Perez-Jurado, L.A. (Luis A.)
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- Female chromosome X mosaicism is age-related and preferentially affects the inactivated X chromosome(Nature Publishing Group: Nature Communications, 2016) Machiela, M.J. (Mitchell J.); Goldstein, A.M. (Alisa M.); Hu, N. (Nan); Koh, W.P. (Woon-Puay); Stevens, V.L. (Victoria L.); Wiencke, J.K. (John K.); Hunter, D.J. (David J.); Patiño-García, A. (Ana); Chen, C. (Chu); Seow, A. (Adeline); Khaw, K.T. (Kay-Tee); Kim, Y.T. (Young Tae); Schwartz, A.G. (Ann G.); Wong, M.P. (Maria Pik); Hsiung, C.A. (Chao A.); Xia, L. (Lucy); Hankinson, S.E. (Susan E.); Liao, L. (Linda); Fuchs, C.S. (Charles S.); Zhou, W. (Weiyin); Silverman, D.T. (Debra T.); Sampson, J. (Joshua); Chen, C. (Constance); McNeill, L.H. (Lorna H.); Li, D. (Donghui); McWilliams, R.R. (Robert R.); Park, J.Y. (Jae Yong); Zheng, W. (Wei); Olson, S.H. (Sara H.); Wu, Y.L. (Yi-Long); Magliocco, A.M. (Anthony M.); Tang, Z.Z. (Ze-Zhong); Arslan, A.A. (Alan A.); Jenab, M. (Mazda); Hu, W. (Wei); Mitchell, J.M. (J. Machiela); Wolpin, B.M. (Brian M.); Canzian, F. (Federico); Chaffee, K.G. (Kari G.); Amundadottir, L. (Laufey); Qiao, Y.L. (You-Lin); Butler, M.A. (Mary A.); Schwartz, K.L. (Kendra L.); Lu, L. (Lingeng); Purdue, M. (Mark); Hoover, R.N. (Robert N.); Davis, F.G. (Faith G.); Johansen, C. (Christoffer); Lissowska, J. (Jolanta); Hutchinson, A. (Amy); Kooperberg, C. (Charles); Freedman, N.D. (Neal D.); Chang, I.S. ( I-Shou); Stram, D. (Daniel); Wunder, J.S. (Jay S.); Harris, C.C. (Curtis C.); Petersen, G. (Gloria); Doherty, J. (Jennifer); Stolzenberg-Solomon, R.Z. (Rachael Z.); Wentzensen, N. (Nicolas); Setiawan, V.W. (Veronica Wendy); Garcia-Closas, M. (Montserrat); Liang, X. (Xiaolin); Wacholder, S. (Sholom); Kim, Y.H. (Yeul Hong); Brinton, L.A. (Louise A.); Zeleniuch-Jacquotte, A. (Anne); Friedenreich, C.M. (Christine M.); Duell, E.J. (Eric J.); Beane-Freeman, L.E. (Laura E.); Gallinger, S. (Steven); Zanetti, K.A. (Krista A.); Blot, W.J. (William J.); Teras, L.R. (Lauren R.); Wang, Z. (Zhaoming); Fraumeni, J.F. (Joseph F.); Hautman, C. (Christopher); Klein, R. (Robert); White, E. (Emily); Kraft, P. (Peter); Buring, J.E. (Julie E.); Giovannucci, E.L. (Edward L.); Figueroa, J.D. (Jonine