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2. Tuberculosis infection and lung adenocarcinoma: Mendelian randomization and pathway analysis of genome-wide association study data from never-smoking Asian women

Author

Wong, J.Y.Y., Hsiung, C.A., Matsuo, K., Wong, M.P., Seow, W.J., Song, M., Chang, I.-S., Chatterjee, N., Hu, W., Wu, C., Mitsudomi, T., Zheng, W., Kim, J.H., Seow, A., Caporaso, N.E., Shin, M.-H., Chung, L.P., An, S.-J., Zheng, H., Yatabe, Y., Kim, Y.T., Cai, Q., Kim, Y.-C., Bassig, B.A., Ho, J.C.M., Ji, B.-T., Daigo, Y., Ito, H., Momozawa, Y., Ashikawa, K., Kamatani, Y., Honda, T., Hosgood, H.D., Sakamoto, H., Kunitoh, H., Tsuta, K., Watanabe, S.-I., Kubo, M., Miyagi, Y., Nakayama, H., Matsumoto, S., Tsuboi, M., Goto, K., Song, L., Hua, X., Takahashi, A., Goto, A., Minamiya, Y., Shimizu, K., Tanaka, K., Wei, F., Matsuda, F., Kim, Y.H., Oh, I.-J., Song, F., Su, W.-C., Chang, G.-C., Chen, K.-Y., Chien, L.-H., Xiang, Y.-B., Kweon, S.-S., Lee, K.-M., Blechter, B., Qian, B., Lu, D., Jeon, H.-S., Hsiao, C.-F., Sung, J.S., Tsai, Y.-H., Jung, Y.J., Chung, C.C., Burdett, L., Yeager, M., Hutchinson, A., Berndt, S.I., Pang, H., Choi, J.E., Park, K.H., Sung, S.W., Zhu, M., Guan, P., Tan, W., Hsin, M., Sit, K.-Y., Ho, J., Choi, Y.Y., Kim, J.S., Yoon, H.I., Park, I.K., Xu, P., He, Q., Perng, R.-P., Vermeulen, R., Lim, W.-Y., Chen, K.-C., Jin, L., Jiang, S.-S., Yamaji, T., Hicks, B., Wyatt, K., Dai, J., Jin, G., Song, B., Cheng, S., Cui, P., Iwasaki, M., Shimazu, T., Tsugane, S., Fei, K., Wu, G., Lin, H.-C., Fang, Y.-H., Tsai, F.-Y., Hsieh, W.-S., Yu, J., Stevens, V.L., Laird-Offringa, I.A., Marconett, C.N., Rieswijk, L., Chao, A., Shu, X.-O., Lin, D., Chen, K., Zhou, B., Kohno, T., Shen, H., Chanock, S.J., Rothman, N., Lan, Q., IRAS OH Epidemiology Chemical Agents, and dIRAS RA-2

Subjects
Lung adenocarcinoma, Pathway analysis, Mendelian randomization, Tuberculosis, Lung cancer
Abstract

We investigated whether genetic susceptibility to tuberculosis (TB) influences lung adenocarcinoma development among never-smokers using TB genome-wide association study (GWAS) results within the Female Lung Cancer Consortium in Asia. Pathway analysis with the adaptive rank truncated product method was used to assess the association between a TB-related gene-set and lung adenocarcinoma using GWAS data from 5512 lung adenocarcinoma cases and 6277 controls. The gene-set consisted of 31 genes containing known/suggestive associations with genetic variants from previous TB-GWAS. Subsequently, we followed-up with Mendelian Randomization to evaluate the association between TB and lung adenocarcinoma using three genome-wide significant variants from previous TB-GWAS in East Asians. The TB-related gene-set was associated with lung adenocarcinoma (p = 0.016). Additionally, the Mendelian Randomization showed an association between TB and lung adenocarcinoma (OR = 1.31, 95% CI: 1.03, 1.66, p = 0.027). Our findings support TB as a causal risk factor for lung cancer development among never-smoking Asian women.

Published
2020

3. Tuberculosis infection and lung adenocarcinoma: Mendelian randomization and pathway analysis of genome-wide association study data from never-smoking Asian women

Author

IRAS OH Epidemiology Chemical Agents, dIRAS RA-2, Wong, J.Y.Y., Hsiung, C.A., Matsuo, K., Wong, M.P., Seow, W.J., Song, M., Chang, I.-S., Chatterjee, N., Hu, W., Wu, C., Mitsudomi, T., Zheng, W., Kim, J.H., Seow, A., Caporaso, N.E., Shin, M.-H., Chung, L.P., An, S.-J., Zheng, H., Yatabe, Y., Kim, Y.T., Cai, Q., Kim, Y.-C., Bassig, B.A., Ho, J.C.M., Ji, B.-T., Daigo, Y., Ito, H., Momozawa, Y., Ashikawa, K., Kamatani, Y., Honda, T., Hosgood, H.D., Sakamoto, H., Kunitoh, H., Tsuta, K., Watanabe, S.-I., Kubo, M., Miyagi, Y., Nakayama, H., Matsumoto, S., Tsuboi, M., Goto, K., Song, L., Hua, X., Takahashi, A., Goto, A., Minamiya, Y., Shimizu, K., Tanaka, K., Wei, F., Matsuda, F., Kim, Y.H., Oh, I.-J., Song, F., Su, W.-C., Chang, G.-C., Chen, K.-Y., Chien, L.-H., Xiang, Y.-B., Kweon, S.-S., Lee, K.-M., Blechter, B., Qian, B., Lu, D., Jeon, H.-S., Hsiao, C.-F., Sung, J.S., Tsai, Y.-H., Jung, Y.J., Chung, C.C., Burdett, L., Yeager, M., Hutchinson, A., Berndt, S.I., Pang, H., Choi, J.E., Park, K.H., Sung, S.W., Zhu, M., Guan, P., Tan, W., Hsin, M., Sit, K.-Y., Ho, J., Choi, Y.Y., Kim, J.S., Yoon, H.I., Park, I.K., Xu, P., He, Q., Perng, R.-P., Vermeulen, R., Lim, W.-Y., Chen, K.-C., Jin, L., Jiang, S.-S., Yamaji, T., Hicks, B., Wyatt, K., Dai, J., Jin, G., Song, B., Cheng, S., Cui, P., Iwasaki, M., Shimazu, T., Tsugane, S., Fei, K., Wu, G., Lin, H.-C., Fang, Y.-H., Tsai, F.-Y., Hsieh, W.-S., Yu, J., Stevens, V.L., Laird-Offringa, I.A., Marconett, C.N., Rieswijk, L., Chao, A., Shu, X.-O., Lin, D., Chen, K., Zhou, B., Kohno, T., Shen, H., Chanock, S.J., Rothman, N., Lan, Q., IRAS OH Epidemiology Chemical Agents, dIRAS RA-2, Wong, J.Y.Y., Hsiung, C.A., Matsuo, K., Wong, M.P., Seow, W.J., Song, M., Chang, I.-S., Chatterjee, N., Hu, W., Wu, C., Mitsudomi, T., Zheng, W., Kim, J.H., Seow, A., Caporaso, N.E., Shin, M.-H., Chung, L.P., An, S.-J., Zheng, H., Yatabe, Y., Kim, Y.T., Cai, Q., Kim, Y.-C., Bassig, B.A., Ho, J.C.M., Ji, B.-T., Daigo, Y., Ito, H., Momozawa, Y., Ashikawa, K., Kamatani, Y., Honda, T., Hosgood, H.D., Sakamoto, H., Kunitoh, H., Tsuta, K., Watanabe, S.-I., Kubo, M., Miyagi, Y., Nakayama, H., Matsumoto, S., Tsuboi, M., Goto, K., Song, L., Hua, X., Takahashi, A., Goto, A., Minamiya, Y., Shimizu, K., Tanaka, K., Wei, F., Matsuda, F., Kim, Y.H., Oh, I.-J., Song, F., Su, W.-C., Chang, G.-C., Chen, K.-Y., Chien, L.-H., Xiang, Y.-B., Kweon, S.-S., Lee, K.-M., Blechter, B., Qian, B., Lu, D., Jeon, H.-S., Hsiao, C.-F., Sung, J.S., Tsai, Y.-H., Jung, Y.J., Chung, C.C., Burdett, L., Yeager, M., Hutchinson, A., Berndt, S.I., Pang, H., Choi, J.E., Park, K.H., Sung, S.W., Zhu, M., Guan, P., Tan, W., Hsin, M., Sit, K.-Y., Ho, J., Choi, Y.Y., Kim, J.S., Yoon, H.I., Park, I.K., Xu, P., He, Q., Perng, R.-P., Vermeulen, R., Lim, W.-Y., Chen, K.-C., Jin, L., Jiang, S.-S., Yamaji, T., Hicks, B., Wyatt, K., Dai, J., Jin, G., Song, B., Cheng, S., Cui, P., Iwasaki, M., Shimazu, T., Tsugane, S., Fei, K., Wu, G., Lin, H.-C., Fang, Y.-H., Tsai, F.-Y., Hsieh, W.-S., Yu, J., Stevens, V.L., Laird-Offringa, I.A., Marconett, C.N., Rieswijk, L., Chao, A., Shu, X.-O., Lin, D., Chen, K., Zhou, B., Kohno, T., Shen, H., Chanock, S.J., Rothman, N., and Lan, Q.

Published
2020

7. Genome-wide association study identifies multiple new loci associated with Ewing sarcoma susceptibility

Author

Machiela, M.J. (Mitchell J.), Grünewald, T.G.P. (Thomas G. P.), Surdez, D. (Didier), Reynaud, S. (Stephanie), Mirabeau, O. (Olivier), Karlins, E. (Eric), Rubio, R.A. (Rebeca Alba), Zaidi, S. (Sakina), Grossetete-Lalami, S. (Sandrine), Ballet, S. (Stelly), Lapouble, E. (Eve), Laurence, V. (Valérie), Michon, J. (Jean), Pierron, G. (Gaelle), Kovar, H. (Heinrich), Gaspar, N. (Nathalie), Kontny, U. (Udo), Gonzalez-Neira, A. (Anna), Picci, P. (Piero), Alonso, J. (Javier), Patiño-García, A. (Ana), Corradini, N. (Nadege), Bérard, P.M. (Perrine Marec), Freedman, N.D. (Neal D.), Rothman, N. (Nathaniel), Dagnall, C. (Casey), Burdett, L. (Laurie), Jones, K. (Krisitine), Manning, M. (Michelle), Wyatt, K. (Kathleen), Zhou, W. (Weiyin), Yeager, M. (Meredith), Cox, D.G. (David G.), Hoover, R.N. (Robert N.), Khan, J. (Javed), Armstrong, G.T. (Gregory T.), Leisenring, W.M. (Wendy M.), Bhatia, S. (Smita), Robison, L.L. (Leslie L.), Kulozik, A. (Andreas E.), Kriebel, J. (Jennifer), Meitinger, T. (Thomas), Metzler, M. (Markus), Hartmann, W. (Wolfgang), Strauch, K. (Konstantin), Kirchner, T. (Thomas), Dirksen, U. (Uta), Morton, L.M. (Lindsay M.), Mirabello, L. (Lisa), Tucker, M. (Margaret), Tirode, F. (Franck), Chanock, S.J. (Stephen J.), and Delattre, O. (Olivier)

Subjects
Genome-wide association study, Ewing sarcoma (EWS), Pediatric cancer
Abstract

Ewing sarcoma (EWS) is a pediatric cancer characterized by the EWSR1-FLI1 fusion. We performed a genome-wide association study of 733 EWS cases and 1346 unaffected individuals of European ancestry. Our study replicates previously reported susceptibility loci at 1p36.22, 10q21.3 and 15q15.1, and identifies new loci at 6p25.1, 20p11.22 and 20p11.23. Effect estimates exhibit odds ratios in excess of 1.7, which is high for cancer GWAS, and striking in light of the rarity of EWS cases in familial cancer syndromes. Expression quantitative trait locus (eQTL) analyses identify candidate genes at 6p25.1 (RREB1) and 20p11.23 (KIZ). The 20p11.22 locus is near NKX2-2, a highly overexpressed gene in EWS. Interestingly, most loci reside near GGAA repeat sequences and may disrupt binding of the EWSR1-FLI1 fusion protein. The high locus to case discovery ratio from 733 EWS cases suggests a genetic architecture in which moderate risk SNPs constitute a significant fraction of risk.

Published
2018

11. The ets Family of Genes: Molecular Biology and Functional Implications

Author

Papas, T. S., Fisher, R. J., Bhat, N., Fujiwara, S., Watson, D. K., Lautenberger, J., Seth, A., Chen, Z. Q., Burdett, L., Pribyl, L., Schweinfest, C. W., Ascione, R., Compans, R. W., editor, Cooper, M., editor, Koprowski, H., editor, McConell, I., editor, Melchers, F., editor, Nussenzweig, V., editor, Oldstone, M., editor, Olsnes, S., editor, Saedler, H., editor, Vogt, P. K., editor, Wagner, H., editor, Wilson, I., editor, Shen-Ong, Grace L. C., editor, Potter, Michael, editor, and Copeland, Neal G., editor

Published
1989
Full Text
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12. Female chromosome X mosaicism is age-related and preferentially affects the inactivated X chromosome

Author

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

Subjects
Chromosome X, Age-related
Abstract

To investigate large structural clonal mosaicism of chromosome X, we analysed the SNP microarray intensity data of 38,303 women from cancer genome-wide association studies (20,878 cases and 17,425 controls) and detected 124 mosaic X events42Mb in 97 (0.25%) women. Here we show rates for X-chromosome mosaicism are four times higher than mean autosomal rates; X mosaic events more often include the entire chromosome and participants with X events more likely harbour autosomal mosaic events. X mosaicism frequency increases with age (0.11% in 50-year olds; 0.45% in 75-year olds), as reported for Y and autosomes. Methylation array analyses of 33 women with X mosaicism indicate events preferentially involve the inactive X chromosome. Our results provide further evidence that the sex chromosomes undergo mosaic events more frequently than autosomes, which could have implications for understanding the underlying mechanisms of mosaic events and their possible contribution to risk for chronic diseases.

Published
2016

13. Identification of a novel susceptibility locus at 13q34 and refinement of the 20p12.2 region as a multi-signal locus associated with bladder cancer risk in individuals of European ancestry

Author

Figueroa, J.D., Middlebrooks, C.D., Banday, A.R., Ye, Y., Garcia-Closas, M., Chatterjee, N., Koutros, S., Kiemeney, L.A., Rafnar, T., Bishop, T., Furberg, H., Matullo, G., Golka, K., Gago-Dominguez, M., Taylor, J.A., Fletcher, T., Siddiq, A., Cortessis, V.K., Kooperberg, C., Cussenot, O., Benhamou, S., Prescott, J., Porru, S., Dinney, C.P., Malats, N., Baris, D., Purdue, M.P., Jacobs, E.J., Albanes, D., Wang, Z., Chung, C.C., Vermeulen, S.H., Aben, K.K.H., Galesloot, T.E., Thorleifsson, G., Sulem, P., Stefansson, K., Kiltie, A.E., Harland, M., Teo, M., Offit, K., Vijai, J., Bajorin, D., Kopp, R., Fiorito, G., Guarrera, S., Sacerdote, C., Selinski, S., Hengstler, J.G., Gerullis, H., Ovsiannikov, D., Blaszkewicz, M., Castelao, J.E., Calaza, M., Martinez, M.E., Cordeiro, P., Xu, Z., Panduri, V., Kumar, R., Gurzau, E, Koppova, K., Bueno-de-Mesquita, H.B., Ljungberg, B., Clavel-Chapelon, F., Weiderpass, E., Krogh, V., Dorronsoro, M., Travis, R.C., Tjonneland, A., Brennan, P., Chang-Claude, J., Riboli, E., Conti, D., Stern, M.C., Pike, M.C., Berg, D., Yuan, J.M., Hohensee, C., Jeppson, R.P., Cancel-Tassin, G., Roupret, M., Comperat, E., Turman, C., Vivo, I. De, Giovannucci, E., Hunter, D.J., Kraft, P., Lindstrom, S., Carta, A., Pavanello, S., Arici, C., Mastrangelo, G., Kamat, A.M., Zhang, L., Gong, Y., Pu, X., Hutchinson, A., Burdett, L., Wheeler, W.A., Karagas, M.R., et al., Figueroa, J.D., Middlebrooks, C.D., Banday, A.R., Ye, Y., Garcia-Closas, M., Chatterjee, N., Koutros, S., Kiemeney, L.A., Rafnar, T., Bishop, T., Furberg, H., Matullo, G., Golka, K., Gago-Dominguez, M., Taylor, J.A., Fletcher, T., Siddiq, A., Cortessis, V.K., Kooperberg, C., Cussenot, O., Benhamou, S., Prescott, J., Porru, S., Dinney, C.P., Malats, N., Baris, D., Purdue, M.P., Jacobs, E.J., Albanes, D., Wang, Z., Chung, C.C., Vermeulen, S.H., Aben, K.K.H., Galesloot, T.E., Thorleifsson, G., Sulem, P., Stefansson, K., Kiltie, A.E., Harland, M., Teo, M., Offit, K., Vijai, J., Bajorin, D., Kopp, R., Fiorito, G., Guarrera, S., Sacerdote, C., Selinski, S., Hengstler, J.G., Gerullis, H., Ovsiannikov, D., Blaszkewicz, M., Castelao, J.E., Calaza, M., Martinez, M.E., Cordeiro, P., Xu, Z., Panduri, V., Kumar, R., Gurzau, E, Koppova, K., Bueno-de-Mesquita, H.B., Ljungberg, B., Clavel-Chapelon, F., Weiderpass, E., Krogh, V., Dorronsoro, M., Travis, R.C., Tjonneland, A., Brennan, P., Chang-Claude, J., Riboli, E., Conti, D., Stern, M.C., Pike, M.C., Berg, D., Yuan, J.M., Hohensee, C., Jeppson, R.P., Cancel-Tassin, G., Roupret, M., Comperat, E., Turman, C., Vivo, I. De, Giovannucci, E., Hunter, D.J., Kraft, P., Lindstrom, S., Carta, A., Pavanello, S., Arici, C., Mastrangelo, G., Kamat, A.M., Zhang, L., Gong, Y., Pu, X., Hutchinson, A., Burdett, L., Wheeler, W.A., Karagas, M.R., and et al.

