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551 results on '"Jhangiani, Shalini N."'

152. 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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153. Recurrent De Novo and Biallelic Variation of ATAD3A , Encoding a Mitochondrial Membrane Protein, Results in Distinct Neurological Syndromes

Author

Harel, Tamar, primary, Yoon, Wan Hee, additional, Garone, Caterina, additional, Gu, Shen, additional, Coban-Akdemir, Zeynep, additional, Eldomery, Mohammad K., additional, Posey, Jennifer E., additional, Jhangiani, Shalini N., additional, Rosenfeld, Jill A., additional, Cho, Megan T., additional, Fox, Stephanie, additional, Withers, Marjorie, additional, Brooks, Stephanie M., additional, Chiang, Theodore, additional, Duraine, Lita, additional, Erdin, Serkan, additional, Yuan, Bo, additional, Shao, Yunru, additional, Moussallem, Elie, additional, Lamperti, Costanza, additional, Donati, Maria A., additional, Smith, Joshua D., additional, McLaughlin, Heather M., additional, Eng, Christine M., additional, Walkiewicz, Magdalena, additional, Xia, Fan, additional, Pippucci, Tommaso, additional, Magini, Pamela, additional, Seri, Marco, additional, Zeviani, Massimo, additional, Hirano, Michio, additional, Hunter, Jill V., additional, Srour, Myriam, additional, Zanigni, Stefano, additional, Lewis, Richard Alan, additional, Muzny, Donna M., additional, Lotze, Timothy E., additional, Boerwinkle, Eric, additional, Gibbs, Richard A., additional, Hickey, Scott E., additional, Graham, Brett H., additional, Yang, Yaping, additional, Buhas, Daniela, additional, Martin, Donna M., additional, Potocki, Lorraine, additional, Graziano, Claudio, additional, Bellen, Hugo J., additional, and Lupski, James R., additional

Published
2016
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154. Bi-allelic Mutations in PKD1L1 Are Associated with Laterality Defects in Humans

Author

Vetrini, Francesco, primary, D’Alessandro, Lisa C.A., additional, Akdemir, Zeynep C., additional, Braxton, Alicia, additional, Azamian, Mahshid S., additional, Eldomery, Mohammad K., additional, Miller, Kathryn, additional, Kois, Chelsea, additional, Sack, Virginia, additional, Shur, Natasha, additional, Rijhsinghani, Asha, additional, Chandarana, Jignesh, additional, Ding, Yan, additional, Holtzman, Judy, additional, Jhangiani, Shalini N., additional, Muzny, Donna M., additional, Gibbs, Richard A., additional, Eng, Christine M., additional, Hanchard, Neil A., additional, Harel, Tamar, additional, Rosenfeld, Jill A., additional, Belmont, John W., additional, Lupski, James R., additional, and Yang, Yaping, additional

Published
2016
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155. Germline mutations in shelterin complex genes are associated with familial glioma

Author

Bainbridge, Matthew N, Armstrong, Georgina N, Gramatges, M Monica, Bertuch, Alison A, Jhangiani, Shalini N, Doddapaneni, Harsha, Lewis, Lora, Tombrello, Joseph, Tsavachidis, Spyros, Liu, Yanhong, Jalali, Ali, Plon, Sharon E, Lau, Ching C, Parsons, Donald W, Claus, Elizabeth B, Barnholtz-Sloan, Jill, Il'yasova, Dora, Schildkraut, Joellen, Ali-Osman, Francis, Sadetzki, Siegal, Johansen, Christoffer, Houlston, Richard S, Jenkins, Robert B, Lachance, Daniel, Olson, Sara H, Bernstein, Jonine L, Merrell, Ryan T, Wrensch, Margaret R, Walsh, Kyle M, Davis, Faith G, Lai, Rose, Shete, Sanjay, Aldape, Kenneth, Amos, Christopher I, Thompson, Patricia A, Muzny, Donna M, Gibbs, Richard A, Melin, Beatrice S, Bondy, Melissa L, and Gliogene Consortium

Subjects
Adult, Male, Epigenomics, Proteomics, Biomedical Research, Oligodendroglioma, Telomere-Binding Proteins, Oncology and Carcinogenesis, Shelterin Complex, Rare Diseases, Clinical Research, Neoplasms, Genetics, Humans, Metabolomics, Genetic Predisposition to Disease, Exome, Oncology & Carcinogenesis, Germ-Line Mutation, Aged, Cancer, Brain Neoplasms, Gene Expression Profiling, Human Genome, Neurosciences, Gliogene Consortium, Glioma, Genomics, Middle Aged, Pedigree, Brain Disorders, Brain Cancer, Female, Transcriptome, Signal Transduction
Abstract

Gliomas are the most common brain tumor, with several histological subtypes of various malignancy grade. The genetic contribution to familial glioma is not well understood. Using whole exome sequencing of 90 individuals from 55 families, we identified two families with mutations in POT1 (p.G95C, p.E450X), a member of the telomere shelterin complex, shared by both affected individuals in each family and predicted to impact DNA binding and TPP1 binding, respectively. Validation in a separate cohort of 264 individuals from 246 families identified an additional mutation in POT1 (p.D617Efs), also predicted to disrupt TPP1 binding. All families with POT1 mutations had affected members with oligodendroglioma, a specific subtype of glioma more sensitive to irradiation. These findings are important for understanding the origin of glioma and could have importance for the future diagnostics and treatment of glioma.

Published
2015

156. A potential founder variant inCARMIL2/RLTPRin three Norwegian families with warts, molluscum contagiosum, and T-cell dysfunction

Author

Sorte, Hanne S., primary, Osnes, Liv T., additional, Fevang, Børre, additional, Aukrust, Pål, additional, Erichsen, Hans C., additional, Backe, Paul H., additional, Abrahamsen, Tore G., additional, Kittang, Ole B., additional, Øverland, Torstein, additional, Jhangiani, Shalini N., additional, Muzny, Donna M., additional, Vigeland, Magnus D., additional, Samarakoon, Pubudu, additional, Gambin, Tomasz, additional, Akdemir, Zeynep H. C., additional, Gibbs, Richard A., additional, Rødningen, Olaug K., additional, Lyle, Robert, additional, Lupski, James R., additional, and Stray-Pedersen, Asbjørg, additional

Published
2016
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157. Exome sequencing in mostly consanguineous Arab families with neurologic disease provides a high potential molecular diagnosis rate

Author

Charng, Wu-Lin, primary, Karaca, Ender, additional, Coban Akdemir, Zeynep, additional, Gambin, Tomasz, additional, Atik, Mehmed M., additional, Gu, Shen, additional, Posey, Jennifer E., additional, Jhangiani, Shalini N., additional, Muzny, Donna M., additional, Doddapaneni, Harsha, additional, Hu, Jianhong, additional, Boerwinkle, Eric, additional, Gibbs, Richard A., additional, Rosenfeld, Jill A., additional, Cui, Hong, additional, Xia, Fan, additional, Manickam, Kandamurugu, additional, Yang, Yaping, additional, Faqeih, Eissa A., additional, Al Asmari, Ali, additional, Saleh, Mohammed A. M., additional, El-Hattab, Ayman W., additional, and Lupski, James R., additional

Published
2016
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158. Phenotypic expansion of TBX4 mutations to include acinar dysplasia of the lungs

Author

Szafranski, Przemyslaw, primary, Coban‐Akdemir, Zeynep H., additional, Rupps, Rosemarie, additional, Grazioli, Serge, additional, Wensley, David, additional, Jhangiani, Shalini N., additional, Popek, Edwina, additional, Lee, Anna F., additional, Lupski, James R., additional, Boerkoel, Cornelius F., additional, and Stankiewicz, Paweł, additional

Published
2016
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159. PEHO Syndrome May Represent Phenotypic Expansion at the Severe End of the Early-Onset Encephalopathies

