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1. Phenotypic and mutational spectrum of ROR2‐related Robinow syndrome

Author

Lima, Ariadne R, Ferreira, Barbara M, Zhang, Chaofan, Jolly, Angad, Du, Haowei, White, Janson J, Dawood, Moez, Lins, Tulio C, Chiabai, Marcela A, Beusekom, Ellen, Cordoba, Mara S, Rosa, Erica CC Caldas, Kayserili, Hulya, Kimonis, Virginia, Wu, Erica, Mellado, Cecilia, Aggarwal, Vineet, Richieri‐Costa, Antonio, Brunoni, Décio, Canó, Talyta M, Jorge, Alexander AL, Kim, Chong A, Honjo, Rachel, Bertola, Débora R, Dandalo‐Girardi, Raissa M, Bayram, Yavuz, Gezdirici, Alper, Yilmaz‐Gulec, Elif, Gumus, Evren, Yilmaz, Gülay C, Okamoto, Nobuhiko, Ohashi, Hirofumi, Coban–Akdemir, Zeynep, Mitani, Tadahiro, Jhangiani, Shalini N, Muzny, Donna M, Regattieri, Neysa AP, Pogue, Robert, Pereira, Rinaldo W, Otto, Paulo A, Gibbs, Richard A, Ali, Bassam R, Bokhoven, Hans, Brunner, Han G, Sutton, V Reid, Lupski, James R, Vianna‐Morgante, Angela M, Carvalho, Claudia MB, and Mazzeu, Juliana F

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Genetics, Clinical Research, Pediatric, Congenital Structural Anomalies, Aetiology, 2.1 Biological and endogenous factors, Craniofacial Abnormalities, Dwarfism, Genes, Recessive, Humans, Limb Deformities, Congenital, Male, Phenotype, Receptor Tyrosine Kinase-like Orphan Receptors, Urogenital Abnormalities, chromosome microarray analysis, craniofacial morphology, exonic deletion, HPO terms, next-generation sequencing, quantitative phenotyping cluster heatmap, skeletal dysplasia, WNT pathway, Clinical Sciences, Genetics & Heredity, Clinical sciences
Abstract

Robinow syndrome is characterized by a triad of craniofacial dysmorphisms, disproportionate-limb short stature, and genital hypoplasia. A significant degree of phenotypic variability seems to correlate with different genes/loci. Disturbances of the noncanonical WNT-pathway have been identified as the main cause of the syndrome. Biallelic variants in ROR2 cause an autosomal recessive form of the syndrome with distinctive skeletal findings. Twenty-two patients with a clinical diagnosis of autosomal recessive Robinow syndrome were screened for variants in ROR2 using multiple molecular approaches. We identified 25 putatively pathogenic ROR2 variants, 16 novel, including single nucleotide variants and exonic deletions. Detailed phenotypic analyses revealed that all subjects presented with a prominent forehead, hypertelorism, short nose, abnormality of the nasal tip, brachydactyly, mesomelic limb shortening, short stature, and genital hypoplasia in male patients. A total of 19 clinical features were present in more than 75% of the subjects, thus pointing to an overall uniformity of the phenotype. Disease-causing variants in ROR2, contribute to a clinically recognizable autosomal recessive trait phenotype with multiple skeletal defects. A comprehensive quantitative clinical evaluation of this cohort delineated the phenotypic spectrum of ROR2-related Robinow syndrome. The identification of exonic deletion variant alleles further supports the contention of a loss-of-function mechanism in the etiology of the syndrome.

Published
2022

2. Rare variants in CAPN2 increase risk for isolated hypoplastic left heart syndrome

Author

Blue, Elizabeth E., White, Janson J., Dush, Michael K., Gordon, William W., Wyatt, Brent H., White, Peter, Marvin, Colby T., Helle, Emmi, Ojala, Tiina, Priest, James R., Jenkins, Mary M., Almli, Lynn M., Reefhuis, Jennita, Pangilinan, Faith, Brody, Lawrence C., McBride, Kim L., Garg, Vidu, Shaw, Gary M., Romitti, Paul A., Nembhard, Wendy N., Browne, Marilyn L., Werler, Martha M., Kay, Denise M., Mital, Seema, Chong, Jessica X., Nascone-Yoder, Nanette M., and Bamshad, Michael J.

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

Author

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

Published
2022
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4. Exome sequencing identifies novel genes underlying primary congenital glaucoma in the National Birth Defects Prevention Study.

Author

Blue, Elizabeth E., Moore, Kristin J., North, Kari E., Desrosiers, Tania A., Carmichael, Suzan L., White, Janson J., Chong, Jessica X., Bamshad, Michael J., Jenkins, Mary M., Almli, Lynn M., Brody, Lawrence C., Freedman, Sharon F., Reefhuis, Jennita, Romitti, Paul A., Shaw, Gary M., Werler, Martha, Kay, Denise M., Browne, Marilyn L., Feldkamp, Marcia L., and Finnell, Richard H.