Abstract

Contains fulltext : 167299.pdf (publisher's version ) (Closed access), Candidate gene and genome-wide association studies (GWAS) have identified 15 independent genomic regions associated with bladder cancer risk. In search for additional susceptibility variants, we followed up on four promising single-nucleotide polymorphisms (SNPs) that had not achieved genome-wide significance in 6911 cases and 11 814 controls (rs6104690, rs4510656, rs5003154 and rs4907479, P < 1 x 10(-6)), using additional data from existing GWAS datasets and targeted genotyping for studies that did not have GWAS data. In a combined analysis, which included data on up to 15 058 cases and 286 270 controls, two SNPs achieved genome-wide statistical significance: rs6104690 in a gene desert at 20p12.2 (P = 2.19 x 10(-11)) and rs4907479 within the MCF2L gene at 13q34 (P = 3.3 x 10(-10)). Imputation and fine-mapping analyses were performed in these two regions for a subset of 5551 bladder cancer cases and 10 242 controls. Analyses at the 13q34 region suggest a single signal marked by rs4907479. In contrast, we detected two signals in the 20p12.2 region-the first signal is marked by rs6104690, and the second signal is marked by two moderately correlated SNPs (r(2) = 0.53), rs6108803 and the previously reported rs62185668. The second 20p12.2 signal is more strongly associated with the risk of muscle-invasive (T2-T4 stage) compared with non-muscle-invasive (Ta, T1 stage) bladder cancer (case-case P

Published
2016

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

Author

Machiela, MJ, Zhou, W, Karlins, E, Sampson, JN, Freedman, ND, Yang, Q, Hicks, B, Dagnall, C, Hautman, C, Jacobs, KB, Abnet, CC, Aldrich, MC, Amos, C, Amundadottir, LT, Arslan, AA, Beane-Freeman, LE, Berndt, SI, Black, A, Blot, WJ, Bock, CH, Bracci, PM, Brinton, LA, Bueno-de-Mesquita, HB, Burdett, L, Buring, JE, Butler, MA, Canzian, F, Carreon, T, Chaffee, KG, Chang, I-S, Chatterjee, N, Chen, C, Chen, K, Chung, CC, Cook, LS, Bou, MC, Cullen, M, Davis, FG, De Vivo, I, Ding, T, Doherty, J, Duell, EJ, Epstein, CG, Fan, J-H, Figueroa, JD, Fraumeni, JF, Friedenreich, CM, Fuchs, CS, Gallinger, S, Gao, Y-T, Gapstur, SM, Garcia-Closas, M, Gaudet, MM, Gaziano, JM, Giles, GG, Gillanders, EM, Giovannucci, EL, Goldin, L, Goldstein, AM, Haiman, CA, Hallmans, G, Hankinson, SE, Harris, CC, Henriksson, R, Holly, EA, Hong, Y-C, Hoover, RN, Hsiung, CA, Hu, N, Hu, W, Hunter, DJ, Hutchinson, A, Jenab, M, Johansen, C, Khaw, K-T, Kim, HN, Kim, YH, Kim, YT, Klein, AP, Klein, R, Koh, W-P, Kolonel, LN, Kooperberg, C, Kraft, P, Krogh, V, Kurtz, RC, LaCroix, A, Lan, Q, Landi, MT, Le Marchand, L, Li, D, Liang, X, Liao, LM, Lin, D, Liu, J, Lissowska, J, Lu, L, Magliocco, AM, Malats, N, Matsuo, K, McNeill, LH, McWilliams, RR, Melin, BS, Mirabello, L, Moore, L, Olson, SH, Orlow, I, Park, JY, Patino-Garcia, A, Peplonska, B, Peters, U, Petersen, GM, Pooler, L, Prescott, J, Prokunina-Olsson, L, Purdue, MP, Qiao, Y-L, Rajaraman, P, Real, FX, Riboli, E, Risch, HA, Rodriguez-Santiago, B, Ruder, AM, Savage, SA, Schumacher, F, Schwartz, AG, Schwartz, KL, Seow, A, Setiawan, VW, Severi, G, Shen, H, Sheng, X, Shin, M-H, Shu, X-O, Silverman, DT, Spitz, MR, Stevens, VL, Stolzenberg-Solomon, R, Stram, D, Tang, Z-Z, Taylor, PR, Teras, LR, Tobias, GS, Van den Berg, D, Visvanathan, K, Wacholder, S, Wang, J-C, Wang, Z, Wentzensen, N, Wheeler, W, White, E, Wiencke, JK, Wolpin, BM, Wong, MP, Wu, C, Wu, T, Wu, X, Wu, Y-L, Wunder, JS, Xia, L, Yang, HP, Yang, P-C, Yu, K, Zanetti, KA, Zeleniuch-Jacquotte, A, Zheng, W, Zhou, B, Ziegler, RG, Perez-Jurado, LA, Caporaso, NE, Rothman, N, Tucker, M, Dean, MC, Yeager, M, Chanock, SJ, Machiela, MJ, Zhou, W, Karlins, E, Sampson, JN, Freedman, ND, Yang, Q, Hicks, B, Dagnall, C, Hautman, C, Jacobs, KB, Abnet, CC, Aldrich, MC, Amos, C, Amundadottir, LT, Arslan, AA, Beane-Freeman, LE, Berndt, SI, Black, A, Blot, WJ, Bock, CH, Bracci, PM, Brinton, LA, Bueno-de-Mesquita, HB, Burdett, L, Buring, JE, Butler, MA, Canzian, F, Carreon, T, Chaffee, KG, Chang, I-S, Chatterjee, N, Chen, C, Chen, K, Chung, CC, Cook, LS, Bou, MC, Cullen, M, Davis, FG, De Vivo, I, Ding, T, Doherty, J, Duell, EJ, Epstein, CG, Fan, J-H, Figueroa, JD, Fraumeni, JF, Friedenreich, CM, Fuchs, CS, Gallinger, S, Gao, Y-T, Gapstur, SM, Garcia-Closas, M, Gaudet, MM, Gaziano, JM, Giles, GG, Gillanders, EM, Giovannucci, EL, Goldin, L, Goldstein, AM, Haiman, CA, Hallmans, G, Hankinson, SE, Harris, CC, Henriksson, R, Holly, EA, Hong, Y-C, Hoover, RN, Hsiung, CA, Hu, N, Hu, W, Hunter, DJ, Hutchinson, A, Jenab, M, Johansen, C, Khaw, K-T, Kim, HN, Kim, YH, Kim, YT, Klein, AP, Klein, R, Koh, W-P, Kolonel, LN, Kooperberg, C, Kraft, P, Krogh, V, Kurtz, RC, LaCroix, A, Lan, Q, Landi, MT, Le Marchand, L, Li, D, Liang, X, Liao, LM, Lin, D, Liu, J, Lissowska, J, Lu, L, Magliocco, AM, Malats, N, Matsuo, K, McNeill, LH, McWilliams, RR, Melin, BS, Mirabello, L, Moore, L, Olson, SH, Orlow, I, Park, JY, Patino-Garcia, A, Peplonska, B, Peters, U, Petersen, GM, Pooler, L, Prescott, J, Prokunina-Olsson, L, Purdue, MP, Qiao, Y-L, Rajaraman, P, Real, FX, Riboli, E, Risch, HA, Rodriguez-Santiago, B, Ruder, AM, Savage, SA, Schumacher, F, Schwartz, AG, Schwartz, KL, Seow, A, Setiawan, VW, Severi, G, Shen, H, Sheng, X, Shin, M-H, Shu, X-O, Silverman, DT, Spitz, MR, Stevens, VL, Stolzenberg-Solomon, R, Stram, D, Tang, Z-Z, Taylor, PR, Teras, LR, Tobias, GS, Van den Berg, D, Visvanathan, K, Wacholder, S, Wang, J-C, Wang, Z, Wentzensen, N, Wheeler, W, White, E, Wiencke, JK, Wolpin, BM, Wong, MP, Wu, C, Wu, T, Wu, X, Wu, Y-L, Wunder, JS, Xia, L, Yang, HP, Yang, P-C, Yu, K, Zanetti, KA, Zeleniuch-Jacquotte, A, Zheng, W, Zhou, B, Ziegler, RG, Perez-Jurado, LA, Caporaso, NE, Rothman, N, Tucker, M, Dean, MC, Yeager, M, and Chanock, SJ

Abstract

To investigate large structural clonal mosaicism of chromosome X, we analysed the SNP microarray intensity data of 38,303 women from cancer genome-wide association studies (20,878 cases and 17,425 controls) and detected 124 mosaic X events >2 Mb in 97 (0.25%) women. Here we show rates for X-chromosome mosaicism are four times higher than mean autosomal rates; X mosaic events more often include the entire chromosome and participants with X events more likely harbour autosomal mosaic events. X mosaicism frequency increases with age (0.11% in 50-year olds; 0.45% in 75-year olds), as reported for Y and autosomes. Methylation array analyses of 33 women with X mosaicism indicate events preferentially involve the inactive X chromosome. Our results provide further evidence that the sex chromosomes undergo mosaic events more frequently than autosomes, which could have implications for understanding the underlying mechanisms of mosaic events and their possible contribution to risk for chronic diseases.

Published
2016

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

Author

Berndt, SI, Camp, NJ, Skibola, CF, Vijai, J, Wang, Z, Gu, J, Nieters, A, Kelly, RS, Smedby, KE, Monnereau, A, Cozen, W, Cox, A, Wang, SS, Lan, Q, Teras, LR, Machado, M, Yeager, M, Brooks-Wilson, AR, Hartge, P, Purdue, MP, Birmann, BM, Vajdic, CM, Cocco, P, Zhang, Y, Giles, GG, Zeleniuch-Jacquotte, A, Lawrence, C, Montalvan, R, Burdett, L, Hutchinson, A, Ye, Y, Call, TG, Shanafelt, TD, Novak, AJ, Kay, NE, Liebow, M, Cunningham, JM, Allmer, C, Hjalgrim, H, Adami, H-O, Melbye, M, Glimelius, B, Chang, ET, Glenn, M, Curtin, K, Cannon-Albright, LA, Diver, WR, Link, BK, Weiner, GJ, Conde, L, Bracci, PM, Riby, J, Arnett, DK, Zhi, D, Leach, JM, Holly, EA, Jackson, RD, Tinker, LF, Benavente, Y, Sala, N, Casabonne, D, Becker, N, Boffetta, P, Brennan, P, Foretova, L, Maynadie, M, McKay, J, Staines, A, Chaffee, KG, Achenbach, SJ, Vachon, CM, Goldin, LR, Strom, SS, Leis, JF, Weinberg, JB, Caporaso, NE, Norman, AD, De Roos, AJ, Morton, LM, Severson, RK, Riboli, E, Vineis, P, Kaaks, R, Masala, G, Weiderpass, E, Chirlaque, M-D, Vermeulen, RCH, Travis, RC, Southey, MC, Milne, RL, Albanese, D, Virtamo, J, Weinstein, S, Clavel, J, Zheng, T, Holford, TR, Villano, DJ, Maria, A, Spinelli, JJ, Gascoyne, RD, Connors, JM, Bertrand, KA, Giovannucci, E, Kraft, P, Kricker, A, Turner, J, Ennas, MG, Ferri, GM, Miligi, L, Liang, L, Ma, B, Huang, J, Crouch, S, Park, J-H, Chatterjee, N, North, KE, Snowden, JA, Wright, J, Fraumeni, JF, Offit, K, Wu, X, de Sanjose, S, Cerhan, JR, Chanock, SJ, Rothman, N, Slager, SL, Berndt, SI, Camp, NJ, Skibola, CF, Vijai, J, Wang, Z, Gu, J, Nieters, A, Kelly, RS, Smedby, KE, Monnereau, A, Cozen, W, Cox, A, Wang, SS, Lan, Q, Teras, LR, Machado, M, Yeager, M, Brooks-Wilson, AR, Hartge, P, Purdue, MP, Birmann, BM, Vajdic, CM, Cocco, P, Zhang, Y, Giles, GG, Zeleniuch-Jacquotte, A, Lawrence, C, Montalvan, R, Burdett, L, Hutchinson, A, Ye, Y, Call, TG, Shanafelt, TD, Novak, AJ, Kay, NE, Liebow, M, Cunningham, JM, Allmer, C, Hjalgrim, H, Adami, H-O, Melbye, M, Glimelius, B, Chang, ET, Glenn, M, Curtin, K, Cannon-Albright, LA, Diver, WR, Link, BK, Weiner, GJ, Conde, L, Bracci, PM, Riby, J, Arnett, DK, Zhi, D, Leach, JM, Holly, EA, Jackson, RD, Tinker, LF, Benavente, Y, Sala, N, Casabonne, D, Becker, N, Boffetta, P, Brennan, P, Foretova, L, Maynadie, M, McKay, J, Staines, A, Chaffee, KG, Achenbach, SJ, Vachon, CM, Goldin, LR, Strom, SS, Leis, JF, Weinberg, JB, Caporaso, NE, Norman, AD, De Roos, AJ, Morton, LM, Severson, RK, Riboli, E, Vineis, P, Kaaks, R, Masala, G, Weiderpass, E, Chirlaque, M-D, Vermeulen, RCH, Travis, RC, Southey, MC, Milne, RL, Albanese, D, Virtamo, J, Weinstein, S, Clavel, J, Zheng, T, Holford, TR, Villano, DJ, Maria, A, Spinelli, JJ, Gascoyne, RD, Connors, JM, Bertrand, KA, Giovannucci, E, Kraft, P, Kricker, A, Turner, J, Ennas, MG, Ferri, GM, Miligi, L, Liang, L, Ma, B, Huang, J, Crouch, S, Park, J-H, Chatterjee, N, North, KE, Snowden, JA, Wright, J, Fraumeni, JF, Offit, K, Wu, X, de Sanjose, S, Cerhan, JR, Chanock, SJ, Rothman, N, and Slager, SL

Abstract

Chronic lymphocytic leukemia (CLL) is a common lymphoid malignancy with strong heritability. To further understand the genetic susceptibility for CLL and identify common loci associated with risk, we conducted a meta-analysis of four genome-wide association studies (GWAS) composed of 3,100 cases and 7,667 controls with follow-up replication in 1,958 cases and 5,530 controls. Here we report three new loci at 3p24.1 (rs9880772, EOMES, P=2.55 × 10(-11)), 6p25.2 (rs73718779, SERPINB6, P=1.97 × 10(-8)) and 3q28 (rs9815073, LPP, P=3.62 × 10(-8)), as well as a new independent SNP at the known 2q13 locus (rs9308731, BCL2L11, P=1.00 × 10(-11)) in the combined analysis. We find suggestive evidence (P<5 × 10(-7)) for two additional new loci at 4q24 (rs10028805, BANK1, P=7.19 × 10(-8)) and 3p22.2 (rs1274963, CSRNP1, P=2.12 × 10(-7)). Pathway analyses of new and known CLL loci consistently show a strong role for apoptosis, providing further evidence for the importance of this biological pathway in CLL susceptibility.

Published
2016

16. Genetic variants associated with longer telomere length are associated with increased lung cancer risk among never-smoking women in Asia: a report from the female lung cancer consortium in Asia

Author

Mitchell Machiela, Ca, Hsiung, Xo, Shu, Wj, Seow, Wang Z, Matsuo K, Yc, Hong, Seow A, Wu C, Hd, Hosgood Rd, Chen K, Jc, Wang, Wen W, Cawthon R, Chatterjee N, Hu W, Ne, Caporaso, Jy, Park, Cj, Chen, Yh, Kim, Yt, Kim, Mt, Landi, Shen H, Lawrence C, Burdett L, Yeager M, Is, Chang, Mitsudomi T, Hn, Kim, Gc, Chang, Ba, Bassig, Tucker M, Wei F, Yin Z, Sj, An, Qian B, Vh, Lee, Lu D, Liu J, Hs, Jeon, Cf, Hsiao, Js, Sung, Jh, Kim, Yt, Gao, Yh, Tsai, Yj, Jung, Guo H, Hu Z, Hutchinson A, Wc, Wang, Rj, Klein, Cc, Chung, Ij, Oh, Ky, Chen, Si, Berndt, Wu W, Chang J, Xc, Zhang, Ms, Huang, Zheng H, Wang J, Zhao X, Li Y, Je, Choi, Wc, Su, Kh, Park, Sw, Sung, Ym, Chen, Liu L, Hyun Kang C, Hu L, Ch, Chen, Pao W, Yc, Kim, Ty, Yang, Xu J, Guan P, Tan W, Su J, Cl, Wang, Li H, Dart Loon Sihoe A, Zhao Z, Chen Y, Yy, Choi, Jy, Hung, Js, Kim, Hi, Yoon, Cai Q, Cc, Lin, Ik, Park, Xu P, Dong J, Kim C, He Q, Rp, Perng, Kohno T, Ss, Kweon, Cy, Chen, Rc, Vermeulen, Wu J, Wy, Lim, Kc, Chen, Wh, Chow, Bt, Ji, Jk, Chan, Chu M, Yj, Li, Yokota J, Li J, Chen H, Yb, Xiang, Cj, Yu, Kunitoh H, Wu G, Jin L, Yl, Lo, Shiraishi K, Yh, Chen, Hc, Lin, Wu T, Pik Wong M, Yl, Wu, Pc, Yang, Zhou B, Mh, Shin, Jf, Fraumeni Jr, Zheng W, Lin D, Sj, Chanock, Rothman N, Lan Q, Risk Assessment, Infection & Immunity, dIRAS RA-2, dIRAS RA-I&I RA, and LS IRAS EEPI GRA (Gezh.risico-analyse)

Subjects
Asian Continental Ancestry Group, Adult, China, Singapore, Lung Neoplasms, Smoking, Taiwan, Telomere Homeostasis, Middle Aged, Telomere, Polymorphism, Single Nucleotide, Article, Asian People, Japan, Risk Factors, Republic of Korea, Odds Ratio, Hong Kong, Humans, Female, Genetic Predisposition to Disease, Prospective Studies, Aged, Genome-Wide Association Study
Abstract

Recent evidence from several relatively small nested case-control studies in prospective cohorts shows an association between longer telomere length measured phenotypically in peripheral white blood cell (WBC) DNA and increased lung cancer risk. We sought to further explore this relationship by examining a panel of seven telomere-length associated genetic variants in a large study of 5,457 never-smoking female Asian lung cancer cases and 4,493 never-smoking female Asian controls using data from a previously reported genome-wide association study. Using a group of 1,536 individuals with phenotypically measured telomere length in WBCs in the prospective Shanghai Women's Health study, we demonstrated the utility of a genetic risk score (GRS) of seven telomere-length associated variants to predict telomere length in an Asian population. We then found that GRSs used as instrumental variables to predict longer telomere length were associated with increased lung cancer risk (OR = 1.51 (95% CI = 1.34-1.69) for upper vs. lower quartile of the weighted GRS, p value = 4.54 × 10(-14) ) even after removing rs2736100 (p value = 4.81 × 10(-3) ), a SNP in the TERT locus robustly associated with lung cancer risk in prior association studies. Stratified analyses suggested the effect of the telomere-associated GRS is strongest among younger individuals. We found no difference in GRS effect between adenocarcinoma and squamous cell subtypes. Our results indicate that a genetic background that favors longer telomere length may increase lung cancer risk, which is consistent with earlier prospective studies relating longer telomere length with increased lung cancer risk.

