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1. Discovery and fine-mapping of height loci via high-density imputation of GWASs in individuals of African ancestry

Author

Graff, Mariaelisa, Justice, Anne E, Young, Kristin L, Marouli, Eirini, Zhang, Xinruo, Fine, Rebecca S, Lim, Elise, Buchanan, Victoria, Rand, Kristin, Feitosa, Mary F, Wojczynski, Mary K, Yanek, Lisa R, Shao, Yaming, Rohde, Rebecca, Adeyemo, Adebowale A, Aldrich, Melinda C, Allison, Matthew A, Ambrosone, Christine B, Ambs, Stefan, Amos, Christopher, Arnett, Donna K, Atwood, Larry, Bandera, Elisa V, Bartz, Traci, Becker, Diane M, Berndt, Sonja I, Bernstein, Leslie, Bielak, Lawrence F, Blot, William J, Bottinger, Erwin P, Bowden, Donald W, Bradfield, Jonathan P, Brody, Jennifer A, Broeckel, Ulrich, Burke, Gregory, Cade, Brian E, Cai, Qiuyin, Caporaso, Neil, Carlson, Chris, Carpten, John, Casey, Graham, Chanock, Stephen J, Chen, Guanjie, Chen, Minhui, Chen, Yii-Der I, Chen, Wei-Min, Chesi, Alessandra, Chiang, Charleston WK, Chu, Lisa, Coetzee, Gerry A, Conti, David V, Cooper, Richard S, Cushman, Mary, Demerath, Ellen, Deming, Sandra L, Dimitrov, Latchezar, Ding, Jingzhong, Diver, W Ryan, Duan, Qing, Evans, Michele K, Falusi, Adeyinka G, Faul, Jessica D, Fornage, Myriam, Fox, Caroline, Freedman, Barry I, Garcia, Melissa, Gillanders, Elizabeth M, Goodman, Phyllis, Gottesman, Omri, Grant, Struan FA, Guo, Xiuqing, Hakonarson, Hakon, Haritunians, Talin, Harris, Tamara B, Harris, Curtis C, Henderson, Brian E, Hennis, Anselm, Hernandez, Dena G, Hirschhorn, Joel N, McNeill, Lorna Haughton, Howard, Timothy D, Howard, Barbara, Hsing, Ann W, Hsu, Yu-Han H, Hu, Jennifer J, Huff, Chad D, Huo, Dezheng, Ingles, Sue A, Irvin, Marguerite R, John, Esther M, Johnson, Karen C, Jordan, Joanne M, Kabagambe, Edmond K, Kang, Sun J, Kardia, Sharon L, Keating, Brendan J, Kittles, Rick A, Klein, Eric A, Kolb, Suzanne, and Kolonel, Laurence N

Subjects
Human Genome, Genetics, Africa, Black or African American, Black People, Body Height, Europe, Female, Genome-Wide Association Study, Humans, Male, Polymorphism, Single Nucleotide, African ancestry, fine-mapping, genome-wide, height, Biological Sciences, Medical and Health Sciences, Genetics & Heredity
Abstract

Although many loci have been associated with height in European ancestry populations, very few have been identified in African ancestry individuals. Furthermore, many of the known loci have yet to be generalized to and fine-mapped within a large-scale African ancestry sample. We performed sex-combined and sex-stratified meta-analyses in up to 52,764 individuals with height and genome-wide genotyping data from the African Ancestry Anthropometry Genetics Consortium (AAAGC). We additionally combined our African ancestry meta-analysis results with published European genome-wide association study (GWAS) data. In the African ancestry analyses, we identified three novel loci (SLC4A3, NCOA2, ECD/FAM149B1) in sex-combined results and two loci (CRB1, KLF6) in women only. In the African plus European sex-combined GWAS, we identified an additional three novel loci (RCCD1, G6PC3, CEP95) which were equally driven by AAAGC and European results. Among 39 genome-wide significant signals at known loci, conditioning index SNPs from European studies identified 20 secondary signals. Two of the 20 new secondary signals and none of the 8 novel loci had minor allele frequencies (MAF) < 5%. Of 802 known European height signals, 643 displayed directionally consistent associations with height, of which 205 were nominally significant (p < 0.05) in the African ancestry sex-combined sample. Furthermore, 148 of 241 loci contained ≤20 variants in the credible sets that jointly account for 99% of the posterior probability of driving the associations. In summary, trans-ethnic meta-analyses revealed novel signals and further improved fine-mapping of putative causal variants in loci shared between African and European ancestry populations.

Published
2021

2. Genome-wide association study confirms lung cancer susceptibility loci on chromosomes 5p15 and 15q25 in an African-American population

Author

Zanetti, Krista A, Wang, Zhaoming, Aldrich, Melinda, Amos, Christopher I, Blot, William J, Bowman, Elise D, Burdette, Laurie, Cai, Qiuyin, Caporaso, Neil, Chung, Charles C, Gillanders, Elizabeth M, Haiman, Christopher A, Hansen, Helen M, Henderson, Brian E, Kolonel, Laurence N, Le Marchand, Loic, Li, Shengchao, McNeill, Lorna Haughton, Ryan, Bríd M, Schwartz, Ann G, Sison, Jennette D, Spitz, Margaret R, Tucker, Margaret, Wenzlaff, Angela S, Wiencke, John K, Wilkens, Lynne, Wrensch, Margaret R, Wu, Xifeng, Zheng, Wei, Zhou, Weiyin, Christiani, David, Palmer, Julie R, Penning, Trevor M, Rieber, Alyssa G, Rosenberg, Lynn, Ruiz-Narvaez, Edward A, Su, Li, Vachani, Anil, Wei, Yongyue, Whitehead, Alexander S, Chanock, Stephen J, and Harris, Curtis C

Subjects
Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Cancer, Lung, Women's Health, Human Genome, Clinical Research, Prevention, Genetics, Lung Cancer, 2.1 Biological and endogenous factors, Respiratory, Black or African American, Case-Control Studies, Chromosomes, Human, Pair 15, Chromosomes, Human, Pair 5, Genetic Predisposition to Disease, Genome-Wide Association Study, Humans, Lung Neoplasms, Polymorphism, Single Nucleotide, Population Surveillance, Quantitative Trait Loci, Genome-wide association study, Lung neoplasms, Smoking, African Americans, Telomerase, Receptors, Cholinergic, Clinical Sciences, Oncology & Carcinogenesis, Clinical sciences, Oncology and carcinogenesis
Abstract

ObjectivesGenome-wide association studies (GWAS) of lung cancer have identified regions of common genetic variation with lung cancer risk in Europeans who smoke and never-smoking Asian women. This study aimed to conduct a GWAS in African Americans, who have higher rates of lung cancer despite smoking fewer cigarettes per day when compared with Caucasians. This population provides a different genetic architecture based on underlying African ancestry allowing the identification of new regions and exploration of known regions for finer mapping.Materials and methodsWe genotyped 1,024,001 SNPs in 1737 cases and 3602 controls in stage 1, followed by a replication phase of 20 SNPs (p

Published
2016

3. Female chromosome X mosaicism is age-related and preferentially affects the inactivated X chromosome

Author

Machiela, Mitchell J, Zhou, Weiyin, Karlins, Eric, Sampson, Joshua N, Freedman, Neal D, Yang, Qi, Hicks, Belynda, Dagnall, Casey, Hautman, Christopher, Jacobs, Kevin B, Abnet, Christian C, Aldrich, Melinda C, Amos, Christopher, Amundadottir, Laufey T, Arslan, Alan A, Beane-Freeman, Laura E, Berndt, Sonja I, Black, Amanda, Blot, William J, Bock, Cathryn H, Bracci, Paige M, Brinton, Louise A, Bueno-de-Mesquita, H Bas, Burdett, Laurie, Buring, Julie E, Butler, Mary A, Canzian, Federico, Carreon, Tania, Chaffee, Kari G, Chang, I-Shou, Chatterjee, Nilanjan, Chen, Chu, Chen, Constance, Chen, Kexin, Chung, Charles C, Cook, Linda S, Bou, Marta Crous, Cullen, Michael, Davis, Faith G, De Vivo, Immaculata, Ding, Ti, Doherty, Jennifer, Duell, Eric J, Epstein, Caroline G, Fan, Jin-Hu, Figueroa, Jonine D, Fraumeni, Joseph F, Friedenreich, Christine M, Fuchs, Charles S, Gallinger, Steven, Gao, Yu-Tang, Gapstur, Susan M, Garcia-Closas, Montserrat, Gaudet, Mia M, Gaziano, J Michael, Giles, Graham G, Gillanders, Elizabeth M, Giovannucci, Edward L, Goldin, Lynn, Goldstein, Alisa M, Haiman, Christopher A, Hallmans, Goran, Hankinson, Susan E, Harris, Curtis C, Henriksson, Roger, Holly, Elizabeth A, Hong, Yun-Chul, Hoover, Robert N, Hsiung, Chao A, Hu, Nan, Hu, Wei, Hunter, David J, Hutchinson, Amy, Jenab, Mazda, Johansen, Christoffer, Khaw, Kay-Tee, Kim, Hee Nam, Kim, Yeul Hong, Kim, Young Tae, Klein, Alison P, Klein, Robert, Koh, Woon-Puay, Kolonel, Laurence N, Kooperberg, Charles, Kraft, Peter, Krogh, Vittorio, Kurtz, Robert C, LaCroix, Andrea, Lan, Qing, Landi, Maria Teresa, Le Marchand, Loic, Li, Donghui, Liang, Xiaolin, Liao, Linda M, Lin, Dongxin, Liu, Jianjun, Lissowska, Jolanta, Lu, Lingeng, Magliocco, Anthony M, and Malats, Nuria

Published
2016

4. Genome-wide scan of 29,141 African Americans finds no evidence of selection since admixture

Author

Bhatia, Gaurav, Tandon, Arti, Aldrich, Melinda C., Ambrosone, Christine B., Amos, Christopher, Bandera, Elisa V., Berndt, Sonja I., Bernstein, Leslie, Blot, William J., Bock, Cathryn H., Caporaso, Neil, Casey, Graham, Deming, Sandra L., Diver, W. Ryan, Gapstur, Susan M., Gillanders, Elizabeth M., Harris, Curtis C., Henderson, Brian E., Ingles, Sue A., Isaacs, William, John, Esther M., Kittles, Rick A., Larkin, Emma, McNeill, Lorna H., Millikan, Robert C., Murphy, Adam, Neslund-Dudas, Christine, Nyante, Sarah, Press, Michael F., Rodriguez-Gil, Jorge L., Rybicki, Benjamin A., Schwartz, Ann G., Signorello, Lisa B., Spitz, Margaret, Strom, Sara S., Tucker, Margaret A., Wiencke, John K., Witte, John S., Wu, Xifeng, Yamamura, Yuko, Zanetti, Krista A., Zheng, Wei, Ziegler, Regina G., Chanock, Stephen J., Haiman, Christopher A., Reich, David, and Price, Alkes L.

Subjects
Quantitative Biology - Populations and Evolution
Abstract

We scanned through the genomes of 29,141 African Americans, searching for loci where the average proportion of African ancestry deviates significantly from the genome-wide average. We failed to find any genome-wide significant deviations, and conclude that any selection in African Americans since admixture is sufficiently weak that it falls below the threshold of our power to detect it using a large sample size. These results stand in contrast to the findings of a recent study of selection in African Americans. That study, which had 15 times fewer samples, reported six loci with significant deviations. We show that the discrepancy is likely due to insufficient correction for multiple hypothesis testing in the previous study. The same study reported 14 loci that showed greater population differentiation between African Americans and Nigerian Yoruba than would be expected in the absence of natural selection. Four such loci were previously shown to be genome-wide significant and likely to be affected by selection, but we show that most of the 10 additional loci are likely to be false positives. Additionally, the most parsimonious explanation for the loci that have significant evidence of unusual differentiation in frequency between Nigerians and Africans Americans is selection in Africa prior to their forced migration to the Americas.