Abstract

Background: Primary congenital glaucoma (PCG) affects approximately 1 in 10,000 live born infants in the United States (U.S.). PCG has a autosomal recessive inheritance pattern, and variable expressivity and reduced penetrance have been reported. Likely causal variants in the most commonly mutated gene, CYP1B1, are less prevalent in the U.S., suggesting that alternative genes may contribute to the condition. This study utilized exome sequencing to investigate the genetic architecture of PCG in the U.S. and to identify novel genes and variants. Methods: We studied 37 family trios where infants had PCG and were part of the National Birth Defects Prevention Study (births 1997–2011), a U.S. multicenter study of birth defects. Samples underwent exome sequencing and sequence reads were aligned to the human reference sample (NCBI build 37/hg19). Variant filtration was conducted under de novo and Mendelian inheritance models using GEMINI. Results: Among candidate variants, CYP1B1 was most represented (five trios, 13.5%). Twelve probands (32%) had potentially pathogenic variants in other genes not previously linked to PCG but important in eye development and/or to underlie Mendelian conditions with potential phenotypic overlap (e.g., CRYBB2, RXRA, GLI2). Conclusion: Variation in the genes identified in this population‐based study may help to further explain the genetics of PCG. [ABSTRACT FROM AUTHOR]

Published
2024
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5. DVL3 Alleles Resulting in a −1 Frameshift of the Last Exon Mediate Autosomal-Dominant Robinow Syndrome

Author

White, Janson J, Mazzeu, Juliana F, Hoischen, Alexander, Bayram, Yavuz, Withers, Marjorie, Gezdirici, Alper, Kimonis, Virginia, Steehouwer, Marloes, Jhangiani, Shalini N, Muzny, Donna M, Gibbs, Richard A, Genomics, Baylor-Hopkins Center for Mendelian, van Bon, Bregje WM, Sutton, V Reid, Lupski, James R, Brunner, Han G, and Carvalho, Claudia MB

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Genetics, Rare Diseases, Congenital Structural Anomalies, Clinical Research, Pediatric, 2.1 Biological and endogenous factors, Aetiology, Congenital, Adaptor Proteins, Signal Transducing, Alleles, Base Sequence, Codon, Nonsense, Craniofacial Abnormalities, Dishevelled Proteins, Dwarfism, Exons, Female, Frameshift Mutation, Genetic Variation, Humans, Limb Deformities, Congenital, Male, Molecular Sequence Data, Phosphoproteins, Proto-Oncogene Proteins, Receptor Tyrosine Kinase-like Orphan Receptors, Sequence Analysis, DNA, Sequence Deletion, Urogenital Abnormalities, Wnt Proteins, Wnt-5a Protein, Baylor-Hopkins Center for Mendelian Genomics, Medical and Health Sciences, Genetics & Heredity, Biological sciences, Biomedical and clinical sciences, Health sciences
Abstract

Robinow syndrome is a rare congenital disorder characterized by mesomelic limb shortening, genital hypoplasia, and distinctive facial features. Recent reports have identified, in individuals with dominant Robinow syndrome, a specific type of variant characterized by being uniformly located in the penultimate exon of DVL1 and resulting in a -1 frameshift allele with a premature termination codon that escapes nonsense-mediated decay. Here, we studied a cohort of individuals who had been clinically diagnosed with Robinow syndrome but who had not received a molecular diagnosis from variant studies of DVL1, WNT5A, and ROR2. Because of the uniform location of frameshift variants in DVL1-mediated Robinow syndrome and the functional redundancy of DVL1, DVL2, and DVL3, we elected to pursue direct Sanger sequencing of the penultimate exon of DVL1 and its paralogs DVL2 and DVL3 to search for potential disease-associated variants. Remarkably, targeted sequencing identified five unrelated individuals harboring heterozygous, de novo frameshift variants in DVL3, including two splice acceptor mutations and three 1 bp deletions. Similar to the variants observed in DVL1-mediated Robinow syndrome, all variants in DVL3 result in a -1 frameshift, indicating that these highly specific alterations might be a common cause of dominant Robinow syndrome. Here, we review the current knowledge of these peculiar variant alleles in DVL1- and DVL3-mediated Robinow syndrome and further elucidate the phenotypic features present in subjects with DVL1 and DVL3 frameshift mutations.

Published
2016

6. DVL3 Alleles Resulting in a -1 Frameshift of the Last Exon Mediate Autosomal-Dominant Robinow Syndrome.

Author

White, Janson J, Mazzeu, Juliana F, Hoischen, Alexander, Bayram, Yavuz, Withers, Marjorie, Gezdirici, Alper, Kimonis, Virginia, Steehouwer, Marloes, Jhangiani, Shalini N, Muzny, Donna M, Gibbs, Richard A, Baylor-Hopkins Center for Mendelian Genomics, van Bon, Bregje WM, Sutton, V Reid, Lupski, James R, Brunner, Han G, and Carvalho, Claudia MB

Subjects
Baylor-Hopkins Center for Mendelian Genomics, Humans, Dwarfism, Craniofacial Abnormalities, Limb Deformities, Congenital, Urogenital Abnormalities, Adaptor Proteins, Signal Transducing, Proto-Oncogene Proteins, Phosphoproteins, Codon, Nonsense, Sequence Analysis, DNA, Sequence Deletion, Base Sequence, Frameshift Mutation, Alleles, Exons, Molecular Sequence Data, Female, Male, Wnt Proteins, Genetic Variation, Receptor Tyrosine Kinase-like Orphan Receptors, Wnt-5a Protein, Dishevelled Proteins, Rare Diseases, Congenital Structural Anomalies, Clinical Research, Pediatric, Genetics, 2.1 Biological and endogenous factors, Aetiology, Congenital, Biological Sciences, Medical and Health Sciences, Genetics & Heredity
Abstract