Author

Gawlinski, Pawel, primary, Posmyk, Renata, additional, Gambin, Tomasz, additional, Sielicka, Danuta, additional, Chorazy, Monika, additional, Nowakowska, Beata, additional, Jhangiani, Shalini N., additional, Muzny, Donna M., additional, Bekiesinska-Figatowska, Monika, additional, Bal, Jerzy, additional, Boerwinkle, Eric, additional, Gibbs, Richard A., additional, Lupski, James R., additional, and Wiszniewski, Wojciech, additional

Published
2016
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160. The role of combined SNV and CNV burden in patients with distal symmetric polyneuropathy

Author

Pehlivan, Davut, primary, Beck, Christine R., additional, Okamoto, Yuji, additional, Harel, Tamar, additional, Akdemir, Zeynep H.C., additional, Jhangiani, Shalini N., additional, Withers, Marjorie A., additional, Goksungur, Meryem Tuba, additional, Carvalho, Claudia M.B., additional, Czesnik, Dirk, additional, Gonzaga-Jauregui, Claudia, additional, Wiszniewski, Wojciech, additional, Muzny, Donna M., additional, Gibbs, Richard A., additional, Rautenstrauss, Bernd, additional, Sereda, Michael W., additional, and Lupski, James R., additional

Published
2016
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161. Monoallelic and Biallelic Variants in EMC1 Identified in Individuals with Global Developmental Delay, Hypotonia, Scoliosis, and Cerebellar Atrophy

Author

Harel, Tamar, primary, Yesil, Gozde, additional, Bayram, Yavuz, additional, Coban-Akdemir, Zeynep, additional, Charng, Wu-Lin, additional, Karaca, Ender, additional, Al Asmari, Ali, additional, Eldomery, Mohammad K., additional, Hunter, Jill V., additional, Jhangiani, Shalini N., additional, Rosenfeld, Jill A., additional, Pehlivan, Davut, additional, El-Hattab, Ayman W., additional, Saleh, Mohammed A., additional, LeDuc, Charles A., additional, Muzny, Donna, additional, Boerwinkle, Eric, additional, Gibbs, Richard A., additional, Chung, Wendy K., additional, Yang, Yaping, additional, Belmont, John W., additional, and Lupski, James R., additional

Published
2016
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162. Recurrent Muscle Weakness with Rhabdomyolysis, Metabolic Crises, and Cardiac Arrhythmia Due to Bi-allelic TANGO2 Mutations

Author

Lalani, Seema R., primary, Liu, Pengfei, additional, Rosenfeld, Jill A., additional, Watkin, Levi B., additional, Chiang, Theodore, additional, Leduc, Magalie S., additional, Zhu, Wenmiao, additional, Ding, Yan, additional, Pan, Shujuan, additional, Vetrini, Francesco, additional, Miyake, Christina Y., additional, Shinawi, Marwan, additional, Gambin, Tomasz, additional, Eldomery, Mohammad K., additional, Akdemir, Zeynep Hande Coban, additional, Emrick, Lisa, additional, Wilnai, Yael, additional, Schelley, Susan, additional, Koenig, Mary Kay, additional, Memon, Nada, additional, Farach, Laura S., additional, Coe, Bradley P., additional, Azamian, Mahshid, additional, Hernandez, Patricia, additional, Zapata, Gladys, additional, Jhangiani, Shalini N., additional, Muzny, Donna M., additional, Lotze, Timothy, additional, Clark, Gary, additional, Wilfong, Angus, additional, Northrup, Hope, additional, Adesina, Adekunle, additional, Bacino, Carlos A., additional, Scaglia, Fernando, additional, Bonnen, Penelope E., additional, Crosson, Jane, additional, Duis, Jessica, additional, Maegawa, Gustavo H.B., additional, Coman, David, additional, Inwood, Anita, additional, McGill, Jim, additional, Boerwinkle, Eric, additional, Graham, Brett, additional, Beaudet, Art, additional, Eng, Christine M., additional, Hanchard, Neil A., additional, Xia, Fan, additional, Orange, Jordan S., additional, Gibbs, Richard A., additional, Lupski, James R., additional, and Yang, Yaping, additional

Published
2016
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163. POGZ truncating alleles cause syndromic intellectual disability

Author

White, Janson, primary, Beck, Christine R., additional, Harel, Tamar, additional, Posey, Jennifer E., additional, Jhangiani, Shalini N., additional, Tang, Sha, additional, Farwell, Kelly D., additional, Powis, Zöe, additional, Mendelsohn, Nancy J., additional, Baker, Janice A., additional, Pollack, Lynda, additional, Mason, Kati J., additional, Wierenga, Klaas J., additional, Arrington, Daniel K., additional, Hall, Melissa, additional, Psychogios, Apostolos, additional, Fairbrother, Laura, additional, Walkiewicz, Magdalena, additional, Person, Richard E., additional, Niu, Zhiyv, additional, Zhang, Jing, additional, Rosenfeld, Jill A., additional, Muzny, Donna M., additional, Eng, Christine, additional, Beaudet, Arthur L., additional, Lupski, James R., additional, Boerwinkle, Eric, additional, Gibbs, Richard A., additional, Yang, Yaping, additional, Xia, Fan, additional, and Sutton, V. Reid, additional

Published
2016
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164. Biallelic Mutations in UNC80 Cause Persistent Hypotonia, Encephalopathy, Growth Retardation, and Severe Intellectual Disability

Author

Stray-Pedersen, Asbjørg, primary, Cobben, Jan-Maarten, additional, Prescott, Trine E., additional, Lee, Sora, additional, Cang, Chunlei, additional, Aranda, Kimberly, additional, Ahmed, Sohnee, additional, Alders, Marielle, additional, Gerstner, Thorsten, additional, Aslaksen, Kathinka, additional, Tétreault, Martine, additional, Qin, Wen, additional, Hartley, Taila, additional, Jhangiani, Shalini N., additional, Muzny, Donna M., additional, Tarailo-Graovac, Maja, additional, van Karnebeek, Clara D.M., additional, Lupski, James R., additional, Ren, Dejian, additional, and Yoon, Grace, additional

Published
2016
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165. Multiallelic Positions in the Human Genome: Challenges for Genetic Analyses

Author

Campbell, Ian M., primary, Gambin, Tomasz, additional, Jhangiani, Shalini N., additional, Grove, Megan L., additional, Veeraraghavan, Narayanan, additional, Muzny, Donna M., additional, Shaw, Chad A., additional, Gibbs, Richard A., additional, Boerwinkle, Eric, additional, Yu, Fuli, additional, and Lupski, James R., additional

Published
2015
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166. 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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167. Genes that Affect Brain Structure and Function Identified by Rare Variant Analyses of Mendelian Neurologic Disease

Author

Karaca, Ender, primary, Harel, Tamar, additional, Pehlivan, Davut, additional, Jhangiani, Shalini N., additional, Gambin, Tomasz, additional, Coban Akdemir, Zeynep, additional, Gonzaga-Jauregui, Claudia, additional, Erdin, Serkan, additional, Bayram, Yavuz, additional, Campbell, Ian M., additional, Hunter, Jill V., additional, Atik, Mehmed M., additional, Van Esch, Hilde, additional, Yuan, Bo, additional, Wiszniewski, Wojciech, additional, Isikay, Sedat, additional, Yesil, Gozde, additional, Yuregir, Ozge O., additional, Tug Bozdogan, Sevcan, additional, Aslan, Huseyin, additional, Aydin, Hatip, additional, Tos, Tulay, additional, Aksoy, Ayse, additional, De Vivo, Darryl C., additional, Jain, Preti, additional, Geckinli, B. Bilge, additional, Sezer, Ozlem, additional, Gul, Davut, additional, Durmaz, Burak, additional, Cogulu, Ozgur, additional, Ozkinay, Ferda, additional, Topcu, Vehap, additional, Candan, Sukru, additional, Cebi, Alper Han, additional, Ikbal, Mevlit, additional, Yilmaz Gulec, Elif, additional, Gezdirici, Alper, additional, Koparir, Erkan, additional, Ekici, Fatma, additional, Coskun, Salih, additional, Cicek, Salih, additional, Karaer, Kadri, additional, Koparir, Asuman, additional, Duz, Mehmet Bugrahan, additional, Kirat, Emre, additional, Fenercioglu, Elif, additional, Ulucan, Hakan, additional, Seven, Mehmet, additional, Guran, Tulay, additional, Elcioglu, Nursel, additional, Yildirim, Mahmut Selman, additional, Aktas, Dilek, additional, Alikaşifoğlu, Mehmet, additional, Ture, Mehmet, additional, Yakut, Tahsin, additional, Overton, John D., additional, Yuksel, Adnan, additional, Ozen, Mustafa, additional, Muzny, Donna M., additional, Adams, David R., additional, Boerwinkle, Eric, additional, Chung, Wendy K., additional, Gibbs, Richard A., additional, and Lupski, James R., additional

