48 results on '"Jensen, Tanner"'
Search Results
2. Considerations for reporting variants in novel candidate genes identified during clinical genomic testing
- Author
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Abouhala, Siwaar, Albert, Jessica, Almalvez, Miguel, Alvarez, Raquel, Amin, Mutaz, Anderson, Peter, Aradhya, Swaroop, Ashley, Euan, Assimes, Themistocles, Auriga, Light, Austin-Tse, Christina, Bamshad, Mike, Barseghyan, Hayk, Baxter, Samantha, Behera, Sairam, Beheshti, Shaghayegh, Bejerano, Gill, Berger, Seth, Bernstein, Jon, Best, Sabrina, Blankenmeister, Benjamin, Blue, Elizabeth, Boerwinkle, Eric, Bonkowski, Emily, Bonner, Devon, Boone, Philip, Bornhorst, Miriam, Brand, Harrison, Buckingham, Kati, Calame, Daniel, Carter, Jennefer, Casadei, Silvia, Chadwick, Lisa, Chavez, Clarisa, Chen, Ziwei, Chinn, Ivan, Chong, Jessica, Coban-Akdemir, Zeynep, Cohen, Andrea J., Conner, Sarah, Conomos, Matthew, Coveler, Karen, Cui, Ya Allen, Currin, Sara, Daber, Robert, Dardas, Zain, Davis, Colleen, Dawood, Moez, de Dios, Ivan, de Esch, Celine, Delaney, Meghan, Delot, Emmanuele, DiTroia, Stephanie, Doddapaneni, Harsha, Du, Haowei, Duan, Ruizhi, Dugan-Perez, Shannon, Duong, Nhat, Duyzend, Michael, Eichler, Evan, Emami, Sara, Fraser, Jamie, Fusaro, Vincent, Galey, Miranda, Ganesh, Vijay, Garcia, Brandon, Garimella, Kiran, Gibbs, Richard, Gifford, Casey, Ginsburg, Amy, Goddard, Page, Gogarten, Stephanie, Gogate, Nikhita, Gordon, William, Gorzynski, John E., Greenleaf, William, Grochowski, Christopher, Groopman, Emily, Sousa, Rodrigo Guarischi, Gudmundsson, Sanna, Gulati, Ashima, Hall, Stacey, Harvey, William, Hawley, Megan, Heavner, Ben, Horike-Pyne, Martha, Hu, Jianhong, Huang, Yongqing, Hwang, James, Jarvik, Gail, Jensen, Tanner, Jhangiani, Shalini, Jimenez-Morales, David, Jin, Christopher, Saad, Ahmed K., Kahn-Kirby, Amanda, Kain, Jessica, Kaur, Parneet, Keehan, Laura, Knoblach, Susan, Ko, Arthur, Kundaje, Anshul, Kundu, Soumya, Lancaster, Samuel M., Larsson, Katie, Lee, Arthur, Lemire, Gabrielle, Lewis, Richard, Li, Wei, Li, Yidan, Liu, Pengfei, LoTempio, Jonathan, Lupski, James (Jim), Ma, Jialan, MacArthur, Daniel, Mahmoud, Medhat, Malani, Nirav, Mangilog, Brian, Marafi, Dana, Marmolejos, Sofia, Marten, Daniel, Martinez, Eva, Marvin, Colby, Marwaha, Shruti, Mastrorosa, Francesco Kumara, Matalon, Dena, May, Susanne, McGee, Sean, Meador, Lauren, Mefford, Heather, Mendez, Hector Rodrigo, Miller, Alexander, Miller, Danny E., Mitani, Tadahiro, Montgomery, Stephen, Moyses, Mariana, Munderloh, Chloe, Muzny, Donna, Nelson, Sarah, Nguyen, Thuy-mi P., Nguyen, Jonathan, Nussbaum, Robert, Nykamp, Keith, O'Callaghan, William, O'Heir, Emily, O'Leary, Melanie, Olsen, Jeren, Osei-Owusu, Ikeoluwa, O'Donnell-Luria, Anne, Padhi, Evin, Pais, Lynn, Pan, Miao, Panchal, Piyush, Patterson, Karynne, Payne, Sheryl, Pehlivan, Davut, Petrowski, Paul, Pham, Alicia, Pitsava, Georgia, Podesta, Astaria`Sara, Ponce, Sarah, Porter, Elizabeth, Posey, Jennifer, Prosser, Jaime, Quertermous, Thomas, Rai, Archana, Ramani, Arun, Rehm, Heidi, Reuter, Chloe, Reuter, Jason, Richardson, Matthew, Rivera-Munoz, Andres, Rubio, Oriane, Sabo, Aniko, Salani, Monica, Samocha, Kaitlin, Sanchis-Juan, Alba, Savage, Sarah, Scott, Evette, Scott, Stuart, Sedlazeck, Fritz, Shah, Gulalai, Shojaie, Ali, Singh, Mugdha, Smith, Kevin, Smith, Josh, Snow, Hana, Snyder, Michael, Socarras, Kayla, Starita, Lea, Stark, Brigitte, Stenton, Sarah, Stergachis, Andrew, Stilp, Adrienne, Sutton, V. Reid, Tai, Jui-Cheng, Talkowski, Michael (Mike), Tise, Christina, Tong, Catherine (Cat), Tsao, Philip, Ungar, Rachel, VanNoy, Grace, Vilain, Eric, Voutos, Isabella, Walker, Kim, Wei, Chia-Lin, Weisburd, Ben, Weiss, Jeff, Wellington, Chris, Weng, Ziming, Westheimer, Emily, Wheeler, Marsha, Wheeler, Matthew, Wiel, Laurens, Wilson, Michael, Wojcik, Monica, Wong, Quenna, Xiao, Changrui, Yadav, Rachita, Yi, Qian, Yuan, Bo, Zhao, Jianhua, Zhen, Jimmy, Zhou, Harry, Chong, Jessica X., Berger, Seth I., Smith, Erica, Calame, Daniel G., Hawley, Megan H., Rivera-Munoz, E. Andres, Bamshad, Michael J., and Rehm, Heidi L.
- Published
- 2024
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3. Loss of function of FAM177A1, a Golgi complex localized protein, causes a novel neurodevelopmental disorder
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Acosta, Maria T., Adam, Margaret, Adams, David R., Alvarez, Raquel L., Alvey, Justin, Amendola, Laura, Andrews, Ashley, Ashley, Euan A., Bacino, Carlos A., Bademci, Guney, Balasubramanyam, Ashok, Baldridge, Dustin, Bale, Jim, Bamshad, Michael, Barbouth, Deborah, Bayrak-Toydemir, Pinar, Beck, Anita, Beggs, Alan H., Behrens, Edward, Bejerano, Gill, Bellen, Hugo J., Bennett, Jimmy, Berg-Rood, Beverly, Bernstein, Jonathan A., Berry, Gerard T., Bican, Anna, Bivona, Stephanie, Blue, Elizabeth, Bohnsack, John, Bonner, Devon, Botto, Lorenzo, Boyd, Brenna, Briere, Lauren C., Burke, Elizabeth A., Burrage, Lindsay C., Butte, Manish J., Byers, Peter, Byrd, William E., Carey, John, Carrasquillo, Olveen, Cassini, Thomas, Chang, Ta Chen Peter, Chanprasert, Sirisak, Chao, Hsiao-Tuan, Chinn, Ivan, Clark, Gary D., Coakley, Terra R., Cobban, Laurel A., Cogan, Joy D., Coggins, Matthew, Sessions Cole, F., Colley, Heather A., Cope, Heidi, Corner, Brian, Corona, Rosario, Craigen, William J., Crouse, Andrew B., Cunningham, Michael, D’Souza, Precilla, Dai, Hongzheng, Dasari, Surendra, Davis, Joie, Dayal, Jyoti G., Dell’Angelica, Esteban C., Dickson, Patricia, Dipple, Katrina, Doherty, Daniel, Dorrani, Naghmeh, Doss, Argenia L., Douine, Emilie D., Earl, Dawn, Eckstein, David J., Emrick, Lisa T., Eng, Christine M., Ezell, Kimberly, Falk, Marni, Fieg, Elizabeth L., Fisher, Paul G., Fogel, Brent L., Forghani, Irman, Gahl, William A., Glass, Ian, Gochuico, Bernadette, Goddard, Page C., Godfrey, Rena A., Golden-Grant, Katie, Grajewski, Alana, Hadley, Don, Hahn, Sihoun, Halley, Meghan C., Hamid, Rizwan, Hassey, Kelly, Hayes, Nichole, High, Frances, Hing, Anne, Hisama, Fuki M., Holm, Ingrid A., Hom, Jason, Horike-Pyne, Martha, Huang, Alden, Hutchison, Sarah, Introne, Wendy, Isasi, Rosario, Izumi, Kosuke, Jamal, Fariha, Jarvik, Gail P., Jarvik, Jeffrey, Jayadev, Suman, Jean-Marie, Orpa, Jobanputra, Vaidehi, Karaviti, Lefkothea, Ketkar, Shamika, Kiley, Dana, Kilich, Gonench, Kobren, Shilpa N., Kohane, Isaac S., Kohler, Jennefer N., Korrick, Susan, Kozuira, Mary, Krakow, Deborah, Krasnewich, Donna M., Kravets, Elijah, Lalani, Seema R., Lam, Byron, Lam, Christina, Lanpher, Brendan C., Lanza, Ian R., LeBlanc, Kimberly, Lee, Brendan H., Levitt, Roy, Lewis, Richard A., Liu, Pengfei, Liu, Xue Zhong, Longo, Nicola, Loo, Sandra K., Loscalzo, Joseph, Maas, Richard L., Macnamara, Ellen F., MacRae, Calum A., Maduro, Valerie V., Maghiro, AudreyStephannie, Mahoney, Rachel, Malicdan, May Christine V., Mamounas, Laura A., Manolio, Teri A., Mao, Rong, Maravilla, Kenneth, Marom, Ronit, Marth, Gabor, Martin, Beth A., Martin, Martin G., Martínez-Agosto, Julian