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1. 5q35 duplication presents with psychiatric and undergrowth phenotypes mediated by NSD1 overexpression and mTOR signaling downregulation

Author

Kelly L. Jones, Anita E. Beck, Ghayda M. Mirzaa, Derek Wong, Małgorzata J.M. Nowaczyk, Celeste Eno, Dawn L. Earl, Christine Sutanto, Fabiola Quintero-Rivera, and Julian A. Martinez-Agosto

Subjects
Adult, Male, Programmed cell death, medicine.medical_specialty, Adolescent, Down-Regulation, Chromosome Disorders, Article, Young Adult, 03 medical and health sciences, Downregulation and upregulation, Leucine, Gene Duplication, Genetics, medicine, Animals, Humans, Child, Psychiatry, Genetics (clinical), PI3K/AKT/mTOR pathway, 030304 developmental biology, 0303 health sciences, Cell Death, biology, TOR Serine-Threonine Kinases, 030305 genetics & heredity, Histone-Lysine N-Methyltransferase, biology.organism_classification, Phenotype, Pedigree, Insulin receptor, Drosophila melanogaster, Nuclear receptor, Caspases, Child, Preschool, Histone methyltransferase, biology.protein, Chromosomes, Human, Pair 5, Female, Signal Transduction
Abstract

PURPOSE: Nuclear receptor binding SET domain protein 1, NSD1, encodes a histone methyltransferase H3K36. NSD1 is responsible for the phenotype of the reciprocal 5q35.2q35.3 microdeletion-microduplication syndromes. We expand the phenotype and demonstrate the functional role of NSD1 in microduplication 5q35 syndrome. METHODS: Through an international collaboration, we report nine new patients, contributing to the emerging phenotype, highlighting psychiatric phenotypes in older affected individuals. Focusing specifically on the undergrowth phenotype, we have modeled the effects of Mes-4/NSD overexpression in Drosophila melanogaster. RESULTS: The individuals (including a family) from diverse backgrounds with duplications ranging in size from 0.6–4.5 Mb, have a consistent undergrowth phenotype. Mes-4 overexpression in the developing wing causes undergrowth, increased H3K36 methylation, and increased apoptosis. We demonstrate that altering the levels of insulin receptor (IR) rescues the apoptosis and the wing undergrowth phenotype, suggesting changes in mTOR pathway signaling. Leucine supplementation rescued Mes-4/NSD induced cell death, demonstrating decreased mTOR signaling caused by NSD1. CONCLUSION: Given that we show mTOR inhibition as a likely mechanism and amelioration of the phenotype by leucine supplementation in a fly model, we suggest further studies should evaluate the therapeutic potential of leucine or branched chain amino acids as an adjunct possible treatment to ameliorate human growth and psychiatric phenotypes and propose inclusion of 5q35-microduplication as part of the differential diagnosis for children and adults with delayed bone age, short stature, microcephaly, developmental delay, and psychiatric phenotypes.

Published
2021
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2. Biallelic MADD variants cause a phenotypic spectrum ranging from developmental delay to a multisystem disorder

