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2. Erratum: Sequence data and association statistics from 12,940 type 2 diabetes cases and controls.

Author

Flannick, Jason, Fuchsberger, Christian, Mahajan, Anubha, Teslovich, Tanya M, Agarwala, Vineeta, Gaulton, Kyle J, Caulkins, Lizz, Koesterer, Ryan, Ma, Clement, Moutsianas, Loukas, McCarthy, Davis J, Rivas, Manuel A, Perry, John RB, Sim, Xueling, Blackwell, Thomas W, Robertson, Neil R, Rayner, N William, Cingolani, Pablo, Locke, Adam E, Tajes, Juan Fernandez, Highland, Heather M, Dupuis, Josee, Chines, Peter S, Lindgren, Cecilia M, Hartl, Christopher, Jackson, Anne U, Chen, Han, Huyghe, Jeroen R, van de Bunt, Martijn, Pearson, Richard D, Kumar, Ashish, Müller-Nurasyid, Martina, Grarup, Niels, Stringham, Heather M, Gamazon, Eric R, Lee, Jaehoon, Chen, Yuhui, Scott, Robert A, Below, Jennifer E, Chen, Peng, Huang, Jinyan, Go, Min Jin, Stitzel, Michael L, Pasko, Dorota, Parker, Stephen CJ, Varga, Tibor V, Green, Todd, Beer, Nicola L, Day-Williams, Aaron G, Ferreira, Teresa, Fingerlin, Tasha, Horikoshi, Momoko, Hu, Cheng, Huh, Iksoo, Ikram, Mohammad Kamran, Kim, Bong-Jo, Kim, Yongkang, Kim, Young Jin, Kwon, Min-Seok, Lee, Juyoung, Lee, Selyeong, Lin, Keng-Han, Maxwell, Taylor J, Nagai, Yoshihiko, Wang, Xu, Welch, Ryan P, Yoon, Joon, Zhang, Weihua, Barzilai, Nir, Voight, Benjamin F, Han, Bok-Ghee, Jenkinson, Christopher P, Kuulasmaa, Teemu, Kuusisto, Johanna, Manning, Alisa, Ng, Maggie CY, Palmer, Nicholette D, Balkau, Beverley, Stančáková, Alena, Abboud, Hanna E, Boeing, Heiner, Giedraitis, Vilmantas, Prabhakaran, Dorairaj, Gottesman, Omri, Scott, James, Carey, Jason, Kwan, Phoenix, Grant, George, Smith, Joshua D, Neale, Benjamin M, Purcell, Shaun, Butterworth, Adam S, Howson, Joanna MM, Lee, Heung Man, Lu, Yingchang, Kwak, Soo-Heon, Zhao, Wei, Danesh, John, and Lam, Vincent KL

Abstract

This corrects the article DOI: 10.1038/sdata.2017.179.

Published
2018

3. Sequence data and association statistics from 12,940 type 2 diabetes cases and controls.

Author

Flannick, Jason, Fuchsberger, Christian, Mahajan, Anubha, Teslovich, Tanya M, Agarwala, Vineeta, Gaulton, Kyle J, Caulkins, Lizz, Koesterer, Ryan, Ma, Clement, Moutsianas, Loukas, McCarthy, Davis J, Rivas, Manuel A, Perry, John RB, Sim, Xueling, Blackwell, Thomas W, Robertson, Neil R, Rayner, N William, Cingolani, Pablo, Locke, Adam E, Tajes, Juan Fernandez, Highland, Heather M, Dupuis, Josee, Chines, Peter S, Lindgren, Cecilia M, Hartl, Christopher, Jackson, Anne U, Chen, Han, Huyghe, Jeroen R, van de Bunt, Martijn, Pearson, Richard D, Kumar, Ashish, Müller-Nurasyid, Martina, Grarup, Niels, Stringham, Heather M, Gamazon, Eric R, Lee, Jaehoon, Chen, Yuhui, Scott, Robert A, Below, Jennifer E, Chen, Peng, Huang, Jinyan, Go, Min Jin, Stitzel, Michael L, Pasko, Dorota, Parker, Stephen CJ, Varga, Tibor V, Green, Todd, Beer, Nicola L, Day-Williams, Aaron G, Ferreira, Teresa, Fingerlin, Tasha, Horikoshi, Momoko, Hu, Cheng, Huh, Iksoo, Ikram, Mohammad Kamran, Kim, Bong-Jo, Kim, Yongkang, Kim, Young Jin, Kwon, Min-Seok, Lee, Juyoung, Lee, Selyeong, Lin, Keng-Han, Maxwell, Taylor J, Nagai, Yoshihiko, Wang, Xu, Welch, Ryan P, Yoon, Joon, Zhang, Weihua, Barzilai, Nir, Voight, Benjamin F, Han, Bok-Ghee, Jenkinson, Christopher P, Kuulasmaa, Teemu, Kuusisto, Johanna, Manning, Alisa, Ng, Maggie CY, Palmer, Nicholette D, Balkau, Beverley, Stančáková, Alena, Abboud, Hanna E, Boeing, Heiner, Giedraitis, Vilmantas, Prabhakaran, Dorairaj, Gottesman, Omri, Scott, James, Carey, Jason, Kwan, Phoenix, Grant, George, Smith, Joshua D, Neale, Benjamin M, Purcell, Shaun, Butterworth, Adam S, Howson, Joanna MM, Lee, Heung Man, Lu, Yingchang, Kwak, Soo-Heon, Zhao, Wei, Danesh, John, and Lam, Vincent KL

Subjects
Humans, Diabetes Mellitus, Type 2, European Continental Ancestry Group, Genetic Variation, Diabetes, Human Genome, Genetics, 2.1 Biological and endogenous factors, Metabolic and endocrine
Abstract

To investigate the genetic basis of type 2 diabetes (T2D) to high resolution, the GoT2D and T2D-GENES consortia catalogued variation from whole-genome sequencing of 2,657 European individuals and exome sequencing of 12,940 individuals of multiple ancestries. Over 27M SNPs, indels, and structural variants were identified, including 99% of low-frequency (minor allele frequency [MAF] 0.1-5%) non-coding variants in the whole-genome sequenced individuals and 99.7% of low-frequency coding variants in the whole-exome sequenced individuals. Each variant was tested for association with T2D in the sequenced individuals, and, to increase power, most were tested in larger numbers of individuals (>80% of low-frequency coding variants in ~82 K Europeans via the exome chip, and ~90% of low-frequency non-coding variants in ~44 K Europeans via genotype imputation). The variants, genotypes, and association statistics from these analyses provide the largest reference to date of human genetic information relevant to T2D, for use in activities such as T2D-focused genotype imputation, functional characterization of variants or genes, and other novel analyses to detect associations between sequence variation and T2D.

Published
2017

4. Crowdsourced estimation of cognitive decline and resilience in Alzheimer's disease

Author

Allen, Genevera I, Amoroso, Nicola, Anghel, Catalina, Balagurusamy, Venkat, Bare, Christopher J, Beaton, Derek, Bellotti, Roberto, Bennett, David A, Boehme, Kevin L, Boutros, Paul C, Caberlotto, Laura, Caloian, Cristian, Campbell, Frederick, Neto, Elias Chaibub, Chang, Yu‐Chuan, Chen, Beibei, Chen, Chien‐Yu, Chien, Ting‐Ying, Clark, Tim, Das, Sudeshna, Davatzikos, Christos, Deng, Jieyao, Dillenberger, Donna, Dobson, Richard JB, Dong, Qilin, Doshi, Jimit, Duma, Denise, Errico, Rosangela, Erus, Guray, Everett, Evan, Fardo, David W, Friend, Stephen H, Fröhlich, Holger, Gan, Jessica, St George‐Hyslop, Peter, Ghosh, Satrajit S, Glaab, Enrico, Green, Robert C, Guan, Yuanfang, Hong, Ming‐Yi, Huang, Chao, Hwang, Jinseub, Ibrahim, Joseph, Inglese, Paolo, Iyappan, Anandhi, Jiang, Qijia, Katsumata, Yuriko, Kauwe, John SK, Klein, Arno, Kong, Dehan, Krause, Roland, Lalonde, Emilie, Lauria, Mario, Lee, Eunjee, Lin, Xihui, Liu, Zhandong, Livingstone, Julie, Logsdon, Benjamin A, Lovestone, Simon, Ma, Tsung‐wei, Malhotra, Ashutosh, Mangravite, Lara M, Maxwell, Taylor J, Merrill, Emily, Nagorski, John, Namasivayam, Aishwarya, Narayan, Manjari, Naz, Mufassra, Newhouse, Stephen J, Norman, Thea C, Nurtdinov, Ramil N, Oyang, Yen‐Jen, Pawitan, Yudi, Peng, Shengwen, Peters, Mette A, Piccolo, Stephen R, Praveen, Paurush, Priami, Corrado, Sabelnykova, Veronica Y, Senger, Philipp, Shen, Xia, Simmons, Andrew, Sotiras, Aristeidis, Stolovitzky, Gustavo, Tangaro, Sabina, Tateo, Andrea, Tung, Yi‐An, Tustison, Nicholas J, Varol, Erdem, Vradenburg, George, Weiner, Michael W, Xiao, Guanghua, Xie, Lei, Xie, Yang, Xu, Jia, Yang, Hojin, Zhan, Xiaowei, Zhou, Yunyun, Zhu, Fan, and Zhu, Hongtu

Subjects
Biomedical and Clinical Sciences, Biological Psychology, Clinical Sciences, Neurosciences, Psychology, Neurodegenerative, Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD), Alzheimer's Disease, Brain Disorders, Acquired Cognitive Impairment, Prevention, Behavioral and Social Science, Aging, Dementia, 4.1 Discovery and preclinical testing of markers and technologies, Neurological, Alzheimer Disease, Apolipoproteins E, Biomarkers, Cognition Disorders, Computational Biology, Databases, Bibliographic, Humans, Predictive Value of Tests, Azheimer's disease, Crowdsource, Big data, Bioinformatics, Cognitive decline, Imaging, Genetics, Alzheimer's Disease Neuroimaging Initiative, Geriatrics, Clinical sciences, Biological psychology
Abstract

Identifying accurate biomarkers of cognitive decline is essential for advancing early diagnosis and prevention therapies in Alzheimer's disease. The Alzheimer's disease DREAM Challenge was designed as a computational crowdsourced project to benchmark the current state-of-the-art in predicting cognitive outcomes in Alzheimer's disease based on high dimensional, publicly available genetic and structural imaging data. This meta-analysis failed to identify a meaningful predictor developed from either data modality, suggesting that alternate approaches should be considered for prediction of cognitive performance.

