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1. A deep catalogue of protein-coding variation in 983,578 individuals

Author

Sun, Kathie Y., Bai, Xiaodong, Chen, Siying, Bao, Suying, Zhang, Chuanyi, Kapoor, Manav, Backman, Joshua, Joseph, Tyler, Maxwell, Evan, Mitra, George, Gorovits, Alexander, Mansfield, Adam, Boutkov, Boris, Gokhale, Sujit, Habegger, Lukas, Marcketta, Anthony, Locke, Adam E., Ganel, Liron, Hawes, Alicia, Kessler, Michael D., Sharma, Deepika, Staples, Jeffrey, Bovijn, Jonas, Gelfman, Sahar, Di Gioia, Alessandro, Rajagopal, Veera M., Lopez, Alexander, Varela, Jennifer Rico, Alegre-Díaz, Jesús, Berumen, Jaime, Tapia-Conyer, Roberto, Kuri-Morales, Pablo, Torres, Jason, Emberson, Jonathan, Collins, Rory, Cantor, Michael, Thornton, Timothy, Kang, Hyun Min, Overton, John D., Shuldiner, Alan R., Cremona, M. Laura, Nafde, Mona, Baras, Aris, Abecasis, Gonçalo, Marchini, Jonathan, Reid, Jeffrey G., Salerno, William, and Balasubramanian, Suganthi

Published
2024
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2. “PMS2CL interference leading to erroneous identification of a pathogenic PMS2 variant in Black Patients”

Author

Cappadocia, Jacqueline, primary, Aiello, Lisa B., additional, Kelley, Michael J., additional, Katona, Bryson W., additional, Maxwell, Kara N., additional, Verma, Anurag, additional, Verma, Shefali S., additional, Bradford, Yuki, additional, Brock, Ashlei, additional, DerOhannessian, Stephanie, additional, Dudek, Scott, additional, Dunn, Joseph, additional, Drivas, Theodore, additional, Haubein, Ned, additional, Hu-Sain, Khadijah, additional, Judy, Renae, additional, Kloter, Ashley, additional, Ko, Yi-An, additional, Livingstone, Meghan, additional, Morrel, Linda, additional, Morse, Colleen, additional, Poindexter, Afiya, additional, Risman, Marjorie, additional, Tran, Teo, additional, Vadivieso, Fred, additional, Weaver, JoEllen, additional, Rader, Daniel J., additional, Ritchie, Marylyn D., additional, Feldman, Michael D., additional, Beechert, Christina, additional, Forsythe, Caitlin, additional, Fuller, Erin D., additional, Gu, Zhenhua, additional, Lattari, Michael, additional, Lopez, Alexander, additional, Overton, John D., additional, Padilla, Maria Sotiropoulos, additional, Pradhan, Manasi, additional, Manoochehri, Kia, additional, Schleicher, Thomas D., additional, Widom, Louis, additional, Wolf, Sarah E., additional, Ulloa, Ricardo H., additional, Averitt, Amelia, additional, Banerjee, Nilanjana, additional, Cantor, Michael, additional, Li, Dadong, additional, Malhotra, Sameer, additional, Sharma, Deepika, additional, Staples, Jeffrey, additional, Bai, Xiaodong, additional, Balasubramanian, Suganthi, additional, Bao, Suying, additional, Boutkov, Boris, additional, Chen, Siying, additional, Eom, Gisu, additional, Habegger, Lukas, additional, Hawes, Alicia, additional, Khalid, Shareef, additional, Krasheninina, Olga, additional, Lanche, Rouel, additional, Mansfield, Adam J., additional, Maxwell, Evan K., additional, Mitra, George, additional, Nafde, Mona, additional, O’Keeffe, Sean, additional, Panea, Razvan, additional, Polanco, Tommy, additional, Rasool, Ayesha, additional, Reid, Jeffrey G., additional, Salerno, William, additional, Staples, Jeffrey C., additional, Sun, Kathie, additional, Abecasis, Goncalo, additional, Backman, Joshua, additional, Damask, Amy, additional, Dobbyn, Lee, additional, Revez Ferreira, Manuel Allen, additional, Ghosh, Arkopravo, additional, Gillies, Christopher, additional, Gurski, Lauren, additional, Jorgenson, Eric, additional, Kang, Hyun Min, additional, Kessler, Michael, additional, Kosmicki, Jack, additional, Li, Alexander, additional, Lin, Nan, additional, Liu, Daren, additional, Locke, Adam, additional, Marchini, Jonathan, additional, Marcketta, Anthony, additional, Mbatchou, Joelle, additional, Moscati, Arden, additional, Paulding, Charles, additional, Sidore, Carlo, additional, Stahl, Eli, additional, Watanabe, Kyoko, additional, Ye, Bin, additional, Zhang, Blair, additional, Ziyatdinov, Andrey, additional, Ayer, Ariane, additional, Guvenek, Aysegul, additional, Hindy, George, additional, Coppola, Giovanni, additional, Freudenberg, Jan, additional, Bovijn, Jonas, additional, Siminovitch, Katherine, additional, Praveen, Kavita, additional, Lotta, Luca A., additional, Kapoor, Manav, additional, Haas, Mary, additional, Riaz, Moeen, additional, Verweij, Niek, additional, Sosina, Olukayode, additional, Akbari, Parsa, additional, Nakka, Priyanka, additional, Gelfman, Sahar, additional, Gokhale, Sujit, additional, De, Tanima, additional, Rajagopal, Veera, additional, Shuldiner, Alan, additional, Tzoneva, Gannie, additional, Rodriguez-Flores, Juan, additional, Chen, Esteban, additional, Jones, Marcus B., additional, LeBlanc, Michelle G., additional, Mighty, Jason, additional, Mitnaul, Lyndon J., additional, Nishtala, Nirupama, additional, Rana, Nadia, additional, Hernandez, Jaimee, additional, Baras, Aris, additional, Deubler, Andrew, additional, and Economides, Aris, additional