Robinow syndrome is a rare congenital disorder characterized by mesomelic limb shortening, genital hypoplasia, and distinctive facial features. Recent reports have identified, in individuals with dominant Robinow syndrome, a specific type of variant characterized by being uniformly located in the penultimate exon of DVL1 and resulting in a -1 frameshift allele with a premature termination codon that escapes nonsense-mediated decay. Here, we studied a cohort of individuals who had been clinically diagnosed with Robinow syndrome but who had not received a molecular diagnosis from variant studies of DVL1, WNT5A, and ROR2. Because of the uniform location of frameshift variants in DVL1-mediated Robinow syndrome and the functional redundancy of DVL1, DVL2, and DVL3, we elected to pursue direct Sanger sequencing of the penultimate exon of DVL1 and its paralogs DVL2 and DVL3 to search for potential disease-associated variants. Remarkably, targeted sequencing identified five unrelated individuals harboring heterozygous, de novo frameshift variants in DVL3, including two splice acceptor mutations and three 1 bp deletions. Similar to the variants observed in DVL1-mediated Robinow syndrome, all variants in DVL3 result in a -1 frameshift, indicating that these highly specific alterations might be a common cause of dominant Robinow syndrome. Here, we review the current knowledge of these peculiar variant alleles in DVL1- and DVL3-mediated Robinow syndrome and further elucidate the phenotypic features present in subjects with DVL1 and DVL3 frameshift mutations.

Published
2016

7. Paralog Studies Augment Gene Discovery: DDX and DHX Genes

Author

Paine, Ingrid, Posey, Jennifer E., Grochowski, Christopher M., Jhangiani, Shalini N., Rosenheck, Sarah, Kleyner, Robert, Marmorale, Taylor, Yoon, Margaret, Wang, Kai, Robison, Reid, Cappuccio, Gerarda, Pinelli, Michele, Magli, Adriano, Coban Akdemir, Zeynep, Hui, Joannie, Yeung, Wai Lan, Wong, Bibiana K.Y., Ortega, Lucia, Bekheirnia, Mir Reza, Bierhals, Tatjana, Hempel, Maja, Johannsen, Jessika, Santer, René, Aktas, Dilek, Alikasifoglu, Mehmet, Bozdogan, Sevcan, Aydin, Hatip, Karaca, Ender, Bayram, Yavuz, Ityel, Hadas, Dorschner, Michael, White, Janson J., Wilichowski, Ekkehard, Wortmann, Saskia B., Casella, Erasmo B., Kitajima, Joao Paulo, Kok, Fernando, Monteiro, Fabiola, Muzny, Donna M., Bamshad, Michael, Gibbs, Richard A., Sutton, V. Reid, Van Esch, Hilde, Brunetti-Pierri, Nicola, Hildebrandt, Friedhelm, Brautbar, Ariel, Van den Veyver, Ignatia B., Glass, Ian, Lessel, Davor, Lyon, Gholson J., and Lupski, James R.

Published
2019
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8. Insights into genetics, human biology and disease gleaned from family based genomic studies

Author

Posey, Jennifer E., O’Donnell-Luria, Anne H., Chong, Jessica X., Harel, Tamar, Jhangiani, Shalini N., Coban Akdemir, Zeynep H., Buyske, Steven, Pehlivan, Davut, Carvalho, Claudia M.B., Baxter, Samantha, Sobreira, Nara, Liu, Pengfei, Wu, Nan, Rosenfeld, Jill A., Kumar, Sushant, Avramopoulos, Dimitri, White, Janson J., Doheny, Kimberly F., Witmer, P. Dane, Boehm, Corinne, Sutton, V. Reid, Muzny, Donna M., Boerwinkle, Eric, Günel, Murat, Nickerson, Deborah A., Mane, Shrikant, MacArthur, Daniel G., Gibbs, Richard A., Hamosh, Ada, Lifton, Richard P., Matise, Tara C., Rehm, Heidi L., Gerstein, Mark, Bamshad, Michael J., Valle, David, and Lupski, James R.

Published
2019
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11. WNT Signaling Perturbations Underlie the Genetic Heterogeneity of Robinow Syndrome

Author

White, Janson J., Mazzeu, Juliana F., Coban-Akdemir, Zeynep, Bayram, Yavuz, Bahrambeigi, Vahid, Hoischen, Alexander, van Bon, Bregje W.M., Gezdirici, Alper, Gulec, Elif Yilmaz, Ramond, Francis, Touraine, Renaud, Thevenon, Julien, Shinawi, Marwan, Beaver, Erin, Heeley, Jennifer, Hoover-Fong, Julie, Durmaz, Ceren D., Karabulut, Halil Gurhan, Marzioglu-Ozdemir, Ebru, Cayir, Atilla, Duz, Mehmet B., Seven, Mehmet, Price, Susan, Ferreira, Barbara Merfort, Vianna-Morgante, Angela M., Ellard, Sian, Parrish, Andrew, Stals, Karen, Flores-Daboub, Josue, Jhangiani, Shalini N., Gibbs, Richard A., Brunner, Han G., Sutton, V. Reid, Lupski, James R., and Carvalho, Claudia M.B.

Published
2018
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12. De novo missense variants in PPP1CB are associated with intellectual disability and congenital heart disease

Author

Ma, Lijiang, Bayram, Yavuz, McLaughlin, Heather M., Cho, Megan T., Krokosky, Alyson, Turner, Clesson E., Lindstrom, Kristin, Bupp, Caleb P., Mayberry, Katey, Mu, Weiyi, Bodurtha, Joann, Weinstein, Veronique, Zadeh, Neda, Alcaraz, Wendy, Powis, Zöe, Shao, Yunru, Scott, Daryl A., Lewis, Andrea M., White, Janson J., Jhangiani, Shalani N., Gulec, Elif Yilmaz, Lalani, Seema R., Lupski, James R., Retterer, Kyle, Schnur, Rhonda E., Wentzensen, Ingrid M., Bale, Sherri, and Chung, Wendy K.