Published
2016

7. The genetic architecture of type 2 diabetes

Author

Fuchsberger, Christian, Flannick, Jason, Teslovich, Tanya M., Mahajan, Anubha, Agarwala, Vineeta, Gaulton, Kyle J., Ma, Clement, Fontanillas, Pierre, Moutsianas, Loukas, McCarthy, Davis J., Rivas, Manuel A., Perry, John R. B., Sim, Xueling, Blackwell, Thomas W., Robertson, Neil R., Rayner, N. William, Cingolani, Pablo, Locke, Adam E., Tajes, Juan Fernandez, Highland, Heather M., Dupuis, Josee, Chines, Peter S., Lindgren, Cecilia M., Hartl, Christopher, Jackson, Anne U., Chen, Han, Huyghe, Jeroen R., van de Bunt, Martijn, Pearson, Richard D., Kumar, Ashish, Müller-Nurasyid, Martina, Grarup, Niels, Stringham, Heather M., Gamazon, Eric R., Lee, Jaehoon, Chen, Yuhui, Scott, Robert A., Below, Jennifer E., Chen, Peng, Huang, Jinyan, Go, Min Jin, Stitzel, Michael L., Pasko, Dorota, Parker, Stephen C. J., Varga, Tibor V., Green, Todd, Beer, Nicola L., Day-Williams, Aaron G., Ferreira, Teresa, Fingerlin, Tasha, Horikoshi, Momoko, Hu, Cheng, Huh, Iksoo, Ikram, Mohammad Kamran, Kim, Bong-Jo, Kim, Yongkang, Kim, Young Jin, Kwon, Min-Seok, Lee, Juyoung, Lee, Selyeong, Lin, Keng-Han, Maxwell, Taylor J., Nagai, Yoshihiko, Wang, Xu, Welch, Ryan P., Yoon, Joon, Zhang, Weihua, Barzilai, Nir, Voight, Benjamin F., Han, Bok-Ghee, Jenkinson, Christopher P., Kuulasmaa, Teemu, Kuusisto, Johanna, Manning, Alisa, Ng, Maggie C. Y., Palmer, Nicholette D., Balkau, Beverley, Stančáková, Alena, Abboud, Hanna E., Boeing, Heiner, Giedraitis, Vilmantas, Prabhakaran, Dorairaj, Gottesman, Omri, Scott, James, Carey, Jason, Kwan, Phoenix, Grant, George, Smith, Joshua D., Neale, Benjamin M., Purcell, Shaun, Butterworth, Adam S., Howson, Joanna M. M., Lee, Heung Man, Lu, Yingchang, Kwak, Soo-Heon, Zhao, Wei, Danesh, John, Lam, Vincent K. L., Park, Kyong Soo, Saleheen, Danish, So, Wing Yee, Tam, Claudia H. T., Afzal, Uzma, Aguilar, David, Arya, Rector, Aung, Tin, Chan, Edmund, Navarro, Carmen, Cheng, Ching-Yu, Palli, Domenico, Correa, Adolfo, Curran, Joanne E., Rybin, Denis, Farook, Vidya S., Fowler, Sharon P., Freedman, Barry I., Griswold, Michael, Hale, Daniel Esten, Hicks, Pamela J., Khor, Chiea-Chuen, Kumar, Satish, Lehne, Benjamin, Thuillier, Dorothée, Lim, Wei Yen, Liu, Jianjun, van der Schouw, Yvonne T., Loh, Marie, Musani, Solomon K., Puppala, Sobha, Scott, William R., Yengo, Loïc, Tan, Sian-Tsung, Taylor Jr., Herman A., Thameem, Farook, Wilson, Gregory, Wong, Tien Yin, Njølstad, Pål Rasmus, Levy, Jonathan C., Mangino, Massimo, Bonnycastle, Lori L., Schwarzmayr, Thomas, Fadista, João, Surdulescu, Gabriela L., Herder, Christian, Groves, Christopher J., Wieland, Thomas, Bork-Jensen, Jette, Brandslund, Ivan, Christensen, Cramer, Koistinen, Heikki A., Doney, Alex S. F., Kinnunen, Leena, Esko, Tõnu, Farmer, Andrew J., Hakaste, Liisa, Hodgkiss, Dylan, Kravic, Jasmina, Lyssenko, Valeriya, Hollensted, Mette, Jørgensen, Marit E., Jørgensen, Torben, Ladenvall, Claes, Justesen, Johanne Marie, Käräjämäki, Annemari, Kriebel, Jennifer, Rathmann, Wolfgang, Lannfelt, Lars, Lauritzen, Torsten, Narisu, Narisu, Linneberg, Allan, Melander, Olle, Milani, Lili, Neville, Matt, Orho-Melander, Marju, Qi, Lu, Qi, Qibin, Roden, Michael, Rolandsson, Olov, Swift, Amy, Rosengren, Anders H., Stirrups, Kathleen, Wood, Andrew R., Mihailov, Evelin, Blancher, Christine, Carneiro, Mauricio O., Maguire, Jared, Poplin, Ryan, Shakir, Khalid, Fennell, Timothy, DePristo, Mark, Hrabé de Angelis, Martin, Deloukas, Panos, Gjesing, Anette P., Jun, Goo, Nilsson, Peter, Murphy, Jacquelyn, Onofrio, Robert, Thorand, Barbara, Hansen, Torben, Meisinger, Christa, Hu, Frank B., Isomaa, Bo, Karpe, Fredrik, Liang, Liming, Peters, Annette, Huth, Cornelia, O’Rahilly, Stephen P., Palmer, Colin N. A., Pedersen, Oluf, Rauramaa, Rainer, Tuomilehto, Jaakko, Salomaa, Veikko, Watanabe, Richard M., Syvänen, Ann-Christine, Bergman, Richard N., Bharadwaj, Dwaipayan, Bottinger, Erwin P., Cho, Yoon Shin, Chandak, Giriraj R., Chan, Juliana C. N., Chia, Kee Seng, Daly, Mark J., Ebrahim, Shah B., Langenberg, Claudia, Elliott, Paul, Jablonski, Kathleen A., Lehman, Donna M., Jia, Weiping, Ma, Ronald C. W., Pollin, Toni I., Sandhu, Manjinder, Tandon, Nikhil, Froguel, Philippe, Barroso, Inês, Teo, Yik Ying, Zeggini, Eleftheria, Loos, Ruth J. F., Small, Kerrin S., Ried, Janina S., DeFronzo, Ralph A., Grallert, Harald, Glaser, Benjamin, Metspalu, Andres, Wareham, Nicholas J., Walker, Mark, Banks, Eric, Gieger, Christian, Ingelsson, Erik, Im, Hae Kyung, Illig, Thomas, Franks, Paul W., Buck, Gemma, Trakalo, Joseph, Buck, David, Prokopenko, Inga, Mägi, Reedik, Lind, Lars, Farjoun, Yossi, Owen, Katharine R., Gloyn, Anna L., Strauch, Konstantin, Tuomi, Tiinamaija, Kooner, Jaspal Singh, Lee, Jong-Young, Park, Taesung, Donnelly, Peter, Morris, Andrew D., Hattersley, Andrew T., Bowden, Donald W., Collins, Francis S., Atzmon, Gil, Chambers, John C., Spector, Timothy D., Laakso, Markku, Strom, Tim M., Bell, Graeme I., Blangero, John, Duggirala, Ravindranath, Tai, E. Shyong, McVean, Gilean, Hanis, Craig L., Wilson, James G., Seielstad, Mark, Frayling, Timothy M., Meigs, James B., Cox, Nancy J., Sladek, Rob, Lander, Eric S., Gabriel, Stacey, Burtt, Noël P., Mohlke, Karen L., Meitinger, Thomas, Groop, Leif, Abecasis, Goncalo, Florez, Jose C., Scott, Laura J., Morris, Andrew P., Kang, Hyun Min, Boehnke, Michael, Altshuler, David, and McCarthy, Mark I.

Published
2016
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13. A scan of chromosome 10 identifies a novel locus showing strong association with late-onset Alzheimer disease

Author

Grupe, Andrew, Li, Yonghong, Rowland, Charles, Nowotny, Petra, Hinrichs, Anthony L., Smemo, Scott, Kauwe, John S.K., Maxwell, Taylor J., Cherny, Sara, Doil, Lisa, Tacey, Kristina, van Luchene, Ryan, Myers, Amanda, Wavrant-De Vrieze, Fabienne, Kaleem, Mona, Hollingworth, Paul, Jehu, Luke, Foy, Catherine, Archer, Nicola, Hamilton, Gillian, Holmans, Peter, Morris, Chris M., Catanese, Joseph, Sninsky, John, White, Thomas J., Powell, John, Hardy, John, O'Donovan, Michael, Lovestone, Simon, Jones, Lesley, Morris, John C., Thal, Leon, Owen, Michael, Williams, Julie, and Goate, Alison

Subjects
Alzheimer's disease -- Genetic aspects, Alzheimer's disease -- Development and progression, Chromosomes -- Research, Gene expression -- Research, Biological sciences
Published
2006

15. DAPK1 variants are associated with Alzheimer's disease and allele-specific expression

Author

Li, Yonghong, Grupe, Andrew, Rowland, Charles, Nowotny, Petra, Kauwe, John S.K., Smemo, Scott, Hinrichs, Anthony, Tacey, Kristina, Toombs, Timothy A., Kwok, Shirley, Catanese, Joseph, White, Thomas J., Maxwell, Taylor J., Hollingworth, Paul, Abraham, Richard, Rubinsztein, David C., Brayne, Carol, Vrièze, Fabienne Wavrant-De, Hardy, John, OʼDonovan, Michael, Lovestone, Simon, Morris, John C., Thal, Leon J., Owen, Michael, Williams, Julie, and Goate, Alison