Published
2024
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4. PMS2CL interference leading to erroneous identification of a pathogenic PMS2 variant in Black patients

Author

Verma, Anurag, Verma, Shefali S., Bradford, Yuki, Brock, Ashlei, DerOhannessian, Stephanie, Dudek, Scott, Dunn, Joseph, Drivas, Theodore, Haubein, Ned, Hu-Sain, Khadijah, Judy, Renae, Kloter, Ashley, Ko, Yi-An, Livingstone, Meghan, Morrel, Linda, Morse, Colleen, Poindexter, Afiya, Risman, Marjorie, Tran, Teo, Vadivieso, Fred, Weaver, JoEllen, Rader, Daniel J., Ritchie, Marylyn D., Feldman, Michael D., Beechert, Christina, Forsythe, Caitlin, Fuller, Erin D., Gu, Zhenhua, Lattari, Michael, Lopez, Alexander, Overton, John D., Padilla, Maria Sotiropoulos, Pradhan, Manasi, Manoochehri, Kia, Schleicher, Thomas D., Widom, Louis, Wolf, Sarah E., Ulloa, Ricardo H., Averitt, Amelia, Banerjee, Nilanjana, Cantor, Michael, Li, Dadong, Malhotra, Sameer, Sharma, Deepika, Staples, Jeffrey, Bai, Xiaodong, Balasubramanian, Suganthi, Bao, Suying, Boutkov, Boris, Chen, Siying, Eom, Gisu, Habegger, Lukas, Hawes, Alicia, Khalid, Shareef, Krasheninina, Olga, Lanche, Rouel, Mansfield, Adam J., Maxwell, Evan K., Mitra, George, Nafde, Mona, O’Keeffe, Sean, Orelus, Max, Panea, Razvan, Polanco, Tommy, Rasool, Ayesha, Reid, Jeffrey G., Salerno, William, Staples, Jeffrey C., Sun, Kathie, Abecasis, Goncalo, Backman, Joshua, Damask, Amy, Dobbyn, Lee, Ferreira, Manuel Allen Revez, Ghosh, Arkopravo, Gillies, Christopher, Gurski, Lauren, Jorgenson, Eric, Kang, Hyun Min, Kessler, Michael, Kosmicki, Jack, Li, Alexander, Lin, Nan, Liu, Daren, Locke, Adam, Marchini, Jonathan, Marcketta, Anthony, Mbatchou, Joelle, Moscati, Arden, Paulding, Charles, Sidore, Carlo, Stahl, Eli, Watanabe, Kyoko, Ye, Bin, Zhang, Blair, Ziyatdinov, Andrey, Ayer, Ariane, Guvenek, Aysegul, Hindy, George, Coppola, Giovanni, Freudenberg, Jan, Bovijn, Jonas, Siminovitch, Katherine, Praveen, Kavita, Lotta, Luca A., Kapoor, Manav, Haas, Mary, Riaz, Moeen, Verweij, Niek, Sosina, Olukayode, Akbari, Parsa, Nakka, Priyanka, Gelfman, Sahar, Gokhale, Sujit, De, Tanima, Rajagopal, Veera, Shuldiner, Alan, Tzoneva, Gannie, Rodriguez-Flores, Juan, Chen, Esteban, Jones, Marcus B., LeBlanc, Michelle G., Mighty, Jason, Mitnaul, Lyndon J., Nishtala, Nirupama, Rana, Nadia, Hernandez, Jaimee, Baras, Aris, Deubler, Andrew, Economides, Aris, Cappadocia, Jacqueline, Aiello, Lisa B., Kelley, Michael J., Katona, Bryson W., and Maxwell, Kara N.

