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51. Probabilistic approaches to the use of higher order clone relationships in physical map assembly

Author: States, David J., Nowotny, Volker, and Blackwell, Thomas W.
Published: 2001

52. Identification of CFTR variants in Latino patients with cystic fibrosis from the Dominican Republic and Puerto Rico

Author: Zeiger, Andrew M., primary, McGarry, Meghan E., additional, Mak, Angel C. Y., additional, Medina, Vivian, additional, Salazar, Sandra, additional, Eng, Celeste, additional, Liu, Amy K., additional, Oh, Sam S., additional, Nuckton, Thomas J., additional, Jain, Deepti, additional, Blackwell, Thomas W., additional, Kang, Hyun Min, additional, Abecasis, Goncalo, additional, Oñate, Leandra Cordero, additional, Seibold, Max A., additional, Burchard, Esteban G., additional, and Rodriguez‐Santana, Jose, additional
Published: 2019
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53. Mapping the 17q12-21.1 Locus for Variants Associated with Early-Onset Asthma in African Americans.

Author: Hongsheng Gui, Levin, Albert M., Donglei Hu, Sleiman, Patrick, Shujie Xiao, Mak, Angel C. Y., Mao Yang, Barczak, Andrea J., Huntsman, Scott, Eng, Celeste, Hochstadt, Samantha, Zhang, Ellen, Whitehouse, Kyle, Simons, Samantha, Cabral, Whitney, Takriti, Sami, Abecasis, Gonçalo, Blackwell, Thomas W., Hyun Min Kang, and Nickerson, Deborah A.
Subjects: ASTHMA, HEALTH of African Americans, CHROMOSOMES, LINKAGE disequilibrium, GENETIC polymorphisms, RESEARCH funding
Abstract: Rationale: The 17q12-21.1 locus is one of the most highly replicated genetic associations with asthma. Individuals of African descent have lower linkage disequilibrium in this region, which could facilitate identifying causal variants.Objectives: To identify functional variants at 17q12-21.1 associated with early-onset asthma among African American individuals.Methods: We evaluated African American participants from SAPPHIRE (Study of Asthma Phenotypes and Pharmacogenomic Interactions by Race-Ethnicity) (n = 1,940), SAGE II (Study of African Americans, Asthma, Genes and Environment) (n = 885), and GCPD-A (Study of the Genetic Causes of Complex Pediatric Disorders-Asthma) (n = 2,805). Associations with asthma onset at ages under 5 years were meta-analyzed across cohorts. The lead signal was reevaluated considering haplotypes informed by genetic ancestry (i.e., African vs. European). Both an expression-quantitative trait locus analysis and a phenome-wide association study were performed on the lead variant.Measurements and Main Results: The meta-analyzed results from SAPPHIRE, SAGE II, and the GCPD-A identified rs11078928 as the top association for early-onset asthma. A haplotype analysis suggested that the asthma association partitioned most closely with the rs11078928 genotype. Genetic ancestry did not appear to influence the effect of this variant. In the expression-quantitative trait locus analysis, rs11078928 was related to alternative splicing of GSDMB (gasdermin-B) transcripts. The phenome-wide association study of rs11078928 suggested that this variant was predominantly associated with asthma and asthma-associated symptoms.Conclusions: A splice-acceptor polymorphism appears to be a causal variant for asthma at the 17q12-21.1 locus. This variant appears to have the same magnitude of effect in individuals of African and European descent. [ABSTRACT FROM AUTHOR]
Published: 2021
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54. 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

55. 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
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56. Evaluating the contribution of rare variants to type 2 diabetes and related traits using pedigrees

Author: Jun, Goo, primary, Manning, Alisa, additional, Almeida, Marcio, additional, Zawistowski, Matthew, additional, Wood, Andrew R., additional, Teslovich, Tanya M., additional, Fuchsberger, Christian, additional, Feng, Shuang, additional, Cingolani, Pablo, additional, Gaulton, Kyle J., additional, Dyer, Thomas, additional, Blackwell, Thomas W., additional, Chen, Han, additional, Chines, Peter S., additional, Choi, Sungkyoung, additional, Churchhouse, Claire, additional, Fontanillas, Pierre, additional, King, Ryan, additional, Lee, SungYoung, additional, Lincoln, Stephen E., additional, Trubetskoy, Vasily, additional, DePristo, Mark, additional, Fingerlin, Tasha, additional, Grossman, Robert, additional, Grundstad, Jason, additional, Heath, Alison, additional, Kim, Jayoun, additional, Kim, Young Jin, additional, Laramie, Jason, additional, Lee, Jaehoon, additional, Li, Heng, additional, Liu, Xuanyao, additional, Livne, Oren, additional, Locke, Adam E., additional, Maller, Julian, additional, Mazur, Alexander, additional, Morris, Andrew P., additional, Pollin, Toni I., additional, Ragona, Derek, additional, Reich, David, additional, Rivas, Manuel A., additional, Scott, Laura J., additional, Sim, Xueling, additional, Tearle, Rick G., additional, Teo, Yik Ying, additional, Williams, Amy L., additional, Zöllner, Sebastian, additional, Curran, Joanne E., additional, Peralta, Juan, additional, Akolkar, Beena, additional, Bell, Graeme I., additional, Burtt, Noël P., additional, Cox, Nancy J., additional, Florez, Jose C., additional, Hanis, Craig L., additional, McKeon, Catherine, additional, Mohlke, Karen L., additional, Seielstad, Mark, additional, Wilson, James G., additional, Atzmon, Gil, additional, Below, Jennifer E., additional, Dupuis, Josée, additional, Nicolae, Dan L., additional, Lehman, Donna, additional, Park, Taesung, additional, Won, Sungho, additional, Sladek, Robert, additional, Altshuler, David, additional, McCarthy, Mark I., additional, Duggirala, Ravindranath, additional, Boehnke, Michael, additional, Frayling, Timothy M., additional, Abecasis, Gonçalo R., additional, and Blangero, John, additional
Published: 2017
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57. Inherited causes of clonal haematopoiesis in 97,691 whole genomes