Published
2006

17. Sequence data and association statistics from 12,940 type 2 diabetes cases and controls

Author

Massachusetts Institute of Technology. Department of Biology, Altshuler, David M, Jason, Flannick, Fuchsberger, Christian, Mahajan, Anubha, Teslovich, Tanya M., Agarwala, Vineeta, Gaulton, Kyle J., Caulkins, Lizz, Koesterer, Ryan, Ma, Clement, Moutsianas, Loukas, McCarthy, Davis J., Rivas, Manuel A., Perry, John R. B., Sim, Xueling, Blackwell, Thomas W., Robertson, Neil R., Rayner, N William, Cingolani, Pablo, Locke, Adam E., Tajes, Juan Fernandez, Highland, Heather M., Dupuis, Josee, Chines, Peter S., Lindgren, Cecilia M., Hartl, Christopher, Jackson, Anne U., Chen, Han, Huyghe, Jeroen R., van de Bunt, Martijn, Pearson, Richard D., Kumar, Ashish, Müller-Nurasyid, Martina, Grarup, Niels, Stringham, Heather M., Gamazon, Eric R., Chen, Yuhui, Scott, Robert A., Below, Jennifer E., Chen, Peng, Huang, Jinyan, Go, Min Jin, Stitzel, Michael L., Pasko, Dorota, Parker, Stephen C. J., Varga, Tibor V., Green, Todd, Beer, Nicola L., Day-Williams, Aaron G., Ferreira, Teresa, Fingerlin, Tasha, Horikoshi, Momoko, Hu, Cheng, Huh, Iksoo, Ikram, Mohammad Kamran, Kim, Bong-Jo, Kim, Yongkang, Kim, Young Jin, Kwon, Min-Seok, Lee, Juyoung, Lee, Selyeong, Lin, Keng-Han, Maxwell, Taylor J., Nagai, Yoshihiko, Wang, Xu, Welch, Ryan P., Yoon, Joon, Zhang, Weihua, Barzilai, Nir, Voight, Benjamin F., Han, Bok-Ghee, Jenkinson, Christopher P., Kuulasmaa, Teemu, Kuusisto, Johanna, Manning, Alisa, Ng, Maggie C. Y., Palmer, Nicholette D., Balkau, Beverley, Stančáková, Alena, Abboud, Hanna E., Boeing, Heiner, Giedraitis, Vilmantas, Prabhakaran, Dorairaj, Gottesman, Omri, Scott, James, Carey, Jason, Kwan, Phoenix, Grant, George, Smith, Joshua D., Neale, Benjamin M., Purcell, Shaun, Butterworth, Adam S., Howson, Joanna M. M., Lee, Heung Man, Lu, Yingchang, Kwak, Soo-Heon, Zhao, Wei, Danesh, John, Lam, Vincent K. L., Park, Kyong Soo, Saleheen, Danish, So, Wing Yee, Tam, Claudia H. T., Afzal, Uzma, Aguilar, David, Arya, Rector, Aung, Tin, Chan, Edmund, Navarro, Carmen, Cheng, Ching-Yu, Palli, Domenico, Correa, Adolfo, Curran, Joanne E., Rybin, Dennis, Farook, Vidya S., Fowler, Sharon P., Freedman, Barry I., Griswold, Michael, Hale, Daniel Esten, Hicks, Pamela J., Khor, Chiea-Chuen, Kumar, Satish, Lehne, Benjamin, Thuillier, Dorothée, Lim, Wei Yen, Liu, Jianjun, Loh, Marie, Musani, Solomon K., Puppala, Sobha, Scott, William R., Yengo, Loïc, Tan, Sian-Tsung, Taylor, Herman A., Thameem, Farook, Wilson, Gregory, Wong, Tien Yin, Njølstad, Pål Rasmus, Levy, Jonathan C., Mangino, Massimo, Bonnycastle, Lori L., Schwarzmayr, Thomas, Fadista, João, Surdulescu, Gabriela L., Herder, Christian, Groves, Christopher J., Wieland, Thomas, Bork-Jensen, Jette, Brandslund, Ivan, Christensen, Cramer, Koistinen, Heikki A., Doney, Alex S. F., Kinnunen, Leena, Esko, Tõnu, Farmer, Andrew J., Hakaste, Liisa, Hodgkiss, Dylan, Kravic, Jasmina, Lyssenko, Valeri, Hollensted, Mette, Jørgensen, Marit E., Jørgensen, Torben, Ladenvall, Claes, Justesen, Johanne Marie, Käräjämäki, Annemari, Kriebel, Jennifer, Rathmann, Wolfgang, Lannfelt, Lars, Lauritzen, Torsten, Narisu, Narisu, Linneberg, Allan, Melander, Olle, Milani, Lili, Neville, Matt, Orho-Melander, Marju, Qi, Lu, Qi, Qibin, Roden, Michael, Rolandsson, Olov, Altshuler, David, Lee, Jaehoon, Ph. D. Massachusetts Institute of Technology, Massachusetts Institute of Technology. Department of Biology, Altshuler, David M, Jason, Flannick, Fuchsberger, Christian, Mahajan, Anubha, Teslovich, Tanya M., Agarwala, Vineeta, Gaulton, Kyle J., Caulkins, Lizz, Koesterer, Ryan, Ma, Clement, Moutsianas, Loukas, McCarthy, Davis J., Rivas, Manuel A., Perry, John R. B., Sim, Xueling, Blackwell, Thomas W., Robertson, Neil R., Rayner, N William, Cingolani, Pablo, Locke, Adam E., Tajes, Juan Fernandez, Highland, Heather M., Dupuis, Josee, Chines, Peter S., Lindgren, Cecilia M., Hartl, Christopher, Jackson, Anne U., Chen, Han, Huyghe, Jeroen R., van de Bunt, Martijn, Pearson, Richard D., Kumar, Ashish, Müller-Nurasyid, Martina, Grarup, Niels, Stringham, Heather M., Gamazon, Eric R., Chen, Yuhui, Scott, Robert A., Below, Jennifer E., Chen, Peng, Huang, Jinyan, Go, Min Jin, Stitzel, Michael L., Pasko, Dorota, Parker, Stephen C. J., Varga, Tibor V., Green, Todd, Beer, Nicola L., Day-Williams, Aaron G., Ferreira, Teresa, Fingerlin, Tasha, Horikoshi, Momoko, Hu, Cheng, Huh, Iksoo, Ikram, Mohammad Kamran, Kim, Bong-Jo, Kim, Yongkang, Kim, Young Jin, Kwon, Min-Seok, Lee, Juyoung, Lee, Selyeong, Lin, Keng-Han, Maxwell, Taylor J., Nagai, Yoshihiko, Wang, Xu, Welch, Ryan P., Yoon, Joon, Zhang, Weihua, Barzilai, Nir, Voight, Benjamin F., Han, Bok-Ghee, Jenkinson, Christopher P., Kuulasmaa, Teemu, Kuusisto, Johanna, Manning, Alisa, Ng, Maggie C. Y., Palmer, Nicholette D., Balkau, Beverley, Stančáková, Alena, Abboud, Hanna E., Boeing, Heiner, Giedraitis, Vilmantas, Prabhakaran, Dorairaj, Gottesman, Omri, Scott, James, Carey, Jason, Kwan, Phoenix, Grant, George, Smith, Joshua D., Neale, Benjamin M., Purcell, Shaun, Butterworth, Adam S., Howson, Joanna M. M., Lee, Heung Man, Lu, Yingchang, Kwak, Soo-Heon, Zhao, Wei, Danesh, John, Lam, Vincent K. L., Park, Kyong Soo, Saleheen, Danish, So, Wing Yee, Tam, Claudia H. T., Afzal, Uzma, Aguilar, David, Arya, Rector, Aung, Tin, Chan, Edmund, Navarro, Carmen, Cheng, Ching-Yu, Palli, Domenico, Correa, Adolfo, Curran, Joanne E., Rybin, Dennis, Farook, Vidya S., Fowler, Sharon P., Freedman, Barry I., Griswold, Michael, Hale, Daniel Esten, Hicks, Pamela J., Khor, Chiea-Chuen, Kumar, Satish, Lehne, Benjamin, Thuillier, Dorothée, Lim, Wei Yen, Liu, Jianjun, Loh, Marie, Musani, Solomon K., Puppala, Sobha, Scott, William R., Yengo, Loïc, Tan, Sian-Tsung, Taylor, Herman A., Thameem, Farook, Wilson, Gregory, Wong, Tien Yin, Njølstad, Pål Rasmus, Levy, Jonathan C., Mangino, Massimo, Bonnycastle, Lori L., Schwarzmayr, Thomas, Fadista, João, Surdulescu, Gabriela L., Herder, Christian, Groves, Christopher J., Wieland, Thomas, Bork-Jensen, Jette, Brandslund, Ivan, Christensen, Cramer, Koistinen, Heikki A., Doney, Alex S. F., Kinnunen, Leena, Esko, Tõnu, Farmer, Andrew J., Hakaste, Liisa, Hodgkiss, Dylan, Kravic, Jasmina, Lyssenko, Valeri, Hollensted, Mette, Jørgensen, Marit E., Jørgensen, Torben, Ladenvall, Claes, Justesen, Johanne Marie, Käräjämäki, Annemari, Kriebel, Jennifer, Rathmann, Wolfgang, Lannfelt, Lars, Lauritzen, Torsten, Narisu, Narisu, Linneberg, Allan, Melander, Olle, Milani, Lili, Neville, Matt, Orho-Melander, Marju, Qi, Lu, Qi, Qibin, Roden, Michael, Rolandsson, Olov, Altshuler, David, and Lee, Jaehoon, Ph. D. Massachusetts Institute of Technology

Abstract

To investigate the genetic basis of type 2 diabetes (T2D) to high resolution, the GoT2D and T2D-GENES consortia catalogued variation from whole-genome sequencing of 2,657 European individuals and exome sequencing of 12,940 individuals of multiple ancestries. Over 27M SNPs, indels, and structural variants were identified, including 99% of low-frequency (minor allele frequency [MAF] 0.1-5%) non-coding variants in the whole-genome sequenced individuals and 99.7% of low-frequency coding variants in the whole-exome sequenced individuals. Each variant was tested for association with T2D in the sequenced individuals, and, to increase power, most were tested in larger numbers of individuals ( > 80% of low-frequency coding variants in ∼82 K Europeans via the exome chip, and ∼90% of low-frequency non-coding variants in ∼44 K Europeans via genotype imputation). The variants, genotypes, and association statistics from these analyses provide the largest reference to date of human genetic information relevant to T2D, for use in activities such as T2D-focused genotype imputation, functional characterization of variants or genes, and other novel analyses to detect associations between sequence variation and T2D.

Published
2018

18. Data Descriptor : Sequence data and association statistics from 12,940 type 2 diabetes cases and controls

Author

Flannick, Jason, Fuchsberger, Christian, Mahajan, Anubha, Teslovich, Tanya M., Agarwala, Vineeta, Gaulton, Kyle J., Caulkins, Lizz, Koesterer, Ryan, Ma, Clement, Moutsianas, Loukas, McCarthy, Davis J., Rivas, Manuel A., Perry, John R.B., Sim, Xueling, Blackwell, Thomas W., Robertson, Neil R., Rayner, N. William, Cingolani, Pablo, Locke, Adam E., Tajes, Juan Fernandez, Highland, Heather M., Dupuis, Josée, Chines, Peter S., Lindgren, Cecilia M., Hartl, Christopher, Jackson, Anne U., Chen, Han, Huyghe, Jeroen R., Van De Bunt, Martijn, Pearson, Richard D., Kumar, Ashish, Müller-Nurasyid, Martina, Grarup, Niels, Stringham, Heather M., Gamazon, Eric R., Lee, Jaehoon, Chen, Yuhui, Scott, Robert A., Below, Jennifer E., Chen, Peng, Huang, Jinyan, Go, Min Jin, Stitzel, Michael L., Pasko, Dorota, Parker, Stephen C.J., Varga, Tibor V., Green, Todd, Beer, Nicola L., Day-Williams, Aaron G., Ferreira, Teresa, Fingerlin, Tasha, Horikoshi, Momoko, Hu, Cheng, Huh, Iksoo, Ikram, Mohammad Kamran, Kim, Bong Jo, Kim, Yongkang, Kim, Young Jin, Kwon, Min Seok, Lee, Juyoung, Lee, Selyeong, Lin, Keng Han, Maxwell, Taylor J., Nagai, Yoshihiko, Wang, Xu, Welch, Ryan P., Yoon, Joon, Zhang, Weihua, Barzilai, Nir, Voight, Benjamin F., Han, Bok Ghee, Jenkinson, Christopher P., Kuulasmaa, Teemu, Kuusisto, Johanna, Manning, Alisa, Ng, Maggie C.Y., Palmer, Nicholette D., Balkau, Beverley, Stančáková, Alena, Abboud, Hanna E., Boeing, Heiner, Giedraitis, Vilmantas, Prabhakaran, Dorairaj, Gottesman, Omri, Scott, James, Carey, Jason, Kwan, Phoenix, Grant, George, Smith, Joshua D., Neale, Benjamin M., Purcell, Shaun, Butterworth, Adam S., Howson, Joanna M.M., Lee, Heung Man, Lu, Yingchang, Kwak, Soo Heon, Zhao, Wei, Danesh, John, Lam, Vincent K.L., Park, Kyong Soo, Saleheen, Danish, So, Wing Yee, Tam, Claudia H.T., Afzal, Uzma, Aguilar, David, Arya, Rector, Aung, Tin, Chan, Edmund, Navarro, Carmen, Cheng, Ching Yu, Palli, Domenico, Correa, Adolfo, Curran, Joanne E., Rybin, Dennis, Farook, Vidya S., Fowler, Sharon P., Freedman, Barry I., Griswold, Michael, Hale, Daniel Esten, Hicks, Pamela J., Khor, Chiea Chuen, Kumar, Satish, Lehne, Benjamin, Thuillier, Dorothée, Lim, Wei Yen, Liu, Jianjun, Loh, Marie, Musani, Solomon K., Puppala, Sobha, Scott, William R., Yengo, Loïc, Tan, Sian Tsung, Taylor, Herman A., Thameem, Farook, Wilson, Gregory, Wong, Tien Yin, Njølstad, Pål Rasmus, Levy, Jonathan C., Mangino, Massimo, Bonnycastle, Lori L., Schwarzmayr, Thomas, Fadista, João, Surdulescu, Gabriela L., Herder, Christian, Groves, Christopher J., Wieland, Thomas, Bork-Jensen, Jette, Brandslund, Ivan, Christensen, Cramer, Koistinen, Heikki A., Doney, Alex S.F., Kinnunen, Leena, Esko, Tõnu, Farmer, Andrew J., Hakaste, Liisa, Hodgkiss, Dylan, Kravic, Jasmina, Lyssenko, Valeriya, Hollensted, Mette, Jørgensen, Marit E., Jørgensen, Torben, Ladenvall, Claes, Justesen, Johanne Marie, Käräjämäki, Annemari, Kriebel, Jennifer, Rathmann, Wolfgang, Lannfelt, Lars, Lauritzen, Torsten, Narisu, Narisu, Linneberg, Allan, Melander, Olle, Milani, Lili, Neville, Matt, Orho-Melander, Marju, Qi, Lu, Qi, Qibin, Roden, Michael, Rolandsson, Olov, Swift, Amy, Rosengren, Anders H., Stirrups, Kathleen, Wood, Andrew R., Mihailov, Evelin, Blancher, Christine, Carneiro, Mauricio O., Maguire, Jared, Poplin, Ryan, Shakir, Khalid, Fennell, Timothy, DePristo, Mark, De Angelis, Martin Hrabé, Deloukas, Panos, Gjesing, Anette P., Jun, Goo, Nilsson, Peter M., Murphy, Jacquelyn, Onofrio, Robert, Thorand, Barbara, Hansen, Torben, Meisinger, Christa, Hu, Frank B., Isomaa, Bo, Karpe, Fredrik, Liang, Liming, Peters, Annette, Huth, Cornelia, O'Rahilly, Stephen P., Palmer, Colin N.A., Pedersen, Oluf, Rauramaa, Rainer, Tuomilehto, Jaakko, Salomaa, Veikko, Watanabe, Richard M., Syvänen, Ann Christine, Bergman, Richard N., Bharadwaj, Dwaipayan, Bottinger, Erwin P., Cho, Yoon Shin, Chandak, Giriraj R., Chan, Juliana C.N., Chia, Kee Seng, Daly, Mark J., Ebrahim, Shah B., Langenberg, Claudia, Elliott, Paul, Jablonski, Kathleen A., Lehman, Donna M., Jia, Weiping, Ma, Ronald C.W., Pollin, Toni I., Sandhu, Manjinder, Tandon, Nikhil, Froguel, Philippe, Barroso, Inês, Teo, Yik Ying, Zeggini, Eleftheria, Loos, Ruth J.F., Small, Kerrin S., Ried, Janina S., DeFronzo, Ralph A., Grallert, Harald, Glaser, Benjamin, Metspalu, Andres, Wareham, Nicholas J., Walker, Mark, Banks, Eric, Gieger, Christian, Ingelsson, Erik, Im, Hae Kyung, Illig, Thomas, Franks, Paul W., Buck, Gemma, Trakalo, Joseph, Buck, David, Prokopenko, Inga, Mägi, Reedik, Lind, Lars, Farjoun, Yossi, Owen, Katharine R., Gloyn, Anna L., Strauch, Konstantin, Tuomi, Tiinamaija, Kooner, Jaspal Singh, Lee, Jong Young, Park, Taesung, Donnelly, Peter, Morris, Andrew D., Hattersley, Andrew T., Bowden, Donald W., Collins, Francis S., Atzmon, Gil, Chambers, John C., Spector, Timothy D., Laakso, Markku, Strom, Tim M., Bell, Graeme I., Blangero, John, Duggirala, Ravindranath, Tai, Eshyong, McVean, Gilean, Hanis, Craig L., Wilson, James G., Seielstad, Mark, Frayling, Timothy M., Meigs, James B., Cox, Nancy J., Sladek, Rob, Lander, Eric S., Gabriel, Stacey, Mohlke, Karen L., Meitinger, Thomas, Groop, Leif, Abecasis, Goncalo, Scott, Laura J., Morris, Andrew P., Kang, Hyun Min, Altshuler, David, Burtt, Noël P., Florez, Jose C., Boehnke, Michael, McCarthy, Mark I., Clinicum, Department of Medicine, Endokrinologian yksikkö, Research Programs Unit, Diabetes and Obesity Research Program, Institute for Molecular Medicine Finland, HUS Internal Medicine and Rehabilitation, and HUS Abdominal Center