Published
2024
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5. Inference of Causal Relationships Between Genetic Risk Factors for Cardiometabolic Phenotypes and Female‐Specific Health Conditions

Author

Xiao, Brenda, primary, Velez Edwards, Digna R., additional, Lucas, Anastasia, additional, Drivas, Theodore, additional, Gray, Kathryn, additional, Keating, Brendan, additional, Weng, Chunhua, additional, Jarvik, Gail P., additional, Hakonarson, Hakon, additional, Kottyan, Leah, additional, Elhadad, Noemie, additional, Wei, Wei‐Qi, additional, Luo, Yuan, additional, Kim, Dokyoon, additional, Ritchie, Marylyn, additional, Verma, Shefali Setia, additional, Abecasis, Goncalo, additional, Baras, Aris, additional, Cantor, Michael, additional, Coppola, Giovanni, additional, Deubler, Andrew, additional, Economides, Aris, additional, Karalis, Katia, additional, Lotta, Luca A., additional, Overton, John D., additional, Reid, Jeffrey G., additional, Siminovitch, Katherine, additional, Shuldiner, Alan, additional, Beechert, Christina, additional, Forsythe, Caitlin, additional, Fuller, Erin D., additional, Gu, Zhenhua, additional, Lattari, Michael, additional, Lopez, Alexander, additional, Padilla, Maria Sotiropoulos, additional, Pradhan, Manasi, additional, Manoochehri, Kia, additional, Schleicher, Thomas D., additional, Widom, Louis, additional, Wolf, Sarah E., additional, Ulloa, Ricardo H., additional, Averitt, Amelia, additional, Banerjee, Nilanjana, additional, Li, Dadong, additional, Malhotra, Sameer, additional, Sharma, Deepika, additional, Staples, Jeffrey, additional, Bai, Xiaodong, additional, Balasubramanian, Suganthi, additional, Bao, Suying, additional, Boutkov, Boris, additional, Chen, Siying, additional, Eom, Gisu, additional, Habegger, Lukas, additional, Hawes, Alicia, additional, Khalid, Shareef, additional, Krasheninina, Olga, additional, Lanche, Rouel, additional, Mansfield, Adam J., additional, Maxwell, Evan K., additional, Mitra, George, additional, Nafde, Mona, additional, O’Keeffe, Sean, additional, Orelus, Max, additional, Panea, Razvan, additional, Polanco, Tommy, additional, Rasool, Ayesha, additional, Salerno, William, additional, Staples, Jeffrey C., additional, Sun, Kathie, additional, Backman, Joshua, additional, Damask, Amy, additional, Dobbyn, Lee, additional, Ferreira, Manuel Allen Revez, additional, Ghosh, Arkopravo, additional, Gillies, Christopher, additional, Gurski, Lauren, additional, Jorgenson, Eric, additional, Kang, Hyun Min, additional, Kessler, Michael, additional, Kosmicki, Jack, additional, Li, Alexander, additional, Lin, Nan, additional, Liu, Daren, additional, Locke, Adam, additional, Marchini, Jonathan, additional, Marcketta, Anthony, additional, Mbatchou, Joelle, additional, Moscati, Arden, additional, Paulding, Charles, additional, Sidore, Carlo, additional, Stahl, Eli, additional, Watanabe, Kyoko, additional, Ye, Bin, additional, Zhang, Blair, additional, Ziyatdinov, Andrey, additional, Ayer, Ariane, additional, Guvenek, Aysegul, additional, Hindy, George, additional, Freudenberg, Jan, additional, Bovijn, Jonas, additional, Praveen, Kavita, additional, Kapoor, Manav, additional, Haas, Mary, additional, Riaz, Moeen, additional, Verweij, Niek, additional, Sosina, Olukayode, additional, Akbari, Parsa, additional, Nakka, Priyanka, additional, Gelfman, Sahar, additional, Gokhale, Sujit, additional, De, Tanima, additional, Rajagopal, Veera, additional, Tzoneva, Gannie, additional, Rodriguez‐Flores, Juan, additional, Chim, Shek Man, additional, Donato, Valerio, additional, Fernandez, Daniel, additional, Gatta, Giusy Della, additional, Di Gioia, Alessandro, additional, Howell, Kristen, additional, Khrimian, Lori, additional, Kim, Minhee, additional, Martinez, Hector, additional, Miloscio, Lawrence, additional, Nunez, Sheilyn, additional, Pavlopoulos, Elias, additional, Persaud, Trikaldarshi, additional, Chen, Esteban, additional, Jones, Marcus B., additional, LeBlanc, Michelle G., additional, Mighty, Jason, additional, Mitnaul, Lyndon J., additional, Nishtala, Nirupama, additional, and Rana, Nadia, additional

Published
2023
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6. Analysis of rare genetic variation underlying cardiometabolic diseases and traits among 200,000 individuals in the UK Biobank