Author: Bick, Alexander G., Weinstock, Joshua S., Nandakumar, Satish K., Fulco, Charles P., Bao, Erik L., Zekavat, Seyedeh M., Szeto, Mindy D., Liao, Xiaotian, Leventhal, Matthew J., Nasser, Joseph, Chang, Kyle, Laurie, Cecelia, Burugula, Bala Bharathi, Gibson, Christopher J., Lin, Amy E., Taub, Margaret A., Aguet, Francois, Ardlie, Kristin, Mitchell, Braxton D., Barnes, Kathleen C., Moscati, Arden, Fornage, Myriam, Redline, Susan, Psaty, Bruce M., Silverman, Edwin K., Weiss, Scott T., Palmer, Nicholette D., Vasan, Ramachandran S., Burchard, Esteban G., Kardia, Sharon L. R., He, Jiang, Kaplan, Robert C., Smith, Nicholas L., Arnett, Donna K., Schwartz, David A., Correa, Adolfo, de Andrade, Mariza, Guo, Xiuqing, Konkle, Barbara A., Custer, Brian, Peralta, Juan M., Gui, Hongsheng, Meyers, Deborah A., McGarvey, Stephen T., Chen, Ida Yii-Der, Shoemaker, M. Benjamin, Peyser, Patricia A., Broome, Jai G., Gogarten, Stephanie M., Wang, Fei Fei, Wong, Quenna, Montasser, May E., Daya, Michelle, Kenny, Eimear E., North, Kari E., Launer, Lenore J., Cade, Brian E., Bis, Joshua C., Cho, Michael H., Lasky-Su, Jessica, Bowden, Donald W., Cupples, L. Adrienne, Mak, Angel C. Y., Becker, Lewis C., Smith, Jennifer A., Kelly, Tanika N., Aslibekyan, Stella, Heckbert, Susan R., Tiwari, Hemant K., Yang, Ivana V., Heit, John A., Lubitz, Steven A., Johnsen, Jill M., Curran, Joanne E., Wenzel, Sally E., Weeks, Daniel E., Rao, Dabeeru C., Darbar, Dawood, Moon, Jee-Young, Tracy, Russell P., Buth, Erin J., Rafaels, Nicholas, Loos, Ruth J. F., Durda, Peter, Liu, Yongmei, Hou, Lifang, Lee, Jiwon, Kachroo, Priyadarshini, Freedman, Barry I., Levy, Daniel, Bielak, Lawrence F., Hixson, James E., Floyd, James S., Whitsel, Eric A., Ellinor, Patrick T., Irvin, Marguerite R., Fingerlin, Tasha E., Raffield, Laura M., Armasu, Sebastian M., Wheeler, Marsha M., Sabino, Ester C., Blangero, John, Williams, L. Keoki, Levy, Bruce D., Sheu, Wayne Huey-Herng, Roden, Dan M., Boerwinkle, Eric, Manson, JoAnn E., Mathias, Rasika A., Desai, Pinkal, Taylor, Kent D., Johnson, Andrew D., Auer, Paul L., Kooperberg, Charles, Laurie, Cathy C., Blackwell, Thomas W., Smith, Albert V., Zhao, Hongyu, Lange, Ethan, Lange, Leslie, Rich, Stephen S., Rotter, Jerome I., Wilson, James G., Scheet, Paul, Kitzman, Jacob O., Lander, Eric S., Engreitz, Jesse M., Ebert, Benjamin L., Reiner, Alexander P., Jaiswal, Siddhartha, Abecasis, Gonçalo, Sankaran, Vijay G., Kathiresan, Sekar, and Natarajan, Pradeep
Abstract: Age is the dominant risk factor for most chronic human diseases, but the mechanisms through which ageing confers this risk are largely unknown1. The age-related acquisition of somatic mutations that lead to clonal expansion in regenerating haematopoietic stem cell populations has recently been associated with both haematological cancer2–4and coronary heart disease5—this phenomenon is termed clonal haematopoiesis of indeterminate potential (CHIP)6. Simultaneous analyses of germline and somatic whole-genome sequences provide the opportunity to identify root causes of CHIP. Here we analyse high-coverage whole-genome sequences from 97,691 participants of diverse ancestries in the National Heart, Lung, and Blood Institute Trans-omics for Precision Medicine (TOPMed) programme, and identify 4,229 individuals with CHIP. We identify associations with blood cell, lipid and inflammatory traits that are specific to different CHIP driver genes. Association of a genome-wide set of germline genetic variants enabled the identification of three genetic loci associated with CHIP status, including one locus at TET2that was specific to individuals of African ancestry. In silico-informed in vitro evaluation of the TET2germline locus enabled the identification of a causal variant that disrupts a TET2distal enhancer, resulting in increased self-renewal of haematopoietic stem cells. Overall, we observe that germline genetic variation shapes haematopoietic stem cell function, leading to CHIP through mechanisms that are specific to clonal haematopoiesis as well as shared mechanisms that lead to somatic mutations across tissues.
Published: 2020
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58. 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

59. 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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60. 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

61. Evaluating the contribution of rare variants to type 2 diabetes and related traits using pedigrees.

Author: Goo Jun, Manning, Alisa, Almeida, Marcio, Zawistowski, Matthew, Wood, Andrew R., Teslovich, Tanya M., Fuchsberger, Christian, Shuang Feng, Cingolani, Pablo, Gaulton, Kyle J., Dyer, Thomas, Blackwell, Thomas W., Han Chen, Chines, Peter S., Sungkyoung Choi, Churchhouse, Claire, Fontanillas, Pierre, King, Ryan, Sungyoung Lee, and Lincoln, Stephen E.
Subjects: TYPE 2 diabetes, ALLELES, GENETICS, NUCLEOTIDE sequencing, GENOMES, THERAPEUTICS
Abstract: A major challenge in evaluating the contribution of rare variants to complex disease is identifying enough copies of the rare alleles to permit informative statistical analysis. To investigate the contribution of rare variants to the risk of type 2 diabetes (T2D) and related traits, we performed deep whole-genome analysis of 1,034 members of 20 large Mexican-American families with high prevalence of T2D. If rare variants of large effect accounted for much of the diabetes risk in these families, our experiment was powered to detect association. Using gene expression data on 21,677 transcripts for 643 pedigree members, we identified evidence for large-effect rare-variant cis-expression quantitative trait loci that could not be detected in population studies, validating our approach. However, we did not identify any rare variants of large effect associated with T2D, or the related traits of fasting glucose and insulin, suggesting that large-effect rare variants account for only a modest fraction of the genetic risk of these traits in this sample of families. Reliable identification of large-effect rare variants will require larger samples of extended pedigrees or different study designs that further enrich for such variants. [ABSTRACT FROM AUTHOR]
Published: 2018
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62. Integration of Genome and Chromatin Structure with Gene Expression Profiles To Predict c-MYC Recognition Site Binding and Function