Published
2016
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13. Dual molecular diagnosis contributes to atypical Prader–Willi phenotype in monozygotic twins

Author

Jehee, Fernanda S., de Oliveira, Valdirene T., Gurgel‐Giannetti, Juliana, Pietra, Rafaella X., Rubatino, Fernando V. M., Carobin, Natália V., Vianna, Gabrielle S., de Freitas, Mariana L., Fernandes, Karla S., Ribeiro, Beatriz S. V., Brüggenwirth, Hennie T., Ali‐Amin, Roza, White, Janson J., Akdemir, Zeynep C., Jhangiani, Shalini N., Gibbs, Richard A., Lupski, James R., Varela, Monica C., Koiffmann, Célia, Rosenberg, Carla, and Carvalho, Cláudia M. B.

Published
2017
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14. Back Cover, Volume 43, Issue 7

Author

Lima, Ariadne R., primary, Ferreira, Barbara M., additional, Zhang, Chaofan, additional, Jolly, Angad, additional, Du, Haowei, additional, White, Janson J., additional, Dawood, Moez, additional, Lins, Tulio C., additional, Chiabai, Marcela A., additional, van Beusekom, Ellen, additional, Cordoba, Mara S., additional, Caldas Rosa, Erica C.C., additional, Kayserili, Hulya, additional, Kimonis, Virginia, additional, Wu, Erica, additional, Mellado, Cecilia, additional, Aggarwal, Vineet, additional, Richieri‐Costa, Antonio, additional, Brunoni, Décio, additional, Canó, Talyta M., additional, Jorge, Alexander A. L., additional, Kim, Chong A., additional, Honjo, Rachel, additional, Bertola, Débora R., additional, Dandalo‐Girardi, Raissa M., additional, Bayram, Yavuz, additional, Gezdirici, Alper, additional, Yilmaz‐Gulec, Elif, additional, Gumus, Evren, additional, Yilmaz, Gülay C., additional, Okamoto, Nobuhiko, additional, Ohashi, Hirofumi, additional, Coban–Akdemir, Zeynep, additional, Mitani, Tadahiro, additional, Jhangiani, Shalini N., additional, Muzny, Donna M., additional, Regattieri, Neysa A.P., additional, Pogue, Robert, additional, Pereira, Rinaldo W., additional, Otto, Paulo A., additional, Gibbs, Richard A., additional, Ali, Bassam R., additional, van Bokhoven, Hans, additional, Brunner, Han G., additional, Sutton, V. Reid, additional, Lupski, James R., additional, Vianna‐Morgante, Angela M., additional, Carvalho, Claudia M. B., additional, and Mazzeu, Juliana F., additional

Published
2022
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15. 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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16. Further delineation of van den Ende‐Gupta syndrome: Genetic heterogeneity and overlap with congenital heart defects and skeletal malformations syndrome.

Author

Hildebrandt, Clara C., Patel, Nisha, Graham, John M., Bamshad, Michael, Nickerson, Deborah A., White, Janson J., Marvin, Colby T., Miller, Danny E., Grand, Katheryn L., Sanchez‐Lara, Pedro A., Schweitzer, Daniela, Al‐Zaidan, Hamad I., Al Masseri, Zainab, Alkuraya, Fowzan S., and Lin, Angela E.

Abstract

Van den Ende‐Gupta syndrome (VDEGS) is a rare autosomal recessive condition characterized by distinctive facial and skeletal features, and in most affected persons, by biallelic pathogenic variants in SCARF2. We review the type and frequency of the clinical features in 36 reported individuals with features of VDEGS, 15 (42%) of whom had known pathogenic variants in SCARF2, 6 (16%) with negative SCARF2 testing, and 15 (42%) not tested. We also report three new individuals with pathogenic variants in SCARF2 and clinical features of VDEGS. Of the six persons without known pathogenic variants in SCARF2, three remain unsolved despite extensive genetic testing. Three were found to have pathogenic ABL1 variants using whole exome sequencing (WES) or whole genome sequencing (WGS). Their phenotype was consistent with the congenital heart disease and skeletal malformations syndrome (CHDSKM), which has been associated with ABL1 variants. Of the three unsolved cases, two were brothers who underwent WGS and targeted long‐range sequencing of both SCARF2 and ABL1, and the third person who underwent WES and RNA sequencing for SCARF2. Because these affected individuals with classical features of VDEGS lacked a detectable pathogenic SCARF2 variant, genetic heterogeneity is likely. Our study shows the importance of performing genetic testing on individuals with the VDEGS "phenotype," either as a targeted gene analysis (SCARF2, ABL1) or WES/WGS. Additionally, individuals with the combination of arachnodactyly and blepharophimosis should undergo echocardiography while awaiting results of molecular testing due to the overlapping physical features of VDEGS and CHDSKM. [ABSTRACT FROM AUTHOR]

Published
2021
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17. Exome Sequencing of a Primary Ovarian Insufficiency Cohort Reveals Common Molecular Etiologies for a Spectrum of Disease