Author

Jurgens, Sean J., Choi, Seung Hoan, Morrill, Valerie N., Chaffin, Mark, Pirruccello, James P., Halford, Jennifer L., Weng, Lu-Chen, Nauffal, Victor, Roselli, Carolina, Hall, Amelia W., Oetjens, Matthew T., Lagerman, Braxton, vanMaanen, David P., Abecasis, Goncalo, Bai, Xiaodong, Balasubramanian, Suganthi, Baras, Aris, Beechert, Christina, Boutkov, Boris, Cantor, Michael, Coppola, Giovanni, de, Tanima, Deubler, Andrew, Economides, Aris, Eom, Gisu, Ferreira, Manuel A. R., Forsythe, Caitlin, Fuller, Erin D., Gu, Zhenhua, Habegger, Lukas, Hawes, Alicia, Jones, Marcus B., Karalis, Katia, Khalid, Shareef, Krasheninina, Olga, Lanche, Rouel, Lattari, Michael, Li, Dadong, Lopez, Alexander, Lotta, Luca A., Manoochehri, Kia, Mansfield, Adam J., Maxwell, Evan K., Mighty, Jason, Mitnaul, Lyndon J., Nafde, Mona, Nielsen, Jonas, O’Keeffe, Sean, Orelus, Max, Overton, John D., Padilla, Maria Sotiropoulos, Panea, Razvan, Polanco, Tommy, Pradhan, Manasi, Rasool, Ayesha, Reid, Jeffrey G., Salerno, William, Schleicher, Thomas D., Shuldiner, Alan, Siminovitch, Katherine, Staples, Jeffrey C., Ulloa, Ricardo H., Verweij, Niek, Widom, Louis, Wolf, Sarah E., Aragam, Krishna G., Lunetta, Kathryn L., Haggerty, Christopher M., Lubitz, Steven A., Ellinor, Patrick T., Cardiology, Graduate School, and ACS - Amsterdam Cardiovascular Sciences

Subjects
Genetics
Abstract

Cardiometabolic diseases are the leading cause of death worldwide. Despite a known genetic component, our understanding of these diseases remains incomplete. Here, we analyzed the contribution of rare variants to 57 diseases and 26 cardiometabolic traits, using data from 200,337 UK Biobank participants with whole-exome sequencing. We identified 57 gene-based associations, with broad replication of novel signals in Geisinger MyCode. There was a striking risk associated with mutations in known Mendelian disease genes, including MYBPC3, LDLR, GCK, PKD1 and TTN. Many genes showed independent convergence of rare and common variant evidence, including an association between GIGYF1 and type 2 diabetes. We identified several large effect associations for height and 18 unique genes associated with blood lipid or glucose levels. Finally, we found that between 1.0% and 2.4% of participants carried rare potentially pathogenic variants for cardiometabolic disorders. These findings may facilitate studies aimed at therapeutics and screening of these common disorders.

Published
2022

7. Yield of genetic association signals from genomes, exomes and imputation in the UK Biobank

Author

Gaynor, Sheila M., Joseph, Tyler, Bai, Xiaodong, Zou, Yuxin, Boutkov, Boris, Maxwell, Evan K., Delaneau, Olivier, Hofmeister, Robin J., Krasheninina, Olga, Balasubramanian, Suganthi, Marcketta, Anthony, Backman, Joshua, Reid, Jeffrey G., Overton, John D., Lotta, Luca A., Marchini, Jonathan, Salerno, William J., Baras, Aris, Abecasis, Goncalo R., and Thornton, Timothy A.

Abstract

Whole-genome sequencing (WGS), whole-exome sequencing (WES) and array genotyping with imputation (IMP) are common strategies for assessing genetic variation and its association with medically relevant phenotypes. To date, there has been no systematic empirical assessment of the yield of these approaches when applied to hundreds of thousands of samples to enable the discovery of complex trait genetic signals. Using data for 100 complex traits from 149,195 individuals in the UK Biobank, we systematically compare the relative yield of these strategies in genetic association studies. We find that WGS and WES combined with arrays and imputation (WES + IMP) have the largest association yield. Although WGS results in an approximately fivefold increase in the total number of assayed variants over WES + IMP, the number of detected signals differed by only 1% for both single-variant and gene-based association analyses. Given that WES + IMP typically results in savings of lab and computational time and resources expended per sample, we evaluate the potential benefits of applying WES + IMP to larger samples. When we extend our WES + IMP analyses to 468,169 UK Biobank individuals, we observe an approximately fourfold increase in association signals with the threefold increase in sample size. We conclude that prioritizing WES + IMP and large sample sizes rather than contemporary short-read WGS alternatives will maximize the number of discoveries in genetic association studies.

