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Genomics of 1 million parent lifespans implicates novel pathways and common diseases and distinguishes survival chances

Timmers, Paul RHJ, Mounier, Ninon, Lall, Kristi, Fischer, Krista, Ning, Zheng, Feng, Xiao, Bretherick, Andrew D, Clark, David W, eQTLGen Consortium, Agbessi, M, Ahsan, H, Alves, I, Andiappan, A, Awadalla, P, Battle, A, Bonder, MJ, Boomsma, D, Christiansen, M, Claringbould, A, Deelen, P, van Dongen, J, Esko, T, Favé, M, Franke, L, Frayling, T, Gharib, SA, Gibson, G, Hemani, G, Jansen, R, Kalnapenkis, A, Kasela, S, Kettunen, J, Kim, Y, Kirsten, H, Kovacs, P, Krohn, K, Kronberg-Guzman, J, Kukushkina, V, Kutalik, Z, Kähönen, M, Lee, B, Lehtimäki, T, Loeffler, M, Marigorta, U, Metspalu, A, van Meurs, J, Milani, L, Müller-Nurasyid, M, Nauck, M, Nivard, M, Penninx, B, Perola, M, Pervjakova, N, Pierce, B, Powell, J, Prokisch, H, Psaty, BM, Raitakari, O, Ring, S, Ripatti, S, Rotzschke, O, Ruëger, S, Saha, A, Scholz, M, Schramm, K, Seppälä, I, Stumvoll, M, Sullivan, P, Teumer, A, Thiery, J, Tong, L, Tönjes, A, Verlouw, J, Visscher, PM, Võsa, U, Völker, U, Yaghootkar, H, Yang, J, Zeng, B, Zhang, F, Agbessi, M, Ahsan, H, Alves, I, Andiappan, A, Awadalla, P, Battle, A, Bonder, MJ, Boomsma, D, Christiansen, M, Claringbould, A, Deelen, P, van Dongen, J, Esko, T, Favé, M, Franke, L, Frayling, T, Gharib, SA, Gibson, G, Hemani, G, Jansen, R, Kalnapenkis, A, Kasela, S, Kettunen, J, Kim, Y, Kirsten, H, Kovacs, P, Krohn, K, Kronberg-Guzman, J, Kukushkina, V, Kutalik, Z, Kähönen, M, Lee, B, Lehtimäki, T, Loeffler, M, Marigorta, U, Metspalu, A, van Meurs, J, Milani, L, Müller-Nurasyid, M, Nauck, M, Nivard, M, Penninx, B, Perola, M, Pervjakova, N, Pierce, B, Powell, J, Prokisch, H, Psaty, BM, Raitakari, O, Ring, S, Ripatti, S, Rotzschke, O, Ruëger, S, Saha, A, Scholz, M, Schramm, K, Seppälä, I, Stumvoll, M, Sullivan, P, Teumer, A, Thiery, J, Tong, L, Tönjes, A, Verlouw, J, Visscher, PM, Võsa, U, Völker, U, Yaghootkar, H, Yang, J, Zeng, B, Zhang, F, Shen, Xia, Esko, Tõnu, Kutalik, Zoltán, Wilson, James F, Joshi, Peter K·2019·eLife
DOI 10.7554/elife.39856PMC PMC6333444
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Abstract

We use a genome-wide association of 1 million parental lifespans of genotyped subjects and data on mortality risk factors to validate previously unreplicated findings near CDKN2B-AS1, ATXN2/BRAP, FURIN/FES, ZW10, PSORS1C3, and 13q21.31, and identify and replicate novel findings near ABO, ZC3HC1, and IGF2R. We also validate previous findings near 5q33.3/EBF1 and FOXO3, whilst finding contradictory evidence at other loci. Gene set and cell-specific analyses show that expression in foetal brain cells and adult dorsolateral prefrontal cortex is enriched for lifespan variation, as are gene pathways involving lipid proteins and homeostasis, vesicle-mediated transport, and synaptic function. Individual genetic variants that increase dementia, cardiovascular disease, and lung cancer – but not other cancers – explain the most variance. Resulting polygenic scores show a mean lifespan difference of around five years of life across the deciles. Editorial note: This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (see decision letter).