Published
2013

5. Genome-wide association meta-analyses combining multiple risk phenotypes provide insights into the genetic architecture of cutaneous melanoma susceptibility

Author

Landi, Maria Teresa, Bishop, D. Timothy, MacGregor, Stuart, Machiela, Mitchell J., Stratigos, Alexander J., Ghiorzo, Paola, Brossard, Myriam, Calista, Donato, Choi, Jiyeon, Fargnoli, Maria Concetta, Zhang, Tongwu, Rodolfo, Monica, Trower, Adam J., Menin, Chiara, Martinez, Jacobo, Hadjisavvas, Andreas, Song, Lei, Stefanaki, Irene, Scolyer, Richard, Yang, Rose, Goldstein, Alisa M., Potrony, Miriam, Kypreou, Katerina P., Pastorino, Lorenza, Queirolo, Paola, Pellegrini, Cristina, Cattaneo, Laura, Zawistowski, Matthew, Gimenez-Xavier, Pol, Rodriguez, Arantxa, Elefanti, Lisa, Manoukian, Siranoush, Rivoltini, Licia, Smith, Blair H., Loizidou, Maria A., Del Regno, Laura, Massi, Daniela, Mandala, Mario, Khosrotehrani, Kiarash, Akslen, Lars A., Amos, Christopher I., Andresen, Per A., Avril, Marie-Françoise, Azizi, Esther, Soyer, H. Peter, Bataille, Veronique, Dalmasso, Bruna, Bowdler, Lisa M., Burdon, Kathryn P., Chen, Wei V., Codd, Veryan, Craig, Jamie E., Dębniak, Tadeusz, Falchi, Mario, Fang, Shenying, Friedman, Eitan, Simi, Sarah, Galan, Pilar, Garcia-Casado, Zaida, Gillanders, Elizabeth M., Gordon, Scott, Green, Adele, Gruis, Nelleke A., Hansson, Johan, Harland, Mark, Harris, Jessica, Helsing, Per, Henders, Anjali, Hočevar, Marko, Höiom, Veronica, Hunter, David, Ingvar, Christian, Kumar, Rajiv, Lang, Julie, Lathrop, G. Mark, Lee, Jeffrey E., Li, Xin, Lubiński, Jan, Mackie, Rona M., Malt, Maryrose, Malvehy, Josep, McAloney, Kerrie, Mohamdi, Hamida, Molven, Anders, Moses, Eric K., Neale, Rachel E., Novaković, Srdjan, Nyholt, Dale R., Olsson, Håkan, Orr, Nicholas, Fritsche, Lars G., Puig-Butille, Joan Anton, Qureshi, Abrar A., Radford-Smith, Graham L., Randerson-Moor, Juliette, Requena, Celia, Rowe, Casey, Samani, Nilesh J., Sanna, Marianna, Schadendorf, Dirk, Schulze, Hans-Joachim, Simms, Lisa A., Smithers, Mark, Song, Fengju, Swerdlow, Anthony J., van der Stoep, Nienke, Kukutsch, Nicole A., Visconti, Alessia, Wallace, Leanne, Ward, Sarah V., Wheeler, Lawrie, Sturm, Richard A., Hutchinson, Amy, Jones, Kristine, Malasky, Michael, Vogt, Aurelie, Zhou, Weiyin, Pooley, Karen A., Elder, David E., Han, Jiali, Hicks, Belynda, Hayward, Nicholas K., Kanetsky, Peter A., Brummett, Chad, Montgomery, Grant W., Olsen, Catherine M., Hayward, Caroline, Dunning, Alison M., Martin, Nicholas G., Evangelou, Evangelos, Mann, Graham J., Long, Georgina, Pharoah, Paul D. P., Easton, Douglas F., Barrett, Jennifer H., Cust, Anne E., Abecasis, Goncalo, Duffy, David L., Whiteman, David C., Gogas, Helen, De Nicolo, Arcangela, Tucker, Margaret A., Newton-Bishop, Julia A., Peris, Ketty, Chanock, Stephen J., Demenais, Florence, Brown, Kevin M., Puig, Susana, Nagore, Eduardo, Shi, Jianxin, Iles, Mark M., and Law, Matthew H.

Published
2020
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6. Characterization of Large Structural Genetic Mosaicism in Human Autosomes

Author

Machiela, Mitchell J, Zhou, Weiyin, Sampson, Joshua N, Dean, Michael C, Jacobs, Kevin B, Black, Amanda, Brinton, Louise A, Chang, I-Shou, Chen, Chu, Chen, Constance, Chen, Kexin, Cook, Linda S, Bou, Marta Crous, De Vivo, Immaculata, Doherty, Jennifer, Friedenreich, Christine M, Gaudet, Mia M, Haiman, Christopher A, Hankinson, Susan E, Hartge, Patricia, Henderson, Brian E, Hong, Yun-Chul, Hosgood, H Dean, Hsiung, Chao A, Hu, Wei, Hunter, David J, Jessop, Lea, Kim, Hee Nam, Kim, Yeul Hong, Kim, Young Tae, Klein, Robert, Kraft, Peter, Lan, Qing, Lin, Dongxin, Liu, Jianjun, Le Marchand, Loic, Liang, Xiaolin, Lissowska, Jolanta, Lu, Lingeng, Magliocco, Anthony M, Matsuo, Keitaro, Olson, Sara H, Orlow, Irene, Park, Jae Yong, Pooler, Loreall, Prescott, Jennifer, Rastogi, Radhai, Risch, Harvey A, Schumacher, Fredrick, Seow, Adeline, Setiawan, Veronica Wendy, Shen, Hongbing, Sheng, Xin, Shin, Min-Ho, Shu, Xiao-Ou, Berg, David VanDen, Wang, Jiu-Cun, Wentzensen, Nicolas, Wong, Maria Pik, Wu, Chen, Wu, Tangchun, Wu, Yi-Long, Xia, Lucy, Yang, Hannah P, Yang, Pan-Chyr, Zheng, Wei, Zhou, Baosen, Abnet, Christian C, Albanes, Demetrius, Aldrich, Melinda C, Amos, Christopher, Amundadottir, Laufey T, Berndt, Sonja I, Blot, William J, Bock, Cathryn H, Bracci, Paige M, Burdett, Laurie, Buring, Julie E, Butler, Mary A, Carreón, Tania, Chatterjee, Nilanjan, Chung, Charles C, Cook, Michael B, Cullen, Michael, Davis, Faith G, Ding, Ti, Duell, Eric J, Epstein, Caroline G, Fan, Jin-Hu, Figueroa, Jonine D, Fraumeni, Joseph F, Freedman, Neal D, Fuchs, Charles S, Gao, Yu-Tang, Gapstur, Susan M, Patiño-Garcia, Ana, Garcia-Closas, Montserrat, Gaziano, J Michael, Giles, Graham G, and Gillanders, Elizabeth M

Subjects
Biological Sciences, Genetics, Human Genome, Clinical Research, 2.1 Biological and endogenous factors, Aetiology, Aged, Chromosome Aberrations, Female, Genome, Human, Genome-Wide Association Study, Genotype, Humans, Male, Middle Aged, Mosaicism, Neoplasms, Medical and Health Sciences, Genetics & Heredity, Biological sciences, Biomedical and clinical sciences, Health sciences
Abstract

Analyses of genome-wide association study (GWAS) data have revealed that detectable genetic mosaicism involving large (>2 Mb) structural autosomal alterations occurs in a fraction of individuals. We present results for a set of 24,849 genotyped individuals (total GWAS set II [TGSII]) in whom 341 large autosomal abnormalities were observed in 168 (0.68%) individuals. Merging data from the new TGSII set with data from two prior reports (the Gene-Environment Association Studies and the total GWAS set I) generated a large dataset of 127,179 individuals; we then conducted a meta-analysis to investigate the patterns of detectable autosomal mosaicism (n = 1,315 events in 925 [0.73%] individuals). Restricting to events >2 Mb in size, we observed an increase in event frequency as event size decreased. The combined results underscore that the rate of detectable mosaicism increases with age (p value = 5.5 × 10(-31)) and is higher in men (p value = 0.002) but lower in participants of African ancestry (p value = 0.003). In a subset of 47 individuals from whom serial samples were collected up to 6 years apart, complex changes were noted over time and showed an overall increase in the proportion of mosaic cells as age increased. Our large combined sample allowed for a unique ability to characterize detectable genetic mosaicism involving large structural events and strengthens the emerging evidence of non-random erosion of the genome in the aging population.

Published
2015

7. Genetic Simulation Tools for Post‐Genome Wide Association Studies of Complex Diseases

Author

Chen, Huann-Sheng, Hutter, Carolyn M, Mechanic, Leah E, Amos, Christopher I, Bafna, Vineet, Hauser, Elizabeth R, Hernandez, Ryan D, Li, Chun, Liberles, David A, McAllister, Kimberly, Moore, Jason H, Paltoo, Dina N, Papanicolaou, George J, Peng, Bo, Ritchie, Marylyn D, Rosenfeld, Gabriel, Witte, John S, Gillanders, Elizabeth M, and Feuer, Eric J

Subjects
Genetics, Cancer, Biotechnology, Human Genome, Computer Simulation, Disease, Genome-Wide Association Study, Genomics, Humans, Models, Genetic, Molecular Epidemiology, Software, genetic simulation, rare variants, next-generation sequencing, complex phenotypes, computational resources, Public Health and Health Services, Epidemiology
Abstract

Genetic simulation programs are used to model data under specified assumptions to facilitate the understanding and study of complex genetic systems. Standardized data sets generated using genetic simulation are essential for the development and application of novel analytical tools in genetic epidemiology studies. With continuing advances in high-throughput genomic technologies and generation and analysis of larger, more complex data sets, there is a need for updating current approaches in genetic simulation modeling. To provide a forum to address current and emerging challenges in this area, the National Cancer Institute (NCI) sponsored a workshop, entitled "Genetic Simulation Tools for Post-Genome Wide Association Studies of Complex Diseases" at the National Institutes of Health (NIH) in Bethesda, Maryland on March 11-12, 2014. The goals of the workshop were to (1) identify opportunities, challenges, and resource needs for the development and application of genetic simulation models; (2) improve the integration of tools for modeling and analysis of simulated data; and (3) foster collaborations to facilitate development and applications of genetic simulation. During the course of the meeting, the group identified challenges and opportunities for the science of simulation, software and methods development, and collaboration. This paper summarizes key discussions at the meeting, and highlights important challenges and opportunities to advance the field of genetic simulation.

Published
2015

8. Gene‐Environment Interactions in Cancer Epidemiology: A National Cancer Institute Think Tank Report

Author

Hutter, Carolyn M, Mechanic, Leah E, Chatterjee, Nilanjan, Kraft, Peter, and Gillanders, Elizabeth M

Subjects
Human Genome, Cancer, Genetics, Prevention, Aetiology, 2.1 Biological and endogenous factors, Gene-Environment Interaction, Genetic Predisposition to Disease, Genome-Wide Association Study, Humans, Motivation, National Cancer Institute (U.S.), Neoplasms, Public Health, Reproducibility of Results, Research Report, Risk, Sample Size, United States, NCI Gene-Environment Think Tank, complex phenotypes, gene-environment interactions, genetic epidemiology, Public Health and Health Services, Epidemiology
Abstract

Cancer risk is determined by a complex interplay of genetic and environmental factors. Genome-wide association studies (GWAS) have identified hundreds of common (minor allele frequency [MAF] > 0.05) and less common (0.01 < MAF < 0.05) genetic variants associated with cancer. The marginal effects of most of these variants have been small (odds ratios: 1.1-1.4). There remain unanswered questions on how best to incorporate the joint effects of genes and environment, including gene-environment (G × E) interactions, into epidemiologic studies of cancer. To help address these questions, and to better inform research priorities and allocation of resources, the National Cancer Institute sponsored a "Gene-Environment Think Tank" on January 10-11, 2012. The objective of the Think Tank was to facilitate discussions on (1) the state of the science, (2) the goals of G × E interaction studies in cancer epidemiology, and (3) opportunities for developing novel study designs and analysis tools. This report summarizes the Think Tank discussion, with a focus on contemporary approaches to the analysis of G × E interactions. Selecting the appropriate methods requires first identifying the relevant scientific question and rationale, with an important distinction made between analyses aiming to characterize the joint effects of putative or established genetic and environmental factors and analyses aiming to discover novel risk factors or novel interaction effects. Other discussion items include measurement error, statistical power, significance, and replication. Additional designs, exposure assessments, and analytical approaches need to be considered as we move from the current small number of success stories to a fuller understanding of the interplay of genetic and environmental factors.

Published
2013

9. A meta-analysis identifies new loci associated with body mass index in individuals of African ancestry

Author

Monda, Keri L, Chen, Gary K, Taylor, Kira C, Palmer, Cameron, Edwards, Todd L, Lange, Leslie A, Ng, Maggie CY, Adeyemo, Adebowale A, Allison, Matthew A, Bielak, Lawrence F, Chen, Guanjie, Graff, Mariaelisa, Irvin, Marguerite R, Rhie, Suhn K, Li, Guo, Liu, Yongmei, Liu, Youfang, Lu, Yingchang, Nalls, Michael A, Sun, Yan V, Wojczynski, Mary K, Yanek, Lisa R, Aldrich, Melinda C, Ademola, Adeyinka, Amos, Christopher I, Bandera, Elisa V, Bock, Cathryn H, Britton, Angela, Broeckel, Ulrich, Cai, Quiyin, Caporaso, Neil E, Carlson, Chris S, Carpten, John, Casey, Graham, Chen, Wei-Min, Chen, Fang, Chen, Yii-Der I, Chiang, Charleston WK, Coetzee, Gerhard A, Demerath, Ellen, Deming-Halverson, Sandra L, Driver, Ryan W, Dubbert, Patricia, Feitosa, Mary F, Feng, Ye, Freedman, Barry I, Gillanders, Elizabeth M, Gottesman, Omri, Guo, Xiuqing, Haritunians, Talin, Harris, Tamara, Harris, Curtis C, Hennis, Anselm JM, Hernandez, Dena G, McNeill, Lorna H, Howard, Timothy D, Howard, Barbara V, Howard, Virginia J, Johnson, Karen C, Kang, Sun J, Keating, Brendan J, Kolb, Suzanne, Kuller, Lewis H, Kutlar, Abdullah, Langefeld, Carl D, Lettre, Guillaume, Lohman, Kurt, Lotay, Vaneet, Lyon, Helen, Manson, JoAnn E, Maixner, William, Meng, Yan A, Monroe, Kristine R, Morhason-Bello, Imran, Murphy, Adam B, Mychaleckyj, Josyf C, Nadukuru, Rajiv, Nathanson, Katherine L, Nayak, Uma, N'Diaye, Amidou, Nemesure, Barbara, Wu, Suh-Yuh, Leske, M Cristina, Neslund-Dudas, Christine, Neuhouser, Marian, Nyante, Sarah, Ochs-Balcom, Heather, Ogunniyi, Adesola, Ogundiran, Temidayo O, Ojengbede, Oladosu, Olopade, Olufunmilayo I, Palmer, Julie R, Ruiz-Narvaez, Edward A, Palmer, Nicholette D, Press, Michael F, Rampersaud, Evandine, Rasmussen-Torvik, Laura J, Rodriguez-Gil, Jorge L, Salako, Babatunde, and Schadt, Eric E

Subjects
Biological Sciences, Genetics, Human Genome, Black or African American, Body Mass Index, Case-Control Studies, Gene Frequency, Genetic Loci, Genetic Predisposition to Disease, Genome-Wide Association Study, Humans, Linkage Disequilibrium, Obesity, Polymorphism, Single Nucleotide, NABEC Consortium, UKBEC Consortium, BioBank Japan Project, AGEN Consortium, Medical and Health Sciences, Developmental Biology, Agricultural biotechnology, Bioinformatics and computational biology
Abstract

Genome-wide association studies (GWAS) have identified 36 loci associated with body mass index (BMI), predominantly in populations of European ancestry. We conducted a meta-analysis to examine the association of >3.2 million SNPs with BMI in 39,144 men and women of African ancestry and followed up the most significant associations in an additional 32,268 individuals of African ancestry. We identified one new locus at 5q33 (GALNT10, rs7708584, P = 3.4 × 10(-11)) and another at 7p15 when we included data from the GIANT consortium (MIR148A-NFE2L3, rs10261878, P = 1.2 × 10(-10)). We also found suggestive evidence of an association at a third locus at 6q16 in the African-ancestry sample (KLHL32, rs974417, P = 6.9 × 10(-8)). Thirty-two of the 36 previously established BMI variants showed directionally consistent effect estimates in our GWAS (binomial P = 9.7 × 10(-7)), five of which reached genome-wide significance. These findings provide strong support for shared BMI loci across populations, as well as for the utility of studying ancestrally diverse populations.

