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2. Considerations for reporting variants in novel candidate genes identified during clinical genomic testing

Author

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. Variant interpretation using population databases: lessons from gnomAD

Author

Gudmundsson, Sanna, Singer-Berk, Moriel, Watts, Nicholas A., Phu, William, Goodrich, Julia K., Solomonson, Matthew, Consortium, Genome Aggregation Database, Rehm, Heidi L., MacArthur, Daniel G., and ODonnell-Luria, Anne

Subjects
Quantitative Biology - Genomics
Abstract

Reference population databases are an essential tool in variant and gene interpretation. Their use guides the identification of pathogenic variants amidst the sea of benign variation present in every human genome, and supports the discovery of new disease-gene relationships. The Genome Aggregation Database (gnomAD) is currently the largest and most widely used publicly available collection of population variation from harmonized sequencing data. The data is available through the online gnomAD browser (https://gnomad.broadinstitute.org/) that enables rapid and intuitive variant analysis. This review provides guidance on the content of the gnomAD browser, and its usage for variant and gene interpretation. We introduce key features including allele frequency, per-base expression levels, constraint scores, and variant co-occurrence, alongside guidance on how to use these in analysis, with a focus on the interpretation of candidate variants and novel genes in rare disease., Comment: Version 3: Includes updates to mirror the latest features and layouts available on the gnomAD browser and general improvements to text and figures (clarifications, typos, additional references etc.) as well as the addition of Table S1, S2, Figure S1, S2 and S5

Published
2021
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6. Beyond the exome: What’s next in diagnostic testing for Mendelian conditions

Author

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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10. P559: Improved classification framework demonstrates many population predicted loss of function (pLoF) variants in genomic sequencing do not result in LoF*

Author

Singer-Berk, Moriel, primary, Gudmundsson, Sanna, additional, Baxter, Samantha, additional, Seaby, Eleanor, additional, England, Eleina, additional, Wood, Jordan, additional, Son, Rachel, additional, Watts, Nicholas, additional, Karczewski, Konrad, additional, Harrison, Steven, additional, MacArthur, Daniel, additional, Rehm, Heidi, additional, and O'Donnell-Luria, Anne, additional

Published
2023
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12. Centers for Mendelian Genomics: A decade of facilitating gene discovery

