Review

. 2022 Apr;24(4):784-797.

doi: 10.1016/j.gim.2021.12.005. Epub 2022 Feb 9.

Centers for Mendelian Genomics: A decade of facilitating gene discovery

Samantha M Baxter¹, Jennifer E Posey², Nicole J Lake³, Nara Sobreira⁴, Jessica X Chong⁵, Steven Buyske⁶, Elizabeth E Blue⁷, Lisa H Chadwick⁸, Zeynep H Coban-Akdemir⁹, Kimberly F Doheny⁴, Colleen P Davis¹⁰, Monkol Lek¹¹, Christopher Wellington⁸, Shalini N Jhangiani¹², Mark Gerstein¹³, Richard A Gibbs¹⁴, Richard P Lifton¹⁵, Daniel G MacArthur¹⁶, Tara C Matise¹⁷, James R Lupski¹⁸, David Valle⁴, Michael J Bamshad¹⁹, Ada Hamosh⁴, Shrikant Mane²⁰, Deborah A Nickerson²¹; Centers for Mendelian Genomics Consortium; Heidi L Rehm²², Anne O'Donnell-Luria²³

Collaborators, Affiliations

Collaborators

Centers for Mendelian Genomics Consortium:
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, Igna van den Veyver

Affiliations

¹ Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA. Electronic address: samantha@broadinstitute.org.
² Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX.
³ Department of Genetics, Yale School of Medicine, New Haven, CT; Murdoch Children's Research Institute, Melbourne, Victoria, Australia.
⁴ McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD.
⁵ Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA; Brotman Baty Institute for Precision Medicine, Seattle, WA.
⁶ Department of Statistics, Rutgers University, Piscataway, NJ; Department of Genetics, Rutgers University, Piscataway, NJ.
⁷ Brotman Baty Institute for Precision Medicine, Seattle, WA; Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA.
⁸ Division of Genome Sciences, National Human Genome Research Institute, Bethesda, MD.
⁹ Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX.
¹⁰ Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA.
¹¹ Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Department of Genetics, Yale School of Medicine, New Haven, CT.
¹² Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX.
¹³ Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT.
¹⁴ Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX.
¹⁵ Department of Genetics, Yale School of Medicine, New Haven, CT; Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY.
¹⁶ Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Centre for Population Genomics, Garvan Institute of Medical Research and UNSW Sydney, Sydney, New South Wales, Australia; Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.
¹⁷ Department of Genetics, Rutgers University, Piscataway, NJ.
¹⁸ Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX; Department of Pediatrics, Baylor College of Medicine, Houston, TX.
¹⁹ Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA; Brotman Baty Institute for Precision Medicine, Seattle, WA; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA.
²⁰ Department of Genetics, Yale School of Medicine, New Haven, CT.
²¹ Brotman Baty Institute for Precision Medicine, Seattle, WA; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA.
²² Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA. Electronic address: hrehm@broadinstitute.org.
²³ Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA; Department of Pediatrics, Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA. Electronic address: odonnell@broadinstitute.org.

PMID: 35148959
PMCID: PMC9119004
DOI: 10.1016/j.gim.2021.12.005

Review

Centers for Mendelian Genomics: A decade of facilitating gene discovery

Samantha M Baxter et al. Genet Med. 2022 Apr.

. 2022 Apr;24(4):784-797.

doi: 10.1016/j.gim.2021.12.005. Epub 2022 Feb 9.

Authors

Collaborators

Centers for Mendelian Genomics Consortium:
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, Igna van den Veyver

Affiliations

¹ Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA. Electronic address: samantha@broadinstitute.org.
² Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX.
³ Department of Genetics, Yale School of Medicine, New Haven, CT; Murdoch Children's Research Institute, Melbourne, Victoria, Australia.
⁴ McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD.
⁵ Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA; Brotman Baty Institute for Precision Medicine, Seattle, WA.
⁶ Department of Statistics, Rutgers University, Piscataway, NJ; Department of Genetics, Rutgers University, Piscataway, NJ.
⁷ Brotman Baty Institute for Precision Medicine, Seattle, WA; Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA.
⁸ Division of Genome Sciences, National Human Genome Research Institute, Bethesda, MD.
⁹ Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX.
¹⁰ Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA.
¹¹ Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Department of Genetics, Yale School of Medicine, New Haven, CT.
¹² Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX.
¹³ Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT.
¹⁴ Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX.
¹⁵ Department of Genetics, Yale School of Medicine, New Haven, CT; Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY.
¹⁶ Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Centre for Population Genomics, Garvan Institute of Medical Research and UNSW Sydney, Sydney, New South Wales, Australia; Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.
¹⁷ Department of Genetics, Rutgers University, Piscataway, NJ.
¹⁸ Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX; Department of Pediatrics, Baylor College of Medicine, Houston, TX.
¹⁹ Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA; Brotman Baty Institute for Precision Medicine, Seattle, WA; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA.
²⁰ Department of Genetics, Yale School of Medicine, New Haven, CT.
²¹ Brotman Baty Institute for Precision Medicine, Seattle, WA; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA.
²² Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA. Electronic address: hrehm@broadinstitute.org.
²³ Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA; Department of Pediatrics, Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA. Electronic address: odonnell@broadinstitute.org.

PMID: 35148959
PMCID: PMC9119004
DOI: 10.1016/j.gim.2021.12.005

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.

Keywords: Centers for Mendelian Genomics (CMG); Data sharing; Mendelian conditions; Novel gene-disease discovery; Rare disease tools.

PubMed Disclaimer

Conflict of interest statement

Conflict of Interest Baylor College of Medicine and Miraca Holdings Inc have formed a joint venture with shared ownership and governance of Baylor Genetics, formerly the Baylor Miraca Genetics Laboratories, which performs clinical ES and chromosomal microarray analysis for genome-wide detection of copy number variants. J.R.L. serves on the Scientific Advisory Board of Baylor Genetics. J.R.L. has stock ownership in 23andMe, is a paid consultant for Regeneron Pharmaceuticals, and is a coinventor on multiple United States and European patents related to molecular diagnostics for inherited neuropathies, eye diseases, and bacterial genomic fingerprinting. H.L.R. receives funding from Illumina to support rare disease gene discovery and diagnosis. Consortium author conflicts of interest are listed in the Supplement. All other authors have no disclosures relevant to the manuscript.

Figures

**Figure 1. Overview of the Centers for Mendelian Genomics (CMGs) by numbers.**
(A) A high-level summary of activities performed by the CMGs, including the number of collaborators, number of kindreds, volume of testing performed, and discovery rates. (B) Map of CMG collaborators. Blue indicates that the CMGs collaborated with at least 1 researcher in that country (based on country listing in PubMed affiliations). (C) Data-sharing metrics for the CMGs.

**Figure 2. Solve and discovery rates by high-level Human Phenotype Ontology (HPO) category.**
Kindreds were categorized as having phenotypes in 1 HPO high-level system or multiple high-level systems. From there, the solve and discovery types were analyzed for each system. There were 494 kindreds in our Center for Mendelian Genomics (CMG) cohort with no HPO terms available, and therefore they were not able to be included in this analysis. Systems with fewer than 10 kindreds were noted but excluded.

See this image and copyright information in PMC

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Centers for Mendelian Genomics: A decade of facilitating gene discovery

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Centers for Mendelian Genomics: A decade of facilitating gene discovery

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