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1. Expanding the clinical spectrum of biglycan-related Meester-Loeys syndrome

Author

Meester, Josephina A. N., Hebert, Anne, Bastiaansen, Maaike, Rabaut, Laura, Bastianen, Jarl, Boeckx, Nele, Ashcroft, Kathryn, Atwal, Paldeep S., Benichou, Antoine, Billon, Clarisse, Blankensteijn, Jan D., Brennan, Paul, Bucks, Stephanie A., Campbell, Ian M., Conrad, Solène, Curtis, Stephanie L., Dasouki, Majed, Dent, Carolyn L., Eden, James, Goel, Himanshu, Hartill, Verity, Houweling, Arjan C., Isidor, Bertrand, Jackson, Nicola, Koopman, Pieter, Korpioja, Anita, Kraatari-Tiri, Minna, Kuulavainen, Liina, Lee, Kelvin, Low, Karen J., Lu, Alan C., McManus, Morgan L., Oakley, Stephen P., Oliver, James, Organ, Nicole M., Overwater, Eline, Revencu, Nicole, Trainer, Alison H., Trivedi, Bhavya, Turner, Claire L. S., Whittington, Rebecca, Zankl, Andreas, Zentner, Dominica, Van Laer, Lut, Verstraeten, Aline, and Loeys, Bart L.

Published
2024
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2. Expanding the genotypic and phenotypic spectrum in a diverse cohort of 104 individuals with Wiedemann‐Steiner syndrome

Author

Sheppard, Sarah E, Campbell, Ian M, Harr, Margaret H, Gold, Nina, Li, Dong, Bjornsson, Hans T, Cohen, Julie S, Fahrner, Jill A, Fatemi, Ali, Harris, Jacqueline R, Nowak, Catherine, Stevens, Cathy A, Grand, Katheryn, Au, Margaret, Graham, John M, Sanchez‐Lara, Pedro A, Del Campo, Miguel, Jones, Marilyn C, Abdul‐Rahman, Omar, Alkuraya, Fowzan S, Bassetti, Jennifer A, Bergstrom, Katherine, Bhoj, Elizabeth, Dugan, Sarah, Kaplan, Julie D, Derar, Nada, Gripp, Karen W, Hauser, Natalie, Innes, A Micheil, Keena, Beth, Kodra, Neslida, Miller, Rebecca, Nelson, Beverly, Nowaczyk, Malgorzata J, Rahbeeni, Zuhair, Ben‐Shachar, Shay, Shieh, Joseph T, Slavotinek, Anne, Sobering, Andrew K, Abbott, Mary‐Alice, Allain, Dawn C, Amlie‐Wolf, Louise, Au, Ping Yee Billie, Bedoukian, Emma, Beek, Geoffrey, Barry, James, Berg, Janet, Bernstein, Jonathan A, Cytrynbaum, Cheryl, Chung, Brian Hon‐Yin, Donoghue, Sarah, Dorrani, Naghmeh, Eaton, Alison, Flores‐Daboub, Josue A, Dubbs, Holly, Felix, Carolyn A, Fong, Chin‐To, Fung, Jasmine Lee Fong, Gangaram, Balram, Goldstein, Amy, Greenberg, Rotem, Ha, Thoa K, Hersh, Joseph, Izumi, Kosuke, Kallish, Staci, Kravets, Elijah, Kwok, Pui‐Yan, Jobling, Rebekah K, Johnson, Amy E Knight, Kushner, Jessica, Lee, Bo Hoon, Levin, Brooke, Lindstrom, Kristin, Manickam, Kandamurugu, Mardach, Rebecca, McCormick, Elizabeth, McLeod, D Ross, Mentch, Frank D, Minks, Kelly, Muraresku, Colleen, Nelson, Stanley F, Porazzi, Patrizia, Pichurin, Pavel N, Powell‐Hamilton, Nina N, Powis, Zoe, Ritter, Alyssa, Rogers, Caleb, Rohena, Luis, Ronspies, Carey, Schroeder, Audrey, Stark, Zornitza, Starr, Lois, Stoler, Joan, Suwannarat, Pim, Velinov, Milen, Weksberg, Rosanna, Wilnai, Yael, Zadeh, Neda, Zand, Dina J, and Falk, Marni J

