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2. Centers for Mendelian Genomics: A decade of facilitating gene discovery

Author

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

Subjects
Phenotype, Exome Sequencing, Humans, Exome, Genomics, Article, Genetic Association Studies, Genetics (clinical)
Abstract

PURPOSE: Mendelian disease genomic research has undergone a massive transformation over the past decade. With increasing availability of exome and genome sequencing, the role of Mendelian research has expanded beyond data collection, sequencing, and analysis to worldwide data sharing and collaboration. METHODS: Over the past 10 years, the National Institutes of Health–supported Centers for Mendelian Genomics (CMGs) have played a major role in this research and clinical evolution. RESULTS: We highlight the cumulative gene discoveries facilitated by the program, biomedical research leveraged by the approach, and the larger impact on the research community. Beyond generating a list of gene-phenotype relationships and participating in widespread data sharing, the CMGs have created resources, tools, and training for the larger community to foster understanding of genes and genome variation. The CMGs have participated in a wide range of data sharing activities, including deposition of all eligible CMG data into the Analysis, Visualization, and Informatics Lab-space (AnVIL), sharing candidate genes through the Matchmaker Exchange and the CMG website, and sharing variants in Genotypes to Mendelian Phenotypes (Geno2MP) and VariantMatcher. CONCLUSION: The work is far from complete; strengthening communication between research and clinical realms, continued development and sharing of knowledge and tools, and improving access to richly characterized data sets are all required to diagnose the remaining molecularly undiagnosed patients.

Published
2022

3. Comprehensive Structural Variant Detection: From Mosaic to Population-Level

Author

Moritz Smolka, Luis F. Paulin, Christopher M. Grochowski, Medhat Mahmoud, Sairam Behera, Mira Gandhi, Karl Hong, Davut Pehlivan, Sonja W. Scholz, Claudia M.B. Carvalho, Christos Proukakis, and Fritz J Sedlazeck

Abstract

Long-read Structural Variation (SV) calling remains a challenging but highly accurate way to identify complex genomic rearrangements. Here, we present Sniffles2, which is faster and more accurate than state-of-the-art SV caller across different coverages, sequencing technologies, and SV types. Furthermore, Sniffles2 solves the problem of family to population-level SV calling to produce fully genotyped VCF files by introducing a gVCF file concept. Across 31 Mendelian samples, we accurately identified causative SVs around MECP2, including highly complex alleles with three overlapping SVs. Sniffles2 also enables the detection of mosaic SVs in bulk long-read data. This way, we were able to identify multiple mosaic SVs across a multiple system atrophy patient brain. The identified SV showed a remarkable diversity within the cingulate cortex, impacting both genes involved in neuron function and repetitive elements. In summary, we demonstrate the utility and versatility of Sniffles2 to identify SVs from the mosaic to population levels.

Published
2022

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