Published
2013

10. The landscape of recombination in African Americans

Author

Hinch, Anjali G, Tandon, Arti, Patterson, Nick, Song, Yunli, Rohland, Nadin, Palmer, Cameron D, Chen, Gary K, Wang, Kai, Buxbaum, Sarah G, Akylbekova, Ermeg L, Aldrich, Melinda C, Ambrosone, Christine B, Amos, Christopher, Bandera, Elisa V, Berndt, Sonja I, Bernstein, Leslie, Blot, William J, Bock, Cathryn H, Boerwinkle, Eric, Cai, Qiuyin, Caporaso, Neil, Casey, Graham, Adrienne Cupples, L, Deming, Sandra L, Ryan Diver, W, Divers, Jasmin, Fornage, Myriam, Gillanders, Elizabeth M, Glessner, Joseph, Harris, Curtis C, Hu, Jennifer J, Ingles, Sue A, Isaacs, William, John, Esther M, Linda Kao, WH, Keating, Brendan, Kittles, Rick A, Kolonel, Laurence N, Larkin, Emma, Le Marchand, Loic, McNeill, Lorna H, Millikan, Robert C, Murphy, Musani, Solomon, Neslund-Dudas, Christine, Nyante, Sarah, Papanicolaou, George J, Press, Michael F, Psaty, Bruce M, Reiner, Alex P, Rich, Stephen S, Rodriguez-Gil, Jorge L, Rotter, Jerome I, Rybicki, Benjamin A, Schwartz, Ann G, Signorello, Lisa B, Spitz, Margaret, Strom, Sara S, Thun, Michael J, Tucker, Margaret A, Wang, Zhaoming, Wiencke, John K, Witte, John S, Wrensch, Margaret, Wu, Xifeng, Yamamura, Yuko, Zanetti, Krista A, Zheng, Wei, Ziegler, Regina G, Zhu, Xiaofeng, Redline, Susan, Hirschhorn, Joel N, Henderson, Brian E, Taylor Jr, Herman A, Price, Alkes L, Hakonarson, Hakon, Chanock, Stephen J, Haiman, Christopher A, Wilson, James G, Reich, David, and Myers, Simon R

Subjects
Biological Sciences, Genetics, Human Genome, Biotechnology, Africa, Western, Black or African American, Alleles, Amino Acid Motifs, Base Sequence, Chromosome Mapping, Crossing Over, Genetic, Europe, Evolution, Molecular, Female, Gene Frequency, Genetics, Population, Genome, Human, Genomics, Haplotypes, Histone-Lysine N-Methyltransferase, Humans, Male, Molecular Sequence Data, Pedigree, Polymorphism, Single Nucleotide, Probability, White People, General Science & Technology
Abstract

Recombination, together with mutation, gives rise to genetic variation in populations. Here we leverage the recent mixture of people of African and European ancestry in the Americas to build a genetic map measuring the probability of crossing over at each position in the genome, based on about 2.1 million crossovers in 30,000 unrelated African Americans. At intervals of more than three megabases it is nearly identical to a map built in Europeans. At finer scales it differs significantly, and we identify about 2,500 recombination hotspots that are active in people of West African ancestry but nearly inactive in Europeans. The probability of a crossover at these hotspots is almost fully controlled by the alleles an individual carries at PRDM9 (P value

Published
2011

13. Joint effects between five identified risk variants, allergy, and autoimmune conditions on glioma risk

Author

Safaeian, Mahboobeh, Rajaraman, Preetha, Hartge, Patricia, Yeager, Meredith, Linet, Martha, Butler, Mary Ann, Ruder, Avima M., Purdue, Mark P., Hsing, Ann, Beane-Freeman, Laura, Hoppin, Jane A., Albanes, Demetrius, Weinstein, Stephanie J., Inskip, Peter D., Brenner, Alina, Rothman, Nathaniel, Chatterjee, Nilanjan, Gillanders, Elizabeth M., Chanock, Stephen J., and Wang, Sophia S.

Published
2013

14. Genome-wide meta-analysis identifies five new susceptibility loci for cutaneous malignant melanoma

Author

Law, Matthew H, Bishop, D Timothy, Lee, Jeffrey E, Brossard, Myriam, Martin, Nicholas G, Moses, Eric K, Song, Fengju, Barrett, Jennifer H, Kumar, Rajiv, Easton, Douglas F, Pharoah, Paul D P, Swerdlow, Anthony J, Kypreou, Katerina P, Taylor, John C, Harland, Mark, Randerson-Moor, Juliette, Akslen, Lars A, Andresen, Per A, Avril, Marie-Françoise, Azizi, Esther, Scarrà, Giovanna Bianchi, Brown, Kevin M, Dȩbniak, Tadeusz, Duffy, David L, Elder, David E, Fang, Shenying, Friedman, Eitan, Galan, Pilar, Ghiorzo, Paola, Gillanders, Elizabeth M, Goldstein, Alisa M, Gruis, Nelleke A, Hansson, Johan, Helsing, Per, Hočevar, Marko, Höiom, Veronica, Ingvar, Christian, Kanetsky, Peter A, Chen, Wei V, Landi, Maria Teresa, Lang, Julie, Lathrop, G Mark, Lubiński, Jan, Mackie, Rona M, Mann, Graham J, Molven, Anders, Montgomery, Grant W, Novaković, Srdjan, Olsson, Håkan, Puig, Susana, Puig-Butille, Joan Anton, Qureshi, Abrar A, Radford-Smith, Graham L, van der Stoep, Nienke, van Doorn, Remco, Whiteman, David C, Craig, Jamie E, Schadendorf, Dirk, Simms, Lisa A, Burdon, Kathryn P, Nyholt, Dale R, Pooley, Karen A, Orr, Nick, Stratigos, Alexander J, Cust, Anne E, Ward, Sarah V, Hayward, Nicholas K, Han, Jiali, Schulze, Hans-Joachim, Dunning, Alison M, Bishop, Julia A Newton, Demenais, Florence, Amos, Christopher I, MacGregor, Stuart, and Iles, Mark M

Published
2015
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16. The Effect on Melanoma Risk of Genes Previously Associated With Telomere Length

Author

Iles, Mark M., Bishop, D. Timothy, Taylor, John C., Hayward, Nicholas K., Brossard, Myriam, Cust, Anne E., Dunning, Alison M., Lee, Jeffrey E., Moses, Eric K., Akslen, Lars A., Andresen, Per A., Avril, Marie-Françoise, Azizi, Esther, Scarrà, Giovanna Bianchi, Brown, Kevin M., Dębniak, Tadeusz, Elder, David E., Friedman, Eitan, Ghiorzo, Paola, Gillanders, Elizabeth M., Goldstein, Alisa M., Gruis, Nelleke A., Hansson, Johan, Harland, Mark, Helsing, Per, Hočevar, Marko, Höiom, Veronica, Ingvar, Christian, Kanetsky, Peter A., Landi, Maria Teresa, Lang, Julie, Lathrop, G. Mark, Lubiński, Jan, Mackie, Rona M., Martin, Nicholas G., Molven, Anders, Montgomery, Grant W., Novaković, Srdjan, Olsson, Håkan, Puig, Susana, Puig-Butille, Joan Anton, Radford-Smith, Graham L., Randerson-Moor, Juliette, van der Stoep, Nienke, van Doorn, Remco, Whiteman, David C., MacGregor, Stuart, Pooley, Karen A., Ward, Sarah V., Mann, Graham J., Amos, Christopher I., Pharoah, Paul D. P., Demenais, Florence, Law, Matthew H., Newton Bishop, Julia A., and Barrett, Jennifer H.

Published
2014
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17. Fine mapping of genetic susceptibility loci for melanoma reveals a mixture of single variant and multiple variant regions

Author

Barrett, Jennifer H., Taylor, John C., Bright, Chloe, Harland, Mark, Dunning, Alison M., Akslen, Lars A., Andresen, Per A., Avril, Marie-Françoise, Azizi, Esther, Bianchi Scarrà, Giovanna, Brossard, Myriam, Brown, Kevin M., Dębniak, Tadeusz, Elder, David E., Friedman, Eitan, Ghiorzo, Paola, Gillanders, Elizabeth M., Gruis, Nelleke A., Hansson, Johan, Helsing, Per, Hočevar, Marko, Höiom, Veronica, Ingvar, Christian, Landi, Maria Teresa, Lang, Julie, Lathrop, Mark G., Lubiński, Jan, Mackie, Rona M., Molven, Anders, Novaković, Srdjan, Olsson, Håkan, Puig, Susana, Puig-Butille, Joan Anton, van der Stoep, Nienke, van Doorn, Remco, van Workum, Wilbert, Goldstein, Alisa M., Kanetsky, Peter A., Pharoah, Paul D. P., Demenais, Florence, Hayward, Nicholas K., Newton Bishop, Julia A., Bishop, Timothy D., and Iles, Mark M.

Published
2015
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18. Imputation and subset-based association analysis across different cancer types identifies multiple independent risk loci in the TERT-CLPTM1L region on chromosome 5p15.33