Author

Baxter, Samantha M., primary, Posey, Jennifer E., additional, Lake, Nicole J., additional, Sobreira, Nara, additional, Chong, Jessica X., additional, Buyske, Steven, additional, Blue, Elizabeth E., additional, Chadwick, Lisa H., additional, Coban-Akdemir, Zeynep H., additional, Doheny, Kimberly F., additional, Davis, Colleen P., additional, Lek, Monkol, additional, Wellington, Christopher, additional, Jhangiani, Shalini N., additional, Gerstein, Mark, additional, Gibbs, Richard A., additional, Lifton, Richard P., additional, MacArthur, Daniel G., additional, Matise, Tara C., additional, Lupski, James R., additional, Valle, David, additional, Bamshad, Michael J., additional, Hamosh, Ada, additional, Mane, Shrikant, additional, Nickerson, Deborah A., additional, Rehm, Heidi L., additional, O’Donnell-Luria, Anne, additional, Adams, Marcia, additional, Aguet, François, additional, Akay, Gulsen, additional, Anderson, Peter, additional, Antonescu, Corina, additional, Arachchi, Harindra M., additional, Atik, Mehmed M., additional, Austin-Tse, Christina A., additional, Babb, Larry, additional, Bacus, Tamara J., additional, Bahrambeigi, Vahid, additional, Balasubramanian, Suganthi, additional, Bayram, Yavuz, additional, Beaudet, Arthur L., additional, Beck, Christine R., additional, Belmont, John W., additional, Below, Jennifer E., additional, Bilguvar, Kaya, additional, Boehm, Corinne D., additional, Boerwinkle, Eric, additional, Boone, Philip M., additional, Bowne, Sara J., additional, Brand, Harrison, additional, Buckingham, Kati J., additional, Byrne, Alicia B., additional, Calame, Daniel, additional, Campbell, Ian M., additional, Cao, Xiaolong, additional, Carvalho, Claudia, additional, Chander, Varuna, additional, Chang, Jaime, additional, Chao, Katherine R., additional, Chinn, Ivan K., additional, Clarke, Declan, additional, Collins, Ryan L., additional, Cummings, Beryl, additional, Dardas, Zain, additional, Dawood, Moez, additional, Delano, Kayla, additional, DiTroia, Stephanie P., additional, Doddapaneni, Harshavardhan, additional, Du, Haowei, additional, Du, Renqian, additional, Duan, Ruizhi, additional, Eldomery, Mohammad, additional, Eng, Christine M., additional, England, Eleina, additional, Evangelista, Emily, additional, Everett, Selin, additional, Fatih, Jawid, additional, Felsenfeld, Adam, additional, Francioli, Laurent C., additional, Frazar, Christian D., additional, Fu, Jack, additional, Gamarra, Emmanuel, additional, Gambin, Tomasz, additional, Gan, Weiniu, additional, Gandhi, Mira, additional, Ganesh, Vijay S., additional, Garimella, Kiran V., additional, Gauthier, Laura D., additional, Giroux, Danielle, additional, Gonzaga-Jauregui, Claudia, additional, Goodrich, Julia K., additional, Gordon, William W., additional, Griffith, Sean, additional, Grochowski, Christopher M., additional, Gu, Shen, additional, Gudmundsson, Sanna, additional, Hall, Stacey J., additional, Hansen, Adam, additional, Harel, Tamar, additional, Harmanci, Arif O., additional, Herman, Isabella, additional, Hetrick, Kurt, additional, Hijazi, Hadia, additional, Horike-Pyne, Martha, additional, Hsu, Elvin, additional, Hu, Jianhong, additional, Huang, Yongqing, additional, Hurless, Jameson R., additional, Jahl, Steve, additional, Jarvik, Gail P., additional, Jiang, Yunyun, additional, Johanson, Eric, additional, Jolly, Angad, additional, Karaca, Ender, additional, Khayat, Michael, additional, Knight, James, additional, Kolar, J. Thomas, additional, Kumar, Sushant, additional, Lalani, Seema, additional, Laricchia, Kristen M., additional, Larkin, Kathryn E., additional, Leal, Suzanne M., additional, Lemire, Gabrielle, additional, Lewis, Richard A., additional, Li, He, additional, Ling, Hua, additional, Lipson, Rachel B., additional, Liu, Pengfei, additional, Lovgren, Alysia Kern, additional, López-Giráldez, Francesc, additional, MacMillan, Melissa P., additional, Mangilog, Brian E., additional, Mano, Stacy, additional, Marafi, Dana, additional, Marosy, Beth, additional, Marshall, Jamie L., additional, Martin, Renan, additional, Marvin, Colby T., additional, Mawhinney, Michelle, additional, McGee, Sean, additional, McGoldrick, Daniel J., additional, Mehaffey, Michelle, additional, Mekonnen, Betselote, additional, Meng, Xiaolu, additional, Mitani, Tadahiro, additional, Miyake, Christina Y., additional, Mohr, David, additional, Morris, Shaine, additional, Mullen, Thomas E., additional, Murdock, David R., additional, Murugan, Mullai, additional, Muzny, Donna M., additional, Myers, Ben, additional, Neira, Juanita, additional, Nguyen, Kevin K., additional, Nielsen, Patrick M., additional, Nudelman, Natalie, additional, O’Heir, Emily, additional, O’Leary, Melanie C., additional, Ongaco, Chrissie, additional, Orange, Jordan, additional, Osei-Owusu, Ikeoluwa A., additional, Paine, Ingrid S., additional, Pais, Lynn S., additional, Paschall, Justin, additional, Patterson, Karynne, additional, Pehlivan, Davut, additional, Pelle, Benjamin, additional, Penney, Samantha, additional, Perez de Acha Chavez, Jorge, additional, Pierce-Hoffman, Emma, additional, Poli, Cecilia M., additional, Punetha, Jaya, additional, Radhakrishnan, Aparna, additional, Richardson, Matthew A., additional, Rodrigues, Eliete, additional, Roote, Gwendolin T., additional, Rosenfeld, Jill A., additional, Ryke, Erica L., additional, Sabo, Aniko, additional, Sanchez, Alice, additional, Schrauwen, Isabelle, additional, Scott, Daryl A., additional, Sedlazeck, Fritz, additional, Serrano, Jillian, additional, Shaw, Chad A., additional, Shelford, Tameka, additional, Shively, Kathryn M., additional, Singer-Berk, Moriel, additional, Smith, Joshua D., additional, Snow, Hana, additional, Snyder, Grace, additional, Solomonson, Matthew, additional, Son, Rachel G., additional, Song, Xiaofei, additional, Stankiewicz, Pawel, additional, Stephan, Taylorlyn, additional, Sutton, V. Reid, additional, Sveden, Abigail, additional, Sánchez, Diana Cornejo, additional, Tackett, Monica, additional, Talkowski, Michael, additional, Threlkeld, Machiko S., additional, Tiao, Grace, additional, Udler, Miriam S., additional, Vail, Laura, additional, Valivullah, Zaheer, additional, Valkanas, Elise, additional, VanNoy, Grace E., additional, Wang, Qingbo S., additional, Wang, Gao, additional, Wang, Lu, additional, Wangler, Michael F., additional, Watts, Nicholas A., additional, Weisburd, Ben, additional, Weiss, Jeffrey M., additional, Wheeler, Marsha M., additional, White, Janson J., additional, Williamson, Clara E., additional, Wilson, Michael W., additional, Wiszniewski, Wojciech, additional, Withers, Marjorie A., additional, Witmer, Dane, additional, Witzgall, Lauren, additional, Wohler, Elizabeth, additional, Wojcik, Monica H., additional, Wong, Isaac, additional, Wood, Jordan C., additional, Wu, Nan, additional, Xing, Jinchuan, additional, Yang, Yaping, additional, Yi, Qian, additional, Yuan, Bo, additional, Zeiger, Jordan E., additional, Zhang, Chaofan, additional, Zhang, Peng, additional, Zhang, Yan, additional, Zhang, Xiaohong, additional, Zhang, Yeting, additional, Zhang, Shifa, additional, Zoghbi, Huda, additional, and van den Veyver, Igna, additional