Published
2024
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8. Genetic variation of the blood coagulation regulator tissue factor pathway inhibitor and venous thromboembolism among middle‐aged and older adults: A population‐based cohort study

Author

Manderstedt, Eric, primary, Lind‐Halldén, Christina, additional, Halldén, Christer, additional, Elf, Johan, additional, Svensson, Peter J., additional, Engström, Gunnar, additional, Melander, Olle, additional, Baras, Aris, additional, Lotta, Luca A., additional, Zöller, Bengt, additional, Abecasis, Goncalo, additional, Cantor, Michael, additional, Coppola, Giovanni, additional, Economides, Aris, additional, Overton, John D., additional, Reid, Jeffrey G., additional, Shuldiner, Alan, additional, Beechert, Christina, additional, Forsythe, Caitlin, additional, Fuller, Erin D., additional, Gu, Zhenhua, additional, Lattari, Michael, additional, Lopez, Alexander, additional, Schleicher, Thomas D., additional, Padilla, Maria Sotiropoulos, additional, Widom, Louis, additional, Wolf, Sarah E., additional, Pradhan, Manasi, additional, Manoochehri, Kia, additional, Ulloa, Ricardo H., additional, Bai, Xiaodong, additional, Balasubramanian, Suganthi, additional, Blumenfeld, Andrew, additional, Boutkov, Boris, additional, Eom, Gisu, additional, Habegger, Lukas, additional, Hawes, Alicia, additional, Khalid, Shareef, additional, Krasheninina, Olga, additional, Lanche, Rouel, additional, Mansfield, Adam J., additional, Maxwell, Evan K., additional, Nafde, Mrunali, additional, O’Keeffe, Sean, additional, Orelus, Max, additional, Panea, Razvan, additional, Polanco, Tommy, additional, Rasool, Ayesha, additional, Salerno, William, additional, Staples, Jeffrey C., additional, Jones, Marcus B., additional, Mighty, Jason, additional, and Mitnaul, Lyndon J., additional

Published
2022
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9. Thrombotic risk determined by rare and common SERPINA1 variants in a population‐based cohort study

Author

Manderstedt, Eric, primary, Halldén, Christer, additional, Lind‐Halldén, Christina, additional, Elf, Johan, additional, Svensson, Peter J., additional, Engström, Gunnar, additional, Melander, Olle, additional, Baras, Aris, additional, Lotta, Luca A., additional, Zöller, Bengt, additional, Abecasis, Goncalo, additional, Cantor, Michael, additional, Coppola, Giovanni, additional, Economides, Aris, additional, Overton, John D., additional, Reid, Jeffrey G., additional, Shuldiner, Alan, additional, Beechert, Christina, additional, Forsythe, Caitlin, additional, Fuller, Erin D., additional, Gu, Zhenhua, additional, Lattari, Michael, additional, Lopez, Alexander, additional, Manoochehri, Kia, additional, Padilla, Maria Sotiropoulos, additional, Pradhan, Manasi, additional, Schleicher, Thomas D., additional, Ulloa, Ricardo H., additional, Widom, Louis, additional, Wolf, Sarah E., additional, Bai, Xiaodong, additional, Balasubramanian, Suganthi, additional, Blumenfeld, Andrew, additional, Boutkov, Boris, additional, Eom, Gisu, additional, Habegger, Lukas, additional, Hawes, Alicia, additional, Khalid, Shareef, additional, Krasheninina, Olga, additional, Lanche, Rouel, additional, Mansfield, Adam J., additional, Maxwell, Evan K., additional, Nafde, Mrunali, additional, O’Keeffe, Sean, additional, Orelus, Max, additional, Panea, Razvan, additional, Polanco, Tommy, additional, Rasool, Ayesha, additional, Salerno, William, additional, Staples, Jeffrey C., additional, Jones, Marcus B., additional, Mighty, Jason, additional, and Mitnaul, Lyndon J., additional

Published
2022
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10. Performance of polygenic risk scores for cancer prediction in a racially diverse academic biobank

Author

Wang, Louise, primary, Desai, Heena, additional, Verma, Shefali S., additional, Le, Anh, additional, Hausler, Ryan, additional, Verma, Anurag, additional, Judy, Renae, additional, Doucette, Abigail, additional, Gabriel, Peter E., additional, Nathanson, Katherine L., additional, Damrauer, Scott M., additional, Mowery, Danielle L., additional, Ritchie, Marylyn D., additional, Kember, Rachel L., additional, Maxwell, Kara N., additional, Abecasis, Goncalo, additional, Bai, Xiaodong, additional, Balasubramanian, Suganthi, additional, Baras, Aris, additional, Blumenfeld, Andrew, additional, Boutkov, Boris, additional, Cantor, Michael, additional, Coppola, Giovanni, additional, Economides, Aris, additional, Eom, Gisu, additional, Habegger, Lukas, additional, Hawes, Alicia, additional, Jones, Marcus B., additional, Khalid, Shareef, additional, Krasheninina, Olga, additional, Lanche, Rouel, additional, Lotta, Luca A., additional, Mansfield, Adam J., additional, Maxwell, Evan K., additional, Mighty, Jason, additional, Mitnaul, Lyndon J., additional, Nafde, Mrunali, additional, O’Keeffe, Sean, additional, Orelus, Max, additional, Overton, John D., additional, Panea, Razvan, additional, Polanco, Tommy, additional, Rasool, Ayesha, additional, Reid, Jeffrey G., additional, Salerno, William, additional, Staples, Jeffrey C., additional, Shuldiner, Alan, additional, Beechert, Christina, additional, Forsythe, Caitlin, additional, Fuller, Erin D., additional, Gu, Zhenhua, additional, Lattari, Michael, additional, Lopez, Alexander, additional, Manoochehri, Kia, additional, Pradhan, Manasi, additional, Schleicher, Thomas D., additional, Padilla, Maria Sotiropoulos, additional, Ulloa, Ricardo H., additional, Widom, Louis, additional, and Wolf, Sarah E., additional