A., Marwaha, Shruti, McCauley, Jacob, McConkie-Rosell, Allyn, McCray, Alexa T., McGee, Elisabeth, Mefford, Heather, Lawrence Merritt, J., Might, Matthew, Mirzaa, Ghayda, Morava, Eva, Moretti, Paolo, Mulvihill, John, Nakano-Okuno, Mariko, Nelson, Stanley F., Neumann, Serena, Newman, John H., Nicholas, Sarah K., Nickerson, Deborah, Nieves-Rodriguez, Shirley, Novacic, Donna, Oglesbee, Devin, Orengo, James P., Pace, Laura, Pak, Stephen, Carl Pallais, J., Palmer, Christina G.S., Papp, Jeanette C., Parker, Neil H., Phillips, John A., III, Posey, Jennifer E., Potocki, Lorraine, Pusey Swerdzewski, Barbara N., Quinlan, Aaron, Rao, Deepak A., Raper, Anna, Raskind, Wendy, Renteria, Genecee, Reuter, Chloe M., Rives, Lynette, Robertson, Amy K., Rodan, Lance H., Rosenfeld, Jill A., Rosenwasser, Natalie, Rossignol, Francis, Ruzhnikov, Maura, Sacco, Ralph, Sampson, Jacinda B., Saporta, Mario, Schaechter, Judy, Schedl, Timothy, Schoch, Kelly, Scott, Daryl A., Ron Scott, C., Seto, Elaine, Shashi, Vandana, Shin, Jimann, Silverman, Edwin K., Sinsheimer, Janet S., Sisco, Kathy, Smith, Edward C., Smith, Kevin S., Solnica-Krezel, Lilianna, Solomon, Ben, Spillmann, Rebecca C., Stoler, Joan M., Sullivan, Kathleen, Sullivan, Jennifer A., Sun, Angela, Sutton, Shirley, Sweetser, David A., Sybert, Virginia, Tabor, Holly K., Tan, Queenie K.-G., Tan, Amelia L.M., Tarakad, Arjun, Tekin, Mustafa, Telischi, Fred, Thorson, Willa, Tifft, Cynthia J., Toro, Camilo, Tran, Alyssa A., Ungar, Rachel A., Urv, Tiina K., Vanderver, Adeline, Velinder, Matt, Viskochil, Dave, Vogel, Tiphanie P., Wahl, Colleen E., Walker, Melissa, Wallace, Stephanie, Walley, Nicole M., Wambach, Jennifer, Wan, Jijun, Wangler, Michael F., Ward, Patricia A., Wegner, Daniel, Hubshman, Monika Weisz, Wener, Mark, Wenger, Tara, Westerfield, Monte, Wheeler, Matthew T., Whitlock, Jordan, Wolfe, Lynne A., Worley, Kim, Xiao, Changrui, Yamamoto, Shinya, Yang, John, Zhang, Zhe, Zuchner, Stephan, Legro, Nicole R., Bowman, Angela, Ugur, Berrak, Jackstadt, Madelyn M., Shriver, Leah P., Patti, Gary J., Zhang, Bo, Feng, Wenjia, McAdow, Anthony R., Goddard, Pagé, Jensen, Tanner, Fresard, Laure, Alvarez, Raquel, McCormack, Colleen, Holt, James M., Worthey, Elizabeth A., Montgomery, Stephen B., Postlethwait, John, De Camilli, Pietro, and Solnica-Krezel, Lila
- Published
- 2024
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4. Impact of genome build on RNA-seq interpretation and diagnostics
- Author
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Ungar, Rachel A., Goddard, Pagé C., Jensen, Tanner D., Degalez, Fabien, Smith, Kevin S., Jin, Christopher A., Bonner, Devon E., Bernstein, Jonathan A., Wheeler, Matthew T., and Montgomery, Stephen B.
- Published
- 2024
- Full Text
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5. Beyond the exome: What’s next in diagnostic testing for Mendelian conditions
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Abouhala, Siwaar, Albert, Jessica, Almalvez, Miguel, Alvarez, Raquel, Amin, Mutaz, Anderson, Peter, Aradhya, Swaroop, Ashley, Euan, Assimes, Themistocles, Auriga, Light, Austin-Tse, Christina, Bamshad, Mike, Barseghyan, Hayk, Baxter, Samantha, Behera, Sairam, Beheshti, Shaghayegh, Bejerano, Gill, Berger, Seth, Bernstein, Jon, Best, Sabrina, Blankenmeister, Benjamin, Blue, Elizabeth, Boerwinkle, Eric, Bonkowski, Emily, Bonner, Devon, Boone, Philip, Bornhorst, Miriam, Bozkurt-Yozgatli, Tugce, Brand, Harrison, Buckingham, Kati, Calame, Daniel, Casadei, Silvia, Chadwick, Lisa, Chavez, Clarisa, Chen, Ziwei, Chinn, Ivan, Chong, Jessica, Coban-Akdemir, Zeynep, Cohen, Andrea J., Conner, Sarah, Conomos, Matthew, Coveler, Karen, Cui, Ya Allen, Currin, Sara, Daber, Robert, Dardas, Zain, Davis, Colleen, Dawood, Moez, de Dios, Ivan, de Esch, Celine, Delaney, Meghan, Délot, Emmanuèle, DiTroia, Stephanie, Doddapaneni, Harsha, Du, Haowei, Duan, Ruizhi, Dugan-Perez, Shannon, Duong, Nhat, Duyzend, Michael, Eichler, Evan, Emami, Sara, Fatih, Jawid, Fraser, Jamie, Fusaro, Vincent, Galey, Miranda, Ganesh, Vijay, Garimella, Kiran, Gibbs, Richard, Gifford, Casey, Ginsburg, Amy, Goddard, Pagé, Gogarten, Stephanie, Gogate, Nikhita, Gordon, William, Gorzynski, John E., Greenleaf, William, Grochowski, Christopher, Groopman, Emily, Guarischi Sousa, Rodrigo, Gudmundsson, Sanna, Gulati, Ashima, Guo, Daniel, Hale, Walker, Hall, Stacey, Harvey, William, Hawley, Megan, Heavner, Ben, Herman, Isabella, Horike-Pyne, Martha, Hu, Jianhong, Huang, Yongqing, Hwang, James, Jarvik, Gail, Jensen, Tanner, Jhangiani, Shalini, Jimenez-Morales, David, Jin, Christopher, Saad, Ahmed K., Kahn-Kirby, Amanda, Kain, Jessica, Kaur, Parneet, Keehan, Laura, Knoblach, Susan, Ko, Arthur, Kohler, Jennefer, Kundaje, Anshul, Kundu, Soumya, Lancaster, Samuel M., Larsson, Katie, Lemire, Gabrielle, Lewis, Richard, Li, Wei, Li, Yidan, Liu, Pengfei, LoTempio, Jonathan, Lupski, James, Ma, Jialan, MacArthur, Daniel, Mahmoud, Medhat, Malani, Nirav, Mangilog, Brian, Marafi, Dana, Marmolejos, Sofia, Marten, Daniel, Martinez, Eva, Marvin, Colby, Marwaha, Shruti, Kumara Mastrorosa, Francesco, Matalon, Dena, May, Susanne, McGee, Sean, Meador, Lauren, Mefford, Heather, Rodrigo Mendez, Hector, Miller, Alexander, Miller, Danny E., Mitani, Tadahiro, Montgomery, Stephen, Moussa, Hala Mohamed, Moyses, Mariana, Munderloh, Chloe, Muzny, Donna, Nelson, Sarah, Neu, Matthew B., Nguyen, Jonathan, Nguyen, Thuy-mi P., Nussbaum, Robert, Nykamp, Keith, O'Callaghan, William, O'Heir, Emily, O'Leary, Melanie, Olsen, Jeren, Osei-Owusu, Ikeoluwa, O'Donnell-Luria, Anne, Padhi, Evin, Pais, Lynn, Pan, Miao, Panchal, Piyush, Patterson, Karynne, Payne, Sheryl, Pehlivan, Davut, Petrowski, Paul, Pham, Alicia, Pitsava, Georgia, Podesta, Astaria, Ponce, Sarah, Posey, Jennifer, Prosser, Jaime, Quertermous, Thomas, Rai, Archana, Ramani, Arun, Rehm, Heidi, Reuter, Chloe, Reuter, Jason, Richardson, Matthew, Rivera-Munoz, Andres, Rubio, Oriane, Sabo, Aniko, Salani, Monica, Samocha, Kaitlin, Sanchis-Juan, Alba, Savage, Sarah, Scott, Stuart, Scott, Evette, Sedlazeck, Fritz, Shah, Gulalai, Shojaie, Ali, Singh, Mugdha, Smith, Josh, Smith, Kevin, Snow, Hana, Snyder, Michael, Socarras, Kayla, Starita, Lea, Stark, Brigitte, Stenton, Sarah, Stergachis, Andrew, Stilp, Adrienne, Sundaram, Laksshman, Sutton, V. Reid, Tai, Jui-Cheng, Talkowski, Michael, Tise, Christina, Tong, Catherine, Tsao, Philip, Ungar, Rachel, VanNoy, Grace, Vilain, Eric, Voutos, Isabella, Walker, Kim, Weisburd, Ben, Weiss, Jeff, Wellington, Chris, Weng, Ziming, Westheimer, Emily, Wheeler, Marsha, Wheeler, Matthew, Wiel, Laurens, Wilson, Michael, Wojcik, Monica, Wong, Quenna, Wong, Issac, Xiao, Changrui, Yadav, Rachita, Yi, Qian, Yuan, Bo, Zhao, Jianhua, Zhen, Jimmy, Zhou, Harry, Wojcik, Monica H., Reuter, Chloe M., Duyzend, Michael H., Boone, Philip M., Groopman, Emily E., Délot, Emmanuèle C., Jain, Deepti, Starita, Lea M., Montgomery, Stephen B., Bamshad, Michael J., Chong, Jessica X., Wheeler, Matthew T., Berger, Seth I., and Sedlazeck, Fritz J.