Subjects
Congenital Structural Anomalies, Clinical Research, Brain Disorders, Rare Diseases, Pediatric, Aetiology, 2.1 Biological and endogenous factors, Black People, Constipation, Failure to Thrive, Genetic Association Studies, Genetic Predisposition to Disease, Growth Disorders, Histone-Lysine N-Methyltransferase, Humans, Hypertrichosis, Intellectual Disability, Loss of Function Mutation, Myeloid-Lymphoid Leukemia Protein, Retrospective Studies, White People, hypertrichosis, KMT2A, MLL1, syndromic intellectual disability, syndromic short stature, Wiedemann&#8208, Steiner syndrome, Wiedemann-Steiner syndrome, Genetics, Clinical Sciences
Abstract

Wiedemann-Steiner syndrome (WSS) is an autosomal dominant disorder caused by monoallelic variants in KMT2A and characterized by intellectual disability and hypertrichosis. We performed a retrospective, multicenter, observational study of 104 individuals with WSS from five continents to characterize the clinical and molecular spectrum of WSS in diverse populations, to identify physical features that may be more prevalent in White versus Black Indigenous People of Color individuals, to delineate genotype-phenotype correlations, to define developmental milestones, to describe the syndrome through adulthood, and to examine clinicians' differential diagnoses. Sixty-nine of the 82 variants (84%) observed in the study were not previously reported in the literature. Common clinical features identified in the cohort included: developmental delay or intellectual disability (97%), constipation (63.8%), failure to thrive (67.7%), feeding difficulties (66.3%), hypertrichosis cubiti (57%), short stature (57.8%), and vertebral anomalies (46.9%). The median ages at walking and first words were 20 months and 18 months, respectively. Hypotonia was associated with loss of function (LoF) variants, and seizures were associated with non-LoF variants. This study identifies genotype-phenotype correlations as well as race-facial feature associations in an ethnically diverse cohort, and accurately defines developmental trajectories, medical comorbidities, and long-term outcomes in individuals with WSS.

Published
2021

4. Clinical decision support with a comprehensive in-EHR patient tracking system improves genetic testing follow up

Author

Campbell, Ian M, primary, Karavite, Dean J, additional, Mcmanus, Morgan L, additional, Cusick, Fred C, additional, Junod, David C, additional, Sheppard, Sarah E, additional, Lourie, Eli M, additional, Shelov, Eric D, additional, Hakonarson, Hakon, additional, Luberti, Anthony A, additional, Muthu, Naveen, additional, and Grundmeier, Robert W, additional

Published
2023
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6. Malate dehydrogenase 2 deficiency is an emerging cause of pediatric epileptic encephalopathy with a recognizable biochemical signature

Author

Priestley, Jessica R.C., primary, Pace, Lisa M., additional, Sen, Kuntal, additional, Aggarwal, Anjali, additional, Alves, Cesar Augusto P.F., additional, Campbell, Ian M., additional, Cuddapah, Sanmati R., additional, Engelhardt, Nicole M., additional, Eskandar, Marina, additional, Jolín García, Paloma C., additional, Gropman, Andrea, additional, Helbig, Ingo, additional, Hong, Xinying, additional, Gowda, Vykuntaraju K., additional, Lusk, Laina, additional, Trapane, Pamela, additional, Srinivasan, Varunvenkat M., additional, Suwannarat, Pim, additional, and Ganetzky, Rebecca D., additional

Published
2022
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7. Platelet findings in 22q11.2 deletion syndrome correlate with disease manifestations but do not correlate with GPIb surface expression

Author

Campbell, Ian M., primary, Crowley, T. Blaine, additional, Jobaliya, Chintan, additional, Bailey, Alice, additional, McGinn, Daniel E., additional, Gaiser, Kimberly, additional, Bassett, Anne, additional, Gur, Raquel E., additional, Morrow, Bernice, additional, Emanuel, Beverly S., additional, Franco, Aime T., additional, French, Deborah, additional, Zackai, Elaine H., additional, McDonald‐McGinn, Donna M., additional, and Lambert, Michele P., additional

Published
2022
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8. 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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9. Platelet findings in 22q11.2 deletion syndrome correlate with disease manifestations but do not correlate with GPIb surface expression.