Published
2015
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169. A biallelic <italic>ANTXR1</italic> variant expands the anthrax toxin receptor associated phenotype to tooth agenesis.

Author

Dinckan, Nuriye, Du, Renqian, Akdemir, Zeynep C., Bayram, Yavuz, Jhangiani, Shalini N., Doddapaneni, Harsha, Hu, Jianhong, Muzny, Donna M., Guven, Yeliz, Aktoren, Oya, Kayserili, Hulya, Boerwinkle, Eric, Gibbs, Richard A., Posey, Jennifer E., Lupski, James R., Uyguner, Zehra O., and Letra, Ariadne

Abstract

Tooth development is regulated by multiple genetic pathways, which ultimately drive the complex interactions between the oral epithelium and mesenchyme. Disruptions at any time point during this process may lead to failure of tooth development, also known as tooth agenesis (TA). TA is a common craniofacial abnormality in humans and represents the failure to develop one or more permanent teeth. Many genes and potentially subtle variants in these genes contribute to the TA phenotype. We report the clinical and genetic impact of a rare homozygous ANTXR1 variant (c.1312C>T), identified by whole exome sequencing (WES), in a consanguineous Turkish family with TA. Mutations in ANTXR1 have been associated with GAPO (growth retardation, alopecia, pseudoanodontia, and optic atrophy) syndrome and infantile hemangioma, however no clinical characteristics associated with these conditions were observed in our study family. We detected the expression of Antxr1 in oral and dental tissues of developing mouse embryos, further supporting a role for this gene in tooth development. Our findings implicate ANTXR1 as a candidate gene for isolated TA, suggest the involvement of specific hypomorphic alleles, and expand the previously known ANTXR1‐associated phenotypes. [ABSTRACT FROM AUTHOR]

Published
2018
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171. The Genetic Basis of Mendelian Phenotypes: Discoveries, Challenges, and Opportunities

Author

Chong, Jessica X., primary, Buckingham, Kati J., additional, Jhangiani, Shalini N., additional, Boehm, Corinne, additional, Sobreira, Nara, additional, Smith, Joshua D., additional, Harrell, Tanya M., additional, McMillin, Margaret J., additional, Wiszniewski, Wojciech, additional, Gambin, Tomasz, additional, Coban Akdemir, Zeynep H., additional, Doheny, Kimberly, additional, Scott, Alan F., additional, Avramopoulos, Dimitri, additional, Chakravarti, Aravinda, additional, Hoover-Fong, Julie, additional, Mathews, Debra, additional, Witmer, P. Dane, additional, Ling, Hua, additional, Hetrick, Kurt, additional, Watkins, Lee, additional, Patterson, Karynne E., additional, Reinier, Frederic, additional, Blue, Elizabeth, additional, Muzny, Donna, additional, Kircher, Martin, additional, Bilguvar, Kaya, additional, López-Giráldez, Francesc, additional, Sutton, V. Reid, additional, Tabor, Holly K., additional, Leal, Suzanne M., additional, Gunel, Murat, additional, Mane, Shrikant, additional, Gibbs, Richard A., additional, Boerwinkle, Eric, additional, Hamosh, Ada, additional, Shendure, Jay, additional, Lupski, James R., additional, Lifton, Richard P., additional, Valle, David, additional, Nickerson, Deborah A., additional, and Bamshad, Michael J., additional

Published
2015
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172. Exome Sequence Analysis Suggests that Genetic Burden Contributes to Phenotypic Variability and Complex Neuropathy

Author

Gonzaga-Jauregui, Claudia, primary, Harel, Tamar, additional, Gambin, Tomasz, additional, Kousi, Maria, additional, Griffin, Laurie B., additional, Francescatto, Ludmila, additional, Ozes, Burcak, additional, Karaca, Ender, additional, Jhangiani, Shalini N., additional, Bainbridge, Matthew N., additional, Lawson, Kim S., additional, Pehlivan, Davut, additional, Okamoto, Yuji, additional, Withers, Marjorie, additional, Mancias, Pedro, additional, Slavotinek, Anne, additional, Reitnauer, Pamela J., additional, Goksungur, Meryem T., additional, Shy, Michael, additional, Crawford, Thomas O., additional, Koenig, Michel, additional, Willer, Jason, additional, Flores, Brittany N., additional, Pediaditrakis, Igor, additional, Us, Onder, additional, Wiszniewski, Wojciech, additional, Parman, Yesim, additional, Antonellis, Anthony, additional, Muzny, Donna M., additional, Katsanis, Nicholas, additional, Battaloglu, Esra, additional, Boerwinkle, Eric, additional, Gibbs, Richard A., additional, and Lupski, James R., additional

Published
2015
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173. Whole-exome sequencing identifies novel homozygous mutation in NPAS2 in family with nonobstructive azoospermia

Author

Ramasamy, Ranjith, primary, Bakırcıoğlu, M. Emre, additional, Cengiz, Cenk, additional, Karaca, Ender, additional, Scovell, Jason, additional, Jhangiani, Shalini N., additional, Akdemir, Zeynep C., additional, Bainbridge, Matthew, additional, Yu, Yao, additional, Huff, Chad, additional, Gibbs, Richard A., additional, Lupski, James R., additional, and Lamb, Dolores J., additional

Published
2015
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174. Secondary findings and carrier test frequencies in a large multiethnic sample

Author

Gambin, Tomasz, primary, Jhangiani, Shalini N., additional, Below, Jennifer E., additional, Campbell, Ian M., additional, Wiszniewski, Wojciech, additional, Muzny, Donna M., additional, Staples, Jeffrey, additional, Morrison, Alanna C., additional, Bainbridge, Matthew N., additional, Penney, Samantha, additional, McGuire, Amy L., additional, Gibbs, Richard A., additional, Lupski, James R., additional, and Boerwinkle, Eric, additional

Published
2015
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175. Homozygous Loss-of-function Mutations inSOHLH1in Patients With Nonsyndromic Hypergonadotropic Hypogonadism

Author

Bayram, Yavuz, primary, Gulsuner, Suleyman, additional, Guran, Tulay, additional, Abaci, Ayhan, additional, Yesil, Gozde, additional, Gulsuner, Hilal Unal, additional, Atay, Zeynep, additional, Pierce, Sarah B., additional, Gambin, Tomasz, additional, Lee, Ming, additional, Turan, Serap, additional, Bober, Ece, additional, Atik, Mehmed M., additional, Walsh, Tom, additional, Karaca, Ender, additional, Pehlivan, Davut, additional, Jhangiani, Shalini N., additional, Muzny, Donna, additional, Bereket, Abdullah, additional, Buyukgebiz, Atilla, additional, Boerwinkle, Eric, additional, Gibbs, Richard A., additional, King, Mary-Claire, additional, and Lupski, James R., additional

