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Haiman, Christopher

Mayo Clinic

University of Southern California

Citations 10

Abstract 3583: The Breast Cancer Risk Prediction Project: a resource of 1.8 million women with diverse backgrounds from 20 prospective cohorts to improve breast cancer risk prediction and advance breast cancer epidemiology
Kraft, Peter, O’Meara, Ellen S. , Rohan, Thomas, Neuhouser, Marian L, Vachon, Celine M, Haiman, Christopher, White, Emily , Lee, I‐Min , Gaudet, Mia M. , Chatterjee, Nilanjan , Freeman, Laura E. Beane , Palmer, Julie R. , Genkinger, Jeanine M. , Lacey, James V. , Teras, Lauren R. , Visvanathan, Kala , Milne, Roger L. , Chen, Yu , Eliassen, A. Heather , Kitahara, Cari M. , O’Brien, Katie M. , Anderson, Garnet L. , Campbell, Archie I , Fortner, Renée T. , Lagerros, Ylva Trolle , Sandin, Sven , García‐Closas, Montserrat

Cancer Research | April 21, 2025 | Volume: 85 | Issue: 8_Supplement_1 | Pages: 3583-3583

10.1158/1538-7445.am2025-3583 Get It

Abstract Breast cancer risk assessment tools are widely used in clinical practice to guide decisions regarding screening timing and modality, lifestyle interventions, genetic testing, preventive therapy, and risk-reducing surgery. Although a number of tools designed for the general population are used in practice, they face a series of challenges including: (i) modest discriminatory ability due to lack of a unified model that flexibly incorporates a comprehensive set of risk factors; (ii) inability to produce subtype-specific risk estimates, relevant for tailoring screening and/or preventive strategies (e.g. prophylactic endocrine therapy that is effective only for hormone receptor positive tumors); (iii) lack of data from diverse populations to build models that work well for all women; and, (iv) scarcity of opportunities for comparative validation of different models. The Breast Cancer Risk Prediction Project (BCRPP), a collaboration currently including 20 prospective cohorts from the National Cancer Institute’s Cohort Consortium, is addressing these challenges by harmonizing, sharing, and analyzing data on over 1.8 million women, over 115, 000 of whom have developed breast cancer. The BCRPP is developing a comprehensive tool that will predict breast cancer risk, overall and by subtypes, across major racial and ethnic groups in the United States. This tool incorporates known and emerging risk factors (e.g. reproductive history, anthropometry, smoking, alcohol intake, medication use, mammography, family history, and measured genotypes). In parallel to model building and validation efforts, BCRPP investigators are developing privacy-preserving web and mobile interfaces to deliver the risk tools to patients and clinicians. Here we present descriptive data on participating cohorts (e.g. dates of enrollment, ages at enrollment, length of follow up, numbers of cases by subtype), summarize missing data patterns and our approach to model development and validation that accounts for heterogeneity in missingness patterns across cohorts, and describe data governance procedures and data sharing infrastructure (including pooled and federated analyses, to account for policy limitations on sharing individual data). Descriptive information and procedures for requesting and accessing data are available via the BCRPP data platform (https://epidataplatforms.cancer.gov/bcrpp/). Although originally assembled for risk model development, these data on a large and diverse sample of women with extensive harmonized risk factors and covariates can be a resource to address other outstanding questions in breast cancer epidemiology across time, the lifecourse, and diverse populations. Citation Format: Peter Kraft, Laura Beane-Freeman, Julie Palmer, Ellen O'Meara, Jeanine Genkinger, James Lacey, Thomas Rohan, Lauren Teras, Marian L. Neuhouser, Kala Visvanathan, Celine Vachon, Roger Milne, Christopher Haiman, Yu Chen, Heather Eliassen, Cari Kitahara, Katie O'Brien, Emily White, Garnet Anderson, I-Min Lee, Archie Campbell, Renee Fortner, Ylva Lagerros, Sven Sandin, Mia Gaudet, Montserrat Garcia-Closas, Nilanjan Chatterjee. The Breast Cancer Risk Prediction Project: a resource of 1.8 million women with diverse backgrounds from 20 prospective cohorts to improve breast cancer risk prediction and advance breast cancer epidemiology [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 3583.
Abstract GS4-04: Population-based Estimates of contralateral Breast Cancer Risk among Carriers of Germline Pathogenic Variants in ATM, BRCA1, BRCA2, CHEK2, and PALB2
Yadav, Siddhartha , Dunn, Carolyn, Holtegaard, Susan, Patel, Alpa V. , Martínez, Elena, Haiman, Christopher, Ruddy, Kathryn, Ziogas, Argyrios, Goldgar, David E. , Nathanson, Katherine L. , Yadav, Siddhartha , Nathanson, Katherine L , Boddicker, Nicholas , Na, Jie , Polley, Eric C. , Hu, Chunling , Hart, Steven N. , Gnanaolivu, Rohan , Larson, Nicole, Dunn, Carolyn, Huang, Huaizhi , Teras, Lauren R. , Lacey, James V. , Neuhausen, Susan L. , Bernstein, Leslie , Chen, Fei , Ruddy, Kathryn J. , Olson, Janet E. , John, Esther M. , Kurian, Allison W. , Sandler, Dale P. , O’Brien, Katie M. , Taylor, Jack A. , Weinberg, Clarice R. , Anton‐Culver, Hoda , Zirpoli, Gary , Domchek, Susan M. , Palmer, Julie R. , Weitzel, Jeffrey N. , Kraft, Peter , Couch, Fergus J.