Author

Jolly, Angad, primary, Bayram, Yavuz, additional, Turan, Serap, additional, Aycan, Zehra, additional, Tos, Tulay, additional, Abali, Zehra Yavas, additional, Hacihamdioglu, Bulent, additional, Coban Akdemir, Zeynep Hande, additional, Hijazi, Hadia, additional, Bas, Serpil, additional, Atay, Zeynep, additional, Guran, Tulay, additional, Abali, Saygin, additional, Bas, Firdevs, additional, Darendeliler, Feyza, additional, Colombo, Roberto, additional, Barakat, Tahsin Stefan, additional, Rinne, Tuula, additional, White, Janson J, additional, Yesil, Gozde, additional, Gezdirici, Alper, additional, Gulec, Elif Yilmaz, additional, Karaca, Ender, additional, Pehlivan, Davut, additional, Jhangiani, Shalini N, additional, Muzny, Donna M, additional, Poyrazoglu, Sukran, additional, Bereket, Abdullah, additional, Gibbs, Richard A, additional, Posey, Jennifer E, additional, and Lupski, James R, additional

Published
2019
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18. REST Final-Exon-Truncating Mutations Cause Hereditary Gingival Fibromatosis

Author

Bayram, Yavuz, White, Janson J., Elcioglu, Nursel, Cho, Megan T., Zadeh, Neda, Gedikbasi, Asuman, Palanduz, Sukru, Ozturk, Sukru, Cefle, Kivanc, Kasapcopur, Ozgur, Coban Akdemir, Zeynep, Pehlivan, Davut, Begtrup, Amber, Carvalho, Claudia M.B., Paine, Ingrid Sophie, Mentes, Ali, Bektas-Kayhan, Kivanc, Karaca, Ender, Jhangiani, Shalini N., Muzny, Donna M., Gibbs, Richard A., and Lupski, James R.

Published
2017
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20. Identification of a RAI1-associated disease network through integration of exome sequencing, transcriptomics, and 3D genomics

Author

Loviglio, Maria Nicla, primary, Beck, Christine R., additional, White, Janson J., additional, Leleu, Marion, additional, Harel, Tamar, additional, Guex, Nicolas, additional, Niknejad, Anne, additional, Bi, Weimin, additional, Chen, Edward S., additional, Crespo, Isaac, additional, Yan, Jiong, additional, Charng, Wu-Lin, additional, Gu, Shen, additional, Fang, Ping, additional, Coban-Akdemir, Zeynep, additional, Shaw, Chad A., additional, Jhangiani, Shalini N., additional, Muzny, Donna M., additional, Gibbs, Richard A., additional, Rougemont, Jacques, additional, Xenarios, Ioannis, additional, Lupski, James R., additional, and Reymond, Alexandre, additional

Published
2016
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21. Hutterite‐type cataract maps to chromosome 6p21.32‐p21.31, cosegregates with a homozygous mutation inLEMD2, and is associated with sudden cardiac death

Author

Boone, Philip M., primary, Yuan, Bo, additional, Gu, Shen, additional, Ma, Zhiwei, additional, Gambin, Tomasz, additional, Gonzaga‐Jauregui, Claudia, additional, Jain, Mahim, additional, Murdock, Todd J., additional, White, Janson J., additional, Jhangiani, Shalini N., additional, Walker, Kimberly, additional, Wang, Qiaoyan, additional, Muzny, Donna M., additional, Gibbs, Richard A., additional, Hejtmancik, J. Fielding, additional, Lupski, James R., additional, Posey, Jennifer E., additional, and Lewis, Richard A., additional

Published
2015
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22. Hutterite-type cataract maps to chromosome 6p21.32-p21.31, cosegregates with a homozygous mutation in LEMD2, and is associated with sudden cardiac death.

Author

Boone, Philip M., Yuan, Bo, Gu, Shen, Ma, Zhiwei, Gambin, Tomasz, Gonzaga‐Jauregui, Claudia, Jain, Mahim, Murdock, Todd J., White, Janson J., Jhangiani, Shalini N., Walker, Kimberly, Wang, Qiaoyan, Muzny, Donna M., Gibbs, Richard A., Hejtmancik, J. Fielding, Lupski, James R., Posey, Jennifer E., and Lewis, Richard A.

Subjects
CATARACT, CATARACT in children, EXOMES, MISSENSE mutation, POINT mutation (Biology), GENETICS
Abstract

Background Juvenile-onset cataracts are known among the Hutterites of North America. Despite being identified over 30 years ago, this autosomal recessive condition has not been mapped, and the disease gene is unknown. Methods We performed whole exome sequencing of three Hutterite-type cataract trios and follow-up genotyping and mapping in four extended kindreds. Results Trio exomes enabled genome-wide autozygosity mapping, which localized the disease gene to a 9.5-Mb region on chromosome 6p. This region contained two candidate variants, LEMD2 c.T38G and MUC21 c.665delC. Extended pedigrees recruited for variant genotyping revealed multiple additional relatives with juvenile-onset cataract, as well as six deceased relatives with both cataracts and sudden cardiac death. The candidate variants were genotyped in 84 family members, including 17 with cataracts; only the variant in LEMD2 cosegregated with cataracts ( LOD = 9.62). SNP-based fine mapping within the 9.5 Mb linked region supported this finding by refining the cataract locus to a 0.5- to 2.9-Mb subregion (6p21.32-p21.31) containing LEMD2 but not MUC21. LEMD2 is expressed in mouse and human lenses and encodes a LEM domain-containing protein; the c.T38G missense mutation is predicted to mutate a highly conserved residue within this domain (p.Leu13Arg). Conclusion We performed a genetic and genomic study of Hutterite-type cataract and found evidence for an association of this phenotype with sudden cardiac death. Using combined genetic and genomic approaches, we mapped cataracts to a small portion of chromosome 6 and propose that they result from a homozygous missense mutation in LEMD2. [ABSTRACT FROM AUTHOR]

Published
2016
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23. Identification of a RAI1-associated disease network through integration of exome sequencing, transcriptomics, and 3D genomics