Published
2014

17. A genome-wide association study of marginal zone lymphoma shows association to the HLA region

Author

Vijai, J, Wang, Z, Berndt, SI, Skibola, CF, Slager, SL, de Sanjose, S, Melbye, M, Glimelius, B, Bracci, PM, Conde, L, Birmann, BM, Wang, SS, Brooks-Wilson, AR, Lan, Q, de Bakker, PIW, Vermeulen, RCH, Portlock, C, Ansell, SM, Link, BK, Riby, J, North, KE, Gu, J, Hjalgrim, H, Cozen, W, Becker, N, Teras, LR, Spinelli, JJ, Turner, J, Zhang, Y, Purdue, MP, Giles, GG, Kelly, RS, Zeleniuch-Jacquotte, A, Ennas, MG, Monnereau, A, Bertrand, KA, Albanes, D, Lightfoot, T, Yeager, M, Chung, CC, Burdett, L, Hutchinson, A, Lawrence, C, Montalvan, R, Liang, L, Huang, J, Ma, B, Villano, DJ, Maria, A, Corines, M, Thomas, T, Novak, AJ, Dogan, A, Liebow, M, Thompson, CA, Witzig, TE, Habermann, TM, Weiner, GJ, Smith, MT, Holly, EA, Jackson, RD, Tinker, LF, Ye, Y, Adami, H-O, Smedby, KE, De Roos, AJ, Hartge, P, Morton, LM, Severson, RK, Benavente, Y, Boffetta, P, Brennan, P, Foretova, L, Maynadie, M, Mckay, J, Staines, A, Diver, WR, Vajdic, CM, Armstrong, BK, Kricker, A, Zheng, T, Holford, TR, Severi, G, Vineis, P, Ferri, GM, Ricco, R, Miligi, L, Clavel, J, Giovannucci, E, Kraft, P, Virtamo, J, Smith, A, Kane, E, Roman, E, Chiu, BCH, Fraumeni, JF, Wu, X, Cerhan, JR, Offit, K, Chanock, SJ, Rothman, N, Nieters, A, Vijai, J, Wang, Z, Berndt, SI, Skibola, CF, Slager, SL, de Sanjose, S, Melbye, M, Glimelius, B, Bracci, PM, Conde, L, Birmann, BM, Wang, SS, Brooks-Wilson, AR, Lan, Q, de Bakker, PIW, Vermeulen, RCH, Portlock, C, Ansell, SM, Link, BK, Riby, J, North, KE, Gu, J, Hjalgrim, H, Cozen, W, Becker, N, Teras, LR, Spinelli, JJ, Turner, J, Zhang, Y, Purdue, MP, Giles, GG, Kelly, RS, Zeleniuch-Jacquotte, A, Ennas, MG, Monnereau, A, Bertrand, KA, Albanes, D, Lightfoot, T, Yeager, M, Chung, CC, Burdett, L, Hutchinson, A, Lawrence, C, Montalvan, R, Liang, L, Huang, J, Ma, B, Villano, DJ, Maria, A, Corines, M, Thomas, T, Novak, AJ, Dogan, A, Liebow, M, Thompson, CA, Witzig, TE, Habermann, TM, Weiner, GJ, Smith, MT, Holly, EA, Jackson, RD, Tinker, LF, Ye, Y, Adami, H-O, Smedby, KE, De Roos, AJ, Hartge, P, Morton, LM, Severson, RK, Benavente, Y, Boffetta, P, Brennan, P, Foretova, L, Maynadie, M, Mckay, J, Staines, A, Diver, WR, Vajdic, CM, Armstrong, BK, Kricker, A, Zheng, T, Holford, TR, Severi, G, Vineis, P, Ferri, GM, Ricco, R, Miligi, L, Clavel, J, Giovannucci, E, Kraft, P, Virtamo, J, Smith, A, Kane, E, Roman, E, Chiu, BCH, Fraumeni, JF, Wu, X, Cerhan, JR, Offit, K, Chanock, SJ, Rothman, N, and Nieters, A

Abstract

Marginal zone lymphoma (MZL) is the third most common subtype of B-cell non-Hodgkin lymphoma. Here we perform a two-stage GWAS of 1,281 MZL cases and 7,127 controls of European ancestry and identify two independent loci near BTNL2 (rs9461741, P=3.95 × 10(-15)) and HLA-B (rs2922994, P=2.43 × 10(-9)) in the HLA region significantly associated with MZL risk. This is the first evidence that genetic variation in the major histocompatibility complex influences MZL susceptibility.

Published
2015

19. Genome-wide association study identifies multiple susceptibility loci for diffuse large B cell lymphoma

Author

Cerhan, JR, Berndt, SI, Vijai, J, Ghesquieres, H, McKay, J, Wang, SS, Wang, Z, Yeager, M, Conde, L, de Bakker, PIW, Nieters, A, Cox, D, Burdett, L, Monnereau, A, Flowers, CR, De Roos, AJ, Brooks-Wilson, AR, Lan, Q, Severi, G, Melbye, M, Gu, J, Jackson, RD, Kane, E, Teras, LR, Purdue, MP, Vajdic, CM, Spinelli, JJ, Giles, GG, Albanes, D, Kelly, RS, Zucca, M, Bertrand, KA, Zeleniuch-Jacquotte, A, Lawrence, C, Hutchinson, A, Zhi, D, Habermann, TM, Link, BK, Novak, AJ, Dogan, A, Asmann, YW, Liebow, M, Thompson, CA, Ansell, SM, Witzig, TE, Weiner, GJ, Veron, AS, Zelenika, D, Tilly, H, Haioun, C, Molina, TJ, Hjalgrim, H, Glimelius, B, Adami, H-O, Bracci, PM, Riby, J, Smith, MT, Holly, EA, Cozen, W, Hartge, P, Morton, LM, Severson, RK, Tinker, LF, North, KE, Becker, N, Benavente, Y, Boffetta, P, Brennan, P, Foretova, L, Maynadie, M, Staines, A, Lightfoot, T, Crouch, S, Smith, A, Roman, E, Diver, WR, Offit, K, Zelenetz, A, Klein, RJ, Villano, DJ, Zheng, T, Zhang, Y, Holford, TR, Kricker, A, Turner, J, Southey, MC, Clavel, J, Virtamo, J, Weinstein, S, Riboli, E, Vineis, P, Kaaks, R, Trichopoulos, D, Vermeulen, RCH, Boeing, H, Tjonneland, A, Angelucci, E, Di Lollo, S, Rais, M, Birmann, BM, Laden, F, Giovannucci, E, Kraft, P, Huang, J, Ma, B, Ye, Y, Chiu, BCH, Sampson, J, Liang, L, Park, J-H, Chung, CC, Weisenburger, DD, Chatterjee, N, Fraumeni, JF, Slager, SL, Wu, X, de Sanjose, S, Smedby, KE, Salles, G, Skibola, CF, Rothman, N, Chanock, SJ, Cerhan, JR, Berndt, SI, Vijai, J, Ghesquieres, H, McKay, J, Wang, SS, Wang, Z, Yeager, M, Conde, L, de Bakker, PIW, Nieters, A, Cox, D, Burdett, L, Monnereau, A, Flowers, CR, De Roos, AJ, Brooks-Wilson, AR, Lan, Q, Severi, G, Melbye, M, Gu, J, Jackson, RD, Kane, E, Teras, LR, Purdue, MP, Vajdic, CM, Spinelli, JJ, Giles, GG, Albanes, D, Kelly, RS, Zucca, M, Bertrand, KA, Zeleniuch-Jacquotte, A, Lawrence, C, Hutchinson, A, Zhi, D, Habermann, TM, Link, BK, Novak, AJ, Dogan, A, Asmann, YW, Liebow, M, Thompson, CA, Ansell, SM, Witzig, TE, Weiner, GJ, Veron, AS, Zelenika, D, Tilly, H, Haioun, C, Molina, TJ, Hjalgrim, H, Glimelius, B, Adami, H-O, Bracci, PM, Riby, J, Smith, MT, Holly, EA, Cozen, W, Hartge, P, Morton, LM, Severson, RK, Tinker, LF, North, KE, Becker, N, Benavente, Y, Boffetta, P, Brennan, P, Foretova, L, Maynadie, M, Staines, A, Lightfoot, T, Crouch, S, Smith, A, Roman, E, Diver, WR, Offit, K, Zelenetz, A, Klein, RJ, Villano, DJ, Zheng, T, Zhang, Y, Holford, TR, Kricker, A, Turner, J, Southey, MC, Clavel, J, Virtamo, J, Weinstein, S, Riboli, E, Vineis, P, Kaaks, R, Trichopoulos, D, Vermeulen, RCH, Boeing, H, Tjonneland, A, Angelucci, E, Di Lollo, S, Rais, M, Birmann, BM, Laden, F, Giovannucci, E, Kraft, P, Huang, J, Ma, B, Ye, Y, Chiu, BCH, Sampson, J, Liang, L, Park, J-H, Chung, CC, Weisenburger, DD, Chatterjee, N, Fraumeni, JF, Slager, SL, Wu, X, de Sanjose, S, Smedby, KE, Salles, G, Skibola, CF, Rothman, N, and Chanock, SJ

Abstract

Diffuse large B cell lymphoma (DLBCL) is the most common lymphoma subtype and is clinically aggressive. To identify genetic susceptibility loci for DLBCL, we conducted a meta-analysis of 3 new genome-wide association studies (GWAS) and 1 previous scan, totaling 3,857 cases and 7,666 controls of European ancestry, with additional genotyping of 9 promising SNPs in 1,359 cases and 4,557 controls. In our multi-stage analysis, five independent SNPs in four loci achieved genome-wide significance marked by rs116446171 at 6p25.3 (EXOC2; P = 2.33 × 10(-21)), rs2523607 at 6p21.33 (HLA-B; P = 2.40 × 10(-10)), rs79480871 at 2p23.3 (NCOA1; P = 4.23 × 10(-8)) and two independent SNPs, rs13255292 and rs4733601, at 8q24.21 (PVT1; P = 9.98 × 10(-13) and 3.63 × 10(-11), respectively). These data provide substantial new evidence for genetic susceptibility to this B cell malignancy and point to pathways involved in immune recognition and immune function in the pathogenesis of DLBCL.

Published
2014

20. Polymorphisms in innate immunity genes and lung cancer risk in Xuanwei, China

Author

Shen, M., Vermeulen, R.C.H., Rajaraman, P., Menashe, I., He, X., Chapman, R.S., Yeager, M., Thomas, G., Burdett, L., Hutchinson, A., Yuenger, J., Chanock, S., Lan, Q., Risk Assessment of Toxic and Immunomodulatory Agents, and Dep IRAS

Abstract

The high incidence of lung cancer in Xuanwei County, China has been attributed to exposure to indoor smoky coal emissions that contain polycyclic aromatic hydrocarbons (PAHs). The inflammatory response induced by coal smoke components may promote lung tumor development. We studied the association between single nucleotide polymorphisms (SNPs) in genes involved in innate immunity and lung cancer risk in a population-based case-control study (122 cases and 122 controls) in Xuanwei. A total of 1,360 tag SNPs in 149 gene regions were included in the analysis. FCER2 rs7249320 was the most significant SNP (OR: 0.30; 95% CI: 0.16-0.55; P: 0.0001; false discovery rate value, 0.13) for variant carriers. The gene regions ALOX12B/ALOX15B and KLK2 were associated with increased lung cancer risk globally (false discovery rate value

Published
2009

21. Assessing movements of three buoy line types using DSTmilli Loggers: Implications for entanglements of bottlenose dolphins in the crab pot fishery

Author

McFee, W. E., Pennington, P. L., Burdett, L. G., Powell, J. W. B., Schwacke, J. H., and Dockery, F. E.

Subjects
Conservation, Management
Abstract

A study was conducted in October 2006 in the Charleston, South Carolina area to test the movements of three different buoy line types to determine which produced a preferred profile that could reduce the risk of dolphin entanglement. Tests on diamond-braided nylon commonly used in the crab pot fishery were compared with stiffened line of Esterpro and calf types in both shallow and deep water environments using DSTmilli data loggers. Loggers were placed at intervals along the lines to record depth, and thus movements, over a 24 hour period. Three observers viewed video animations and charts created for each of the six trial days from the collected logger data and provided their opinions on the most desirable line type that fit set criteria. A quantitative analysis (ANCOVA) of the data was conducted taking into consideration daily tidal fluctuations and logger movements. Loggers tracking the tides had an r2 value approaching 1.00 and produced little movement other than with the tides. Conversely, r2 values approaching 0.00 were less affected by tidal movement and influenced by currents that cause more erratic movement. Results from this study showed that stiffened line, in particular the medium lay Esterpro type, produced the more desirable profiles that could reduce risk of dolphin entanglement. Combining the observer’s results with the ANCOVA results, Esterpro was chosen nearly 60% of the time as opposed to the nylon line which was only chosen 10% of the time. ANCOVA results showed that the stiffened lines performed better in both the shallow and deep water environments, while the nylon line only performed better during one trial in a deep water set, most probably due to the increased current velocities experienced that day. (58pp.)(PDF contains 68 pages) Center for Coastal Environmental Health and Biomolecular Research

Published
2007

22. Spatial and temporal analysis of bottlenose dolphin strandings in South Carolina, 1992-2005

Author

McFee, W. E. and Burdett, L. G.

Subjects
Ecology, Fisheries, Management
Abstract

This CD contains summary data of bottlenose dolphins stranded in South Carolina using a Geographical Information System (GIS) and contains two published manuscripts in .pdf files. The intent of this CD is to provide data on bottlenose dolphin strandings in South Carolina to marine mammal researchers and managers.This CD is an accumulation of 14 years of stranding data collected through the collaborations of the National Ocean Service, Center for Coastal Environmental Health and Biomolecular Research (CCEHBR), the South Carolina Department of Natural Resources, and numerous volunteers and veterinarians that comprised the South Carolina Marine Mammal Stranding Network.Spatial and temporal information can be visually represented on maps using GIS. For this CD, maps were created to show relationships of stranding densities with land use, human population density, human interaction with dolphins, high geographical regions of live strandings, and seasonal changes. Point maps were also created to show individual strandings within South Carolina.In summary, spatial analysis revealed higher densities of bottlenose dolphin strandings in Charleston and Beaufort Counties, which consist of urban land with agricultural input. This trend was positively correlated with higher human population levels in these coastal counties as compared with other coastal counties. However, spatial analysis revealed that certain areas within a county may have low human population levels but high stranding density, suggesting that the level of effort to respond to strandings is not necessarily positively correlated with the density of strandings in South Carolina.Temporal analysis revealed a significantly higher density of bottlenose dolphin strandings in the northern portion of the State in the fall, mostly due to an increase of neonate strandings. On a finer geographic scale, seasonal stranding densities may fluctuate depending on the region of interest.Charleston Harbor had the highest density of live bottlenose dolphin strandings compared to the rest of the State. This was due in large part to the number of live dolphin entanglements in the crab pot fishery, the largest source of fishery-related mortality for bottlenose dolphins in South Carolina (Burdett and McFee 2004). Spatial density calculations also revealed that Charleston and Beaufort accounted for the majority of dolphins that were involved with human activities.1