Subjects
MUTATIONS, COMMON DISEASES, POPULATION-SCALE, Endocrinology and Diabetes, FRAMEWORK, GENETIC ARCHITECTURE, RARE VARIANTS, DISCOVERY, 3121 General medicine, internal medicine and other clinical medicine, Endokrinologi och diabetes, IMPUTATION, GENOME-WIDE ASSOCIATION, Medical Genetics, METAANALYSIS, Medicinsk genetik
Abstract

Correction: SCIENTIFIC DATA Vol. 5, Article Number: 180182, DOI: 10.1038/sdata.2018.2 Published: JAN 23 2018 To investigate the genetic basis of type 2 diabetes (T2D) to high resolution, the GoT2D and T2D-GENES consortia catalogued variation from whole-genome sequencing of 2,657 European individuals and exome sequencing of 12,940 individuals of multiple ancestries. Over 27M SNPs, indels, and structural variants were identified, including 99% of low-frequency (minor allele frequency [MAF] 0.1-5%) non-coding variants in the whole-genome sequenced individuals and 99.7% of low-frequency coding variants in the whole-exome sequenced individuals. Each variant was tested for association with T2D in the sequenced individuals, and, to increase power, most were tested in larger numbers of individuals (> 80% of low-frequency coding variants in similar to 82 K Europeans via the exome chip, and similar to 90% of low-frequency non-coding variants in similar to 44 K Europeans via genotype imputation). The variants, genotypes, and association statistics from these analyses provide the largest reference to date of human genetic information relevant to T2D, for use in activities such as T2D-focused genotype imputation, functional characterization of variants or genes, and other novel analyses to detect associations between sequence variation and T2D.

Published
2017
Full Text
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20. Data Descriptor:Sequence data and association statistics from 12,940 type 2 diabetes cases and controls

Author

Flannick, Jason, Fuchsberger, Christian, Mahajan, Anubha, Teslovich, Tanya M., Agarwala, Vineeta, Gaulton, Kyle J., Caulkins, Lizz, Koesterer, Ryan, Ma, Clement, Moutsianas, Loukas, McCarthy, Davis J., Rivas, Manuel A., Perry, John R.B., Sim, Xueling, Blackwell, Thomas W., Robertson, Neil R., Rayner, N. William, Cingolani, Pablo, Locke, Adam E., Tajes, Juan Fernandez, Highland, Heather M., Dupuis, Josée, Chines, Peter S., Lindgren, Cecilia M., Hartl, Christopher, Jackson, Anne U., Chen, Han, Huyghe, Jeroen R., Van De Bunt, Martijn, Pearson, Richard D., Kumar, Ashish, Müller-Nurasyid, Martina, Grarup, Niels, Stringham, Heather M., Gamazon, Eric R., Lee, Jaehoon, Chen, Yuhui, Scott, Robert A., Below, Jennifer E., Chen, Peng, Huang, Jinyan, Go, Min Jin, Stitzel, Michael L., Pasko, Dorota, Parker, Stephen C.J., Varga, Tibor V., Green, Todd, Beer, Nicola L., Day-Williams, Aaron G., Ferreira, Teresa, Fingerlin, Tasha, Horikoshi, Momoko, Hu, Cheng, Huh, Iksoo, Ikram, Mohammad Kamran, Kim, Bong Jo, Kim, Yongkang, Kim, Young Jin, Kwon, Min Seok, Lee, Juyoung, Lee, Selyeong, Lin, Keng Han, Maxwell, Taylor J., Nagai, Yoshihiko, Wang, Xu, Welch, Ryan P., Yoon, Joon, Zhang, Weihua, Barzilai, Nir, Voight, Benjamin F., Han, Bok Ghee, Jenkinson, Christopher P., Kuulasmaa, Teemu, Kuusisto, Johanna, Manning, Alisa, Ng, Maggie C.Y., Palmer, Nicholette D., Balkau, Beverley, Stančáková, Alena, Abboud, Hanna E., Boeing, Heiner, Giedraitis, Vilmantas, Prabhakaran, Dorairaj, Gottesman, Omri, Scott, James, Carey, Jason, Kwan, Phoenix, Grant, George, Smith, Joshua D., Neale, Benjamin M., Purcell, Shaun, Butterworth, Adam S., Howson, Joanna M.M., Lee, Heung Man, Lu, Yingchang, Kwak, Soo Heon, Zhao, Wei, Danesh, John, Lam, Vincent K.L., Park, Kyong Soo, Saleheen, Danish, So, Wing Yee, Tam, Claudia H.T., Afzal, Uzma, Aguilar, David, Arya, Rector, Aung, Tin, Chan, Edmund, Navarro, Carmen, Cheng, Ching Yu, Palli, Domenico, Correa, Adolfo, Curran, Joanne E., Rybin, Dennis, Farook, Vidya S., Fowler, Sharon P., Freedman, Barry I., Griswold, Michael, Hale, Daniel Esten, Hicks, Pamela J., Khor, Chiea Chuen, Kumar, Satish, Lehne, Benjamin, Thuillier, Dorothée, Lim, Wei Yen, Liu, Jianjun, Loh, Marie, Musani, Solomon K., Puppala, Sobha, Scott, William R., Yengo, Loïc, Tan, Sian Tsung, Taylor, Herman A., Thameem, Farook, Wilson, Gregory, Wong, Tien Yin, Njølstad, Pål Rasmus, Levy, Jonathan C., Mangino, Massimo, Bonnycastle, Lori L., Schwarzmayr, Thomas, Fadista, João, Surdulescu, Gabriela L., Herder, Christian, Groves, Christopher J., Wieland, Thomas, Bork-Jensen, Jette, Brandslund, Ivan, Christensen, Cramer, Koistinen, Heikki A., Doney, Alex S.F., Kinnunen, Leena, Esko, Tõnu, Farmer, Andrew J., Hakaste, Liisa, Hodgkiss, Dylan, Kravic, Jasmina, Lyssenko, Valeriya, Hollensted, Mette, Jørgensen, Marit E., Jørgensen, Torben, Ladenvall, Claes, Justesen, Johanne Marie, Käräjämäki, Annemari, Kriebel, Jennifer, Rathmann, Wolfgang, Lannfelt, Lars, Lauritzen, Torsten, Narisu, Narisu, Linneberg, Allan, Melander, Olle, Milani, Lili, Neville, Matt, Orho-Melander, Marju, Qi, Lu, Qi, Qibin, Roden, Michael, Rolandsson, Olov, Swift, Amy, Rosengren, Anders H., Stirrups, Kathleen, Wood, Andrew R., Mihailov, Evelin, Blancher, Christine, Carneiro, Mauricio O., Maguire, Jared, Poplin, Ryan, Shakir, Khalid, Fennell, Timothy, DePristo, Mark, De Angelis, Martin Hrabé, Deloukas, Panos, Gjesing, Anette P., Jun, Goo, Nilsson, Peter M., Murphy, Jacquelyn, Onofrio, Robert, Thorand, Barbara, Hansen, Torben, Meisinger, Christa, Hu, Frank B., Isomaa, Bo, Karpe, Fredrik, Liang, Liming, Peters, Annette, Huth, Cornelia, O'Rahilly, Stephen P., Palmer, Colin N.A., Pedersen, Oluf, Rauramaa, Rainer, Tuomilehto, Jaakko, Salomaa, Veikko, Watanabe, Richard M., Syvänen, Ann Christine, Bergman, Richard N., Bharadwaj, Dwaipayan, Bottinger, Erwin P., Cho, Yoon Shin, Chandak, Giriraj R., Chan, Juliana C.N., Chia, Kee Seng, Daly, Mark J., Ebrahim, Shah B., Langenberg, Claudia, Elliott, Paul, Jablonski, Kathleen A., Lehman, Donna M., Jia, Weiping, Ma, Ronald C.W., Pollin, Toni I., Sandhu, Manjinder, Tandon, Nikhil, Froguel, Philippe, Barroso, Inês, Teo, Yik Ying, Zeggini, Eleftheria, Loos, Ruth J.F., Small, Kerrin S., Ried, Janina S., DeFronzo, Ralph A., Grallert, Harald, Glaser, Benjamin, Metspalu, Andres, Wareham, Nicholas J., Walker, Mark, Banks, Eric, Gieger, Christian, Ingelsson, Erik, Im, Hae Kyung, Illig, Thomas, Franks, Paul W., Buck, Gemma, Trakalo, Joseph, Buck, David, Prokopenko, Inga, Mägi, Reedik, Lind, Lars, Farjoun, Yossi, Owen, Katharine R., Gloyn, Anna L., Strauch, Konstantin, Tuomi, Tiinamaija, Kooner, Jaspal Singh, Lee, Jong Young, Park, Taesung, Donnelly, Peter, Morris, Andrew D., Hattersley, Andrew T., Bowden, Donald W., Collins, Francis S., Atzmon, Gil, Chambers, John C., Spector, Timothy D., Laakso, Markku, Strom, Tim M., Bell, Graeme I., Blangero, John, Duggirala, Ravindranath, Tai, Eshyong, McVean, Gilean, Hanis, Craig L., Wilson, James G., Seielstad, Mark, Frayling, Timothy M., Meigs, James B., Cox, Nancy J., Sladek, Rob, Lander, Eric S., Gabriel, Stacey, Mohlke, Karen L., Meitinger, Thomas, Groop, Leif, Abecasis, Goncalo, Scott, Laura J., Morris, Andrew P., Kang, Hyun Min, Altshuler, David, Burtt, Noël P., Florez, Jose C., Boehnke, Michael, McCarthy, Mark I., Flannick, Jason, Fuchsberger, Christian, Mahajan, Anubha, Teslovich, Tanya M., Agarwala, Vineeta, Gaulton, Kyle J., Caulkins, Lizz, Koesterer, Ryan, Ma, Clement, Moutsianas, Loukas, McCarthy, Davis J., Rivas, Manuel A., Perry, John R.B., Sim, Xueling, Blackwell, Thomas W., Robertson, Neil R., Rayner, N. William, Cingolani, Pablo, Locke, Adam E., Tajes, Juan Fernandez, Highland, Heather M., Dupuis, Josée, Chines, Peter S., Lindgren, Cecilia M., Hartl, Christopher, Jackson, Anne U., Chen, Han, Huyghe, Jeroen R., Van De Bunt, Martijn, Pearson, Richard D., Kumar, Ashish, Müller-Nurasyid, Martina, Grarup, Niels, Stringham, Heather M., Gamazon, Eric R., Lee, Jaehoon, Chen, Yuhui, Scott, Robert A., Below, Jennifer E., Chen, Peng, Huang, Jinyan, Go, Min Jin, Stitzel, Michael L., Pasko, Dorota, Parker, Stephen C.J., Varga, Tibor V., Green, Todd, Beer, Nicola L., Day-Williams, Aaron G., Ferreira, Teresa, Fingerlin, Tasha, Horikoshi, Momoko, Hu, Cheng, Huh, Iksoo, Ikram, Mohammad Kamran, Kim, Bong Jo, Kim, Yongkang, Kim, Young Jin, Kwon, Min Seok, Lee, Juyoung, Lee, Selyeong, Lin, Keng Han, Maxwell, Taylor J., Nagai, Yoshihiko, Wang, Xu, Welch, Ryan P., Yoon, Joon, Zhang, Weihua, Barzilai, Nir, Voight, Benjamin F., Han, Bok Ghee, Jenkinson, Christopher P., Kuulasmaa, Teemu, Kuusisto, Johanna, Manning, Alisa, Ng, Maggie C.Y., Palmer, Nicholette D., Balkau, Beverley, Stančáková, Alena, Abboud, Hanna E., Boeing, Heiner, Giedraitis, Vilmantas, Prabhakaran, Dorairaj, Gottesman, Omri, Scott, James, Carey, Jason, Kwan, Phoenix, Grant, George, Smith, Joshua D., Neale, Benjamin M., Purcell, Shaun, Butterworth, Adam S., Howson, Joanna M.M., Lee, Heung Man, Lu, Yingchang, Kwak, Soo Heon, Zhao, Wei, Danesh, John, Lam, Vincent K.L., Park, Kyong Soo, Saleheen, Danish, So, Wing Yee, Tam, Claudia H.T., Afzal, Uzma, Aguilar, David, Arya, Rector, Aung, Tin, Chan, Edmund, Navarro, Carmen, Cheng, Ching Yu, Palli, Domenico, Correa, Adolfo, Curran, Joanne E., Rybin, Dennis, Farook, Vidya S., Fowler, Sharon P., Freedman, Barry I., Griswold, Michael, Hale, Daniel Esten, Hicks, Pamela J., Khor, Chiea Chuen, Kumar, Satish, Lehne, Benjamin, Thuillier, Dorothée, Lim, Wei Yen, Liu, Jianjun, Loh, Marie, Musani, Solomon K., Puppala, Sobha, Scott, William R., Yengo, Loïc, Tan, Sian Tsung, Taylor, Herman A., Thameem, Farook, Wilson, Gregory, Wong, Tien Yin, Njølstad, Pål Rasmus, Levy, Jonathan C., Mangino, Massimo, Bonnycastle, Lori L., Schwarzmayr, Thomas, Fadista, João, Surdulescu, Gabriela L., Herder, Christian, Groves, Christopher J., Wieland, Thomas, Bork-Jensen, Jette, Brandslund, Ivan, Christensen, Cramer, Koistinen, Heikki A., Doney, Alex S.F., Kinnunen, Leena, Esko, Tõnu, Farmer, Andrew J., Hakaste, Liisa, Hodgkiss, Dylan, Kravic, Jasmina, Lyssenko, Valeriya, Hollensted, Mette, Jørgensen, Marit E., Jørgensen, Torben, Ladenvall, Claes, Justesen, Johanne Marie, Käräjämäki, Annemari, Kriebel, Jennifer, Rathmann, Wolfgang, Lannfelt, Lars, Lauritzen, Torsten, Narisu, Narisu, Linneberg, Allan, Melander, Olle, Milani, Lili, Neville, Matt, Orho-Melander, Marju, Qi, Lu, Qi, Qibin, Roden, Michael, Rolandsson, Olov, Swift, Amy, Rosengren, Anders H., Stirrups, Kathleen, Wood, Andrew R., Mihailov, Evelin, Blancher, Christine, Carneiro, Mauricio O., Maguire, Jared, Poplin, Ryan, Shakir, Khalid, Fennell, Timothy, DePristo, Mark, De Angelis, Martin Hrabé, Deloukas, Panos, Gjesing, Anette P., Jun, Goo, Nilsson, Peter M., Murphy, Jacquelyn, Onofrio, Robert, Thorand, Barbara, Hansen, Torben, Meisinger, Christa, Hu, Frank B., Isomaa, Bo, Karpe, Fredrik, Liang, Liming, Peters, Annette, Huth, Cornelia, O'Rahilly, Stephen P., Palmer, Colin N.A., Pedersen, Oluf, Rauramaa, Rainer, Tuomilehto, Jaakko, Salomaa, Veikko, Watanabe, Richard M., Syvänen, Ann Christine, Bergman, Richard N., Bharadwaj, Dwaipayan, Bottinger, Erwin P., Cho, Yoon Shin, Chandak, Giriraj R., Chan, Juliana C.N., Chia, Kee Seng, Daly, Mark J., Ebrahim, Shah B., Langenberg, Claudia, Elliott, Paul, Jablonski, Kathleen A., Lehman, Donna M., Jia, Weiping, Ma, Ronald C.W., Pollin, Toni I., Sandhu, Manjinder, Tandon, Nikhil, Froguel, Philippe, Barroso, Inês, Teo, Yik Ying, Zeggini, Eleftheria, Loos, Ruth J.F., Small, Kerrin S., Ried, Janina S., DeFronzo, Ralph A., Grallert, Harald, Glaser, Benjamin, Metspalu, Andres, Wareham, Nicholas J., Walker, Mark, Banks, Eric, Gieger, Christian, Ingelsson, Erik, Im, Hae Kyung, Illig, Thomas, Franks, Paul W., Buck, Gemma, Trakalo, Joseph, Buck, David, Prokopenko, Inga, Mägi, Reedik, Lind, Lars, Farjoun, Yossi, Owen, Katharine R., Gloyn, Anna L., Strauch, Konstantin, Tuomi, Tiinamaija, Kooner, Jaspal Singh, Lee, Jong Young, Park, Taesung, Donnelly, Peter, Morris, Andrew D., Hattersley, Andrew T., Bowden, Donald W., Collins, Francis S., Atzmon, Gil, Chambers, John C., Spector, Timothy D., Laakso, Markku, Strom, Tim M., Bell, Graeme I., Blangero, John, Duggirala, Ravindranath, Tai, Eshyong, McVean, Gilean, Hanis, Craig L., Wilson, James G., Seielstad, Mark, Frayling, Timothy M., Meigs, James B., Cox, Nancy J., Sladek, Rob, Lander, Eric S., Gabriel, Stacey, Mohlke, Karen L., Meitinger, Thomas, Groop, Leif, Abecasis, Goncalo, Scott, Laura J., Morris, Andrew P., Kang, Hyun Min, Altshuler, David, Burtt, Noël P., Florez, Jose C., Boehnke, Michael, and McCarthy, Mark I.

