Rare Non-coding Variation Identified by Large Scale Whole Genome Sequencing Reveals Unexplained Heritability of Type 2 Diabetes

ChangJiang Xu, Ioanna Tachmazidou, Klaudia Walter, Antonio Ciampi, Eleftheria Zeggini, Celia M. T. Greenwood, , Estimating genome-wide significance for whole-genome sequencing studies. Genetic Epidemiology. ,vol. 38, pp. 281- 290 ,(2014) , 10.1002/GEPI.21797

Hilary K Finucane, Brendan Bulik-Sullivan, Alexander Gusev, Gosia Trynka, Yakir Reshef, Po-Ru Loh, Verneri Anttila, Han Xu, Chongzhi Zang, Kyle Farh, Stephan Ripke, Felix R Day, ReproGen Consortium, Schizophrenia Working Group of the Psychiatric Genomics Consortium, Raci Consortium, Shaun Purcell, Eli Stahl, Sara Lindstrom, John RB Perry, Yukinori Okada, Soumya Raychaudhuri, Mark J Daly, Nick Patterson, Benjamin M Neale, Alkes L Price, None, Partitioning heritability by functional annotation using genome-wide association summary statistics Nature Genetics. ,vol. 47, pp. 1228- 1235 ,(2015) , 10.1038/NG.3404

Jana Marie Schwarz, David N Cooper, Markus Schuelke, Dominik Seelow, MutationTaster2: mutation prediction for the deep-sequencing age Nature Methods. ,vol. 11, pp. 361- 362 ,(2014) , 10.1038/NMETH.2890

Prateek Kumar, Steven Henikoff, Pauline C Ng, Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nature Protocols. ,vol. 4, pp. 1073- 1081 ,(2009) , 10.1038/NPROT.2009.86

Sang Hong Lee, Naomi R. Wray, Michael E. Goddard, Peter M. Visscher, Estimating Missing Heritability for Disease from Genome-wide Association Studies American Journal of Human Genetics. ,vol. 88, pp. 294- 305 ,(2011) , 10.1016/J.AJHG.2011.02.002

J. Fadista, P. Vikman, E. O. Laakso, I. G. Mollet, J. L. Esguerra, J. Taneera, P. Storm, P. Osmark, C. Ladenvall, R. B. Prasad, K. B. Hansson, F. Finotello, K. Uvebrant, J. K. Ofori, B. Di Camillo, U. Krus, C. M. Cilio, O. Hansson, L. Eliasson, A. H. Rosengren, E. Renstrom, C. B. Wollheim, L. Groop, Global genomic and transcriptomic analysis of human pancreatic islets reveals novel genes influencing glucose metabolism Proceedings of the National Academy of Sciences of the United States of America. ,vol. 111, pp. 13924- 13929 ,(2014) , 10.1073/PNAS.1402665111

Matthew P. Conomos, Michael B. Miller, Timothy A. Thornton, Robust inference of population structure for ancestry prediction and correction of stratification in the presence of relatedness. Genetic Epidemiology. ,vol. 39, pp. 276- 293 ,(2015) , 10.1002/GEPI.21896

Sharon R. Browning, Brian L. Browning, Population Structure Can Inflate SNP-Based Heritability Estimates American Journal of Human Genetics. ,vol. 89, pp. 191- 193 ,(2011) , 10.1016/J.AJHG.2011.05.025

Anubha Mahajan, Xueling Sim, Hui Jin Ng, Alisa Manning, Manuel A Rivas, Heather M Highland, Adam E Locke, Niels Grarup, Hae Kyung Im, Pablo Cingolani, Jason Flannick, Pierre Fontanillas, Christian Fuchsberger, Kyle J Gaulton, Tanya M Teslovich, N William Rayner, Neil R Robertson, Nicola L Beer, Jana K Rundle, Jette Bork-Jensen, Claes Ladenvall, Christine Blancher, David Buck, Gemma Buck, Noël P Burtt, Stacey Gabriel, Anette P Gjesing, Christopher J Groves, Mette Hollensted, Jeroen R Huyghe, Anne U Jackson, Goo Jun, Johanne Marie Justesen, Massimo Mangino, Jacquelyn Murphy, Matt Neville, Robert Onofrio, Kerrin S Small, Heather M Stringham, Ann-Christine Syvänen, Joseph Trakalo, Goncalo Abecasis, Graeme I Bell, John Blangero, Nancy J Cox, Ravindranath Duggirala, Craig L Hanis, Mark Seielstad, James G Wilson, Cramer Christensen, Ivan Brandslund, Rainer Rauramaa, Gabriela L Surdulescu, Alex SF Doney, Lars Lannfelt, Allan Linneberg, Bo Isomaa, Tiinamaija Tuomi, Marit E Jørgensen, Torben Jørgensen, Johanna Kuusisto, Matti Uusitupa, Veikko Salomaa, Timothy D Spector, Andrew D Morris, Colin NA Palmer, Francis S Collins, Karen L Mohlke, Richard N Bergman, Erik Ingelsson, Lars Lind, Jaakko Tuomilehto, Torben Hansen, Richard M Watanabe, Inga Prokopenko, Josee Dupuis, Fredrik Karpe, Leif Groop, Markku Laakso, Oluf Pedersen, Jose C Florez, Andrew P Morris, David Altshuler, James B Meigs, Michael Boehnke, Mark I McCarthy, Cecilia M Lindgren, Anna L Gloyn, T2D-GENES consortium and GoT2D consortium, None, Identification and Functional Characterization of G6PC2 Coding Variants Influencing Glycemic Traits Define an Effector Transcript at the G6PC2-ABCB11 Locus PLOS Genetics. ,vol. 11, pp. e1004876- ,(2015) , 10.1371/JOURNAL.PGEN.1004876