Author

Campbell, Ian M., Crowley, T. Blaine, Jobaliya, Chintan, Bailey, Alice, McGinn, Daniel E., Gaiser, Kimberly, Bassett, Anne, Gur, Raquel E., Morrow, Bernice, Emanuel, Beverly S., Franco, Aime T., French, Deborah, Zackai, Elaine H., McDonald‐McGinn, Donna M., and Lambert, Michele P.

Subjects
*DIGEORGE syndrome, *MEAN platelet volume, *BLOOD platelets, *IDIOPATHIC thrombocytopenic purpura, *CONGENITAL heart disease, *PLATELET count, *THYROID hormone receptors, *THROMBOPOIETIN receptors
Abstract

Prior studies have demonstrated that patients with chromosome 22q11.2 deletion syndrome (22q11.2DS) have lower platelet counts (PC) compared to non‐deleted populations. They also have an increased mean platelet volume. The mechanism for this has been postulated to be haploinsufficiency of the GPIBB gene. We examined platelet parameters, deletion size and factors known to influence counts, including status of thyroid hormone and congenital heart disease (CHD), in a population of 825 patients with 22q11.2DS. We also measured surface expression of GPIB‐IX complex by flow cytometry. The major determinant of PC was deletion status of GP1BB, regardless of surface expression or other factors. Patients with nested distal chromosome 22q11.2 deletions (those with GP1BB present) had higher PCs than those with proximal deletions where GP1BB is deleted. Patients with 22q11.2DS also demonstrated an accelerated PC decrease with age, occurring in childhood. These data demonstrate that genes within the proximal deletion segment drive PC differences in 22q11.2DS and suggest that PC reference ranges may need to be adjusted for age and deletion size in 22q11.2DS populations. Bleeding did not correlate with either platelet count or GPIb expression. Further studies into drivers of expression of GPIb and associations with severe thrombocytopenia and immune thrombocytopenia are needed to inform clinical care. [ABSTRACT FROM AUTHOR]

Published
2023
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17. Clinical exome sequencing data reveal high diagnostic yields for congenital diaphragmatic hernia plus (CDH+) and new phenotypic expansions involving CDH.

Author

Scott, Tiana M., Campbell, Ian M., Hernandez-Garcia, Andres, Lalani, Seema R., Pengfei Liu, Shaw, Chad A., Rosenfeld, Jill A., and Scott, Daryl A.

Abstract

Background Congenital diaphragmatic hernia (CDH) is a life-threatening birth defect that often co-occurs with non-hernia-related anomalies (CDH+). While copy number variant (CNV) analysis is often employed as a diagnostic test for CDH+, clinical exome sequencing (ES) has not been universally adopted. Methods We analysed a clinical database of ~12 000 test results to determine the diagnostic yields of ES in CDH+ and to identify new phenotypic expansions. Results Among the 76 cases with an indication of CDH+, a molecular diagnosis was made in 28 cases for a diagnostic yield of 37% (28/76). A provisional diagnosis was made in seven other cases (9%; 7/76). Four individuals had a diagnosis of Kabuki syndrome caused by frameshift variants in KMT2D. Putatively deleterious variants in ALG12 and EP300 were each found in two individuals, supporting their role in CDH development. We also identified individuals with de novo pathogenic variants in FOXP1 and SMARCA4, and compound heterozygous pathogenic variants in BRCA2. The role of these genes in CDH development is supported by the expression of their mouse homologs in the developing diaphragm, their high CDH-specific pathogenicity scores generated using a previously validated algorithm for genome-scale knowledge synthesis and previously published case reports. Conclusion We conclude that ES should be ordered in cases of CDH+ when a specific diagnosis is not suspected and CNV analyses are negative. Our results also provide evidence in favour of phenotypic expansions involving CDH for genes associated with ALG12-congenital disorder of glycosylation, Rubinstein-Taybi syndrome, Fanconi anaemia, Coffin-Siris syndrome and FOXP1-related disorders. [ABSTRACT FROM AUTHOR]

Published
2022
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20. An Organismal CNV Mutator Phenotype Restricted to Early Human Development

