 phosphorylation.Conclusions:Burden analyses, biallelic inactivation, and functional evidence support the role of NBN as contributing to a broad cancer spectrum. Further studies in large pan-cancer series and the assessment of epistatic and environmental interactions are warranted to further define these associations.

Published
2023

46. 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

47. Supplementary Tables 1-4 from Common Variants at the 19p13.1 and ZNF365 Loci Are Associated with ER Subtypes of Breast Cancer and Ovarian Cancer Risk in BRCA1 and BRCA2 Mutation Carriers

Author

Jacques Simard, Kenneth Offit, Georgia Chenevix-Trench, Douglas F. Easton, Phuong L. Mai, Mark H. Greene, Paolo Radice, Liliana Varesco, Giuseppe Giannini, Alessandra Viel, Loris Bernard, Monica Barile, Daniela Zaffaroni, Bernard Peissel, Siranoush Manoukian, Paolo Peterlongo, V. Shane Pankratz, Zachary Fredericksen, Noralane M. Lindor, Yuan Chun Ding, Susan L. Neuhausen, Amanda B. Spurdle, Marc D. Tischkowitz, Heli Nevanlinna, Taru A. Muranen, Miguel de la Hoya, Trinidad Caldes, Wolfram Heinritz, Britta Fiebig, Karin Kast, Christian Sutter, Andrea Gehrig, Helmut Deissler, Raymonda Varon-Mateeva, Dorothea Gadzicki, Sabine Preisler-Adams, Dieter Niederacher, Simone Heidemann, Norbert Arnold, Nina Ditsch, Alfons Meindl, Christoph Engel, Barbara Wappenschmidt, Rita K. Schmutzler, Ava Kwong, Orland Diez, Cecelia M. Dorfling, Elizabeth J. van Rensburg, Mary S. Beattie, Patricia A. Ganz, Soo Hwang Teo, Edith Olah, Christine S. Walsh, Beth Y. Karlan, Kunle O. Odunsi, Paul P.D. Pharoah, Simon A. Gayther, Joan Brunet, Lidia Feliubadalo, Ignacio Blanco, Conxi Lazaro, Ramunas Janavicius, Claudine Isaacs, Evgeny N. Imyanitov, Simona Agata, Marco Montagna, Amanda Ewart-Toland, Katie Wakeley, John Boggess, Wendy S. Rubinstein, Jack Basil, Kelly Phillips, Marion Piedmonte, Mark E. Robson, Kara Sarrel, Sohela Shah, Joseph Vijai, Aðalgeir Arason, Finn C. Nielsen, Thomas V.O. Hansen, Anneliese Fink-Retter, Muy-Kheng M. Tea, Christine Rappaport, Christian F. Singer, David E. Goldgar, John L. Hopper, Melissa C. Southey, Alexander Miron, Esther M. John, Wendy K. Chung, MaryBeth Terry, Mary B. Daly, Saundra S. Buys, Carrie L. Snyder, Henry T. Lynch, Linda Akloul, Capucine Delnatte, Isabelle Coupier, Pascal Pujol, Olivier Caron, Brigitte Bressac-de Paillerets, Nadia Boutry-Kryza, Mélanie Léoné, Sylvie Mazoyer, François Cornelis, Laurent Castera, Marion Fassy-Colcombet, Dominique Stoppa-Lyonnet, Andrew K. Godwin, Betsy Bove, Lucy E. Side, M. John Kennedy, Mary E. Porteous, Lisa Walker, Patrick J. Morrison, Shirley V. Hodgson, Fiona Douglas, Carole Brewer, Joan Paterson, Jackie Cook, Trevor Cole, Diana M. Eccles, Rosemarie Davidson, Julian Adlard, Rosalind A. Eeles, Chris Jacobs, D. Gareth Evans, Elena Fineberg, Radka Platte, Steve D. Ellis, Debra Frost, Susan Peock, Margreet G.E.M. Ausems, Rogier A. Oldenburg, Maartje J. Hooning, Marleen Kets, Marinus J. Blok, Juul Wijnen, Hanne E.J. Meijers-Heijboer, Flora E. van Leeuwen, Theo A. van Os, Frans B.L. Hogervorst, Ute Hamann, Javier Benitez, María Isabel Tejada, Mercedes Durán, Ana Osorio, Bohdan Górski, Cezary Cybulski, Jacek Gronwald, Tomasz Byrski, Tomasz Huzarski, Elżbieta Złowocka, Katarzyna Durda, Katarzyna Jaworska, Jan Lubinski, Ania Jakubowska, Susan M. Domchek, Timothy R. Rebbeck, Katherine L. Nathanson, Per Karlsson, Hans Ehrencrona, Maria Soller, Niklas Loman, Gisela Barbany-Bustinza, Anna von Wachenfeldt, Maria A. Caligo, Torben A. Kruse, Anne-Bine Skytte, Uffe Birk Jensen, Anne-Marie Gerdes, Mads Thomassen, Anna Marie Mulligan, Hilmi Ozcelik, Irene L. Andrulis, Olga M. Sinilnikova, Sue Healey, Andrew Lee, Daniel Barrowdale, Lesley McGuffog, Tomas Kirchhoff, Xianshu Wang, Xiaoqing Chen, Jonathan Beesley, Penny Soucy, Karoline B. Kuchenbaecker, Susan J. Ramus, Antonis C. Antoniou, Mia M. Gaudet, and Fergus J. Couch

Abstract

PDF file - 90K

Published
2023

48. Supplementary Tables S2-S5 from Targeting Germline- and Tumor-Associated Nucleotide Excision Repair Defects in Cancer

Author

Kenneth Offit, Joseph Vijai, Elisa de Stanchina, Barry S. Taylor, Jonathan E. Rosenberg, Dean F. Bajorin, Michael F. Berger, David B. Solit, Semanti Mukherjee, Steven M. Lipkin, Gopa Iyer, Charles M. Rudin, Ouathek Ouerfelli, Helena Furberg, Mogens Winkel Madsen, Chaitanya Bandlamudi, Yelena Kemel, Kaitlyn Tkachuk, Vignesh Ravichandran, Zoe Steinsnyder, and Sabine Topka

Abstract

Supplementary Tables S2-S5

Published
2023

49. Supplementary Data from Targeting Germline- and Tumor-Associated Nucleotide Excision Repair Defects in Cancer

Author

Kenneth Offit, Joseph Vijai, Elisa de Stanchina, Barry S. Taylor, Jonathan E. Rosenberg, Dean F. Bajorin, Michael F. Berger, David B. Solit, Semanti Mukherjee, Steven M. Lipkin, Gopa Iyer, Charles M. Rudin, Ouathek Ouerfelli, Helena Furberg, Mogens Winkel Madsen, Chaitanya Bandlamudi, Yelena Kemel, Kaitlyn Tkachuk, Vignesh Ravichandran, Zoe Steinsnyder, and Sabine Topka

Abstract

Supplementary Methods, Supplementary Figures S1-S11, Supplementary Tables S1, S6, S8-11

Published
2023

50. 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

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