Abstract

To investigate the genetic basis of type 2 diabetes (T2D) to high resolution, the GoT2D and T2D-GENES consortia catalogued variation from whole-genome sequencing of 2,657 European individuals and exome sequencing of 12,940 individuals of multiple ancestries. Over 27M SNPs, indels, and structural variants were identified, including 99% of low-frequency (minor allele frequency [MAF] 0.1-5%) non-coding variants in the whole-genome sequenced individuals and 99.7% of low-frequency coding variants in the whole-exome sequenced individuals. Each variant was tested for association with T2D in the sequenced individuals, and, to increase power, most were tested in larger numbers of individuals (>80% of low-frequency coding variants in ∼82 K Europeans via the exome chip, and ∼90% of low-frequency non-coding variants in ∼44 K Europeans via genotype imputation). The variants, genotypes, and association statistics from these analyses provide the largest reference to date of human genetic information relevant to T2D, for use in activities such as T2D-focused genotype imputation, functional characterization of variants or genes, and other novel analyses to detect associations between sequence variation and T2D.

Published
2017

21. Identification and Functional Characterization of G6PC2 Coding Variants Influencing Glycemic Traits Define an Effector Transcript at the G6PC2-ABCB11 Locus

Author

Mahajan, Anubha, Sim, Xueling, Ng, Hui Jin, Manning, Alisa, Rivas, Manuel A., Highland, Heather M., Locke, Adam E., Grarup, Niels, Im, Hae Kyung, Cingolani, Pablo, Flannick, Jason, Fontanillas, Pierre, Fuchsberger, Christian, Gaulton, Kyle J., Teslovich, Tanya M., Rayner, N. William, Robertson, Neil R., Beer, Nicola L., Rundle, Jana K., Bork-Jensen, Jette, Ladenvall, Claes, Blancher, Christine, Buck, David, Buck, Gemma, Burtt, Noël P., Gabriel, Stacey, Gjesing, Anette P., Groves, Christopher J., Hollensted, Mette, Huyghe, Jeroen R., Jackson, Anne U., Jun, Goo, Justesen, Johanne Marie, Mangino, Massimo, Murphy, Jacquelyn, Neville, Matt, Onofrio, Robert, Small, Kerrin S., Stringham, Heather M., Syvänen, Ann Christine, Trakalo, Joseph, Abecasis, Goncalo, Bell, Graeme I., Blangero, John, Cox, Nancy J., Duggirala, Ravindranath, Hanis, Craig L., Seielstad, Mark, Wilson, James G., Christensen, Cramer, Brandslund, Ivan, Rauramaa, Rainer, Surdulescu, Gabriela L., Doney, Alex S F, Lannfelt, Lars, Linneberg, Allan, Isomaa, Bo, Tuomi, Tiinamaija, Jørgensen, Marit E., Jørgensen, Torben, Kuusisto, Johanna, Uusitupa, Matti, Salomaa, Veikko, Spector, Timothy D., Morris, Andrew D., Palmer, Colin N A, Collins, Francis S., Mohlke, Karen L., Bergman, Richard N., Ingelsson, Erik, Lind, Lars, Tuomilehto, Jaakko, Hansen, Torben, Watanabe, Richard M., Prokopenko, Inga, Dupuis, Josee, Karpe, Fredrik, Groop, Leif, Laakso, Markku, Pedersen, Oluf, Florez, Jose C., Morris, Andrew P., Altshuler, David, Meigs, James B., Boehnke, Michael, McCarthy, Mark I., Lindgren, Cecilia M., Gloyn, Anna L., Abboud, Hanna E., Afzal, Uzma, Aguilar, David, Arya, Rector, Atzmon, Gil, Aung, Tin, Banks, Eric, Barroso, Inês, Barzilai, Nir, Below, Jennifer E., Bharadwaj, Dwaipayan, Blackwell, Thomas W., Bonnycastle, Lori L., Bowden, Don, Carey, Jason, Carneiro, Mauricio O., Chambers, John C., Chan, Edmund, Chan, Juliana, Chandak, Giriraj R., Chen, Peng, Chen, Yuhui, Chen, Han, Cheng, Ching Yu, Chia, Kee Seng, Cho, Yoon Shin, Correa, Adolfo, Curran, Joanne E., Daly, Mark J., Day-Williams, Aaron G., DeFronzo, Ralph A., DePristo, Mark, Donnelly, Peter J., Ebrahim, Shah B., Elliott, Paul, Esko, Tõnu, Fadista, João, Farjoun, Yossi, Farmer, Andrew J., Farook, Vidya S., Fennell, Timothy, Ferreira, Teresa, Fingerlin, Tasha, Forsén, Tom, Fowler, Sharon P., Franks, Paul W., Frayling, Timothy M., Freedman, Barry I., Froguel, Philippe, Gamazon, Eric R., Gieger, Christian, Glaser, Benjamin, Go, Min Jin, Goldstein, Jacqueline I., Grallert, Harald, Grant, George, Green, Todd, Griswold, Michael, Hale, Daniel Esten, Han, Bok Ghee, Hartl, Christopher, Hattersley, Andrew T., Hicks, Pamela J., Hodgkiss, Dylan, Horikoshi, Momoko, Hrabé de Angelis, Martin, Hu, Cheng, Hu, Frank B., Huh, Iksoo, Kamran Ikram, Mohammad, Illig, Thomas, Jablonski, Kathleen A., Jenkinson, Christopher P., Jia, Weiping, Kang, Hyun Min, Khor, Chiea Chuen, Kim, Yongkang, Kim, Young Jin, Kim, Bong Jo, Kinnunen, Leena, Kooner, Jaspal Singh, Kravic, Jasmina, Kriebel, Jennifer, Kumar, Ashish, Kumar, Satish, Kuulasmaa, Teemu, Kwon, Min Seok, Langenberg, Claudia, Lauritzen, Torsten, Lee, Selyeong, Lee, Jaehoon, Lee, Juyoung, Lee, Jong Young, Lehman, Donna M., Lehne, Benjamin, Levy, Jonathan C., Li, Jiang, Liang, Liming, Lim, Wei Yen, Lin, Keng Han, Liu, Jianjun, Loh, Marie, Ma, Ronald C W, Ma, Clement, Mägi, Reedik, Maguire, Jared, Maxwell, Taylor J., McVean, Gilean, Meisinger, Christa, Meitinger, Thomas, Melander, Olle, Metspalu, Andres, Mihailov, Evelin, Milani, Lili, Moutsianas, Loukas, Müller-Nurasyid, Martina, K. Musani, Solomon, Nagai, Yoshihiko, Narisu, Narisu, Neale, Benjamin M., Ng, Maggie C Y, Nilsson, Peter, O'Rahilly, Stephen P., Orho-Melander, Marju, Owen, Katharine R., Palmer, Nicholette D., Park, Taesung, Pasko, Dorota, Pearson, Richard D., Perry, John R B, Peters, Annette, Pollin, Toni I., Poplin, Ryan, Prabhakaran, Dorairaj, Puppala, Sobha, Purcell, Shaun, Qi, Lu, Qi, Qibin, Roden, Michael, Rolandsson, Olov, Rosengren, Anders H., Sandhu, Manjinder, Schwarzmayr, Thomas, Scott, Laura J., Scott, Robert A., Scott, James, Scott, William R., Sehmi, Jobanpreet, Shakir, Khalid, Sladek, Rob, Smith, Joshua D., Stancáková, Alena, Strauch, Konstantin, Strom, Tim M., Swift, Amy, Tai, E. Shyong, Tajes, Juan Fernandez, Tan, Sian Tsung, Tandon, Nikhil, Taylor, Herman A., Teo, Yik Ying, Thameem, Farook, Thorand, Barbara, van de Bunt, Martijn, Varga, Tibor V., Walker, Mark, Wareham, Nicholas J., Welch, Ryan P., Wieland, Thomas, Wilson, Gregory, Wong, Tien Yin, Wood, Andrew R., Yoon, Joon, Zeggini, Eleftheria, and Zhang, Weihua