Author

Wang, Zhaoming, Zhu, Bin, Zhang, Mingfeng, Parikh, Hemang, Jia, Jinping, Chung, Charles C., Sampson, Joshua N., Hoskins, Jason W., Hutchinson, Amy, Burdette, Laurie, Ibrahim, Abdisamad, Hautman, Christopher, Raj, Preethi S., Abnet, Christian C., Adjei, Andrew A., Ahlbom, Anders, Albanes, Demetrius, Allen, Naomi E., Ambrosone, Christine B., Aldrich, Melinda, Amiano, Pilar, Amos, Christopher, Andersson, Ulrika, Andriole, Gerald, Jr, Andrulis, Irene L., Arici, Cecilia, Arslan, Alan A., Austin, Melissa A., Baris, Dalsu, Barkauskas, Donald A., Bassig, Bryan A., Beane Freeman, Laura E., Berg, Christine D., Berndt, Sonja I., Bertazzi, Pier Alberto, Biritwum, Richard B., Black, Amanda, Blot, William, Boeing, Heiner, Boffetta, Paolo, Bolton, Kelly, Boutron-Ruault, Marie-Christine, Bracci, Paige M., Brennan, Paul, Brinton, Louise A., Brotzman, Michelle, Bueno-de-Mesquita, H. Bas, Buring, Julie E., Butler, Mary Ann, Cai, Qiuyin, Cancel-Tassin, Geraldine, Canzian, Federico, Cao, Guangwen, Caporaso, Neil E., Carrato, Alfredo, Carreon, Tania, Carta, Angela, Chang, Gee-Chen, Chang, I-Shou, Chang-Claude, Jenny, Che, Xu, Chen, Chien-Jen, Chen, Chih-Yi, Chen, Chung-Hsing, Chen, Constance, Chen, Kuan-Yu, Chen, Yuh-Min, Chokkalingam, Anand P., Chu, Lisa W., Clavel-Chapelon, Francoise, Colditz, Graham A., Colt, Joanne S., Conti, David, Cook, Michael B., Cortessis, Victoria K., Crawford, E. David, Cussenot, Olivier, Davis, Faith G., De Vivo, Immaculata, Deng, Xiang, Ding, Ti, Dinney, Colin P., Di Stefano, Anna Luisa, Diver, W. Ryan, Duell, Eric J., Elena, Joanne W., Fan, Jin-Hu, Feigelson, Heather Spencer, Feychting, Maria, Figueroa, Jonine D., Flanagan, Adrienne M., Fraumeni, Joseph F., Jr, Freedman, Neal D., Fridley, Brooke L., Fuchs, Charles S., Gago-Dominguez, Manuela, Gallinger, Steven, Gao, Yu-Tang, Gapstur, Susan M., Garcia-Closas, Montserrat, Garcia-Closas, Reina, Gastier-Foster, Julie M., Gaziano, J. Michael, Gerhard, Daniela S., Giffen, Carol A., Giles, Graham G., Gillanders, Elizabeth M., Giovannucci, Edward L., Goggins, Michael, Gokgoz, Nalan, Goldstein, Alisa M., Gonzalez, Carlos, Gorlick, Richard, Greene, Mark H., Gross, Myron, Grossman, H. Barton, Grubb, Robert, III, Gu, Jian, Guan, Peng, Haiman, Christopher A., Hallmans, Goran, Hankinson, Susan E., Harris, Curtis C., Hartge, Patricia, Hattinger, Claudia, Hayes, Richard B., He, Qincheng, Helman, Lee, Henderson, Brian E., Henriksson, Roger, Hoffman-Bolton, Judith, Hohensee, Chancellor, Holly, Elizabeth A., Hong, Yun-Chul, Hoover, Robert N., Hosgood, H. Dean, III, Hsiao, Chin-Fu, Hsing, Ann W., Hsiung, Chao Agnes, Hu, Nan, Hu, Wei, Hu, Zhibin, Huang, Ming-Shyan, Hunter, David J., Inskip, Peter D., Ito, Hidemi, Jacobs, Eric J., Jacobs, Kevin B., Jenab, Mazda, Ji, Bu-Tian, Johansen, Christoffer, Johansson, Mattias, Johnson, Alison, Kaaks, Rudolf, Kamat, Ashish M., Kamineni, Aruna, Karagas, Margaret, Khanna, Chand, Khaw, Kay-Tee, Kim, Christopher, Kim, In-Sam, Kim, Jin Hee, Kim, Yeul Hong, Kim, Young-Chul, Kim, Young Tae, Kang, Chang Hyun, Jung, Yoo Jin, Kitahara, Cari M., Klein, Alison P., Klein, Robert, Kogevinas, Manolis, Koh, Woon-Puay, Kohno, Takashi, Kolonel, Laurence N., Kooperberg, Charles, Kratz, Christian P., Krogh, Vittorio, Kunitoh, Hideo, Kurtz, Robert C., Kurucu, Nilgun, Lan, Qing, Lathrop, Mark, Lau, Ching C., Lecanda, Fernando, Lee, Kyoung-Mu, Lee, Maxwell P., Le Marchand, Loic, Lerner, Seth P., Li, Donghui, Liao, Linda M., Lim, Wei-Yen, Lin, Dongxin, Lin, Jie, Lindstrom, Sara, Linet, Martha S., Lissowska, Jolanta, Liu, Jianjun, Ljungberg, Börje, Lloreta, Josep, Lu, Daru, Ma, Jing, Malats, Nuria, Mannisto, Satu, Marina, Neyssa, Mastrangelo, Giuseppe, Matsuo, Keitaro, McGlynn, Katherine A., McKean-Cowdin, Roberta, McNeill, Lorna H., McWilliams, Robert R., Melin, Beatrice S., Meltzer, Paul S., Mensah, James E., Miao, Xiaoping, Michaud, Dominique S., Mondul, Alison M., Moore, Lee E., Muir, Kenneth, Niwa, Shelley, Olson, Sara H., Orr, Nick, Panico, Salvatore, Park, Jae Yong, Patel, Alpa V., Patino-Garcia, Ana, Pavanello, Sofia, Peeters, Petra H. M., Peplonska, Beata, Peters, Ulrike, Petersen, Gloria M., Picci, Piero, Pike, Malcolm C., Porru, Stefano, Prescott, Jennifer, Pu, Xia, Purdue, Mark P., Qiao, You-Lin, Rajaraman, Preetha, Riboli, Elio, Risch, Harvey A., Rodabough, Rebecca J., Rothman, Nathaniel, Ruder, Avima M., Ryu, Jeong-Seon, Sanson, Marc, Schned, Alan, Schumacher, Fredrick R., Schwartz, Ann G., Schwartz, Kendra L., Schwenn, Molly, Scotlandi, Katia, Seow, Adeline, Serra, Consol, Serra, Massimo, Sesso, Howard D., Severi, Gianluca, Shen, Hongbing, Shen, Min, Shete, Sanjay, Shiraishi, Kouya, Shu, Xiao-Ou, Siddiq, Afshan, Sierrasesumaga, Luis, Sierri, Sabina, Loon Sihoe, Alan Dart, Silverman, Debra T., Simon, Matthias, Southey, Melissa C., Spector, Logan, Spitz, Margaret, Stampfer, Meir, Stattin, Par, Stern, Mariana C., Stevens, Victoria L., Stolzenberg-Solomon, Rachael Z., Stram, Daniel O., Strom, Sara S., Su, Wu-Chou, Sund, Malin, Sung, Sook Whan, Swerdlow, Anthony, Tan, Wen, Tanaka, Hideo, Tang, Wei, Tang, Ze-Zhang, Tardon, Adonina, Tay, Evelyn, Taylor, Philip R., Tettey, Yao, Thomas, David M., Tirabosco, Roberto, Tjonneland, Anne, Tobias, Geoffrey S., Toro, Jorge R., Travis, Ruth C., Trichopoulos, Dimitrios, Troisi, Rebecca, Truelove, Ann, Tsai, Ying-Huang, Tucker, Margaret A., Tumino, Rosario, Van Den Berg, David, Van Den Eeden, Stephen K., Vermeulen, Roel, Vineis, Paolo, Visvanathan, Kala, Vogel, Ulla, Wang, Chaoyu, Wang, Chengfeng, Wang, Junwen, Wang, Sophia S., Weiderpass, Elisabete, Weinstein, Stephanie J., Wentzensen, Nicolas, Wheeler, William, White, Emily, Wiencke, John K., Wolk, Alicja, Wolpin, Brian M., Wong, Maria Pik, Wrensch, Margaret, Wu, Chen, Wu, Tangchun, Wu, Xifeng, Wu, Yi-Long, Wunder, Jay S., Xiang, Yong-Bing, Xu, Jun, Yang, Hannah P., Yang, Pan-Chyr, Yatabe, Yasushi, Ye, Yuanqing, Yeboah, Edward D., Yin, Zhihua, Ying, Chen, Yu, Chong-Jen, Yu, Kai, Yuan, Jian-Min, Zanetti, Krista A., Zeleniuch-Jacquotte, Anne, Zheng, Wei, Zhou, Baosen, Mirabello, Lisa, Savage, Sharon A., Kraft, Peter, Chanock, Stephen J., Yeager, Meredith, Landi, Maria Terese, Shi, Jianxin, Chatterjee, Nilanjan, and Amundadottir, Laufey T.

Published
2014
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21. Epidemiologic Research of Rare Cancers: Trends, Resources, and Challenges

Author

Gallicchio, Lisa, primary, Daee, Danielle L., additional, Rotunno, Melissa, additional, Barajas, Rolando, additional, Fagan, Sarah, additional, Carrick, Danielle M., additional, Divi, Rao L., additional, Filipski, Kelly K., additional, Freedman, Andrew N., additional, Gillanders, Elizabeth M., additional, Lam, Tram K., additional, Martin, Damali N., additional, Rogers, Scott, additional, Verma, Mukesh, additional, and Nelson, Stefanie A., additional

Published
2021
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24. Two-locus genome-wide linkage scan for prostate cancer susceptibility genes with an interaction effect

Author

Chang, Bao-Li, Lange, Ethan M., Dimitrov, Latchezar, Valis, Christopher J., Gillanders, Elizabeth M., Lange, Leslie A., Wiley, Kathleen E., Isaacs, Sarah D., Wiklund, Fredrik, Baffoe-Bonnie, Agnes, Langefeld, Carl D, Zheng, S. Lilly, Matikainen, Mika P., Ikonen, Tarja, Fredriksson, Henna, Tammela, Teuvo, Walsh, Patrick C., Bailey-Wilson, Joan E., Schleutker, Johanna, Gronberg, Henrik, Cooney, Kathleen A., Isaacs, William B., Suh, Edward, Trent, Jeffrey M., and Xu, Jianfeng

Published
2006
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25. A major locus for hereditary prostate cancer in Finland: localization by linkage disequilibrium of a haplotype in the HPCX region

Author

Baffoe-Bonnie, Agnes B., Smith, Jeffrey R., Stephan, Dietrich A., Schleutker, Johanna, Carpten, John D., Kainu, Tommi, Gillanders, Elizabeth M., Matikainen, Mika, Teslovich, Tanya M., Tammela, Teuvo, Sood, Raman, Balshem, Andrew M., Scarborough, Sheehan D., Xu, Jianfeng, Isaacs, William B., Trent, Jeffrey M., Kallioniemi, Olli-P., and Bailey-Wilson, Joan E.

Published
2005
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29. Publisher Correction: Novel pleiotropic risk loci for melanoma and nevus density implicate multiple biological pathways

Author

Duffy, David L., Zhu, Gu, Li, Xin, Sanna, Marianna, Jacobs, Leonie C., Evans, David M., Yazar, Seyhan, Beesley, Jonathan, Lawrence, Matthew H., Kraft, Peter, Visconti, Alessia, Taylor, John C., Lui, Fan, Wright, Margaret J., Henders, Anjali K., Bowdler, Lisa, Glass, Dan, Ikram, Arfan M., Uitterlinden, André G., Madden, Pamela A., Heath, Andrew C., Nelson, Elliot C., Green, Adele C., Chanock, Stephen, Barrett, Jennifer H., Brown, Matthew A., Hayward, Nicholas K., MacGregor, Stuart, Sturm, Richard A., Hewitt, Alex W., Leenhardt, Jeffrey E., Brossard, Myriam, Moses, Eric K., Song, Fengju, Kumar, Rajiv, Easton, Douglas F., Pharoah, Paul D. P., Swerdlow, Anthony J., Kypreou, Katerina P., Harland, Mark, Randerson-Moor, Juliette, Akslen, Lars A., Andresen, Per A., Avril, Marie-Françoise, Azizi, Esther, Scarrà, Giovanna Bianchi, Brown, Kevin M., Dębniak, Tadeusz, Elder, David E., Fang, Shenying, Friedman, Eitan, Galan, Pilar, Ghiorzo, Paola, Gillanders, Elizabeth M., Goldstein, Alisa M., Gruis, Nelleke A., Hansson, Johan, Helsing, Per, Hočevar, Marko, Höiom, Veronica, Ingvar, Christian, Kanetsky, Peter A., Chen, Wei V., Landi, Maria Teresa, Lang, Julie, Lathrop, G. Mark, Lubiński, Jan, Mackie, Rona M., Mann, Graham J., Molven, Anders, Novaković, Srdjan, Olsson, Håkan, Puig, Susana, Puig-Butille, Joan Anton, Radford-Smith, Graham L., van Doorn, Remco, Whiteman, David C., Craig, Jamie E., Schadendorf, Dirk, Simms, Lisa A., Burdon, Kathryn P., Nyholt, Dale R., Pooley, Karen A., Orr, Nicholas, Stratigos, Alexander J., Cust, Anne E., Ward, Sarah V., Schulze, Hans-Joachim, Dunning, Alison M., Demenais, Florence, Amos, Christopher I., Kayser, Manfred, Hunter, David J., Newton Bishop, Julia A., Spector, Timothy D., Montgomery, Grant W., Mackey, David A., Smith, George Davey, Nijsten, Tamar E., Bishop, D. Timothy, Bataille, Veronique, Falchi, Mario, Han, Jiali, and Martin, Nicholas G.

Subjects
0301 basic medicine, Skin Neoplasms, Medizin, General Physics and Astronomy, 02 engineering and technology, Receptors, G-Protein-Coupled, Guanine Nucleotide Exchange Factors, skin and connective tissue diseases, lcsh:Science, Melanoma, Telomerase, Nevus, Pigmented, Stem Cell Factor, Multidisciplinary, Microfilament Proteins, Nuclear Proteins, RNA-Binding Proteins, Genetic Pleiotropy, 021001 nanoscience & nanotechnology, Publisher Correction, Spelling, Cytochrome P-450 CYP1B1, Interferon Regulatory Factors, 0210 nano-technology, Science, Telomere-Binding Proteins, Nerve Tissue Proteins, Computational biology, Biology, Polymorphism, Single Nucleotide, General Biochemistry, Genetics and Molecular Biology, Article, Histone Deacetylases, White People, Group VI Phospholipases A2, 03 medical and health sciences, medicine, Nevus, Humans, Genetic Predisposition to Disease, General Chemistry, medicine.disease, Repressor Proteins, MicroRNAs, 030104 developmental biology, RNA, lcsh:Q, Carrier Proteins, Genome-Wide Association Study
Abstract

The total number of acquired melanocytic nevi on the skin is strongly correlated with melanoma risk. Here we report a meta-analysis of 11 nevus GWAS from Australia, Netherlands, UK, and USA comprising 52,506 individuals. We confirm known loci including MTAP, PLA2G6, and IRF4, and detect novel SNPs in KITLG and a region of 9q32. In a bivariate analysis combining the nevus results with a recent melanoma GWAS meta-analysis (12,874 cases, 23,203 controls), SNPs near GPRC5A, CYP1B1, PPARGC1B, HDAC4, FAM208B, DOCK8, and SYNE2 reached global significance, and other loci, including MIR146A and OBFC1, reached a suggestive level. Overall, we conclude that most nevus genes affect melanoma risk (KITLG an exception), while many melanoma risk loci do not alter nevus count. For example, variants in TERC and OBFC1 affect both traits, but other telomere length maintenance genes seem to affect melanoma risk only. Our findings implicate multiple pathways in nevogenesis., Melanocytic nevus count is associated with melanoma risk. In this study, a meta-analysis of 11 nevus GWAS studies identifies novel SNPs in KITLG and 9q32, and bivariate analysis with melanoma GWAS meta-analysis reveals that most nevus genes affect melanoma risk, while melanoma risk loci do not alter the nevus count.