Published
2015
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177. Tu2021 High-Throughput Analyses of Liver Nucleic Acids Failed to Unravel a Common Etiology of Biliary Atresia

Author

Kellermayer, Richard, primary, Nagy-Szakal, Dorottya, additional, Harris, Ronald A., additional, Tamara, Pereira N., additional, Lewindon, Peter, additional, Jhangiani, Shalini N., additional, Gambin, Tomasz, additional, Harpavat, Sanjiv, additional, Wiszniewski, Wojciech K., additional, Xavier, Daniela Dias, additional, Bernardi, Mylinh, additional, White, Lisa D., additional, Gibbs, Richard, additional, Finegold, Milton J., additional, Lupski, James R., additional, Belmont, John W., additional, Ramm, Grant A., additional, and Shepherd, Ross W., additional

Published
2015
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178. DVL1 Frameshift Mutations Clustering in the Penultimate Exon Cause Autosomal-Dominant Robinow Syndrome

Author

White, Janson, primary, Mazzeu, Juliana F., additional, Hoischen, Alexander, additional, Jhangiani, Shalini N., additional, Gambin, Tomasz, additional, Alcino, Michele Calijorne, additional, Penney, Samantha, additional, Saraiva, Jorge M., additional, Hove, Hanne, additional, Skovby, Flemming, additional, Kayserili, Hülya, additional, Estrella, Elicia, additional, Vulto-van Silfhout, Anneke T., additional, Steehouwer, Marloes, additional, Muzny, Donna M., additional, Sutton, V. Reid, additional, Gibbs, Richard A., additional, Lupski, James R., additional, Brunner, Han G., additional, van Bon, Bregje W.M., additional, and Carvalho, Claudia M.B., additional

Published
2015
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179. A Massive Expansion of Effector Genes Underlies Gall-Formation in the Wheat Pest Mayetiola destructor

Author

Zhao, Chaoyang, primary, Escalante, Lucio Navarro, additional, Chen, Hang, additional, Benatti, Thiago R., additional, Qu, Jiaxin, additional, Chellapilla, Sanjay, additional, Waterhouse, Robert M., additional, Wheeler, David, additional, Andersson, Martin N., additional, Bao, Riyue, additional, Batterton, Matthew, additional, Behura, Susanta K., additional, Blankenburg, Kerstin P., additional, Caragea, Doina, additional, Carolan, James C., additional, Coyle, Marcus, additional, El-Bouhssini, Mustapha, additional, Francisco, Liezl, additional, Friedrich, Markus, additional, Gill, Navdeep, additional, Grace, Tony, additional, Grimmelikhuijzen, Cornelis J.P., additional, Han, Yi, additional, Hauser, Frank, additional, Herndon, Nicolae, additional, Holder, Michael, additional, Ioannidis, Panagiotis, additional, Jackson, LaRonda, additional, Javaid, Mehwish, additional, Jhangiani, Shalini N., additional, Johnson, Alisha J., additional, Kalra, Divya, additional, Korchina, Viktoriya, additional, Kovar, Christie L., additional, Lara, Fremiet, additional, Lee, Sandra L., additional, Liu, Xuming, additional, Löfstedt, Christer, additional, Mata, Robert, additional, Mathew, Tittu, additional, Muzny, Donna M., additional, Nagar, Swapnil, additional, Nazareth, Lynne V., additional, Okwuonu, Geoffrey, additional, Ongeri, Fiona, additional, Perales, Lora, additional, Peterson, Brittany F., additional, Pu, Ling-Ling, additional, Robertson, Hugh M., additional, Schemerhorn, Brandon J., additional, Scherer, Steven E., additional, Shreve, Jacob T., additional, Simmons, DeNard, additional, Subramanyam, Subhashree, additional, Thornton, Rebecca L., additional, Xue, Kun, additional, Weissenberger, George M., additional, Williams, Christie E., additional, Worley, Kim C., additional, Zhu, Dianhui, additional, Zhu, Yiming, additional, Harris, Marion O., additional, Shukle, Richard H., additional, Werren, John H., additional, Zdobnov, Evgeny M., additional, Chen, Ming-Shun, additional, Brown, Susan J., additional, Stuart, Jeffery J., additional, and Richards, Stephen, additional

Published
2015
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180. Targeted Sequencing in Chromosome 17q Linkage Region Identifies Familial Glioma Candidates in the Gliogene Consortium

Author

Jalali, Ali, primary, Amirian, E. Susan, additional, Bainbridge, Matthew N., additional, Armstrong, Georgina N., additional, Liu, Yanhong, additional, Tsavachidis, Spyros, additional, Jhangiani, Shalini N., additional, Plon, Sharon E., additional, Lau, Ching C., additional, Claus, Elizabeth B., additional, Barnholtz-Sloan, Jill S., additional, Il'yasova, Dora, additional, Schildkraut, Joellen, additional, Ali-Osman, Francis, additional, Sadetzki, Siegal, additional, Johansen, Christoffer, additional, Houlston, Richard S., additional, Jenkins, Robert B., additional, Lachance, Daniel, additional, Olson, Sara H., additional, Bernstein, Jonine L., additional, Merrell, Ryan T., additional, Wrensch, Margaret R., additional, Davis, Faith G., additional, Lai, Rose, additional, Shete, Sanjay, additional, Aldape, Kenneth, additional, Amos, Christopher I., additional, Muzny, Donna M., additional, Gibbs, Richard A., additional, Melin, Beatrice S., additional, and Bondy, Melissa L., additional

Published
2015
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181. Germline Mutations in Shelterin Complex Genes Are Associated With Familial Glioma

Author

Bainbridge, Matthew N., primary, Armstrong, Georgina N., additional, Gramatges, M. Monica, additional, Bertuch, Alison A., additional, Jhangiani, Shalini N., additional, Doddapaneni, Harsha, additional, Lewis, Lora, additional, Tombrello, Joseph, additional, Tsavachidis, Spyros, additional, Liu, Yanhong, additional, Jalali, Ali, additional, Plon, Sharon E., additional, Lau, Ching C., additional, Parsons, Donald W., additional, Claus, Elizabeth B., additional, Barnholtz-Sloan, Jill, additional, Il’yasova, Dora, additional, Schildkraut, Joellen, additional, Ali-Osman, Francis, additional, Sadetzki, Siegal, additional, Johansen, Christoffer, additional, Houlston, Richard S., additional, Jenkins, Robert B., additional, Lachance, Daniel, additional, Olson, Sara H., additional, Bernstein, Jonine L., additional, Merrell, Ryan T., additional, Wrensch, Margaret R., additional, Walsh, Kyle M., additional, Davis, Faith G., additional, Lai, Rose, additional, Shete, Sanjay, additional, Aldape, Kenneth, additional, Amos, Christopher I., additional, Thompson, Patricia A., additional, Muzny, Donna M., additional, Gibbs, Richard A., additional, Melin, Beatrice S., additional, and Bondy, Melissa L., additional

Published
2014
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182. A potential founder variant in CARMIL2/RLTPR in three Norwegian families with warts, molluscum contagiosum, and T-cell dysfunction.

