Alternative genomic diagnoses for individuals with a clinical diagnosis of Dubowitz syndrome
David A. Dyment, Anne O’Donnell‐Luria, Pankaj B. Agrawal, Zeynep Coban‐Akdemir, Kyrieckos A. Aleck, Danny Antaki, Hind Al Sharhan, Ping Yee Billie Au, Hatip Aydın, Alan H. Beggs, Kaya Bilgüvar, Eric Boerwinkle, Harrison Brand, Catherine A. Brownstein, Steven Buyske, Bernard Chodirker, Jungmin Choi, Albert E. Chudley, Carol L. Clericuzio, Gerald F. Cox, Cynthia J. Curry, Elke de Boer, Bert B.A. de Vries, Kathryn Dunn, Cullen M. Dutmer, Eleina England, Jill A. Fahrner, Bilgen Bilge Geçkinli, Casie A. Genetti, Alper Gezdirici, William T. Gibson, Joseph G. Gleeson, Cheryl R. Greenberg, April Hall, Ada Hamosh, Taila Hartley, Shalini N. Jhangiani, Ender Karaca, Kristin D. Kernohan, Julie Lauzon, M. E. Suzanne Lewis, R. Brian Lowry, Francesc López‐Giráldez, Tara C. Matise, Jennifer McEvoy‐Venneri, Brenda McInnes, Aziz Mhanni, Sixto García Miñaúr, Jukka S. Moilanen, An Nguyen, Małgorzata J.M. Nowaczyk, Jennifer E. Posey, Katrin Õunap, Davut Pehli̇van, Sander Pajusalu, Lynette S. Penney, Timothy Poterba, Paolo Prontera, Maria Juliana Rodovalho Doriqui, Sarah L. Sawyer, Nara Sobreira, Valentina Stanley, Deniz Torun, David S. Wargowski, P. Dane Witmer, Isaac Wong, Jinchuan Xing, Maha S. Zaki, Yeting Zhang, Kym M. Boycott, Michael J. Bamshad, Deborah A. Nickerson, Elizabeth Blue, A. Micheil Innes
Abstract
Dubowitz syndrome (DubS) is considered a recognizable syndrome characterized by a distinctive facial appearance and deficits in growth and development. There have been over 200 individuals reported with Dubowitz or a "Dubowitz-like" condition, although no single gene has been implicated as responsible for its cause. We have performed exome (ES) or genome sequencing (GS) for 31 individuals clinically diagnosed with DubS. After genome-wide sequencing, rare variant filtering and computational and Mendelian genomic analyses, a presumptive molecular diagnosis was made in 13/27 (48%) families. The molecular diagnoses included biallelic variants in SKIV2L, SLC35C1, BRCA1, NSUN2; de novo variants in ARID1B, ARID1A, CREBBP, POGZ, TAF1, HDAC8, and copy-number variation at1p36.11(ARID1A), 8q22.2(VPS13B), Xp22, and Xq13(HDAC8). Variants of unknown significance in known disease genes, and also in genes of uncertain significance, were observed in 7/27 (26%) additional families. Only one gene, HDAC8, could explain the phenotype in more than one family (N = 2). All but two of the genomic diagnoses were for genes discovered, or for conditions recognized, since the introduction of next-generation sequencing. Overall, the DubS-like clinical phenotype is associated with extensive locus heterogeneity and the molecular diagnoses made are for emerging clinical conditions sharing characteristic features that overlap the DubS phenotype.