- Published
- 2023
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6. Accelerated identification of disease-causing variants with ultra-rapid nanopore genome sequencing
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Goenka, Sneha D., Gorzynski, John E., Shafin, Kishwar, Fisk, Dianna G., Pesout, Trevor, Jensen, Tanner D., Monlong, Jean, Chang, Pi-Chuan, Baid, Gunjan, Bernstein, Jonathan A., Christle, Jeffrey W., Dalton, Karen P., Garalde, Daniel R., Grove, Megan E., Guillory, Joseph, Kolesnikov, Alexey, Nattestad, Maria, Ruzhnikov, Maura R. Z., Samadi, Mehrzad, Sethia, Ankit, Spiteri, Elizabeth, Wright, Christopher J., Xiong, Katherine, Zhu, Tong, Jain, Miten, Sedlazeck, Fritz J., Carroll, Andrew, Paten, Benedict, and Ashley, Euan A.
- Published
- 2022
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7. Widespread choroid plexus contamination in sampling and profiling of brain tissue
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Olney, Kimberly C., Todd, Kennedi T., Pallegar, Praveen N., Jensen, Tanner D., Cadiz, Mika P., Gibson, Katelin A., Barnett, Joseph H., de Ávila, Camila, Bouchal, Samantha M., Rabichow, Benjamin E., Ding, Zonghui, Wojtas, Aleksandra M., Wilson, Melissa A., and Fryer, John D.
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- 2022
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8. Culture shock: microglial heterogeneity, activation, and disrupted single-cell microglial networks in vitro
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Cadiz, Mika P., Jensen, Tanner D., Sens, Jonathon P., Zhu, Kuixi, Song, Won-Min, Zhang, Bin, Ebbert, Mark, Chang, Rui, and Fryer, John D.
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- 2022
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9. A 3′UTR Insertion Is a Candidate Causal Variant at the TMEM106B Locus Associated With Increased Risk for FTLD-TDP
- Author
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Chemparathy, Augustine, primary, Le Guen, Yann, additional, Zeng, Yi, additional, Gorzynski, John, additional, Jensen, Tanner D., additional, Yang, Chengran, additional, Kasireddy, Nandita, additional, Talozzi, Lia, additional, Belloy, Michael, additional, Stewart, Ilaria, additional, Gitler, Aaron D., additional, Wagner, Anthony D., additional, Mormino, Elizabeth, additional, Henderson, Victor W., additional, Wyss-Coray, Tony, additional, Ashley, Euan, additional, Cruchaga, Carlos, additional, and Greicius, Michael D., additional
- Published
- 2024
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10. Novel characterization of Alzheimer’s disease genetic loci using long‐read sequencing
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Talozzi, Lia, primary, Chemparathy, Augustine, additional, Jensen, Tanner D., additional, Gorzynski, John, additional, Belloy, Michael E, additional, Guen, Yann Le, additional, Kasireddy, Nandita, additional, Dailey, Maddie, additional, Stewart, Ilaria, additional, Ashley, Euan, additional, and Greicius, Michael D, additional
- Published
- 2023
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11. Clusterin ameliorates tau pathology in vivo by inhibiting fibril formation
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Wojtas, Aleksandra M., Carlomagno, Yari, Sens, Jonathon P., Kang, Silvia S., Jensen, Tanner D., Kurti, Aishe, Baker, Kelsey E., Berry, Taylor J., Phillips, Virginia R., Castanedes, Monica Casey, Awan, Ayesha, DeTure, Michael, De Castro, Cristhoper H. Fernandez, Librero, Ariston L., Yue, Mei, Daughrity, Lillian, Jansen-West, Karen R., Cook, Casey N., Dickson, Dennis W., Petrucelli, Leonard, and Fryer, John D.
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- 2020
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12. APOE loss-of-function variants: Compatible with longevity and associated with resistance to Alzheimer’s disease pathology
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Chemparathy, Augustine, Le Guen, Yann, Chen, Sunny, Lee, Eun-Gyung, Leong, Lesley, Gorzynski, John E., Jensen, Tanner D., Ferrasse, Alexis, Xu, Guangxue, Xiang, Hong, Belloy, Michael E., Kasireddy, Nandita, Peña-Tauber, Andrés, Williams, Kennedy, Stewart, Ilaria, Talozzi, Lia, Wingo, Thomas S., Lah, James J., Jayadev, Suman, Hales, Chadwick M., Peskind, Elaine, Child, Daniel D., Roeber, Sigrun, Keene, C. Dirk, Cong, Le, Ashley, Euan A., Yu, Chang-En, and Greicius, Michael D.
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- 2024
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13. A 3’UTR Insertion Is a Candidate Causal Variant at theTMEM106BLocus Associated with Increased Risk for FTLD-TDP
- Author
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Chemparathy, Augustine, primary, Le Guen, Yann, additional, Zeng, Yi, additional, Gorzynski, John, additional, Jensen, Tanner, additional, Yang, Chengran, additional, Kasireddy, Nandita, additional, Talozzi, Lia, additional, Belloy, Michael E., additional, Stewart, Ilaria, additional, Gitler, Aaron D., additional, Wagner, Anthony D., additional, Mormino, Elizabeth, additional, Henderson, Victor W., additional, Wyss-Coray, Tony, additional, Ashley, Euan, additional, Cruchaga, Carlos, additional, and Greicius, Michael D., additional
- Published
- 2023
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14. Video of Procedure
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Zander, Ben, Black, Travis, Davis, Dylan, Jensen, Tanner, Lyon, Brielle, and Wiggins, Bradford
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Acquiescence ,Intuition - Published
- 2022
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15. Reducing Acquiescence by Demonstrating Faulty Logic
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Black, Travis, Davis, Dylan, Jensen, Tanner, Lyon, Brielle, Zander, Ben, and Wiggins, Bradford
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Monty Hall ,Acquiescence ,Intuition - Abstract
This study is based off of Walco & Risen's 2017 study The Empirical Case for Acquiescing to Intuition. This study was conducted at BYU-Idaho by five undergraduate students during Winter 2019 under the direction of Dr. Bradford Wiggins, Ph.D. This study is inspired by Walco and Risen's, "Empirical Case of Acquiescence" published in 2016, focusing on study two.
- Published
- 2022
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16. Ethics Review
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Zander, Ben, Black, Travis, Davis, Dylan, Jensen, Tanner, Lyon, Brielle, and Wiggins, Bradford
- Subjects
Acquiescence ,Intuition - Published
- 2022
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17. Method and Materials
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Zander, Ben, Black, Travis, Davis, Dylan, Jensen, Tanner, Lyon, Brielle, and Wiggins, Bradford
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Acquiescence ,Intuition - Published
- 2022
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18. Data and Stats File
- Author
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Zander, Ben, Black, Travis, Davis, Dylan, Jensen, Tanner, Lyon, Brielle, and Wiggins, Bradford
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Acquiescence ,Intuition - Published
- 2022
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19. Near-fatal Legionella pneumonia in a neonate linked to home humidifier by metagenomic next generation sequencing
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West, Patrick T., primary, Brooks, Erin F., additional, Costales, Cristina, additional, Moreno, Angel, additional, Jensen, Tanner Dean, additional, Budvytiene, Indre, additional, Khan, Aslam, additional, Pham, Trung H.M., additional, Schwenk, Hayden T., additional, Bhatt, Ami S., additional, and Banaei, Niaz, additional
- Published
- 2022
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20. The effect of sudden-onset distractors on reading efficiency and comprehension
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Luke, Steven G, primary and Jensen, Tanner, additional
- Published
- 2022
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21. The effect of sudden-onset distractors on reading efficiency and comprehension.