Published
2022
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14. A form of muscular dystrophy associated with pathogenic variants in JAG2

Author

Coppens, Sandra, primary, Barnard, Alison M., additional, Puusepp, Sanna, additional, Pajusalu, Sander, additional, Õunap, Katrin, additional, Vargas-Franco, Dorianmarie, additional, Bruels, Christine C., additional, Donkervoort, Sandra, additional, Pais, Lynn, additional, Chao, Katherine R., additional, Goodrich, Julia K., additional, England, Eleina M., additional, Weisburd, Ben, additional, Ganesh, Vijay S., additional, Gudmundsson, Sanna, additional, O’Donnell-Luria, Anne, additional, Nigul, Mait, additional, Ilves, Pilvi, additional, Mohassel, Payam, additional, Siddique, Teepu, additional, Milone, Margherita, additional, Nicolau, Stefan, additional, Maroofian, Reza, additional, Houlden, Henry, additional, Hanna, Michael G., additional, Quinlivan, Ros, additional, Toosi, Mehran Beiraghi, additional, Karimiani, Ehsan Ghayoor, additional, Costagliola, Sabine, additional, Deconinck, Nicolas, additional, Kadhim, Hazim, additional, Macke, Erica, additional, Lanpher, Brendan C., additional, Klee, Eric W., additional, Łusakowska, Anna, additional, Kostera-Pruszczyk, Anna, additional, Hahn, Andreas, additional, Schrank, Bertold, additional, Nishino, Ichizo, additional, Ogasawara, Masashi, additional, El Sherif, Rasha, additional, Stojkovic, Tanya, additional, Nelson, Isabelle, additional, Bonne, Gisèle, additional, Cohen, Enzo, additional, Boland-Augé, Anne, additional, Deleuze, Jean-François, additional, Meng, Yao, additional, Töpf, Ana, additional, Vilain, Catheline, additional, Pacak, Christina A., additional, Rivera-Zengotita, Marie L., additional, Bönnemann, Carsten G., additional, Straub, Volker, additional, Handford, Penny A., additional, Draper, Isabelle, additional, Walter, Glenn A., additional, and Kang, Peter B., additional

Published
2021
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16. Delineation of phenotypes and genotypes related to cohesin structural protein RAD21

Author

Krab, Lianne C., primary, Marcos-Alcalde, Iñigo, additional, Assaf, Melissa, additional, Balasubramanian, Meena, additional, Andersen, Janne Bayer, additional, Bisgaard, Anne-Marie, additional, Fitzpatrick, David R., additional, Gudmundsson, Sanna, additional, Huisman, Sylvia A., additional, Kalayci, Tugba, additional, Maas, Saskia M., additional, Martinez, Francisco, additional, McKee, Shane, additional, Menke, Leonie A., additional, Mulder, Paul A., additional, Murch, Oliver D., additional, Parker, Michael, additional, Pie, Juan, additional, Ramos, Feliciano J., additional, Rieubland, Claudine, additional, Rosenfeld Mokry, Jill A., additional, Scarano, Emanuela, additional, Shinawi, Marwan, additional, Gómez-Puertas, Paulino, additional, Tümer, Zeynep, additional, and Hennekam, Raoul C., additional