Cancer Research | March 2, 2023 | Volume: 83 | Issue: 5_Supplement | Pages: GS4-04-GS4-04

10.1158/1538-7445.sabcs22-gs4-04 Get It

Abstract Purpose To estimate the risk of contralateral breast cancer (CBC) among women in the general population with germline pathogenic variants (PVs) in ATM, BRCA1, BRCA2, CHEK2, and PALB2. Methods Among 15,104 prospectively followed women within the CARRIERS study treated with ipsilateral surgery for invasive breast cancer, a subset of 14,237 women were identified from population-based studies. The risk of CBC was estimated for PV carriers in each gene compared to women without PVs in a multivariate proportional hazard regression analysis accounting for the competing risk of death and adjusting for patient and tumor characteristics. The primary analyses focused on the overall cohort and on women from the general population. Secondary analyses examined associations by race/ethnicity, age at primary breast cancer diagnosis, menopausal status, and tumor estrogen receptor status. Results Germline BRCA1, BRCA2, and CHEK2 PV carriers with breast cancer were at significantly elevated risk (Hazard ratio ≥ 1.9, p< 0.05) of CBC, whereas only the PALB2 PV carriers with ER-negative breast cancer had elevated risks. In contrast, ATM PV carriers did not have significantly increased CBC risks. African American PV carriers had similarly elevated risks of CBC as non-Hispanic White PV carriers. Among premenopausal women, the 15-year cumulative incidence of CBC was >20% for BRCA1, BRCA2 and CHEK2 PV carriers with breast cancer, and for PALB2 PV carriers with ER-negative breast cancer. The 15-year cumulative incidence of CBC among postmenopausal PV carriers was < 20% for PV carriers in any of the 5 genes. Conclusions Women diagnosed with breast cancer and known to carry germline PVs in BRCA1, BRCA2, CHEK2, or PALB2 are at substantially increased risk of CBC and may benefit from enhanced surveillance and risk-reduction strategies. Citation Format: Siddhartha Yadav, Nicholas J. Boddicker, Jie Na, Eric C. Polley, Chunling Hu, Steven N. Hart, Rohan D. Gnanaolivu, Nicole Larson, Carolyn Dunn, Susan Holtegaard, Huaizhi Huang, Lauren R. Teras, Alpa V. Patel, James V. Lacey Jr., Susan Neuhausen, Leslie Bernstein, Elena Martinez, Christopher Haiman, Fei Chen, Kathryn Ruddy, Janet Olson, Esther John, Allison W. Kurian, Dale P. Sandler, Katie M. O’Brien, Jack A. Taylor, Clarice R. Weinberg, Hoda Anton-Culver, Argyrios Ziogas, Gary R. Zirpoli, David E. Goldgar, Katherine L. Nathanson, Susan Domchek, Julie R. Palmer, Jeffrey Weitzel, Peter Kraft, Fergus J. Couch. Population-based Estimates of contralateral Breast Cancer Risk among Carriers of Germline Pathogenic Variants in ATM, BRCA1, BRCA2, CHEK2, and PALB2 [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr GS4-04.
Breast Cancer Screening Strategies for Women With ATM, CHEK2, and PALB2 Pathogenic Variants
Lowry, Kathryn P. , Geuzinge, H. Amarens , Stout, Natasha K. , Alagöz, Oğuzhan , Hampton, John M. , Koning, Harry J. de , Miglioretti, Diana L. , Ravesteyn, Nicolien T. van , Sprague, Brian L. , Tosteson, Anna N.A. , Weaver, Donald L. , Yaffe, Martin J. , Mandelblatt, Jeanne S. , Kurian, Allison W. , Auer, Paul L. , Berstein, Leslie, Carter, Brian D., Gaudet, Mia M. , Haiman, Christopher, Jacobs, Eric J. , John, Esther M. , Lindström, Sara , Martínez, Elena, Patel, Alpa V. , Reid, Sonya , Taylor, Jack A. , Teras, Lauren R., Vachon, Celine M. , Yao, Song, Ziogas, Argyrios, Goldgar, David E. , Chen, Chen , Chen, C , Miglioretti, Diana L , John, Esther M , Taylor, Jack A , de Koning, Harry J , Kurian, Allison W , Kerlikowske, Karla , Schechter, Clyde B. , Trentham‐Dietz, Amy , Yeh, Jennifer M. , Couch, Fergus J. , Hu, Chunling , Kraft, Peter , Polley, Eric C. , Robson, Mark E. , Hart, Steven N. , Nathanson, Katherine L. , Domchek, Susan M. , Ambrosone, Christine B. , Anton‐Culver, Hoda , Bandera, Elisa V. , Bertrand, Kimberly A. , Burnside, Elizabeth S. , Eliassen, A. Heather , Hodge, James M. , Hunter, David J. , Kooperberg, Charles , Lacey, James V. , Marchand, Loı̈c Le , Ma, Huiyan , Neuhausen, Susan L. , Newcomb, Polly A. , O’Brien, Katie M. , Olson, Janet E. , Ong, Irene M. , Pal, Tuya , Palmer, Julie R. , Rosenberg, Lynn A. , Sandler, Dale P. , Tamimi, Rulla M. , Teras, Lauren R. , Vachon, Celine M. , Weinberg, Clarice R. , Yadav, Siddhartha , Yao, Song , Weitzel, Jeffrey N.