Published
2019

30. Novel pleiotropic risk loci for melanoma and nevus density implicate multiple biological pathways (vol 9, 4774, 2018)

Author

Duffy, David L. Zhu, Gu Li, Xin Sanna, Marianna Iles, Mark M. Jacobs, Leonie C. Evans, David M. Yazar, Seyhan and Beesley, Jonathan Law, Matthew H. Kraft, Peter Visconti, Alessia Taylor, John C. Liu, Fan Wright, Margaret J. and Henders, Anjali K. Bowdler, Lisa Glass, Dan Ikram, M. Arfan and Uitterlinden, Andre G. Madden, Pamela A. Heath, Andrew C. and Nelson, Elliot C. Green, Adele C. Chanock, Stephen and Barrett, Jennifer H. Brown, Matthew A. Hayward, Nicholas K. and MacGregor, Stuart Sturm, Richard A. Hewitt, Alex W. Kayser, Manfred Hunter, David J. Bishop, Julia A. Newton Spector, Timothy D. Montgomery, Grant W. Mackey, David A. Smith, George Davey Nijsten, Tamar E. Bishop, D. Timothy Bataille, Veronique Falchi, Mario Han, Jiali Martin, Nicholas G. and Lee, Jeffrey E. Brossard, Myriam Moses, Eric K. Song, Fengju and Kumar, Rajiv Easton, Douglas F. Pharoah, Paul D. P. and Swerdlow, Anthony J. Kypreou, Katerina P. Harland, Mark and Randerson-Moor, Juliette Akslen, Lars A. Andresen, Per A. and Avril, Marie-Francoise Azizi, Esther Scarra, Giovanna Bianchi and Brown, Kevin M. Debniak, Tadeusz Elder, David E. Fang, Shenying Friedman, Eitan Galan, Pilar Ghiorzo, Paola and Gillanders, Elizabeth M. Goldstein, Alisa M. Gruis, Nelleke A. and Hansson, Johan Helsing, Per Hocevar, Marko Hoiom, Veronica Ingvar, Christian Kanetsky, Peter A. Chen, Wei V. and Landi, Maria Teresa Lang, Julie Lathrop, G. Mark and Lubinski, Jan Mackie, Rona M. Mann, Graham J. Molven, Anders and Novakovic, Srdjan Olsson, Hakan Puig, Susana and Puig-Butille, Joan Anton Radford-Smith, Graham L. van der Stoep, Nienke van Doorn, Remco Whiteman, David C. Craig, Jamie E. and Schadendorf, Dirk Simms, Lisa A. Burdon, Kathryn P. and Nyholt, Dale R. Pooley, Karen A. Orr, Nicholas Stratigos, Alexander J. Cust, Anne E. Ward, Sarah V. Schulze, Hans-Joachim Dunning, Alison M. Demenais, Florence Amos, Christopher I. Melanoma GWAS Consortium

Published
2019

31. Features associated with germline CDKN2A mutations: a GenoMEL study of melanoma-prone families from three continents

Author

Goldstein, Alisa M, Chan, May, Harland, Mark, Hayward, Nicholas K, Demenais, Florence, Bishop, D Timothy, Azizi, Esther, Bergman, Wilma, Bianchi-Scarra, Giovanna, Bruno, William, Calista, Donato, Albright, Lisa A Cannon, Chaudru, Valerie, Chompret, Agnes, Cuellar, Francisco, Elder, David E, Ghiorzo, Paola, Gillanders, Elizabeth M, Gruis, Nelleke A, Hansson, Johan, Hogg, David, Holland, Elizabeth A, Kanetsky, Peter A, Kefford, Richard F, Landi, Maria Teresa, Lang, Julie, Leachman, Sancy A, MacKie, Rona M, Magnusson, Veronica, Mann, Graham J, Bishop, Julia Teresa, Palmer, Jane M, Puig, Susana, Puig-Butille, Joan A, Stark, Mitchell, Tsao, Hensin, Tucker, Margaret A, Whitaker, Linda, and Yakobson, Emanuel

Published
2007

34. Combined Genome-Wide Scan for Prostate Cancer Susceptibility Genes

Author

Gillanders, Elizabeth M., Xu, Jianfeng, Chang, Bao-li, Lange, Ethan M., Wiklund, Fredrik, Bailey-Wilson, Joan E., Baffoe-Bonnie, Agnes, Jones, MaryPat, Gildea, Derek, Riedesel, Erica, Albertus, Julie, Isaacs, Sarah D., Wiley, Kathleen E., Mohai, Caroline E., Matikainen, Mika P., Tammela, Teuvo L. J., Zheng, S. Lilly, Brown, W. Mark, Rökman, Annika, Carpten, John D., Meyers, Deborah A., Walsh, Patrick C., Schleutker, Johanna, Gronberg, Henrik, Cooney, Kathleen A., Isaacs, William B., and Trent, Jeffrey M.

Published
2004

36. Establishing an adjusted p-value threshold to control the family-wide type 1 error in genome wide association studies

Author

Bailey-Wilson Joan E, Holmes Taura N, Gillanders Elizabeth M, and Duggal Priya

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background By assaying hundreds of thousands of single nucleotide polymorphisms, genome wide association studies (GWAS) allow for a powerful, unbiased review of the entire genome to localize common genetic variants that influence health and disease. Although it is widely recognized that some correction for multiple testing is necessary, in order to control the family-wide Type 1 Error in genetic association studies, it is not clear which method to utilize. One simple approach is to perform a Bonferroni correction using all n single nucleotide polymorphisms (SNPs) across the genome; however this approach is highly conservative and would "overcorrect" for SNPs that are not truly independent. Many SNPs fall within regions of strong linkage disequilibrium (LD) ("blocks") and should not be considered "independent". Results We proposed to approximate the number of "independent" SNPs by counting 1 SNP per LD block, plus all SNPs outside of blocks (interblock SNPs). We examined the effective number of independent SNPs for Genome Wide Association Study (GWAS) panels. In the CEPH Utah (CEU) population, by considering the interdependence of SNPs, we could reduce the total number of effective tests within the Affymetrix and Illumina SNP panels from 500,000 and 317,000 to 67,000 and 82,000 "independent" SNPs, respectively. For the Affymetrix 500 K and Illumina 317 K GWAS SNP panels we recommend using 10-5, 10-7 and 10-8 and for the Phase II HapMap CEPH Utah and Yoruba populations we recommend using 10-6, 10-7 and 10-9 as "suggestive", "significant" and "highly significant" p-value thresholds to properly control the family-wide Type 1 error. Conclusion By approximating the effective number of independent SNPs across the genome we are able to 'correct' for a more accurate number of tests and therefore develop 'LD adjusted' Bonferroni corrected p-value thresholds that account for the interdepdendence of SNPs on well-utilized commercially available SNP "chips". These thresholds will serve as guides to researchers trying to decide which regions of the genome should be studied further.

Published
2008
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37. GeneLink: a database to facilitate genetic studies of complex traits

Author

Wolfsberg Tyra G, Trout Ken, Ibay Grace, Freas-Lutz Diana, Klein Alison P, Jones Mary, Duggal Priya, Umayam Lowell, Gildea Derek, Masiello Anthony, Gillanders Elizabeth M, Trent Jeffrey M, Bailey-Wilson Joan E, and Baxevanis Andreas D

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background In contrast to gene-mapping studies of simple Mendelian disorders, genetic analyses of complex traits are far more challenging, and high quality data management systems are often critical to the success of these projects. To minimize the difficulties inherent in complex trait studies, we have developed GeneLink, a Web-accessible, password-protected Sybase database. Results GeneLink is a powerful tool for complex trait mapping, enabling genotypic data to be easily merged with pedigree and extensive phenotypic data. Specifically designed to facilitate large-scale (multi-center) genetic linkage or association studies, GeneLink securely and efficiently handles large amounts of data and provides additional features to facilitate data analysis by existing software packages and quality control. These include the ability to download chromosome-specific data files containing marker data in map order in various formats appropriate for downstream analyses (e.g., GAS and LINKAGE). Furthermore, an unlimited number of phenotypes (either qualitative or quantitative) can be stored and analyzed. Finally, GeneLink generates several quality assurance reports, including genotyping success rates of specified DNA samples or success and heterozygosity rates for specified markers. Conclusions GeneLink has already proven an invaluable tool for complex trait mapping studies and is discussed primarily in the context of our large, multi-center study of hereditary prostate cancer (HPC). GeneLink is freely available at http://research.nhgri.nih.gov/genelink.

Published
2004
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38. Abstract LB-161: GAME-ON and OncoArray: Understanding the genetic architecture of cancer risk

Author

Nelson, Stefanie A., primary, Caga-Anan, Charlisse, additional, Daee, Danielle, additional, Costello, Maura Kate, additional, Seminara, Daniela, additional, Amos, Christopher I., additional, Gruber, Stephen B., additional, Haiman, Christopher, additional, Hunter, David, additional, Kraft, Peter, additional, Sellers, Thomas, additional, and Gillanders, Elizabeth M., additional

Published
2017
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39. Genome-wide meta-analysis identifies five new susceptibility loci for cutaneous malignant melanoma

Author

Law, Matthew H. Bishop, D. Timothy Lee, Jeffrey E. Brossard, Myriam Martin, Nicholas G. Moses, Eric K. Song, Fengju and Barrett, Jennifer H. Kumar, Rajiv Easton, Douglas F. and Pharoah, Paul D. P. Swerdlow, Anthony J. Kypreou, Katerina P. and Taylor, John C. Harland, Mark Randerson-Moor, Juliette and Akslen, Lars A. Andresen, Per A. Avril, Marie-Franoise and Azizi, Esther Scarra, Giovanna Bianchi Brown, Kevin M. and Debniak, Tadeusz Duffy, David L. Elder, David E. Fang, Shenying Friedman, Eitan Galan, Pilar Ghiorzo, Paola and Gillanders, Elizabeth M. Goldstein, Alisa M. Gruis, Nelleke A. and Hansson, Johan Helsing, Per Hocevar, Marko Hoeiom, Veronica Ingvar, Christian Kanetsky, Peter A. Chen, Wei V. and Landi, Maria Teresa Lang, Julie Lathrop, G. Mark and Lubinski, Jan Mackie, Rona M. Mann, Graham J. Molven, Anders and Montgomery, Grant W. Novakovic, Srdjan Olsson, Hakan and Puig, Susana Puig-Butille, Joan Anton Qureshi, Abrar A. and Radford-Smith, Graham L. van der Stoep, Nienke van Doorn, Remco and Whiteman, David C. Craig, Jamie E. Schadendorf, Dirk and Simms, Lisa A. Burdon, Kathryn P. Nyholt, Dale R. Pooley, Karen A. Orr, Nick Stratigos, Alexander J. Cust, Anne E. and Ward, Sarah V. Hayward, Nicholas K. Han, Jiali Schulze, Hans-Joachim Dunning, Alison M. Bishop, Julia A. Newton and Demenais, Florence Amos, Christopher I. MacGregor, Stuart and Iles, Mark M. GenoMEL Consortium Essen-Heidelberg Investigators and SDH Study Grp Q-MEGA QTWIN Investigators AMFS Investigators and ATHENS Melanoma Study Grp

Abstract

Thirteen common susceptibility loci have been reproducibly associated with cutaneous malignant melanoma (CMM). We report the results of an international 2-stage meta-analysis of CMM genome-wide association studies (GWAS). This meta-analysis combines 11 GWAS (5 previously unpublished) and a further three stage 2 data sets, totaling 15,990 CMM cases and 26,409 controls. Five loci not previously associated with CMM risk reached genome-wide significance (P < 5 x 10(-8)), as did 2 previously reported but unreplicated loci and all 13 established loci. Newly associated SNPs fall within putative melanocyte regulatory elements, and bioinformatic and expression quantitative trait locus (eQTL) data highlight candidate genes in the associated regions, including one involved in telomere biology.

Published
2015

40. Genome-wide Scan of 29,141 African Americans Finds No Evidence of Directional Selection since Admixture

Author

Deming, Sandra L., Casey, Graham, Murphy, Adam, Press, Michael F., Bock, Cathryn H., Aldrich, Melinda C., McNeill, Lorna H., Bernstein, Leslie, Tandon, Arti, Caporaso, Neil, De Jager, Phillip L., Bhatia, Gaurav, Ambrosone, Christine B., Larkin, Emma, Amos, Christopher, Blot, William J., Ingles, Sue A., Bandera, Elisa V., Harris, Curtis C., Isaacs, William, Rodriguez-Gil, Jorge L., Millikan, Robert C., Diver, W. Ryan, Patterson, Nick, Berndt, Sonja I., Kittles, Rick A., Gapstur, Susan M., Neslund-Dudas, Christine, Henderson, Brian E., Gillanders, Elizabeth M., Nyante, Sarah, and John, Esther M.

Abstract

The extent of recent selection in admixed populations is currently an unresolved question. We scanned the genomes of 29,141 African Americans and failed to find any genome-wide-significant deviations in local ancestry, indicating no evidence of selection influencing ancestry after admixture. A recent analysis of data from 1,890 African Americans reported that there was evidence of selection in African Americans after their ancestors left Africa, both before and after admixture. Selection after admixture was reported on the basis of deviations in local ancestry, and selection before admixture was reported on the basis of allele-frequency differences between African Americans and African populations. The local-ancestry deviations reported by the previous study did not replicate in our very large sample, and we show that such deviations were expected purely by chance, given the number of hypotheses tested. We further show that the previous study’s conclusion of selection in African Americans before admixture is also subject to doubt. This is because the FST statistics they used were inflated and because true signals of unusual allele-frequency differences between African Americans and African populations would be best explained by selection that occurred in Africa prior to migration to the Americas.