Author

Loviglio, Maria Nicla, Beck, Christine R., White, Janson J., Leleu, Marion, Harel, Tamar, Guex, Nicolas, Niknejad, Anne, Bi, Weimin, Chen, Edward S., Crespo, Isaac, Yan, Jiong, Charng, Wu-Lin, Gu, Shen, Fang, Ping, Coban-Akdemir, Zeynep, Shaw, Chad A., Jhangiani, Shalini N., Muzny, Donna M., Gibbs, Richard A., Rougemont, Jacques, Xenarios, Ioannis, Lupski, James R., and Reymond, Alexandre

Subjects
Male, Text mining, lcsh:QH426-470, Intellectual disability, lcsh:Medicine, Real-Time Polymerase Chain Reaction, Disease network, Mice, Genetics, Animals, Humans, Exome, Gene Regulatory Networks, Chromatin conformation, Diagnostic, Genetics(clinical), RNA, Messenger, Molecular Biology, Mice, Knockout, Reverse Transcriptase Polymerase Chain Reaction, Research, lcsh:R, Genomics, Embryo, Mammalian, Mice, Inbred C57BL, lcsh:Genetics, Phenotype, Mutation, Trans-Activators, Molecular Medicine, Female, Smith-Magenis Syndrome, Transcriptome, Transcription Factors
Abstract

Background Smith-Magenis syndrome (SMS) is a developmental disability/multiple congenital anomaly disorder resulting from haploinsufficiency of RAI1. It is characterized by distinctive facial features, brachydactyly, sleep disturbances, and stereotypic behaviors. Methods We investigated a cohort of 15 individuals with a clinical suspicion of SMS who showed neither deletion in the SMS critical region nor damaging variants in RAI1 using whole exome sequencing. A combination of network analysis (co-expression and biomedical text mining), transcriptomics, and circularized chromatin conformation capture (4C-seq) was applied to verify whether modified genes are part of the same disease network as known SMS-causing genes. Results Potentially deleterious variants were identified in nine of these individuals using whole-exome sequencing. Eight of these changes affect KMT2D, ZEB2, MAP2K2, GLDC, CASK, MECP2, KDM5C, and POGZ, known to be associated with Kabuki syndrome 1, Mowat-Wilson syndrome, cardiofaciocutaneous syndrome, glycine encephalopathy, mental retardation and microcephaly with pontine and cerebellar hypoplasia, X-linked mental retardation 13, X-linked mental retardation Claes-Jensen type, and White-Sutton syndrome, respectively. The ninth individual carries a de novo variant in JAKMIP1, a regulator of neuronal translation that was recently found deleted in a patient with autism spectrum disorder. Analyses of co-expression and biomedical text mining suggest that these pathologies and SMS are part of the same disease network. Further support for this hypothesis was obtained from transcriptome profiling that showed that the expression levels of both Zeb2 and Map2k2 are perturbed in Rai1 –/– mice. As an orthogonal approach to potentially contributory disease gene variants, we used chromatin conformation capture to reveal chromatin contacts between RAI1 and the loci flanking ZEB2 and GLDC, as well as between RAI1 and human orthologs of the genes that show perturbed expression in our Rai1 –/– mouse model. Conclusions These holistic studies of RAI1 and its interactions allow insights into SMS and other disorders associated with intellectual disability and behavioral abnormalities. Our findings support a pan-genomic approach to the molecular diagnosis of a distinctive disorder. Electronic supplementary material The online version of this article (doi:10.1186/s13073-016-0359-z) contains supplementary material, which is available to authorized users.

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24. Exome Sequencing of a Primary Ovarian Insufficiency Cohort Reveals Common Molecular Etiologies for a Spectrum of Disease

Author

Serap Turan, Zeynep Coban Akdemir, Angad Jolly, Firdevs Bas, Davut Pehlivan, Hadia Hijazi, Zehra Yavas Abali, Tuula Rinne, Jennifer E. Posey, Yavuz Bayram, Tahsin Stefan Barakat, Tulay Tos, Roberto Colombo, Shalini N. Jhangiani, Gozde Yesil, Sukran Poyrazoglu, Zeynep Atay, Alper Gezdirici, James R. Lupski, Donna M. Muzny, Tulay Guran, Zehra Aycan, Richard A. Gibbs, Elif Yilmaz Gulec, Janson White, Serpil Bas, Ender Karaca, Feyza Darendeliler, Abdullah Bereket, Bülent Hacıhamdioğlu, Saygin Abali, İstinye Üniversitesi, Tıp Fakültesi, Dahili Tıp Bilimleri Bölümü, Bülent Hacıhamdioğlu / 0000-0001-7070-6429, Hacihamdioglu, Bulent, Bülent Hacıhamdioğlu / GBK-6773-2022, Bülent Hacıhamdioğlu / 22134579900, Clinical Genetics, YEŞİL, Gözde, Jolly, Angad, Bayram, Yavuz, Turan, Serap, Aycan, Zehra, Tos, Tulay, Abali, Zehra Yavas, Akdemir, Zeynep Hande Coban, Hijazi, Hadia, Bas, Serpil, Atay, Zeynep, Guran, Tulay, Abali, Saygin, Bas, Firdevs, Darendeliler, Feyza, Colombo, Roberto, Barakat, Tahsin Stefan, Rinne, Tuula, White, Janson J., Yesil, Gozde, Gezdirici, Alper, Gulec, Elif Yilmaz, Karaca, Ender, Pehlivan, Davut, Jhangiani, Shalini N., Muzny, Donna M., Poyrazoglu, Sukran, Bereket, Abdullah, Gibbs, Richard A., Posey, Jennifer E., and Lupski, James R.