JAMA Oncology | February 17, 2022 | Volume: 8 | Issue: 4 | Pages: 587

10.1001/jamaoncol.2021.6204 Get It

A large-scale multi-ethnic genome-wide association study of coronary artery disease
Tcheandjieu, Catherine , Zhu, Xiang , Clarke, Shoa L. , Lee, Kyung Min , Chen, Fei , Pyarajan, Saiju , Song, Rebecca J. , Plomondon, Mary E. , Waldo, Stephen W. , Sinnott-Armstrong, Nasa , Wojcik, Genevieve L. , Haessler, Jeffrey, Do, Ron , North, Kari, Haiman, Christopher, Bis, Joshua, Shen, Botong, Lange, Leslie A., Lu, Yingchang , Stanaway, Ian B. , Hebbring, Scott J. , Namjou, Bahram , Kaufman, Kenneth M. , Kamatani, Yoichiro, Ritchie, Marylyn D. , Baras, Aris , Natarajan, Pradeep , Raghavan, Sridharan , Lee, Jennifer , Tang, Hua, Sun, Yan V. , O’Donnell, Christopher J. , Kathiresan, Sekar , Saleheen, Danish , Gaziano, J. Michael , Reaven, Peter D. , Cho, Kelly , Graff, Mariaelisa , Huang, Jie , Clarke, Shoa L , Do, Ron , Natarajan, Pradeep , Min Lee, Kyung , Assimes, Themistocles L. , Hilliard, Austin T. , Napolioni, Valerio , Ma, Shining , Fang, Huaying , Gorman, Bryan R. , Maddox, Thomas M , Ho, Yuk-Lam Anne , Buyske, Steven , Kooperberg, Charles , Loos, Ruth J. F. , Verbanck, Marie , Chaudhary, Kumardeep , Avery, Christy L. , Marchand, Loı̈c Le , Wilkens, Lynne R. , Leonard, Hampton L. , Giri, Ayush , Dikilitas, Ozan , Kullo, Iftikhar J. , Jarvik, Gail P. , Gordon, Adam, Koyama, Satoshi , Ito, Kaoru , Ishigaki, Kazuyoshi , Kamatani, Yoichiro, Tsao, Noah L. , Verma, Shefali S. , Kember, Rachel L. , Lotta, Luca Andrea , Levin, Michael G. , Hauser, Elizabeth R. , Miller, Donald Ray , Vujković, Marijana , Huffman, Jennifer E. , Klarin, Derek , Voight, Benjamin F. , Rader, Daniel J , Chang, Kyong‐Mi , Damrauer, Scott M , Lynch, Julie A. , Wilson, Peter W.F. , Tsao, Philip S. , Bick, Alexander G.

No container title available | March 10, 2021 | Volume: No volume available | Issue: No issue available | Pages: No page available

10.21203/rs.3.rs-275591/v1 Get It

Abstract Coronary artery disease (CAD) is a leading cause of death, yet its genetic determinants are not fully elucidated. We report a multi-ethnic genome-wide association study of CAD involving nearly a quarter of a million cases, incorporating the largest cohorts to date of Whites, Blacks, and Hispanics from the Million Veteran Program with existing studies including CARDIoGRAMplusC4D, UK Biobank, and Biobank Japan. We verify substantial and nearly equivalent heritability of CAD across multiple ancestral groups, discover 107 novel loci including the first nine on the X-chromosome, identify the first eight genome-wide significant loci among Blacks and Hispanics, and demonstrate that two common haplotypes are largely responsible for the risk stratification at the well-known 9p21 locus in most populations except those of African origin where both haplotypes are virtually absent. We identify 15 loci for angiographically derived burden of coronary atherosclerosis, which robustly overlap with the strongest and earliest loci reported to date for clinical CAD. Phenome-wide association analyses of novel loci and externally validated polygenic risk scores (PRS) augment signals from the insulin resistance cluster of risk factors and consequences, extend previously established pleiotropic associations of loci with traditional risk factors to include smoking and family history, and confirm a substantially reduced transferability of existing PRS to Blacks. Downstream integrative genomic analyses reinforce the critical role of endothelial, fibroblast, and smooth muscle cells within the coronary vessel wall in CAD susceptibility. Our study highlights the value of a multi-ethnic design in efficiently characterizing the genetic architecture of CAD across all human populations.
Abstract PD3-02: Polygenic risk scores provide clinically meaningful risk stratification among women carrying moderate penetrance pathogenic variants in breast cancer predisposition genes: Results from the CARRIERS study
Gao, Chi , Samara, Raed, Auer, Paul, Gaudet, Mia M. , Haiman, Christopher, Goldgar, David E. , Nathanson, Katherine L. , Nathanson, Katherine L , Polley, Eric C. , Hu, Chunling , Hart, Steven N. , Gnanaolivu, Rohan , Lee, Kun Y. , Na, Jie , Boddicker, Nicholas , Bernstein, Leslie , Trentham‐Dietz, Amy , Yao, Song , Olson, Janet E. , Neuhausen, Susan L. , Weitzel, Jeffrey N. , Domchek, Susan M. , Couch, Fergus J. , Kraft, Peter

Cancer Research | March 26, 2020 | Volume: 80 | Issue: 4_Supplement | Pages: PD3-02-PD3-02