D.); Yang, P.C. (Pan-Chyr); Chung, C.C. (Charles C.); Pooler, L. (Loreall); Tobias, G.S. (Geoffrey S.); Severi, G. (Gianluca); Hong, Y.C. (Yun-Chul); Mirabello, L. (Lisa); Prokunina-Olsson, L. (Ludmila); Burdett, L. (Laurie); Wu, C. (Chen); Haiman, C.A. (Christopher A.); Black, A. (Amanda); Holly, E.A. (Elizabeth A.); Liu, J. (Jianjun); Ruder, A.M. (Avima M.); Hicks, B. (Belynda); Peplonska, B. (Beata); LaCroix, A. (Andrea); Gaziano, J.M. (J. Michael); Caporaso, N.E. (Neil E.); Shin, M.H. (Min-Ho); Shu, X.O. (Xiao-Ou); Zhou, B. (Baosen); Lan, Q. (Qing); Dagnall, C. (Casey); Bock, C.H. (Cathryn H.); Real, F.X. (Francisco X.); Yang, Q. (Qi); Yu, K. (Kai); Gaudet, M.M. (Mia M.); Prescott, J. (Jennifer); Wu, T. (Tangchun); Kolonel, L.N. (Laurence N.); Malats, N. (Nuria); Visvanathan, K. (Kala); Savage, S.A. (Sharon A.); Aldrich, M.C. (Melinda C.); Chanock, S.J. (Stephen J.); Bracci, P.M. (Paige M.); Rodriguez-Santiago, B. (Benjamin); Riboli, E. (Elio); Klein, A.P. (Alison P.); Spitz, M.R. (Margaret R.); Risch, H.A. (Harvey A.); Perez-Jurado, L.A. (Luis A.); Lin, D. (Dongxin); Chen, K. (Kexin); Gillanders, E.M. (Elizabeth M.); Taylor, P.R. (Philip R.); Yang, H.P. (Hannah P.); Jacobs, K. (Kevin); Ding, T. (Ti); Abnet, C.C. (Christian C.); Wu, Y.Q. (Yan Q.); Peters, U. (Ulrike); Sheng, X. (Xin); Landi, M.T. (María Teresa); Le-Marchand, L. (Loic); Goldin, L. (Lynn); Gao, Y.T. (Yu-Tang); Fan, J.H. (Jin-Hu); Orlow, I. (Irene); Berndt, S.I. (Sonja I.); Epstein, C.G. (Caroline G.); Karlins, E. (Eric); Chatterjee, N. (Nilanjan); Cullen, M. (Michael); Moore, L.E. (Lee E.); Kim, H.N. (Hee Nam); Wheeler, W. (William); Melin, B.S. (Beatrice S.); De Vivo, I. (Immaculata); Giles, G.G. (Graham G.); Krogh, V. (Vittorio); Amos, C. (Christopher); Shen, H. (Hongbing); Crous Bou, M. (Marta); Yeager, M. (Meredith); Wang, J.C. (Jiu-Cun); Tucker, M. (Margaret); Schumacher, F. (Fredrick); Carreon, T. (Tania); Ziegler, R.G. (Regina G.); Kurtz, R.C. (Robert C.); Van Den Berg, D. (David); Henriksson, R. (Roger); Gapstur, S.M. (Susan M.); Hallmans, G. (Goran); Bueno-de-Mesquita, H.B. (H. Bas); Rothman, N. (Nathaniel); Dean, M.C. (Michael C.); Cook, L.S. (Linda S.); Matsuo, K. (Keitaro); Rajaraman, P. (Preetha)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.