Published
2014
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41. Imputation and subset-based association analysis across different cancer types identifies multiple independent risk loci in the TERT-CLPTM1L region on chromosome 5p15.33

Author

Wang, Zhaoming Zhu, Bin Zhang, Mingfeng Parikh, Hemang and Jia, Jinping Chung, Charles C. Sampson, Joshua N. Hoskins, Jason W. Hutchinson, Amy Burdette, Laurie Ibrahim, Abdisamad and Hautman, Christopher Raj, Preethi S. Abnet, Christian C. and Adjei, Andrew A. Ahlbom, Anders Albanes, Demetrius Allen, Naomi E. Ambrosone, Christine B. Aldrich, Melinda Amiano, Pilar Amos, Christopher Andersson, Ulrika Andriole, Jr., Gerald Andrulis, Irene L. Arici, Cecilia Arslan, Alan A. and Austin, Melissa A. Baris, Dalsu Barkauskas, Donald A. and Bassig, Bryan A. Freeman, Laura E. Beane Berg, Christine D. and Berndt, Sonja I. Bertazzi, Pier Alberto Biritwum, Richard B. and Black, Amanda Blot, William Boeing, Heiner Boffetta, Paolo and Bolton, Kelly Boutron-Ruault, Marie-Christine Bracci, Paige M. Brennan, Paul Brinton, Louise A. Brotzman, Michelle and Bueno-de-Mesquita, H. Bas Buring, Julie E. Butler, Mary Ann and Cai, Qiuyin Cancel-Tassin, Geraldine Canzian, Federico Cao, Guangwen Caporaso, Neil E. Carrato, Alfredo Carreon, Tania and Carta, Angela Chang, Gee-Chen Chang, I-Shou and Chang-Claude, Jenny Che, Xu Chen, Chien-Jen Chen, Chih-Yi and Chen, Chung-Hsing Chen, Constance Chen, Kuan-Yu Chen, Yuh-Min Chokkalingam, Anand P. Chu, Lisa W. Clavel-Chapelon, Francoise Colditz, Graham A. Colt, Joanne S. Conti, David and Cook, Michael B. Cortessis, Victoria K. Crawford, E. David and Cussenot, Olivier Davis, Faith G. De Vivo, Immaculata and Deng, Xiang Ding, Ti Dinney, Colin P. Di Stefano, Anna Luisa and Diver, W. Ryan Duell, Eric J. Elena, Joanne W. Fan, Jin-Hu Feigelson, Heather Spencer Feychting, Maria Figueroa, Jonine D. Flanagan, Adrienne M. Fraumeni, Jr., Joseph F. and Freedman, Neal D. Fridley, Brooke L. Fuchs, Charles S. and Gago-Dominguez, Manuela Gallinger, Steven Gao, Yu-Tang and Gapstur, Susan M. Garcia-Closas, Montserrat Garcia-Closas, Reina and Gastier-Foster, Julie M. Gaziano, J. Michael Gerhard, Daniela S. Giffen, Carol A. Giles, Graham G. Gillanders, Elizabeth M. Giovannucci, Edward L. Goggins, Michael Gokgoz, Nalan Goldstein, Alisa M. Gonzalez, Carlos Gorlick, Richard and Greene, Mark H. Gross, Myron Grossman, H. Barton Grubb, III, Robert Gu, Jian Guan, Peng Haiman, Christopher A. and Hallmans, Goran Hankinson, Susan E. Harris, Curtis C. and Hartge, Patricia Hattinger, Claudia Hayes, Richard B. He, Qincheng Helman, Lee Henderson, Brian E. Henriksson, Roger and Hoffman-Bolton, Judith Hohensee, Chancellor Holly, Elizabeth A. Hong, Yun-Chul Hoover, Robert N. Hosgood, H. Dean and Hsiao, Chin-Fu Hsing, Ann W. Hsiung, Chao Agnes Hu, Nan and Hu, Wei Hu, Zhibin Huang, Ming-Shyan Hunter, David J. and Inskip, Peter D. Ito, Hidemi Jacobs, Eric J. Jacobs, Kevin B. Jenab, Mazda Ji, Bu-Tian Johansen, Christoffer and Johansson, Mattias Johnson, Alison Kaaks, Rudolf Kamat, Ashish M. Kamineni, Aruna Karagas, Margaret Khanna, Chand and Khaw, Kay-Tee Kim, Christopher Kim, In-Sam Kim, Jin Hee and Kim, Yeul Hong Kim, Young-Chul Kim, Young Tae Kang, Chang Hyun Jung, Yoo Jin Kitahara, Cari M. Klein, Alison P. and Klein, Robert Kogevinas, Manolis Koh, Woon-Puay Kohno, Takashi Kolonel, Laurence N. Kooperberg, Charles Kratz, Christian P. Krogh, Vittorio Kunitoh, Hideo Kurtz, Robert C. and Kurucu, Nilgun Lan, Qing Lathrop, Mark Lau, Ching C. and Lecanda, Fernando Lee, Kyoung-Mu Lee, Maxwell P. Le Marchand, Loic Lerner, Seth P. Li, Donghui Liao, Linda M. and Lim, Wei-Yen Lin, Dongxin Lin, Jie Lindstrom, Sara and Linet, Martha S. Lissowska, Jolanta Liu, Jianjun Ljungberg, Boerje Lloreta, Josep Lu, Daru Ma, Jing Malats, Nuria and Mannisto, Satu Marina, Neyssa Mastrangelo, Giuseppe and Matsuo, Keitaro McGlynn, Katherine A. McKean-Cowdin, Roberta and McNeill, Lorna H. McWilliams, Robert R. Melin, Beatrice S. and Meltzer, Paul S. Mensah, James E. Miao, Xiaoping Michaud, Dominique S. Mondul, Alison M. Moore, Lee E. Muir, Kenneth and Niwa, Shelley Olson, Sara H. Orr, Nick Panico, Salvatore and Park, Jae Yong Patel, Alpa V. Patino-Garcia, Ana and Pavanello, Sofia Peeters, Petra H. M. Peplonska, Beata and Peters, Ulrike Petersen, Gloria M. Picci, Piero Pike, Malcolm C. Porru, Stefano Prescott, Jennifer Pu, Xia and Purdue, Mark P. Qiao, You-Lin Rajaraman, Preetha Riboli, Elio Risch, Harvey A. Rodabough, Rebecca J. Rothman, Nathaniel Ruder, Avima M. Ryu, Jeong-Seon Sanson, Marc and Schned, Alan Schumacher, Fredrick R. Schwartz, Ann G. and Schwartz, Kendra L. Schwenn, Molly Scotlandi, Katia Seow, Adeline Serra, Consol Serra, Massimo Sesso, Howard D. and Severi, Gianluca Shen, Hongbing Shen, Min Shete, Sanjay and Shiraishi, Kouya Shu, Xiao-Ou Siddiq, Afshan Sierrasesumaga, Luis Sierri, Sabina Sihoe, Alan Dart Loon Silverman, Debra T. Simon, Matthias Southey, Melissa C. Spector, Logan and Spitz, Margaret Stampfer, Meir Stattin, Par Stern, Mariana C. Stevens, Victoria L. Stolzenberg-Solomon, Rachael Z. and Stram, Daniel O. Strom, Sara S. Su, Wu-Chou Sund, Malin and Sung, Sook Whan Swerdlow, Anthony Tan, Wen Tanaka, Hideo and Tang, Wei Tang, Ze-Zhang Tardon, Adonina Tay, Evelyn and Taylor, Philip R. Tettey, Yao Thomas, David M. Tirabosco, Roberto Tjonneland, Anne Tobias, Geoffrey S. Toro, Jorge R. and Travis, Ruth C. Trichopoulos, Dimitrios Troisi, Rebecca and Truelove, Ann Tsai, Ying-Huang Tucker, Margaret A. Tumino, Rosario Van Den Berg, David Van Den Eeden, Stephen K. and Vermeulen, Roel Vineis, Paolo Visvanathan, Kala Vogel, Ulla and Wang, Chaoyu Wang, Chengfeng Wang, Junwen Wang, Sophia S. Weiderpass, Elisabete Weinstein, Stephanie J. Wentzensen, Nicolas Wheeler, William White, Emily Wiencke, John K. and Wolk, Alicja Wolpin, Brian M. Wong, Maria Pik Wrensch, Margaret Wu, Chen Wu, Tangchun Wu, Xifeng Wu, Yi-Long and Wunder, Jay S. Xiang, Yong-Bing Xu, Jun Yang, Hannah P. and Yang, Pan-Chyr Yatabe, Yasushi Ye, Yuanqing Yeboah, Edward D. Yin, Zhihua Ying, Chen Yu, Chong-Jen Yu, Kai and Yuan, Jian-Min Zanetti, Krista A. Zeleniuch-Jacquotte, Anne and Zheng, Wei Zhou, Baosen Mirabello, Lisa Savage, Sharon A. Kraft, Peter Chanock, Stephen J. Yeager, Meredith and Landi, Maria Terese Shi, Jianxin Chatterjee, Nilanjan and Amundadottir, Laufey T.

Abstract

Genome-wide association studies (GWAS) have mapped risk alleles for at least 10 distinct cancers to a small region of 63 000 bp on chromosome 5p15.33. This region harbors the TERT and CLPTM1L genes; the former encodes the catalytic subunit of telomerase reverse transcriptase and the latter may play a role in apoptosis. To investigate further the genetic architecture of common susceptibility alleles in this region, we conducted an agnostic subset-based meta-analysis (association analysis based on subsets) across six distinct cancers in 34 248 cases and 45 036 controls. Based on sequential conditional analysis, we identified as many as six independent risk loci marked by common single-nucleotide polymorphisms: five in the TERT gene (Region 1: rs7726159, P = 2.10 x 10(-39); Region 3: rs2853677, P = 3.30 x 10(-36) and P-Conditional = 2.36 x 10(-8); Region 4: rs2736098, P = 3.87 x 10(-12) and P-Conditional = 5.19 x 10(-6), Region 5: rs13172201, P = 0.041 and P-Conditional = 2.04 x 10(-6); and Region 6: rs10069690, P = 7.49 x 10 215 and P-Conditional = 5.35 x 10(-7)) and one in the neighboring CLPTM1L gene(Region 2: rs451360; P = 1.90 x 10(-18) and P-Conditional = 7.06 x 10(-16)). Between three and five cancers mapped to each independent locus with both risk-enhancing and protective effects. Allele-specific effects on DNA methylation were seen for a subset of risk loci, indicating that methylation and subsequent effects on gene expression may contribute to the biology of risk variants on 5p15.33. Our results provide strong support for extensive pleiotropy across this region of 5p15.33, to an extent not previously observed in other cancer susceptibility loci.

Published
2014

42. Genome-wide association study confirms lung cancer susceptibility loci on chromosomes 5p15 and 15q25 in an African-American population

Author

Zanetti, Krista A., primary, Wang, Zhaoming, additional, Aldrich, Melinda, additional, Amos, Christopher I., additional, Blot, William J., additional, Bowman, Elise D., additional, Burdette, Laurie, additional, Cai, Qiuyin, additional, Caporaso, Neil, additional, Chung, Charles C., additional, Gillanders, Elizabeth M., additional, Haiman, Christopher A., additional, Hansen, Helen M., additional, Henderson, Brian E., additional, Kolonel, Laurence N., additional, Marchand, Loic Le, additional, Li, Shengchao, additional, McNeill, Lorna Haughton, additional, Ryan, Bríd M., additional, Schwartz, Ann G., additional, Sison, Jennette D., additional, Spitz, Margaret R., additional, Tucker, Margaret, additional, Wenzlaff, Angela S., additional, Wiencke, John K., additional, Wilkens, Lynne, additional, Wrensch, Margaret R., additional, Wu, Xifeng, additional, Zheng, Wei, additional, Zhou, Weiyin, additional, Christiani, David, additional, Palmer, Julie R., additional, Penning, Trevor M., additional, Rieber, Alyssa G., additional, Rosenberg, Lynn, additional, Ruiz-Narvaez, Edward A., additional, Su, Li, additional, Vachani, Anil, additional, Wei, Yongyue, additional, Whitehead, Alexander S., additional, Chanock, Stephen J., additional, and Harris, Curtis C., additional

Published
2016
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43. Female chromosome X mosaicism is age-related and preferentially affects the inactivated X chromosome