10.1158/1538-7445.sabcs19-pd3-02 Get It

Abstract Background: Pathogenic variants detected in multi-gene cancer predisposition panels are increasingly used to counsel women regarding their risk for breast cancer. However, the clinical implications of moderate penetrance genes (e.g. CHEK2, ATM) remain unclear. Breast MRI is indicated for women with a lifetime risk of breast cancer of >20%, and polygenic risk scores (PRS) based on common variants discovered in recent genome-wide association studies (GWAS) may identify women with pathogenic variants in CHEK2 and ATM who are above or below this level of risk. PRS may also stratify carriers with substantially elevated lifetime risks of breast cancer. Previous work found that PRS modified breast cancer risk in carriers of pathogenic variant in BRCA1 or BRCA2, but the joint effects of pathogenic variants and PRS have not been studied in samples drawn from the general population. There is also no published study evaluating the effect of PRS among women with pathogenic variants in genes other than BRCA1/2 and CHEK2. Here, we evaluated the joint effects of PRS and pathogenic variants in ten established breast cancer predisposition genes in a population-based case-control sample. Method: We analyzed 43,144 non-Hispanic European-ancestry individuals (20,988 controls and 22,120 cases) drawn from 7 cohorts and 2 population-based case-control studies in the CAnceR RIsk Estimates Related to Susceptibility” (CARRIERS) consortium. Targeted sequencing was performed using a dual bar-coded QIAseq panel of breast cancer predisposition genes. Variant calling was conducted with Haplotype Caller and Vardict. The PRS was calculated based on 106 common variants using effect estimates from the largest published breast cancer GWAS. Genetic status was evaluated for 10 breast cancer predisposition genes: ATM, BARD1, BRCA1, BRCA2, BRIP1, CDH1, CHEK2, NF1, PALB2 and TP53. Lasso Penalized regression was performed to assess the combined effect on overall breast cancer of pathogenic variants and common variants (including main and interaction effects between age, family history, carrier status and PRS). The fraction of women at >2-fold increased risk (which is associated with approximately 20% lifetime risk of breast cancer) was calculated for pathogenic variant carriers and non-carriers of different family history and age groups (<40, 40-50, 50-60, 60-70, >70yrs old). Results: Among non-carriers, one standard deviation change in the PRS was associated with a 1.63x change in odds of breast cancer. The best-fitting risk model did not include any PRS-by-carrier interaction terms, implying the relative risk gradient associated with PRS among women with pathogenic variants is similar to that among non-carriers. For carriers of pathogenic variants in moderate penetrance genes with no family history of breast cancer, the PRS can identify 60.6% of ATM pathogenic variant carriers and 30% of CHEK2 pathogenic variant carriers that have less than 2-fold risk of breast cancer; when carriers have a family history of breast cancer, the PRS can identify 30% of ATM pathogenic variant carriers and 11.8% of CHEK2 pathogenic variant carriers with less than 2-fold risk of breast cancer. Conclusion: In our large, population-based case-control study, the effect of the PRS among pathogenic variant carriers was not significantly different than among non-carriers. However, the PRS may be particularly important for estimating breast cancer risk among carriers of pathogenic variants in moderate penetrance genes such as CHEK2 and ATM, enabling a more precise approach for MRI screening strategy and breast cancer risk management. Citation Format: Chi Gao, Eric C. Polley, Chunling Hu, Steven N. Hart, Rohan Gnanaolivu, Kun Y. Lee, Jie Na, Nicholas J. Boddicker, Raed Samara, Paul Auer, Leslie Bernstein, Mia Gaudet, Amy Trentham-Dietz, Song Yao, Christopher Haiman, Janet E. Olson, Susan Neuhausen, Jeffrey N. Weitzel, David E. Goldgar, Susan Domchek, Katherine L. Nathanson, Fergus J. Couch, Peter Kraft, on behalf of the CARRIERS consortium. Polygenic risk scores provide clinically meaningful risk stratification among women carrying moderate penetrance pathogenic variants in breast cancer predisposition genes: Results from the CARRIERS study [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr PD3-02.
A Transcriptome-Wide Association Study Identifies Novel Candidate Susceptibility Genes for Pancreatic Cancer
Zhong, Jun, Jermusyk, Ashley , Wu, Lang , Hoskins, Jason W. , Collins, Irene , Mocci, Evelina , Song, Lei , Chung, Charles C., Xiao, Wenming , Andreotti, Gabriella , Arslan, Alan A. , Babić, Ana , Berndt, Sonja, Borgida, Ayelet , Bracci, Paige M. , Brennan, Paul , Bueno‐de‐Mesquita, Bas , Buring, Julie E. , Childs, Erica J., Du, Mengmeng , Fuchs, Charles S. , Gallinger, Steven , Gaziano, J. Michael, Giovannucci, Edward L. , Goodman, Gary E. , Goodman, Phyllis J. , Haiman, Christopher, Hartge, Patricia, Hasan, Manal , Helzlsouer, Kathy J., Holly, Elizabeth A., Klein, Eric A. , Kogevinas, Manolis, Kurtz, Robert J., Ng, Kimmie , Obazee, Ofure , Oberg, Ann L. , Patel, Alpa V. , Peters, Ulrike , Porta, Miquel , Rothman, Nathaniel , Scélo, Ghislaine , Sesso, Howard D. , Sieri, Sabina , Tjønneland, Anne , Thornquist, Mark, Trichopoulou, Antonia , Visvanathan, Kala , Wactawski‐Wende, Jean , Wentzensen, Nicolas , Yuan, Chen , Zeleniuch‐Jacquotte, Anne , Hoover, Robert N. , Brown, Kevin M. , Jacobs, Eric J. , Li, Donghui , Yu, Kai , Wolpin, Brian M. , Chatterjee, Nilanjan , Shi, Jianxin , Petersen, Gloria M. , Zhong, Jun , Arslan, Alan A , Tjønneland, Anne , Wactawski-Wende, Jean , Visvanathan, Kala , Klein, Eric A , Porta, Miquel , Zeleniuch-Jacquotte, Anne , Zhong, Jun , Yuan, Chen , Hoskins, Jason W , Zhang, Mingfeng , Zhang, Tongwu , Albanes, Demetrius , Bamlet, William R. , Freeman, Laura E. Beane , Brais, Lauren K , Canzian, Federico , Cotterchio, Michelle , Duell, Eric J. , Giles, Graham G. , Goggins, Michael , Marchand, Loı̈c Le , Malats, Núria , Männistö, Satu , Milne, Roger L. , Neale, Rachel Ε. , Orlow, Irene , Rothman, Nathaniel , Severi, Gianluca , Silverman, Debra T. , Sund, Malin , Tobias, Geoffrey S. , Van Den Eeden, Stephen K , White, Emily , Yu, Kai , Kooperberg, Charles , Risch, Harvey A. , Shu, Xiao‐Ou , Chanock, Stephen Jacob , Stolzenberg‐Solomon, Rachael Z. , Klein, Alison P. , Smith, Jill Palmer , Kraft, Peter , Zheng, Wei , Ámundadóttir, Laufey T.