Published
2020
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17. Translational Research of Mendelian Disorders : Applications of Cutting-Edge Sequencing Techniques and Molecular Tools

Author

Gudmundsson, Sanna

Subjects
Mendelian disorders, translational research, intellectual disability, sequencing technologies, Genetics, Genetik
Abstract

Up to 8% of all live-born children are affected with a congenital disorder. Some are Mendelian disorders of known etiology, but many are of undetermined genetic cause and mechanism, limiting diagnosis and treatment. This project aims to investigate the underlying causes of unresolved Mendelian disorders, and especially syndromes associated with intellectual disability, by using cutting-edge sequencing techniques and molecular tools in a translational setting that intends to directly benefit affected families. In Paper I, we report the first keratitis-ichthyosis-deafness syndrome patient presenting with reversion of disease phenotype, a phenomenon known as revertant mosaicism. Third-generation sequencing and a cell assay were used to pin-point the mechanism of the somatic variants giving rise to healthy looking skin in the patient. In Paper II, we describe a novel approach to investigate parental origin, gonadal mosaicism, and estimate recurrence risk of disease in two families. Third-generation sequencing was used for haplotype phasing and detection of low-frequency variants in paternal sperm. The recurrence risk in future offspring in the families affected with Noonan syndrome and Treacher Collins syndrome was determined to be 40% and

Published
2019

18. Additional file 1: of Targeted high-throughput sequencing of candidate genes for chronic obstructive pulmonary disease

Author

Matsson, Hans, Söderhäll, Cilla, Einarsdottir, Elisabet, Lamontagne, Maxime, Gudmundsson, Sanna, Backman, Helena, Lindberg, Anne, Rönmark, Eva, Kere, Juha, Sin, Don, Postma, Dirkje, Yohan Bossé, Lundbäck, Bo, and Klar, Joakim

Abstract

Supplementary methods. Detailed methods description regarding classification of COPD, sequencing protocol and linkage disequilibrium analysis. (DOCX 123 kb)

Published
2016
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19. Additional file 2: of Targeted high-throughput sequencing of candidate genes for chronic obstructive pulmonary disease

Author

Matsson, Hans, Söderhäll, Cilla, Einarsdottir, Elisabet, Lamontagne, Maxime, Gudmundsson, Sanna, Backman, Helena, Lindberg, Anne, Rönmark, Eva, Kere, Juha, Sin, Don, Postma, Dirkje, Yohan Bossé, Lundbäck, Bo, and Klar, Joakim

Abstract

Targeted genes and variants for targeted high throughput sequencing. The table lists the selected genes and variants included in the study. (DOCX 79 kb)

Published
2016
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20. Additional file 7 of Targeted high-throughput sequencing of candidate genes for chronic obstructive pulmonary disease

Author

Matsson, Hans, Söderhäll, Cilla, Einarsdottir, Elisabet, Lamontagne, Maxime, Gudmundsson, Sanna, Backman, Helena, Lindberg, Anne, Rönmark, Eva, Kere, Juha, Sin, Don, Postma, Dirkje, Yohan Bossé, Lundbäck, Bo, and Klar, Joakim

Subjects
fungi, respiratory system, human activities, respiratory tract diseases
Abstract

Probe sets replicated in both replication sets (UBC and Groningen) in the lung eQTL analyses. A table of replicated probe sets in the lung eQTL analysis. (DOCX 38 kb)

Published
2016
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21. Additional file 5: of Targeted high-throughput sequencing of candidate genes for chronic obstructive pulmonary disease

Author

Matsson, Hans, Söderhäll, Cilla, Einarsdottir, Elisabet, Lamontagne, Maxime, Gudmundsson, Sanna, Backman, Helena, Lindberg, Anne, Rönmark, Eva, Kere, Juha, Sin, Don, Postma, Dirkje, Yohan Bossé, Lundbäck, Bo, and Klar, Joakim

Subjects
humanities
Abstract

Pairwise linkage disequilibrium (LD) of associated variants. A list of detected genetic variants found to be in LD. (DOCX 46 kb)

Published
2016
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22. Additional file 6 of Targeted high-throughput sequencing of candidate genes for chronic obstructive pulmonary disease

Author

Matsson, Hans, Söderhäll, Cilla, Einarsdottir, Elisabet, Lamontagne, Maxime, Gudmundsson, Sanna, Backman, Helena, Lindberg, Anne, Rönmark, Eva, Kere, Juha, Sin, Don, Postma, Dirkje, Yohan Bossé, Lundbäck, Bo, and Klar, Joakim