Abstract

Genome wide association studies (GWAS) for fasting glucose (FG) and insulin (FI) have identified common variant signals which explain 4.8% and 1.2% of trait variance, respectively. It is hypothesized that low-frequency and rare variants could contribute substantially to unexplained genetic variance. To test this, we analyzed exome-array data from up to 33,231 non-diabetic individuals of European ancestry. We found exome-wide significant (P

Published
2015
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23. A family-based joint test for mean and variance heterogeneity for quantitative traits

Author

CAO, YING, MAXWELL, TAYLOR J., and WEI, PENG

Subjects
Phenotype, Models, Genetic, Quantitative Trait Loci, Linear Models, Humans, Computer Simulation, Gene-Environment Interaction, Polymorphism, Single Nucleotide, Article, Body Mass Index
Abstract

Traditional quantitative trait locus (QTL) analysis focuses on identifying loci associated with mean heterogeneity. Recent research has discovered loci associated with phenotype variance heterogeneity (vQTL), which is important in studying genetic association with complex traits, especially for identifying gene-gene and gene-environment interactions. While several tests have been proposed to detect vQTL for unrelated individuals, there are no tests for related individuals, commonly seen in family-based genetic studies. Here we introduce a likelihood ratio test (LRT) for identifying mean and variance heterogeneity simultaneously or for either effect alone, adjusting for covariates and family relatedness using a linear mixed effect model approach. The LRT test statistic for normally distributed quantitative traits approximately follows χ(2)-distributions. To correct for inflated Type I error for non-normally distributed quantitative traits, we propose a parametric bootstrap-based LRT that removes the best linear unbiased prediction (BLUP) of family random effect. Simulation studies show that our family-based test controls Type I error and has good power, while Type I error inflation is observed when family relatedness is ignored. We demonstrate the utility and efficiency gains of the proposed method using data from the Framingham Heart Study to detect loci associated with body mass index (BMI) variability.

Published
2014

24. The genetic architecture of type 2 diabetes

Author

JC onderzoeksprogramma Cardiovasculaire Epidemiologie, Circulatory Health, Cardiovasculaire Epidemiologie, Fuchsberger, Christian, Flannick, Jason, Teslovich, Tanya M, Mahajan, Anubha, Agarwala, Vineeta, Gaulton, Kyle J, Ma, Clement, Fontanillas, Pierre, Moutsianas, Loukas, McCarthy, Davis J, Rivas, Manuel A, Perry, John R B, Sim, Xueling, Blackwell, Thomas W, Robertson, Neil R, Rayner, N William, Cingolani, Pablo, Locke, Adam E, Tajes, Juan Fernandez, Highland, Heather M, Dupuis, Josee, Chines, Peter S, Lindgren, Cecilia M, Hartl, Christopher, Jackson, Anne U, Chen, Han, Huyghe, Jeroen R, van de Bunt, Martijn, Pearson, Richard D, Kumar, Ashish, Müller-Nurasyid, Martina, Grarup, Niels, Stringham, Heather M, Gamazon, Eric R, Lee, Jaehoon, Chen, Yuhui, Scott, Robert A, Below, Jennifer E, Chen, Peng, Huang, Jinyan, Go, Min Jin, Stitzel, Michael L, Pasko, Dorota, Parker, Stephen C J, Varga, Tibor V, Green, Todd, Beer, Nicola L, Day-Williams, Aaron G, Ferreira, Teresa, Fingerlin, Tasha, Horikoshi, Momoko, Hu, Cheng, Huh, Iksoo, Ikram, Mohammad Kamran, Kim, Bong-Jo, Kim, Yongkang, Kim, Young Jin, Kwon, Min-Seok, Lee, Juyoung, Lee, Selyeong, Lin, Keng-Han, Maxwell, Taylor J, Nagai, Yoshihiko, Wang, Xu, Welch, Ryan P, Yoon, Joon, Zhang, Weihua, Barzilai, Nir, Voight, Benjamin F, Han, Bok-Ghee, Jenkinson, Christopher P, Kuulasmaa, Teemu, Kuusisto, Johanna, Manning, Alisa, Ng, Maggie C Y, Palmer, Nicholette D, Balkau, Beverley, Stančáková, Alena, Abboud, Hanna E, Boeing, Heiner, Giedraitis, Vilmantas, Prabhakaran, Dorairaj, Gottesman, Omri, Scott, James, Carey, Jason, Kwan, Phoenix, Grant, George, Smith, Joshua D, Neale, Benjamin M, Purcell, Shaun, Butterworth, Adam S, Howson, Joanna M M, Lee, Heung Man, Lu, Yingchang, Kwak, Soo-Heon, Zhao, Wei, Danesh, John, Lam, Vincent K L, Park, Kyong Soo, Saleheen, Danish, So, Wing Yee, Tam, Claudia H T, Afzal, Uzma, Aguilar, David, Arya, Rector, Aung, Tin, Chan, Edmund, Navarro, Carmen, Cheng, Ching-Yu, Palli, Domenico, Correa, Adolfo, Curran, Joanne E, Rybin, Denis, Farook, Vidya S, Fowler, Sharon P, Freedman, Barry I, Griswold, Michael, Hale, Daniel Esten, Hicks, Pamela J, Khor, Chiea-Chuen, Kumar, Satish, Lehne, Benjamin, Thuillier, Dorothée, Lim, Wei Yen, Liu, Jianjun, van der Schouw, Yvonne T, Loh, Marie, Musani, Solomon K, Puppala, Sobha, Scott, William R, Yengo, Loïc, Tan, Sian-Tsung, Taylor, Herman A, Thameem, Farook, Wilson, Gregory, Wong, Tien Yin, Njølstad, Pål Rasmus, Levy, Jonathan C, Mangino, Massimo, Bonnycastle, Lori L, Schwarzmayr, Thomas, Fadista, João, Surdulescu, Gabriela L, Herder, Christian, Groves, Christopher J, Wieland, Thomas, Bork-Jensen, Jette, Brandslund, Ivan, Christensen, Cramer, Koistinen, Heikki A, Doney, Alex S F, Kinnunen, Leena, Esko, Tõnu, Farmer, Andrew J, Hakaste, Liisa, Hodgkiss, Dylan, Kravic, Jasmina, Lyssenko, Valeriya, Hollensted, Mette, Jørgensen, Marit E, Jørgensen, Torben, Ladenvall, Claes, Justesen, Johanne Marie, Käräjämäki, Annemari, Kriebel, Jennifer, Rathmann, Wolfgang, Lannfelt, Lars, Lauritzen, Torsten, Narisu, Narisu, Linneberg, Allan, Melander, Olle, Milani, Lili, Neville, Matt, Orho-Melander, Marju, Qi, Lu, Qi, Qibin, Roden, Michael, Rolandsson, Olov, Swift, Amy, Rosengren, Anders H, Stirrups, Kathleen, Wood, Andrew R, Mihailov, Evelin, Blancher, Christine, Carneiro, Mauricio O, Maguire, Jared, Poplin, Ryan, Shakir, Khalid, Fennell, Timothy, DePristo, Mark, Hrabé de Angelis, Martin, Deloukas, Panos, Gjesing, Anette P, Jun, Goo, Nilsson, Peter, Murphy, Jacquelyn, Onofrio, Robert, Thorand, Barbara, Hansen, Torben, Meisinger, Christa, Hu, Frank B, Isomaa, Bo, Karpe, Fredrik, Liang, Liming, Peters, Annette, Huth, Cornelia, O'Rahilly, Stephen P, Palmer, Colin N A, Pedersen, Oluf, Rauramaa, Rainer, Tuomilehto, Jaakko, Salomaa, Veikko, Watanabe, Richard M, Syvänen, Ann-Christine, Bergman, Richard N, Bharadwaj, Dwaipayan, Bottinger, Erwin P, Cho, Yoon Shin, Chandak, Giriraj R, Chan, Juliana C N, Chia, Kee Seng, Daly, Mark J, Ebrahim, Shah B, Langenberg, Claudia, Elliott, Paul, Jablonski, Kathleen A, Lehman, Donna M, Jia, Weiping, Ma, Ronald C W, Pollin, Toni I, Sandhu, Manjinder, Tandon, Nikhil, Froguel, Philippe, Barroso, Inês, Teo, Yik Ying, Zeggini, Eleftheria, Loos, Ruth J F, Small, Kerrin S, Ried, Janina S, DeFronzo, Ralph A, Grallert, Harald, Glaser, Benjamin, Metspalu, Andres, Wareham, Nicholas J, Walker, Mark, Banks, Eric, Gieger, Christian, Ingelsson, Erik, Im, Hae Kyung, Illig, Thomas, Franks, Paul W, Buck, Gemma, Trakalo, Joseph, Buck, David, Prokopenko, Inga, Mägi, Reedik, Lind, Lars, Farjoun, Yossi, Owen, Katharine R, Gloyn, Anna L, Strauch, Konstantin, Tuomi, Tiinamaija, Kooner, Jaspal Singh, Lee, Jong-Young, Park, Taesung, Donnelly, Peter, Morris, Andrew D, Hattersley, Andrew T, Bowden, Donald W, Collins, Francis S, Atzmon, Gil, Chambers, John C, Spector, Timothy D, Laakso, Markku, Strom, Tim M, Bell, Graeme I, Blangero, John, Duggirala, Ravindranath, Tai, E Shyong, McVean, Gilean, Hanis, Craig L, Wilson, James G, Seielstad, Mark, Frayling, Timothy M, Meigs, James B, Cox, Nancy J, Sladek, Rob, Lander, Eric S, Gabriel, Stacey, Burtt, Noël P, Mohlke, Karen L, Meitinger, Thomas, Groop, Leif, Abecasis, Goncalo, Florez, Jose C, Scott, Laura J, Morris, Andrew P, Kang, Hyun Min, Boehnke, Michael, Altshuler, David, McCarthy, Mark I, JC onderzoeksprogramma Cardiovasculaire Epidemiologie, Circulatory Health, Cardiovasculaire Epidemiologie, Fuchsberger, Christian, Flannick, Jason, Teslovich, Tanya M, Mahajan, Anubha, Agarwala, Vineeta, Gaulton, Kyle J, Ma, Clement, Fontanillas, Pierre, Moutsianas, Loukas, McCarthy, Davis J, Rivas, Manuel A, Perry, John R B, Sim, Xueling, Blackwell, Thomas W, Robertson, Neil R, Rayner, N William, Cingolani, Pablo, Locke, Adam E, Tajes, Juan Fernandez, Highland, Heather M, Dupuis, Josee, Chines, Peter S, Lindgren, Cecilia M, Hartl, Christopher, Jackson, Anne U, Chen, Han, Huyghe, Jeroen R, van de Bunt, Martijn, Pearson, Richard D, Kumar, Ashish, Müller-Nurasyid, Martina, Grarup, Niels, Stringham, Heather M, Gamazon, Eric R, Lee, Jaehoon, Chen, Yuhui, Scott, Robert A, Below, Jennifer E, Chen, Peng, Huang, Jinyan, Go, Min Jin, Stitzel, Michael L, Pasko, Dorota, Parker, Stephen C J, Varga, Tibor V, Green, Todd, Beer, Nicola L, Day-Williams, Aaron G, Ferreira, Teresa, Fingerlin, Tasha, Horikoshi, Momoko, Hu, Cheng, Huh, Iksoo, Ikram, Mohammad Kamran, Kim, Bong-Jo, Kim, Yongkang, Kim, Young Jin, Kwon, Min-Seok, Lee, Juyoung, Lee, Selyeong, Lin, Keng-Han, Maxwell, Taylor J, Nagai, Yoshihiko, Wang, Xu, Welch, Ryan P, Yoon, Joon, Zhang, Weihua, Barzilai, Nir, Voight, Benjamin F, Han, Bok-Ghee, Jenkinson, Christopher P, Kuulasmaa, Teemu, Kuusisto, Johanna, Manning, Alisa, Ng, Maggie C Y, Palmer, Nicholette D, Balkau, Beverley, Stančáková, Alena, Abboud, Hanna E, Boeing, Heiner, Giedraitis, Vilmantas, Prabhakaran, Dorairaj, Gottesman, Omri, Scott, James, Carey, Jason, Kwan, Phoenix, Grant, George, Smith, Joshua D, Neale, Benjamin M, Purcell, Shaun, Butterworth, Adam S, Howson, Joanna M M, Lee, Heung Man, Lu, Yingchang, Kwak, Soo-Heon, Zhao, Wei, Danesh, John, Lam, Vincent K L, Park, Kyong Soo, Saleheen, Danish, So, Wing Yee, Tam, Claudia H T, Afzal, Uzma, Aguilar, David, Arya, Rector, Aung, Tin, Chan, Edmund, Navarro, Carmen, Cheng, Ching-Yu, Palli, Domenico, Correa, Adolfo, Curran, Joanne E, Rybin, Denis, Farook, Vidya S, Fowler, Sharon P, Freedman, Barry I, Griswold, Michael, Hale, Daniel Esten, Hicks, Pamela J, Khor, Chiea-Chuen, Kumar, Satish, Lehne, Benjamin, Thuillier, Dorothée, Lim, Wei Yen, Liu, Jianjun, van der Schouw, Yvonne T, Loh, Marie, Musani, Solomon K, Puppala, Sobha, Scott, William R, Yengo, Loïc, Tan, Sian-Tsung, Taylor, Herman A, Thameem, Farook, Wilson, Gregory, Wong, Tien Yin, Njølstad, Pål Rasmus, Levy, Jonathan C, Mangino, Massimo, Bonnycastle, Lori L, Schwarzmayr, Thomas, Fadista, João, Surdulescu, Gabriela L, Herder, Christian, Groves, Christopher J, Wieland, Thomas, Bork-Jensen, Jette, Brandslund, Ivan, Christensen, Cramer, Koistinen, Heikki A, Doney, Alex S F, Kinnunen, Leena, Esko, Tõnu, Farmer, Andrew J, Hakaste, Liisa, Hodgkiss, Dylan, Kravic, Jasmina, Lyssenko, Valeriya, Hollensted, Mette, Jørgensen, Marit E, Jørgensen, Torben, Ladenvall, Claes, Justesen, Johanne Marie, Käräjämäki, Annemari, Kriebel, Jennifer, Rathmann, Wolfgang, Lannfelt, Lars, Lauritzen, Torsten, Narisu, Narisu, Linneberg, Allan, Melander, Olle, Milani, Lili, Neville, Matt, Orho-Melander, Marju, Qi, Lu, Qi, Qibin, Roden, Michael, Rolandsson, Olov, Swift, Amy, Rosengren, Anders H, Stirrups, Kathleen, Wood, Andrew R, Mihailov, Evelin, Blancher, Christine, Carneiro, Mauricio O, Maguire, Jared, Poplin, Ryan, Shakir, Khalid, Fennell, Timothy, DePristo, Mark, Hrabé de Angelis, Martin, Deloukas, Panos, Gjesing, Anette P, Jun, Goo, Nilsson, Peter, Murphy, Jacquelyn, Onofrio, Robert, Thorand, Barbara, Hansen, Torben, Meisinger, Christa, Hu, Frank B, Isomaa, Bo, Karpe, Fredrik, Liang, Liming, Peters, Annette, Huth, Cornelia, O'Rahilly, Stephen P, Palmer, Colin N A, Pedersen, Oluf, Rauramaa, Rainer, Tuomilehto, Jaakko, Salomaa, Veikko, Watanabe, Richard M, Syvänen, Ann-Christine, Bergman, Richard N, Bharadwaj, Dwaipayan, Bottinger, Erwin P, Cho, Yoon Shin, Chandak, Giriraj R, Chan, Juliana C N, Chia, Kee Seng, Daly, Mark J, Ebrahim, Shah B, Langenberg, Claudia, Elliott, Paul, Jablonski, Kathleen A, Lehman, Donna M, Jia, Weiping, Ma, Ronald C W, Pollin, Toni I, Sandhu, Manjinder, Tandon, Nikhil, Froguel, Philippe, Barroso, Inês, Teo, Yik Ying, Zeggini, Eleftheria, Loos, Ruth J F, Small, Kerrin S, Ried, Janina S, DeFronzo, Ralph A, Grallert, Harald, Glaser, Benjamin, Metspalu, Andres, Wareham, Nicholas J, Walker, Mark, Banks, Eric, Gieger, Christian, Ingelsson, Erik, Im, Hae Kyung, Illig, Thomas, Franks, Paul W, Buck, Gemma, Trakalo, Joseph, Buck, David, Prokopenko, Inga, Mägi, Reedik, Lind, Lars, Farjoun, Yossi, Owen, Katharine R, Gloyn, Anna L, Strauch, Konstantin, Tuomi, Tiinamaija, Kooner, Jaspal Singh, Lee, Jong-Young, Park, Taesung, Donnelly, Peter, Morris, Andrew D, Hattersley, Andrew T, Bowden, Donald W, Collins, Francis S, Atzmon, Gil, Chambers, John C, Spector, Timothy D, Laakso, Markku, Strom, Tim M, Bell, Graeme I, Blangero, John, Duggirala, Ravindranath, Tai, E Shyong, McVean, Gilean, Hanis, Craig L, Wilson, James G, Seielstad, Mark, Frayling, Timothy M, Meigs, James B, Cox, Nancy J, Sladek, Rob, Lander, Eric S, Gabriel, Stacey, Burtt, Noël P, Mohlke, Karen L, Meitinger, Thomas, Groop, Leif, Abecasis, Goncalo, Florez, Jose C, Scott, Laura J, Morris, Andrew P, Kang, Hyun Min, Boehnke, Michael, Altshuler, David, and McCarthy, Mark I