JNCI: Journal of the National Cancer Institute | December 31, 2019 | Volume: 112 | Issue: 10 | Pages: 1003-1012

10.1093/jnci/djz246 Get It

Abstract Background Although 20 pancreatic cancer susceptibility loci have been identified through genome-wide association studies in individuals of European ancestry, much of its heritability remains unexplained and the genes responsible largely unknown. Methods To discover novel pancreatic cancer risk loci and possible causal genes, we performed a pancreatic cancer transcriptome-wide association study in Europeans using three approaches: FUSION, MetaXcan, and Summary-MulTiXcan. We integrated genome-wide association studies summary statistics from 9040 pancreatic cancer cases and 12 496 controls, with gene expression prediction models built using transcriptome data from histologically normal pancreatic tissue samples (NCI Laboratory of Translational Genomics [n = 95] and Genotype-Tissue Expression v7 [n = 174] datasets) and data from 48 different tissues (Genotype-Tissue Expression v7, n = 74–421 samples). Results We identified 25 genes whose genetically predicted expression was statistically significantly associated with pancreatic cancer risk (false discovery rate < .05), including 14 candidate genes at 11 novel loci (1p36.12: CELA3B; 9q31.1: SMC2, SMC2-AS1; 10q23.31: RP11-80H5.9; 12q13.13: SMUG1; 14q32.33: BTBD6; 15q23: HEXA; 15q26.1: RCCD1; 17q12: PNMT, CDK12, PGAP3; 17q22: SUPT4H1; 18q11.22: RP11-888D10.3; and 19p13.11: PGPEP1) and 11 at six known risk loci (5p15.33: TERT, CLPTM1L, ZDHHC11B; 7p14.1: INHBA; 9q34.2: ABO; 13q12.2: PDX1; 13q22.1: KLF5; and 16q23.1: WDR59, CFDP1, BCAR1, TMEM170A). The association for 12 of these genes (CELA3B, SMC2, and PNMT at novel risk loci and TERT, CLPTM1L, INHBA, ABO, PDX1, KLF5, WDR59, CFDP1, and BCAR1 at known loci) remained statistically significant after Bonferroni correction. Conclusions By integrating gene expression and genotype data, we identified novel pancreatic cancer risk loci and candidate functional genes that warrant further investigation.
A Meta-Analysis Of Genome-Wide Association Studies Of Multiple Myeloma In Cases and Controls Of European Origin Identifies a Risk Locus In 12q23.1
Rand, Kristin A. , Camp, Nicola J. , Déan, Eric, Serie, Daniel, Edlund, Christopher K., Curtin, Karen , Huntsman, Scott , Roos, Anneclaire De, Brown, Elizabeth E. , Spinelli, John J. , Severson, Richard K., Bracci, Paige M. , Mohrbacher, Ann, Tricot, Guido , Campa, Daniele , Martin, Thomas G. , Henderson, Brian E., Zangari, Maurizio , Rothman, Nathaniel , Kumar, Shaji , Kolonel, Laurence N. , Wolf, Jeffrey L. , Munshi, Nikhil C. , Haiman, Christopher, Conti, David V. , Vachon, Celine M. , Conti, David V , Martino, Alessandro, Hu, Donglei , Berg, David Van Den , Giles, Graham G. , Ailawadhi, Sikander , Birmann, Brenda M. , Brooks‐Wilson, Angela , Gebregziabher, Mulugeta , Tomasson, Michael H. , Rothman, Nathaniel , Chanock, Stephen Jacob , Colditz, Graham A. , Rajkumar, S. Vincent , Anderson, Kenneth C. , Canzian, Federico , Vachon, Celine M. , Ziv, Elad , Cozen, Wendy