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Luke, Steven G and Jensen, Tanner
- Subjects
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DIGITAL technology , *EYE movements , *READING disability , *EYE tracking , *DISTRACTION , *DYSLEXIA , *PROSPECTIVE memory - Abstract
Reading is an essential skill that requires focused attention. However, much reading is done in non-optimal environments. These days, reading is often done on digital devices or with a digital device nearby. These devices often introduce momentary distractions during reading, interrupting with alerts, notifications, and pop-ups. In two eye-tracking experiments, we investigated how such momentary distractions affect reading. Participants read paragraphs while their eye movements were monitored. During half of the paragraphs, distractions appeared periodically on the screen that required a response from the participants. In Experiment 1, the distractions were arrows that the participant had to respond to and then could immediately forget. In Experiment 2, the participants performed a 1-back task that required them to remember the identity of the last distractor. Compared with the no-distraction condition, the respond-and-forget distractors of Experiment 1 had minimal impact on reading behaviour and comprehension, but the working-memory-load distractors of Experiment 2 led to increased rereading and decreased reading comprehension. It seems a simple pop-up does not disrupt reading, but a message you must remember will. [ABSTRACT FROM AUTHOR]
- Published
- 2023
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22. Ultra-Rapid Nanopore Whole Genome Genetic Diagnosis of Dilated Cardiomyopathy in an Adolescent With Cardiogenic Shock
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Gorzynski, John E., primary, Goenka, Sneha D., additional, Shafin, Kishwar, additional, Jensen, Tanner D., additional, Fisk, Dianna G., additional, Grove, Megan E., additional, Spiteri, Elizabeth, additional, Pesout, Trevor, additional, Monlong, Jean, additional, Bernstein, Jonathan A., additional, Ceresnak, Scott, additional, Chang, Pi-Chuan, additional, Christle, Jeffrey W., additional, Chubb, Henry, additional, Dunn, Kyla, additional, Garalde, Daniel R., additional, Guillory, Joseph, additional, Ruzhnikov, Maura R.Z., additional, Wright, Chris, additional, Wusthoff, Courtney J., additional, Xiong, Katherine, additional, Hollander, Seth A., additional, Berry, Gerald J., additional, Jain, Miten, additional, Sedlazeck, Fritz J., additional, Carroll, Andrew, additional, Paten, Benedict, additional, and Ashley, Euan A., additional
- Published
- 2022
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23. Additional file 4 of Culture shock: microglial heterogeneity, activation, and disrupted single-cell microglial networks in vitro
- Author
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Cadiz, Mika P., Jensen, Tanner D., Sens, Jonathon P., Zhu, Kuixi, Song, Won-Min, Zhang, Bin, Ebbert, Mark, Chang, Rui, and Fryer, John D.
- Subjects
nervous system ,human activities - Abstract
Additional file 4: Figure S3. Key drivers of the cultured microglia phenotype. Top 100 of 444 total key drivers with prioritized rank derived from the astro-plated microglia and micro-isolated microglia networks.
- Published
- 2022
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24. Additional file 1 of Culture shock: microglial heterogeneity, activation, and disrupted single-cell microglial networks in vitro
- Author
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Cadiz, Mika P., Jensen, Tanner D., Sens, Jonathon P., Zhu, Kuixi, Song, Won-Min, Zhang, Bin, Ebbert, Mark, Chang, Rui, and Fryer, John D.
- Abstract
Additional file 1: Table S1. Genes differentially expressed in each cluster of primary cultured astrocyte-plated microglial cells. All genes displayed have an adjusted p value of less than 0.05 and are expressed in a minimum of 25% of cells in each cluster.
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- 2022
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25. Additional file 2 of Culture shock: microglial heterogeneity, activation, and disrupted single-cell microglial networks in vitro
- Author
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Cadiz, Mika P., Jensen, Tanner D., Sens, Jonathon P., Zhu, Kuixi, Song, Won-Min, Zhang, Bin, Ebbert, Mark, Chang, Rui, and Fryer, John D.
- Abstract
Additional file 2: Figure S1. MEGENA network analysis of freshly isolated cells establishes a reference transcriptional network for microglia. (a) Transcriptional regulatory network for freshly isolated microglia inferred by MEGENA. Nodes represent genes, and an edge between nodes represents the significant correlation of those two genes. Bar graph shows relative strength of these top 20 nodes and highlights the module to which each gene belongs. Heatmap shows the scaled expression of the top 100 genes of each of the 3 core MEGENA modules. Heatmap is represented by a downsampled 2000 of the freshly isolated cells. (b) Subnetwork of module 2. Weighted module expression is calculated by calculating the sum of the expression of each gene in the module, weighted by its strength in the network, and signed by whether that gene has positive or negative correlation with the largest hub of that module. Plotting the module weighted sum in a violin and feature plot shows strong, significant association of module 2 with the activated cluster (two-tailed t-test between activated vs homeostatic cluster, p-value = 1.93e-15). Metascape gene ontology (GO) enrichment suggests that this module is related to inflammatory response and the transcriptional response to stress. (c) Subnetwork of module 3, containing many homeostatic microglia markers. Weighted module expression is highest in the homeostatic cluster and significantly decreases in cells from the activated cluster (two-tailed t-test between activated vs homeostatic cluster, p-value = 4.34e-60). Metascape shows that pathways enriched for this module include ribonucleoprotein complex formation, functioning of the lysosome, and immune pathways like neutrophil degranulation and myeloid activation. (d) Network of the subnetwork for module 4, which contains many interferon-related genes. Module weighted sum is significantly increased in the interferon cluster compared to the homeostatic cluster (two-tailed t-test, p-value = 7.65e-23). Metascape enrichment analysis shows pathways related to interferon signaling and cytokine production.
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- 2022
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26. Additional file 3 of Culture shock: microglial heterogeneity, activation, and disrupted single-cell microglial networks in vitro
- Author
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Cadiz, Mika P., Jensen, Tanner D., Sens, Jonathon P., Zhu, Kuixi, Song, Won-Min, Zhang, Bin, Ebbert, Mark, Chang, Rui, and Fryer, John D.
- Abstract
Additional file 3: Figure S2. In vitro microglia networks are disrupted and dissimilar to the freshly isolated network. (a) Transcriptional regulatory network for astrocyte-plated in vitro cells inferred by MEGENA. Top 50 nodes are labelled, and nodes are colored corresponding to the 5 core modules identified by MEGENA clustering analysis. (b) Bar graph of the top 40 nodes shows from a relative strength between nodes. (c) Heatmap of the scaled expression of the top 75 genes of each core module across 2000 downsampled cells. Modules strongly associate with specific clusters. Module 9 contains genes highly expressed in the macrophage-like cluster. Module 5 contains genes associated with the microglia-like 1, and monocyte-like 1 and 2 clusters. Module 6 contains hubs of ribosomal genes and is downregulated in microglia-like cluster 2 and upregulated in microglia-like cluster 3. Modules 7 and 8 contain cell cycle genes associated with proliferation cluster. (d) Subnetwork of module 5, a heterogenous module that contains a variety of hubs. Hubs like Cx3cr1, Fcrls, and Fcer1g are markers of resting microglia, while hubs like Apoe, Lgals1, Lgals3 are activation markers. Smaller hubs like Anxa1 and S100a4 are unique to monocyte-like cells. The weighted module expression of this module is strongest in the microglia-like 1 cluster, but expression of this module is robust across all clusters. Metascape GO enrichment shows enrichment for immune and cell death processes. (e) Subnetwork of module 7, a cell cycle module whose module weighted expression is significantly higher in proliferation cluster 6 (two-tailed t-test, p-value = 1.62e-166). Metascape analysis of this clusters shows enrichment of cell cycle processes. (f) Subnetwork of module 9, with hubs Mrc1 and Stab1 that are unique markers of macrophages. Weighted module expression of this module is expressed robustly in all clusters, but is highest in macrophage-like cluster 0 (two-tailed t-test, p-value = 8.23e-7). Metascape GO enrichment shows this module is related to lysosomal and vesicle transport pathways.