- Detectable clonal mosaicism and its relationship to aging and cancer(Nature Publishing Group, 2012-12) Johnson, A. (Alison); Goldstein, A.M. (Alisa M.); Hu, N. (Nan); Koh, W.P. (Woon-Puay); Landgren, A. (Annelie); Stevens, V.L. (Victoria L.); Wiencke, J.K. (John K.); Hunter, D.J. (David J.); Patiño-García, A. (Ana); Khaw, K.T. (Kay-Tee); Virtamo, J. (Jarmo); Schwartz, A.G. (Ann G.); Yuan, J.M. (Jian-Min); Rybicki, B.A. (Benjamin A.); Boutron-Ruault, M.C. (Marie-Christine); Wolk, A. (Alicja); Mandelson, M.T. (Margaret T.); McGlynn, K.A. (Katherine A.); Hankinson, S.E. (Susan E.); Liao, L. (Linda); Fuchs, C.S. (Charles S.); Zhou, W. (Weiyin); Erickson, R.L. (Ralph L.); Silverman, D.T. (Debra T.); Sampson, J. (Joshua); Hassan, M. (Manal); McNeill, L.H. (Lorna H.); Li, D. (Donghui); McWilliams, R.R. (Robert R.); Zheng, W. (Wei); Olson, S.H. (Sara H.); Thomas, G. (Gilles); Tang, Z.Z. (Ze-Zhong); Arslan, A.A. (Alan A.); Jenab, M. (Mazda); Elena, J.W. (Joanne W.); Rabe, K.G. (Kari G.); Villa, O. (Olaya); Wolpin, B.M. (Brian M.); Canzian, F. (Federico); Amundadottir, L. (Laufey); Qiao, Y.L. (You-Lin); Butler, M.A. (Mary A.); Cotterchio, M. (Michelle); Schwartz, K.L. (Kendra L.); Liu, C. (Chenwei); Kogevinas, M. (Manolis); Purdue, M. (Mark); Hoover, R.N. (Robert N.); Davis, F.G. (Faith G.); Johansen, C. (Christoffer); Lissowska, J. (Jolanta); Mendelsohn, J.B. (Julie B.); Hutchinson, A. (Amy); Kooperberg, C. (Charles); Marenne, G. (Gaelle); Freedman, N.D. (Neal D.); Sesso, H.D. (Howard D.); Stram, D. (Daniel); Wunder, J.S. (Jay S.); Harris, C.C. (Curtis C.); Jiao, L. (Li); Henderson, B.E. (Brian E.); Petersen, G. (Gloria); Stolzenberg-Solomon, R.Z. (Rachael Z.); Ahlbom, A. (Anders); Wentzensen, N. (Nicolas); Garcia-Closas, M. (Montserrat); Wacholder, S. (Sholom); McKean-Cowdin, R. (Roberta); Brinton, L.A. (Louise A.); Zeleniuch-Jacquotte, A. (Anne); Duell, E.J. (Eric J.); Andersson, U. (Ulrika); Beane-Freeman, L.E. (Laura E.); Kovaks, J. (Joseph); Berg, C.D. (Christine D.); Gallinger, S. (Steven); Zanetti, K.A. (Krista A.); Sierrasesumaga, L. (Luis); Blot, W.J. (William J.); Teras, L.R. (Lauren R.); Wang, Z. (Zhaoming); Fraumeni, J.F. (Joseph F.); Schwenn, M. (Molly); White, E. (Emily); Kraft, P. (Peter); Buring, J.E. (Julie E.); Giovannucci, E.L. (Edward L.); Figueroa, J.D. (Jonine D.); Albanes, D. (Demetrius); Chung, C.C. (Charles C.); Hoffman-Bolton, J.A. (Judith A.); Tobias, G.S. (Geoffrey S.); Severi, G. (Gianluca); Mirabello, L. (Lisa); Prokunina-Olsson, L. (Ludmila); Burdett, L. (Laurie); Barkauskas, D.A. (Donald A.); Feychting, M. (Maria); Haiman, C.A. (Christopher A.); Black, A. (Amanda); Michaud, D.S. (Dominique S.); Holly, E.A. (Elizabeth A.); Cook, M.B. (Michael B.); Ruder, A.M. (Avima M.); Gorlick, R.G. (Richard G.); Wrensch, M. (Margaret); Peplonska, B. (Beata); LaCroix, A. (Andrea); Weinstein, S.J. (Stephanie J.); Chow, W.H. (Wong-Ho); Gaziano, J.M. (J. Michael); Caporaso, N.E. (Neil E.); Chang, K. (Kenneth); Shu, X.O. (Xiao-Ou); Hsing, A.W. (Ann W.); Gonzalez, J.R. (Juan R.); Bock, C.H. (Cathryn H.); Real, F.X. (Francisco X.); Kratz, C.P. (Christian P.); Yu, K. (Kai); Rotunno, M. (Melissa); Gaudet, M.M. (Mia M.); Consonni, D. (Dario); Kolonel, L.N. (Laurence N.); Malats, N. (Nuria); Visvanathan, K. (Kala); Savage, S.A. (Sharon