Blood | October 14, 2019 | Volume: 122 | Issue: 21 | Pages: 3111-3111

10.1182/blood.v122.21.3111.3111 Get It

Abstract Introduction The 2-3 fold excess risk of multiple myeloma (MM) among family members of cases suggests a heritable contribution to risk. Recently, a genome-wide association study (GWAS) identified two genome-wide significant and one promising novel loci associated with multiple myeloma risk. To confirm these associations and identify additional novel risk loci, we performed a four-center, genome-wide association meta-analysis. Methods A fixed effects model was used for the meta-analysis which included a total of 1248 cases and 1485 controls, all of European descent, genotyped and analyzed at four separate centers with samples contributed by 10 studies. After quality control and imputation using the 1000 Genomes Project, the analysis included ∼9.5 million variants (λ=1.024). Associations between (single nucleotide polymorphisms) SNP genotypes and MM risk were evaluated under a log-additive model of inheritance, with each study adjusting for age, sex, and up to 10 principal components to control for population stratification. Promising results were replicated in an independent set of 1587 cases and 1770 controls using TaqMan, for a total of 2835 and 3255 cases and controls, respectively, in a combined meta-analysis. Results The discovery meta-analysis did not reveal any genome-wide significant associations (defined as p<5 x 10-8). We used a novel pruning algorithm to identify the top 35 most promising single nucleotide polymorphisms (SNPs) to advance to replication. We successfully genotyped 22 SNPs in the replication set. In the combined discovery and replication meta-analysis, rs1345359 at 12q23.1 was the most strongly associated SNP (P=9 x 10-8, Table 1). The variant allele C was associated with reduced risk (odds ratio discovery set [OR]= 0.69, OR replication set = 0.78, OR combined = 0.74). A second locus at 20q13.2 (rs150220835), was associated with a two-fold increased risk (P=1.22 x 10-6), a borderline increased risk (P=0.0900) and 45% increased risk (P=2.44 X 10-5) in the discovery, replication, and combined analysis sets respectively (Table 1). We also confirmed the association between MM risk and two previously published SNPs (rs4487645, p=0.0007and rs105251, p=0.0044) (Broderick et al., Nat. Genet., 2011). The third previously suggested SNP (rs6746082) was of nominal significance (p=0.0517) in the meta-analysis. Discussion We confirmed the association between MM risk and two previously published SNPs and identified a possible association with a novel SNP in chromosome 12q23.1 (rs1345359). This SNP is not located in a gene nor associated with biofeatures in ENCODE, thus further examination of correlated SNPs is necessary to identify a functional SNP linked to this locus. We also found suggestive evidence for a second locus at 20q13.2 requiring additional replication. Larger studies would improve risk variant discovery for this rare hematologic malignancy. Disclosures: Wolf: Celgene: Honoraria, Research Funding; Millenium: Honoraria; Onyx: Honoraria. Anderson:Celgene, Millennium, BMS, Onyx: Membership on an entity’s Board of Directors or advisory committees; Acetylon, Oncopep: Scientific Founder , Scientific Founder Other.
Genetic Susceptibility Markers of Multiple Myeloma in African-Americans
Rand, Kristin A. , Song, Chi , Hwang, Amie E. , Huff, Carol Ann , Bernal‐Mizrachi, Leon , Sheng, Xin , Graff, John J., Zimmerman, Todd M., Pawlish, Karen , Stram, Alexander , Strom, Sara S., Terebelo, Howard R. , Stanford, Janet L. , Goodman, Phyllis J. , Berndt, Sonja I. , Carpten, John, Hennis, Anselm , Chu, Lisa W., Driver, W. Ryan, Leske, M. Christina, Murphy, Adam B. , Stevens, Victoria L. , Pettaway, Curtis A. , Witte, John S. , Zheng, Siqun L., Xu, Jianfeng , Munshi, Nikhil C. , Hsing, Ann W. , Mehta, Jayesh, Signorello, Lisa B., Nemesure, Barbara , Mohrbacher, Ann, Janakiraman, Nalini, Blot, William J. , Henderson, Brian E., Kolonel, Laurence N. , Zonder, Jeffrey A. , Haiman, Christopher, Tomasson, Michael H. , Ailawadhi, Sikander , Berg, David Van Den , Conti, David V. , Peters, Edward , Singhal, Seema , Bock, Cathryn Hufford , Colditz, Graham A. , Stram, Alex , Rybicki, Benjamin A. , Kittles, Rick A. , Casey, Graham , Klein, Eric A. , John, Esther M. , Neslund-Dudas, Christine M , Zheng, Wei , Wu, Szu‐Yuan , Ingles, Sue A. , Chanock, Stephen Jacob , Anderson, Kenneth C. , Chiu, Brian C.‐H. , Orlowski, Robert Z. , Lonial, Sagar , Stram, Daniel O. , Cozen, Wendy