Published
2022
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11. Classic Thrombophilias and Thrombotic Risk Among Middle‐Aged and Older Adults: A Population‐Based Cohort Study

Author

Manderstedt, Eric, primary, Lind‐Halldén, Christina, additional, Halldén, Christer, additional, Elf, Johan, additional, Svensson, Peter J., additional, Dahlbäck, Björn, additional, Engström, Gunnar, additional, Melander, Olle, additional, Baras, Aris, additional, Lotta, Luca A., additional, Zöller, Bengt, additional, Abecasis, Goncalo, additional, Cantor, Michael, additional, Coppola, Giovanni, additional, Economides, Aris, additional, Lotta, Luca A, additional, Overton, John D, additional, Reid, Jeffrey G, additional, Shuldiner, Alan, additional, Beechert, Christina, additional, Forsythe, Caitlin, additional, Fuller, Erin D, additional, Gu, Zhenhua, additional, Lattari, Michael, additional, Lopez, Alexander, additional, Schleicher, Thomas D, additional, Padilla, Maria Sotiropoulos, additional, Widom, Louis, additional, Wolf, Sarah E, additional, Pradhan, Manasi, additional, Manoochehri, Kia, additional, Ulloa, Ricardo H, additional, Bai, Xiaodong, additional, Balasubramanian, Suganthi, additional, Blumenfeld, Andrew, additional, Boutkov, Boris, additional, Eom, Gisu, additional, Habegger, Lukas, additional, Hawes, Alicia, additional, Khalid, Shareef, additional, Krasheninina, Olga, additional, Lanche, Rouel, additional, Mansfield, Adam J, additional, Maxwell, Evan K, additional, Nafde, Mrunali, additional, O’Keeffe, Sean, additional, Orelus, Max, additional, Panea, Razvan, additional, Polanco, Tommy, additional, Rasool, Ayesha, additional, Salerno, William, additional, Staples, Jeffrey C, additional, Jones, Marcus B, additional, Mighty, Jason, additional, and Mitnaul, Lyndon J, additional

Published
2022
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12. Thrombotic Risk Determined by STAB 2 Variants in a Population-Based Cohort Study

Author

Manderstedt, Eric, primary, Halldén, Christer, additional, Lind-Halldén, Christina, additional, Elf, Johan, additional, Svensson, Peter J., additional, Engström, Gunnar, additional, Melander, Olle, additional, Baras, Aris, additional, Lotta, Luca A, additional, Zöller, Bengt, additional, Abecasis, Goncalo, additional, Cantor, Michael, additional, Coppola, Giovanni, additional, Overton, John D., additional, Reid, Jeffrey G., additional, Shuldiner, Alan, additional, Karalis, Katia, additional, Siminovitch, Katherine, additional, Beechert, Christina, additional, Forsythe, Caitlin, additional, Fuller, Erin D., additional, Gu, Zhenhua, additional, Lattari, Michael, additional, Lopez, Alexander, additional, Schleicher, Thomas D., additional, Sotiropoulos Padilla, Maria, additional, Widom, Louis, additional, Wolf, Sarah E., additional, Pradhan, Manasi, additional, Manoochehri, Kia, additional, Ulloa, Ricardo H., additional, Bai, Xiaodong, additional, Balasubramanian, Suganthi, additional, Blumenfeld, Andrew, additional, Boutkov, Boris, additional, Eom, Gisu, additional, Habegger, Lukas, additional, Hawes, Alicia, additional, Khalid, Shareef, additional, Krasheninina, Olga, additional, Lanche, Rouel, additional, Mansfield, Adam J., additional, Maxwell, Evan K., additional, Nafde, Mrunali, additional, O’Keeffe, Sean, additional, Orelus, Max, additional, Panea, Razvan, additional, Polanco, Tommy, additional, Rasool, Ayesha, additional, Salerno, William, additional, Staples, Jeffrey C., additional, Verweij, Niek, additional, Nielsen, Jonas, additional, De, Tanima, additional, Jones, Marcus B., additional, Mighty, Jason, additional, LeBlanc, Michelle G., additional, and Mitnaul, Lyndon J., additional

Published
2021
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13. Deciphering osteoarthritis genetics across 826,690 individuals from 9 populations