Published
2007

24. Detectable clonal mosaicism and its relationship to aging and cancer

Author

Jacobs, KB, Yeager, M, Zhou, W, Wacholder, S, Wang, Z, Rodriguez-Santiago, B, Hutchinson, A, Deng, X, Liu, C, Horner, M-J, Cullen, M, Epstein, CG, Burdett, L, Dean, MC, Chatterjee, N, Sampson, J, Chung, CC, Kovaks, J, Gapstur, SM, Stevens, VL, Teras, LT, Gaudet, MM, Albanes, D, Weinstein, SJ, Virtamo, J, Taylor, PR, Freedman, ND, Abnet, CC, Goldstein, AM, Hu, N, Yu, K, Yuan, J-M, Liao, L, Ding, T, Qiao, Y-L, Gao, Y-T, Koh, W-P, Xiang, Y-B, Tang, Z-Z, Fan, J-H, Aldrich, MC, Amos, C, Blot, WJ, Bock, CH, Gillanders, EM, Harris, CC, Haiman, CA, Henderson, BE, Kolonel, LN, Le Marchand, L, McNeill, LH, Rybicki, BA, Schwartz, AG, Signorello, LB, Spitz, MR, Wiencke, JK, Wrensch, M, Wu, X, Zanetti, KA, Ziegler, RG, Figueroa, JD, Garcia-Closas, M, Malats, N, Marenne, G, Prokunina-Olsson, L, Baris, D, Schwenn, M, Johnson, A, Landi, MT, Goldin, L, Consonni, D, Bertazzi, PA, Rotunno, M, Rajaraman, P, Andersson, U, Freeman, LEB, Berg, CD, Buring, JE, Butler, MA, Carreon, T, Feychting, M, Ahlbom, A, Gaziano, JM, Giles, GG, Hallmans, G, Hankinson, SE, Hartge, P, Henriksson, R, Inskip, PD, Johansen, C, Landgren, A, McKean-Cowdin, R, Michaud, DS, Melin, BS, Peters, U, Ruder, AM, Sesso, HD, Severi, G, Shu, X-O, Visvanathan, K, White, E, Wolk, A, Zeleniuch-Jacquotte, A, Zheng, W, Silverman, DT, Kogevinas, M, Gonzalez, JR, Villa, O, Li, D, Duell, EJ, Risch, HA, Olson, SH, Kooperberg, C, Wolpin, BM, Jiao, L, Hassan, M, Wheeler, W, Arslan, AA, Bueno-de-Mesquita, HB, Fuchs, CS, Gallinger, S, Gross, MD, Holly, EA, Klein, AP, LaCroix, A, Mandelson, MT, Petersen, G, Boutron-Ruault, M-C, Bracci, PM, Canzian, F, Chang, K, Cotterchio, M, Giovannucci, EL, Goggins, M, Bolton, JAH, Jenab, M, Khaw, K-T, Krogh, V, Kurtz, RC, McWilliams, RR, Mendelsohn, JB, Rabe, KG, Riboli, E, Tjonneland, A, Tobias, GS, Trichopoulos, D, Elena, JW, Yu, H, Amundadottir, L, Stolzenberg-Solomon, RZ, Kraft, P, Schumacher, F, Stram, D, Savage, SA, Mirabello, L, Andrulis, IL, Wunder, JS, Patino Garcia, A, Sierrasesumaga, L, Barkauskas, DA, Gorlick, RG, Purdue, M, Chow, W-H, Moore, LE, Schwartz, KL, Davis, FG, Hsing, AW, Berndt, SI, Black, A, Wentzensen, N, Brinton, LA, Lissowska, J, Peplonska, B, McGlynn, KA, Cook, MB, Graubard, BI, Kratz, CP, Greene, MH, Erickson, RL, Hunter, DJ, Thomas, G, Hoover, RN, Real, FX, Fraumeni, JF, Caporaso, NE, Tucker, M, Rothman, N, Perez-Jurado, LA, Chanock, SJ, Jacobs, KB, Yeager, M, Zhou, W, Wacholder, S, Wang, Z, Rodriguez-Santiago, B, Hutchinson, A, Deng, X, Liu, C, Horner, M-J, Cullen, M, Epstein, CG, Burdett, L, Dean, MC, Chatterjee, N, Sampson, J, Chung, CC, Kovaks, J, Gapstur, SM, Stevens, VL, Teras, LT, Gaudet, MM, Albanes, D, Weinstein, SJ, Virtamo, J, Taylor, PR, Freedman, ND, Abnet, CC, Goldstein, AM, Hu, N, Yu, K, Yuan, J-M, Liao, L, Ding, T, Qiao, Y-L, Gao, Y-T, Koh, W-P, Xiang, Y-B, Tang, Z-Z, Fan, J-H, Aldrich, MC, Amos, C, Blot, WJ, Bock, CH, Gillanders, EM, Harris, CC, Haiman, CA, Henderson, BE, Kolonel, LN, Le Marchand, L, McNeill, LH, Rybicki, BA, Schwartz, AG, Signorello, LB, Spitz, MR, Wiencke, JK, Wrensch, M, Wu, X, Zanetti, KA, Ziegler, RG, Figueroa, JD, Garcia-Closas, M, Malats, N, Marenne, G, Prokunina-Olsson, L, Baris, D, Schwenn, M, Johnson, A, Landi, MT, Goldin, L, Consonni, D, Bertazzi, PA, Rotunno, M, Rajaraman, P, Andersson, U, Freeman, LEB, Berg, CD, Buring, JE, Butler, MA, Carreon, T, Feychting, M, Ahlbom, A, Gaziano, JM, Giles, GG, Hallmans, G, Hankinson, SE, Hartge, P, Henriksson, R, Inskip, PD, Johansen, C, Landgren, A, McKean-Cowdin, R, Michaud, DS, Melin, BS, Peters, U, Ruder, AM, Sesso, HD, Severi, G, Shu, X-O, Visvanathan, K, White, E, Wolk, A, Zeleniuch-Jacquotte, A, Zheng, W, Silverman, DT, Kogevinas, M, Gonzalez, JR, Villa, O, Li, D, Duell, EJ, Risch, HA, Olson, SH, Kooperberg, C, Wolpin, BM, Jiao, L, Hassan, M, Wheeler, W, Arslan, AA, Bueno-de-Mesquita, HB, Fuchs, CS, Gallinger, S, Gross, MD, Holly, EA, Klein, AP, LaCroix, A, Mandelson, MT, Petersen, G, Boutron-Ruault, M-C, Bracci, PM, Canzian, F, Chang, K, Cotterchio, M, Giovannucci, EL, Goggins, M, Bolton, JAH, Jenab, M, Khaw, K-T, Krogh, V, Kurtz, RC, McWilliams, RR, Mendelsohn, JB, Rabe, KG, Riboli, E, Tjonneland, A, Tobias, GS, Trichopoulos, D, Elena, JW, Yu, H, Amundadottir, L, Stolzenberg-Solomon, RZ, Kraft, P, Schumacher, F, Stram, D, Savage, SA, Mirabello, L, Andrulis, IL, Wunder, JS, Patino Garcia, A, Sierrasesumaga, L, Barkauskas, DA, Gorlick, RG, Purdue, M, Chow, W-H, Moore, LE, Schwartz, KL, Davis, FG, Hsing, AW, Berndt, SI, Black, A, Wentzensen, N, Brinton, LA, Lissowska, J, Peplonska, B, McGlynn, KA, Cook, MB, Graubard, BI, Kratz, CP, Greene, MH, Erickson, RL, Hunter, DJ, Thomas, G, Hoover, RN, Real, FX, Fraumeni, JF, Caporaso, NE, Tucker, M, Rothman, N, Perez-Jurado, LA, and Chanock, SJ

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 × 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 × 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

25. A multi-stage genome-wide association study of bladder cancer identifies multiple susceptibility loci.

Author

Garcia-Closas, M., Chatterjee, N., Malats, N., Wu, X., Figueroa, J.D., Real, F.X., Berg, D.P.G. van den, Matullo, G., Baris, D., Thun, M., Kiemeney, L.A.L.M., Vilneis, P., De Vivo, I., Albanes, D., Purdue, M., Rafnar, T., Hildebrandt, M.A.T., Kiltie, A.E., Cussenot, O., Golka, K., Kumar, R., Taylor, J.A., Mayordomo, J.I., Jacobs, K.B., Kogevinas, M., Hutchinson, A., Wang, Z., Fu, Y., Prokunina-Olsson, L., Burdett, L., Yeager, M., Wheeler, W., Tardon, A., Serra, C., Carrato, A., Garcia-Closas, R., Lloreta, J., Johnson, A., Schwenn, M., Karagas, M.R., Schned, A., Andriole, G.L., Grubb, R., Black, A., Jacobs, E.J., Diver, W.R., Gapstur, S.M., Weinstein, S.J., Virtamo, J., Cortessis, V.K., Gago-Dominguez, M., Pike, M.C., Stern, M.C., Yuan, J.M., Hunter, D.J., McGrath, M., Dinney, C.P., Czerniak, B., Chen, M., Yang, H., Vermeulen, S., Aben, K.K.H., Witjes, J.A., Makkinje, R.R., Sulem, P., Besenbacher, S., Riboli, E., Brennan, P., Panico, S., Navarro, C, Allen, N.E., Bueno-De-Mesquita, H.B., Trichopoulos, D., Caporaso, N., Landi, M.T., Canzian, F., Ljungberg, B, Tjonneland, A., Clavel-Chapelon, F., Bishop, D.T., Teo, M.T., Knowles, M.A., Guarrera, S., Polidoro, S., Ricceri, F., Sacerdote, C., Allione, A., Cancel-Tassin, G., Selinski, S., Hengstler, J.G., Dietrich, H., Fletcher, T., Rudnai, P., Gurzau, E, Koppova, K., Bolick, S.C., Godfrey, A., Xu, Z., Garcia-Closas, M., Chatterjee, N., Malats, N., Wu, X., Figueroa, J.D., Real, F.X., Berg, D.P.G. van den, Matullo, G., Baris, D., Thun, M., Kiemeney, L.A.L.M., Vilneis, P., De Vivo, I., Albanes, D., Purdue, M., Rafnar, T., Hildebrandt, M.A.T., Kiltie, A.E., Cussenot, O., Golka, K., Kumar, R., Taylor, J.A., Mayordomo, J.I., Jacobs, K.B., Kogevinas, M., Hutchinson, A., Wang, Z., Fu, Y., Prokunina-Olsson, L., Burdett, L., Yeager, M., Wheeler, W., Tardon, A., Serra, C., Carrato, A., Garcia-Closas, R., Lloreta, J., Johnson, A., Schwenn, M., Karagas, M.R., Schned, A., Andriole, G.L., Grubb, R., Black, A., Jacobs, E.J., Diver, W.R., Gapstur, S.M., Weinstein, S.J., Virtamo, J., Cortessis, V.K., Gago-Dominguez, M., Pike, M.C., Stern, M.C., Yuan, J.M., Hunter, D.J., McGrath, M., Dinney, C.P., Czerniak, B., Chen, M., Yang, H., Vermeulen, S., Aben, K.K.H., Witjes, J.A., Makkinje, R.R., Sulem, P., Besenbacher, S., Riboli, E., Brennan, P., Panico, S., Navarro, C, Allen, N.E., Bueno-De-Mesquita, H.B., Trichopoulos, D., Caporaso, N., Landi, M.T., Canzian, F., Ljungberg, B, Tjonneland, A., Clavel-Chapelon, F., Bishop, D.T., Teo, M.T., Knowles, M.A., Guarrera, S., Polidoro, S., Ricceri, F., Sacerdote, C., Allione, A., Cancel-Tassin, G., Selinski, S., Hengstler, J.G., Dietrich, H., Fletcher, T., Rudnai, P., Gurzau, E, Koppova, K., Bolick, S.C., Godfrey, A., and Xu, Z.

Abstract

Contains fulltext : 88946.pdf (publisher's version ) (Closed access)

Published
2010

26. Polymorphisms in innate immunity genes and lung cancer risk in Xuanwei, China.

Author

Risk Assessment of Toxic and Immunomodulatory Agents, Dep IRAS, Shen, M., Vermeulen, R.C.H., Rajaraman, P., Menashe, I., He, X., Chapman, R.S., Yeager, M., Thomas, G., Burdett, L., Hutchinson, A., Yuenger, J., Chanock, S., Lan, Q., Risk Assessment of Toxic and Immunomodulatory Agents, Dep IRAS, Shen, M., Vermeulen, R.C.H., Rajaraman, P., Menashe, I., He, X., Chapman, R.S., Yeager, M., Thomas, G., Burdett, L., Hutchinson, A., Yuenger, J., Chanock, S., and Lan, Q.

Published
2009

27. Digital Cultural Communication: tools and methods for community co-creation

Author

Burdett, L, Watkins, Jerry, Russo, Angelina, Burdett, L, Watkins, Jerry, and Russo, Angelina

Abstract

Only now are the communication technologies familiar to higher-end users becoming available to communities. When such technologies are married to traditional forms such as community narratives, they present an opportunity for communities to preserve their stories and distribute this knowledge to a wider audience. In some of the most remote parts of Australia, communities are partnering with cultural institutions to create digital cultural content. When communities create content in partnership with cultural institutions, both contribute to the sharing of cultural knowledge and distribution of this knowledge to a wider audience. In Queensland, a new initiative has created a mobile digital platform which travels into outlying areas of the community not just to capture and disseminate digital culture but to promote and train in new literacy. Livingstone (2003) suggests that the new literacy has limited value to communities if they cannot access technologies, nor have reason to. This paper introduces Digital Cultural Communication, an interaction design-derived Solutions Architecture which weds new literacy to multiplatform communication design by providing a cost-effective strategic infrastructure. Cultural institutions can supply training in new literacy for community co-creation and by promoting the end product, stimulate demand. Using an ambitious and exciting case study from Queensland’s cultural sector, this paper illustrates how communities can engage in the co-creation of content which both extends their digital literacy and strengthens their cultural identity. Further, by framing this case study within the domain of Digital Cultural Communication, the paper illustrates the advantages of partnerships between communities and cultural institutions in the capture, display and distribution of knowledge.

Published
2005

29. Abstract LB-337: Synergistic effects of twelve common genetic polymorphisms and smoking habits on absolute risk of bladder cancer

Author

García-Closas, M., primary, Rothman, N., additional, Figueroa, J. D., additional, Prokunina-Olsson, L., additional, Han, S., additional, Baris, D., additional, Jacobs, E., additional, Malats, N., additional, Vivo, I. De, additional, Albanes, D., additional, Purdue, M. P., additional, Sharma, S., additional, Fu, Y. P., additional, Kogevinas, M., additional, Wang, Z., additional, Tang, W., additional, Tardón, A., additional, Serra, C., additional, Carrato, A., additional, García-Closas, R., additional, Lloreta, J., additional, Johnson, A., additional, Schwenn, M., additional, Karagas, M. R., additional, Schned, A., additional, Andriole, G., additional, Grubb, R., additional, Black, A., additional, Gapstur, S. M., additional, Thun, M., additional, Diver, W. R., additional, Weinstein, S. J., additional, Virtamo, J., additional, Hunter, D. J., additional, Caporaso, N., additional, Landi, M. T., additional, Hutchinson, A., additional, Burdett, L., additional, Jacobs, K. B., additional, Yeager, M., additional, Fraumeni, J. F., additional, Chanock, S. J., additional, Silverman, D. T., additional, and Chatterjee, N., additional

Published
2012
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38. A comprehensive candidate gene approach identifies genetic variation associated with osteosarcoma

Author

Grotmol Tom, Hutchinson Amy, Uzoka Arinze, Teshome Kedest, Chowdhury Salma, Wang Zhaoming, Burdett Laurie, Berndt Sonja I, Yu Kai, Mirabello Lisa, Douglass Chester, Hayes Richard B, Hoover Robert N, and Savage Sharon A

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

Abstract Background Osteosarcoma (OS) is a bone malignancy which occurs primarily in adolescents. Since it occurs during a period of rapid growth, genes important in bone formation and growth are plausible modifiers of risk. Genes involved in DNA repair and ribosomal function may contribute to OS pathogenesis, because they maintain the integrity of critical cellular processes. We evaluated these hypotheses in an OS association study of genes from growth/hormone, bone formation, DNA repair, and ribosomal pathways. Methods We evaluated 4836 tag-SNPs across 255 candidate genes in 96 OS cases and 1426 controls. Logistic regression models were used to estimate the odds ratios (OR) and 95% confidence intervals (CI). Results Twelve SNPs in growth or DNA repair genes were significantly associated with OS after Bonferroni correction. Four SNPs in the DNA repair gene FANCM (ORs 1.9-2.0, P = 0.003-0.004) and 2 SNPs downstream of the growth hormone gene GH1 (OR 1.6, P = 0.002; OR 0.5, P = 0.0009) were significantly associated with OS. One SNP in the region of each of the following genes was significant: MDM2, MPG, FGF2, FGFR3, GNRH2, and IGF1. Conclusions Our results suggest that several SNPs in biologically plausible pathways are associated with OS. Larger studies are required to confirm our findings.

Published
2011
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39. Genotypes and haplotypes in the insulin-like growth factors, their receptors and binding proteins in relation to plasma metabolic levels and mammographic density

Author

Chanock Stephen J, Bremnes Yngve, Fagerheim Toril, Alnaes Grethe IG, Solvang Hiroko K, Johansen Fredrik, Brill Ilene, Gram Inger T, Biong Margarethe, Burdett Laurie, Yeager Meredith, Ursin Giske, and Kristensen Vessela N

Subjects
Internal medicine, RC31-1245, Genetics, QH426-470
Abstract

Abstract Background Increased mammographic density is one of the strongest independent risk factors for breast cancer. It is believed that one third of breast cancers are derived from breasts with more than 50% density. Mammographic density is affected by age, BMI, parity, and genetic predisposition. It is also greatly influenced by hormonal and growth factor changes in a woman's life cycle, spanning from puberty through adult to menopause. Genetic variations in genes coding for hormones and growth factors involved in development of the breast are therefore of great interest. The associations between genetic polymorphisms in genes from the IGF pathway on mammographic density and circulating levels of IGF1, its binding protein IGFBP3, and their ratio in postmenopausal women are reported here. Methods Samples from 964 postmenopausal Norwegian women aged 55-71 years were collected as a part of the Tromsø Mammography and Breast Cancer Study. All samples were genotyped for 25 SNPs in IGF1, IGF2, IGF1R, IGF2R, IGFALS and IGFBP3 using Taqman (ABI). The main statistical analyses were conducted with the PROC HAPLOTYPE procedure within SAS/GENETICS™ (SAS 9.1.3). Results The haplotype analysis revealed six haploblocks within the studied genes. Of those, four had significant associations with circulating levels of IGF1 or IGFBP3 and/or mammographic density. One haplotype variant in the IGF1 gene was found to be associated with mammographic density. Within the IGF2 gene one haplotype variant was associated with levels of both IGF1 and IGFBP3. Two haplotype variants in the IGF2R were associated with the level of IGF1. Both variants of the IGFBP3 haplotype were associated with the IGFBP3 level and indicate regulation in cis. Conclusion Polymorphisms within the IGF1 gene and related genes were associated with plasma levels of IGF1, IGFBP3 and mammographic density in this study of postmenopausal women.

Published
2010
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40. Genome-wide association study identifies five susceptibility loci for follicular lymphoma outside the HLA region

Author

Joseph Vijai, W. Ryan Diver, Degui Zhi, Brenda M. Birmann, Henrik Hjalgrim, Bruce K. Armstrong, Gianluca Severi, Pierluigi Cocco, Joseph F. Fraumeni, Xifeng Wu, Graham G. Giles, Eleanor Kane, Herve Ghesquieres, Eve Roman, Edward Giovannucci, Mads Melbye, Rudolph Kaaks, Lindsay M. Morton, Nicholas K. Akers, Elizabeth A. Holly, Liming Liang, Patrizio Mazza, Kari E. North, John J. Spinelli, Carrie A. Thompson, Bodil Ohlsson, Yuanqing Ye, Anneclaire J. De Roos, Stephen J. Chanock, Theodore R. Holford, Paul Brennan, Jianjun Liu, Roel Vermeulen, Thomas E. Witzig, Angela Brooks-Wilson, Mark P. Purdue, Ahmet Dogan, Gilles Salles, Kenneth Offit, Lucia Conde, Laurie Burdett, George J. Weiner, Anne Kricker, James McKay, Peter Kraft, Sonja I. Berndt, Attilio Gabbas, Rebecca Montalvan, Rebecca D. Jackson, Baoshan Ma, Zhaoming Wang, Patricia Hartge, Danylo J. Villano, Marc Maynadie, Mortimer J. Lacher, Lauren R. Teras, Susan L. Slager, Lenka Foretova, Rachel S. Kelly, Martha S. Linet, Brian K. Link, Jarmo Virtamo, Charles C. Chung, Anne Zeleniuch-Jacquotte, Martyn T. Smith, Tracy Lightfoot, Jacques Riby, Paolo Boffetta, Meredith Yeager, Brian C.-H. Chiu, Grzegorz S. Nowakowski, Yolanda Benavente, Bengt Glimelius, Mark Liebow, Saioa Chamosa, Charles E. Lawrence, Karin E. Smedby, Nikolaus Becker, Thomas M. Habermann, Jacqueline Clavel, Qing Lan, Alexandra Nieters, Maryjean Schenk, Sophia S. Wang, Demetrius Albanes, Lesley F. Tinker, Alex Smith, Anthony Staines, Amy Hutchinson, Wendy Cozen, Hans-Olov Adami, Anne J. Novak, Christine F. Skibola, Ann Maria, Elisabete Weiderpass, Kimberly A. Bertrand, James R. Cerhan, Maria Grazia Ennas, Claire M. Vajdic, Jinyan Huang, Paul I.W. de Bakker, Paige M. Bracci, Tongzhang Zheng, Ruth C. Travis, Paolo Vineis, Jia Nee Foo, Jennifer Turner, Alain Monnereau, Silvia de Sanjosé, Nathaniel Rothman, Yawei Zhang, Jian Gu, Skibola, C.F., Berndt, S.I., Vijai, J., Conde, L., Wang, Z., Yeager, M., De Bakker, P.I.W., Birmann, B.M., Vajdic, C.M., Foo, J.-N., Bracci, P.M., Vermeulen, R.C.H., Slager, S.L., De Sanjose, S., Wang, S.S., Linet, M.S., Salles, G., Lan, Q., Severi, G., Hjalgrim, H., Lightfoot, T., Melbye, M., Gu, J., Ghesquières, H., Link, B.K., Morton, L.M., Holly, E.A., Smith, A., Tinker, L.F., Teras, L.R., Kricker, A., Becker, N., Purdue, M.P., Spinelli, J.J., Zhang, Y., Giles, G.G., Vineis, P., Monnereau, A., Bertrand, K.A., Albanes, D., Zeleniuch-Jacquotte, A., Gabbas, A., Chung, C.C., Burdett, L., Hutchinson, A., Lawrence, C., Montalvan, R., Liang, L., Huang, J., Ma, B., Liu, J., Adami, H.-O., Glimelius, B., Ye, Y., Nowakowski, G.S., Dogan, A., Thompson, C.A., Habermann, T.M., Novak, A.J., Liebow, M., Witzig, T.E., Weiner, G.J., Schenk, M., Hartge, P., De Roos, A.J., Cozen, W., Zhi, D., Akers, N.K., Riby, J., Smith, M.T., Lacher, M., Villano, D.J., Maria, A., Roman, E., Kane, E., Jackson, R.D., North, K.E., Diver, W.R., Turner, J., Armstrong, B.K., Benavente, Y., Boffetta, P., Brennan, P., Foretova, L., Maynadie, M., Staines, A., McKay, J., Brooks-Wilson, A.R., Zheng, T., Holford, T.R., Chamosa, S., Kaaks, R., Kelly, R.S., Ohlsson, B., Travis, R.C., Weiderpass, E., Clavel, J., Giovannucci, E., Kraft, P., Virtamo, J., Mazza, P., Cocco, P., Ennas, M.G., Chiu, B.C.H., Fraumeni, J.F., Jr., Nieters, A., Offit, K., Wu, X., Cerhan, J.R., Smedby, K.E., Chanock, S.J., and Rothman, N.

