Identifying rare variants from exome scans: The GAW17 experience

Saurabh Ghosh, Heike Bickeböller, Julia Bailey, Joan E. Bailey-Wilson, Rita Cantor, Robert Culverhouse, Warwick Daw, Anita L. Destefano, Corinne D. Engelman, Anthony Hinrichs, Jeanine Houwing-Duistermaat, Inke R. König, Jack Kent, Nan Laird, Nathan Pankratz, Andrew Paterson, Elizabeth Pugh, Brian Suarez, Yan Sun, Alun ThomasNathan Tintle, Xiaofeng Zhu, Andreas Ziegler, Jean W. MacCluer, Laura Almasy

Research output: Contribution to journalArticlepeer-review

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Abstract

Genetic Analysis Workshop 17 (GAW17) provided a platform for evaluating existing statistical genetic methods and for developing novel methods to analyze rare variants that modulate complex traits. In this article, we present an overview of the 1000 Genomes Project exome data and simulated phenotype data that were distributed to GAW17 participants for analyses, the different issues addressed by the participants, and the process of preparation of manuscripts resulting from the discussions during the workshop.

Original languageEnglish (US)
Article numberS1
JournalBMC Proceedings
Volume5
Issue numberSUPPL. 9
DOIs
StatePublished - 2011