Author

Machiela, Mitchell J., primary, Zhou, Weiyin, additional, Karlins, Eric, additional, Sampson, Joshua N., additional, Freedman, Neal D., additional, Yang, Qi, additional, Hicks, Belynda, additional, Dagnall, Casey, additional, Hautman, Christopher, additional, Jacobs, Kevin B., additional, Abnet, Christian C., additional, Aldrich, Melinda C., additional, Amos, Christopher, additional, Amundadottir, Laufey T., additional, Arslan, Alan A., additional, Beane-Freeman, Laura E., additional, Berndt, Sonja I., additional, Black, Amanda, additional, Blot, William J., additional, Bock, Cathryn H., additional, Bracci, Paige M., additional, Brinton, Louise A., additional, Bueno-de-Mesquita, H Bas, additional, Burdett, Laurie, additional, Buring, Julie E., additional, Butler, Mary A., additional, Canzian, Federico, additional, Carreón, Tania, additional, Chaffee, Kari G., additional, Chang, I-Shou, additional, Chatterjee, Nilanjan, additional, Chen, Chu, additional, Chen, Constance, additional, Chen, Kexin, additional, Chung, Charles C., additional, Cook, Linda S., additional, Crous Bou, Marta, additional, Cullen, Michael, additional, Davis, Faith G., additional, De Vivo, Immaculata, additional, Ding, Ti, additional, Doherty, Jennifer, additional, Duell, Eric J., additional, Epstein, Caroline G., additional, Fan, Jin-Hu, additional, Figueroa, Jonine D., additional, Fraumeni, Joseph F., additional, Friedenreich, Christine M., additional, Fuchs, Charles S., additional, Gallinger, Steven, additional, Gao, Yu-Tang, additional, Gapstur, Susan M., additional, Garcia-Closas, Montserrat, additional, Gaudet, Mia M., additional, Gaziano, J. Michael, additional, Giles, Graham G., additional, Gillanders, Elizabeth M., additional, Giovannucci, Edward L., additional, Goldin, Lynn, additional, Goldstein, Alisa M., additional, Haiman, Christopher A., additional, Hallmans, Goran, additional, Hankinson, Susan E., additional, Harris, Curtis C., additional, Henriksson, Roger, additional, Holly, Elizabeth A., additional, Hong, Yun-Chul, additional, Hoover, Robert N., additional, Hsiung, Chao A., additional, Hu, Nan, additional, Hu, Wei, additional, Hunter, David J., additional, Hutchinson, Amy, additional, Jenab, Mazda, additional, Johansen, Christoffer, additional, Khaw, Kay-Tee, additional, Kim, Hee Nam, additional, Kim, Yeul Hong, additional, Kim, Young Tae, additional, Klein, Alison P., additional, Klein, Robert, additional, Koh, Woon-Puay, additional, Kolonel, Laurence N., additional, Kooperberg, Charles, additional, Kraft, Peter, additional, Krogh, Vittorio, additional, Kurtz, Robert C., additional, LaCroix, Andrea, additional, Lan, Qing, additional, Landi, Maria Teresa, additional, Marchand, Loic Le, additional, Li, Donghui, additional, Liang, Xiaolin, additional, Liao, Linda M., additional, Lin, Dongxin, additional, Liu, Jianjun, additional, Lissowska, Jolanta, additional, Lu, Lingeng, additional, Magliocco, Anthony M., additional, Malats, Nuria, additional, Matsuo, Keitaro, additional, McNeill, Lorna H., additional, McWilliams, Robert R., additional, Melin, Beatrice S., additional, Mirabello, Lisa, additional, Moore, Lee, additional, Olson, Sara H., additional, Orlow, Irene, additional, Park, Jae Yong, additional, Patiño-Garcia, Ana, additional, Peplonska, Beata, additional, Peters, Ulrike, additional, Petersen, Gloria M., additional, Pooler, Loreall, additional, Prescott, Jennifer, additional, Prokunina-Olsson, Ludmila, additional, Purdue, Mark P., additional, Qiao, You-Lin, additional, Rajaraman, Preetha, additional, Real, Francisco X., additional, Riboli, Elio, additional, Risch, Harvey A., additional, Rodriguez-Santiago, Benjamin, additional, Ruder, Avima M., additional, Savage, Sharon A., additional, Schumacher, Fredrick, additional, Schwartz, Ann G., additional, Schwartz, Kendra L., additional, Seow, Adeline, additional, Wendy Setiawan, Veronica, additional, Severi, Gianluca, additional, Shen, Hongbing, additional, Sheng, Xin, additional, Shin, Min-Ho, additional, Shu, Xiao-Ou, additional, Silverman, Debra T., additional, Spitz, Margaret R., additional, Stevens, Victoria L., additional, Stolzenberg-Solomon, Rachael, additional, Stram, Daniel, additional, Tang, Ze-Zhong, additional, Taylor, Philip R., additional, Teras, Lauren R., additional, Tobias, Geoffrey S., additional, Van Den Berg, David, additional, Visvanathan, Kala, additional, Wacholder, Sholom, additional, Wang, Jiu-Cun, additional, Wang, Zhaoming, additional, Wentzensen, Nicolas, additional, Wheeler, William, additional, White, Emily, additional, Wiencke, John K., additional, Wolpin, Brian M., additional, Wong, Maria Pik, additional, Wu, Chen, additional, Wu, Tangchun, additional, Wu, Xifeng, additional, Wu, Yi-Long, additional, Wunder, Jay S., additional, Xia, Lucy, additional, Yang, Hannah P., additional, Yang, Pan-Chyr, additional, Yu, Kai, additional, Zanetti, Krista A., additional, Zeleniuch-Jacquotte, Anne, additional, Zheng, Wei, additional, Zhou, Baosen, additional, Ziegler, Regina G., additional, Perez-Jurado, Luis A., additional, Caporaso, Neil E., additional, Rothman, Nathaniel, additional, Tucker, Margaret, additional, Dean, Michael C., additional, Yeager, Meredith, additional, and Chanock, Stephen J., additional

Published
2016
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44. Multiple Myeloma Mortality in Relation to Obesity Among African Americans

Author

Sonderman, Jennifer S., primary, Bethea, Traci N., additional, Kitahara, Cari M., additional, Patel, Alpa V., additional, Harvey, Chinonye, additional, Knutsen, Synnøve F., additional, Park, Yikyung, additional, Park, Song-Yi, additional, Fraser, Gary E., additional, Teras, Lauren R., additional, Purdue, Mark P., additional, Stolzenberg-Solomon, Rachael Z., additional, Gillanders, Elizabeth M., additional, Palmer, Julie R., additional, Kolonel, Laurence N., additional, and Blot, William J., additional

Published
2016
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46. Characterization of Large Structural Genetic Mosaicism in Human Autosomes

Author

Machiela, Mitchell J., Zhou, Weiyin, Sampson, Joshua N., Dean, Michael C., Jacobs, Kevin B., Black, Amanda, Brinton, Louise A., Chang, I-Shou, Chen, Chu, Chen, Constance, Chen, Kexin, Cook, Linda S., Bou, Marta Crous, De Vivo, Immaculata, Doherty, Jennifer, Friedenreich, Christine M., Gaudet, Mia M., Haiman, Christopher A., Hankinson, Susan E., Hartge, Patricia, Henderson, Brian E., Hong, Yun-Chul, Hosgood, H. Dean, III, Hsiung, Chao A., Hu, Wei, Hunter, David J., Jessop, Lea, Kim, Hee Nam, Kim, Yeul Hong, Kim, Young Tae, Klein, Robert, Kraft, Peter, Lan, Qing, Lin, Dongxin, Liu, Jianjun, Le Marchand, Loic, Liang, Xiaolin, Lissowska, Jolanta, Lu, Lingeng, Magliocco, Anthony M., Matsuo, Keitaro, Olson, Sara H., Orlow, Irene, Park, Jae Yong, Pooler, Loreall, Prescott, Jennifer, Rastogi, Radhai, Risch, Harvey A., Schumacher, Fredrick, Seow, Adeline, Setiawan, Veronica Wendy, Shen, Hongbing, Sheng, Xin, Shin, Min-Ho, Shu, Xiao-Ou, VanDen Berg, David, Wang, Jiu-Cun, Wentzensen, Nicolas, Wong, Maria Pik, Wu, Chen, Wu, Tangchun, Wu, Yi-Long, Xia, Lucy, Yang, Hannah P., Yang, Pan-Chyr, Zheng, Wei, Zhou, Baosen, Abnet, Christian C., Albanes, Demetrius, Aldrich, Melinda C., Amos, Christopher, Amundadottir, Laufey T., Berndt, Sonja I., Blot, William J., Bock, Cathryn H., Bracci, Paige M., Burdett, Laurie, Buring, Julie E., Butler, Mary A., Carreon, Tania, Chatterjee, Nilanjan, Chung, Charles C., Cook, Michael B., Cullen, Michael, Davis, Faith G., Ding, Ti, Duell, Eric J., Epstein, Caroline G., Fan, Jin-Hu, Figueroa, Jonine D., Fraumeni, Joseph F., Jr., Freedman, Neal D., Fuchs, Charles S., Gao, Yu-Tang, Gapstur, Susan M., Patino-Garcia, Ana, Garcia-Closas, Montserrat, Gaziano, J. Michael, Giles, Graham G., Gillanders, Elizabeth M., Giovannucci, Edward L., Goldin, Lynn, Goldstein, Alisa M., Greene, Mark H., Hallmans, Göran, Harris, Curtis C., Henriksson, Roger, Holly, Elizabeth A., Hoover, Robert N., Hu, Nan, Hutchinson, Amy, Jenab, Mazda, Johansen, Christoffer, Khaw, Kay-Tee, Koh, Woon-Puay, Kolonel, Laurence N., Kooperberg, Charles, Krogh, Vittorio, Kurtz, Robert C., LaCroix, Andrea, Landgren, Annelie, Landi, Maria Teresa, Li, Donghui, Liao, Linda M., Malats, Nuria, McGlynn, Katherine A., McNeill, Lorna H., McWilliams, Robert R., Melin, Beatrice S., Mirabello, Lisa, Peplonska, Beata, Peters, Ulrike, Petersen, Gloria M., Prokunina-Olsson, Ludmila, Purdue, Mark, Qiao, You-Lin, Rabe, Kari G., Rajaraman, Preetha, Real, Francisco X., Riboli, Elio, Rodriguez-Santiago, Benjamin, Rothman, Nathaniel, Ruder, Avima M., Savage, Sharon A., Schwartz, Ann G., Schwartz, Kendra L., Sesso, Howard D., Severi, Gianluca, Silverman, Debra T., Spitz, Margaret R., Stevens, Victoria L., Stolzenberg-Solomon, Rachael, Stram, Daniel, Tang, Ze-Zhong, Taylor, Philip R., Teras, Lauren R., Tobias, Geoffrey S., Viswanathan, Kala, Wacholder, Sholom, Wang, Zhaoming, Weinstein, Stephanie J., Wheeler, William, White, Emily, Wiencke, John K., Wolpin, Brian M., Wu, Xifeng, Wunder, Jay S., Yu, Kai, Zanetti, Krista A., Zeleniuch-Jacquotte, Anne, Ziegler, Regina G., De Andrade, Mariza, Barnes, Kathleen C., Beaty, Terri H., Bierut, Laura J., Desch, Karl C., Doheny, Kimberly F., Feenstra, Bjarke, Ginsburg, David, Heit, John A., Kang, Jae H., Laurie, Cecilia A., Li, Jun Z., Lowe, William L., Marazita, Mary L., Melbye, Mads, Mirel, Daniel B., Murray, Jeffrey C., Nelson, Sarah C., Pasquale, Louis R., Rice, Kenneth, Wiggs, Janey L., Wise, Anastasia, Tucker, Margaret, Perez-Jurado, Luis A., Laurie, Cathy C., Caporaso, Neil E., Yeager, Meredith, Chanock, Stephen J., Machiela, Mitchell J., Zhou, Weiyin, Sampson, Joshua N., Dean, Michael C., Jacobs, Kevin B., Black, Amanda, Brinton, Louise A., Chang, I-Shou, Chen, Chu, Chen, Constance, Chen, Kexin, Cook, Linda S., Bou, Marta Crous, De Vivo, Immaculata, Doherty, Jennifer, Friedenreich, Christine M., Gaudet, Mia M., Haiman, Christopher A., Hankinson, Susan E., Hartge, Patricia, Henderson, Brian E., Hong, Yun-Chul, Hosgood, H. Dean, III, Hsiung, Chao A., Hu, Wei, Hunter, David J., Jessop, Lea, Kim, Hee Nam, Kim, Yeul Hong, Kim, Young Tae, Klein, Robert, Kraft, Peter, Lan, Qing, Lin, Dongxin, Liu, Jianjun, Le Marchand, Loic, Liang, Xiaolin, Lissowska, Jolanta, Lu, Lingeng, Magliocco, Anthony M., Matsuo, Keitaro, Olson, Sara H., Orlow, Irene, Park, Jae Yong, Pooler, Loreall, Prescott, Jennifer, Rastogi, Radhai, Risch, Harvey A., Schumacher, Fredrick, Seow, Adeline, Setiawan, Veronica Wendy, Shen, Hongbing, Sheng, Xin, Shin, Min-Ho, Shu, Xiao-Ou, VanDen Berg, David, Wang, Jiu-Cun, Wentzensen, Nicolas, Wong, Maria Pik, Wu, Chen, Wu, Tangchun, Wu, Yi-Long, Xia, Lucy, Yang, Hannah P., Yang, Pan-Chyr, Zheng, Wei, Zhou, Baosen, Abnet, Christian C., Albanes, Demetrius, Aldrich, Melinda C., Amos, Christopher, Amundadottir, Laufey T., Berndt, Sonja I., Blot, William J., Bock, Cathryn H., Bracci, Paige M., Burdett, Laurie, Buring, Julie E., Butler, Mary A., Carreon, Tania, Chatterjee, Nilanjan, Chung, Charles C., Cook, Michael B., Cullen, Michael, Davis, Faith G., Ding, Ti, Duell, Eric J., Epstein, Caroline G., Fan, Jin-Hu, Figueroa, Jonine D., Fraumeni, Joseph F., Jr., Freedman, Neal D., Fuchs, Charles S., Gao, Yu-Tang, Gapstur, Susan M., Patino-Garcia, Ana, Garcia-Closas, Montserrat, Gaziano, J. Michael, Giles, Graham G., Gillanders, Elizabeth M., Giovannucci, Edward L., Goldin, Lynn, Goldstein, Alisa M., Greene, Mark H., Hallmans, Göran, Harris, Curtis C., Henriksson, Roger, Holly, Elizabeth A., Hoover, Robert N., Hu, Nan, Hutchinson, Amy, Jenab, Mazda, Johansen, Christoffer, Khaw, Kay-Tee, Koh, Woon-Puay, Kolonel, Laurence N., Kooperberg, Charles, Krogh, Vittorio, Kurtz, Robert C., LaCroix, Andrea, Landgren, Annelie, Landi, Maria Teresa, Li, Donghui, Liao, Linda M., Malats, Nuria, McGlynn, Katherine A., McNeill, Lorna H., McWilliams, Robert R., Melin, Beatrice S., Mirabello, Lisa, Peplonska, Beata, Peters, Ulrike, Petersen, Gloria M., Prokunina-Olsson, Ludmila, Purdue, Mark, Qiao, You-Lin, Rabe, Kari G., Rajaraman, Preetha, Real, Francisco X., Riboli, Elio, Rodriguez-Santiago, Benjamin, Rothman, Nathaniel, Ruder, Avima M., Savage, Sharon A., Schwartz, Ann G., Schwartz, Kendra L., Sesso, Howard D., Severi, Gianluca, Silverman, Debra T., Spitz, Margaret R., Stevens, Victoria L., Stolzenberg-Solomon, Rachael, Stram, Daniel, Tang, Ze-Zhong, Taylor, Philip R., Teras, Lauren R., Tobias, Geoffrey S., Viswanathan, Kala, Wacholder, Sholom, Wang, Zhaoming, Weinstein, Stephanie J., Wheeler, William, White, Emily, Wiencke, John K., Wolpin, Brian M., Wu, Xifeng, Wunder, Jay S., Yu, Kai, Zanetti, Krista A., Zeleniuch-Jacquotte, Anne, Ziegler, Regina G., De Andrade, Mariza, Barnes, Kathleen C., Beaty, Terri H., Bierut, Laura J., Desch, Karl C., Doheny, Kimberly F., Feenstra, Bjarke, Ginsburg, David, Heit, John A., Kang, Jae H., Laurie, Cecilia A., Li, Jun Z., Lowe, William L., Marazita, Mary L., Melbye, Mads, Mirel, Daniel B., Murray, Jeffrey C., Nelson, Sarah C., Pasquale, Louis R., Rice, Kenneth, Wiggs, Janey L., Wise, Anastasia, Tucker, Margaret, Perez-Jurado, Luis A., Laurie, Cathy C., Caporaso, Neil E., Yeager, Meredith, and Chanock, Stephen J.