Subjects
EXPRESSION, Follicular lymphoma, Single-nucleotide polymorphism, Genome-wide association study, Human leukocyte antigen, Biology, VARIANTS, Polymorphism, Single Nucleotide, follicular lymphoma, HLA Antigens, Polymorphism (computer science), Report, CLASS-I, RESOURCE, Biomarkers, Tumor, Genetics, medicine, Chromosomes, Human, Humans, TOOL, Genetic Predisposition to Disease, Genetics(clinical), PEPTIDE, Allele, Lymphoma, Follicular, Alleles, Genetics (clinical), Genetic association, SNPS, RISK, Genome-wide association, Haplotype, medicine.disease, HLA, Haplotypes, Case-Control Studies, UNIVERSITY, SET, Genome-Wide Association Study
Abstract

Genome-wide association studies (GWASs) of follicular lymphoma (FL) have previously identified human leukocyte antigen (HLA) gene variants. To identify additional FL susceptibility loci, we conducted a large-scale two-stage GWAS in 4,523 case subjects and 13,344 control subjects of European ancestry. Five non-HLA loci were associated with FL risk: 11q23.3 (rs4938573, p = 5.79 × 10 -20) near CXCR5; 11q24.3 (rs4937362, p = 6.76 × 10 -11) near ETS1; 3q28 (rs6444305, p = 1.10 × 10 -10) in LPP; 18q21.33 (rs17749561, p = 8.28 × 10 -10) near BCL2; and 8q24.21 (rs13254990, p = 1.06 × 10 -8) near PVT1. In an analysis of the HLA region, we identified four linked HLA-DRß1 multiallelic amino acids at positions 11, 13, 28, and 30 that were associated with FL risk (pomnibus = 4.20 × 10 -67 to 2.67 × 10 -70). Additional independent signals included rs17203612 in HLA class II (odds ratio [ORper-allele] = 1.44; p = 4.59 × 10 -16) and rs3130437 in HLA class I (ORper-allele = 1.23; p = 8.23 × 10 -9). Our findings further expand the number of loci associated with FL and provide evidence that multiple common variants outside the HLA region make a significant contribution to FL risk. © 2014 by The American Society of Human Genetics. All rights reserved.

Published
2016

41. Genetically predicted longer telomere length is associated with increased risk of B-cell lymphoma subtypes

Author

Henrik Hjalgrim, Joseph Vijai, Bengt Glimelius, Kimberly A. Bertrand, Immaculata De Vivo, Eve Roman, Martha Glenn, Nathaniel Rothman, Yolanda Benavente, Zhaoming Wang, Ju-Hyun Park, Anneclaire J. De Roos, John J. Spinelli, Demetrius Albanes, Paul Brennan, Emanuele Angelucci, Mariagrazia Zucca, Qing Lan, Kari E. North, Paige M. Bracci, Mark P. Purdue, Marco Rais, Melissa C. Southey, Alain Monnereau, Ahmet Dogan, Graham G. Giles, Robert J. Klein, Peter Kraft, Lesley F. Tinker, Laurie Burdett, Lucia Conde, Carrie A. Thompson, James McKay, Martyn T. Smith, Göran Roos, Yan W. Asmann, Dennis D. Weisenburger, Elizabeth A. Holly, Thomas E. Witzig, Liming Liang, Paul I.W. de Bakker, Alex Smith, Jarmo Virtamo, Charles E. Lawrence, Patricia Hartge, Karen Curtin, Anthony Staines, Nikolaus Becker, Nicola J. Camp, Charles C. Chung, Degui Zhi, Brenda M. Birmann, W. Ryan Diver, Roel Vermeulen, Sonja I. Berndt, Tongzhang Zheng, Silvia de Sanjosé, Eleanor Kane, James R. Cerhan, Christopher R. Flowers, Joseph F. Fraumeni, Stephen J. Chanock, Stephen M. Ansell, Angela Brooks-Wilson, Kenneth Offit, Jinyan Huang, Mads Melbye, Edward Giovannucci, Baoshan Ma, Tracy Lightfoot, Brian K. Link, Richard K. Severson, Theodore R. Holford, Yawei Zhang, Anne Tjønneland, Meredith Yeager, Wendy Cozen, Anne J. Novak, Lauren R. Teras, Claire M. Vajdic, Lisa A. Cannon-Albright, Lenka Foretova, Christine F. Skibola, Sophia S. Wang, Hans-Olov Adami, Andrew D. Zelenetz, Jenny Turner, Paolo Vineis, Corinne Haioun, Hervé Tilly, Anne Zeleniuch-Jacquotte, Thomas M. Habermann, Paolo Boffetta, Jacqueline Clavel, Herve Ghesquieres, Stephanie J. Weinstein, Lindsay M. Morton, Susan L. Slager, Simon Crouch, Gilles Salles, Rachel S. Kelly, Karin E. Smedby, Amy Hutchinson, David G. Cox, Elio Riboli, Jacques Riby, Rebecca D. Jackson, Mark Liebow, Thierry Jo Molina, Danylo J. Villano, Marc Maynadie, Yuanqing Ye, Heiner Boeing, Jian Gu, Brian C.-H. Chiu, Simonetta Di Lollo, Mitchell J. Machiela, Alexandra Nieters, Xifeng Wu, Rudolph Kaaks, Machiela, M.J., Lan, Q., Slager, S.L., Vermeulen, R.C.H., Teras, L.R., Camp, N.J., Cerhan, J.R., Spinelli, J.J., Wang, S.S., Nieters, A., Vijai, J., Yeager, M., Wang, Z., Ghesquières, H., McKay, J., Conde, L., de Bakker, P.I.W., Cox, D.G., Burdett, L., Monnereau, A., Flowers, C.R., De Roos, A.J., Brooks-Wilson, A.R., Giles, G.G., Melbye, M., Gu, J., Jackson, R.D., Kane, E., Purdue, M.P., Vajdic, C.M., Albanes, D., Kelly, R.S., Zucca, M., Bertrand, K.A., Zeleniuch-Jacquotte, A., Lawrence, C., Hutchinson, A., Zhi, D., Habermann, T.M., Link, B.K., Novak, A.J., Dogan, A., Asmann, Y.W., Liebow, M., Thompson, C.A., Ansell, S.M., Witzig, T.E., Tilly, H., Haioun, C., Molina, T.J., Hjalgrim, H., Glimelius, B., Adami, H.-O., Roos, G., Bracci, P.M., Riby, J., Smith, M.T., Holly, E.A., Cozen, W., Hartge, P., Morton, L.M., Severson, R.K., Tinker, L.F., North, K.E., Becker, N., Benavente, Y., Boffetta, P., Brennan, P., Foretova, L., Maynadie, M., Staines, A., Lightfoot, T., Crouch, S., Smith, A., Roman, E., Ryan Diver, W., Offit, K., Zelenetz, A., Klein, R.J., Villano, D.J., Zheng, T., Zhang, Y., Holford, T.R., Turner, J., Southey, M.C., Clavel, J., Virtamo, J., Weinstein, S., Riboli, E., Vineis, P., Kaaks, R., Boeing, H., Tjønneland, A., Angelucci, E., Di Lollo, S., Rais, M., De Vivo, I., Giovannucci, E., Kraft, P., Huang, J., Ma, B., Ye, Y., Chiu, B.C.H., Liang, L., Park, J.-H., Chung, C.C., Weisenburger, D.D., Fraumeni, J.F., Jr and Salles, G., Glenn, M., Cannon-Albright, L., Curtin, K., Wu, X., Smedby, K.E., de Sanjose, S., Skibola, C.F., Berndt, S.I., Birmann, B.M., Chanock, S.J., Rothman, N., LS IRAS EEPI GRA (Gezh.risico-analyse), Sub Atmospheric physics and chemistry, dIRAS RA-I&I RA, dIRAS RA-2, Service d’Hématologie [Centre Hospitalier Lyon Sud - HCL], Centre Hospitalier Lyon Sud [CHU - HCL] ( CHLS ), Hospices Civils de Lyon ( HCL ) -Hospices Civils de Lyon ( HCL ), Centre de Recherche en Cancérologie de Lyon ( CRCL ), Centre Léon Bérard [Lyon]-Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Cancer environnement ( EPICENE ), Bordeaux population health ( BPH ), Université de Bordeaux ( UB ) -Institut de Santé Publique, d'Épidémiologie et de Développement (ISPED)-Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Université de Bordeaux ( UB ) -Institut de Santé Publique, d'Épidémiologie et de Développement (ISPED)-Institut National de la Santé et de la Recherche Médicale ( INSERM ), Registre des hémopathies malignes de la Gironde, Institut Bergonié - CRLCC Bordeaux, Department of Agronomy, University of Wisconsin-Madison [Madison], Service hématologie Poitiers, CHU, Service d'hématologie clinique, Assistance publique - Hôpitaux de Paris (AP-HP)-Hôpital Henri Mondor-Université Paris-Est Créteil Val-de-Marne - Paris 12 ( UPEC UP12 ), Université Paris Descartes - Paris 5 ( UPD5 ), Oslo and Akershus University College ( OAUC ), Laboratoire de mécanique Biomécanique Polymère Structures ( LaBPS ), Université de Lorraine ( UL ), The Tisch Cancer Institute, Mount Sinai School of Medicine, International Agency for Cancer Research ( IACR ), International Agency for Cancer Research, Registre des hémopathies malignes de Côte d'Or, Centre d'épidémiologie des populations ( CEP ), Université de Bourgogne ( UB ) -Centre Régional de Lutte contre le cancer - Centre Georges-François Leclerc ( CRLCC - CGFL ), University of Chicago Medicine, Institut National de la Santé et de la Recherche Médicale ( INSERM ), French National Registry of Childhood Hematological malignancies (NRCH), NRCH, Division of Epidemiology, Public Health and Primary Care, Imperial College London, Unit of Cancer Epidemiology, AOU S. Giovanni Battista, CPO Piemonte, CeRMS, University of Torino, Department of Epidemiology and Public Health, Department Cancer Epidemiology, German Cancer Research Center, Institute of Human Nutrition Potsdam-Rehbruecke, Diet, Cancer and Health, Danish Cancer Society, Justus Liebig University Giessen, Sino French Research Center for Biomedical Imaging ( HIT-INSA ), Institut National des Sciences Appliquées de Lyon ( INSA Lyon ), Université de Lyon-Institut National des Sciences Appliquées ( INSA ) -Université de Lyon-Institut National des Sciences Appliquées ( INSA ) -Harbin Institute of Technology ( HIT ), Centre de Recherche en Acquisition et Traitement de l'Image pour la Santé ( CREATIS ), Hospices Civils de Lyon ( HCL ) -Université Jean Monnet [Saint-Étienne] ( UJM ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon ( INSA Lyon ), Université de Lyon-Institut National des Sciences Appliquées ( INSA ) -Institut National des Sciences Appliquées ( INSA ), Institut de Physique Nucléaire d'Orsay ( IPNO ), Université Paris-Sud - Paris 11 ( UP11 ) -Institut National de Physique Nucléaire et de Physique des Particules du CNRS ( IN2P3 ) -Centre National de la Recherche Scientifique ( CNRS ), Chinese Academy of Sciences [Beijing] ( CAS ), Centre Hospitalier Lyon Sud [CHU - HCL] (CHLS), Hospices Civils de Lyon (HCL)-Hospices Civils de Lyon (HCL), Centre de Recherche en Cancérologie de Lyon (UNICANCER/CRCL), Centre Léon Bérard [Lyon]-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Cancer environnement (EPICENE ), Bordeaux population health (BPH), Université de Bordeaux (UB)-Institut de Santé Publique, d'Épidémiologie et de Développement (ISPED)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Bordeaux (UB)-Institut de Santé Publique, d'Épidémiologie et de Développement (ISPED)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Bergonié [Bordeaux], UNICANCER-UNICANCER, University of Wisconsin-Madison, Centre hospitalier universitaire de Poitiers (CHU Poitiers), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Henri Mondor-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Université Paris Descartes - Paris 5 (UPD5), Akershus University College, Laboratoire de mécanique Biomécanique Polymère Structures (LaBPS), Université de Lorraine (UL), Icahn School of Medicine at Mount Sinai [New York] (MSSM), International Agency for Cancer Research (IACR), Centre d'épidémiologie des populations (CEP), Université de Bourgogne (UB)-Centre Régional de Lutte contre le cancer Georges-François Leclerc [Dijon] (UNICANCER/CRLCC-CGFL), Institut National de la Santé et de la Recherche Médicale (INSERM), German Cancer Research Center - Deutsches Krebsforschungszentrum [Heidelberg] (DKFZ), Deutsches Institut für Ernährungsforschung Potsdam-Rehbrücke (DifE), Leibniz Association, Justus-Liebig-Universität Gießen (JLU), Sino French Research Center for Biomedical Imaging (HIT-INSA), Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Harbin Institute of Technology (HIT), Centre de Recherche en Acquisition et Traitement de l'Image pour la Santé (CREATIS), Université Jean Monnet [Saint-Étienne] (UJM)-Hospices Civils de Lyon (HCL)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Chinese Academy of Sciences [Beijing] (CAS), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Università degli studi di Torino = University of Turin (UNITO), Justus-Liebig-Universität Gießen = Justus Liebig University (JLU), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Harbin Institute of Technology (HIT), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Hospices Civils de Lyon (HCL)-Université Jean Monnet [Saint-Étienne] (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre de Recherche en Cancérologie de Lyon (CRCL), Université de Lyon-Université de Lyon-Centre Léon Bérard [Lyon]-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Hôpital Henri Mondor-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Oslo and Akershus University College (OAUC), Université de Bourgogne (UB)-Centre Régional de Lutte contre le cancer - Centre Georges-François Leclerc (CRLCC - CGFL), and Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université Claude Bernard Lyon 1 (UCBL)

Subjects
0301 basic medicine, Serum, Male, Lymphoma, analysis, Chronic lymphocytic leukemia, Follicular lymphoma, Global Health, [ SDV.CAN ] Life Sciences [q-bio]/Cancer, immunology, surgery, 0302 clinical medicine, Endocrinology, immune system diseases, single nucleotide polymorphism, Germany, hemic and lymphatic diseases, London, 80 and over, Odds Ratio, genetics, Prospective Studies, B-cell lymphoma, Association Studies Article, Genetics (clinical), Aged, 80 and over, education.field_of_study, telomere, Genome, Leukemia, Age Factors, General Medicine, Environmental exposure, Genomics, Middle Aged, b-cell lymphoma, small cell lymphoma, Italy, 030220 oncology & carcinogenesis, Medicine, epidemiology, Female, France, Risk of B-cell lymphoma subtypes, Risk, Adult, Canada, China, Lymphoma, B-Cell, Genotype, Adolescent, leukocytes, etiology, Population, [SDV.CAN]Life Sciences [q-bio]/Cancer, Biology, Environment, Risk Assessment, methods, Time, 03 medical and health sciences, medicine, Humans, Family, Genetic Predisposition to Disease, education, Molecular Biology, Alleles, Occupational Health, Genetic Association Studies, Aged, B-Cell, International Agencies, Odds ratio, Environmental Exposure, medicine.disease, Telomere, Non-Hodgkin's lymphoma, 030104 developmental biology, Immunology, physiology, Chronic Disease, pathology, Laboratories, metabolism
Abstract

International audience; Evidence from a small number of studies suggests that longer telomere length measured in peripheral leukocytes is associated with an increased risk of non-Hodgkin lymphoma (NHL). However, these studies may be biased by reverse causation, confounded by unmeasured environmental exposures and might miss time points for which prospective telomere measurement would best reveal a relationship between telomere length and NHL risk. We performed an analysis of genetically inferred telomere length and NHL risk in a study of 10 102 NHL cases of the four most common B-cell histologic types and 9562 controls using a genetic risk score (GRS) comprising nine telomere length-associated single-nucleotide polymorphisms. This approach uses existing genotype data and estimates telomere length by weighing the number of telomere length-associated variant alleles an individual carries with the published change in kb of telomere length. The analysis of the telomere length GRS resulted in an association between longer telomere length and increased NHL risk [four B-cell histologic types combined; odds ratio (OR) = 1.49, 95% CI 1.22-1.82,P-value = 8.5 x 10(-5)]. Subtype-specific analyses indicated that chronic lymphocytic leukemia or small lymphocytic lymphoma (CLL/SLL) was the principal NHL subtype contributing to this association (OR = 2.60, 95% CI 1.93-3.51,P-value = 4.0 x 10(-10)). Significant interactions were observed across strata of sex for CLL/SLL and marginal zone lymphoma subtypes as well as age for the follicular lymphoma subtype. Our results indicate that a genetic background that favors longer telomere length may increase NHL risk, particularly risk of CLL/SLL, and are consistent with earlier studies relating longer telomere length with increased NHL risk

