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1. Fine-mapping type 2 diabetes loci to single-variant resolution using high-density imputation and islet-specific epigenome maps.

Author

Mahajan A, Taliun D, Thurner M, Robertson NR, Torres JM, Rayner NW, Payne AJ, Steinthorsdottir V, Scott RA, Grarup N, Cook JP, Schmidt EM, Wuttke M, Sarnowski C, Mägi R, Nano J, Gieger C, Trompet S, Lecoeur C, Preuss MH, Prins BP, Guo X, Bielak LF, Below JE, Bowden DW, Chambers JC, Kim YJ, Ng MCY, Petty LE, Sim X, Zhang W, Bennett AJ, Bork-Jensen J, Brummett CM, Canouil M, Ec Kardt KU, Fischer K, Kardia SLR, Kronenberg F, Läll K, Liu CT, Locke AE, Luan J, Ntalla I, Nylander V, Schönherr S, Schurmann C, Yengo L, Bottinger EP, Brandslund I, Christensen C, Dedoussis G, Florez JC, Ford I, Franco OH, Frayling TM, Giedraitis V, Hackinger S, Hattersley AT, Herder C, Ikram MA, Ingelsson M, Jørgensen ME, Jørgensen T, Kriebel J, Kuusisto J, Ligthart S, Lindgren CM, Linneberg A, Lyssenko V, Mamakou V, Meitinger T, Mohlke KL, Morris AD, Nadkarni G, Pankow JS, Peters A, Sattar N, Stančáková A, Strauch K, Taylor KD, Thorand B, Thorleifsson G, Thorsteinsdottir U, Tuomilehto J, Witte DR, Dupuis J, Peyser PA, Zeggini E, Loos RJF, Froguel P, Ingelsson E, Lind L, Groop L, Laakso M, Collins FS, Jukema JW, Palmer CNA, Grallert H, Metspalu A, Dehghan A, Köttgen A, Abecasis GR, Meigs JB, Rotter JI, Marchini J, Pedersen O, Hansen T, Langenberg C, Wareham NJ, Stefansson K, Gloyn AL, Morris AP, Boehnke M, and McCarthy MI

Subjects
Body Mass Index, Case-Control Studies, Diabetes Mellitus, Type 2 epidemiology, Diabetes Mellitus, Type 2 pathology, Female, Gene Frequency, Genetic Loci genetics, Genetic Predisposition to Disease, Genome-Wide Association Study, High-Throughput Screening Assays methods, Humans, Islets of Langerhans pathology, Linkage Disequilibrium, Male, Meta-Analysis as Topic, Sex Factors, White People genetics, Chromosome Mapping methods, Diabetes Mellitus, Type 2 genetics, Epigenesis, Genetic, Genome, Human genetics, Islets of Langerhans metabolism, Polymorphism, Single Nucleotide
Abstract

We expanded GWAS discovery for type 2 diabetes (T2D) by combining data from 898,130 European-descent individuals (9% cases), after imputation to high-density reference panels. With these data, we (i) extend the inventory of T2D-risk variants (243 loci, 135 newly implicated in T2D predisposition, comprising 403 distinct association signals); (ii) enrich discovery of lower-frequency risk alleles (80 index variants with minor allele frequency <5%, 14 with estimated allelic odds ratio >2); (iii) substantially improve fine-mapping of causal variants (at 51 signals, one variant accounted for >80% posterior probability of association (PPA)); (iv) extend fine-mapping through integration of tissue-specific epigenomic information (islet regulatory annotations extend the number of variants with PPA >80% to 73); (v) highlight validated therapeutic targets (18 genes with associations attributable to coding variants); and (vi) demonstrate enhanced potential for clinical translation (genome-wide chip heritability explains 18% of T2D risk; individuals in the extremes of a T2D polygenic risk score differ more than ninefold in prevalence).

Published
2018
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2. Refining the accuracy of validated target identification through coding variant fine-mapping in type 2 diabetes.