Andrew P Morris, Benjamin F Voight, Tanya M Teslovich, Teresa Ferreira, Ayellet V Segre, Valgerdur Steinthorsdottir, Rona J Strawbridge, Hassan Khan, Harald Grallert, Anubha Mahajan, Inga Prokopenko, Hyun Min Kang, Christian Dina, Tonu Esko, Ross M Fraser, Stavroula Kanoni, Ashish Kumar, Vasiliki Lagou, Claudia Langenberg, Jian'an Luan, Cecilia M Lindgren, Martina Müller-Nurasyid, Sonali Pechlivanis, N William Rayner, Laura J Scott, Steven Wiltshire, Loic Yengo, Leena Kinnunen, Elizabeth J Rossin, Soumya Raychaudhuri, Andrew D Johnson, Antigone S Dimas, Ruth JF Loos, Sailaja Vedantam, Han Chen, Jose C Florez, Caroline Fox, Ching-Ti Liu, Denis Rybin, David J Couper, Wen Hong L Kao, Man Li, Marilyn C Cornelis, Peter Kraft, Qi Sun, Rob M Van Dam, Heather M Stringham, Peter S Chines, Krista Fischer, Pierre Fontanillas, Oddgeir L Holmen, Sarah E Hunt, Anne U Jackson, Augustine Kong, Robert Lawrence, Julia Meyer, John RB Perry, Carl GP Platou, Simon Potter, Emil Rehnberg, Neil Robertson, Suthesh Sivapalaratnam, Alena Stančáková, Kathleen Stirrups, Gudmar Thorleifsson, Emmi Tikkanen, Andrew R Wood, Peter Almgren, Mustafa Atalay, Rafn Benediktsson, Lori L Bonnycastle, Noël Burtt, Jason Carey, Guillaume Charpentier, Andrew T Crenshaw, Alex SF Doney, Mozhgan Dorkhan, Sarah Edkins, Valur Emilsson, Elodie Eury, Tom Forsen, Karl Gertow, Bruna Gigante, George B Grant, Christopher J Groves, Candace Guiducci, Christian Herder, Astradur B Hreidarsson, Jennie Hui, Alan James, Anna Jonsson, Wolfgang Rathmann, Norman Klopp, Jasmina Kravic, Kaarel Krjutškov, Cordelia Langford, Karin Leander, Eero Lindholm, Stéphane Lobbens, Satu Männistö, Ghazala Mirza, Thomas W Mühleisen, Bill Musk, Melissa Parkin, Loukianos Rallidis, Jouko Saramies, Bengt Sennblad, Sonia Shah, Gunnar Sigurðsson, Angela Silveira, Gerald Steinbach, Barbara Thorand, Joseph Trakalo, Fabrizio Veglia, Roman Wennauer, Wendy Winckler, Delilah Zabaneh, Harry Campbell, Cornelia Van Duijn, Andre G Uitterlinden, Albert Hofman, Eric Sijbrands, Goncalo R Abecasis, Katharine R Owen, Eleftheria Zeggini, Mieke D Trip, Nita G Forouhi, Ann-Christine Syvänen, Johan G Eriksson, Leena Peltonen, Markus M Nöthen, Beverley Balkau, Colin NA Palmer, Valeriya Lyssenko, Tiinamaija Tuomi, Bo Isomaa, David J Hunter, Lu Qi, Alan R Shuldiner, Michael Roden, Ines Barroso, Tom Wilsgaard, John Beilby, Kees Hovingh, Jackie F Price, James F Wilson, Rainer Rauramaa, Timo A Lakka, Lars Lind, George Dedoussis, Large-scale association analysis provides insights into the genetic architecture and pathophysiology of type 2 diabetes Nature Genetics. ,vol. 44, pp. 981- 990 ,(2012) , 10.1038/NG.2383