Author

Sorte, Hanne S., Osnes, Liv T., Fevang, Børre, Aukrust, Pål, Erichsen, Hans C., Backe, Paul H., Abrahamsen, Tore G., Kittang, Ole B., Øverland, Torstein, Jhangiani, Shalini N., Muzny, Donna M., Vigeland, Magnus D., Samarakoon, Pubudu, Gambin, Tomasz, Akdemir, Zeynep H. C., Gibbs, Richard A., Rødningen, Olaug K., Lyle, Robert, Lupski, James R., and Stray ‐ Pedersen, Asbjørg

Subjects
HETEROZYGOSITY, WARTS, MOLLUSCUM contagiosum, T cells, EXOMES, IMMUNODEFICIENCY
Abstract

Background Four patients from three Norwegian families presented with a common skin phenotype of warts, molluscum contagiosum, and dermatitis since early childhood, and various other immunological features. Warts are a common manifestation of human papilloma virus ( HPV), but when they are overwhelming, disseminated and/or persistent, and presenting together with other immunological features, a primary immunodeficiency disease ( PIDD) may be suspected. Methods and results The four patients were exome sequenced as part of a larger study for detecting genetic causes of primary immunodeficiencies. No disease-causing variants were identified in known primary immunodeficiency genes or in other disease-related OMIM genes. However, the same homozygous missense variant in CARMIL2 (also known as RLTPR) was identified in all four patients. In each family, the variant was located within a narrow region of homozygosity, representing a potential region of autozygosity. CARMIL2 is a protein of undetermined function. A role in T-cell activation has been suggested and the mouse protein homolog (Rltpr) is essential for costimulation of T-cell activation via CD28, and for the development of regulatory T cells. Immunophenotyping demonstrated reduced regulatory, CD4+ memory, and CD4+ follicular T cells in all four patients. In addition, they all seem to have a deficiency in IFN γ -synthesis in CD4+ T cells and NK cells. Conclusions We report a novel primary immunodeficiency, and a differential molecular diagnosis to CXCR4-, DOCK8-, GATA2-, MAGT1-, MCM4-, STK4-, RHOH-, TMC6-, and TMC8-related diseases. The specific variant may represent a Norwegian founder variant segregating on a population-specific haplotype. [ABSTRACT FROM AUTHOR]

Published
2016
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183. A Drosophila Genetic Resource of Mutants to Study Mechanisms Underlying Human Genetic Diseases

Author

Yamamoto, Shinya, primary, Jaiswal, Manish, additional, Charng, Wu-Lin, additional, Gambin, Tomasz, additional, Karaca, Ender, additional, Mirzaa, Ghayda, additional, Wiszniewski, Wojciech, additional, Sandoval, Hector, additional, Haelterman, Nele A., additional, Xiong, Bo, additional, Zhang, Ke, additional, Bayat, Vafa, additional, David, Gabriela, additional, Li, Tongchao, additional, Chen, Kuchuan, additional, Gala, Upasana, additional, Harel, Tamar, additional, Pehlivan, Davut, additional, Penney, Samantha, additional, Vissers, Lisenka E.L.M., additional, de Ligt, Joep, additional, Jhangiani, Shalini N., additional, Xie, Yajing, additional, Tsang, Stephen H., additional, Parman, Yesim, additional, Sivaci, Merve, additional, Battaloglu, Esra, additional, Muzny, Donna, additional, Wan, Ying-Wooi, additional, Liu, Zhandong, additional, Lin-Moore, Alexander T., additional, Clark, Robin D., additional, Curry, Cynthia J., additional, Link, Nichole, additional, Schulze, Karen L., additional, Boerwinkle, Eric, additional, Dobyns, William B., additional, Allikmets, Rando, additional, Gibbs, Richard A., additional, Chen, Rui, additional, Lupski, James R., additional, Wangler, Michael F., additional, and Bellen, Hugo J., additional

Published
2014
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184. PGM3 Mutations Cause a Congenital Disorder of Glycosylation with Severe Immunodeficiency and Skeletal Dysplasia

Author

Stray-Pedersen, Asbjørg, primary, Backe, Paul H., additional, Sorte, Hanne S., additional, Mørkrid, Lars, additional, Chokshi, Niti Y., additional, Erichsen, Hans Christian, additional, Gambin, Tomasz, additional, Elgstøen, Katja B.P., additional, Bjørås, Magnar, additional, Wlodarski, Marcin W., additional, Krüger, Marcus, additional, Jhangiani, Shalini N., additional, Muzny, Donna M., additional, Patel, Ankita, additional, Raymond, Kimiyo M., additional, Sasa, Ghadir S., additional, Krance, Robert A., additional, Martinez, Caridad A., additional, Abraham, Shirley M., additional, Speckmann, Carsten, additional, Ehl, Stephan, additional, Hall, Patricia, additional, Forbes, Lisa R., additional, Merckoll, Else, additional, Westvik, Jostein, additional, Nishimura, Gen, additional, Rustad, Cecilie F., additional, Abrahamsen, Tore G., additional, Rønnestad, Arild, additional, Osnes, Liv T., additional, Egeland, Torstein, additional, Rødningen, Olaug K., additional, Beck, Christine R., additional, Boerwinkle, Eric A., additional, Gibbs, Richard A., additional, Lupski, James R., additional, Orange, Jordan S., additional, Lausch, Ekkehart, additional, and Hanson, I. Celine, additional

Published
2014
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185. Structural variation and missense mutation in SBDSassociated with Shwachman-Diamond syndrome

Author

Carvalho, Claudia M B, primary, Zuccherato, Luciana W, additional, Williams, Christopher L, additional, Neill, Nicholas J, additional, Murdock, David R, additional, Bainbridge, Matthew, additional, Jhangiani, Shalini N, additional, Muzny, Donna M, additional, Gibbs, Richard A, additional, Ip, Wan, additional, Guillerman, Robert Paul, additional, Lupski, James R, additional, and Bertuch, Alison A, additional

Published
2014
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186. Human CLP1 Mutations Alter tRNA Biogenesis, Affecting Both Peripheral and Central Nervous System Function

Author

Karaca, Ender, primary, Weitzer, Stefan, additional, Pehlivan, Davut, additional, Shiraishi, Hiroshi, additional, Gogakos, Tasos, additional, Hanada, Toshikatsu, additional, Jhangiani, Shalini N., additional, Wiszniewski, Wojciech, additional, Withers, Marjorie, additional, Campbell, Ian M., additional, Erdin, Serkan, additional, Isikay, Sedat, additional, Franco, Luis M., additional, Gonzaga-Jauregui, Claudia, additional, Gambin, Tomasz, additional, Gelowani, Violet, additional, Hunter, Jill V., additional, Yesil, Gozde, additional, Koparir, Erkan, additional, Yilmaz, Sarenur, additional, Brown, Miguel, additional, Briskin, Daniel, additional, Hafner, Markus, additional, Morozov, Pavel, additional, Farazi, Thalia A., additional, Bernreuther, Christian, additional, Glatzel, Markus, additional, Trattnig, Siegfried, additional, Friske, Joachim, additional, Kronnerwetter, Claudia, additional, Bainbridge, Matthew N., additional, Gezdirici, Alper, additional, Seven, Mehmet, additional, Muzny, Donna M., additional, Boerwinkle, Eric, additional, Ozen, Mustafa, additional, Clausen, Tim, additional, Tuschl, Thomas, additional, Yuksel, Adnan, additional, Hess, Andreas, additional, Gibbs, Richard A., additional, Martinez, Javier, additional, Penninger, Josef M., additional, and Lupski, James R., additional

Published
2014
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187. Expanding the phenotypic spectrum of ARID1B-mediated disorders and identification of altered cell-cycle dynamics due to ARID1B haploinsufficiency

Author

Sim, Joe C H, primary, White, Susan M, additional, Fitzpatrick, Elizabeth, additional, Wilson, Gabrielle R, additional, Gillies, Greta, additional, Pope, Kate, additional, Mountford, Hayley S, additional, Torring, Pernille M, additional, McKee, Shane, additional, Vulto-van Silfhout, Anneke T, additional, Jhangiani, Shalini N, additional, Muzny, Donna M, additional, Leventer, Richard J, additional, Delatycki, Martin B, additional, Amor, David J, additional, and Lockhart, Paul J, additional

Published
2014
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188. Mutations inVRK1Associated With Complex Motor and Sensory Axonal Neuropathy Plus Microcephaly

Author

Gonzaga-Jauregui, Claudia, primary, Lotze, Timothy, additional, Jamal, Leila, additional, Penney, Samantha, additional, Campbell, Ian M., additional, Pehlivan, Davut, additional, Hunter, Jill V., additional, Woodbury, Suzanne L., additional, Raymond, Gerald, additional, Adesina, Adekunle M., additional, Jhangiani, Shalini N., additional, Reid, Jeffrey G., additional, Muzny, Donna M., additional, Boerwinkle, Eric, additional, Lupski, James R., additional, Gibbs, Richard A., additional, and Wiszniewski, Wojciech, additional

Published
2013
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189. Exome sequencing in mostly consanguineous Arab families with neurologic disease provides a high potential molecular diagnosis rate.