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- 2022
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27. Ultrarapid Nanopore Genome Sequencing in a Critical Care Setting
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Gorzynski, John E., primary, Goenka, Sneha D., additional, Shafin, Kishwar, additional, Jensen, Tanner D., additional, Fisk, Dianna G., additional, Grove, Megan E., additional, Spiteri, Elizabeth, additional, Pesout, Trevor, additional, Monlong, Jean, additional, Baid, Gunjan, additional, Bernstein, Jonathan A., additional, Ceresnak, Scott, additional, Chang, Pi-Chuan, additional, Christle, Jeffrey W., additional, Chubb, Henry, additional, Dalton, Karen P., additional, Dunn, Kyla, additional, Garalde, Daniel R., additional, Guillory, Joseph, additional, Knowles, Joshua W., additional, Kolesnikov, Alexey, additional, Ma, Michael, additional, Moscarello, Tia, additional, Nattestad, Maria, additional, Perez, Marco, additional, Ruzhnikov, Maura R.Z., additional, Samadi, Mehrzad, additional, Setia, Ankit, additional, Wright, Chris, additional, Wusthoff, Courtney J., additional, Xiong, Katherine, additional, Zhu, Tong, additional, Jain, Miten, additional, Sedlazeck, Fritz J., additional, Carroll, Andrew, additional, Paten, Benedict, additional, and Ashley, Euan A., additional
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- 2022
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28. Considerations for reporting variants in novel candidate genes identified during clinical genomic testing
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Chong, Jessica X., Berger, Seth I., Baxter, Samantha, Smith, Erica, Xiao, Changrui, Calame, Daniel G., Hawley, Megan H., Rivera-Munoz, E. Andres, DiTroia, Stephanie, Abouhala, Siwaar, Albert, Jessica, Almalvez, Miguel, Alvarez, Raquel, Amin, Mutaz, Anderson, Peter, Aradhya, Swaroop, Ashley, Euan, Assimes, Themistocles, Auriga, Light, Austin-Tse, Christina, Bamshad, Mike, Barseghyan, Hayk, Baxter, Samantha, Behera, Sairam, Beheshti, Shaghayegh, Bejerano, Gill, Berger, Seth, Bernstein, Jon, Best, Sabrina, Blankenmeister, Benjamin, Blue, Elizabeth, Boerwinkle, Eric, Bonkowski, Emily, Bonner, Devon, Boone, Philip, Bornhorst, Miriam, Brand, Harrison, Buckingham, Kati, Calame, Daniel, Carter, Jennefer, Casadei, Silvia, Chadwick, Lisa, Chavez, Clarisa, Chen, Ziwei, Chinn, Ivan, Chong, Jessica, Coban-Akdemir, Zeynep, Cohen, Andrea J., Conner, Sarah, Conomos, Matthew, Coveler, Karen, Cui, Ya Allen, Currin, Sara, Daber, Robert, Dardas, Zain, Davis, Colleen, Dawood, Moez, de Dios, Ivan, de Esch, Celine, Delaney, Meghan, Delot, Emmanuele, DiTroia, Stephanie, Doddapaneni, Harsha, Du, Haowei, Duan, Ruizhi, Dugan-Perez, Shannon, Duong, Nhat, Duyzend, Michael, Eichler, Evan, Emami, Sara, Fraser, Jamie, Fusaro, Vincent, Galey, Miranda, Ganesh, Vijay, Garcia, Brandon, Garimella, Kiran, Gibbs, Richard, Gifford, Casey, Ginsburg, Amy, Goddard, Page, Gogarten, Stephanie, Gogate, Nikhita, Gordon, William, Gorzynski, John E., Greenleaf, William, Grochowski, Christopher, Groopman, Emily, Sousa, Rodrigo Guarischi, Gudmundsson, Sanna, Gulati, Ashima, Hall, Stacey, Harvey, William, Hawley, Megan, Heavner, Ben, Horike-Pyne, Martha, Hu, Jianhong, Huang, Yongqing, Hwang, James, Jarvik, Gail, Jensen, Tanner, Jhangiani, Shalini, Jimenez-Morales, David, Jin, Christopher, Saad, Ahmed K., Kahn-Kirby, Amanda, Kain, Jessica, Kaur, Parneet, Keehan, Laura, Knoblach, Susan, Ko, Arthur, Kundaje, Anshul, Kundu, Soumya, Lancaster, Samuel M., Larsson, Katie, Lee, Arthur, Lemire, Gabrielle, Lewis, Richard, Li, Wei, Li, Yidan, Liu, Pengfei, LoTempio, Jonathan, Lupski, James (Jim), Ma, Jialan, MacArthur, Daniel, Mahmoud, Medhat, Malani, Nirav, Mangilog, Brian, Marafi, Dana, Marmolejos, Sofia, Marten, Daniel, Martinez, Eva, Marvin, Colby, Marwaha, Shruti, Mastrorosa, Francesco Kumara, Matalon, Dena, May, Susanne, McGee, Sean, Meador, Lauren, Mefford, Heather, Mendez, Hector Rodrigo, Miller, Alexander, Miller, Danny E., Mitani, Tadahiro, Montgomery, Stephen, Moyses, Mariana, Munderloh, Chloe, Muzny, Donna, Nelson, Sarah, Nguyen, Thuy-mi P., Nguyen, Jonathan, Nussbaum, Robert, Nykamp, Keith, O'Callaghan, William, O'Heir, Emily, O'Leary, Melanie, Olsen, Jeren, Osei-Owusu, Ikeoluwa, O'Donnell-Luria, Anne, Padhi, Evin, Pais, Lynn, Pan, Miao, Panchal, Piyush, Patterson, Karynne, Payne, Sheryl, Pehlivan, Davut, Petrowski, Paul, Pham, Alicia, Pitsava, Georgia, Podesta, Astaria`Sara, Ponce, Sarah, Porter, Elizabeth, Posey, Jennifer, Prosser, Jaime, Quertermous, Thomas, Rai, Archana, Ramani, Arun, Rehm, Heidi, Reuter, Chloe, Reuter, Jason, Richardson, Matthew, Rivera-Munoz, Andres, Rubio, Oriane, Sabo, Aniko, Salani, Monica, Samocha, Kaitlin, Sanchis-Juan, Alba, Savage, Sarah, Scott, Evette, Scott, Stuart, Sedlazeck, Fritz, Shah, Gulalai, Shojaie, Ali, Singh, Mugdha, Smith, Kevin, Smith, Josh, Snow, Hana, Snyder, Michael, Socarras, Kayla, Starita, Lea, Stark, Brigitte, Stenton, Sarah, Stergachis, Andrew, Stilp, Adrienne, Sutton, V. Reid, Tai, Jui-Cheng, Talkowski, Michael (Mike), Tise, Christina, Tong, Catherine (Cat), Tsao, Philip, Ungar, Rachel, VanNoy, Grace, Vilain, Eric, Voutos, Isabella, Walker, Kim, Wei, Chia-Lin, Weisburd, Ben, Weiss, Jeff, Wellington, Chris, Weng, Ziming, Westheimer, Emily, Wheeler, Marsha, Wheeler, Matthew, Wiel, Laurens, Wilson, Michael, Wojcik, Monica, Wong, Quenna, Xiao, Changrui, Yadav, Rachita, Yi, Qian, Yuan, Bo, Zhao, Jianhua, Zhen, Jimmy, Zhou, Harry, Bamshad, Michael J., and Rehm, Heidi L.
- Abstract
Since the first novel gene discovery for a Mendelian condition was made via exome sequencing, the rapid increase in the number of genes known to underlie Mendelian conditions coupled with the adoption of exome (and more recently, genome) sequencing by diagnostic testing labs has changed the landscape of genomic testing for rare diseases. Specifically, many individuals suspected to have a Mendelian condition are now routinely offered clinical ES. This commonly results in a precise genetic diagnosis but frequently overlooks the identification of novel candidate genes. Such candidates are also less likely to be identified in the absence of large-scale gene discovery research programs. Accordingly, clinical laboratories have both the opportunity, and some might argue a responsibility, to contribute to novel gene discovery, which should, in turn, increase the diagnostic yield for many conditions. However, clinical diagnostic laboratories must necessarily balance priorities for throughput, turnaround time, cost efficiency, clinician preferences, and regulatory constraints and often do not have the infrastructure or resources to effectively participate in either clinical translational or basic genome science research efforts. For these and other reasons, many laboratories have historically refrained from broadly sharing potentially pathogenic variants in novel genes via networks such as Matchmaker Exchange, much less reporting such results to ordering providers. Efforts to report such results are further complicated by a lack of guidelines for clinical reporting and interpretation of variants in novel candidate genes. Nevertheless, there are myriad benefits for many stakeholders, including patients/families, clinicians, and researchers, if clinical laboratories systematically and routinely identify, share, and report novel candidate genes. To facilitate this change in practice, we developed criteria for triaging, sharing, and reporting novel candidate genes that are most likely to be promptly validated as underlying a Mendelian condition and translated to use in clinical settings.