Author

Liu, Pengfei, primary, Yuan, Bo, additional, Carvalho, Claudia M.B., additional, Wuster, Arthur, additional, Walter, Klaudia, additional, Zhang, Ling, additional, Gambin, Tomasz, additional, Chong, Zechen, additional, Campbell, Ian M., additional, Coban Akdemir, Zeynep, additional, Gelowani, Violet, additional, Writzl, Karin, additional, Bacino, Carlos A., additional, Lindsay, Sarah J., additional, Withers, Marjorie, additional, Gonzaga-Jauregui, Claudia, additional, Wiszniewska, Joanna, additional, Scull, Jennifer, additional, Stankiewicz, Paweł, additional, Jhangiani, Shalini N., additional, Muzny, Donna M., additional, Zhang, Feng, additional, Chen, Ken, additional, Gibbs, Richard A., additional, Rautenstrauss, Bernd, additional, Cheung, Sau Wai, additional, Smith, Janice, additional, Breman, Amy, additional, Shaw, Chad A., additional, Patel, Ankita, additional, Hurles, Matthew E., additional, and Lupski, James R., additional

Published
2017
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21. A visual and curatorial approach to clinical variant prioritization and disease gene discovery in genome-wide diagnostics

Author

James, Regis A., primary, Campbell, Ian M., additional, Chen, Edward S., additional, Boone, Philip M., additional, Rao, Mitchell A., additional, Bainbridge, Matthew N., additional, Lupski, James R., additional, Yang, Yaping, additional, Eng, Christine M., additional, Posey, Jennifer E., additional, and Shaw, Chad A., additional

Published
2016
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22. Comparative Genomic Analyses of the Human NPHP1 Locus Reveal Complex Genomic Architecture and Its Regional Evolution in Primates

Author

Yuan, Bo, primary, Liu, Pengfei, additional, Gupta, Aditya, additional, Beck, Christine R., additional, Tejomurtula, Anusha, additional, Campbell, Ian M., additional, Gambin, Tomasz, additional, Simmons, Alexandra D., additional, Withers, Marjorie A., additional, Harris, R. Alan, additional, Rogers, Jeffrey, additional, Schwartz, David C., additional, and Lupski, James R., additional

Published
2015
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23. 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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25. 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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29. The Alu-Rich Genomic Architecture of SPAST Predisposes to Diverse and Functionally Distinct Disease-Associated CNV Alleles

Author

Boone, Philip M., primary, Yuan, Bo, additional, Campbell, Ian M., additional, Scull, Jennifer C., additional, Withers, Marjorie A., additional, Baggett, Brett C., additional, Beck, Christine R., additional, Shaw, Christine J., additional, Stankiewicz, Pawel, additional, Moretti, Paolo, additional, Goodwin, Wendy E., additional, Hein, Nichole, additional, Fink, John K., additional, Seong, Moon-Woo, additional, Seo, Soo Hyun, additional, Park, Sung Sup, additional, Karbassi, Izabela D., additional, Batish, Sat Dev, additional, Ordóñez-Ugalde, Andrés, additional, Quintáns, Beatriz, additional, Sobrido, María-Jesús, additional, Stemmler, Susanne, additional, and Lupski, James R., additional

Published
2014
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30. Parental Somatic Mosaicism Is Underrecognized and Influences Recurrence Risk of Genomic Disorders

Author

Campbell, Ian M., primary, Yuan, Bo, additional, Robberecht, Caroline, additional, Pfundt, Rolph, additional, Szafranski, Przemyslaw, additional, McEntagart, Meriel E., additional, Nagamani, Sandesh C.S., additional, Erez, Ayelet, additional, Bartnik, Magdalena, additional, Wiśniowiecka-Kowalnik, Barbara, additional, Plunkett, Katie S., additional, Pursley, Amber N., additional, Kang, Sung-Hae L., additional, Bi, Weimin, additional, Lalani, Seema R., additional, Bacino, Carlos A., additional, Vast, Mala, additional, Marks, Karen, additional, Patton, Michael, additional, Olofsson, Peter, additional, Patel, Ankita, additional, Veltman, Joris A., additional, Cheung, Sau Wai, additional, Shaw, Chad A., additional, Vissers, Lisenka E.L.M., additional, Vermeesch, Joris R., additional, Lupski, James R., additional, and Stankiewicz, Paweł, additional

Published
2014
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31. 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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32. Fusion of Large-Scale Genomic Knowledge and Frequency Data Computationally Prioritizes Variants in Epilepsy