Author: Chen, Yili, primary, Blackwell, Thomas W, additional, Chen, Ji, additional, Gao, Jing, additional, Lee, Angel W, additional, and States, David J, additional
Published: 2007
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63. Evolutionary-conserved Gene Expression Response Profiles Across Mammalian Tissues

Author: Chen, Ji, primary, Blackwell, Thomas W., additional, Fermin, Damian, additional, Menon, Rajasree, additional, Chen, Yili, additional, Gao, Jing, additional, Lee, Angel W., additional, and States, David J., additional
Published: 2007
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64. Computational Prediction of c-MYC Binding and Action by Integration of Multiple Data Sources.

Author: Chen, Yili, primary, Blackwell, Thomas W., primary, Gao, Jing, primary, Hewagama, Anura, primary, Grifka, Heather M., primary, Lee, Angel W., primary, and States, David J., primary
Published: 2006
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65. Identifying Novel Blood Proteins and Protein Isoforms Using Tandem Mass Spectra.

Author: Fermin, Damian, primary, Allen, Baxter B., additional, Blackwell, Thomas W., additional, Menon, Rajasree, additional, Adamski, Marcin, additional, and States, David J., additional
Published: 2006
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66. Challenges in deriving high-confidence protein identifications from data gathered by a HUPO plasma proteome collaborative study

Author: States, David J, primary, Omenn, Gilbert S, additional, Blackwell, Thomas W, additional, Fermin, Damian, additional, Eng, Jimmy, additional, Speicher, David W, additional, and Hanash, Samir M, additional
Published: 2006
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67. Overview of the HUPO Plasma Proteome Project: Results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database

Author: Omenn, Gilbert S., primary, States, David J., additional, Adamski, Marcin, additional, Blackwell, Thomas W., additional, Menon, Rajasree, additional, Hermjakob, Henning, additional, Apweiler, Rolf, additional, Haab, Brian B., additional, Simpson, Richard J., additional, Eddes, James S., additional, Kapp, Eugene A., additional, Moritz, Robert L., additional, Chan, Daniel W., additional, Rai, Alex J., additional, Admon, Arie, additional, Aebersold, Ruedi, additional, Eng, Jimmy, additional, Hancock, William S., additional, Hefta, Stanley A., additional, Meyer, Helmut, additional, Paik, Young-Ki, additional, Yoo, Jong-Shin, additional, Ping, Peipei, additional, Pounds, Joel, additional, Adkins, Joshua, additional, Qian, Xiaohong, additional, Wang, Rong, additional, Wasinger, Valerie, additional, Wu, Chi Yue, additional, Zhao, Xiaohang, additional, Zeng, Rong, additional, Archakov, Alexander, additional, Tsugita, Akira, additional, Beer, Ilan, additional, Pandey, Akhilesh, additional, Pisano, Michael, additional, Andrews, Philip, additional, Tammen, Harald, additional, Speicher, David W., additional, and Hanash, Samir M., additional
Published: 2005
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68. Integration of Genome and Chromatin Structure with Gene Expression Profiles To Predict c-MYC Recognition Site Binding and Function.

Author: Yili Chen, Blackwell, Thomas W., Ji Chen, Jing Gao, Lee, Angel W., and States, David J.
Subjects: *BINDING sites, *MYC proteins, *DNA-binding proteins, *CHROMATIN, *GENOMES, *TRANSCRIPTION factors
Abstract: The MYC genes encode nuclear sequence specific-binding DNA-binding proteins that are pleiotropic regulators of cellular function, and the c-MYC proto-oncogene is deregulated and/or mutated in most human cancers. Experimental studies of MYC binding to the genome are not fully consistent. While many c-MYC recognition sites can be identified in c-MYC responsive genes, other motif matches-even experimentally confirmed sites-are associated with genes showing no c-MYC response. We have developed a computational model that integrates multiple sources of evidence to predict which genes will bind and be regulated by MYC in vivo. First, a Bayesian network classifier is used to predict those c-MYC recognition sites that are most likely to exhibit high-occupancy binding in chromatin immunoprecipitation studies. This classifier incorporates genomic sequence, experimentally determined genomic chromatin acetylation islands, and predicted methylation status from a computational model estimating the likelihood of genomic DNA methylation. We find that the predictions from this classifier are also applicable to other transcription factors, such as cAMP-response element-binding protein, whose binding sites are sensitive to DNA methylation. Second, the MYC binding probability is combined with the gene expression profile data from nine independent microarray datasets in multiple tissues. Finally, we may consider gene function annotations in Gene Ontology to predict the c-MYC targets. We assess the performance of our prediction results by comparing them with the c-myc targets identified in the biomedical literature. In total, we predict 460 likely c-MYC target genes in the human genome, of which 67 have been reported to be both bound and regulated by MYC, 68 are bound by MYC, and another 80 are MYC-regulated. The approach thus successfully identifies many known c-MYC targets and suggests many novel sites. Our findings suggest that to identify c-MYC genomic targets, integration of different data sources helps to improve the accuracy. [ABSTRACT FROM AUTHOR]
Published: 2007
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69. Author Correction: Inherited causes of clonal haematopoiesis in 97,691 whole genomes