Author

Wu-Lin Charng, Karaca, Ender, Coban Akdemir, Zeynep, Gambin, Tomasz, Atik, Mehmed M., Shen Gu, Posey, Jennifer E., Jhangiani, Shalini N., Muzny, Donna M., Doddapaneni, Harsha, Jianhong Hu, Boerwinkle, Eric, Gibbs, Richard A., Rosenfeld, Jill A., Hong Cui, Fan Xia, Manickam, Kandamurugu, Yaping Yang, Faqeih, Eissa A., and Al Asmari, Ali

Subjects
EXOMES, NUCLEOTIDE sequencing, DNA analysis, NUCLEOTIDE analysis, NEURODEVELOPMENTAL treatment
Abstract

Background: Neurodevelopment is orchestrated by a wide range of genes, and the genetic causes of neurodevelopmental disorders are thus heterogeneous. We applied whole exome sequencing (WES) for molecular diagnosis and in silico analysis to identify novel disease gene candidates in a cohort from Saudi Arabia with primarily Mendelian neurologic diseases. Methods: We performed WES in 31 mostly consanguineous Arab families and analyzed both single nucleotide and copy number variants (CNVs) from WES data. Interaction/expression network and pathway analyses, as well as paralog studies were utilized to investigate potential pathogenicity and disease association of novel candidate genes. Additional cases for candidate genes were identified through the clinical WES database at Baylor Miraca Genetics Laboratories and GeneMatcher. Results: We found known pathogenic or novel variants in known disease genes with phenotypic expansion in 6 families, disease-associated CNVs in 2 families, and 12 novel disease gene candidates in 11 families, including KIF5B, GRM7, FOXP4, MLLT1, and KDM2B. Overall, a potential molecular diagnosis was provided by variants in known disease genes in 17 families (54.8 %) and by novel candidate disease genes in an additional 11 families, making the potential molecular diagnostic rate ~90 %. Conclusions: Molecular diagnostic rate from WES is improved by exome-predicted CNVs. Novel candidate disease gene discovery is facilitated by paralog studies and through the use of informatics tools and available databases to identify additional evidence for pathogenicity. Trial registration: Not applicable. [ABSTRACT FROM AUTHOR]

Published
2016
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190. Multiallelic Positions in the Human Genome: Challenges for Genetic Analyses.

Author

Campbell, Ian M., Gambin, Tomasz, Jhangiani, Shalini N., Grove, Megan L., Veeraraghavan, Narayanan, Muzny, Donna M., Shaw, Chad A., Gibbs, Richard A., Boerwinkle, Eric, Yu, Fuli, and Lupski, James R.

Abstract

ABSTRACT As the amount of human genomic sequence available from personal genomes and exomes has increased, so too has the observation of genomic positions having two or more alternative alleles, so-called multiallelic sites. For portions of the haploid genome that are present in more than one copy, including segmental duplications, variation at such multisite variant positions becomes even more complex. Despite the frequency of multiallelic variants, a number of commonly used resources and tools in genomic research and diagnostics do not support these multiallelic variants all together or require special modifications. Here, we explore the frequency of multiallelic sites in large samples with whole exome sequencing and discuss potential outcomes of failing to account for multiple variant alleles. We also briefly discuss some commonly utilized resources that fully support multiallelic sites. [ABSTRACT FROM AUTHOR]

Published
2016
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191. 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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192. Rare variants in the notch signaling pathway describe a novel type of autosomal recessive Klippel-Feil syndrome.

Author

Karaca, Ender, Yuregir, Ozge O., Bozdogan, Sevcan T., Aslan, Huseyin, Pehlivan, Davut, Jhangiani, Shalini N., Akdemir, Zeynep C., Gambin, Tomasz, Bayram, Yavuz, Atik, Mehmed M., Erdin, Serkan, Muzny, Donna, Gibbs, Richard A., and Lupski, James R.

Abstract

Klippel-Feil syndrome is a rare disorder represented by a subgroup of segmentation defects of the vertebrae and characterized by fusion of the cervical vertebrae, low posterior hairline, and short neck with limited motion. Both autosomal dominant and recessive inheritance patterns were reported in families with Klippel-Feil. Mutated genes for both dominant ( GDF6 and GDF3) and recessive ( MEOX1) forms of Klippel-Feil syndrome have been shown to be involved in somite development via transcription regulation and signaling pathways. Heterotaxy arises from defects in proteins that function in the development of left-right asymmetry of the developing embryo. We describe a consanguineous family with a male proband who presents with classical Klippel-Feil syndrome together with heterotaxy (situs inversus totalis). The present patient also had Sprengel's deformity, deformity of the sternum, and a solitary kidney. Using exome sequencing, we identified a homozygous frameshift mutation (c.299delT; p.L100fs) in RIPPLY2, a gene shown to play a crucial role in somitogenesis and participate in the Notch signaling pathway via negatively regulating Tbx6. Our data confirm RIPPLY2 as a novel gene for autosomal recessive Klippel-Feil syndrome, and in addition-from a mechanistic standpoint-suggest the possibility that mutations in RIPPLY2 could also lead to heterotaxy. © 2015 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Published
2015
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193. Epistasis dominates the genetic architecture of Drosophila quantitative traits

Author

Huang, Wen, primary, Richards, Stephen, additional, Carbone, Mary Anna, additional, Zhu, Dianhui, additional, Anholt, Robert R. H., additional, Ayroles, Julien F., additional, Duncan, Laura, additional, Jordan, Katherine W., additional, Lawrence, Faye, additional, Magwire, Michael M., additional, Warner, Crystal B., additional, Blankenburg, Kerstin, additional, Han, Yi, additional, Javaid, Mehwish, additional, Jayaseelan, Joy, additional, Jhangiani, Shalini N., additional, Muzny, Donna, additional, Ongeri, Fiona, additional, Perales, Lora, additional, Wu, Yuan-Qing, additional, Zhang, Yiqing, additional, Zou, Xiaoyan, additional, Stone, Eric A., additional, Gibbs, Richard A., additional, and Mackay, Trudy F. C., additional

Published
2012
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194. The Drosophila melanogaster Genetic Reference Panel

Author

Mackay, Trudy F. C., primary, Richards, Stephen, additional, Stone, Eric A., additional, Barbadilla, Antonio, additional, Ayroles, Julien F., additional, Zhu, Dianhui, additional, Casillas, Sònia, additional, Han, Yi, additional, Magwire, Michael M., additional, Cridland, Julie M., additional, Richardson, Mark F., additional, Anholt, Robert R. H., additional, Barrón, Maite, additional, Bess, Crystal, additional, Blankenburg, Kerstin Petra, additional, Carbone, Mary Anna, additional, Castellano, David, additional, Chaboub, Lesley, additional, Duncan, Laura, additional, Harris, Zeke, additional, Javaid, Mehwish, additional, Jayaseelan, Joy Christina, additional, Jhangiani, Shalini N., additional, Jordan, Katherine W., additional, Lara, Fremiet, additional, Lawrence, Faye, additional, Lee, Sandra L., additional, Librado, Pablo, additional, Linheiro, Raquel S., additional, Lyman, Richard F., additional, Mackey, Aaron J., additional, Munidasa, Mala, additional, Muzny, Donna Marie, additional, Nazareth, Lynne, additional, Newsham, Irene, additional, Perales, Lora, additional, Pu, Ling-Ling, additional, Qu, Carson, additional, Ràmia, Miquel, additional, Reid, Jeffrey G., additional, Rollmann, Stephanie M., additional, Rozas, Julio, additional, Saada, Nehad, additional, Turlapati, Lavanya, additional, Worley, Kim C., additional, Wu, Yuan-Qing, additional, Yamamoto, Akihiko, additional, Zhu, Yiming, additional, Bergman, Casey M., additional, Thornton, Kevin R., additional, Mittelman, David, additional, and Gibbs, Richard A., additional

Published
2012
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195. Enrichment of mutations in chromatin regulators in people with Rett syndrome lacking mutations in MECP2

Author

Sajan, Samin A., Jhangiani, Shalini N., Muzny, Donna M., Gibbs, Richard A., Lupski, James R., Glaze, Daniel G., Kaufmann, Walter E., Skinner, Steven A., Annese, Fran, Friez, Michael J., Lane, Jane, Percy, Alan K., and Neul, Jeffrey L.