Author

Campbell, Ian M., primary, Rao, Mitchell, additional, Arredondo, Sean D., additional, Lalani, Seema R., additional, Xia, Zhilian, additional, Kang, Sung-Hae L., additional, Bi, Weimin, additional, Breman, Amy M., additional, Smith, Janice L., additional, Bacino, Carlos A., additional, Beaudet, Arthur L., additional, Patel, Ankita, additional, Cheung, Sau Wai, additional, Lupski, James R., additional, Stankiewicz, Paweł, additional, Ramocki, Melissa B., additional, and Shaw, Chad A., additional

Published
2013
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33. TM4SF20 Ancestral Deletion and Susceptibility to a Pediatric Disorder of Early Language Delay and Cerebral White Matter Hyperintensities

Author

Wiszniewski, Wojciech, primary, Hunter, Jill V., additional, Hanchard, Neil A., additional, Willer, Jason R., additional, Shaw, Chad, additional, Tian, Qi, additional, Illner, Anna, additional, Wang, Xueqing, additional, Cheung, Sau W., additional, Patel, Ankita, additional, Campbell, Ian M., additional, Gelowani, Violet, additional, Hixson, Patricia, additional, Ester, Audrey R., additional, Azamian, Mahshid S., additional, Potocki, Lorraine, additional, Zapata, Gladys, additional, Hernandez, Patricia P., additional, Ramocki, Melissa B., additional, Santos-Cortez, Regie L.P., additional, Wang, Gao, additional, York, Michele K., additional, Justice, Monica J., additional, Chu, Zili D., additional, Bader, Patricia I., additional, Omo-Griffith, Lisa, additional, Madduri, Nirupama S., additional, Scharer, Gunter, additional, Crawford, Heather P., additional, Yanatatsaneejit, Pattamawadee, additional, Eifert, Anna, additional, Kerr, Jeffery, additional, Bacino, Carlos A., additional, Franklin, Adiaha I.A., additional, Goin-Kochel, Robin, additional, Simpson, Gayle, additional, Immken, Ladonna, additional, Haque, Muhammad E., additional, Stosic, Marija, additional, Williams, Misti D., additional, Morgan, Thomas M., additional, Pruthi, Sumit, additional, Omary, Reed, additional, Boyadjiev, Simeon A., additional, Win, Kay K., additional, Thida, Aye, additional, Hurles, Matthew, additional, Hibberd, Martin Lloyd, additional, Khor, Chiea Chuen, additional, Van Vinh Chau, Nguyen, additional, Gallagher, Thomas E., additional, Mutirangura, Apiwat, additional, Stankiewicz, Pawel, additional, Beaudet, Arthur L., additional, Maletic-Savatic, Mirjana, additional, Rosenfeld, Jill A., additional, Shaffer, Lisa G., additional, Davis, Erica E., additional, Belmont, John W., additional, Dunstan, Sarah, additional, Simmons, Cameron P., additional, Bonnen, Penelope E., additional, Leal, Suzanne M., additional, Katsanis, Nicholas, additional, Lupski, James R., additional, and Lalani, Seema R., additional

Published
2013
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34. Deletions of recessive disease genes: CNV contribution to carrier states and disease-causing alleles

Author

Boone, Philip M., primary, Campbell, Ian M., additional, Baggett, Brett C., additional, Soens, Zachry T., additional, Rao, Mitchell M., additional, Hixson, Patricia M., additional, Patel, Ankita, additional, Bi, Weimin, additional, Cheung, Sau Wai, additional, Lalani, Seema R., additional, Beaudet, Arthur L., additional, Stankiewicz, Pawel, additional, Shaw, Chad A., additional, and Lupski, James R., additional

Published
2013
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36. Novel 9q34.11 gene deletions encompassing combinations of four Mendelian disease genes: STXBP1, SPTAN1, ENG, and TOR1A

Author

Campbell, Ian M., primary, Yatsenko, Svetlana A., additional, Hixson, Patricia, additional, Reimschisel, Tyler, additional, Thomas, Matthew, additional, Wilson, William, additional, Dayal, Usha, additional, Wheless, James W., additional, Crunk, Amy, additional, Curry, Cynthia, additional, Parkinson, Nicole, additional, Fishman, Leona, additional, Riviello, James J., additional, Nowaczyk, Malgorzata J.M., additional, Zeesman, Susan, additional, Rosenfeld, Jill A., additional, Bejjani, Bassem A., additional, Shaffer, Lisa G., additional, Cheung, Sau Wai, additional, Lupski, James R., additional, Stankiewicz, Pawel, additional, and Scaglia, Fernando, additional

Published
2012
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41. Human endogenous retroviral elements promote genome instability via nonallelic homologous recombination.