Author

Katherine Wesseling Perry, Archana Raja, Emilie D. Douine, Xue Zhong Liu, Brent L. Fogel, Stan F. Nelson, Kenneth R. Maravilla, Eva H. Baker, Dave Viskochil, Kerstin Kutsche, Jordan H. Whitlock, Susan L. Samson, Christine M. Eng, Chloe M. Reuter, Suman Jayadev, David R. Adams, Sihoun Hahn, Rebecca C. Spillmann, Margaret Adam, Heather C Mefford, John C. Carey, Ehsan Ghayoor Karimiani, Donna M. Krasnewich, David Goldstein, Susan A. Korrick, Guoyun Yu, Tomas Honzik, Henry Houlden, Andrea L. Gropman, David A. Sweetser, Anna Bican, Carlos A. Bacino, Liliana Fernandez, Gabrielle Brown, Justin Alvey, Hane Lee, Emanuele G. Coci, Hongzheng Dai, Mario Saporta, Laurel A. Cobban, John F. Bohnsack, Stephanie Fox, Heidi Cope, Tyra Estwick, Lorraine Potocki, Nichole Hayes, Elizabeth A. Burke, Rizwan Hamid, Aaron R. Quinlan, Kelly Hassey, Lindsay C. Burrage, Jane Juusola, Adeline Vanderver, Malik Alawi, Teri A. Manolio, Maja Hempel, Esther M. Maier, Jennifer Kennedy, Bruce D. Gelb, Martha Horike-Pyne, Amarilis Sanchez-Valle, Euan A. Ashley, Surendra Dasari, Elizabeth Blue, Eva Morava-Kozicz, Natalie Rosenwasser, Alan H. Beggs, Bryn D. Webb, Isaac S. Kohane, Kelly Schoch, C. Christopher Lau, Nicole M. Walley, Laura M. Amendola, Genecee Renteria, Catherine H. Sillari, Jonathan A. Bernstein, Pinar Bayrak-Toydemir, R. Frank Kooy, Mariko Nakano-Okuno, Manuela Siekmeyer, Marije E. C. Meuwissen, Stephanie Bivona, Mark Wener, Precilla D'Souza, Olveen Carrasquillo, Paolo Moretti, Diane B. Zastrow, David J. Eckstein, Janet S. Sinsheimer, Kathy Sisco, Holly K. Tabor, William E. Byrd, Esteban C. Dell'Angelica, Rosario Isasi, Jacinda B. Sampson, Carsten Bonnenmann, J. Lawrence Merritt, Joan M. Stoler, Richard L. Maas, Paul G. Fisher, Jeanette C. Papp, Kimberly LeBlanc, Lilianna Solnica-Krezel, Mustafa Tekin, Mathias Woidy, Andrew B. Crouse, Katleen Ballon, David Murphy, Matthew T. Wheeler, Joseph Loscalzo, Ellen Macnamara, Cecelia P. Tamburro, Lefkothea P. Karaviti, Chunli Zhao, Ingrid A. Holm, Pankaj B. Agrawal, Alana L. Grajewski, Stephen C. Pak, Ian R. Lanza, Mohammad Doosti, Jennifer E. Posey, Rebecca Signer, Katie Golden-Grant, Christopher A. Walsh, Alica M. Goldman, Jyoti G. Dayal, Queenie K.-G. Tan, Martin G. Martin, Joy D. Cogan, Kevin S. Smith, Deborah A. Nickerson, Elisabeth McGee, Laure Fresard, Rena A. Godfrey, Sharyn A. Lincoln, Kathleen E. Sullivan, Mariska Davids, Melissa A. Walker, Prashant Sharma, Maria Iascone, Neil H. Parker, Carlos Ferreira, Elizabeth L. Fieg, Edwin K. Silverman, Michael L. Cunningham, Pengfei Liu, Edward M. Behrens, Sandra K. Loo, David R. Murdock, F. Sessions Cole, C. Ron Scott, Dan Doherty, Elly Brokamp, John H. Newman, Alden Y. Huang, Laura A. Pace, Avi Nath, Jimmy Bennet, Georg Christoph Korenke, Alyssa