Author: Bick, Alexander G., Weinstock, Joshua S., Nandakumar, Satish K., Fulco, Charles P., Bao, Erik L., Zekavat, Seyedeh M., Szeto, Mindy D., Liao, Xiaotian, Leventhal, Matthew J., Nasser, Joseph, Chang, Kyle, Laurie, Cecelia, Burugula, Bala Bharathi, Gibson, Christopher J., Niroula, Abhishek, Lin, Amy E., Taub, Margaret A., Aguet, Francois, Ardlie, Kristin, Mitchell, Braxton D., Barnes, Kathleen C., Moscati, Arden, Fornage, Myriam, Redline, Susan, Psaty, Bruce M., Silverman, Edwin K., Weiss, Scott T., Palmer, Nicholette D., Vasan, Ramachandran S., Burchard, Esteban G., Kardia, Sharon L. R., He, Jiang, Kaplan, Robert C., Smith, Nicholas L., Arnett, Donna K., Schwartz, David A., Correa, Adolfo, de Andrade, Mariza, Guo, Xiuqing, Konkle, Barbara A., Custer, Brian, Peralta, Juan M., Gui, Hongsheng, Meyers, Deborah A., McGarvey, Stephen T., Chen, Ida Yii-Der, Shoemaker, M. Benjamin, Peyser, Patricia A., Broome, Jai G., Gogarten, Stephanie M., Wang, Fei Fei, Wong, Quenna, Montasser, May E., Daya, Michelle, Kenny, Eimear E., North, Kari E., Launer, Lenore J., Cade, Brian E., Bis, Joshua C., Cho, Michael H., Lasky-Su, Jessica, Bowden, Donald W., Cupples, L. Adrienne, Mak, Angel C. Y., Becker, Lewis C., Smith, Jennifer A., Kelly, Tanika N., Aslibekyan, Stella, Heckbert, Susan R., Tiwari, Hemant K., Yang, Ivana V., Heit, John A., Lubitz, Steven A., Johnsen, Jill M., Curran, Joanne E., Wenzel, Sally E., Weeks, Daniel E., Rao, Dabeeru C., Darbar, Dawood, Moon, Jee-Young, Tracy, Russell P., Buth, Erin J., Rafaels, Nicholas, Loos, Ruth J. F., Durda, Peter, Liu, Yongmei, Hou, Lifang, Lee, Jiwon, Kachroo, Priyadarshini, Freedman, Barry I., Levy, Daniel, Bielak, Lawrence F., Hixson, James E., Floyd, James S., Whitsel, Eric A., Ellinor, Patrick T., Irvin, Marguerite R., Fingerlin, Tasha E., Raffield, Laura M., Armasu, Sebastian M., Wheeler, Marsha M., Sabino, Ester C., Blangero, John, Williams, L. Keoki, Levy, Bruce D., Sheu, Wayne Huey-Herng, Roden, Dan M., Boerwinkle, Eric, Manson, JoAnn E., Mathias, Rasika A., Desai, Pinkal, Taylor, Kent D., Johnson, Andrew D., Auer, Paul L., Kooperberg, Charles, Laurie, Cathy C., Blackwell, Thomas W., Smith, Albert V., Zhao, Hongyu, Lange, Ethan, Lange, Leslie, Rich, Stephen S., Rotter, Jerome I., Wilson, James G., Scheet, Paul, Kitzman, Jacob O., Lander, Eric S., Engreitz, Jesse M., Ebert, Benjamin L., Reiner, Alexander P., Jaiswal, Siddhartha, Abecasis, Gonçalo, Sankaran, Vijay G., Kathiresan, Sekar, and Natarajan, Pradeep
Abstract: A Correction to this paper has been published: https://doi.org/10.1038/s41586-021-03280-1.
Published: 2021
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70. Whole genome sequence analysis of platelet traits in the NHLBI Trans-Omics for Precision Medicine (TOPMed) initiative

Author: Little, Amarise, Hu, Yao, Sun, Quan, Jain, Deepti, Broome, Jai, Chen, Ming-Huei, Thibord, Florian, McHugh, Caitlin, Surendran, Praveen, Blackwell, Thomas W, Brody, Jennifer A, Bhan, Arunoday, Chami, Nathalie, De Vries, Paul S, Ekunwe, Lynette, Heard-Costa, Nancy, Hobbs, Brian D, Manichaikul, Ani, Moon, Jee-Young, Preuss, Michael H, Ryan, Kathleen, Wang, Zhe, Wheeler, Marsha, Yanek, Lisa R, Abecasis, Goncalo R, Almasy, Laura, Beaty, Terri H, Becker, Lewis C, Blangero, John, Boerwinkle, Eric, Butterworth, Adam S, Choquet, Hélène, Correa, Adolfo, Curran, Joanne E, Faraday, Nauder, Fornage, Myriam, Glahn, David C, Hou, Lifang, Jorgenson, Eric, Kooperberg, Charles, Lewis, Joshua P, Lloyd-Jones, Donald M, Loos, Ruth JF, Min, Yuan-I, Mitchell, Braxton D, Morrison, Alanna C, Nickerson, Deborah A, North, Kari E, O'Connell, Jeffrey R, Pankratz, Nathan, Psaty, Bruce M, Vasan, Ramachandran S, Rich, Stephen S, Rotter, Jerome I, Smith, Albert V, Smith, Nicholas L, Tang, Hua, Tracy, Russell P, Conomos, Matthew P, Laurie, Cecelia A, Mathias, Rasika A, Li, Yun, Auer, Paul L, NHLBI Trans-Omics For Precision Medicine (TOPMed) Consortium, Thornton, Timothy, Reiner, Alexander P, Johnson, Andrew D, and Raffield, Laura M
Subjects: Blood Platelets, Phenotype, Humans, Precision Medicine, National Heart, Lung, and Blood Institute (U.S.), Polymorphism, Single Nucleotide, United States, 3. Good health, Genome-Wide Association Study
Abstract: Platelets play a key role in thrombosis and hemostasis. Platelet count (PLT) and mean platelet volume (MPV) are highly heritable quantitative traits, with hundreds of genetic signals previously identified, mostly in European ancestry populations. We here utilize whole genome sequencing (WGS) from NHLBI's Trans-Omics for Precision Medicine initiative (TOPMed) in a large multi-ethnic sample to further explore common and rare variation contributing to PLT (n = 61 200) and MPV (n = 23 485). We identified and replicated secondary signals at MPL (rs532784633) and PECAM1 (rs73345162), both more common in African ancestry populations. We also observed rare variation in Mendelian platelet-related disorder genes influencing variation in platelet traits in TOPMed cohorts (not enriched for blood disorders). For example, association of GP9 with lower PLT and higher MPV was partly driven by a pathogenic Bernard-Soulier syndrome variant (rs5030764, p.Asn61Ser), and the signals at TUBB1 and CD36 were partly driven by loss of function variants not annotated as pathogenic in ClinVar (rs199948010 and rs571975065). However, residual signal remained for these gene-based signals after adjusting for lead variants, suggesting that additional variants in Mendelian genes with impacts in general population cohorts remain to be identified. Gene-based signals were also identified at several genome-wide association study identified loci for genes not annotated for Mendelian platelet disorders (PTPRH, TET2, CHEK2), with somatic variation driving the result at TET2. These results highlight the value of WGS in populations of diverse genetic ancestry to identify novel regulatory and coding signals, even for well-studied traits like platelet traits.