Author

Campbell, Ian M., Gambin, Tomasz, Dittwald, Piotr, Beck, Christine R., Shuvarikov, Andrey, Hixson, Patricia, Patel, Ankita, Gambin, Anna, Shaw, Chad A., Rosenfeld, Jill A., and Stankiewicz1, Paweł

Subjects
*PATHOGENIC microorganisms, *RETROVIRUS diseases, *GENETIC recombination, *HUMAN genome, *HOMOLOGY (Biology)
Abstract

Background Recurrent rearrangements of the human genome resulting in disease and variation are mainly mediated by nonallelic homologous recombination (NAHR) between low-copy repeats. However, other genomic structures, including AT rich palindromes and retroviruses, have also been also reported to underlie recurrent structural rearrangements. Notably, recurrent deletions of Yq12 conveying azoospermia, as well as non-pathogenic reciprocal duplications, are mediated by human endogenous retroviral elements (HERVs). We hypothesized that HERV elements throughout the genome can serve as substrates for genomic instability and result in human copy-number variation (CNV). Results We developed parameters to identify HERV elements similar to those that mediate Yq12 rearrangements as well as recurrent deletions of 3q13.2q13.31. We used these parameters to identify HERV pairs genome-wide that may cause instability. Our analysis highlighted 170 pairs, flanking 12.1% of the genome. We cross-referenced these predicted susceptibility regions with CNVs from our clinical databases for potentially HERV-mediated rearrangements and identified 78 CNVs. We subsequently molecularly confirmed recurrent deletion and duplication rearrangements at four loci in 10 individuals, including reciprocal rearrangements at two loci. Breakpoint sequencing revealed clustering in regions of high sequence identity enriched in PRDM9 mediated recombination hotspot motifs. Conclusions The presence of deletions and reciprocal duplications suggests NAHR as the causative mechanism of HERV-mediated CNV, even though the length and the sequence homology of the HERV elements are less than currently thought to be required for NAHR. We propose that in addition to HERVs, other repetitive elements such as LINEs may also be responsible for the formation of recurrent CNVs via NAHR. [ABSTRACT FROM AUTHOR]

Published
2014
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42. Genes that Affect Brain Structure and Function Identified by Rare Variant Analyses of Mendelian Neurologic Disease

Author

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

Subjects
Male, PONTOCEREBELLAR HYPOPLASIA, Candidate gene, Rna Helicases, PROTEIN, Cohort Studies, 0302 clinical medicine, Snx14 Cause, Databases, Genetic, Gene Regulatory Networks, Copy-number variation, Pontocerebellar Hypoplasia, Exome sequencing, Alzheimers-Disease, Genetics, 0303 health sciences, H-Prune, General Neuroscience, Brain, Mendelian Randomization Analysis, Neurologic Disease, Pedigree, 3. Good health, ALZHEIMERS-DISEASE, H-PRUNE, symbols, Female, Mutations, Neuroscience(all), SNX14 CAUSE, Biology, TRIPLE T COMPLEX, Article, 03 medical and health sciences, symbols.namesake, Genetic variation, CHROMATIN REMODELING COMPLEX, Humans, Allele, Gene, Genetic Association Studies, 030304 developmental biology, RNA HELICASES, MUTATIONS, Protein, Genetic Variation, Triple T Complex, INTELLECTUAL-DISABILITY SYNDROME, Intellectual-Disability Syndrome, Mendelian inheritance, Chromatin Remodeling Complex, Nervous System Diseases, 030217 neurology & neurosurgery
Abstract