A.); Aldrich, M.C. (Melinda C.); Chanock, S.J. (Stephen J.); Bracci, P.M. (Paige M.); Rodriguez-Santiago, B. (Benjamin); Riboli, E. (Elio); Baris, D. (Dalsu); Klein, A.P. (Alison P.); Spitz, M.R. (Margaret R.); Deng, X. (Xiang); Risch, H.A. (Harvey A.); Perez-Jurado, L.A. (Luis A.); Gross, M.D. (Myron D.); Gillanders, E.M. (Elizabeth M.); Taylor, P.R. (Philip R.); Jacobs, K. (Kevin); Ding, T. (Ti); Hartge, P. (Patricia); Greene, M.H. (Mark H.); Abnet, C.C. (Christian C.); Wu, Y.Q. (Yan Q.); Peters, U. (Ulrike); Trichopoulos, D. (Dimitrios); Landi, M.T. (María Teresa); Horner, M.J. (Marie-Josephe); Le-Marchand, L. (Loic); Goldin, L. (Lynn); Gao, Y.T. (Yu-Tang); Fan, J.H. (Jin-Hu); Berndt, S.I. (Sonja I.); Epstein, C.G. (Caroline G.); Signorello, L.B. (Lisa B.); Chatterjee, N. (Nilanjan); Cullen, M. (Michael); Moore, L.E. (Lee E.); Wheeler, W. (William); Melin, B.S. (Beatrice S.); Giles, G.G. (Graham G.); Tjonneland, A. (Anne); Inskip, P.D. (Peter D.); Krogh, V. (Vittorio); Amos, C. (Christopher); Graubard, B.I. (Barry I.); Bertazzi, P.A. (Pier Alberto); Yeager, M. (Meredith); Goggins, M. (Michael); Yu, H. (Herbert); Tucker, M. (Margaret); Schumacher, F. (Fredrick); Carreon, T. (Tania); Ziegler, R.G. (Regina G.); Kurtz, R.C. (Robert C.); Henriksson, R. (Roger); Gapstur, S.M. (Susan M.); Hallmans, G. (Goran); Xiang, Y.B. (Yong-Bing); Bueno-de-Mesquita, H.B. (H. Bas); Rothman, N. (Nathaniel); Andrulis, I.L. (Irene L.); Dean, M.C. (Michael C.); Rajaraman, P. (Preetha)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.
- NetActivity enhances transcriptional signals by combining gene expression into robust gene set activity scores through interpretable autoencoders(Oxford University Press, 2024) Ruiz, C. (Carlos); Wang, L. (Liewei); Perez-Jurado, L.A. (Luis A.); Ochoa, I. (Idoia); Hernaez, M. (Mikel); Marín-Goñi, I. (Irene)Grouping gene expression into gene set activity scores (GSAS) provides better biological insights than studying individual genes. However, existing gene set projection methods cannot return representative, robust, and interpretable GSAS. We developed NetActivity, a machine learning framework that generates GSAS based on a sparsely-connected autoencoder, where each neuron in the inner layer represents a gene set. We proposed a three-tier training that yielded representative, robust, and interpretable GSAS. NetActivity model was trained with 1518 GO biological processes terms and KEGG pathways and all GTEx samples. NetActivity generates GSAS robust to the initialization parameters and representative of the original transcriptome, and assigned higher importance to more biologically relevant genes. Moreover, NetActivity returns GSAS with a more consistent definition and higher interpretability than GSVA and hipathia, state-of-the-art gene set projection methods. Finally, NetActivity enables combining bulk RNA-seq and microarray datasets in a meta-analysis of prostate cancer progression, highlighting gene sets related to cell division, key for disease progression. When applied to metastatic prostate cancer, gene sets associated with cancer progression were also altered due to drug resistance, while a classical enrichment analysis identified gene sets irrelevant to the phenotype. NetActivity is publicly available in Bioconductor and GitHub.