Abstract

Purpose:Rett syndrome (RTT) is a neurodevelopmental disorder caused primarily by de novo mutations in MECP2 and sometimes in CDKL5 and FOXG1. However, some RTT patients lack mutations in these genes.Methods:Twenty-two RTT patients without apparent MECP2, CDKL5, and FOXG1 mutations were subjected to both whole-exome sequencing and single-nucleotide polymorphism array–based copy-number variant (CNV) analyses.Results:Three patients had MECP2 mutations initially missed by clinical testing. Of the remaining 19, 17 (89.5%) had 29 other likely pathogenic intragenic mutations and/or CNVs (10 patients had 2 or more). Interestingly, 13 patients had mutations in a gene/region previously reported in other neurodevelopmental disorders (NDDs), thereby providing a potential diagnostic yield of 68.4%. These mutations were significantly enriched in chromatin regulators (corrected P = 0.0068) and moderately enriched in postsynaptic cell membrane molecules (corrected P = 0.076), implicating glutamate receptor signaling.Conclusion:The genetic etiology of RTT without MECP2, CDKL5, and FOXG1 mutations is heterogeneous, overlaps with other NDDs, and complicated by a high mutation burden. Dysregulation of chromatin structure and abnormal excitatory synaptic signaling may form two common pathological bases of RTT.Genet Med 19 1, 13–19.

Published
2017
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196. CAV3mutation in a patient with transient hyperCKemia and myalgia

Author

Macias, Anna, Gambin, Tomasz, Szafranski, Przemyslaw, Jhangiani, Shalini N., Kolasa, Anna, Obersztyn, Ewa, Lupski, James R., Stankiewicz, Pawel, and Kaminska, Anna

Abstract

Mutations in caveolin-3(CAV3) can lead to different clinical phenotypes affecting skeletal or cardiac muscles. Here, we describe a patient with Klinefelter syndrome, ulcerative colitis and Sjögren syndrome, who developed transient hyperCKemia, myalgia and mild muscular weakness. Using whole exome sequencing (WES), a missense mutation G169A was found in the CAV3gene. In addition, we identified a homozygous frameshift deletion in MS4A12that may contribute to inflammatory bowel disease, further demonstrating usefulness of WES in dual molecular diagnoses.

Published
2016
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197. Novel mutations in LRP6highlight the role of WNT signaling in tooth agenesis

Author

Ockeloen, Charlotte W., Khandelwal, Kriti D., Dreesen, Karoline, Ludwig, Kerstin U., Sullivan, Robert, van Rooij, Iris A.L.M., Thonissen, Michelle, Swinnen, Steven, Phan, Milien, Conte, Federica, Ishorst, Nina, Gilissen, Christian, Roa Fuentes, Laury, van de Vorst, Maartje, Henkes, Arjen, Steehouwer, Marloes, van Beusekom, Ellen, Bloemen, Marjon, Vankeirsbilck, Bruno, Bergé, Stefaan, Hens, Greet, Schoenaers, Joseph, Vander Poorten, Vincent, Roosenboom, Jasmien, Verdonck, An, Devriendt, Koen, Roeleveldt, Nel, Jhangiani, Shalini N., Vissers, Lisenka E.L.M., Lupski, James R., de Ligt, Joep, Von den Hoff, Johannes W., Pfundt, Rolph, Brunner, Han G., Zhou, Huiqing, Dixon, Jill, Mangold, Elisabeth, van Bokhoven, Hans, Dixon, Michael J., Kleefstra, Tjitske, Hoischen, Alexander, and Carels, Carine E.L.

Abstract

We aimed to identify a novel genetic cause of tooth agenesis (TA) and/or orofacial clefting (OFC) by combining whole-exome sequencing (WES) and targeted resequencing in a large cohort of TA and OFC patients.

Published
2016
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198. Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development

Author

Renfree, Marilyn B, primary, Papenfuss, Anthony T, additional, Deakin, Janine E, additional, Lindsay, James, additional, Heider, Thomas, additional, Belov, Katherine, additional, Rens, Willem, additional, Waters, Paul D, additional, Pharo, Elizabeth A, additional, Shaw, Geoff, additional, Wong, Emily SW, additional, Lefèvre, Christophe M, additional, Nicholas, Kevin R, additional, Kuroki, Yoko, additional, Wakefield, Matthew J, additional, Zenger, Kyall R, additional, Wang, Chenwei, additional, Ferguson-Smith, Malcolm, additional, Nicholas, Frank W, additional, Hickford, Danielle, additional, Yu, Hongshi, additional, Short, Kirsty R, additional, Siddle, Hannah V, additional, Frankenberg, Stephen R, additional, Chew, Keng Y, additional, Menzies, Brandon R, additional, Stringer, Jessica M, additional, Suzuki, Shunsuke, additional, Hore, Timothy A, additional, Delbridge, Margaret L, additional, Patel, Hardip, additional, Mohammadi, Amir, additional, Schneider, Nanette Y, additional, Hu, Yanqiu, additional, O'Hara, William, additional, Al Nadaf, Shafagh, additional, Wu, Chen, additional, Feng, Zhi-Ping, additional, Cocks, Benjamin G, additional, Wang, Jianghui, additional, Flicek, Paul, additional, Searle, Stephen MJ, additional, Fairley, Susan, additional, Beal, Kathryn, additional, Herrero, Javier, additional, Carone, Dawn M, additional, Suzuki, Yutaka, additional, Sugano, Sumio, additional, Toyoda, Atsushi, additional, Sakaki, Yoshiyuki, additional, Kondo, Shinji, additional, Nishida, Yuichiro, additional, Tatsumoto, Shoji, additional, Mandiou, Ion, additional, Hsu, Arthur, additional, McColl, Kaighin A, additional, Lansdell, Benjamin, additional, Weinstock, George, additional, Kuczek, Elizabeth, additional, McGrath, Annette, additional, Wilson, Peter, additional, Men, Artem, additional, Hazar-Rethinam, Mehlika, additional, Hall, Allison, additional, Davis, John, additional, Wood, David, additional, Williams, Sarah, additional, Sundaravadanam, Yogi, additional, Muzny, Donna M, additional, Jhangiani, Shalini N, additional, Lewis, Lora R, additional, Morgan, Margaret B, additional, Okwuonu, Geoffrey O, additional, Ruiz, San J, additional, Santibanez, Jireh, additional, Nazareth, Lynne, additional, Cree, Andrew, additional, Fowler, Gerald, additional, Kovar, Christie L, additional, Dinh, Huyen H, additional, Joshi, Vandita, additional, Jing, Chyn, additional, Lara, Fremiet, additional, Thornton, Rebecca, additional, Chen, Lei, additional, Deng, Jixin, additional, Liu, Yue, additional, Shen, Joshua Y, additional, Song, Xing-Zhi, additional, Edson, Janette, additional, Troon, Carmen, additional, Thomas, Daniel, additional, Stephens, Amber, additional, Yapa, Lankesha, additional, Levchenko, Tanya, additional, Gibbs, Richard A, additional, Cooper, Desmond W, additional, Speed, Terence P, additional, Fujiyama, Asao, additional, M Graves, Jennifer A, additional, O'Neill, Rachel J, additional, Pask, Andrew J, additional, Forrest, Susan M, additional, and Worley, Kim C, additional