Published
2016

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

Author

Nathaniel Rothman, Yolanda Benavente, Paul Brennan, Qing Lan, Pierluigi Cocco, Simon Crouch, Anneclaire J. De Roos, Josh Wright, Christine F. Skibola, Mark P. Purdue, Elisabete Weiderpass, James R. Cerhan, Randy D. Gascoyne, Maria Grazia Ennas, Kari E. North, Zhaoming Wang, Jinyan Huang, Julie M. Cunningham, Alain Monnereau, Peter Kraft, Patricia Hartge, Edward Giovannucci, Karen Curtin, Giovanna Masala, Jacqueline Clavel, Neil E. Kay, Jacques Riby, María Dolores Chirlaque, John J. Spinelli, Delphine Casabonne, Jenny Turner, Lucia Conde, Lesley F. Tinker, Martha Glenn, Sara S. Strom, Donna K. Arnett, Rebecca Montalvan, Ju-Hyun Park, Melissa C. Southey, Ann Maria, Karin E. Smedby, Lindsay M. Morton, Marc Maynadié, Laurie Burdett, Amy Hutchinson, Bengt Glimelius, W. Ryan Diver, Elio Riboli, Sonja I. Berndt, Lisa A. Cannon-Albright, Kimberly A. Bertrand, Aaron D. Norman, Sara J. Achenbach, Celine M. Vachon, Angela Cox, Xifeng Wu, Theodore R. Holford, Neil E. Caporaso, Joseph F. Fraumeni, Roel Vermeulen, Rudolph Kaaks, Mads Melbye, Joseph Vijai, Kari G. Chaffee, Lauren R. Teras, Rebecca D. Jackson, Lenka Foretova, J. Brice Weinberg, Paige M. Bracci, Sophia S. Wang, Demetrius Albanes, Stephen J. Chanock, Wendy Cozen, Mark Liebow, Anne J. Novak, Hans-Olov Adami, George J. Weiner, Angela Brooks-Wilson, Kenneth Offit, Anne Kricker, Claire M. Vajdic, James McKay, Ellen T. Chang, Baoshan Ma, Cristine Allmer, Susan L. Slager, Brian K. Link, Elizabeth A. Holly, Anthony Staines, Liming Liang, Jarmo Virtamo, Timothy G. Call, Nicola J. Camp, Ruth C. Travis, Alexandra Nieters, Degui Zhi, Brenda M. Birmann, Tait D. Shanafelt, Rachel S. Kelly, Graham G. Giles, Nilanjan Chatterjee, John A. Snowden, Yuanqing Ye, Núria Sala, Tongzhang Zheng, Paolo Boffetta, Lynn R. Goldin, Danylo J. Villano, Jose F. Leis, Paolo Vineis, Lucia Miligi, Jian Gu, Justin M. Leach, Silvia de Sanjosé, Richard K. Severson, Yawei Zhang, Henrik Hjalgrim, Roger L. Milne, Charles E. Lawrence, Meredith Yeager, Moara Machado, Nikolaus Becker, Joseph M. Connors, Anne Zeleniuch-Jacquotte, Giovanni Maria Ferri, Stephanie J. Weinstein, LS IRAS EEPI GRA (Gezh.risico-analyse), Sub Atmospheric physics and chemistry, dIRAS RA-I&I RA, dIRAS RA-2, Berndt, S.I., Camp, N.J., Skibola, C.F., Vijai, J., Wang, Z., Gu, J., Nieters, A., Kelly, R.S., Smedby, K.E., Monnereau, A., Cozen, W., Cox, A., Wang, S.S., Lan, Q., Teras, L.R., Machado, M., Yeager, M., Brooks-Wilson, A.R., Hartge, P., Purdue, M.P., Birmann, B.M., Vajdic, C.M., Cocco, P., Zhang, Y., Giles, G.G., Zeleniuch-Jacquotte, A., Lawrence, C., Montalvan, R., Burdett, L., Hutchinson, A., Ye, Y., Call, T.G., Shanafelt, T.D., Novak, A.J., Kay, N.E., Liebow, M., Cunningham, J.M., Allmer, C., Hjalgrim, H., Adami, H.-O., Melbye, M., Glimelius, B., Chang, E.T., Glenn, M., Curtin, K., Cannon-Albright, L.A., Diver, W.R., Link, B.K., Weiner, G.J., Conde, L., Bracci, P.M., Riby, J., Arnett, D.K., Zhi, D., Leach, J.M., Holly, E.A., Jackson, R.D., Tinker, L.F., Benavente, Y., Sala, N., Casabonne, D., Becker, N., Boffetta, P., Brennan, P., Foretova, L., Maynadie, M., McKay, J., Staines, A., Chaffee, K.G., Achenbach, S.J., Vachon, C.M., Goldin, L.R., Strom, S.S., Leis, J.F., Weinberg, J.B., Caporaso, N.E., Norman, A.D., De Roos, A.J., Morton, L.M., Severson, R.K., Riboli, E., Vineis, P., Kaaks, R., Masala, G., Weiderpass, E., Chirlaque, M.-D., Vermeulen, R.C.H., Travis, R.C., Southey, M.C., Milne, R.L., Albanes, D., Virtamo, J., Weinstein, S., Clavel, J., Zheng, T., Holford, T.R., Villano, D.J., Maria, A., Spinelli, J.J., Gascoyne, R.D., Connors, J.M., Bertrand, K.A., Giovannucci, E., Kraft, P., Kricker, A., Turner, J., Ennas, M.G., Ferri, G.M., Miligi, L., Liang, L., Ma, B., Huang, J., Crouch, S., Park, J.-H., Chatterjee, N., North, K.E., Snowden, J.A., Wright, J., Fraumeni, J.F., Offit, K., Wu, X., De Sanjose, S., Cerhan, J.R., Chanock, S.J., Rothman, N., Slager, S.L., National Cancer Institute ( NIH ), Centre d'épidémiologie des populations ( CEP ), Université de Bourgogne ( UB ) -Centre Régional de Lutte contre le cancer - Centre Georges-François Leclerc ( CRLCC - CGFL ), Registre des hémopathies malignes de Côte d'Or, Mayo Clinic [Rochester], National Cancer Institute [Bethesda] (NCI-NIH), National Institutes of Health [Bethesda] (NIH), Centre d'épidémiologie des populations (CEP), Université de Bourgogne (UB)-Centre Régional de Lutte contre le cancer Georges-François Leclerc [Dijon] (UNICANCER/CRLCC-CGFL), and UNICANCER-UNICANCER

Subjects
0301 basic medicine, Medicin och hälsovetenskap, Chronic lymphocytic leukemia, General Physics and Astronomy, Genome-wide association study, VARIANTS, Medical and Health Sciences, Malalties hereditàries, [ SDV.MHEP.HEM ] Life Sciences [q-bio]/Human health and pathology/Hematology, Chronic, Genetics, RISK, Leukemia, Multidisciplinary, BANK1, VDP::Medisinske Fag: 700::Helsefag: 800::Samfunnsmedisin, sosialmedisin: 801, Bcl-2-Like Protein 11, Adaptor Proteins, [SDV.MHEP.HEM]Life Sciences [q-bio]/Human health and pathology/Hematology, Single Nucleotide, Lymphocytic, 3. Good health, PRIORITIZATION, Multidisciplinary Sciences, medicine.anatomical_structure, Science & Technology - Other Topics, TRANSCRIPTION FACTOR EOMESODERMIN, Genetic disorders, EXPRESSION, SUSCEPTIBILITY LOCI, Science, European Continental Ancestry Group, FAS GENE-MUTATIONS, Locus (genetics), Biology, Polymorphism, Single Nucleotide, General Biochemistry, Genetics and Molecular Biology, CLASSIFICATION, White People, Article, 03 medical and health sciences, Proto-Oncogene Proteins, MD Multidisciplinary, medicine, Genetic predisposition, SNP, Humans, Leucèmia limfocítica crònica, Genetic Predisposition to Disease, Polymorphism, B cell, Serpins, Genetic association, Adaptor Proteins, Signal Transducing, Science & Technology, Signal Transducing, B-Cell, Membrane Proteins, General Chemistry, medicine.disease, Leukemia, Lymphocytic, Chronic, B-Cell, 030104 developmental biology, VDP::Medical disciplines: 700::Health sciences: 800::Community medicine, Social medicine: 801, Apoptosis Regulatory Proteins, T-Box Domain Proteins, FOLLICULAR LYMPHOMA, Genome-Wide Association Study
Abstract

Chronic lymphocytic leukemia (CLL) is a common lymphoid malignancy with strong heritability. To further understand the genetic susceptibility for CLL and identify common loci associated with risk, we conducted a meta-analysis of four genome-wide association studies (GWAS) composed of 3,100 cases and 7,667 controls with follow-up replication in 1,958 cases and 5,530 controls. Here we report three new loci at 3p24.1 (rs9880772, EOMES, P=2.55 × 10−11), 6p25.2 (rs73718779, SERPINB6, P=1.97 × 10−8) and 3q28 (rs9815073, LPP, P=3.62 × 10−8), as well as a new independent SNP at the known 2q13 locus (rs9308731, BCL2L11, P=1.00 × 10−11) in the combined analysis. We find suggestive evidence (P, Chronic lymphocytic leukemia is a highly inheritable cancer. Here the authors conduct a metaanalysis of four genome-wide association studies and identify three novel loci located near EOMES, SERPINB6 and LPP associated with risk of this disease.

Published
2016

43. The chromosome 2p21 region harbors a complex genetic architecture for association with risk for renal cell carcinoma

Author

Susan M. Gapstur, Michael J. Thun, Victoria L. Stevens, Robert L. Grubb, Lee E. Moore, Summer S. Han, Kendra L. Schwartz, Philip S. Rosenberg, Mattias Johansson, Valerie Gaborieau, Ruth M. Pfeiffer, Jarmo Virtamo, Dana Mates, Lenka Foretova, Stephanie J. Weinstein, Paolo Boffetta, Christine D. Berg, Marie Navratilova, Mark P. Purdue, Vladimir Janout, Meredith Yeager, Demetrius Albanes, Ghislaine Scelo, Faith G. Davis, Ming Hui Wei, Wong Ho Chow, Ousmane Toure, James D. McKay, Jorge R. Toro, Margaret A. Tucker, Stephen J. Chanock, Vladimir Bencko, Nilanjan Chatterjee, W. Ryan Diver, Nathaniel Rothman, Joanne S. Colt, David Zaridze, Paul Brennan, Laurie Burdett, Vsevolod Matveev, Antonin Brisuda, Joseph F. Fraumeni, Neonilia Szeszenia-Dabrowska, Charles C. Chung, Han, S.S., Yeager, M., Moore, L.E., Wei, M.-H., Pfeiffer, R., Toure, O., Purdue, M.P., Johansson, M., Scelo, G., Chung, C.C., Gaborieau, V., Zaridze, D., Schwartz, K., Szeszenia-Dabrowska, N., Davis, F., Bencko, V., Colt, J.S., Janout, V., Matveev, V., Foretova, L., Mates, D., Navratilova, M., Boffetta, P., Berg, C.D., Grubb, R.L., Stevens, V.L., Thun, M.J., Diver, W.R., Gapstur, S.M., Albanes, D., Weinstein, S.J., Virtamo, J., Burdett, L., Brisuda, A., McKay, J.D., Fraumeni, J.F., Chatterjee, N., Rosenberg, P.S., Rothman, N., Brennan, P., Chow, W.-H., Tucker, M.A., Chanock, S.J., and Toro, J.R.

Subjects
Male, Genotype, Genome-wide association study, Single-nucleotide polymorphism, Locus (genetics), HapMap Project, Biology, Chromosome, Polymorphism, Single Nucleotide, Odds Ratio, Basic Helix-Loop-Helix Transcription Factors, Genetics, Humans, Genetic Predisposition to Disease, 1000 Genomes Project, International HapMap Project, Carcinoma, Renal Cell, Molecular Biology, Genetics (clinical), Allele, Genome, Association Studies Articles, Smoking, Haplotype, Renal Cell Carcinoma, Chromosome Mapping, General Medicine, Kidney Neoplasms, Haplotypes, Case-Control Studies, Chromosomes, Human, Pair 2, Single Nucleotide Polymorphism, Female, Confidence Interval, Imputation (genetics), Genome-Wide Association Study
Abstract

In follow-up of a recent genome-wide association study (GWAS) that identified a locus in chromosome 2p21 associated with risk for renal cell carcinoma (RCC), we conducted a fine mapping analysis of a 120 kb region that includes EPAS1. We genotyped 59 tagged common single-nucleotide polymorphisms (SNPs) in 2278 RCC and 3719 controls of European background and observed a novel signal for rs9679290 [P=5 5.75× 3 10 -8, per-allele odds ratio (OR) = 1.27, 95% confidence interval (CI): 1.17-1.39]. Imputation of common SNPs surrounding rs9679290 using HapMap 3 and 1000 Genomes data yielded two additional signals, rs4953346 (P = 4.09 × 10 -14) and rs12617313 (P = 7.48 × 10 -12), both highly correlated withrs9679290 (r 2 > 0.95), but interestingly not correlated with the two SNPs reported in the GWAS: rs11894252 and rs7579899 (r 2 < 0.1 with rs9679290). Genotype analysis of rs12617313 confirmed an association with RCC risk (P = 1.72 × 10 -9, per-allele OR = 1.28, 95% CI: 1.18-1.39) In conclusion, we report that chromosome 2p21 harbors a complex genetic architecture for common RCC risk variants. Published by Oxford University Press 2011.

Published
2011

44. Genome-wide association study identifies multiple susceptibility loci for diffuse large B cell lymphoma

Author

Lenka Foretova, Sophia S. Wang, Hans-Olov Adami, Demetrius Albanes, Andrew D. Zelenetz, Emanuele Angelucci, Paige M. Bracci, Hervé Tilly, Hervé Ghesquières, John J. Spinelli, Kimberly A. Bertrand, Francine Laden, Rebecca D. Jackson, Wendy Cozen, Anne J. Novak, Charles C. Chung, Meredith Yeager, Brian C.-H. Chiu, Jenny Turner, Melissa C. Southey, Gianluca Severi, Simonetta Di Lollo, Lindsay M. Morton, Mark Liebow, Theodore R. Holford, Paolo Boffetta, Paul I.W. de Bakker, Joseph Vijai, Claire M. Vajdic, Anne Kricker, Mark P. Purdue, Stephanie J. Weinstein, Ahmet Dogan, Alain Monnereau, Patricia Hartge, Degui Zhi, Amy K. Hutchinson, Brenda M. Birmann, Charles Lawrence, Elizabeth A. Holly, Marco Rais, Anneclaire J. De Roos, Karin E. Smedby, Sonja I. Berndt, Stephen J. Chanock, Lucia Conde, Stephen M. Ansell, Yan W. Asmann, Yuanqing Ye, David G. Cox, Elio Riboli, Joseph F. Fraumeni, Christine F. Skibola, Christopher R. Flowers, Angela Brooks-Wilson, Amelie S. Veron, Jarmo Virtamo, Danylo J. Villano, Thierry Jo Molina, W. Ryan Diver, James D. McKay, Kenneth Offit, Eve Roman, Jinyan Huang, Xifeng Wu, Marc Maynadie, Yolanda Benavente, Baoshan Ma, Brian K. Link, Thomas E. Witzig, Mads Melbye, George J. Weiner, Zhaoming Wang, Corinne Haioun, Alex Smith, Anthony Staines, Anne Zeleniuch-Jacquotte, Martyn T. Smith, Paul Brennan, Nilanjan Chatterjee, Tracy Lightfoot, Eleanor Kane, Bengt Glimelius, Ju-Hyun Park, Robert J. Klein, Alexandra Nieters, Heiner Boeing, Mariagrazia Zucca, Nathaniel Rothman, Jacqueline Clavel, Qing Lan, Susan L. Slager, Rudolph Kaaks, Diana Zelenika, Nikolaus Becker, Henrik Hjalgrim, Rachel S. Kelly, Roel Vermeulen, Graham G. Giles, Anne Tjønneland, Carrie A. Thompson, Laurie Burdett, Richard K. Severson, Dimitrios Trichopoulos, Yawei Zhang, Kari E. North, Tongzhang Zheng, Jian Gu, Edward Giovannucci, Jacques Riby, Simon Crouch, Gilles Salles, Silvia de Sanjosé, Dennis D. Weisenburger, Thomas M. Habermann, Paolo Vineis, Lesley F. Tinker, Joshua N. Sampson, Liming Liang, Peter Kraft, James R. Cerhan, Lauren R. Teras, Cerhan, J.R., Berndt, S.I., Vijai, J., Ghesquières, H., McKay, J., Wang, S.S., Wang, Z., Yeager, M., Conde, L., De Bakker, P.I.W., Nieters, A., Cox, D., Burdett, L., Monnereau, A., Flowers, C.R., De Roos, A.J., Brooks-Wilson, A.R., Lan, Q., Severi, G., Melbye, M., Gu, J., Jackson, R.D., Kane, E., Teras, L.R., Purdue, M.P., Vajdic, C.M., Spinelli, J.J., Giles, G.G., Albanes, D., Kelly, R.S., Zucca, M., Bertrand, K.A., Zeleniuch-Jacquotte, A., Lawrence, C., Hutchinson, A., Zhi, D., Habermann, T.M., Link, B.K., Novak, A.J., Dogan, A., Asmann, Y.W., Liebow, M., Thompson, C.A., Ansell, S.M., Witzig, T.E., Weiner, G.J., Veron, A.S., Zelenika, D., Tilly, H., Haioun, C., Molina, T.J., Hjalgrim, H., Glimelius, B., Adami, H.-O., Bracci, P.M., Riby, J., Smith, M.T., Holly, E.A., Cozen, W., Hartge, P., Morton, L.M., Severson, R.K., Tinker, L.F., North, K.E., Becker, N., Benavente, Y., Boffetta, P., Brennan, P., Foretova, L., Maynadie, M., Staines, A., Lightfoot, T., Crouch, S., Smith, A., Roman, E., Diver, W.R., Offit, K., Zelenetz, A., Klein, R.J., Villano, D.J., Zheng, T., Zhang, Y., Holford, T.R., Kricker, A., Turner, J., Southey, M.C., Clavel, J., Virtamo, J., Weinstein, S., Riboli, E., Vineis, P., Kaaks, R., Trichopoulos, D., Vermeulen, R.C.H., Boeing, H., Tjonneland, A., Angelucci, E., Di Lollo, S., Rais, M., Birmann, B.M., Laden, F., Giovannucci, E., Kraft, P., Huang, J., Ma, B., Ye, Y., Chiu, B.C.H., Sampson, J., Liang, L., Park, J.-H., Chung, C.C., Weisenburger, D.D., Chatterjee, N., Fraumeni, J.F., Slager, S.L., Wu, X., De Sanjose, S., Smedby, K.E., Salles, G., Skibola, C.F., Rothman, N., and Chanock, S.J.