Subjects
MECHANISM, 0301 basic medicine, endocrine system diseases, Endocrinology, Diabetes and Metabolism, Clinical Biochemistry, PROTEIN, Cell Cycle Proteins, Disease, Primary Ovarian Insufficiency, VARIANTS, Biochemistry, Cohort Studies, 0302 clinical medicine, Endocrinology, Gene Frequency, Locus heterogeneity, FAILURE, Exome sequencing, Jolly A., Bayram Y., Turan S., Aycan Z., Tos T., Abali Z. Y. , Hacihamdioglu B., Akdemir Z. H. C. , Hijazi H., Bas S., et al., -Exome Sequencing of a Primary Ovarian Insufficiency Cohort Reveals Common Molecular Etiologies for a Spectrum of Disease-, JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM, cilt.104, ss.3049-3067, 2019, Genetics, 030219 obstetrics & reproductive medicine, Minichromosome Maintenance Proteins, REARRANGEMENTS, Oligogenic Inheritance, DNA-Binding Proteins, INSIGHTS, Female, medicine.medical_specialty, Immunoglobulins, Locus (genetics), Genomics, Biology, 03 medical and health sciences, Hypergonadotropic hypogonadism, All institutes and research themes of the Radboud University Medical Center, Internal medicine, Exome Sequencing, medicine, Humans, HOP2-MND1, Settore BIO/10 - BIOCHIMICA, Allele frequency, Clinical Research Articles, Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], IDENTIFICATION, MUTATIONS, Hypogonadism, Biochemistry (medical), DNA Helicases, medicine.disease, GENE, 030104 developmental biology, exome
Abstract

Context: Primary ovarian insufficiency (POI) encompasses a spectrum of premature menopause, including both primary and secondary amenorrhea. For 75% to 90% of individuals with hyper-gonadotropic hypogonadism presenting as POI, the molecular etiology is unknown. Common etiologies include chromosomal abnormalities, environmental factors, and congenital disorders affecting ovarian development and function, as well as syndromic and nonsyndromic single gene disorders suggesting POI represents a complex trait. Objective: To characterize the contribution of known disease genes to POI and identify molecular etiologies and biological underpinnings of POI. Design, Setting, and Participants: We applied exome sequencing (ES) and family-based genomics to 42 affected female individuals from 36 unrelated Turkish families, including 31 with reported parental consanguinity. Results: This analysis identified likely damaging, potentially contributing variants and molecular diagnoses in 16 families (44%), including 11 families with likely damaging variants in known genes and five families with predicted deleterious variants in disease genes (IGSF10, MND1, MRPS22, and SOHLH1) not previously associated with POI. Of the 16 families, 2 (13%) had evidence for potentially pathogenic variants at more than one locus. Absence of heterozygosity consistent with identity-by-descent mediated recessive disease burden contributes to molecular diagnosis in 15 of 16 (94%) families. GeneMatcher allowed identification of additional families from diverse genetic backgrounds. Conclusions: ES analysis of a POI cohort further characterized locus heterogeneity, reaffirmed the association of genes integral to meiotic recombination, demonstrated the likely contribution of genes involved in hypothalamic development, and documented multilocus pathogenic variation suggesting the potential for oligogenic inheritance contributing to the development of POI. National Human Genome Research Institute (NHGRI)United States Department of Health & Human ServicesNational Institutes of Health (NIH) - USANIH National Human Genome Research Institute (NHGRI); National Heart Lung and Blood Institute (NHBLI)United States Department of Health & Human ServicesNational Institutes of Health (NIH) - USANIH National Heart Lung & Blood Institute (NHLBI) [UM1 HG006542]; National Institute of Neurologic Disorders and Stroke (NINDS)United States Department of Health & Human ServicesNational Institutes of Health (NIH) - USANIH National Institute of Neurological Disorders & Stroke (NINDS) [R35NS105078]; NHGRIUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USANIH National Human Genome Research Institute (NHGRI) [K08 HG008986, U54HG003273]; Howard Hughes Medical Research Fellows Program; Baylor College of Medicine Medical Scientist Training Program; Clinical Research Training Scholarship in Neuromuscular Disease; American Academy of Neurology (AAN); American Brain Foundation (ABF); Netherlands Organization for Scientific Research (ZonMW Veni)Netherlands Organization for Scientific Research (NWO) [91617021]; NARSAD Young Investigator Grant from the Brain & Behavior Research FoundationNARSAD; Muscle Study Group (MSG) This study was supported in part by the National Human Genome Research Institute (NHGRI) and National Heart Lung and Blood Institute (NHBLI) to the Baylor-Hopkins Center for Mendelian Genomics (BHCMG; UM1 HG006542 to J.R.L.); NHGRI grant to Baylor College of Medicine Human Genome Sequencing Center (U54HG003273 to R.A.G.), and National Institute of Neurologic Disorders and Stroke (NINDS; R35NS105078 to J.R.L.). J.E.P. was supported by NHGRI K08 HG008986. A.J. was supported in part by the Howard Hughes Medical Research Fellows Program and the Baylor College of Medicine Medical Scientist Training Program. D. P. is supported by Clinical Research Training Scholarship in Neuromuscular Disease partnered by the American Academy of Neurology (AAN), American Brain Foundation (ABF), and Muscle Study Group (MSG). T.S.B. was supported by the Netherlands Organization for Scientific Research (ZonMW Veni, Grant 91617021) and by an NARSAD Young Investigator Grant from the Brain & Behavior Research Foundation. WOS:000482558500001 31042289 Q1