71. 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.

72. Computational Prediction of c-MYCBinding and Action by Integration of Multiple Data Sources.

Author: Chen, Yili, Blackwell, Thomas W., Gao, Jing, Hewagama, Anura, Grifka, Heather M., Lee, Angel W., and States, David J.
Abstract: c-MYCis an important proto-oncogene. Its actions are mediated by sequence specific binding of the c-MYCprotein to genomic DNA. While many c-MYCrecognition sites can be identified in c-MYCresponsive genes, many others are associated with genes showing no c-MYCresponse. It is not yet known how the cell determines which of the many c-MYCrecognition sites are biologically active and directly bind c-MYCprotein to regulate gene expression. We have developed a computational model that predict c-MYCbinding and functional activation as distinct processes. Our model integrates four types of evidence to predict functional c-MYCtargets: genomic sequence, MYC binding, gene expression and gene function annotations. First, a Bayesian network classifier is used to predict c-MYCrecognition sites likely to exhibit high occupancy binding in chromatin immunoprecipitation studies using several types of sequence information, including predicted DNA methylation using a computational model to estimate the likelihood of genomic DNA methylation. In the second step, the DNA binding probability of MYC is combined with the gene expression information from 9 independent microarray datasets in multiple tissues and the gene function annotations in Gene Ontology to predict the c-MYCtargets. The prediction results were compared with the c-MYCtargets in public MYC target database [www.myccancergene.org], which collected the c-MYCtargets identified in biomedical literatures. In total, we predicted 599 likely c-MYCgenes on human genome, of which 73 have been reported to be both bound and regulated by MYC, 83 are bound by MYC in vivo and another 93 are MYC regulated. The approach thus successfully identified many known c-MYCtargets as well as suggesting many novel sites including many sites that are remote from the transcription start site. Our findings suggest that to identify c-MYCgenomic targets, any study based on single high throughput dataset is likely to be insufficient. Using multiple gene expression datasets helps to improve the sensitivity and integration of different data sources helps to improve the specificity.
Published: 2006
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73. Epigenome-wide Association Analysis of Mitochondrial Heteroplasmy Provides Insight into Molecular Mechanisms of Disease.

Author: Lai M, Kim K, Zheng Y, Castellani CA, Ratliff SM, Wang M, Liu X, Haessler J, Huan T, Bielak LF, Zhao W, Joehanes R, Ma J, Guo X, Manson JE, Grove ML, Bressler J, Taylor KD, Lappalainen T, Kasela S, Blackwell TW, Lake NJ, Faul JD, Ferrier KR, Hou L, Kooperberg C, Reiner AP, Zhang K, Peyser PA, Fornage M, Boerwinkle E, Raffield LM, Carson AP, Rich SS, Liu Y, Levy D, Rotter JI, Smith JA, Arking DE, and Liu C
Abstract: The relationship between mitochondrial DNA (mtDNA) heteroplasmy and nuclear DNA (nDNA) methylation (CpGs) remains to be studied. We conducted an epigenome-wide association analysis of heteroplasmy burden scores across 10,986 participants (mean age 77, 63% women, and 54% non-White races/ethnicities) from seven population-based observational cohorts. We identified 412 CpGs (FDR p < 0.05) associated with mtDNA heteroplasmy. Higher levels of heteroplasmy burden were associated with lower nDNA methylation levels at most significant CpGs. Functional inference analyses of genes annotated to heteroplasmy-associated CpGs emphasized mitochondrial functions and showed enrichment in cardiometabolic conditions and traits. We developed CpG-scores based on heteroplasmy-count associated CpGs (MHC-CpG scores) using elastic net Cox regression in a training cohort. A one-unit higher level of the standardized MHC-CpG scores were associated with 1.26-fold higher hazard of all-cause mortality (95% CI: 1.14, 1.39) and 1.09-fold higher hazard of CVD (95% CI: 1.01-1.17) in the meta-analysis of testing cohorts, adjusting for age, sex, and smoking. These findings shed light on the relationship between mtDNA heteroplasmy and DNA methylation, and the role of heteroplasmy-associated CpGs as biomarkers in predicting all-cause mortality and cardiovascular disease.
Published: 2024
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74. Proteome-wide association studies for blood lipids and comparison with transcriptome-wide association studies.

Author: Zhang D, Gao B, Feng Q, Manichaikul A, Peloso GM, Tracy RP, Durda P, Taylor KD, Liu Y, Johnson WC, Gabriel S, Gupta N, Smith JD, Aguet F, Ardlie KG, Blackwell TW, Gerszten RE, Rich SS, Rotter JI, Scott LJ, Zhou X, and Lee S
Abstract: Blood lipid traits are treatable and heritable risk factors for heart disease, a leading cause of mortality worldwide. Although genome-wide association studies (GWASs) have discovered hundreds of variants associated with lipids in humans, most of the causal mechanisms of lipids remain unknown. To better understand the biological processes underlying lipid metabolism, we investigated the associations of plasma protein levels with total cholesterol (TC), triglycerides (TG), high-density lipoprotein (HDL) cholesterol, and low-density lipoprotein (LDL) cholesterol in blood. We trained protein prediction models based on samples in the Multi-Ethnic Study of Atherosclerosis (MESA) and applied them to conduct proteome-wide association studies (PWASs) for lipids using the Global Lipids Genetics Consortium (GLGC) data. Of the 749 proteins tested, 42 were significantly associated with at least one lipid trait. Furthermore, we performed transcriptome-wide association studies (TWASs) for lipids using 9,714 gene expression prediction models trained on samples from peripheral blood mononuclear cells (PBMCs) in MESA and 49 tissues in the Genotype-Tissue Expression (GTEx) project. We found that although PWASs and TWASs can show different directions of associations in an individual gene, 40 out of 49 tissues showed a positive correlation between PWAS and TWAS signed p values across all the genes, which suggests high-level consistency between proteome-lipid associations and transcriptome-lipid associations., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)
Published: 2024
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75. The Genetic Determinants and Genomic Consequences of Non-Leukemogenic Somatic Point Mutations.