A. Tran, Gabriel F. Batzli, Jimann Shin, Matthew A. Deardorff, Naghmeh Dorrani, Diane Beysen, Irma Gutierrez, Stanislav Kmoch, Majid Alfadhel, Fred F. Telischi, Jennifer A. Sullivan, William A. Gahl, María Palomares-Bralo, Gerard T. Berry, Colleen E. McCormack, Lance H. Rodan, Reza Maroofian, Lenka Nosková, Judy Schaechter, Lynne A. Wolfe, Deborah Krakow, Daryl A. Scott, Tara Wenger, Jason Hom, Dustin Baldridge, Lynette Rives, Lee-kai Wang, Dawn L. Earl, Ralph L. Sacco, Fernando Santos-Simarro, Irman Forghani, Fuki M. Hisama, Terra R. Coakley, Hsiao-Tuan Chao, Jeremy D. Woods, Emily G. Kelley, Jean M. Johnston, Neil A. Hanchard, Amy K. Robertson, Matt Velinder, Byron L. Lam, Wendy H. Raskind, William J. Craigen, Stephan Züchner, Guney Bademci, Julian A. Martinez-Agosto, Mary Koziura, Beth A. Martin, Angela Sun, John A. Phillips, Seema R. Lalani, Daniela Buhas, Emily Solem, Gary D. Clark, Gill Bejerano, Ingo Kurth, Deborah Barbouth, Tiina K. Urv, Fanny Kortüm, Ian A. Glass, Ta Chen Peter Chang, Yong Huang, Roy C. Levitt, Paola Francesca Ajmone, Brenna Boyd, René Santer, Tim Schedl, David D. Draper, Ghayda M. Mirzaa, Aroa Rodríguez Alonso, Stephanie Wallace, Colleen E. Wahl, Calum A. MacRae, Gail P. Jarvik, Jacob L. McCauley, Jill A. Rosenfeld, Ronit Marom, Monte Westerfield, Matthew Might, Poupak Javaher-Haghighi, Brendan C. Lanpher, Devon Bonner, Cynthia J. Tifft, Cecilia Esteves, May Christine V. Malicdan, Jim Bale, Fariha Jamal, Nicola Longo, Christina G.S. Palmer, Lisa Emrick, Peter H. Byers, Vandana Shashi, Tiphanie P. Vogel, Richard A. Lewis, Jijun Wan, Barbara N. Pusey, Maria T. Acosta, Jaak Jaeken, Allyn McConkie-Rosell, Shirley Sutton, John Yang, Lorenzo D. Botto, Hilde Peeters, Rong Mao, Catherine Groden, Brendan Lee, Marta M. Majcherska, Rami Abou Jamra, Ashok Balasubramanyam, Joel B. Krier, Majid Mojarrad, Maria Francesca Bedeschi, Mahshid S. Azamian, Shruti Marwaha, Heather A. Colley, Katrina M. Dipple, Sirisak Chanprasert, Alexa T. McCray, Nicholas Stong, Anne V. Hing, Laura A. Mamounas, Edward C. Smith, Lauren C. Briere, John J.E. Mulvihill, Virginia P. Sybert, Maura R.Z. Ruzhnikov, Valerie Maduro, Frances A. High, Manish J. Butte, Willa Thorson, J. Carl Pallais, Jennefer N. Kohler, Dana Kiley, Raphael Bernier, Christina Lam, Michael J. Bamshad, Patricia A. Ward, Michael F. Wangler, Anita E. Beck, Shinya Yamamoto, Beverly Berg-Rood, Robb Rowley, Gabor T. Marth, Cynthia M. Cooper, Jeffrey G. Jarvik, Thomas C. Markello, Saskia Biskup, Devin Oglesbee, Laura Duncan, Elijah Kravets, Daniel J. Wegner, Mercedes E. Alejandro, Sarah K. Nicholas, Jennifer A. Wambach, Marni J. Falk, Brianna M. Tucker, Marie Morimoto, Corina Heller, Donna Novacic, Camilo Toro, Ashley Andrews, James P. Orengo, Shweta U. Dhar, and Pauline E. Schneeberger