Published
2011
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199. Evolutionary and Biomedical Insights from the Rhesus Macaque Genome

Author

Gibbs, Richard A., primary, Rogers, Jeffrey, additional, Katze, Michael G., additional, Bumgarner, Roger, additional, Weinstock, George M., additional, Mardis, Elaine R., additional, Remington, Karin A., additional, Strausberg, Robert L., additional, Venter, J. Craig, additional, Wilson, Richard K., additional, Batzer, Mark A., additional, Bustamante, Carlos D., additional, Eichler, Evan E., additional, Hahn, Matthew W., additional, Hardison, Ross C., additional, Makova, Kateryna D., additional, Miller, Webb, additional, Milosavljevic, Aleksandar, additional, Palermo, Robert E., additional, Siepel, Adam, additional, Sikela, James M., additional, Attaway, Tony, additional, Bell, Stephanie, additional, Bernard, Kelly E., additional, Buhay, Christian J., additional, Chandrabose, Mimi N., additional, Dao, Marvin, additional, Davis, Clay, additional, Delehaunty, Kimberly D., additional, Ding, Yan, additional, Dinh, Huyen H., additional, Dugan-Rocha, Shannon, additional, Fulton, Lucinda A., additional, Gabisi, Ramatu Ayiesha, additional, Garner, Toni T., additional, Godfrey, Jennifer, additional, Hawes, Alicia C., additional, Hernandez, Judith, additional, Hines, Sandra, additional, Holder, Michael, additional, Hume, Jennifer, additional, Jhangiani, Shalini N., additional, Joshi, Vandita, additional, Khan, Ziad Mohid, additional, Kirkness, Ewen F., additional, Cree, Andrew, additional, Fowler, R. Gerald, additional, Lee, Sandra, additional, Lewis, Lora R., additional, Li, Zhangwan, additional, Liu, Yih-shin, additional, Moore, Stephanie M., additional, Muzny, Donna, additional, Nazareth, Lynne V., additional, Ngo, Dinh Ngoc, additional, Okwuonu, Geoffrey O., additional, Pai, Grace, additional, Parker, David, additional, Paul, Heidie A., additional, Pfannkoch, Cynthia, additional, Pohl, Craig S., additional, Rogers, Yu-Hui, additional, Ruiz, San Juana, additional, Sabo, Aniko, additional, Santibanez, Jireh, additional, Schneider, Brian W., additional, Smith, Scott M., additional, Sodergren, Erica, additional, Svatek, Amanda F., additional, Utterback, Teresa R., additional, Vattathil, Selina, additional, Warren, Wesley, additional, White, Courtney Sherell, additional, Chinwalla, Asif T., additional, Feng, Yucheng, additional, Halpern, Aaron L., additional, Hillier, LaDeana W., additional, Huang, Xiaoqiu, additional, Minx, Pat, additional, Nelson, Joanne O., additional, Pepin, Kymberlie H., additional, Qin, Xiang, additional, Sutton, Granger G., additional, Venter, Eli, additional, Walenz, Brian P., additional, Wallis, John W., additional, Worley, Kim C., additional, Yang, Shiaw-Pyng, additional, Jones, Steven M., additional, Marra, Marco A., additional, Rocchi, Mariano, additional, Schein, Jacqueline E., additional, Baertsch, Robert, additional, Clarke, Laura, additional, Csürös, Miklós, additional, Glasscock, Jarret, additional, Harris, R. Alan, additional, Havlak, Paul, additional, Jackson, Andrew R., additional, Jiang, Huaiyang, additional, Liu, Yue, additional, Messina, David N., additional, Shen, Yufeng, additional, Song, Henry Xing-Zhi, additional, Wylie, Todd, additional, Zhang, Lan, additional, Birney, Ewan, additional, Han, Kyudong, additional, Konkel, Miriam K., additional, Lee, Jungnam, additional, Smit, Arian F. A., additional, Ullmer, Brygg, additional, Wang, Hui, additional, Xing, Jinchuan, additional, Burhans, Richard, additional, Cheng, Ze, additional, Karro, John E., additional, Ma, Jian, additional, Raney, Brian, additional, She, Xinwei, additional, Cox, Michael J., additional, Demuth, Jeffery P., additional, Dumas, Laura J., additional, Han, Sang-Gook, additional, Hopkins, Janet, additional, Karimpour-Fard, Anis, additional, Kim, Young H., additional, Pollack, Jonathan R., additional, Vinar, Tomas, additional, Addo-Quaye, Charles, additional, Degenhardt, Jeremiah, additional, Denby, Alexandra, additional, Hubisz, Melissa J., additional, Indap, Amit, additional, Kosiol, Carolin, additional, Lahn, Bruce T., additional, Lawson, Heather A., additional, Marklein, Alison, additional, Nielsen, Rasmus, additional, Vallender, Eric J., additional, Clark, Andrew G., additional, Ferguson, Betsy, additional, Hernandez, Ryan D., additional, Hirani, Kashif, additional, Kehrer-Sawatzki, Hildegard, additional, Kolb, Jessica, additional, Patil, Shobha, additional, Pu, Ling-Ling, additional, Ren, Yanru, additional, Smith, David Glenn, additional, Wheeler, David A., additional, Schenck, Ian, additional, Ball, Edward V., additional, Chen, Rui, additional, Cooper, David N., additional, Giardine, Belinda, additional, Hsu, Fan, additional, Kent, W. James, additional, Lesk, Arthur, additional, Nelson, David L., additional, O'Brien, William E., additional, Prüfer, Kay, additional, Stenson, Peter D., additional, Wallace, James C., additional, Ke, Hui, additional, Liu, Xiao-Ming, additional, Wang, Peng, additional, Xiang, Andy Peng, additional, Yang, Fan, additional, Barber, Galt P., additional, Haussler, David, additional, Karolchik, Donna, additional, Kern, Andy D., additional, Kuhn, Robert M., additional, Smith, Kayla E., additional, and Zwieg, Ann S., additional

Published
2007
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200. Exome sequencing identifies a homozygous C5orf42 variant in a Turkish kindred with oral-facial-digital syndrome type VI.

Author

Bayram, Yavuz, Aydin, Hatip, Gambin, Tomasz, Akdemir, Zeynep Coban, Atik, Mehmed M., Karaca, Ender, Karaman, Ali, Pehlivan, Davut, Jhangiani, Shalini N., Gibbs, Richard A., and Lupski, James R.

Abstract

Oral-facial-digital syndrome type VI (OFDVI) is a rare ciliopathy in the spectrum of Joubert syndrome (JS) and distinguished from other oral-facial-digital syndromes by metacarpal abnormalities with central polydactyly and by a molar tooth sign on cranial MRI. Additional characteristic features include short stature, micrognathia, posteriorly rotated low-set ears, hypertelorism, epicanthal folds, broad nasal tip, tongue hamartoma, upper lip notch, intraoral frenula, cleft lip/palate, and renal anomalies. Recently, novel mutations in C5orf42 were identified in 9 out of 11 OFDVI families. In a subsequent study C5orf42 was found to be mutated in only 2 out of 17 OFDVI probands while 28 patients with a pure JS phenotype also had pathogenic mutations of C5orf42. We report on two affected cousins diagnosed with OFDVI who were born from first degree cousin marriages. Whole exome sequencing (WES) identified a homozygous predicted damaging missense mutation (c.4034A > G; p.Gln1345Arg) in the C5orf42 gene. Our data contribute to the evidence that C5orf42 is one of the causative genes for OFDVI. © 2015 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Published
2015
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