Subjects
Limfomes, Genotype, Chronic lymphocytic leukemia, Cèl·lules B, Quantitative Trait Loci, Population, Follicular lymphoma, Genome-wide association study, Single-nucleotide polymorphism, Biology, Polymorphism, Single Nucleotide, Article, White People, Genetics, Genetic predisposition, medicine, Humans, Genetic Predisposition to Disease, education, Genetic association, Likelihood Functions, education.field_of_study, B cells, Chromosome Mapping, Computational Biology, medicine.disease, Genetic Loci, large B cell lymphoma (DLBCL), Lymphomas, Lymphoma, Large B-Cell, Diffuse, Diffuse large B-cell lymphoma, Genome-Wide Association Study
Abstract

Diffuse large B cell lymphoma (DLBCL) is the most common lymphoma subtype and is clinically aggressive. To identify genetic susceptibility loci for DLBCL, we conducted a meta-analysis of 3 new genome-wide association studies (GWAS) and 1 previous scan, totaling 3,857 cases and 7,666 controls of European ancestry, with additional genotyping of 9 promising SNPs in 1,359 cases and 4,557 controls. In our multi-stage analysis, five independent SNPs in four loci achieved genome-wide significance marked by rs116446171 at 6p25.3 (EXOC2; P = 2.33 × 10 '21), rs2523607 at 6p21.33 (HLA-B; P = 2.40 × 10 '10), rs79480871 at 2p23.3 (NCOA1; P = 4.23 × 10 '8) and two independent SNPs, rs13255292 and rs4733601, at 8q24.21 (PVT1; P = 9.98 × 10 '13 and 3.63 × 10 '11, respectively). These data provide substantial new evidence for genetic susceptibility to this B cell malignancy and point to pathways involved in immune recognition and immune function in the pathogenesis of DLBCL. © 2014 Nature America, Inc. All rights reserved.

Published
2014

45. A multi-stage genome-wide association study of bladder cancer identifies multiple susceptibility loci

Author

Rajesh Kumar, Gerald L. Andriole, Robert L. Grubb, Monica McGrath, Amanda Black, Manuela Gago-Dominguez, Margaret A. Knowles, Francisco X. Real, Nilanjan Chatterjee, Thorunn Rafnar, Kevin B. Jacobs, Silvia Polidoro, Debra T. Silverman, Sita H. Vermeulen, Manuel Sanchez, Núria Malats, Salvatore Panico, Amy Hutchinson, William Wheeler, Carmen Navarro, Montserrat Garcia-Closas, Carlotta Sacerdote, Gabriel Valdivia, Yi-Ping Fu, Kari Stefansson, Michelle A.T. Hildebrandt, Alessandra Allione, Katja K.H. Aben, Alison Johnson, W. Ryan Diver, Laurie Burdett, Sophia C.E. Bolick, David J. Hunter, Jarmo Virtamo, Jack A. Taylor, Ludmila Prokunina-Olsson, José I Sanz-Velez, Mark P. Purdue, Fulvio Ricceri, Elio Riboli, Maria Teresa Landi, Susan M. Gapstur, Søren Besenbacher, Joseph F. Fraumeni, Olivier Cussenot, J. Alfred Witjes, Victoria K. Cortessis, Paul Brennan, Tony Fletcher, David Van Den Berg, Börje Ljungberg, Lambertus A. Kiemeney, Dalsu Baris, Mark Teo, Zongli Xu, Geraldine Cancel-Tassin, Holger Dietrich, Zhaoming Wang, Maria D. Garcia-Prats, Françoise Clavel-Chapelon, Adonina Tardón, Paolo Vineis, Peter Rudnai, Margaret R. Karagas, Naomi E. Allen, H. Bas Bueno-de-Mesquita, Molly Schwenn, Jose I. Mayordomo, Ashley C. Godfrey, Manolis Kogevinas, Silvia Selinski, Stephen J. Chanock, Jonine D. Figueroa, Alan R. Schned, Stefano Porru, Mariana C. Stern, Demetrius Albanes, Simonetta Guarrera, Patrick Sulem, Immaculata De Vivo, Hushan Yang, Robert N. Hoover, Kvetoslava Koppova, Michael J. Thun, Malcolm C. Pike, Giuseppe Matullo, D T Bishop, Neil E. Caporaso, Klaus Golka, Eugen Gurzau, Colin P.N. Dinney, Josep Lloreta, Nathaniel Rothman, Eric J. Jacobs, Simone Benhamou, Alfredo Carrato, Federico Canzian, Xifeng Wu, Consol Serra, Anne Tjønneland, Jian-Min Yuan, Meredith Yeager, Reina García-Closas, Stephanie J. Weinstein, Jan G. Hengstler, Dimitrios Trichopoulos, Remco R. R. Makkinje, Anne E. Kiltie, Bogdan Czerniak, Meng Chen, Rothman, N, Garcia Closas, M, Chatterjee, N, Malats, N, Wu, X, Figueroa, Jd, Real, Fx, Van Den Berg, D, Matullo, G, Baris, D, Thun, M, Kiemeney, La, Vineis, P, De Vivo, I, Albanes, D, Purdue, Mp, Rafnar, T, Hildebrandt, Ma, Kiltie, Ae, Cussenot, O, Golka, K, Kumar, R, Taylor, Ja, Mayordomo, Ji, Jacobs, Kb, Kogevinas, M, Hutchinson, A, Wang, Z, Fu, Yp, Prokunina Olsson, L, Burdett, L, Yeager, M, Wheeler, W, Tardón, A, Serra, C, Carrato, A, García Closas, R, Lloreta, J, Johnson, A, Schwenn, M, Karagas, Mr, Schned, A, Andriole G., Jr, Grubb R., 3rd, Black, A, Jacobs, Ej, Diver, Wr, Gapstur, Sm, Weinstein, Sj, Virtamo, J, Cortessis, Vk, Gago Dominguez, M, Pike, Mc, Stern, Mc, Yuan, Jm, Hunter, Dj, Mcgrath, M, Dinney, Cp, Czerniak, B, Chen, M, Yang, H, Vermeulen, Sh, Aben, Kk, Witjes, Ja, Makkinje, Rr, Sulem, P, Besenbacher, S, Stefansson, K, Riboli, E, Brennan, P, Panico, Salvatore, Navarro, C, Allen, Ne, Bueno de Mesquita, Hb, Trichopoulos, D, Caporaso, Nicola, Landi, Mt, Canzian, F, Ljungberg, B, Tjonneland, A, Clavel Chapelon, F, Bishop, Dt, Teo, Mt, Knowles, Ma, Guarrera, S, Polidoro, S, Ricceri, F, Sacerdote, C, Allione, A, Cancel Tassin, G, Selinski, S, Hengstler, Jg, Dietrich, H, Fletcher, T, Rudnai, P, Gurzau, E, Koppova, K, Bolick, Sc, Godfrey, A, Xu, Z, Sanz Velez, Ji, D., García Prats M, Sanchez, M, Valdivia, G, Porru, S, Benhamou, S, Hoover, Rn, Fraumeni JF, Jr, Silverman, Dt, and Chanock, Sj

Subjects
Male, Arylamine N-Acetyltransferase, Chromosomes, Human, Pair 22, Genome-wide association study, Aetiology, screening and detection [ONCOL 5], medicine.disease_cause, Genome-wide association studies, Risk Factors, genome-wide association, bladder cancer, Psychology, Genetics, Sex Characteristics, Incidence, Bladder cancer, Smoking, Chromosome Mapping, Single Nucleotide, Tag SNP, Europe, Chromosomes, Human, Pair 2, Pair 2, Female, Human, Locus (genetics), Single-nucleotide polymorphism, Biology, Polymorphism, Single Nucleotide, Risk Assessment, Chromosomes, Article, Molecular epidemiology [NCEBP 1], Translational research [ONCOL 3], medicine, Humans, Family, Genetic Predisposition to Disease, Polymorphism, Pair 18, Pair 22, Genome-Wide Association Study, Neoplasm Staging, Spain, United States, Urinary Bladder Neoplasms, Cancer, Chromosome, medicine.disease, Evaluation of complex medical interventions [NCEBP 2], Carcinogenesis, Chromosomes, Human, Pair 18
Abstract

We conducted a multi-stage, genome-wide association study of bladder cancer with a primary scan of 591,637 SNPs in 3,532 affected individuals (cases) and 5,120 controls of European descent from five studies followed by a replication strategy, which included 8,382 cases and 48,275 controls from 16 studies. In a combined analysis, we identified three new regions associated with bladder cancer on chromosomes 22q13.1, 19q12 and 2q37.1: rs1014971, (P = 8 × 10⁻¹²) maps to a non-genic region of chromosome 22q13.1, rs8102137 (P = 2 × 10⁻¹¹) on 19q12 maps to CCNE1 and rs11892031 (P = 1 × 10⁻⁷) maps to the UGT1A cluster on 2q37.1. We confirmed four previously identified genome-wide associations on chromosomes 3q28, 4p16.3, 8q24.21 and 8q24.3, validated previous candidate associations for the GSTM1 deletion (P = 4 × 10⁻¹¹) and a tag SNP for NAT2 acetylation status (P = 4 × 10⁻¹¹), and found interactions with smoking in both regions. Our findings on common variants associated with bladder cancer risk should provide new insights into the mechanisms of carcinogenesis.

Published
2010

46. Analysis of Heritability and Shared Heritability Based on Genome-Wide Association Studies for Thirteen Cancer Types

Author

Yeul Hong Kim, Sonja I. Berndt, José María Huerta, Morgan Rouprêt, Reury Perng Perng, Yi Young Choi, Lindsay M. Morton, Roberto Tirabosco, H. Bas Bueno-de-Mesquita, Wendy Cozen, Neil E. Caporaso, Stephen J. Chanock, Zhenhong Zhao, Dina Halai, Neyssa Marina, Ann L. Oberg, Stephen M. Ansell, Zhibin Hu, Donghui Li, Anne J. Novak, Jenny Turner, Wen Tan, Julie E. Buring, Stefano Porru, Qincheng He, Tania Carreón, Guoping Wu, Graham G. Giles, Claire M. Vajdic, Rudolf Kaaks, Ulrika Andersson, Susan L. Slager, Jen Yu Hung, Luis Sierrasesúmaga, Roel Vermeulen, Louise A. Brinton, Myron D. Gross, Jennifer Prescott, E. Lund, Chih Yi Chen, Jin Eun Choi, Chaoyu Wang, George J. Weiner, H. Dean Hosgood, Haixin Li, Carrie A. Thompson, Núria Malats, James McKay, Stephanie J. Weinstein, Young Tae Kim, Emily White, Pan-Chyr Yang, Orestis A. Panagiotou, Robert J. Klein, Joseph Vijai, Josep Lloreta, Immaculata De Vivo, Sofia Pavanello, Thomas E. Witzig, Montserrat Garcia-Closas, Roger Henriksson, Bryan A. Bassig, Tait D. Shanafelt, Rachel S. Kelly, Joseph M. Connors, Marco Rais, Wu Chou Su, Alex Smith, John J. Spinelli, Julie M. Gastier-Foster, Anne Kricker, In Kyu Park, Marc J. Gunter, Chancellor Hohensee, Simon Crouch, Jarmo Virtamo, M. G. Ennas, Lucia Conde, Lotte Maxild Mortensen, Lenka Foretova, Eric J. Duell, Anthony Staines, Hongyan Chen, Baosen Zhou, Brian M. Wolpin, Simone Benhamou, Zhaoming Wang, Françoise Clavel-Chapelon, Charles C. Chung, Nan Hu, Domenico Palli, Rebecca Montalvan, Thomas M. Habermann, Debra T. Silverman, Preetha Rajaraman, Christian C. Abnet, Wei-Yen Lim, Yuh Min Chen, Michelle Cotterchio, Lucia Miligi, Claudia Maria Hattinger, Eve Roman, Christopher Kim, Federico Canzian, Alan D. L. Sihoe, Sharon A. Savage, Mark P. Purdue, Maria Teresa Landi, Susan M. Gapstur, M Zucca, Yuanqing Ye, Jian Su, Chong-Jen Yu, Edward Giovannucci, Alain Monnereau, Afshan Siddiq, Ralph L. Erickson, Katherine A. McGlynn, Petra H.M. Peeters, W. Ryan Diver, David Van Den Berg, Gloria M. Petersen, Judith Hoffman-Bolton, Xiao-Ou Shu, Ying Chen, Eric J. Jacobs, Heiner Boeing, Sophia S. Wang, Hans-Olov Adami, Yuqing Li, Jacqueline Clavel, Ellen T. Chang, Tongzhang Zheng, William Pao, Hideo Kunitoh, Ulrike Peters, Jenny Chang-Claude, Alexandra Nieters, Silvia de Sanjosé, Chen Wu, Anders Ahlbom, Jun Suk Kim, Fredrick R. Schumacher, Roberta McKean-Cowdin, Laurence N. Kolonel, Herbert Yu, Li Liu, Vittorio Krogh, Tangchun Wu, Ho Il Yoon, Joseph F. Fraumeni, Olivier Cussenot, Jae Sook Sung, Kari E. North, Andrew D. Zelenetz, Ana Patiño-García, Anne Zeleniuch-Jacquotte, Christopher A. Haiman, Biyun Qian, Giovanni Maria Ferri, Rebecca Rodabough, Xifeng Wu, Maria Feychting, Kuan-Yu Chen, Laure Dossus, Jianjun Liu, Jean Wactawski-Wende, Constance Chen, Robert L. Grubb, Paolo Vineis, Mads Melbye, Chien Chung Lin, Malin Sund, Wei Zheng, Jun Xu, Yi Song Chen, Kay-Tee Khaw, Richard K. Severson, Kun-Chieh Chen, Jian-Min Yuan, Bu Tian Ji, Simonetta Di Lollo, Ping Xu, Howard D. Sesso, Yoo Jin Jung, Margaret R. Karagas, Piero Picci, Gianluca Severi, Margaret A. Tucker, Ti Ding, Gee-Chen Chang, Li Hsin Chien, She-Juan An, Maria Pik Wong, Chien-Jen Chen, Jonine D. Figueroa, Sun-Seog Kweon, Katia Scotlandi, Sara H. Olson, Kendra Schwartz, Chang Hyun Kang, Marta Crous-Bou, Yawei Zhang, Ludmila Prokunina-Olsson, Yolanda Benavente, Christine D. Berg, Kala Visvanathan, Loic Le Marchand, Takashi Kohno, Nilanjan Chatterjee, Tracy Lightfoot, Zhihua Yin, Lee E. Moore, Joanne S. Colt, Laurie Burdett, Tetsuya Mitsudomi, Harvey A. Risch, Alfredo Carrato, Hyo Sung Jeon, Victoria L. Stevens, Richard Gorlick, Danylo J. Villano, Alison P. Klein, Angela Brooks-Wilson, Joshua N. Sampson, Chu Chen, You-Lin Qiao, Kouya Shiraishi, Alan R. Schned, Dominique S. Michaud, Peng Guan, Philip R. Taylor, Gerald L. Andriole, John K.C. Chan, Eva Comperat, Randy D. Gascoyne, Marc Maynadie, Kyong Hwa Park, Amanda Black, Charles Kooperberg, Andrea La Croix, Kenneth Offit, Peter Kraft, David Thomas, Manuela Gago-Dominguez, Manolis Kogevinas, Theodore R. Holford, Pamela L. Horn-Ross, Xingzhou He, Massimo Serra, Satu Männistö, Christoffer Johansen, Meredith Yeager, Robert N. Hoover, Mary Ann Butler, William Wheeler, Jian Gu, Wei Wu, Ying Hsiang Chen, Leslie Bernstein, Yao Jen Li, David J. Hunter, In-Jae Oh, Jay S. Wunder, Meng Zhu, Henrik Hjalgrim, Martyn T. Smith, Alisa M. Goldstein, Linda M. Liao, Chao Agnes Hsiung, Ruth C. Travis, Jiucun Wang, Marie-Christine Boutron-Ruault, Daru Lu, Reina García-Closas, Avima M. Ruder, Martha S. Linet, Wei Tang, Geraldine Cancel-Tassin, Brian K. Link, Rebecca D. Jackson, J. Michael Gaziano, Malcolm C. Pike, Yu-Tang Gao, Lisa Mirabello, Alan A. Arslan, Hong Zheng, Nicolas Wentzensen, Chung Hsing Chen, I. Shou Chang, Meir J. Stampfer, Brenda M. Birmann, Alison Johnson, Wong-Ho Chow, Chin-Fu Hsiao, Neal D. Freedman, Robert C. Kurtz, Donald A. Barkauskas, Steven Gallinger, Junwen Wang, Simina M. Boca, Irene L. Andrulis, Hongbing Shen, Adrienne M. Flanagan, Cosmeri Rizzato, Marianna C. Stern, Angela Carta, Melissa C. Southey, Corrado Magnani, Sook Whan Sung, Lesley F. Tinker, M. Dorronsoro, Guangfu Jin, Giovanna Masala, Yi-Long Wu, Min-Ho Shin, Ming Shyan Huang, Göran Hallmans, Xueying Zhao, Jacques Riby, Beatrice Melin, Adonina Tardón, Börje Ljungberg, Mark Liebow, Elizabeth A. Holly, Carol Giffen, Paolo Boffetta, Maria Fernanda Amary, Jihua Li, Mazda Jenab, Keitaro Matsuo, Nalan Gokgoz, Karin E. Smedby, Cari M. Kitahara, Mia M. Gaudet, Cecilia Arici, Brian E. Henderson, Amy Hutchinson, Elio Riboli, Patricia Hartge, Victoria K. Cortessis, Kexin Chen, Dalsu Baris, Michael Goggins, Young-Chul Kim, Tsung-Ying Yang, Fusheng Wei, Peter D. Inskip, Demetrius Albanes, Fang Yu Tsai, Qing Lan, Li Jin, Charles E. Lawrence, Nikolaus Becker, Rachael S. Stolzenberg-Solomon, Bengt Glimelius, Wei Hu, Maria Dolores Chirlaque, Kimberly A. Bertrand, Bruce K. Armstrong, Veronica Wendy Setiawan, Kathy J. Helzlsouer, Manal M. Hassan, Jun Yokota, David V. Conti, Kai Yu, Chenwei Liu, Christine F. Skibola, Jae Yong Park, Fernando Lecanda, Dimitrios Trichopoulos, Eleanor Kane, Dongxin Lin, Yun-Chul Hong, Consol Serra, Anne Tjønneland, Melissa A. Austin, X. Zhang, Charles S. Fuchs, Nathaniel Rothman, Paul Brennan, Chih-Liang Wang, Wei Shen, Ying-Huang Tsai, Hee Nam Kim, Ghislaine Scelo, Faith G. Davis, Sara Lindström, Molly Schwenn, Giuseppe Mastrangelo, Adeline Seow, Laufey T. Amundadottir, Laura E. Beane Freeman, Huan Guo, Victor Ho-Fun Lee, Aruna Kamineni, Pierluigi Cocco, Jiang Chang, Emanuele Angelucci, Paige M. Bracci, Yong-Bing Xiang, G. M. Monawar Hosain, Elisabete Weiderpass, James R. Cerhan, Junjie Wu, Lauren R. Teras, Jin Hee Kim, Qiuyin Cai, Sampson, J.N., Wheeler, W.A., Yeager, M., Panagiotou, O., Wang, Z., Berndt, S.I., Lan, Q., Abnet, C.C., Amundadottir, L.T., Figueroa, J.D., Landi, M.T., Mirabello, L., Savage, S.A., Taylor, P.R., De Vivo, I., McGlynn, K.A., Purdue, M.P., Rajaraman, P., Adami, H.-O., Ahlbom, A., Albanes, D., Amary, M.F., An, S.-J., Andersson, U., Andriole, G., Jr., Andrulis, I.L., Angelucci, E., Ansell, S.M., Arici, C., Armstrong, B.K., Arslan, A.A., Austin, M.A., Baris, D., Barkauskas, D.A., Bassig, B.A., Becker, N., Benavente, Y., Benhamou, S., Berg, C., Van Den Berg, D., Bernstein, L., Bertrand, K.A., Birmann, B.M., Black, A., Boeing, H., Boffetta, P., Boutron-Ruault, M.-C., Bracci, P.M., Brinton, L., Brooks-Wilson, A.R., Bueno-De-Mesquita, H.B., Burdett, L., Buring, J., Butler, M.A., Cai, Q., Cancel-Tassin, G., Canzian, F., Carrato, A., Carreon, T., Carta, A., Chan, J.K.C., Chang, E.T., Chang, G.-C., Chang, I.S., Chang, J., Chang-Claude, J., Chen, C.-J., Chen, C.-Y., Chen, C., Chen, C.-H., Chen, H., Chen, K., Chen, K.-Y., Chen, K.-C., Chen, Y., Chen, Y.-H., Chen, Y.-S., Chen, Y.-M., Chien, L.-H., Chirlaque, M.-D., Choi, J.E., Choi, Y.Y., Chow, W.-H., Chung, C.C., Clavel, J., Clavel-Chapelon, F., Cocco, P., Colt, J.S., Comperat, E., Conde, L., Connors, J.M., Conti, D., Cortessis, V.K., Cotterchio, M., Cozen, W., Crouch, S., Crous-Bou, M., Cussenot, O., Davis, F.G., Ding, T., Diver, W.R., Dorronsoro, M., Dossus, L., Duell, E.J., Ennas, M.G., Erickson, R.L., Feychting, M., Flanagan, A.M., Foretova, L., Fraumeni, J.F., Jr., Freedman, N.D., Freeman, L.E.B., Fuchs, C., Gago-Dominguez, M., Gallinger, S., Gao, Y.-T., Gapstur, S.M., Garcia-Closas, M., García-Closas, R., Gascoyne, R.D., Gastier-Foster, J., Gaudet, M.M., Gaziano, J.M., Giffen, C., Giles, G.G., Giovannucci, E., Glimelius, B., Goggins, M., Gokgoz, N., Goldstein, A.M., Gorlick, R., Gross, M., Grubb, R., III and Gu, J., Guan, P., Gunter, M., Guo, H., Habermann, T.M., Haiman, C.A., Halai, D., Hallmans, G., Hassan, M., Hattinger, C., He, Q., He, X., Helzlsouer, K., Henderson, B., Henriksson, R., Hjalgrim, H., Hoffman-Bolton, J., Hohensee, C., Holford, T.R., Holly, E.A., Hong, Y.-C., Hoover, R.N., Horn-Ross, P.L., Hosain, G.M.M., Hosgood, H.D., III and Hsiao, C.-F., Hu, N., Hu, W., Hu, Z., Huang, M.-S., Huerta, J.-M., Hung, J.-Y., Hutchinson, A., Inskip, P.D., Jackson, R.D., Jacobs, E.J., Jenab, M., Jeon, H.-S., Ji, B.-T., Jin, G., Jin, L., Johansen, C., Johnson, A., Jung, Y.J., Kaaks, R., Kamineni, A., Kane, E., Kang, C.H., Karagas, M.R., Kelly, R.S., Khaw, K.-T., Kim, C., Kim, H.N., Kim, J.H., Kim, J.S., Kim, Y.H., Kim, Y.T., Kim, Y.-C., Kitahara, C.M., Klein, A.P., Klein, R.J., Kogevinas, M., Kohno, T., Kolonel, L.N., Kooperberg, C., Kricker, A., Krogh, V., Kunitoh, H., Kurtz, R.C., Kweon, S.-S., La Croix, A., Lawrence, C., Lecanda, F., Lee, V.H.F., Li, D., Li, H., Li, J., Li, Y.-J., Li, Y., Liao, L.M., Liebow, M., Lightfoot, T., Lim, W.-Y., Lin, C.-C., Lin, D., Lindstrom, S., Linet, M.S., Link, B.K., Liu, C., Liu, J., Liu, L., Ljungberg, B., Lloreta, J., Di Lollo, S., Lu, D., Lund, E., Malats, N., Mannisto, S., Marchand, L.L., Marina, N., Masala, G., Mastrangelo, G., Matsuo, K., Maynadie, M., McKay, J., McKean-Cowdin, R., Melbye, M., Melin, B.S., Michaud, D.S., Mitsudomi, T., Monnereau, A., Montalvan, R., Moore, L.E., Mortensen, L.M., Nieters, A., North, K.E., Novak, A.J., Oberg, A.L., Offit, K., Oh, I.-J., Olson, S.H., Palli, D., Pao, W., Park, I.K., Park, J.Y., Park, K.H., Patiño-Garcia, A., Pavanello, S., Peeters, P.H.M., Perng, R.-P., Peters, U., Petersen, G.M., Picci, P., Pike, M.C., Porru, S., Prescott, J., Prokunina-Olsson, L., Qian, B., Qiao, Y.-L., Rais, M., Riboli, E., Riby, J., Risch, H.A., Rizzato, C., Rodabough, R., Roman, E., Roupret, M., Ruder, A.M., De Sanjose, S., Scelo, G., Schned, A., Schumacher, F., Schwartz, K., Schwenn, M., Scotlandi, K., Seow, A., Serra, C., Serra, M., Sesso, H.D., Setiawan, V.W., Severi, G., Severson, R.K., 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Subjects
Male, Cancer Research, Lung Neoplasms, Lymphoma, Genome-wide association study, Polymorphism (computer science), Neoplasms, Medicine, Chronic, Genetics, Osteosarcoma, Oncology And Carcinogenesis, Leukemia, Smoking, Family aggregation, Single Nucleotide, Middle Aged, Familial risk, Diffuse, Kidney Neoplasms, Lymphocytic, Oncology, Adult, Aged, Asian Continental Ancestry Group, Bone Neoplasms, European Continental Ancestry Group, Female, Humans, Leukemia, Lymphocytic, Chronic, B-Cell, Lymphoma, Large B-Cell, Diffuse, Polymorphism, Single Nucleotide, Testicular Neoplasms, Tissue Array Analysis, Urinary Bladder Neoplasms, Genetic Predisposition to Disease, Genome-Wide Association Study, Genetic correlation, Large B-Cell, Oncology & Carcinogenesis, Polymorphism, business.industry, Extramural, B-Cell, Cancer, Heritability, Genome-wide association studies for thirteen cancer types, medicine.disease, business
Abstract