Subjects
0301 basic medicine, MAPK/ERK pathway, Death Domain Receptor Signaling Adaptor Proteins, Programmed cell death, Developmental Disabilities, Biology, 03 medical and health sciences, 0302 clinical medicine, Epidermal growth factor, medicine, Guanine Nucleotide Exchange Factors, Humans, Death domain, Kinase, Original Articles, Phenotype, Hypotonia, Protein Transport, 030104 developmental biology, Mutation, Cancer research, Human medicine, Neurology (clinical), Nervous System Diseases, Signal transduction, medicine.symptom, 030217 neurology & neurosurgery, Signal Transduction
Abstract

In pleiotropic diseases, multiple organ systems are affected causing a variety of clinical manifestations. Here, we report a pleiotropic disorder with a unique constellation of neurological, endocrine, exocrine, and haematological findings that is caused by biallelic MADD variants. MADD, the mitogen-activated protein kinase (MAPK) activating death domain protein, regulates various cellular functions, such as vesicle trafficking, activity of the Rab3 and Rab27 small GTPases, tumour necrosis factor-α (TNF-α)-induced signalling and prevention of cell death. Through national collaboration and GeneMatcher, we collected 23 patients with 21 different pathogenic MADD variants identified by next-generation sequencing. We clinically evaluated the series of patients and categorized the phenotypes in two groups. Group 1 consists of 14 patients with severe developmental delay, endo- and exocrine dysfunction, impairment of the sensory and autonomic nervous system, and haematological anomalies. The clinical course during the first years of life can be potentially fatal. The nine patients in Group 2 have a predominant neurological phenotype comprising mild-to-severe developmental delay, hypotonia, speech impairment, and seizures. Analysis of mRNA revealed multiple aberrant MADD transcripts in two patient-derived fibroblast cell lines. Relative quantification of MADD mRNA and protein in fibroblasts of five affected individuals showed a drastic reduction or loss of MADD. We conducted functional tests to determine the impact of the variants on different pathways. Treatment of patient-derived fibroblasts with TNF-α resulted in reduced phosphorylation of the extracellular signal-regulated kinases 1 and 2, enhanced activation of the pro-apoptotic enzymes caspase-3 and -7 and increased apoptosis compared to control cells. We analysed internalization of epidermal growth factor in patient cells and identified a defect in endocytosis of epidermal growth factor. We conclude that MADD deficiency underlies multiple cellular defects that can be attributed to alterations of TNF-α-dependent signalling pathways and defects in vesicular trafficking. Our data highlight the multifaceted role of MADD as a signalling molecule in different organs and reveal its physiological role in regulating the function of the sensory and autonomic nervous system and endo- and exocrine glands.

Published
2020
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3. Phenotypic spectrum and transcriptomic profile associated with germline variants in TRAF7