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- 2024
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29. Loss of function of FAM177A1, a Golgi complex localized protein, causes a novel neurodevelopmental disorder
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Kohler, Jennefer N., Legro, Nicole R., Baldridge, Dustin, Shin, Jimann, Bowman, Angela, Ugur, Berrak, Jackstadt, Madelyn M., Shriver, Leah P., Patti, Gary J., Zhang, Bo, Feng, Wenjia, McAdow, Anthony R., Goddard, Pagé, Ungar, Rachel A., Jensen, Tanner, Smith, Kevin S., Fresard, Laure, Alvarez, Raquel, Bonner, Devon, Reuter, Chloe M., McCormack, Colleen, Kravets, Elijah, Marwaha, Shruti, Holt, James M., Acosta, Maria T., Adam, Margaret, Adams, David R., Alvarez, Raquel L., Alvey, Justin, Amendola, Laura, Andrews, Ashley, Ashley, Euan A., Bacino, Carlos A., Bademci, Guney, Balasubramanyam, Ashok, Baldridge, Dustin, Bale, Jim, Bamshad, Michael, Barbouth, Deborah, Bayrak-Toydemir, Pinar, Beck, Anita, Beggs, Alan H., Behrens, Edward, Bejerano, Gill, Bellen, Hugo J., Bennett, Jimmy, Berg-Rood, Beverly, Bernstein, Jonathan A., Berry, Gerard T., Bican, Anna, Bivona, Stephanie, Blue, Elizabeth, Bohnsack, John, Bonner, Devon, Botto, Lorenzo, Boyd, Brenna, Briere, Lauren C., Burke, Elizabeth A., Burrage, Lindsay C., Butte, Manish J., Byers, Peter, Byrd, William E., Carey, John, Carrasquillo, Olveen, Cassini, Thomas, Chang, Ta Chen Peter, Chanprasert, Sirisak, Chao, Hsiao-Tuan, Chinn, Ivan, Clark, Gary D., Coakley, Terra R., Cobban, Laurel A., Cogan, Joy D., Coggins, Matthew, Sessions Cole, F., Colley, Heather A., Cope, Heidi, Corner, Brian, Corona, Rosario, Craigen, William J., Crouse, Andrew B., Cunningham, Michael, D’Souza, Precilla, Dai, Hongzheng, Dasari, Surendra, Davis, Joie, Dayal, Jyoti G., Dell’Angelica, Esteban C., Dickson, Patricia, Dipple, Katrina, Doherty, Daniel, Dorrani, Naghmeh, Doss, Argenia L., Douine, Emilie D., Earl, Dawn, Eckstein, David J., Emrick, Lisa T., Eng, Christine M., Ezell, Kimberly, Falk, Marni, Fieg, Elizabeth L., Fisher, Paul G., Fogel, Brent L., Forghani, Irman, Gahl, William A., Glass, Ian, Gochuico, Bernadette, Goddard, Page C., Godfrey, Rena A., Golden-Grant, Katie, Grajewski, Alana, Hadley, Don, Hahn, Sihoun, Halley, Meghan C., Hamid, Rizwan, Hassey, Kelly, Hayes, Nichole, High, Frances, Hing, Anne, Hisama, Fuki M., Holm, Ingrid A., Hom, Jason, Horike-Pyne, Martha, Huang, Alden, Hutchison, Sarah, Introne, Wendy, Isasi, Rosario, Izumi, Kosuke, Jamal, Fariha, Jarvik, Gail P., Jarvik, Jeffrey, Jayadev, Suman, Jean-Marie, Orpa, Jobanputra, Vaidehi, Karaviti, Lefkothea, Ketkar, Shamika, Kiley, Dana, Kilich, Gonench, Kobren, Shilpa N., Kohane, Isaac S., Kohler, Jennefer N., Korrick, Susan, Kozuira, Mary, Krakow, Deborah, Krasnewich, Donna M., Kravets, Elijah, Lalani, Seema R., Lam, Byron, Lam, Christina, Lanpher, Brendan C., Lanza, Ian R., LeBlanc, Kimberly, Lee, Brendan H., Levitt, Roy, Lewis, Richard A., Liu, Pengfei, Liu, Xue Zhong, Longo, Nicola, Loo, Sandra K., Loscalzo, Joseph, Maas, Richard L., Macnamara, Ellen F., MacRae, Calum A., Maduro, Valerie V., Maghiro, AudreyStephannie, Mahoney, Rachel, Malicdan, May Christine V., Mamounas, Laura A., Manolio, Teri A., Mao, Rong, Maravilla, Kenneth, Marom, Ronit, Marth, Gabor, Martin, Beth A., Martin, Martin G., Martínez-Agosto, Julian A., Marwaha, Shruti, McCauley, Jacob, McConkie-Rosell, Allyn, McCray, Alexa T., McGee, Elisabeth, Mefford, Heather, Lawrence Merritt, J., Might, Matthew, Mirzaa, Ghayda, Morava, Eva, Moretti, Paolo, Mulvihill, John, Nakano-Okuno, Mariko, Nelson, Stanley F., Neumann, Serena, Newman, John H., Nicholas, Sarah K., Nickerson, Deborah, Nieves-Rodriguez, Shirley, Novacic, Donna, Oglesbee, Devin, Orengo, James P., Pace, Laura, Pak, Stephen, Carl Pallais, J., Palmer, Christina G.S., Papp, Jeanette C., Parker, Neil H., Phillips, John A., Posey, Jennifer E., Potocki, Lorraine, Pusey Swerdzewski, Barbara N., Quinlan, Aaron, Rao, Deepak A., Raper, Anna, Raskind, Wendy, Renteria, Genecee, Reuter, Chloe M., Rives, Lynette, Robertson, Amy K., Rodan, Lance H., Rosenfeld, Jill A., Rosenwasser, Natalie, Rossignol, Francis, Ruzhnikov, Maura, Sacco, Ralph, Sampson, Jacinda B., Saporta, Mario, Schaechter, Judy, Schedl, Timothy, Schoch, Kelly, Scott, Daryl A., Ron Scott, C., Seto, Elaine, Shashi, Vandana, Shin, Jimann, Silverman, Edwin K., Sinsheimer, Janet S., Sisco, Kathy, Smith, Edward C., Smith, Kevin S., Solnica-Krezel, Lilianna, Solomon, Ben, Spillmann, Rebecca C., Stoler, Joan M., Sullivan, Kathleen, Sullivan, Jennifer A., Sun, Angela, Sutton, Shirley, Sweetser, David A., Sybert, Virginia, Tabor, Holly K., Tan, Queenie K.-G., Tan, Amelia L.M., Tarakad, Arjun, Tekin, Mustafa, Telischi, Fred, Thorson, Willa, Tifft, Cynthia J., Toro, Camilo, Tran, Alyssa A., Ungar, Rachel A., Urv, Tiina K., Vanderver, Adeline, Velinder, Matt, Viskochil, Dave, Vogel, Tiphanie P., Wahl, Colleen E., Walker, Melissa, Wallace, Stephanie, Walley, Nicole M., Wambach, Jennifer, Wan, Jijun, Wangler, Michael F., Ward, Patricia A., Wegner, Daniel, Hubshman, Monika Weisz, Wener, Mark, Wenger, Tara, Westerfield, Monte, Wheeler, Matthew T., Whitlock, Jordan, Wolfe, Lynne A., Worley, Kim, Xiao, Changrui, Yamamoto, Shinya, Yang, John, Zhang, Zhe, Zuchner, Stephan, Worthey, Elizabeth A., Ashley, Euan A., Montgomery, Stephen B., Fisher, Paul G., Postlethwait, John, De Camilli, Pietro, Solnica-Krezel, Lila, Bernstein, Jonathan A., and Wheeler, Matthew T.
- Abstract
The function of FAM177A1and its relationship to human disease is largely unknown. Recent studies have demonstrated FAM177A1to be a critical immune-associated gene. One previous case study has linked FAM177A1to a neurodevelopmental disorder in 4 siblings.
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- 2024
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30. Additional file 1 of Clusterin ameliorates tau pathology in vivo by inhibiting fibril formation
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Wojtas, Aleksandra M., Yari Carlomagno, Sens, Jonathon P., Kang, Silvia S., Jensen, Tanner D., Kurti, Aishe, Baker, Kelsey E., Berry, Taylor J., Phillips, Virginia R., Castanedes, Monica Casey, Awan, Ayesha, DeTure, Michael, Cristhoper H. Fernandez De Castro, Ariston L. Librero, Yue, Mei, Daughrity, Lillian, Jansen-West, Karen R., Cook, Casey N., Dickson, Dennis W., Petrucelli, Leonard, and Fryer, John D.