Blood | October 10, 2019 | Volume: 124 | Issue: 21 | Pages: 2030-2030

10.1182/blood.v124.21.2030.2030 Get It

Abstract Multiple myeloma (MM) is 2-3 times more common among African-Americans compared to non-Hispanic whites. The 2-3-fold increased risk among family members of cases suggests a genetic contribution to risk. Genome-wide association studies (GWAS) in populations of European ancestry have identified seven novel risk loci at 2p23.3 (rs6746082), 3q26.2 (rs10936599), 3p22.1 (rs1052501), 6p21.32 (rs2285803), 7p15.3 (rs4487645), 17p11.2 (rs4273077) and 22q13.1 (rs877529) (Broderick, et al. Nat Genet, 2011, Chubb, et al. Nat Genet, 2013), three of which were replicated in another European series (Martino et al., Br J Haematol, 2012). Here we examined the index signals and conducted fine-mapping for each locus in a case-control study of 1,049 multiple myeloma cases and 7,084 controls of African ancestry to identify better markers of risk and novel independent loci in seven previously reported regions in this high risk population. Incident cases were recruited from 10 clinical centers and SEER cancer registries from 2011 to 2013 and genotyped using the Illumina HumanCore GWAS array. Control data were obtained from previous genome-wide studies of breast and prostate cancer, genotyped using the Illumina 1M-Duo in 4425 male controls from the African Ancestry Prostate Cancer Consortium (consisting of 14 independent studies) and 2632 female controls from a breast cancer GWAS of African-American women (consisting of 9 independent studies). Imputation to 1000 Genomes (March 2012 release) was conducted for regions around six of the previously identified single nucleotide polymorphisms [SNPs] (the HLA region harboring rs2285803 is still being imputed, results will be presented). A case-control analysis of SNPs/indels >1% frequency within 250 kb of each index variant was conducted using unconditional multivariable logistic regression adjusting for age, sex and five leading principal components. Region-specific alpha levels were determined through permutation tests. The minimum alpha level across the six regions was α=0.002. All previously reported risk variants were common in African-Americans (minor allele frequency [MAF] >0.05). For five of the six SNPs, we had ≥94% power to detect the same effect observed in non-Hispanic whites, and 64% power for the less common variant rs10936599 (MAF=0.07). We observed directionally consistent effects (odds ratio [OR]>1) for the six risk variants tested, with three replicating at p≤0.05 (7p15.3, p=1.4x10-7; 17p11.2, p=0.05; 22q13.1, p=0.02). For three of the six regions, we observed better markers of risk in African-Americans that were correlated with the index SNP in Europeans (7p15.3, rs56333627, p=1.5x10-5, r2=0.89; 17p11.2, rs34562254, p=2.9x10-3, r2=0.90; 22q13.1, rs2092410, p=1.1x10-4 r2=.71). The missense variant identified in the 17p11.2 region (rs34562254, Pro251Leu) is located in TNFRSF13B, which encodes the protein TACI, a B cell surface receptor which plays a role in B cell maturation, apoptosis and antibody production by inducing activation of transcription factors including NFAT and NFκβ. In addition, there is evidence suggesting that TACI is involved in MM pathogenesis. Our results demonstrate that many of the risk loci for MM found in European ancestry populations are also risk loci in men and women of African ancestry and that by fine-mapping, we are able to identify variants that better capture risk in populations of African ancestry. Disclosures Terebelo: Celgene Corp: Membership on an entity's Board of Directors or advisory committees. Lonial:Millennium: The Takeda Oncology Company: Consultancy, Research Funding; Celgene: Consultancy, Research Funding; Novartis: Consultancy, Research Funding; Bristol-Myers Squibb: Consultancy, Research Funding; Onyx Pharmaceuticals: Consultancy, Research Funding.
Abstract 4177: The joint effects of polygenic risk scores and pathogenic variants in cancer predisposition genes on breast cancer risk in the general population: results from the CARRIERS study
Gao, Chi , Lilyquist, Jenna , Eckloff, Bruce W., Samara, Raed, Klebba, Josh, Auer, Paul, Gaudet, Mia M. , Haiman, Christopher, Goldgar, David E. , Nathanson, Katherine L. , Nathanson, Katherine L , Hu, Chunling , Hart, Steven N. , Gnanaolivu, Rohan , Lee, Kun Y. , Boddicker, Nicholas , Bernstein, Leslie , Anton‐Culver, Hoda , Trentham‐Dietz, Amy , Palmer, Julie R. , Yao, Song , Olson, Janet E. , Domchek, Susan M. , Weitzel, Jeffrey N. , Polley, Eric C. , Couch, Fergus J. , Kraft, Peter

Cancer Research | August 7, 2019 | Volume: 79 | Issue: 13_Supplement | Pages: 4177-4177