Author

Robert A. Hegele, Maria Iascone, Kevin A. Shapiro, Nicolas Chatron, Marwan Shinawi, Joel Charrow, Jeffrey W. Innis, Luitgard Graul-Neumann, Joanna Goes Castro Meira, Anna Lehman, Dawn L. Earl, Victoria R. Sanders, Shannon Rego, David A. Sweetser, Clémantine Dimartino, Wilhelmina S. Kerstjens-Frederikse, Antonio Vitobello, Davor Lessel, Daniel Grinberg, Laurence Faivre, Ryan Peretz, Katherine M. Christensen, Emma Reesor, Erin Beaver, Elizabeth Wohler, Margot R.F. Reijnders, Deborah Barbouth, Anna Cereda, Kaja Kristine Selmer, Melissa A. Walker, Barbro Stadheim, Alessandro Serretti, Helen Kingston, Jill Clayton-Smith, Raymond Lewandowski, Bernarda Lozić, Robert Stratton, Amelia Kirby, Anne H. O’Donnell-Luria, Sara Gabbiadini, Susanna Balcells, Myriam Oufadem, Christel Thauvin, Maha Aly, Wendy K. Chung, Susan M. White, Lauren C. Briere, Thomas Smol, Stanislas Lyonnet, Roberto Colombo, Catherine E. Keegan, Marie T. McDonald, Melanie Parisot, Tiong Yang Tan, Brian Wong, Christopher T. Gordon, Magnus Dehli Vigeland, Frances A. High, Emily Bryant, Audrey Labalme, Nara Sobreira, Arnold Munnich, Jeanne Amiel, Dayna Morel Swols, Raquel Rabionet, Laura Castilla-Vallmanya, Jennifer Heeley, Gunnar Houge, Michael J. Gambello, Bernardo Blanco-Sánchez, Lynn Pais, Olena M. Vaske, Roser Urreizti, Alison Wray, Veronique Pingault, Damien Sanlaville, John Christodoulou, John Millichap, Valérie Cormier-Daire, Parul Jayakar, Helen Cox, Frédéric Tran Mau-Them, Belinda Chong, Victoria Mok Siu, Anne Slavotinek, Antonie J. van Essen, Ingvild Aukrust, Lorne A. Clarke, Rachel Gannaway, Anne Dieux-Coeslier, Patrick Nitschké, Tony Yao, Simon Sadedin, Danielle Karlowicz, Christelle Rougeot, Christine Bole-Feysot, Sandra Yang, Megan T. Cho, Gaetan Lesca, Christiane Zweier, Castilla-Vallmanya L., Selmer K.K., Dimartino C., Rabionet R., Blanco-Sanchez B., Yang S., Reijnders M.R.F., van Essen A.J., Oufadem M., Vigeland M.D., Stadheim B., Houge G., Cox H., Kingston H., Clayton-Smith J., Innis J.W., Iascone M., Cereda A., Gabbiadini S., Chung W.K., Sanders V., Charrow J., Bryant E., Millichap J., Vitobello A., Thauvin C., Mau-Them F.T., Faivre L., Lesca G., Labalme A., Rougeot C., Chatron N., Sanlaville D., Christensen K.M., Kirby A., Lewandowski R., Gannaway R., Aly M., Lehman A., Clarke L., Graul-Neumann L., Zweier C., Lessel D., Lozic B., Aukrust I., Peretz R., Stratton R., Smol T., Dieux-Coeslier A., Meira J., Wohler E., Sobreira N., Beaver E.M., Heeley J., Briere L.C., High F.A., Sweetser D.A., Walker M.A., Keegan C.E., Jayakar P., Shinawi M., Kerstjens-Frederikse W.S., Earl D.L., Siu V.M., Reesor E., Yao T., Hegele R.A., Vaske O.M., Rego S., Shapiro K.A., Wong B., Gambello M.J., McDonald M., Karlowicz D., Colombo R., Serretti A., Pais L., O'Donnell-Luria A., Wray A., Sadedin S., Chong B., Tan T.Y., Christodoulou J., White S.M., Slavotinek A., Barbouth D., Morel Swols D., Parisot M., Bole-Feysot C., Nitschke P., Pingault V., Munnich A., Cho M.T., Cormier-Daire V., Balcells S., Lyonnet S., Grinberg D., Amiel J., Urreizti R., Gordon C.T., MUMC+: DA KG Polikliniek (9), and RS: FHML non-thematic output

Subjects
0301 basic medicine, NF-KAPPA-B, PROTEIN, 030105 genetics & heredity, medicine.disease_cause, Germline, Transcriptome, ACTIVATION, POLYUBIQUITINATION, Missense mutation, Exome, Genetics (clinical), Genetics, Sanger sequencing, Mutation, leads, Necrosi, craniofacial development, Phenotype, Tumor Necrosis Factor Receptor-Associated Peptides and Proteins, intellectual disability, patent ductus arteriosu, symbols, Mutation, Missense, Biology, traf7, Article, akt1, target, 03 medical and health sciences, symbols.namesake, Necrosis, patent ductus arteriosus, medicine, Humans, blepharophimosi, Tumors, MUTATIONS, Fibroblasts, medicine.disease, Blepharophimosis, TRAF7, blepharophimosis, GENOMIC ANALYSIS, Germ Cells, 030104 developmental biology, MENINGIOMAS
Abstract

PURPOSE: Somatic variants in tumor necrosis factor receptor-associated factor 7 (TRAF7) cause meningioma, while germline variants have recently been identified in seven patients with developmental delay and cardiac, facial, and digital anomalies. We aimed to define the clinical and mutational spectrum associated with TRAF7 germline variants in a large series of patients, and to determine the molecular effects of the variants through transcriptomic analysis of patient fibroblasts.METHODS: We performed exome, targeted capture, and Sanger sequencing of patients with undiagnosed developmental disorders, in multiple independent diagnostic or research centers. Phenotypic and mutational comparisons were facilitated through data exchange platforms. Whole-transcriptome sequencing was performed on RNA from patient- and control-derived fibroblasts.RESULTS: We identified heterozygous missense variants in TRAF7 as the cause of a developmental delay-malformation syndrome in 45 patients. Major features include a recognizable facial gestalt (characterized in particular by blepharophimosis), short neck, pectus carinatum, digital deviations, and patent ductus arteriosus. Almost all variants occur in the WD40 repeats and most are recurrent. Several differentially expressed genes were identified in patient fibroblasts.CONCLUSION: We provide the first large-scale analysis of the clinical and mutational spectrum associated with the TRAF7 developmental syndrome, and we shed light on its molecular etiology through transcriptome studies.