BACKGROUND: Studies of related individuals have consistently demonstrated notable familial aggregation of cancer. We aim to estimate the heritability and genetic correlation attributable to the additive effects of common single-nucleotide polymorphisms (SNPs) for cancer at 13 anatomical sites.METHODS: Between 2007 and 2014, the US National Cancer Institute has generated data from genome-wide association studies (GWAS) for 49 492 cancer case patients and 34 131 control patients. We apply novel mixed model methodology (GCTA) to this GWAS data to estimate the heritability of individual cancers, as well as the proportion of heritability attributable to cigarette smoking in smoking-related cancers, and the genetic correlation between pairs of cancers.RESULTS: GWAS heritability was statistically significant at nearly all sites, with the estimates of array-based heritability, hl (2), on the liability threshold (LT) scale ranging from 0.05 to 0.38. Estimating the combined heritability of multiple smoking characteristics, we calculate that at least 24% (95% confidence interval [CI] = 14% to 37%) and 7% (95% CI = 4% to 11%) of the heritability for lung and bladder cancer, respectively, can be attributed to genetic determinants of smoking. Most pairs of cancers studied did not show evidence of strong genetic correlation. We found only four pairs of cancers with marginally statistically significant correlations, specifically kidney and testes (ρ = 0.73, SE = 0.28), diffuse large B-cell lymphoma (DLBCL) and pediatric osteosarcoma (ρ = 0.53, SE = 0.21), DLBCL and chronic lymphocytic leukemia (CLL) (ρ = 0.51, SE =0.18), and bladder and lung (ρ = 0.35, SE = 0.14). Correlation analysis also indicates that the genetic architecture of lung cancer differs between a smoking population of European ancestry and a nonsmoking Asian population, allowing for the possibility that the genetic etiology for the same disease can vary by population and environmental exposures.CONCLUSION: Our results provide important insights into the genetic architecture of cancers and suggest new avenues for investigation.

Published
2015

47. Diversity in the Glucose Transporter-4 Gene (SLC2A4) in Humans Reflects the Action of Natural Selection along the Old-World Primates Evolution

Author

Laurie Burdett, Meredith Yeager, Wagner C. S. Magalhães, Davide Pettener, Stephen J. Chanock, Andrew Crenshaw, Cristina Fabbri, Eduardo Tarazona-Santos, Tarazona-Santos E, Fabbri C, Yeager M, Magalhaes WC, Burdett L, Crenshaw A, Pettener D, and Chanock SJ

Subjects
SLC2A4, Genotype, Pan troglodytes, medicine.medical_treatment, lcsh:Medicine, Adipose tissue, Evolution, Molecular, Genetics and Genomics/Population Genetics, Ethnicity, medicine, Animals, Humans, Insulin, Glucose homeostasis, lcsh:Science, Muscle, Skeletal, Gene, HUMAN EVOLUTION AND BIODIVERSITY, SNPS, Genetics, Evolutionary Biology, Glucose Transporter Type 4, Multidisciplinary, biology, Myocardium, lcsh:R, Glucose transporter, Genetic Variation, Skeletal muscle, Genetics and Genomics, Transporter, Sequence Analysis, DNA, Macaca mulatta, Protein Structure, Tertiary, Evolutionary Biology/Human Evolution, medicine.anatomical_structure, Adipose Tissue, biology.protein, GLUCOSE TRANSPORTERS, lcsh:Q, GLUT4, NATURAL SELECTION, Research Article
Abstract

Background: Glucose is an important source of energy for living organisms. In vertebrates it is ingested with the diet and transported into the cells by conserved mechanisms and molecules, such as the trans-membrane Glucose Transporters (GLUTs). Members of this family have tissue specific expression, biochemical properties and physiologic functions that together regulate glucose levels and distribution. GLUT4 –coded by SLC2A4 (17p13) is an insulin-sensitive transporter with a critical role in glucose homeostasis and diabetes pathogenesis, preferentially expressed in the adipose tissue, heart muscle and skeletal muscle. We tested the hypothesis that natural selection acted on SLC2A4. Methodology/Principal Findings: We re-sequenced SLC2A4 and genotyped 104 SNPs along a ,1 Mb region flanking this gene in 102 ethnically diverse individuals. Across the studied populations (African, European, Asian and Latin-American), all the eight common SNPs are concentrated in the N-terminal region upstream of exon 7 (,3700 bp), while the C-terminal region downstream of intron 6 (,2600 bp) harbors only 6 singletons, a pattern that is not compatible with neutrality for this part of the gene. Tests of neutrality based on comparative genomics suggest that: (1) episodes of natural selection (likely a selective sweep) predating the coalescent of human lineages, within the last 25 million years, account for the observed reduced diversity downstream of intron 6 and, (2) the target of natural selection may not be in the SLC2A4 coding sequence. Conclusions: We propose that the contrast in the pattern of genetic variation between the N-terminal and C-terminal regions are signatures of the action of natural selection and thus follow-up studies should investigate the functional importance of differnet regions of the SLC2A4 gene.

Published
2010

48. Somatic mutations in 3929 HPV positive cervical cells associated with infection outcome and HPV type.

Author

Pinheiro M, Wentzensen N, Dean M, Yeager M, Chen Z, Shastry A, Boland JF, Bass S, Burdett L, Lorey T, Mishra S, Castle PE, Schiffman M, Burk RD, Zhu B, and Mirabello L

Subjects
Humans, Female, Adult, Middle Aged, Papillomaviridae genetics, Human papillomavirus 16 genetics, Human papillomavirus 16 isolation & purification, High-Throughput Nucleotide Sequencing, Uterine Cervical Dysplasia virology, Uterine Cervical Dysplasia genetics, Uterine Cervical Dysplasia pathology, Uterine Cervical Neoplasms virology, Uterine Cervical Neoplasms genetics, Uterine Cervical Neoplasms pathology, Papillomavirus Infections virology, Papillomavirus Infections genetics, Mutation, Cervix Uteri virology, Cervix Uteri pathology
Abstract

Invasive cervical cancers (ICC), caused by HPV infections, have a heterogeneous molecular landscape. We investigate the detection, timing, and HPV type specificity of somatic mutations in 3929 HPV-positive exfoliated cervical cell samples from individuals undergoing cervical screening in the U.S. using deep targeted sequencing in ICC cases, precancers, and HPV-positive controls. We discover a subset of hotspot mutations rare in controls (2.6%) but significantly more prevalent in precancers, particularly glandular precancer lesions (10.2%), and cancers (25.7%), supporting their involvement in ICC carcinogenesis. Hotspot mutations differ by HPV type, and HPV18/45-positive ICC are more likely to have multiple hotspot mutations compared to HPV16-positive ICC. The proportion of cells containing hotspot mutations is higher (i.e., higher variant allele fraction) in ICC and mutations are detectable up to 6 years prior to cancer diagnosis. Our findings demonstrate the feasibility of using exfoliated cervical cells for detection of somatic mutations as potential diagnostic biomarkers., (© 2024. This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.)

Published
2024
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49. A critical literature review highlighting the methodological differences within epidemiological studies: Pedal Amputations in England.

Author

Bowling FL, Burdett L, Foley K, Hodge S, Davies M, and Ahmad N

Subjects
Humans, England epidemiology, Epidemiologic Studies, Lower Extremity surgery, Amputation, Surgical statistics & numerical data, Diabetic Foot surgery, Diabetic Foot epidemiology
Abstract

Introduction: There is an absence in the application of standardised epidemiological principles when calculating and reporting on lower extremity amputation (LEA) rates [1]. The rates of minor LEAs in the diabetic population range from 1.2-362.9 per 100,000 and in the population without diabetes 0.9-109.4 per 100,000. The reported rates of major lower limb amputations vary from 5.6-600 per 100,000 in the diabetic population and 3.6-58.7 per 100,000 in the total population [1]. The variation in methodology does not facilitate comparison across populations and time. All studies published using the population from England, UK, describing minor amputations were systematically reviewed and rates and methodologies compared., Method: A systematic search was carried out using (PRISMA) guidelines [2] to reveal primary data of minor lower extremity amputation rates in England between 1988-2018. This was carried out using electronic databases, grey literature and reference list searching. The search yielded eleven studies that were eligible for review., Results: Significant variation in the reporting of minor lower extremity amputation rates across regional and gender groups in England was found. Rates in the diabetic and non-diabetic population varied from 1.2 to 362.9 per 100,000 and 0.9 to 109.4 per 100,000 respectively. This was predominately a result of poorly describing numerator and denominator populations and defining minor amputations differently. As a result, there was an inability to confidently establish regional, gender and time trends., Conclusion: The inconsistent nature of reporting minor amputations makes drawing conclusions on temporal and population change difficult. Future studies should describe and present basic numerator and denominator population characteristics e.g. number, age and sex and use the standard definition of minor amputation as one that is at or below the ankle., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier Ltd.)

Published
2024
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50. Improved detection of low-frequency within-host variants from deep sequencing: A case study with human papillomavirus.

Author

Mishra SK, Nelson CW, Zhu B, Pinheiro M, Lee HJ, Dean M, Burdett L, Yeager M, and Mirabello L

Abstract

High-coverage sequencing allows the study of variants occurring at low frequencies within samples, but is susceptible to false-positives caused by sequencing error. Ion Torrent has a very low single nucleotide variant (SNV) error rate and has been employed for the majority of human papillomavirus (HPV) whole genome sequences. However, benchmarking of intrahost SNVs (iSNVs) has been challenging, partly due to limitations imposed by the HPV life cycle. We address this problem by deep sequencing three replicates for each of 31 samples of HPV type 18 (HPV18). Errors, defined as iSNVs observed in only one of three replicates, are dominated by C→T (G→A) changes, independently of trinucleotide context. True iSNVs, defined as those observed in all three replicates, instead show a more diverse SNV type distribution, with particularly elevated C→T rates in CCG context (CCG→CTG; CGG→CAG) and C→A rates in ACG context (ACG→AAG; CGT→CTT). Characterization of true iSNVs allowed us to develop two methods for detecting true variants: (1) VCFgenie, a dynamic binomial filtering tool which uses each variant's allele count and coverage instead of fixed frequency cut-offs; and (2) a machine learning binary classifier which trains eXtreme Gradient Boosting models on variant features such as quality and trinucleotide context. Each approach outperforms fixed-cut-off filtering of iSNVs, and performance is enhanced when both are used together. Our results provide improved methods for identifying true iSNVs in within-host applications across sequencing platforms, specifically using HPV18 as a case study., Competing Interests: The authors declare no conflicts of interest. Maisa Pinheiro is currently an employee of GlaxoSmithKline (GSK) (Rockville, Maryland) but completed all work associated with this project while employed at the NCI., (Published by Oxford University Press 2024. This work is written by (a) US Government employee(s) and is in the public domain in the US.)

Published
2024
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