Abstract

Analyses of genome-wide association study (GWAS) data have revealed that detectable genetic mosaicism involving large (>2 Mb) structural autosomal alterations occurs in a fraction of individuals. We present results for a set of 24,849 genotyped individuals (total GWAS set II [TGSII]) in whom 341 large autosomal abnormalities were observed in 168 (0.68%) individuals. Merging data from the new TGSII set with data from two prior reports (the Gene-Environment Association Studies and the total GWAS set I) generated a large dataset of 127,179 individuals; we then conducted a meta-analysis to investigate the patterns of detectable autosomal mosaicism (n = 1,315 events in 925 [0.73%] individuals). Restricting to events >2 Mb in size, we observed an increase in event frequency as event size decreased. The combined results underscore that the rate of detectable mosaicism increases with age (p value = 5.5 x 3 10(-31)) and is higher in men (p value = 0.002) but lower in participants of African ancestry (p value = 0.003). In a subset of 47 individuals from whom serial samples were collected up to 6 years apart, complex changes were noted over time and showed an overall increase in the proportion of mosaic cells as age increased. Our large combined sample allowed for a unique ability to characterize detectable genetic mosaicism involving large structural events and strengthens the emerging evidence of non-random erosion of the genome in the aging population.

Published
2015
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47. Detectable clonal mosaicism and its relationship to aging and cancer

Author

Jacobs, Kevin B. Yeager, Meredith Zhou, Weiyin Wacholder, Sholom Wang, Zhaoming Rodriguez-Santiago, Benjamin and Hutchinson, Amy Deng, Xiang Liu, Chenwei Horner, Marie-Josephe Cullen, Michael Epstein, Caroline G. Burdett, Laurie Dean, Michael C. Chatterjee, Nilanjan Sampson, Joshua and Chung, Charles C. Kovaks, Joseph Gapstur, Susan M. and Stevens, Victoria L. Teras, Lauren T. Gaudet, Mia M. and Albanes, Demetrius Weinstein, Stephanie J. Virtamo, Jarmo and Taylor, Philip R. Freedman, Neal D. Abnet, Christian C. and Goldstein, Alisa M. Hu, Nan Yu, Kai Yuan, Jian-Min Liao, Linda Ding, Ti Qiao, You-Lin Gao, Yu-Tang Koh, Woon-Puay and Xiang, Yong-Bing Tang, Ze-Zhong Fan, Jin-Hu Aldrich, Melinda C. Amos, Christopher Blot, William J. Bock, Cathryn H. Gillanders, Elizabeth M. Harris, Curtis C. Haiman, Christopher A. Henderson, Brian E. Kolonel, Laurence N. Le Marchand, Loic McNeill, Lorna H. Rybicki, Benjamin A. and Schwartz, Ann G. Signorello, Lisa B. Spitz, Margaret R. and Wiencke, John K. Wrensch, Margaret Wu, Xifeng Zanetti, Krista A. Ziegler, Regina G. Figueroa, Jonine D. and Garcia-Closas, Montserrat Malats, Nuria Marenne, Gaelle and Prokunina-Olsson, Ludmila Baris, Dalsu Schwenn, Molly and Johnson, Alison Landi, Maria Teresa Goldin, Lynn Consonni, Dario Bertazzi, Pier Alberto Rotunno, Melissa Rajaraman, Preetha Andersson, Ulrika Freeman, Laura E. Beane Berg, Christine D. Buring, Julie E. Butler, Mary A. Carreon, Tania and Feychting, Maria Ahlbom, Anders Gaziano, J. Michael and Giles, Graham G. Hallmans, Goran Hankinson, Susan E. Hartge, Patricia Henriksson, Roger Inskip, Peter D. Johansen, Christoffer Landgren, Annelie McKean-Cowdin, Roberta and Michaud, Dominique S. Melin, Beatrice S. Peters, Ulrike and Ruder, Avima M. Sesso, Howard D. Severi, Gianluca Shu, Xiao-Ou Visvanathan, Kala White, Emily Wolk, Alicja and Zeleniuch-Jacquotte, Anne Zheng, Wei Silverman, Debra T. and Kogevinas, Manolis Gonzalez, Juan R. Villa, Olaya Li, Donghui Duell, Eric J. Risch, Harvey A. Olson, Sara H. and Kooperberg, Charles Wolpin, Brian M. Jiao, Li Hassan, Manal and Wheeler, William Arslan, Alan A. Bueno-de-Mesquita, H. Bas and Fuchs, Charles S. Gallinger, Steven Gross, Myron D. and Holly, Elizabeth A. Klein, Alison P. LaCroix, Andrea and Mandelson, Margaret T. Petersen, Gloria Boutron-Ruault, Marie-Christine Bracci, Paige M. Canzian, Federico Chang, Kenneth Cotterchio, Michelle Giovannucci, Edward L. Goggins, Michael Bolton, Judith A. Hoffman Jenab, Mazda Khaw, Kay-Tee and Krogh, Vittorio Kurtz, Robert C. McWilliams, Robert R. and Mendelsohn, Julie B. Rabe, Kari G. Riboli, Elio Tjonneland, Anne Tobias, Geoffrey S. Trichopoulos, Dimitrios Elena, Joanne W. Yu, Herbert Amundadottir, Laufey and Stolzenberg-Solomon, Rachael Z. Kraft, Peter Schumacher, Fredrick Stram, Daniel Savage, Sharon A. Mirabello, Lisa and Andrulis, Irene L. Wunder, Jay S. Patino Garcia, Ana and Sierrasesumaga, Luis Barkauskas, Donald A. Gorlick, Richard G. and Purdue, Mark Chow, Wong-Ho Moore, Lee E. Schwartz, Kendra L. Davis, Faith G. Hsing, Ann W. Berndt, Sonja I. and Black, Amanda Wentzensen, Nicolas Brinton, Louise A. and Lissowska, Jolanta Peplonska, Beata McGlynn, Katherine A. and Cook, Michael B. Graubard, Barry I. Kratz, Christian P. and Greene, Mark H. Erickson, Ralph L. Hunter, David J. Thomas, Gilles Hoover, Robert N. Real, Francisco X. Fraumeni, Jr., Joseph F. Caporaso, Neil E. Tucker, Margaret Rothman, Nathaniel Perez-Jurado, Luis A. Chanock, Stephen J.

Abstract

In an analysis of 31,717 cancer cases and 26,136 cancer-free controls from 13 genome-wide association studies, we observed large chromosomal abnormalities in a subset of clones in DNA obtained from blood or buccal samples. We observed mosaic abnormalities, either aneuploidy or copy-neutral loss of heterozygosity, of > 2 Mb in size in autosomes of 517 individuals (0.89%), with abnormal cell proportions of between 7% and 95%. In cancer-free individuals, frequency increased with age, from 0.23% under 50 years to 1.91% between 75 and 79 years (P = 4.8 x 10(-8)). Mosaic abnormalities were more frequent in individuals with solid tumors (0.97% versus 0.74% in cancer-free individuals; odds ratio (OR) = 1.25; P = 0.016), with stronger association with cases who had DNA collected before diagnosis or treatment (OR = 1.45; P = 0.0005). Detectable mosaicism was also more common in individuals for whom DNA was collected at least 1 year before diagnosis with leukemia compared to cancer-free individuals (OR = 35.4; P = 3.8 x 10(-11)). These findings underscore the time-dependent nature of somatic events in the etiology of cancer and potentially other late-onset diseases.

Published
2012

48. Next Generation Analytic Tools for Large Scale Genetic Epidemiology Studies of Complex Diseases

Author

Mechanic, Leah E., Chen, Huann-Sheng, Amos, Christopher I., Chatterjee, Nilanjan, Cox, Nancy J., Divi, Rao L., Fan, Ruzong, Harris, Emily L., Jacobs, Kevin, Kraft, Peter, Leal, Suzanne M., McAllister, Kimberly, Moore, Jason H., Paltoo, Dina N., Province, Michael A., Ramos, Erin M., Ritchie, Marylyn D., Roeder, Kathryn, Schaid, Daniel J., Stephens, Matthew, Thomas, Duncan C., Weinberg, Clarice R., Witte, John S., Zhang, Shunpu, Zöllner, Sebastian, Feuer, Eric J., and Gillanders, Elizabeth M.

Subjects
Article
Abstract

Over the past several years, genome-wide association studies (GWAS) have succeeded in identifying hundreds of genetic markers associated with common diseases. However, most of these markers confer relatively small increments of risk and explain only a small proportion of familial clustering. To identify obstacles to future progress in genetic epidemiology research and provide recommendations to NIH for overcoming these barriers, the National Cancer Institute sponsored a workshop entitled “Next Generation Analytic Tools for Large-Scale Genetic Epidemiology Studies of Complex Diseases” on September 15–16, 2010. The goal of the workshop was to facilitate discussions on (1) statistical strategies and methods to efficiently identify genetic and environmental factors contributing to the risk of complex disease; and (2) how to develop, apply, and evaluate these strategies for the design, analysis, and interpretation of large-scale complex disease association studies in order to guide NIH in setting the future agenda in this area of research. The workshop was organized as a series of short presentations covering scientific (gene-gene and gene-environment interaction, complex phenotypes, and rare variants and next generation sequencing) and methodological (simulation modeling and computational resources and data management) topic areas. Specific needs to advance the field were identified during each session and are summarized.

Published
2011

49. The landscape of recombination in African Americans

Author

Gillanders, Elizabeth M., Ryan Diver, W., Buxbaum, Sarah G., Ingles, Sue A., Berndt, Sonja I., Boerwinkle, Eric, Rohland, Nadin, Patterson, Nick, Caporaso, Neil, Blot, William J., Harris, Curtis C., Song, Yunli, Deming, Sandra L., Hinch, Anjali G., Palmer, Cameron D., Glessner, Joseph, Casey, Graham, Divers, Jasmin, Hu, Jennifer J., Chen, Gary K., Fornage, Myriam, Adrienne Cupples, L., Bock, Cathryn H., Aldrich, Melinda C., Wang, Kai, Bandera, Elisa V., Tandon, Arti, Akylbekova, Ermeg L., Bernstein, Leslie, Ambrosone, Christine B., Cai, Qiuyin, and Amos, Christopher

Abstract

Recombination, together with mutation, is the ultimate source of genetic variation in populations. We leverage the recent mixture of people of African and European ancestry in the Americas to build a genetic map measuring the probability of crossing-over at each position in the genome, based on about 2.1 million crossovers in 30,000 unrelated African Americans. At intervals of more than three megabases it is nearly identical to a map built in Europeans. At finer scales it differs significantly, and we identify about 2,500 recombination hotspots that are active in people of West African ancestry but nearly inactive in Europeans. The probability of a crossover at these hotspots is almost fully controlled by the alleles an individual carries at PRDM9 (P

Published
2011
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50. Robustness of Next Generation Sequencing on Older Formalin-Fixed Paraffin-Embedded Tissue

Author

Carrick, Danielle Mercatante, primary, Mehaffey, Michele G., additional, Sachs, Michael C., additional, Altekruse, Sean, additional, Camalier, Corinne, additional, Chuaqui, Rodrigo, additional, Cozen, Wendy, additional, Das, Biswajit, additional, Hernandez, Brenda Y., additional, Lih, Chih-Jian, additional, Lynch, Charles F., additional, Makhlouf, Hala, additional, McGregor, Paul, additional, McShane, Lisa M., additional, Phillips Rohan, JoyAnn, additional, Walsh, William D., additional, Williams, Paul M., additional, Gillanders, Elizabeth M., additional, Mechanic, Leah E., additional, and Schully, Sheri D., additional

Published
2015
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