Subjects
fungi, mental disorders
Abstract

A plot containing genomic positions and p-values of variants in the CHRNA3/CHRNA5 gene locus with rs8040869 and rs16969968 highlighted. (PDF 144 kb)

Published
2016
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23. Additional file 4: of Targeted high-throughput sequencing of candidate genes for chronic obstructive pulmonary disease

Author

Matsson, Hans, Söderhäll, Cilla, Einarsdottir, Elisabet, Lamontagne, Maxime, Gudmundsson, Sanna, Backman, Helena, Lindberg, Anne, Rönmark, Eva, Kere, Juha, Sin, Don, Postma, Dirkje, Yohan Bossé, Lundbäck, Bo, and Klar, Joakim

Abstract

Gene burden analysis of common variants. The table present the SKAT analysis of gene burden of common variants. (DOCX 86 kb)

Published
2016
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24. Additional file 3: of Targeted high-throughput sequencing of candidate genes for chronic obstructive pulmonary disease

Author

Matsson, Hans, Söderhäll, Cilla, Einarsdottir, Elisabet, Lamontagne, Maxime, Gudmundsson, Sanna, Backman, Helena, Lindberg, Anne, Rönmark, Eva, Kere, Juha, Sin, Don, Postma, Dirkje, Yohan Bossé, Lundbäck, Bo, and Klar, Joakim

Abstract

Number of rare variants found uniquely in cases and controls. The table present data of the UNIQ test of rare variants in cases versus controls. (DOCX 78 kb)

Published
2016
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25. Targeted high-throughput sequencing of candidate genes for chronic obstructive pulmonary disease

Author

Matsson, Hans, primary, Söderhäll, Cilla, additional, Einarsdottir, Elisabet, additional, Lamontagne, Maxime, additional, Gudmundsson, Sanna, additional, Backman, Helena, additional, Lindberg, Anne, additional, Rönmark, Eva, additional, Kere, Juha, additional, Sin, Don, additional, Postma, Dirkje S., additional, Bossé, Yohan, additional, Lundbäck, Bo, additional, and Klar, Joakim, additional

Published
2016
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26. Addendum: The mutational constraint spectrum quantified from variation in 141,456 humans.

Author

Gudmundsson, Sanna, Karczewski, Konrad J., Francioli, Laurent C., Tiao, Grace, Cummings, Beryl B., Alföldi, Jessica, Wang, Qingbo, Collins, Ryan L., Laricchia, Kristen M., Ganna, Andrea, Birnbaum, Daniel P., Gauthier, Laura D., Brand, Harrison, Solomonson, Matthew, Watts, Nicholas A., Rhodes, Daniel, Singer-Berk, Moriel, England, Eleina M., Seaby, Eleanor G., and Kosmicki, Jack A.

Published
2021
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27. Exploring penetrance of clinically relevant variants in over 800,000 humans from the Genome Aggregation Database.

Author

Gudmundsson S, Singer-Berk M, Stenton SL, Goodrich JK, Wilson MW, Einson J, Watts NA, Lappalainen T, Rehm HL, MacArthur DG, and O'Donnell-Luria A

Abstract

Incomplete penetrance, or absence of disease phenotype in an individual with a disease-associated variant, is a major challenge in variant interpretation. Studying individuals with apparent incomplete penetrance can shed light on underlying drivers of altered phenotype penetrance. Here, we investigate clinically relevant variants from ClinVar in 807,162 individuals from the Genome Aggregation Database (gnomAD), demonstrating improved representation in gnomAD version 4. We then conduct a comprehensive case-by-case assessment of 734 predicted loss of function variants (pLoF) in 77 genes associated with severe, early-onset, highly penetrant haploinsufficient disease. We identified explanations for the presumed lack of disease manifestation in 701 of the variants (95%). Individuals with unexplained lack of disease manifestation in this set of disorders rarely occur, underscoring the need and power of deep case-by-case assessment presented here to minimize false assignments of disease risk, particularly in unaffected individuals with higher rates of secondary properties that result in rescue., Competing Interests: COMPETING INTERESTS A.O-D.L. is on the scientific advisory board for Congenica, receives research funding in the form of reagents from Pacific Biosciences, and is a paid advisor to Addition Therapeutics and former advisor to Tome Biosciences and Ono Pharma USA. D.G.M. is a paid adviser to GlaxoSmithKline, Insitro, and Overtone Therapeutics, and receives research funding from Microsoft Corporation. H.L.R. receives research funding from Microsoft. T.L. is an advisor and has equity in Variant Bio.

Published
2024
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