Author

Mahajan, Anubha, Wessel, Jennifer, Willems, Sara M, Zhao, Wei, Robertson, Neil R, Chu, Audrey Y, Gan, Wei, Kitajima, Hidetoshi, Taliun, Daniel, Rayner, N William, Guo, Xiuqing, Lu, Yingchang, Li, Man, Jensen, Richard A, Hu, Yao, Huo, Shaofeng, Lohman, Kurt K, Zhang, Weihua, Cook, James P, Prins, Bram Peter, Flannick, Jason, Grarup, Niels, Trubetskoy, Vassily Vladimirovich, Kravic, Jasmina, Kim, Young Jin, Rybin, Denis V, Yaghootkar, Hanieh, Müller-Nurasyid, Martina, Meidtner, Karina, Li-Gao, Ruifang, Varga, Tibor V, Marten, Jonathan, Li, Jin, Smith, Albert Vernon, An, Ping, Ligthart, Symen, Gustafsson, Stefan, Malerba, Giovanni, Demirkan, Ayse, Tajes, Juan Fernandez, Steinthorsdottir, Valgerdur, Wuttke, Matthias, Lecoeur, Cécile, Preuss, Michael, Bielak, Lawrence F, Graff, Marielisa, Highland, Heather M, Justice, Anne E, Liu, Dajiang J, Marouli, Eirini, Peloso, Gina Marie, Warren, Helen R, ExomeBP Consortium, MAGIC Consortium, GIANT Consortium, Afaq, Saima, Afzal, Shoaib, Ahlqvist, Emma, Almgren, Peter, Amin, Najaf, Bang, Lia B, Bertoni, Alain G, Bombieri, Cristina, Bork-Jensen, Jette, Brandslund, Ivan, Brody, Jennifer A, Burtt, Noël P, Canouil, Mickaël, Chen, Yii-Der Ida, Cho, Yoon Shin, Christensen, Cramer, Eastwood, Sophie V, Eckardt, Kai-Uwe, Fischer, Krista, Gambaro, Giovanni, Giedraitis, Vilmantas, Grove, Megan L, de Haan, Hugoline G, Hackinger, Sophie, Hai, Yang, Han, Sohee, Tybjærg-Hansen, Anne, Hivert, Marie-France, Isomaa, Bo, Jäger, Susanne, Jørgensen, Marit E, Jørgensen, Torben, Käräjämäki, Annemari, Kim, Bong-Jo, Kim, Sung Soo, Koistinen, Heikki A, Kovacs, Peter, Kriebel, Jennifer, Kronenberg, Florian, Läll, Kristi, Lange, Leslie A, Lee, Jung-Jin, Lehne, Benjamin, Li, Huaixing, and Lin, Keng-Hung

Subjects
ExomeBP Consortium, MAGIC Consortium, GIANT Consortium, Humans, Diabetes Mellitus, Type 2, Genetic Predisposition to Disease, Chromosome Mapping, Alleles, European Continental Ancestry Group, Female, Male, Genetic Variation, Genome-Wide Association Study, Whole Exome Sequencing, Diabetes Mellitus, Type 2, Developmental Biology, Biological Sciences, Medical and Health Sciences
Abstract

We aggregated coding variant data for 81,412 type 2 diabetes cases and 370,832 controls of diverse ancestry, identifying 40 coding variant association signals (P

Published
2018

3. Fine-mapping type 2 diabetes loci to single-variant resolution using high-density imputation and islet-specific epigenome maps