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Metadata

Authors
Timmers, P. R., Mounier, N., Lall, K., Fischer, K., Ning, Z., Feng, X., Bretherick, A. D., Clark, D. W., eQTLGen Consortium, Agbessi, M., Ahsan, H., Alves, I., Andiappan, A., Awadalla, P., Battle, A., Bonder, M., Boomsma, D., Christiansen, M., Claringbould, A., Deelen, P., van Dongen, J., Esko, T., Favé, M., Franke, L., Frayling, T., Gharib, S., Gibson, G., Hemani, G., Jansen, R., Kalnapenkis, A., Kasela, S., Kettunen, J., Kim, Y., Kirsten, H., Kovacs, P., Krohn, K., Kronberg-Guzman, J., Kukushkina, V, Kutalik, Z., Kähönen, M., Lee, B., Lehtimäki, T., Loeffler, M., Marigorta, U., Metspalu, A., van Meurs, J., Milani, L., Müller-Nurasyid, M., Nauck, M., Nivard, M., Penninx, B., Perola, M., Pervjakova, N., Pierce, B., Powell, J., Prokisch, H., Psaty, B., Raitakari, O., Ring, S., Ripatti, S., Rotzschke, O., Ruëger, S., Saha, A., Scholz, M., Schramm, K., Seppälä, I., Stumvoll, M., Sullivan, P., Teumer, A., Thiery, J., Tong, L., Tönjes, A., Verlouw, J., Visscher, P., Võsa, U., Völker, U., Yaghootkar, H., Yang, J., Zeng, B., Zhang, F., Agbessi, M., Ahsan, H., Alves, I., Andiappan, A., Awadalla, P., Battle, A., Bonder, M., Boomsma, D., Christiansen, M., Claringbould, A., Deelen, P., van Dongen, J., Esko, T., Favé, M., Franke, L., Frayling, T., Gharib, S., Gibson, G., Hemani, G., Jansen, R., Kalnapenkis, A., Kasela, S., Kettunen, J., Kim, Y., Kirsten, H., Kovacs, P., Krohn, K., Kronberg-Guzman, J., Kukushkina, V, Kutalik, Z., Kähönen, M., Lee, B., Lehtimäki, T., Loeffler, M., Marigorta, U., Metspalu, A., van Meurs, J., Milani, L., Müller-Nurasyid, M., Nauck, M., Nivard, M., Penninx, B., Perola, M., Pervjakova, N., Pierce, B., Powell, J., Prokisch, H., Psaty, B., Raitakari, O., Ring, S., Ripatti, S., Rotzschke, O., Ruëger, S., Saha, A., Scholz, M., Schramm, K., Seppälä, I., Stumvoll, M., Sullivan, P., Teumer, A., Thiery, J., Tong, L., Tönjes, A., Verlouw, J., Visscher, P., Võsa, U., Völker, U., Yaghootkar, H., Yang, J., Zeng, B., Zhang, F., Shen, X., Esko, T., Kutalik, Z., Wilson, J. F., & Joshi, P. K.
Affiliations
  • Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, United Kingdom
  • Institute of Social and Preventive Medicine, University Hospital of Lausanne, Lausanne, Switzerland
  • Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
  • Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
  • State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
  • MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
ORCID
Venue
eLife
Publisher
eLife Sciences Publications, Ltd
Published
2019-01-15
Volume
8
ISSN
2050-084X
DOI
10.7554/elife.39856
PMC
PMC6333444
Cited by
259
References
18
Language
en
Licence
Funders
  • Medical Research Council (DTP in Precision Medicine MR/N013166/1,HGU QTL in health and disease)
  • Estonian Research Competency Council (PUT 1665)
  • Wellcome Trust (PhD Training Fellowship for Clinicians)
  • Edinburgh Clinical Academic Track (204979/Z/16/Z)
  • Svenska Forskningsrådet Formas (2014-00371, 2017-02543)
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (31003A_169929)
  • SystemsX.ch (51RTP0_151019)
  • AXA Research Fund

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