Author: Weinstock JS, Chaudhry SA, Ioannou M, Viskadourou M, Reventun P, Jakubek YA, Liggett LA, Laurie C, Broome JG, Khan A, Taylor KD, Guo X, Peyser PA, Boerwinkle E, Chami N, Kenny EE, Loos RJ, Psaty BM, Russell TP, Brody JA, Yun JH, Cho MH, Vasan RS, Kardia SL, Smith JA, Raffield LM, Bidulescu A, O'Brien E, de Andrade M, Rotter JI, Rich SS, Tracy RP, Chen YI, Gu CC, Hsiung CA, Kooperberg C, Haring B, Nassir R, Mathias R, Reiner A, Sankaran V, Lowenstein CJ, Blackwell TW, Abecasis GR, Smith AV, Kang HM, Natarajan P, Jaiswal S, Bick A, Post WS, Scheet P, Auer P, Karantanos T, Battle A, and Arvanitis M
Abstract: Clonal hematopoiesis (CH) is defined by the expansion of a lineage of genetically identical cells in blood. Genetic lesions that confer a fitness advantage, such as point mutations or mosaic chromosomal alterations (mCAs) in genes associated with hematologic malignancy, are frequent mediators of CH. However, recent analyses of both single cell-derived colonies of hematopoietic cells and population sequencing cohorts have revealed CH frequently occurs in the absence of known driver genetic lesions. To characterize CH without known driver genetic lesions, we used 51,399 deeply sequenced whole genomes from the NHLBI TOPMed sequencing initiative to perform simultaneous germline and somatic mutation analyses among individuals without leukemogenic point mutations (LPM), which we term CH-LPMneg. We quantified CH by estimating the total mutation burden. Because estimating somatic mutation burden without a paired-tissue sample is challenging, we developed a novel statistical method, the Genomic and Epigenomic informed Mutation (GEM) rate, that uses external genomic and epigenomic data sources to distinguish artifactual signals from true somatic mutations. We performed a genome-wide association study of GEM to discover the germline determinants of CH-LPMneg. After fine-mapping and variant-to-gene analyses, we identified seven genes associated with CH-LPMneg ( TCL1A, TERT, SMC4, NRIP1, PRDM16 , MSRA , SCARB1 ), and one locus associated with a sex-associated mutation pathway ( SRGAP2C) . We performed a secondary analysis excluding individuals with mCAs, finding that the genetic architecture was largely unaffected by their inclusion. Functional analyses of SMC4 and NRIP1 implicated altered HSC self-renewal and proliferation as the primary mediator of mutation burden in blood. We then performed comprehensive multi-tissue transcriptomic analyses, finding that the expression levels of 404 genes are associated with GEM. Finally, we performed phenotypic association meta-analyses across four cohorts, finding that GEM is associated with increased white blood cell count and increased risk for incident peripheral artery disease, but is not significantly associated with incident stroke or coronary disease events. Overall, we develop GEM for quantifying mutation burden from WGS without a paired-tissue sample and use GEM to discover the genetic, genomic, and phenotypic correlates of CH-LPMneg., Competing Interests: Competing Interests Declaration L.M.R. is a consultant for the TOPMed Administrative Coordinating Center (through Westat). B.M.P. serves on the Steering Committee of the Yale Open Data Access Project funded by Johnson & Johnson. J.Y. reports grant support from Bayer. M.C. reports grant support from Bayer and GSK, Consulting and speaking fees from Illumina and AstraZeneca. A.G.B., P.N, and S.J. are cofounders, equity holders, and on the scientific advisory board of TenSixteen Bio. G.R.A. is an employee of Regeneron Pharmaceuticals and receives salary, stock and stock options as compensation.
Published: 2024
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76. Genetic Architecture and Analysis Practices of Circulating Metabolites in the NHLBI Trans-Omics for Precision Medicine (TOPMed) Program.

Author: Wang N, Ockerman FP, Zhou LY, Grove ML, Alkis T, Barnard J, Bowler RP, Clish CB, Chung S, Drzymalla E, Evans AM, Franceschini N, Gerszten RE, Gillman MG, Hutton SR, Kelly RS, Kooperberg C, Larson MG, Lasky-Su J, Meyers DA, Woodruff PG, Reiner AP, Rich SS, Rotter JI, Silverman EK, Ramachandran VS, Weiss ST, Wong KE, Wood AC, Wu L, Yarden R, Blackwell TW, Smith AV, Chen H, Raffield LM, and Yu B
Abstract: Circulating metabolite levels partly reflect the state of human health and diseases, and can be impacted by genetic determinants. Hundreds of loci associated with circulating metabolites have been identified; however, most findings focus on predominantly European ancestry or single study analyses. Leveraging the rich metabolomics resources generated by the NHLBI Trans-Omics for Precision Medicine (TOPMed) Program, we harmonized and accessibly cataloged 1,729 circulating metabolites among 25,058 ancestrally-diverse samples. We provided recommendations for outlier and imputation handling to process metabolite data, as well as a general analytical framework. We further performed a pooled analysis following our practical recommendations and discovered 1,778 independent loci associated with 667 metabolites. Among 108 novel locus - metabolite pairs, we detected not only novel loci within previously implicated metabolite associated genes, but also novel genes (such as GAB3 and VSIG4 located in the X chromosome) that have putative roles in metabolic regulation. In the sex-stratified analysis, we revealed 85 independent locus-metabolite pairs with evidence of sexual dimorphism, including well-known metabolic genes such as FADS2 , D2HGDH , SUGP1 , UTG2B17 , strongly supporting the importance of exploring sex difference in the human metabolome. Taken together, our study depicted the genetic contribution to circulating metabolite levels, providing additional insight into the understanding of human health.
Published: 2024
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77. Proteome-Wide Association Studies for Blood Lipids and Comparison with Transcriptome-Wide Association Studies.