Author

Mahajan, Anubha, Taliun, Daniel, Thurner, Matthias, Robertson, Neil R, Torres, Jason M, Rayner, N William, Payne, Anthony J, Steinthorsdottir, Valgerdur, Scott, Robert A, Grarup, Niels, Cook, James P, Schmidt, Ellen M, Wuttke, Matthias, Sarnowski, Chloé, Mägi, Reedik, Nano, Jana, Gieger, Christian, Trompet, Stella, Lecoeur, Cécile, Preuss, Michael H, Prins, Bram Peter, Guo, Xiuqing, Bielak, Lawrence F, Below, Jennifer E, Bowden, Donald W, Chambers, John Campbell, Kim, Young Jin, Ng, Maggie CY, Petty, Lauren E, Sim, Xueling, Zhang, Weihua, Bennett, Amanda J, Bork-Jensen, Jette, Brummett, Chad M, Canouil, Mickaël, Ec Kardt, Kai-Uwe, Fischer, Krista, Kardia, Sharon LR, Kronenberg, Florian, Läll, Kristi, Liu, Ching-Ti, Locke, Adam E, Luan, Jian'an, Ntalla, Ioanna, Nylander, Vibe, Schönherr, Sebastian, Schurmann, Claudia, Yengo, Loïc, Bottinger, Erwin P, Brandslund, Ivan, Christensen, Cramer, Dedoussis, George, Florez, Jose C, Ford, Ian, Franco, Oscar H, Frayling, Timothy M, Giedraitis, Vilmantas, Hackinger, Sophie, Hattersley, Andrew T, Herder, Christian, Ikram, M Arfan, Ingelsson, Martin, Jørgensen, Marit E, Jørgensen, Torben, Kriebel, Jennifer, Kuusisto, Johanna, Ligthart, Symen, Lindgren, Cecilia M, Linneberg, Allan, Lyssenko, Valeriya, Mamakou, Vasiliki, Meitinger, Thomas, Mohlke, Karen L, Morris, Andrew D, Nadkarni, Girish, Pankow, James S, Peters, Annette, Sattar, Naveed, Stančáková, Alena, Strauch, Konstantin, Taylor, Kent D, Thorand, Barbara, Thorleifsson, Gudmar, Thorsteinsdottir, Unnur, Tuomilehto, Jaakko, Witte, Daniel R, Dupuis, Josée, Peyser, Patricia A, Zeggini, Eleftheria, Loos, Ruth JF, Froguel, Philippe, Ingelsson, Erik, Lind, Lars, Groop, Leif, Laakso, Markku, Collins, Francis S, Jukema, J Wouter, Palmer, Colin NA, Grallert, Harald, Metspalu, Andres, Dehghan, Abbas, Köttgen, Anna, Abecasis, Goncalo R, Meigs, James B, Rotter, Jerome I, Marchini, Jonathan, Pedersen, Oluf, Hansen, Torben, Langenberg, Claudia, Wareham, Nicholas J, Stefansson, Kari, Gloyn, Anna L, Morris, Andrew P, Boehnke, Michael, and McCarthy, Mark I

Subjects
Male, endocrine system diseases, Genome, Human, Chromosome Mapping, Polymorphism, Single Nucleotide, Linkage Disequilibrium, White People, 3. Good health, Body Mass Index, Epigenesis, Genetic, High-Throughput Screening Assays, Islets of Langerhans, Sex Factors, Diabetes Mellitus, Type 2, Gene Frequency, Meta-Analysis as Topic, Genetic Loci, Case-Control Studies, Humans, Female, Genetic Predisposition to Disease, Genome-Wide Association Study
Abstract

We expanded GWAS discovery for type 2 diabetes (T2D) by combining data from 898,130 European-descent individuals (9% cases), after imputation to high-density reference panels. With these data, we (i) extend the inventory of T2D-risk variants (243 loci, 135 newly implicated in T2D predisposition, comprising 403 distinct association signals); (ii) enrich discovery of lower-frequency risk alleles (80 index variants with minor allele frequency 2); (iii) substantially improve fine-mapping of causal variants (at 51 signals, one variant accounted for >80% posterior probability of association (PPA)); (iv) extend fine-mapping through integration of tissue-specific epigenomic information (islet regulatory annotations extend the number of variants with PPA >80% to 73); (v) highlight validated therapeutic targets (18 genes with associations attributable to coding variants); and (vi) demonstrate enhanced potential for clinical translation (genome-wide chip heritability explains 18% of T2D risk; individuals in the extremes of a T2D polygenic risk score differ more than ninefold in prevalence).

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