Published
2016

27. Mitochondrial genomic variation associated with higher mitochondrial copy number: the Cache County Study on Memory Health and Aging

Author

Ridge, Perry G, primary, Maxwell, Taylor J, additional, Foutz, Spencer J, additional, Bailey, Matthew H, additional, Corcoran, Christopher D, additional, Tschanz, JoAnn T, additional, Norton, Maria C, additional, Munger, Ronald G, additional, O'Brien, Elizabeth, additional, Kerber, Richard A, additional, Cawthon, Richard M, additional, and Kauwe, John SK, additional

Published
2014
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31. Mitochondrial Genomic Analysis of Late Onset Alzheimer’s Disease Reveals Protective Haplogroups H6A1A/H6A1B: The Cache County Study on Memory in Aging

Author

Ridge, Perry G., primary, Maxwell, Taylor J., additional, Corcoran, Christopher D., additional, Norton, Maria C., additional, Tschanz, JoAnn T., additional, O’Brien, Elizabeth, additional, Kerber, Richard A., additional, Cawthon, Richard M., additional, Munger, Ronald G., additional, and Kauwe, John S. K., additional

Published
2012
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32. Diet-Dependent Genetic and Genomic Imprinting Effects on Obesity in Mice

Author

Cheverud, James M., primary, Lawson, Heather A., additional, Fawcett, Gloria L., additional, Wang, Bing, additional, Pletscher, L. Susan, additional, Fox, Ashley R., additional, Maxwell, Taylor J., additional, Ehrich, Thomas H., additional, Kenney-Hunt, Jane P., additional, Wolf, Jason B., additional, and Semenkovich, Clay F., additional

Published
2011
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33. Deep resequencing reveals excess rare recent variants consistent with explosive population growth

Author

Coventry, Alex, primary, Bull-Otterson, Lara M., additional, Liu, Xiaoming, additional, Clark, Andrew G., additional, Maxwell, Taylor J., additional, Crosby, Jacy, additional, Hixson, James E., additional, Rea, Thomas J., additional, Muzny, Donna M., additional, Lewis, Lora R., additional, Wheeler, David A., additional, Sabo, Aniko, additional, Lusk, Christine, additional, Weiss, Kenneth G., additional, Akbar, Humeira, additional, Cree, Andrew, additional, Hawes, Alicia C., additional, Newsham, Irene, additional, Varghese, Robin T., additional, Villasana, Donna, additional, Gross, Shannon, additional, Joshi, Vandita, additional, Santibanez, Jireh, additional, Morgan, Margaret, additional, Chang, Kyle, additional, IV, Walker Hale, additional, Templeton, Alan R., additional, Boerwinkle, Eric, additional, Gibbs, Richard, additional, and Sing, Charles F., additional

Published
2010
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38. Mitochondrial Haplotypes Associated with Biomarkers for Alzheimer’s Disease.

Author

Ridge, Perry G., Koop, Andre, Maxwell, Taylor J., Bailey, Matthew H., Swerdlow, Russell H., Kauwe, John S. K., and Honea, Robyn A.

Subjects
MITOCHONDRIA, HAPLOTYPES, BIOMARKERS, ALZHEIMER'S disease, LONGITUDINAL method, BRAIN imaging, MAGNETIC resonance imaging
Abstract

Various studies have suggested that the mitochondrial genome plays a role in late-onset Alzheimer’s disease, although results are mixed. We used an endophenotype-based approach to further characterize mitochondrial genetic variation and its relationship to risk markers for Alzheimer’s disease. We analyzed longitudinal data from non-demented, mild cognitive impairment, and late-onset Alzheimer’s disease participants in the Alzheimer’s Disease Neuroimaging Initiative with genetic, brain imaging, and behavioral data. We assessed the relationship of structural MRI and cognitive biomarkers with mitochondrial genome variation using TreeScanning, a haplotype-based approach that concentrates statistical power by analyzing evolutionarily meaningful groups (or clades) of haplotypes together for association with a phenotype. Four clades were associated with three different endophenotypes: whole brain volume, percent change in temporal pole thickness, and left hippocampal atrophy over two years. This is the first study of its kind to identify mitochondrial variation associated with brain imaging endophenotypes of Alzheimer’s disease. Our results provide additional evidence that the mitochondrial genome plays a role in risk for Alzheimer’s disease. [ABSTRACT FROM AUTHOR]

Published
2013
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40. Replication of long-bone length QTL in the F9-F10 LG,SM advanced intercross.

Author

Norgard, Elizabeth A., Jarvis, Joseph P., Roseman, Charles C., Maxwell, Taylor J., Kenney-Hunt, Jane P., Samocha, Kaitlin E., Pletscher, L. Susan, Wang, Bing, Fawcett, Gloria L., Leatherwood, Christopher J., Wolf, Jason B., and Cheverud, James M.