Published
2020

4. BCL11A intellectual developmental disorder: defining the clinical spectrum and genotype-phenotype correlations

Author

Øyvind L. Busk, Kimberley Bradbury, Arjan Bouman, Philippe M. Campeau, Lynne M. Bird, Cornelia Kraus, Colleen Carlston, Rong Mao, Juliette Piard, Laurence Faivre, Amanda Openshaw, Catherine Ward Melver, Mohnish Suri, Christiane Zweier, François Guillemot, Rolph Pfundt, Janice C. Palumbos, Parthiv Haldipur, Jane A. Hurst, Kimberly McDonald, Margaux Serey-Gaut, Luitgard Graul-Neumann, Karen J. Low, Jenny Carmichael, Patrick Ferrerira, Birgit Elisabeth Kristiansen, Ange-Line Bruel, Constance Motter, Andrea Accogli, Darrah N. Haffner, Suhair Hanna, Ruta Marcinkute, Angela Peron, Marcella Zollino, Sofia Maia, James Lespinasse, Claire E. Turner, Sally Ann Lynch, Richard E. Person, Valeria Capra, Kimberly A. Aldinger, Constance Smith-Hicks, Gyri Aasland Gradek, Ingrid M. Wentzensen, Megha Desai, Manuela Morleo, Aditi Shah Parikh, Marcello Scala, Cristina Dias, Gunnar Houge, Telethon Undiagnosed Disease Program, Anne Slavotinek, Roberta Battini, Mary J. Green, Anna Chassevent, Tara Montgomery, David Viskochil, Tatiana Tvrdik, Dawn L. Earl, Karin Weiss, Felice D'Arco, William B. Dobyns, Ping Yee Billie Au, Daniah Beleford, Erica F. Andersen, Bert B.A. de Vries, Jill Clayton-Smith, Christophe Philippe, and Michael J. Bamshad

Subjects
business.industry, Postnatal microcephaly, Microdeletion syndrome, medicine.disease, Bioinformatics, Hypotonia, Developmental disorder, Autism spectrum disorder, Intellectual disability, Fetal hemoglobin, medicine, Missense mutation, medicine.symptom, business
Abstract

PurposeHeterozygous variants in BCL11A underlie an intellectual developmental disorder with persistence of fetal hemoglobin (BCL11A-IDD, a.k.a. Dias-Logan syndrome). We sought to delineate the genotypic and phenotypic spectrum of BCL11A-IDD.MethodsWe performed an in-depth analysis of 42 patients with BCL11A-IDD ascertained through a collaborative network of clinical and research colleagues. We also reviewed 33 additional affected individuals previously reported in the literature or available through public repositories with clinical information.ResultsMolecular and clinical data analysis of 75 patients with BCL11A-IDD identified 60 unique variants (30 frameshift, 7 missense, 6 splice-site, 17 stop-gain) and 8 unique CNVs (microdeletions involving BCL11A only). We redefined the most frequent manifestations of the condition: intellectual disability, hypotonia, behavioral abnormalities, postnatal microcephaly and autism spectrum disorder. Two thirds of patients have brain MRI abnormalities, and we identified a recurrent posterior fossa phenotype of vermian hypoplasia and/or small brainstem. Truncating BCL11A variants, particularly those affecting the long (BCL11A-L) and extra-long (-XL) isoforms, sparing the short (-S) isoform, were associated with increased severity.ConclusionsWe expand the clinical delineation of BCL11A-IDD and identify a potential isoform-specific genotype-phenotype correlation. We show that BCL11A-IDD is associated with posterior fossa anomalies and highlight the differences between BCL11A-IDD and 2p16.1p15 microdeletion syndrome.