Published
2019
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25. REST Final-Exon-Truncating Mutations Cause Hereditary Gingival Fibromatosis

Author

Janson White, Megan T. Cho, James R. Lupski, Kivanc Cefle, Claudia M.B. Carvalho, Donna M. Muzny, Kivanc Bektas-Kayhan, Yavuz Bayram, Ender Karaca, Nursel Elcioglu, Richard A. Gibbs, Shalini N. Jhangiani, Amber Begtrup, Ali Menteş, Neda Zadeh, Zeynep Coban Akdemir, Sukru Ozturk, Ozgur Kasapcopur, Ingrid S. Paine, Asuman Gedikbasi, Davut Pehlivan, Sukru Palanduz, Bayram, Yavuz, White, Janson J., Elcioglu, Nursel, Cho, Megan T., Zadeh, Neda, Gedikbasi, Asuman, Palanduz, Sukru, Ozturk, Sukru, Cefle, Kivanc, Kasapcopur, Ozgur, Akdemir, Zeynep Coban, Pehlivan, Davut, Begtrup, Amber, Carvalho, Claudia M. B., Paine, Ingrid Sophie, Mentes, Ali, Bektas-Kayhan, Kivanc, Karaca, Ender, Jhangiani, Shalini N., Muzny, Donna M., Gibbs, Richard A., and Lupski, James R.

Subjects
0301 basic medicine, Male, NEUROENDOCRINE DIFFERENTIATION, FIBROBLASTS, Adolescent, PROTEIN, RE1-silencing transcription factor, Biology, medicine.disease_cause, Germline, 03 medical and health sciences, Exon, 0302 clinical medicine, TUMOR, Report, Chromosome Segregation, Genetics, medicine, Humans, Family, Genetic Predisposition to Disease, Genetics (clinical), Exome sequencing, GENE-EXPRESSION, Fibromatosis, Gingival, Mutation, Autosome, Base Sequence, Genetic heterogeneity, REPRESSOR, 030206 dentistry, TRANSCRIPTION FACTOR REST, Exons, Middle Aged, medicine.disease, CANCER, Hereditary gingival fibromatosis, Pedigree, Repressor Proteins, 030104 developmental biology, biology.protein, Female, SIGNALING PATHWAY, RESTRICTIVE SILENCER FACTOR
Abstract

Hereditary gingival fibromatosis (HGF) is the most common genetic form of gingival fibromatosis that develops as a slowly progressive, benign, localized or generalized enlargement of keratinized gingiva. HGF is a genetically heterogeneous disorder and can be transmitted either as an autosomal-dominant or autosomal-recessive trait or appear sporadically. To date, four loci (2p22.1, 2p23.3–p22.3, 5q13–q22, and 11p15) have been mapped to autosomes and one gene ( SOS1 ) has been associated with the HGF trait observed to segregate in a dominant inheritance pattern. Here we report 11 individuals with HGF from three unrelated families. Whole-exome sequencing (WES) revealed three different truncating mutations including two frameshifts and one nonsense variant in RE1-silencing transcription factor ( REST ) in the probands from all families and further genetic and genomic analyses confirmed the WES-identified findings. REST is a transcriptional repressor that is expressed throughout the body; it has different roles in different cellular contexts, such as oncogenic and tumor-suppressor functions and hematopoietic and cardiac differentiation. Here we show the consequences of germline final-exon-truncating mutations in REST for organismal development and the association with the HGF phenotype.

Published
2017

26. Hutterite-type cataract maps to chromosome 6p21.32-p21.31, cosegregates with a homozygous mutation in LEMD2, and is associated with sudden cardiac death.

Author

Boone PM, Yuan B, Gu S, Ma Z, Gambin T, Gonzaga-Jauregui C, Jain M, Murdock TJ, White JJ, Jhangiani SN, Walker K, Wang Q, Muzny DM, Gibbs RA, Hejtmancik JF, Lupski JR, Posey JE, and Lewis RA

Abstract

Background: Juvenile-onset cataracts are known among the Hutterites of North America. Despite being identified over 30 years ago, this autosomal recessive condition has not been mapped, and the disease gene is unknown., Methods: We performed whole exome sequencing of three Hutterite-type cataract trios and follow-up genotyping and mapping in four extended kindreds., Results: Trio exomes enabled genome-wide autozygosity mapping, which localized the disease gene to a 9.5-Mb region on chromosome 6p. This region contained two candidate variants, LEMD2 c.T38G and MUC21 c.665delC. Extended pedigrees recruited for variant genotyping revealed multiple additional relatives with juvenile-onset cataract, as well as six deceased relatives with both cataracts and sudden cardiac death. The candidate variants were genotyped in 84 family members, including 17 with cataracts; only the variant in LEMD2 cosegregated with cataracts (LOD = 9.62). SNP-based fine mapping within the 9.5 Mb linked region supported this finding by refining the cataract locus to a 0.5- to 2.9-Mb subregion (6p21.32-p21.31) containing LEMD2 but not MUC21. LEMD2 is expressed in mouse and human lenses and encodes a LEM domain-containing protein; the c.T38G missense mutation is predicted to mutate a highly conserved residue within this domain (p.Leu13Arg)., Conclusion: We performed a genetic and genomic study of Hutterite-type cataract and found evidence for an association of this phenotype with sudden cardiac death. Using combined genetic and genomic approaches, we mapped cataracts to a small portion of chromosome 6 and propose that they result from a homozygous missense mutation in LEMD2.

Published
2015
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