10.1158/1538-7445.am2019-4177 Get It

Abstract Background: Understanding the joint effect on breast cancer risk of rare pathogenic variants in cancer predisposition genes and polygenic risk scores (PRS) from common variants can enable a precision approach to breast cancer management. Previous work found that PRS were associated with breast cancer risk in BRCA1 and BRCA2 mutation carriers recruited from cancer genetics clinics (Kuchenbaecker et al. JNCI 2017). The joint effects of pathogenic variants and PRS have not been studied in samples drawn from the general population. There is also no existing study evaluating the effect of PRS in mutation carriers in genes other than BRCA1/2. Here we evaluate the joint effects of PRS and pathogenic mutations in established cancer predisposition genes in a population-based case-control sample. Method: We analyzed 53,199 European-ancestry individuals (20,730 controls and 21,272 cases) drawn from 7 cohorts and 2 population-based case-control studies in the CAnceR RIsk Estimates Related to Susceptibility” (CARRIERS) consortium. Targeted sequencing was performed using dual bar-coded QIAseq. Mutation calling was conducted with Haplotype Caller and Vardict. We sequenced 18 breast cancer predisposition genes: ATM, BARD1, BRCA1, BRCA2, BRIP1, CDH1, CDKN2A, CHECK2, FANCC, MLH1, MSH2, MSH6, NF1, PALB2, PTEN, RAD51C, RAD51D and TP53. The PRS was calculated based on 128 common variants using effect estimates from the largest published breast cancer GWAS. The PRS was standardized to a mean of 0 and standard deviation of 1. Logistic regression was performed to assess the combined effect of identified mutation and common variants (including main and interaction effects for carrier status and PRS). Results: A total of 1,770 pathogenic mutations were observed. About 1% of the study sample had mutations in either BRCA1 (n=209) or BRCA2 gene (n=305), and 2.2% had mutations in other genes (n=1,176). The effect of PRS in BRCA1 carriers was OR= 0.97 (95%CI: 0.62, 1.52); however, this is not statistically significantly different from the PRS in non-carriers [OR=1.23 (95%CI: 1.20, 1.25)] or previous estimates in carriers [OR: 1.14, 95%CI: 1.11-1.17]. The effect of PRS in BRCA2 carriers was OR=1.87 (95%CI: 1.31, 2.78) which was statistically significantly different from that of the non-carriers. Among the mutation carriers in genes other than BRCA, the effect of PRS on breast cancer was OR=1.00 (95%CI: 0.88,1.15). Conclusion: Consistent with previous studies, we did not find evidence that the effect of the PRS among BRCA1 carriers was statistically significantly different than non-carriers. We found some evidence that the PRS effect may be larger among BRCA2 carriers than non-carriers. Our results also suggest that PRS may not have a strong effect on breast cancer risk in mutation carriers of other predisposition genes; further work is needed for verification. Citation Format: Chi Gao, Chunling Hu, Steven N. Hart, Rohan Gnanaolivu, Kun Y. Lee, Jenna Lilyquist, Nicholas J. Boddicker, Bruce Eckloff, Raed Samara, Josh Klebba, Paul Auer, Leslie Bernstein, Mia Gaudet, Hoda Anton-Culver, Amy Trentham-Dietz, Julie R. Palmer, Song Yao, Christopher Haiman, Janet E. Olson, Susan Domchek, Jeffrey Weitzel, David Goldgar, Katherine L. Nathanson, Eric C. Polley, Fergus J. Couch, Peter Kraft. The joint effects of polygenic risk scores and pathogenic variants in cancer predisposition genes on breast cancer risk in the general population: results from the CARRIERS study [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4177.
Abstract LB-282: Transethnic genome-wide association study of colorectal cancer identifies a new susceptibility locus in VTI1A
Wang, Hansong, Burnett, Terrilea, Kono, Suminori , Haiman, Christopher, Loo, Lenora W. M. , Kolonel, Laurence, Henderson, Brian E., Signorello, Lisa B., Blot, William J. , West, Dee W., Bezieau, Stéphane , Berndt, Sonja I. , Zanke, Brent W., Lindor, Noralane M. , Jenkins, Mark A. , Gallinger, Steven , Casey, Graham , Stenzel, Stephanie L., Peters, Ulrike , Gruber, Stephen B. , Stram, D. O., Iwasaki, Motoki , Wilkens, Lynne R. , Berg, David Van Den , Keku, Temitope O , Sandler, Robert S. , Newcomb, Polly A. , Pande, Mala , Amos, Christopher I. , Hsu, Li , Haile, Robert W. , Hopper, John L. , Schumacher, Fredrick R. , Tsugane, Shoichiro , Marchand, Loı̈c Le , Jenkins, Mark A , Bézieau, Stéphane

Cancer Research | May 1, 2015 | Volume: 74 | Issue: 19_Supplement | Pages: LB-282-LB-282

10.1158/1538-7445.am2014-lb-282 Get It

Abstract To identify genetic variants that contribute to colorectal cancer (CRC) susceptibility, we performed a meta-analysis of two genome-wide association studies in 2,627 cases and 3,797 controls of Japanese ancestry and 1,894 cases and 4,703 controls of African ancestry, followed by a replication of genome-wide statistically significant associations (P &lt; 5E-8) in 16,823 cases and 18,211 controls of European ancestry. This study revealed a new pan-ethnic CRC risk locus at 10q25 (rs12241008, intronic to VTI1A; P=1.5E-9), providing additional insight into the etiology of CRC and highlighting the value of association mapping in diverse populations. Citation Format: Hansong Wang, Terrilea Burnett, Suminori Kono, Christopher Haiman, Motoki Iwasaki, Lynne Wilkens, Lenora Loo, David Van Den Berg, Laurence Kolonel, Brian Henderson, Temitope Keku, Robert Sandler, Lisa Signorello, William Blot, Polly Newcomb, Mala Pande, Christopher Amos, Dee West, Stéphane Bézieau, Sonja Berndt, Brent Zanke, Li Hsu, Noralane Lindor, Robert Haile, John Hopper, Mark Jenkins, Steven Gallinger, Graham Casey, Stephanie Stenzel, Fredrick Schumacher, Ulrike Peters, Stephen Gruber, Shoichiro Tsugane, Dan Stram, Loic Le Marchand. Transethnic genome-wide association study of colorectal cancer identifies a new susceptibility locus in VTI1A. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr LB-282. doi:10.1158/1538-7445.AM2014-LB-282