Author

Boer, Cindy G., primary, Hatzikotoulas, Konstantinos, additional, Southam, Lorraine, additional, Stefánsdóttir, Lilja, additional, Zhang, Yanfei, additional, Coutinho de Almeida, Rodrigo, additional, Wu, Tian T., additional, Zheng, Jie, additional, Hartley, April, additional, Teder-Laving, Maris, additional, Skogholt, Anne Heidi, additional, Terao, Chikashi, additional, Zengini, Eleni, additional, Alexiadis, George, additional, Barysenka, Andrei, additional, Bjornsdottir, Gyda, additional, Gabrielsen, Maiken E., additional, Gilly, Arthur, additional, Ingvarsson, Thorvaldur, additional, Johnsen, Marianne B., additional, Jonsson, Helgi, additional, Kloppenburg, Margreet, additional, Luetge, Almut, additional, Lund, Sigrun H., additional, Mägi, Reedik, additional, Mangino, Massimo, additional, Nelissen, Rob R.G.H.H., additional, Shivakumar, Manu, additional, Steinberg, Julia, additional, Takuwa, Hiroshi, additional, Thomas, Laurent F., additional, Tuerlings, Margo, additional, Babis, George C., additional, Cheung, Jason Pui Yin, additional, Kang, Jae Hee, additional, Kraft, Peter, additional, Lietman, Steven A., additional, Samartzis, Dino, additional, Slagboom, P. Eline, additional, Stefansson, Kari, additional, Thorsteinsdottir, Unnur, additional, Tobias, Jonathan H., additional, Uitterlinden, André G., additional, Winsvold, Bendik, additional, Zwart, John-Anker, additional, Davey Smith, George, additional, Sham, Pak Chung, additional, Thorleifsson, Gudmar, additional, Gaunt, Tom R., additional, Morris, Andrew P., additional, Valdes, Ana M., additional, Tsezou, Aspasia, additional, Cheah, Kathryn S.E., additional, Ikegawa, Shiro, additional, Hveem, Kristian, additional, Esko, Tõnu, additional, Wilkinson, J. Mark, additional, Meulenbelt, Ingrid, additional, Lee, Ming Ta Michael, additional, van Meurs, Joyce B.J., additional, Styrkársdóttir, Unnur, additional, Zeggini, Eleftheria, additional, Loughlin, John, additional, Arden, Nigel, additional, Birrell, Fraser, additional, Carr, Andrew, additional, Deloukas, Panos, additional, Doherty, Michael, additional, McCaskie, Andrew W., additional, Ollier, William E.R., additional, Rai, Ashok, additional, Ralston, Stuart H., additional, Spector, Tim D., additional, Wallis, Gillian A., additional, Martinsen, Amy E., additional, Willer, Cristen, additional, Fors, Egil Andreas, additional, Mundal, Ingunn, additional, Hagen, Knut, additional, Nilsen, Kristian Bernhard, additional, Lie, Marie Udnesseter, additional, Børte, Sigrid, additional, Brumpton, Ben, additional, Nielsen, Jonas Bille, additional, Fritsche, Lars G., additional, Zhou, Wei, additional, Heuch, Ingrid, additional, Storheim, Kjersti, additional, Tyrpenou, Evangelos, additional, Koukakis, Athanasios, additional, Chytas, Dimitrios, additional, Evangelopoulos, Dimitrios Stergios, additional, Efstathios, Chronopoulos, additional, Pneumaticos, Spiros, additional, Nikolaou, Vasileios S., additional, Malizos, Konstantinos, additional, Anastasopoulou, Lydia, additional, Abecasis, Goncalo, additional, Baras, Aris, additional, Cantor, Michael, additional, Coppola, Giovanni, additional, Deubler, Andrew, additional, Economides, Aris, additional, Lotta, Luca A., additional, Overton, John D., additional, Reid, Jeffrey G., additional, Shuldiner, Alan, additional, Karalis, Katia, additional, Siminovitch, Katherine, additional, Beechert, Christina, additional, Forsythe, Caitlin, additional, Fuller, Erin D., additional, Gu, Zhenhua, additional, Lattari, Michael, additional, Lopez, Alexander, additional, Schleicher, Thomas D., additional, Padilla, Maria Sotiropoulos, additional, Widom, Louis, additional, Wolf, Sarah E., additional, Pradhan, Manasi, additional, Manoochehri, Kia, additional, Bai, Xiaodong, additional, Balasubramanian, Suganthi, additional, Boutkov, Boris, additional, Eom, Gisu, additional, Habegger, Lukas, additional, Hawes, Alicia, additional, Krasheninina, Olga, additional, Lanche, Rouel, additional, Mansfield, Adam J., additional, Maxwell, Evan K., additional, Nafde, Mona, additional, O’Keeffe, Sean, additional, Orelus, Max, additional, Panea, Razvan, additional, Polanco, Tommy, additional, Rasool, Ayesha, additional, Salerno, William, additional, Staples, Jeffrey C., additional, Li, Dadong, additional, Sharma, Deepika, additional, Banerjee, Ilanjana, additional, Bovijn, Jonas, additional, Locke, Adam, additional, Verweij, Niek, additional, Haas, Mary, additional, Hindy, George, additional, De, Tanima, additional, Akbari, Parsa, additional, Sosina, Olukayode, additional, Ferreira, Manuel A.R., additional, Jones, Marcus B., additional, Mighty, Jason, additional, LeBlanc, Michelle G., additional, and Mitnaul, Lyndon J., additional

