Browsing by Author "Task Force for Neonatal Genomics"

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    A Genocentric Approach to Discovery of Mendelian Disorders.
    (American journal of human genetics, 2019-11) Hansen, Adam W; Murugan, Mullai; Li, He; Khayat, Michael M; Wang, Liwen; Rosenfeld, Jill; Andrews, B Kim; Jhangiani, Shalini N; Coban Akdemir, Zeynep H; Sedlazeck, Fritz J; Ashley-Koch, Allison E; Liu, Pengfei; Muzny, Donna M; Task Force for Neonatal Genomics; Davis, Erica E; Katsanis, Nicholas; Sabo, Aniko; Posey, Jennifer E; Yang, Yaping; Wangler, Michael F; Eng, Christine M; Sutton, V Reid; Lupski, James R; Boerwinkle, Eric; Gibbs, Richard A
    The advent of inexpensive, clinical exome sequencing (ES) has led to the accumulation of genetic data from thousands of samples from individuals affected with a wide range of diseases, but for whom the underlying genetic and molecular etiology of their clinical phenotype remains unknown. In many cases, detailed phenotypes are unavailable or poorly recorded and there is little family history to guide study. To accelerate discovery, we integrated ES data from 18,696 individuals referred for suspected Mendelian disease, together with relatives, in an Apache Hadoop data lake (Hadoop Architecture Lake of Exomes [HARLEE]) and implemented a genocentric analysis that rapidly identified 154 genes harboring variants suspected to cause Mendelian disorders. The approach did not rely on case-specific phenotypic classifications but was driven by optimization of gene- and variant-level filter parameters utilizing historical Mendelian disease-gene association discovery data. Variants in 19 of the 154 candidate genes were subsequently reported as causative of a Mendelian trait and additional data support the association of all other candidate genes with disease endpoints.
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    De Novo Pathogenic Variants in CACNA1E Cause Developmental and Epileptic Encephalopathy with Contractures, Macrocephaly, and Dyskinesias.
    (American journal of human genetics, 2019-03) Helbig, Katherine L; Lauerer, Robert J; Bahr, Jacqueline C; Souza, Ivana A; Myers, Candace T; Uysal, Betül; Schwarz, Niklas; Gandini, Maria A; Huang, Sun; Keren, Boris; Mignot, Cyril; Afenjar, Alexandra; Billette de Villemeur, Thierry; Héron, Delphine; Nava, Caroline; Valence, Stéphanie; Buratti, Julien; Fagerberg, Christina R; Soerensen, Kristina P; Kibaek, Maria; Kamsteeg, Erik-Jan; Koolen, David A; Gunning, Boudewijn; Schelhaas, H Jurgen; Kruer, Michael C; Fox, Jordana; Bakhtiari, Somayeh; Jarrar, Randa; Padilla-Lopez, Sergio; Lindstrom, Kristin; Jin, Sheng Chih; Zeng, Xue; Bilguvar, Kaya; Papavasileiou, Antigone; Xing, Qinghe; Zhu, Changlian; Boysen, Katja; Vairo, Filippo; Lanpher, Brendan C; Klee, Eric W; Tillema, Jan-Mendelt; Payne, Eric T; Cousin, Margot A; Kruisselbrink, Teresa M; Wick, Myra J; Baker, Joshua; Haan, Eric; Smith, Nicholas; Sadeghpour, Azita; Davis, Erica E; Katsanis, Nicholas; Task Force for Neonatal Genomics; Corbett, Mark A; MacLennan, Alastair H; Gecz, Jozef; Biskup, Saskia; Goldmann, Eva; Rodan, Lance H; Kichula, Elizabeth; Segal, Eric; Jackson, Kelly E; Asamoah, Alexander; Dimmock, David; McCarrier, Julie; Botto, Lorenzo D; Filloux, Francis; Tvrdik, Tatiana; Cascino, Gregory D; Klingerman, Sherry; Neumann, Catherine; Wang, Raymond; Jacobsen, Jessie C; Nolan, Melinda A; Snell, Russell G; Lehnert, Klaus; Sadleir, Lynette G; Anderlid, Britt-Marie; Kvarnung, Malin; Guerrini, Renzo; Friez, Michael J; Lyons, Michael J; Leonhard, Jennifer; Kringlen, Gabriel; Casas, Kari; El Achkar, Christelle M; Smith, Lacey A; Rotenberg, Alexander; Poduri, Annapurna; Sanchis-Juan, Alba; Carss, Keren J; Rankin, Julia; Zeman, Adam; Raymond, F Lucy; Blyth, Moira; Kerr, Bronwyn; Ruiz, Karla; Urquhart, Jill; Hughes, Imelda; Banka, Siddharth; Deciphering Developmental Disorders Study; Hedrich, Ulrike BS; Scheffer, Ingrid E; Helbig, Ingo; Zamponi, Gerald W; Lerche, Holger; Mefford, Heather C
    (The American Journal of Human Genetics 103, 666–678; November 1, 2018) In the version of this article originally published online, Qinghe Xing's name was misspelled as Qinghe Xin. Also, Azita Sadeghpour, Erica E. Davis, and Nicholas Katsanis (all at Center for Human Disease Modeling, Duke University Medical Center, Durham, NC 27701, USA) and the Task Force for Neonatal Genomics were omitted from the author list. The members of the Task Force for Neonatal Genomics are as follows: Alexander Allori, Misha Angrist, Patricia Ashley, Margarita Bidegain, Brita Boyd, Eileen Chambers, Heidi Cope, C. Michael Cotten, Theresa Curington, Erica E. Davis, Sarah Ellestad, Kimberley Fisher, Amanda French, William Gallentine, Ronald Goldberg, Kevin Hill, Sujay Kansagra, Nicholas Katsanis, Sara Katsanis, Joanne Kurtzberg, Jeffrey Marcus, Marie McDonald, Mohammed Mikati, Stephen Miller, Amy Murtha, Yezmin Perilla, Carolyn Pizoli, Todd Purves, Sherry Ross, Azita Sadeghpour, Edward Smith, and John Wiener. The authors apologize for these omissions.