Author: Zhang D, Gao B, Feng Q, Manichaikul A, Peloso GM, Tracy RP, Durda P, Taylor KD, Liu Y, Johnson WC, Gabriel S, Gupta N, Smith JD, Aguet F, Ardlie KG, Blackwell TW, Gerszten RE, Rich SS, Rotter JI, Scott LJ, Zhou X, and Lee S
Abstract: Blood lipid traits are treatable and heritable risk factors for heart disease, a leading cause of mortality worldwide. Although genome-wide association studies (GWAS) have discovered hundreds of variants associated with lipids in humans, most of the causal mechanisms of lipids remain unknown. To better understand the biological processes underlying lipid metabolism, we investigated the associations of plasma protein levels with total cholesterol (TC), triglycerides (TG), high-density lipoprotein cholesterol (HDL), and low-density lipoprotein cholesterol (LDL) in blood. We trained protein prediction models based on samples in the Multi-Ethnic Study of Atherosclerosis (MESA) and applied them to conduct proteome-wide association studies (PWAS) for lipids using the Global Lipids Genetics Consortium (GLGC) data. Of the 749 proteins tested, 42 were significantly associated with at least one lipid trait. Furthermore, we performed transcriptome-wide association studies (TWAS) for lipids using 9,714 gene expression prediction models trained on samples from peripheral blood mononuclear cells (PBMCs) in MESA and 49 tissues in the Genotype-Tissue Expression (GTEx) project. We found that although PWAS and TWAS can show different directions of associations in an individual gene, 40 out of 49 tissues showed a positive correlation between PWAS and TWAS signed p-values across all the genes, which suggests a high-level consistency between proteome-lipid associations and transcriptome-lipid associations.
Published: 2023
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78. Interaction molecular QTL mapping discovers cellular and environmental modifiers of genetic regulatory effects.

Author: Kasela S, Aguet F, Kim-Hellmuth S, Brown BC, Nachun DC, Tracy RP, Durda P, Liu Y, Taylor KD, Craig Johnson W, Berg DVD, Gabriel S, Gupta N, Smith JD, Blackwell TW, Rotter JI, Ardlie KG, Manichaikul A, Rich SS, Graham Barr R, and Lappalainen T
Abstract: Bulk tissue molecular quantitative trait loci (QTLs) have been the starting point for interpreting disease-associated variants, while context-specific QTLs show particular relevance for disease. Here, we present the results of mapping interaction QTLs (iQTLs) for cell type, age, and other phenotypic variables in multi-omic, longitudinal data from blood of individuals of diverse ancestries. By modeling the interaction between genotype and estimated cell type proportions, we demonstrate that cell type iQTLs could be considered as proxies for cell type-specific QTL effects. The interpretation of age iQTLs, however, warrants caution as the moderation effect of age on the genotype and molecular phenotype association may be mediated by changes in cell type composition. Finally, we show that cell type iQTLs contribute to cell type-specific enrichment of diseases that, in combination with additional functional data, may guide future functional studies. Overall, this study highlights iQTLs to gain insights into the context-specificity of regulatory effects., Competing Interests: Declaration of interests T.L. advises Variant Bio, Goldfinch Bio, GlaxoSmithKline, and Pfizer and has equity in Variant Bio.
Published: 2023
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79. Association Between Titin Loss-of-Function Variants and Early-Onset Atrial Fibrillation.

Author: Choi SH, Weng LC, Roselli C, Lin H, Haggerty CM, Shoemaker MB, Barnard J, Arking DE, Chasman DI, Albert CM, Chaffin M, Tucker NR, Smith JD, Gupta N, Gabriel S, Margolin L, Shea MA, Shaffer CM, Yoneda ZT, Boerwinkle E, Smith NL, Silverman EK, Redline S, Vasan RS, Burchard EG, Gogarten SM, Laurie C, Blackwell TW, Abecasis G, Carey DJ, Fornwalt BK, Smelser DT, Baras A, Dewey FE, Jaquish CE, Papanicolaou GJ, Sotoodehnia N, Van Wagoner DR, Psaty BM, Kathiresan S, Darbar D, Alonso A, Heckbert SR, Chung MK, Roden DM, Benjamin EJ, Murray MF, Lunetta KL, Lubitz SA, and Ellinor PT
Subjects: Adult, Age of Onset, Case-Control Studies, Female, Genetic Predisposition to Disease, Genome-Wide Association Study, Heterozygote, Humans, Male, Middle Aged, Quality Control, Atrial Fibrillation genetics, Connectin genetics, Loss of Function Mutation
Abstract: Importance: Atrial fibrillation (AF) is the most common arrhythmia affecting 1% of the population. Young individuals with AF have a strong genetic association with the disease, but the mechanisms remain incompletely understood., Objective: To perform large-scale whole-genome sequencing to identify genetic variants related to AF., Design, Setting, and Participants: The National Heart, Lung, and Blood Institute's Trans-Omics for Precision Medicine Program includes longitudinal and cohort studies that underwent high-depth whole-genome sequencing between 2014 and 2017 in 18 526 individuals from the United States, Mexico, Puerto Rico, Costa Rica, Barbados, and Samoa. This case-control study included 2781 patients with early-onset AF from 9 studies and identified 4959 controls of European ancestry from the remaining participants. Results were replicated in the UK Biobank (346 546 participants) and the MyCode Study (42 782 participants)., Exposures: Loss-of-function (LOF) variants in genes at AF loci and common genetic variation across the whole genome., Main Outcomes and Measures: Early-onset AF (defined as AF onset in persons <66 years of age). Due to multiple testing, the significance threshold for the rare variant analysis was P = 4.55 × 10-3., Results: Among 2781 participants with early-onset AF (the case group), 72.1% were men, and the mean (SD) age of AF onset was 48.7 (10.2) years. Participants underwent whole-genome sequencing at a mean depth of 37.8 fold and mean genome coverage of 99.1%. At least 1 LOF variant in TTN, the gene encoding the sarcomeric protein titin, was present in 2.1% of case participants compared with 1.1% in control participants (odds ratio [OR], 1.76 [95% CI, 1.04-2.97]). The proportion of individuals with early-onset AF who carried a LOF variant in TTN increased with an earlier age of AF onset (P value for trend, 4.92 × 10-4), and 6.5% of individuals with AF onset prior to age 30 carried a TTN LOF variant (OR, 5.94 [95% CI, 2.64-13.35]; P = 1.65 × 10-5). The association between TTN LOF variants and AF was replicated in an independent study of 1582 patients with early-onset AF (cases) and 41 200 control participants (OR, 2.16 [95% CI, 1.19-3.92]; P = .01)., Conclusions and Relevance: In a case-control study, there was a statistically significant association between an LOF variant in the TTN gene and early-onset AF, with the variant present in a small percentage of participants with early-onset AF (the case group). Further research is necessary to understand whether this is a causal relationship.
Published: 2018
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80. Evolutionary-conserved gene expression response profiles across mammalian tissues.