Published
2021
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14. Computationally efficient whole genome regression for quantitative and binary traits

Author

Mbatchou, Joelle, primary, Barnard, Leland, additional, Backman, Joshua, additional, Marcketta, Anthony, additional, Kosmicki, Jack A., additional, Ziyatdinov, Andrey, additional, Benner, Christian, additional, O’Dushlaine, Colm, additional, Barber, Mathew, additional, Boutkov, Boris, additional, Habegger, Lukas, additional, Ferreira, Manuel, additional, Baras, Aris, additional, Reid, Jeffrey, additional, Abecasis, Gonçalo, additional, Maxwell, Evan, additional, and Marchini, Jonathan, additional

Published
2020
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15. Thrombotic risk determined by rare and common SERPINA1variants in a population‐based cohort study

Author

Manderstedt, Eric, Halldén, Christer, Lind‐Halldén, Christina, Elf, Johan, Svensson, Peter J., Engström, Gunnar, Melander, Olle, Baras, Aris, Lotta, Luca A., Zöller, Bengt, Abecasis, Goncalo, Cantor, Michael, Coppola, Giovanni, Economides, Aris, Overton, John D., Reid, Jeffrey G., Shuldiner, Alan, Beechert, Christina, Forsythe, Caitlin, Fuller, Erin D., Gu, Zhenhua, Lattari, Michael, Lopez, Alexander, Manoochehri, Kia, Overton, John D., Padilla, Maria Sotiropoulos, Pradhan, Manasi, Schleicher, Thomas D., Ulloa, Ricardo H., Widom, Louis, Wolf, Sarah E., Bai, Xiaodong, Balasubramanian, Suganthi, Blumenfeld, Andrew, Boutkov, Boris, Eom, Gisu, Habegger, Lukas, Hawes, Alicia, Khalid, Shareef, Krasheninina, Olga, Lanche, Rouel, Mansfield, Adam J., Maxwell, Evan K., Nafde, Mrunali, O’Keeffe, Sean, Orelus, Max, Panea, Razvan, Polanco, Tommy, Rasool, Ayesha, Reid, Jeffrey G., Salerno, William, Staples, Jeffrey C., Jones, Marcus B., Mighty, Jason, and Mitnaul, Lyndon J.

Abstract

Severe alpha‐1‐antitrypsin deficiency (AATD), phenotype PiZZ, was associated with venous thromboembolism (VTE) in a case‐control study.

Published
2022
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17. A deep catalog of protein-coding variation in 985,830 individuals.

Author

Sun KY, Bai X, Chen S, Bao S, Kapoor M, Zhang C, Backman J, Joseph T, Maxwell E, Mitra G, Gorovits A, Mansfield A, Boutkov B, Gokhale S, Habegger L, Marcketta A, Locke A, Kessler MD, Sharma D, Staples J, Bovijn J, Gelfman S, Gioia AD, Rajagopal V, Lopez A, Varela JR, Alegre J, Berumen J, Tapia-Conyer R, Kuri-Morales P, Torres J, Emberson J, Collins R, Cantor M, Thornton T, Kang HM, Overton J, Shuldiner AR, Cremona ML, Nafde M, Baras A, Abecasis G, Marchini J, Reid JG, Salerno W, and Balasubramanian S

Abstract

Coding variants that have significant impact on function can provide insights into the biology of a gene but are typically rare in the population. Identifying and ascertaining the frequency of such rare variants requires very large sample sizes. Here, we present the largest catalog of human protein-coding variation to date, derived from exome sequencing of 985,830 individuals of diverse ancestry to serve as a rich resource for studying rare coding variants. Individuals of African, Admixed American, East Asian, Middle Eastern, and South Asian ancestry account for 20% of this Exome dataset. Our catalog of variants includes approximately 10.5 million missense (54% novel) and 1.1 million predicted loss-of-function (pLOF) variants (65% novel, 53% observed only once). We identified individuals with rare homozygous pLOF variants in 4,874 genes, and for 1,838 of these this work is the first to document at least one pLOF homozygote. Additional insights from the RGC-ME dataset include 1) improved estimates of selection against heterozygous loss-of-function and identification of 3,459 genes intolerant to loss-of-function, 83 of which were previously assessed as tolerant to loss-of-function and 1,241 that lack disease annotations; 2) identification of regions depleted of missense variation in 457 genes that are tolerant to loss-of-function; 3) functional interpretation for 10,708 variants of unknown or conflicting significance reported in ClinVar as cryptic splice sites using splicing score thresholds based on empirical variant deleteriousness scores derived from RGC-ME; and 4) an observation that approximately 3% of sequenced individuals carry a clinically actionable genetic variant in the ACMG SF 3.1 list of genes. We make this important resource of coding variation available to the public through a variant allele frequency browser. We anticipate that this report and the RGC-ME dataset will serve as a valuable reference for understanding rare coding variation and help advance precision medicine efforts.

Published
2023
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