Subjects
GENETIC research, STATISTICAL hypothesis testing, HOMOGRAFTS, GENOMICS, GENOMES
Abstract

Quantitative trait locus (QTL) mapping techniques are frequently used to identify genomic regions associated with variation in phenotypes of interest. However, the F2 intercross and congenic strain populations usually employed have limited genetic resolution resulting in relatively large confidence intervals that greatly inhibit functional confirmation of statistical results. Here we use the increased resolution of the combined F9 and F10 generations ( n = 1455) of the LG,SM advanced intercross to fine-map previously identified QTL associated with the lengths of the humerus, ulna, femur, and tibia. We detected 81 QTL affecting long-bone lengths. Of these, 49 were previously identified in the combined F2-F3 population of this intercross, while 32 represent novel contributors to trait variance. Pleiotropy analysis suggests that most QTL affect three to four long bones or serially homologous limb segments. We also identified 72 epistatic interactions involving 38 QTL and 88 novel regions. This analysis shows that using later generations of an advanced intercross greatly facilitates fine-mapping of confidence intervals, resolving three F2-F3 QTL into multiple linked loci and narrowing confidence intervals of other loci, as well as allowing identification of additional QTL. Further characterization of the biological bases of these QTL will help provide a better understanding of the genetics of small variations in long-bone length. [ABSTRACT FROM AUTHOR]

Published
2009
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41. Sequence data and association statistics from 12,940 type 2 diabetes cases and controls

Author

Flannick, Jason, Fuchsberger, Christian, Mahajan, Anubha, Teslovich, Tanya M, Agarwala, Vineeta, Gaulton, Kyle J, Caulkins, Lizz, Koesterer, Ryan, Ma, Clement, Moutsianas, Loukas, McCarthy, Davis J, Rivas, Manuel A, Perry, John RB, Sim, Xueling, Blackwell, Thomas W, Robertson, Neil R, Rayner, N William, Cingolani, Pablo, Locke, Adam E, Tajes, Juan Fernandez, Highland, Heather M, Dupuis, Josee, Chines, Peter S, Lindgren, Cecilia M, Hartl, Christopher, Jackson, Anne U, Chen, Han, Huyghe, Jeroen R, Van De Bunt, Martijn, Pearson, Richard D, Kumar, Ashish, Müller-Nurasyid, Martina, Grarup, Niels, Stringham, Heather M, Gamazon, Eric R, Lee, Jaehoon, Chen, Yuhui, Scott, Robert A, Below, Jennifer E, Chen, Peng, Huang, Jinyan, Go, Min Jin, Stitzel, Michael L, Pasko, Dorota, Parker, Stephen CJ, Varga, Tibor V, Green, Todd, Beer, Nicola L, Day-Williams, Aaron G, Ferreira, Teresa, Fingerlin, Tasha, Horikoshi, Momoko, Hu, Cheng, Huh, Iksoo, Ikram, Mohammad Kamran, Kim, Bong-Jo, Kim, Yongkang, Kim, Young Jin, Kwon, Min-Seok, Lee, Juyoung, Lee, Selyeong, Lin, Keng-Han, Maxwell, Taylor J, Nagai, Yoshihiko, Wang, Xu, Welch, Ryan P, Yoon, Joon, Zhang, Weihua, Barzilai, Nir, Voight, Benjamin F, Han, Bok-Ghee, Jenkinson, Christopher P, Kuulasmaa, Teemu, Kuusisto, Johanna, Manning, Alisa, Ng, Maggie CY, Palmer, Nicholette D, Balkau, Beverley, Stančáková, Alena, Abboud, Hanna E, Boeing, Heiner, Giedraitis, Vilmantas, Prabhakaran, Dorairaj, Gottesman, Omri, Scott, James, Carey, Jason, Kwan, Phoenix, Grant, George, Smith, Joshua D, Neale, Benjamin M, Purcell, Shaun, Butterworth, Adam S, Howson, Joanna MM, Lee, Heung Man, Lu, Yingchang, Kwak, Soo-Heon, Zhao, Wei, Danesh, John, Lam, Vincent KL, Park, Kyong Soo, Saleheen, Danish, So, Wing Yee, Tam, Claudia HT, Afzal, Uzma, Aguilar, David, Arya, Rector, Aung, Tin, Chan, Edmund, Navarro, Carmen, Cheng, Ching-Yu, Palli, Domenico, Correa, Adolfo, Curran, Joanne E, Rybin, Dennis, Farook, Vidya S, Fowler, Sharon P, Freedman, Barry I, Griswold, Michael, Hale, Daniel Esten, Hicks, Pamela J, Khor, Chiea-Chuen, Kumar, Satish, Lehne, Benjamin, Thuillier, Dorothée, Lim, Wei Yen, Liu, Jianjun, Loh, Marie, Musani, Solomon K, Puppala, Sobha, Scott, William R, Yengo, Loïc, Tan, Sian-Tsung, Taylor, Herman A, Thameem, Farook, Wilson, Gregory, Wong, Tien Yin, Njølstad, Pål Rasmus, Levy, Jonathan C, Mangino, Massimo, Bonnycastle, Lori L, Schwarzmayr, Thomas, Fadista, João, Surdulescu, Gabriela L, Herder, Christian, Groves, Christopher J, Wieland, Thomas, Bork-Jensen, Jette, Brandslund, Ivan, Christensen, Cramer, Koistinen, Heikki A, Doney, Alex SF, Kinnunen, Leena, Esko, Tõnu, Farmer, Andrew J, Hakaste, Liisa, Hodgkiss, Dylan, Kravic, Jasmina, Lyssenko, Valeri, Hollensted, Mette, Jørgensen, Marit E, Jørgensen, Torben, Ladenvall, Claes, Justesen, Johanne Marie, Käräjämäki, Annemari, Kriebel, Jennifer, Rathmann, Wolfgang, Lannfelt, Lars, Lauritzen, Torsten, Narisu, Narisu, Linneberg, Allan, Melander, Olle, Milani, Lili, Neville, Matt, Orho-Melander, Marju, Qi, Lu, Qi, Qibin, Roden, Michael, Rolandsson, Olov, Swift, Amy, Rosengren, Anders H, Stirrups, Kathleen, Wood, Andrew R, Mihailov, Evelin, Blancher, Christine, Carneiro, Mauricio O, Maguire, Jared, Poplin, Ryan, Shakir, Khalid, Fennell, Timothy, DePristo, Mark, De Angelis, Martin Hrabé, Deloukas, Panos, Gjesing, Anette P, Jun, Goo, Nilsson, Peter, Murphy, Jacquelyn, Onofrio, Robert, Thorand, Barbara, Hansen, Torben, Meisinger, Christa, Hu, Frank B, Isomaa, Bo, Karpe, Fredrik, Liang, Liming, Peters, Annette, Huth, Cornelia, O'Rahilly, Stephen P, Palmer, Colin NA, Pedersen, Oluf, Rauramaa, Rainer, Tuomilehto, Jaakko, Salomaa, Veikko, Watanabe, Richard M, Syvänen, Ann-Christine, Bergman, Richard N, Bharadwaj, Dwaipayan, Bottinger, Erwin P, Cho, Yoon Shin, Chandak, Giriraj R, Chan, Juliana Cn, Chia, Kee Seng, Daly, Mark J, Ebrahim, Shah B, Langenberg, Claudia, Elliott, Paul, Jablonski, Kathleen A, Lehman, Donna M, Jia, Weiping, Ma, Ronald CW, Pollin, Toni I, Sandhu, Manjinder, Tandon, Nikhil, Froguel, Philippe, Barroso, Inês, Teo, Yik Ying, Zeggini, Eleftheria, Loos, Ruth JF, Small, Kerrin S, Ried, Janina S, DeFronzo, Ralph A, Grallert, Harald, Glaser, Benjamin, Metspalu, Andres, Wareham, Nicholas J, Walker, Mark, Banks, Eric, Gieger, Christian, Ingelsson, Erik, Im, Hae Kyung, Illig, Thomas, Franks, Paul W, Buck, Gemma, Trakalo, Joseph, Buck, David, Prokopenko, Inga, Mägi, Reedik, Lind, Lars, Farjoun, Yossi, Owen, Katharine R, Gloyn, Anna L, Strauch, Konstantin, Tuomi, Tiinamaija, Kooner, Jaspal Singh, Lee, Jong-Young, Park, Taesung, Donnelly, Peter, Morris, Andrew D, Hattersley, Andrew T, Bowden, Donald W, Collins, Francis S, Atzmon, Gil, Chambers, John C, Spector, Timothy D, Laakso, Markku, Strom, Tim M, Bell, Graeme I, Blangero, John, Duggirala, Ravindranath, Tai, E Shyong, McVean, Gilean, Hanis, Craig L, Wilson, James G, Seielstad, Mark, Frayling, Timothy M, Meigs, James B, Cox, Nancy J, Sladek, Rob, Lander, Eric S, Gabriel, Stacey, Mohlke, Karen L, Meitinger, Thomas, Groop, Leif, Abecasis, Goncalo, Scott, Laura J, Morris, Andrew P, Kang, Hyun Min, Altshuler, David, Burtt, Noël P, Florez, Jose C, Boehnke, Michael, and McCarthy, Mark I

Subjects
Diabetes Mellitus, Type 2, Genetic Variation, Humans, White People, 3. Good health
Abstract

To investigate the genetic basis of type 2 diabetes (T2D) to high resolution, the GoT2D and T2D-GENES consortia catalogued variation from whole-genome sequencing of 2,657 European individuals and exome sequencing of 12,940 individuals of multiple ancestries. Over 27M SNPs, indels, and structural variants were identified, including 99% of low-frequency (minor allele frequency [MAF] 0.1-5%) non-coding variants in the whole-genome sequenced individuals and 99.7% of low-frequency coding variants in the whole-exome sequenced individuals. Each variant was tested for association with T2D in the sequenced individuals, and, to increase power, most were tested in larger numbers of individuals (>80% of low-frequency coding variants in ~82 K Europeans via the exome chip, and ~90% of low-frequency non-coding variants in ~44 K Europeans via genotype imputation). The variants, genotypes, and association statistics from these analyses provide the largest reference to date of human genetic information relevant to T2D, for use in activities such as T2D-focused genotype imputation, functional characterization of variants or genes, and other novel analyses to detect associations between sequence variation and T2D.

42. Estimating population genetic parameters and comparing model goodness-of-fit using DNA sequences with error.

Author

Liu X, Fu YX, Maxwell TJ, and Boerwinkle E

Subjects
Black or African American genetics, Angiopoietin-Like Protein 4, Black People genetics, Computer Simulation, Humans, Likelihood Functions, Mutation, White People genetics, Angiopoietins genetics, Base Sequence, Computational Biology methods, Genetics, Population, Models, Genetic, Polymorphism, Single Nucleotide genetics
Abstract

It is known that sequencing error can bias estimation of evolutionary or population genetic parameters. This problem is more prominent in deep resequencing studies because of their large sample size n, and a higher probability of error at each nucleotide site. We propose a new method based on the composite likelihood of the observed SNP configurations to infer population mutation rate theta = 4N(e)micro, population exponential growth rate R, and error rate epsilon, simultaneously. Using simulation, we show the combined effects of the parameters, theta, n, epsilon, and R on the accuracy of parameter estimation. We compared our maximum composite likelihood estimator (MCLE) of theta with other theta estimators that take into account the error. The results show the MCLE performs well when the sample size is large or the error rate is high. Using parametric bootstrap, composite likelihood can also be used as a statistic for testing the model goodness-of-fit of the observed DNA sequences. The MCLE method is applied to sequence data on the ANGPTL4 gene in 1832 African American and 1045 European American individuals.

Published
2010
Full Text
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43. Beta-2 adrenergic receptor genotypes and haplotypes in different ethnic groups.

Author

Maxwell TJ, Ameyaw MM, Pritchard S, Thornton N, Folayan G, Githang'a J, Indalo A, Tariq M, Mobarek A, Evans DA, Ofori-Adjei D, Templeton AR, and McLeod HL

Subjects
Alleles, Asian People genetics, Black People genetics, Gene Frequency, Genotype, Humans, Phylogeny, Polymorphism, Single Nucleotide, White People genetics, Haplotypes genetics, Receptors, Adrenergic, beta-2 genetics
Abstract

The human beta-2 adrenergic receptor (beta2AR) is responsible for the binding of endogenous catecholamines and their exogenously administered agonists and antagonists. Three functional polymorphisms in codons 16, 27 and 164 have been described which have clinical importance for several diseases, including asthma, hypertension, heart failure, cystic fibrosis and obesity, as well as response to beta-agonist therapy. These were evaluated in 726 individuals from 8 distinct ethnic populations (Chinese, Filipino, Southwest Asian, Saudi, Ghanaian, Kenyan, Sudanese, and European from Scotland). The results show that most haplotypes are shared among all populations, yet there are marked differences in their frequency distributions geographically. The genetic distance tree is different from standard human population distance trees, implying a different mode of evolution for this locus than that for human population gene-flow history. The multilocus frequency differences between the observed clusters of populations correspond to historical haplotype groupings that have been found to be functionally different with respect to multiple medically related phenotypes. Further studies are needed to see if functional relationships are the same across populations.

Published
2005

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