WOS: 000365765400011, PubMed ID: 26539891, Development of the human nervous system involves complex interactions among fundamental cellular processes and requires a multitude of genes, many of which remain to be associated with human disease. We applied whole exome sequencing to 128 mostly consanguineous families with neurogenetic disorders that often included brain malformations. Rare variant analyses for both single nucleotide variant (SNV) and copy number variant (CNV) alleles allowed for identification of 45 novel variants in 43 known disease genes, 41 candidate genes, and CNVs in 10 families, with an overall potential molecular cause identified in >85% of families studied. Among the candidate genes identified, we found PRUNE, VARS, and DHX37 in multiple families and homozygous loss-of-function variants in AGBL2, SLC18A2, SMARCA1, UBQLN1, and CPLX1. Neuroimaging and in silico analysis of functional and expression proximity between candidate and known disease genes allowed for further understanding of genetic networks underlying specific types of brain malformations., U.S. National Human Genome Research Institute (NHGRI) NHLBI grant [U54HG006542]; NINDSUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USANIH National Institute of Neurological Disorders & Stroke (NINDS) [RO1 NS058529, K23NS078056]; NHGRIUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USANIH National Human Genome Research Institute (NHGRI) [5U54HG003273]; Medical Genetics Research Fellowship Program [T32 GM07526]; Regeneron, We thank all the family members and collaborators who participated in this study. This work was supported by U.S. National Human Genome Research Institute (NHGRI) NHLBI grant U54HG006542 to the Baylor-Hopkins Center for Mendelian Genomics, NINDS grant RO1 NS058529 to J. R. L., and NHGRI 5U54HG003273 to R. A. G. T. H. is supported by the Medical Genetics Research Fellowship Program (T32 GM07526). W. W. is supported by Career Development Award K23NS078056 from NINDS. The authors would like to thank the ExAC and the groups that provided exome variant data for comparison. A full list of contributing groups can be found at http://exac.broadinstitute.org/about. J.R.L. has stock ownership in 23andMe and Lasergen and is a paid consultant for Regeneron. J. R. L. is also a coinventor on multiple United States and European patents related to molecular diagnostics for inherited neuropathies, eye diseases, and bacterial genomic fingerprinting. The Department of Molecular and Human Genetics at Baylor College of Medicine derives revenue from the chromosomal microarray analysis and clinical exome sequencing offered in the Medical Genetics Laboratory (https://www.bcm.edu/geneticlabs/). W. K. C. is a paid consultant for Regeneron and BioReference Laboratories. C.G.-J. and J. D. O. are employees of the RGC.

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43. Predicting human genes susceptible to genomic instability associated with Alu / Alu -mediated rearrangements.

Author

Song X, Beck CR, Du R, Campbell IM, Coban-Akdemir Z, Gu S, Breman AM, Stankiewicz P, Ira G, Shaw CA, and Lupski JR

Subjects
Gene Duplication genetics, Genome, Human genetics, Humans, Sequence Deletion, Alu Elements genetics, DNA Copy Number Variations genetics, Genomic Instability genetics
Abstract

Alu elements, the short interspersed element numbering more than 1 million copies per human genome, can mediate the formation of copy number variants (CNVs) between substrate pairs. These Alu / Alu -mediated rearrangements (AAMRs) can result in pathogenic variants that cause diseases. To investigate the impact of AAMR on gene variation and human health, we first characterized Alu s that are involved in mediating CNVs (CNV- Alu s) and observed that these Alu s tend to be evolutionarily younger. We then computationally generated, with the assistance of a supercomputer, a test data set consisting of 78 million Alu pairs and predicted ∼18% of them are potentially susceptible to AAMR. We further determined the relative risk of AAMR in 12,074 OMIM genes using the count of predicted CNV- Alu pairs and experimentally validated the predictions with 89 samples selected by correlating predicted hotspots with a database of CNVs identified by clinical chromosomal microarrays (CMAs) on the genomes of approximately 54,000 subjects. We fine-mapped 47 duplications, 40 deletions, and two complex rearrangements and examined a total of 52 breakpoint junctions of simple CNVs. Overall, 94% of the candidate breakpoints were at least partially Alu mediated. We successfully predicted all (100%) of Alu pairs that mediated deletions ( n = 21) and achieved an 87% positive predictive value overall when including AAMR-generated deletions and duplications. We provided a tool, AluAluCNVpredictor, for assessing AAMR hotspots and their role in human disease. These results demonstrate the utility of our predictive model and provide insights into the genomic features and molecular mechanisms underlying AAMR., (© 2018 Song et al.; Published by Cold Spring Harbor Laboratory Press.)

Published
2018
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