Author: Chen J, Blackwell TW, Fermin D, Menon R, Chen Y, Gao J, Lee AW, and States DJ
Subjects: Animals, Binding Sites, Cluster Analysis, Conserved Sequence, Evolution, Molecular, Gene Expression Regulation, Humans, Mice, Models, Statistical, Oligonucleotide Array Sequence Analysis, Principal Component Analysis, Species Specificity, Transcription Factors metabolism, Gene Expression Profiling
Abstract: Gene expression responses are complex and frequently involve the actions of many genes to effect coordinated patterns. We hypothesized these coordinated responses are evolutionarily conserved and used a comparison of human and mouse gene expression profiles to identify the most prominent conserved features across a set of normal mammalian tissues. Based on data from multiple studies across multiple tissues in human and mouse, 13 gene expression modes across multiple tissues were identified in each of these species using principal component analysis. Strikingly, 1-to-1 pairing of human and mouse modes was observed in 12 out of 13 modes obtained from the two species independently. These paired modes define evolutionarily conserved gene expression response modes (CGEMs). Notably, in this study we were able to extract biological responses that are not overwhelmed by laboratory-to-laboratory or species-to-species variation. Of the variation in our gene expression dataset, 84% can be explained using these CGEMs. Functional annotation was performed using Gene Ontology, pathway, and transcription factor binding site over representation. Our conclusion is that we found an unbiased way of obtaining conserved gene response modes that accounts for a considerable portion of gene expression variation in a given dataset, as well as validates the conservation of major gene expression response modes across the mammals.
Published: 2007
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81. Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics.

Author: Fermin D, Allen BB, Blackwell TW, Menon R, Adamski M, Xu Y, Ulintz P, Omenn GS, and States DJ
Subjects: Blood Proteins genetics, Databases, Protein, Expressed Sequence Tags, Genes, Genomics, Humans, Models, Genetic, Peptides blood, Poisson Distribution, Proteins genetics, Alternative Splicing, Genome, Human, Open Reading Frames, Peptides genetics, Proteomics methods
Abstract: Background: Defining the location of genes and the precise nature of gene products remains a fundamental challenge in genome annotation. Interrogating tandem mass spectrometry data using genomic sequence provides an unbiased method to identify novel translation products. A six-frame translation of the entire human genome was used as the query database to search for novel blood proteins in the data from the Human Proteome Organization Plasma Proteome Project. Because this target database is orders of magnitude larger than the databases traditionally employed in tandem mass spectra analysis, careful attention to significance testing is required. Confidence of identification is assessed using our previously described Poisson statistic, which estimates the significance of multi-peptide identifications incorporating the length of the matching sequence, number of spectra searched and size of the target sequence database., Results: Applying a false discovery rate threshold of 0.05, we identified 282 significant open reading frames, each containing two or more peptide matches. There were 627 novel peptides associated with these open reading frames that mapped to a unique genomic coordinate placed within the start/stop points of previously annotated genes. These peptides matched 1,110 distinct tandem MS spectra. Peptides fell into four categories based upon where their genomic coordinates placed them relative to annotated exons within the parent gene., Conclusion: This work provides evidence for novel alternative splice variants in many previously annotated genes. These findings suggest that annotation of the genome is not yet complete and that proteomics has the potential to further add to our understanding of gene structures.
Published: 2006
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81 results on '"Blackwell, Thomas W"'

51. Probabilistic approaches to the use of higher order clone relationships in physical map assembly

52. Identification of CFTR variants in Latino patients with cystic fibrosis from the Dominican Republic and Puerto Rico

53. Mapping the 17q12-21.1 Locus for Variants Associated with Early-Onset Asthma in African Americans.

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

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

56. Evaluating the contribution of rare variants to type 2 diabetes and related traits using pedigrees

57. Inherited causes of clonal haematopoiesis in 97,691 whole genomes

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

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

60. The genetic architecture of type 2 diabetes

61. Evaluating the contribution of rare variants to type 2 diabetes and related traits using pedigrees.

62. Integration of Genome and Chromatin Structure with Gene Expression Profiles To Predict c-MYC Recognition Site Binding and Function

63. Evolutionary-conserved Gene Expression Response Profiles Across Mammalian Tissues

64. Computational Prediction of c-MYC Binding and Action by Integration of Multiple Data Sources.

65. Identifying Novel Blood Proteins and Protein Isoforms Using Tandem Mass Spectra.

66. Challenges in deriving high-confidence protein identifications from data gathered by a HUPO plasma proteome collaborative study

67. Overview of the HUPO Plasma Proteome Project: Results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database

68. Integration of Genome and Chromatin Structure with Gene Expression Profiles To Predict c-MYC Recognition Site Binding and Function.

69. Author Correction: Inherited causes of clonal haematopoiesis in 97,691 whole genomes

70. Whole genome sequence analysis of platelet traits in the NHLBI Trans-Omics for Precision Medicine (TOPMed) initiative

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

72. Computational Prediction of c-MYCBinding and Action by Integration of Multiple Data Sources.

73. Epigenome-wide Association Analysis of Mitochondrial Heteroplasmy Provides Insight into Molecular Mechanisms of Disease.

74. Proteome-wide association studies for blood lipids and comparison with transcriptome-wide association studies.

75. The Genetic Determinants and Genomic Consequences of Non-Leukemogenic Somatic Point Mutations.

76. Genetic Architecture and Analysis Practices of Circulating Metabolites in the NHLBI Trans-Omics for Precision Medicine (TOPMed) Program.

77. Proteome-Wide Association Studies for Blood Lipids and Comparison with Transcriptome-Wide Association Studies.

78. Interaction molecular QTL mapping discovers cellular and environmental modifiers of genetic regulatory effects.

79. Association Between Titin Loss-of-Function Variants and Early-Onset Atrial Fibrillation.

80. Evolutionary-conserved gene expression response profiles across mammalian tissues.

81. Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics.

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81 results on '"Blackwell, Thomas W"'

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