Bibliographical note

Funding Information:
The Genetic Analysis Workshops would not succeed without the dedicated efforts of a huge number of individuals. These include those who help to select workshop topics, provide real and simulated data sets to be distributed to workshop participants, make local arrangements and staff the registration desk at the workshop, lead presentation groups, write summary papers, review manuscripts, and edit these proceedings. Contributions to GAW17 were organized into discussion and presentation groups focused on various methodological and analytic themes. Twenty-two people generously volunteered to lead these groups, initiating interactions among group members before GAW17, leading group meetings at GAW17, organizing summary presentations for the larger GAW17 audience, serving as editors for the publication and peer review process for this volume, and taking responsibility for the preparation of a summary paper for Genetic Epidemiology. Their efforts deserve special recognition. We are grateful to the following people, who led the group discussions and prepared the summary presentations: Julia Bailey, Joan Bailey-Wilson, Heike Bickeböller, Rita Cantor, Rob Culverhouse, E. Warwick Daw, Anita DeStefano, Corrine Engleman, Anthony Hinrichs, Jeanine Houwing-Duistermaat, Jack Kent Jr, Inke König, Nan Laird, Nathan Pankratz, Andrew Paterson, Elizabeth Pugh, Brian Suarez, Yan Sun, Alun Thomas, Nathan Tintle, Xiaofeng Zhu, and Andreas Ziegler. Useful comments and criticisms of the papers in this volume were provided by 125 scientific reviewers: Alexandre Alcais, Laura Almasy, Christopher Amos, Ping An, Allison Ashley-Koch, Beth Atkinson, Christy Avery, Marie-Claude Babron, Michael Badzioch, Raji Balasubramanian, M. Michael Barmada, Jenny Barrett, Saonli Basu, Justo Lorenzo Bermejo, Joanna Biernacka, Timothy Bishop, Michael Boehnke, Stefan Boehringer, Karl Broman, Sharon Browning, Alfonso Buil, Shelley Bull, Alexandre Bureau, William Bush, Andrea Callegaro, Nicola Camp, Daniel Chassmen, Wei-Min Chen, Ching-Yu Cheng, Erica Childs, Andy Collins, Heather Cordell, Karen Cuenco, Mariza de Andrade, Marcella Devoto, Marie-Pierre Dube, Priya Duggal, Josee Dupuis, Jeanette Eckel-Passow, Paul Eilers, Sarah Ennis, Cathy Falk, Dani Fallin, Cathy Fann, Christine Fischer, Nora Franceschini, France Gagnon, Xiaoyi Gao, Chad Garner, Emanuelle Genin, Lynn Goldin, Alisa Goldstein, Ellen Goode, Harald Göring, Celia Greenwood, Fangyi Gu, Johathan Haines, Elizabeth Hauser, Yuan Jiang, Suh-Hang Hank Juo, Cristina Justice, Xiayi Ke, Abbas Khalili, Alison Klein, Daniel L. Koller, Aldi Kradja, Peter Kraft, Ake Ku, Kenneth Lange, Carl Langfeld, Bingshan Li, Chun Li, Wentian Li, Liming Liang, Jian’an Luan, Brion Maher, Partha Pratim Majumder, James Malley, Lisa Martin, Maria Martinez, Brett McKinney, Nancy Mendall, Yan Meng, Brackie Mitchell, Andrew Morris, Alison Motsinger-Reif, Cassandra Mucray, Indranil Mukhopadhyay, Nandita Mukhopadhyay, Bertram Muller-Myhsok, Rosalind Neuman, Nora Nock, Kari North, Michael Nothnagel, Jeff O’Connell, George Papanicolaou, Andrew Paterson, Ruth Pfeiffer, Dajun Qian, Evadnie Rampersaud, John Rice, Steve Rich, Marylyn Ritchie, Andre Scherag, Audrey Schnell, Mary Sehl, Claire Simpson, Janet Sinsheimer, Anne Spence, Hans Stassen, Catherine M. Stein, Marc Suchard, Yun Ju Sun, Heejong Sung, Michael Swartz, Silke Szymczak, Duncan Thomas, Asuman Turkmen, Kai Wang, Shuang Wang, Ellen Wijsman, Marsha Wilcox, Mary Wojczynski, Qunyuan Zhang, Hongyu Zhou. We are grateful for their contributions. Since GAW7 in 1991, Vanessa Olmo has had major responsibility for all aspects of workshop organization. Over the years, as the workshops have increased in size and complexity, she has taken on greatly increased responsibilities. She has primary responsibility for workshop logistics, including interaction with participants, organizers, editors, and publisher; data distribution; site selection and liaison with local organizers; maintenance of the Genetic Analysis Workshops web site and mailing list; and preparation of the proceedings. The workshops could not succeed without her commitment and her enthusiasm. We also thank Selina Flores, Gene Hopstetter, Richard Polich, Rene Sandoval, Rudy Sandoval, and Gerry Vest, who helped with data distribution, communications with participants, and preparation of the online preworkshop volume; and Thomas Dyer, John Blangero, Juan Peralta, Joanne Curran, Jack Kent, and Jac Charlesworth, who worked on simulating the mini-exome data set for GAW17 and prepared the data for distribution. Mimi Braverman assisted with the editing of the GAW17 proceedings, and Maria Messenger and Malinda Mann formatted the articles and prepared the files. Local arrangements for GAW17 required many hours of planning and organization. We are grateful to local organizer Adrienne Cupples as well as volunteers Yansong Cheng, Seung Hoan Choi, Wei Gao, Audrey Hendricks, Susan Hwang, Denver Lybarger, Alisa Manning, Julius Ngwa, Ed Olmo, Jing Wang, Zheng Xiang, Baiyun Yao, and Vivian Zhuang for welcoming us to Boston and for their efforts to ensure a successful workshop. The GAW Advisory Committee, which has a rotating membership, has overall responsibility for long-term planning for the workshops. Its membership at the time of GAW17 included Laura Almasy (chair), Ingrid Borecki, Adrienne Cupples, Saurabh Ghosh, Elizabeth Hauser, Jean MacCluer, Maria Martinez, Glen Satten, Ellen Wijsman, John Witte, Xiaofeng Zhu, and Andreas Ziegler. Continuous funding for the Genetic Analysis Workshops has been provided since 1982 by the National Institute of General Medical Sciences (NIGMS), through National Institutes of Health grant R01 GM31575 awarded to Jean MacCluer and Laura Almasy. This grant also provided scholarship funds to help defray travel costs for 40 graduate students and postdoctoral trainees attending GAW17. We wish to thank Donna Krasnewich for her interest in the Genetic Analysis Workshops and for her efforts as Program Director for the workshop grant at the time of GAW17. We are also grateful to Irene Eckstrand of NIGMS for her enthusiasm and interest in the workshops since they were first envisioned in 1981. The workshop’s results, published in BMC Proceedings (2011), would not be possible without the support of these individuals and NIGMS. We particularly thank Jean MacCluer, who envisioned the need for genetic analysis workshops and pursued and obtained funding for them. Her leadership has been indispensable to the success of the workshops. As always, we wish to express our appreciation to the Genetic Analysis Workshop participants, without whose ongoing, enthusiastic support the workshops could not have enjoyed their continuing success. This article has been published as part of BMC Proceedings Volume 5 Supplement 9, 2011: Genetic Analysis Workshop 17. The full contents of the supplement are available online at http://www.biomedcentral.com/1753-6561/5?issue=S9.

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