- Subjects
viruses - Abstract
Additional file 1. Table S1 Neuropathological information of samples used in the histological study. Table S2 Demographics and neuropathological characteristics of human subjects. Figure S1 CLU is present in tau aggregates and is upregulated in AAV-TauP301L animals. a Brain tissues of 6-month-old wild-type (WT) mice injected with AAV-GFP (Ctrl) and AAV-TauP301L. Arrows show CLU co-localization with tau deposits. Arrowheads represent tau tangles without CLU immunoreactivity. Scale bar, 100 μm. b Quantification of CLU protein levels in cortex of WT mice injected with AAV-GFP (Ctrl) and AAV-TauP301. N = 15–16 mice/group. Data presented as mean ± S.E.M. and analyzed with Student’s t test, *p
- Published
- 2020
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31. Analysis of Identification Method for Bacterial Species and Antibiotic Resistance Genes Using Optical Data From DNA Oligomers
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Wood, Ryan L., primary, Jensen, Tanner, additional, Wadsworth, Cindi, additional, Clement, Mark, additional, Nagpal, Prashant, additional, and Pitt, William G., additional
- Published
- 2020
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32. Additional file 1: of Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight
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Ebbert, Mark, Jensen, Tanner, Jansen-West, Karen, Sens, Jonathon, Reddy, Joseph, Ridge, Perry, Kauwe, John, Belzil, Veronique, Pregent, Luc, Carrasquillo, Minerva, Keene, Dirk, Larson, Eric, Crane, Paul, Asmann, Yan, Nilufer Ertekin-Taner, Younkin, Steven, Ross, Owen, Rademakers, Rosa, Petrucelli, Leonard, and Fryer, John
- Abstract
Supplemental figures. (DOCX 3853 kb)
- Published
- 2019
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33. Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight
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Ebbert, Mark T. W., primary, Jensen, Tanner D., additional, Jansen-West, Karen, additional, Sens, Jonathon P., additional, Reddy, Joseph S., additional, Ridge, Perry G., additional, Kauwe, John S. K., additional, Belzil, Veronique, additional, Pregent, Luc, additional, Carrasquillo, Minerva M., additional, Keene, Dirk, additional, Larson, Eric, additional, Crane, Paul, additional, Asmann, Yan W., additional, Ertekin-Taner, Nilufer, additional, Younkin, Steven G., additional, Ross, Owen A., additional, Rademakers, Rosa, additional, Petrucelli, Leonard, additional, and Fryer, John D., additional
- Published
- 2019
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34. Systematic analysis of dark and camouflaged genes: disease-relevant genes hiding in plain sight
- Author
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Ebbert, Mark T. W., primary, Jensen, Tanner D., additional, Jansen-West, Karen, additional, Sens, Jonathon P., additional, Reddy, Joseph S., additional, Ridge, Perry G., additional, Kauwe, John S. K., additional, Belzil, Veronique, additional, Pregent, Luc, additional, Carrasquillo, Minerva M., additional, Keene, Dirk, additional, Larson, Eric, additional, Crane, Paul, additional, Asmann, Yan W., additional, Ertekin-Taner, Nilufer, additional, Younkin, Steven G., additional, Ross, Owen A., additional, Rademakers, Rosa, additional, Petrucelli, Leonard, additional, and Fryer, John D., additional
- Published
- 2019
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35. The Weight of Ignorance: Personal Finance Among College Students
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Jensen, Tanner
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College students ,Personal finance ,Investment management ,News, opinion and commentary ,Sports and fitness - Abstract
Byline: Tanner Jensen BVU students investigate personal finance and money management experiences among BVU college [...]
- Published
- 2019
36. Room for Growth: Space Concerns in the CAE
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Jensen, Tanner
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Company growth ,News, opinion and commentary ,Sports and fitness - Abstract
Byline: Tanner Jensen Donna Musel explains the culture of the Center for Academic Excellence and possible options for its growth in the coming [...]
- Published
- 2019
37. Journalistic Objectivity in the Era of Trump
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Jensen, Tanner
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Journalism -- Objectivity ,News, opinion and commentary ,Sports and fitness - Abstract
Byline: Tanner Jensen Journalism has long held the position of the watchdog of society: the educator of the public, the advocate for change, the critical analyst of government action. Their [...]
- Published
- 2018
38. Not an Absolute: Freedom of Speech on a Private Campus
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Jensen, Tanner
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Student rights ,Freedom of speech ,Public enterprises ,Freedom of expression ,Private schools ,Democracy ,News, opinion and commentary ,Sports and fitness - Abstract
Byline: Tanner JensenMany regard their first amendments rights as absolutes, fundamentally protecting their right to free expression. It's for this reason that many students of private schools are surprised to [...]
- Published
- 2018
39. Not an Absolute: Freedom of the Press on a Private Campus
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Jensen, Tanner
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Journalism ,Freedom of speech ,Freedom of the press ,Judgments (Law) ,Public enterprises ,Censorship ,Freedom of expression ,Litigation ,Private schools ,News, opinion and commentary ,Sports and fitness - Abstract
Byline: Tanner JensenThe rights guaranteed in the first amendment are often considered the most important in protecting the freedom of personal expression in the United States, a long history of [...]
- Published
- 2018
40. Near-fatal Legionella pneumoniain a neonate linked to home humidifier by metagenomic next generation sequencing
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West, Patrick T., Brooks, Erin F., Costales, Cristina, Moreno, Angel, Jensen, Tanner Dean, Budvytiene, Indre, Khan, Aslam, Pham, Trung H.M., Schwenk, Hayden T., Bhatt, Ami S., and Banaei, Niaz
- Published
- 2022
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41. The PepSeq Pipeline
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Jensen, Tanner D., primary, Bresciano, Kristi A., additional, Dallon, Emma, additional, Fujimoto, M. Stanley, additional, Lyman, Cole A., additional, Stewart, Enoch, additional, Griffitts, Joel, additional, and Clement, Mark J., additional
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- 2018
- Full Text
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42. Honors students present final projects
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Jensen, Tanner
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Students -- Appreciation ,News, opinion and commentary ,Sports and fitness - Abstract
Byline: Tanner Jensen Last Wednesday, April 25, the latest group of Honors students presented their research projects. After several semesters of designing, conducting, and reporting on a research project of [...]
- Published
- 2018
43. McFadden set to retire after more than two decades at BVU
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Jensen, Tanner
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News, opinion and commentary ,Sports and fitness - Abstract
Byline: Tanner Jensen After more than 20 years of teaching at Buena Vista University, Dr. James McFadden will be retiring at the end of the spring semester, citing health issues [...]
- Published
- 2018
44. High-coverage nanopore sequencing of samples from the 1000 Genomes Project to build a comprehensive catalog of human genetic variation.
- Author
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Gustafson JA, Gibson SB, Damaraju N, Zalusky MPG, Hoekzema K, Twesigomwe D, Yang L, Snead AA, Richmond PA, De Coster W, Olson ND, Guarracino A, Li Q, Miller AL, Goffena J, Anderson ZB, Storz SHR, Ward SA, Sinha M, Gonzaga-Jauregui C, Clarke WE, Basile AO, Corvelo A, Reeves C, Helland A, Musunuri RL, Revsine M, Patterson KE, Paschal CR, Zakarian C, Goodwin S, Jensen TD, Robb E, McCombie WR, Sedlazeck FJ, Zook JM, Montgomery SB, Garrison E, Kolmogorov M, Schatz MC, McLaughlin RN Jr, Dashnow H, Zody MC, Loose M, Jain M, Eichler EE, and Miller DE
- Abstract
Fewer than half of individuals with a suspected Mendelian or monogenic condition receive a precise molecular diagnosis after comprehensive clinical genetic testing. Improvements in data quality and costs have heightened interest in using long-read sequencing (LRS) to streamline clinical genomic testing, but the absence of control data sets for variant filtering and prioritization has made tertiary analysis of LRS data challenging. To address this, the 1000 Genomes Project (1KGP) Oxford Nanopore Technologies Sequencing Consortium aims to generate LRS data from at least 800 of the 1KGP samples. Our goal is to use LRS to identify a broader spectrum of variation so we may improve our understanding of normal patterns of human variation. Here, we present data from analysis of the first 100 samples, representing all 5 superpopulations and 19 subpopulations. These samples, sequenced to an average depth of coverage of 37× and sequence read N50 of 54 kbp, have high concordance with previous studies for identifying single nucleotide and indel variants outside of homopolymer regions. Using multiple structural variant (SV) callers, we identify an average of 24,543 high-confidence SVs per genome, including shared and private SVs likely to disrupt gene function as well as pathogenic expansions within disease-associated repeats that were not detected using short reads. Evaluation of methylation signatures revealed expected patterns at known imprinted loci, samples with skewed X-inactivation patterns, and novel differentially methylated regions. All raw sequencing data, processed data, and summary statistics are publicly available, providing a valuable resource for the clinical genetics community to discover pathogenic SVs., (© 2024 Gustafson et al.; Published by Cold Spring Harbor Laboratory Press.)
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- 2024
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45. Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease.