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    Identification of cis-suppression of human disease mutations by comparative genomics.
    (Nature, 2015-08) Jordan, Daniel M; Frangakis, Stephan G; Golzio, Christelle; Cassa, Christopher A; Kurtzberg, Joanne; Task Force for Neonatal Genomics; Davis, Erica E; Sunyaev, Shamil R; Katsanis, Nicholas
    Patterns of amino acid conservation have served as a tool for understanding protein evolution. The same principles have also found broad application in human genomics, driven by the need to interpret the pathogenic potential of variants in patients. Here we performed a systematic comparative genomics analysis of human disease-causing missense variants. We found that an appreciable fraction of disease-causing alleles are fixed in the genomes of other species, suggesting a role for genomic context. We developed a model of genetic interactions that predicts most of these to be simple pairwise compensations. Functional testing of this model on two known human disease genes revealed discrete cis amino acid residues that, although benign on their own, could rescue the human mutations in vivo. This approach was also applied to ab initio gene discovery to support the identification of a de novo disease driver in BTG2 that is subject to protective cis-modification in more than 50 species. Finally, on the basis of our data and models, we developed a computational tool to predict candidate residues subject to compensation. Taken together, our data highlight the importance of cis-genomic context as a contributor to protein evolution; they provide an insight into the complexity of allele effect on phenotype; and they are likely to assist methods for predicting allele pathogenicity.
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    Mutations in NCAPG2 Cause a Severe Neurodevelopmental Syndrome that Expands the Phenotypic Spectrum of Condensinopathies.
    (American journal of human genetics, 2019-01) Khan, Tahir N; Khan, Kamal; Sadeghpour, Azita; Reynolds, Hannah; Perilla, Yezmin; McDonald, Marie T; Gallentine, William B; Baig, Shahid M; Task Force for Neonatal Genomics; Davis, Erica E; Katsanis, Nicholas
    The use of whole-exome and whole-genome sequencing has been a catalyst for a genotype-first approach to diagnostics. Under this paradigm, we have implemented systematic sequencing of neonates and young children with a suspected genetic disorder. Here, we report on two families with recessive mutations in NCAPG2 and overlapping clinical phenotypes that include severe neurodevelopmental defects, failure to thrive, ocular abnormalities, and defects in urogenital and limb morphogenesis. NCAPG2 encodes a member of the condensin II complex, necessary for the condensation of chromosomes prior to cell division. Consistent with a causal role for NCAPG2, we found abnormal chromosome condensation, augmented anaphase chromatin-bridge formation, and micronuclei in daughter cells of proband skin fibroblasts. To test the functional relevance of the discovered variants, we generated an ncapg2 zebrafish model. Morphants displayed clinically relevant phenotypes, such as renal anomalies, microcephaly, and concomitant increases in apoptosis and altered mitotic progression. These could be rescued by wild-type but not mutant human NCAPG2 mRNA and were recapitulated in CRISPR-Cas9 F0 mutants. Finally, we noted that the individual with a complex urogenital defect also harbored a heterozygous NPHP1 deletion, a common contributor to nephronophthisis. To test whether sensitization at the NPHP1 locus might contribute to a more severe renal phenotype, we co-suppressed nphp1 and ncapg2, which resulted in significantly more dysplastic renal tubules in zebrafish larvae. Together, our data suggest that impaired function of NCAPG2 results in a severe condensinopathy, and they highlight the potential utility of examining candidate pathogenic lesions beyond the primary disease locus.