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Jensen TD, Ni B, Reuter CM, Gorzynski JE, Fazal S, Bonner D, Ungar RA, Goddard PC, Raja A, Ashley EA, Bernstein JA, Zuchner S, Greicius MD, Montgomery SB, Schatz MC, Wheeler MT, and Battle A
- Abstract
Rare structural variants (SVs) - insertions, deletions, and complex rearrangements - can cause Mendelian disease, yet they remain difficult to accurately detect and interpret. We sequenced and analyzed Oxford Nanopore long-read genomes of 68 individuals from the Undiagnosed Disease Network (UDN) with no previously identified diagnostic mutations from short-read sequencing. Using our optimized SV detection pipelines and 571 control long-read genomes, we detected 716 long-read rare (MAF < 0.01) SV alleles per genome on average, achieving a 2.4x increase from short-reads. To characterize the functional effects of rare SVs, we assessed their relationship with gene expression from blood or fibroblasts from the same individuals, and found that rare SVs overlapping enhancers were enriched (LOR = 0.46) near expression outliers. We also evaluated tandem repeat expansions (TREs) and found 14 rare TREs per genome; notably these TREs were also enriched near overexpression outliers. To prioritize candidate functional SVs, we developed Watershed-SV, a probabilistic model that integrates expression data with SV-specific genomic annotations, which significantly outperforms baseline models that don't incorporate expression data. Watershed-SV identified a median of eight high-confidence functional SVs per UDN genome. Notably, this included compound heterozygous deletions in FAM177A1 shared by two siblings, which were likely causal for a rare neurodevelopmental disorder. Our observations demonstrate the promise of integrating long-read sequencing with gene expression towards improving the prioritization of functional SVs and TREs in rare disease patients., Competing Interests: COMPETING INTEREST STATEMENT SBM is an advisor to BioMarin, Myome and Tenaya Therapeutics. AB is a co-founder of CellCipher, Inc, is a shareholder in Alphabet, Inc, and has consulted for Third Rock Ventures, LLC. EAA is the founder of Personalis, Deepcell, Svexa, RCD Co, Parameter Health, an advisor for SequenceBio, Foresite Labs, PacBio, a non-executive director at AstraZeneca, hold stocks in Oxford Nanopore, Pacific Biosciences, AstraZeneca, and offers collaborative support in kind to Illumina, Pacific Biosciences, Oxford Nanopore
- Published
- 2024
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46. Nanopore sequencing of 1000 Genomes Project samples to build a comprehensive catalog of human genetic variation.
- Author
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Gustafson JA, Gibson SB, Damaraju N, Zalusky MP, Hoekzema K, Twesigomwe D, Yang L, Snead AA, Richmond PA, De Coster W, Olson ND, Guarracino A, Li Q, Miller AL, Goffena J, Anderson Z, Storz SH, Ward SA, Sinha M, Gonzaga-Jauregui C, Clarke WE, Basile AO, Corvelo A, Reeves C, Helland A, Musunuri RL, Revsine M, Patterson KE, Paschal CR, Zakarian C, Goodwin S, Jensen TD, Robb E, McCombie WR, Sedlazeck FJ, Zook JM, Montgomery SB, Garrison E, Kolmogorov M, Schatz MC, McLaughlin RN Jr, Dashnow H, Zody MC, Loose M, Jain M, Eichler EE, and Miller DE
- Abstract
Less than half of individuals with a suspected Mendelian condition receive a precise molecular diagnosis after comprehensive clinical genetic testing. Improvements in data quality and costs have heightened interest in using long-read sequencing (LRS) to streamline clinical genomic testing, but the absence of control datasets for variant filtering and prioritization has made tertiary analysis of LRS data challenging. To address this, the 1000 Genomes Project ONT Sequencing Consortium aims to generate LRS data from at least 800 of the 1000 Genomes Project samples. Our goal is to use LRS to identify a broader spectrum of variation so we may improve our understanding of normal patterns of human variation. Here, we present data from analysis of the first 100 samples, representing all 5 superpopulations and 19 subpopulations. These samples, sequenced to an average depth of coverage of 37x and sequence read N50 of 54 kbp, have high concordance with previous studies for identifying single nucleotide and indel variants outside of homopolymer regions. Using multiple structural variant (SV) callers, we identify an average of 24,543 high-confidence SVs per genome, including shared and private SVs likely to disrupt gene function as well as pathogenic expansions within disease-associated repeats that were not detected using short reads. Evaluation of methylation signatures revealed expected patterns at known imprinted loci, samples with skewed X-inactivation patterns, and novel differentially methylated regions. All raw sequencing data, processed data, and summary statistics are publicly available, providing a valuable resource for the clinical genetics community to discover pathogenic SVs., Competing Interests: COMPETING INTEREST STATEMENT WDC, ML, FS, and DEM have received research support and/or consumables from ONT. WDC, JG, FS, and DEM have received travel funding to speak on behalf of ONT. DEM is on a scientific advisory board at ONT. FS has received research support from Illumina, Genetech, and PacBio. SBM is an advisor to BioMarin, MyOme, and Tenaya Therapeutics. EEE is a scientific advisory board (SAB) member of Variant Bio, Inc. DEM holds stock options in MyOme.
- Published
- 2024
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47. Impact of genome build on RNA-seq interpretation and diagnostics.
- Author
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Ungar RA, Goddard PC, Jensen TD, Degalez F, Smith KS, Jin CA, Bonner DE, Bernstein JA, Wheeler MT, and Montgomery SB
- Abstract
Transcriptomics is a powerful tool for unraveling the molecular effects of genetic variants and disease diagnosis. Prior studies have demonstrated that choice of genome build impacts variant interpretation and diagnostic yield for genomic analyses. To identify the extent genome build also impacts transcriptomics analyses, we studied the effect of the hg19, hg38, and CHM13 genome builds on expression quantification and outlier detection in 386 rare disease and familial control samples from both the Undiagnosed Diseases Network (UDN) and Genomics Research to Elucidate the Genetics of Rare Disease (GREGoR) Consortium. We identified 2,800 genes with build-dependent quantification across six routinely-collected biospecimens, including 1,391 protein-coding genes and 341 known rare disease genes. We further observed multiple genes that only have detectable expression in a subset of genome builds. Finally, we characterized how genome build impacts the detection of outlier transcriptomic events. Combined, we provide a database of genes impacted by build choice, and recommend that transcriptomics-guided analyses and diagnoses are cross-referenced with these data for robustness., Competing Interests: Declaration of interests During this project R.A.U. was employed for an internship by Vertex Pharmaceuticals. P.C.G. is a consultant for BioMarin. S.B.M. is an advisor to BioMarin, MyOme, and Tenaya Therapeutics.
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- 2024
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48. A 3'UTR Insertion Is a Candidate Causal Variant at the TMEM106B Locus Associated with Increased Risk for FTLD-TDP.
- Author
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Chemparathy A, Guen YL, Zeng Y, Gorzynski J, Jensen T, Yang C, Kasireddy N, Talozzi L, Belloy ME, Stewart I, Gitler AD, Wagner AD, Mormino E, Henderson VW, Wyss-Coray T, Ashley E, Cruchaga C, and Greicius MD
- Abstract
Background and Objectives: Single nucleotide variants near TMEM106B associate with risk of frontotemporal lobar dementia with TDP-43 inclusions (FTLD-TDP) and Alzheimer's disease (AD) in genome-wide association studies (GWAS), but the causal variant at this locus remains unclear. Here we asked whether a novel structural variant on TMEM106B is the causal variant., Methods: An exploratory analysis identified structural variants on neurodegeneration-related genes. Subsequent analyses focused on an Alu element insertion on the 3'UTR of TMEM106B . This study included data from longitudinal aging and neurogenerative disease cohorts at Stanford University, case-control cohorts in the Alzheimer's Disease Sequencing Project (ADSP), and expression and proteomics data from Washington University in St. Louis (WUSTL). 432 individuals from two Stanford aging cohorts were whole-genome long-read and short-read sequenced. 16,906 samples from ADSP were short-read sequenced. Genotypes, transcriptomics, and proteomics data were available in 1,979 participants from an aging and dementia cohort at WUSTL. Selection criteria were specific to each cohort. In primary analyses, the linkage disequilibrium between the TMEM106B locus variants in the FTLD-TDP GWAS and the 3'UTR insertion was estimated. We then estimated linkage by ancestry in the ADSP and evaluated the effect of the TMEM106B lead variant on mRNA and protein levels., Results: The primary analysis included 432 participants (52.5% females, age range 45-92 years old). We identified a 316 bp Alu insertion overlapping the TMEM106B 3'UTR tightly linked with top GWAS variants rs3173615(C) and rs1990622(A). In ADSP European-ancestry participants, this insertion is in equivalent linkage with rs1990622(A) (R
2 =0.962, D'=0.998) and rs3173615(C) (R2 =0.960, D'=0.996). In African-ancestry participants, the insertion is in stronger linkage with rs1990622(A) (R2 =0.992, D'=0.998) than with rs3173615(C) (R2 =0.811, D'=0.994). In public datasets, rs1990622 was consistently associated with TMEM106B protein levels but not with mRNA expression. In the WUSTL dataset, rs1990622 is associated with TMEM106B protein levels in plasma and cerebrospinal fluid, but not with TMEM106B mRNA expression., Discussion: We identified a novel Alu element insertion in the 3'UTR of TMEM106B in tight linkage with the lead FTLD-TDP risk variant. The lead variant is associated with TMEM106B protein levels, but not expression. The 3'UTR insertion is a lead candidate for the causal variant at this complex locus, pending confirmation with functional studies.- Published
- 2023
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