Published
2021
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5. Targeted long-read sequencing identifies missing disease-causing variation

Author

Tim Cherry, Seth J. Perlman, Rando Allikmets, Christina Lam, Katrina M Dipple, Alexias Safi, Hailey Loucks, Penny M Chow, Ian A. Glass, Xue Zou, Heather C Mefford, Angela Sun, Deborah A. Nickerson, Danny E. Miller, Dawn L. Earl, James T. Bennett, Alexandra P. Lewis, Stephanie Austin, Margaret P Adam, Apoorva K Iyengar, Arvis Sulovari, Edith P Almanza Fuerte, Andrew S. Allen, Audrey Squire, Karynne E. Patterson, Erin Huggins, Winston Lee, William H. Majoros, Emily S Bonkowski, Tianyun Wang, Priya S. Kishnani, Robin L. Bennett, Mary Claire King, Tara L. Wenger, Erika Beckman, Kendra Hoekzema, Gregory E. Crawford, Timothy E. Reddy, Evan E. Eichler, Irene Chang, Anne V. Hing, Zoe Nelson, Thomas J. Walsh, Dan Doherty, Megan C. Sikes, Michael J. Bamshad, Catherine R Paschal, Jessica X. Chong, Jenny Thies, and Katherine M. Munson

Subjects
Male, DNA Copy Number Variations, Computational biology, Disease, Biology, Article, 03 medical and health sciences, symbols.namesake, 0302 clinical medicine, Genetics, Humans, Genetic Predisposition to Disease, Genetic Testing, Gene, Genetics (clinical), 030304 developmental biology, Sequence (medicine), Data source, Chromosome Aberrations, 0303 health sciences, Genome, Human, Genetic Diseases, Inborn, High-Throughput Nucleotide Sequencing, Sequence Analysis, DNA, Phenotype, Karyotyping, Mutation (genetic algorithm), Cytogenetic Analysis, Mutation, Mendelian inheritance, symbols, Female, Nanopore sequencing, 030217 neurology & neurosurgery
Abstract

Despite widespread clinical genetic testing, many individuals with suspected genetic conditions lack a precise diagnosis, limiting their opportunity to take advantage of state-of-the-art treatments. In some cases, testing reveals difficult-to-evaluate structural differences, candidate variants that do not fully explain the phenotype, single pathogenic variants in recessive disorders, or no variants in genes of interest. Thus, there is a need for better tools to identify a precise genetic diagnosis in individuals when conventional testing approaches have been exhausted. We performed targeted long-read sequencing (T-LRS) using adaptive sampling on the Oxford Nanopore platform on 40 individuals, 10 of whom lacked a complete molecular diagnosis. We computationally targeted up to 151 Mbp of sequence per individual and searched for pathogenic substitutions, structural variants, and methylation differences using a single data source. We detected all genomic aberrations-including single-nucleotide variants, copy number changes, repeat expansions, and methylation differences-identified by prior clinical testing. In 8/8 individuals with complex structural rearrangements, T-LRS enabled more precise resolution of the mutation, leading to changes in clinical management in one case. In ten individuals with suspected Mendelian conditions lacking a precise genetic diagnosis, T-LRS identified pathogenic or likely pathogenic variants in six and variants of uncertain significance in two others. T-LRS accurately identifies pathogenic structural variants, resolves complex rearrangements, and identifies Mendelian variants not detected by other technologies. T-LRS represents an efficient and cost-effective strategy to evaluate high-priority genes and regions or complex clinical testing results.

Published
2021

6. Variants in the degron of AFF3 are associated with intellectual disability, mesomelic dysplasia, horseshoe kidney, and epileptic encephalopathy

Author

Rhonda E. Schnur, Fabio Sirchia, Olga Levchenko, Caroline Nava, Jane Juusola, Sarah Verheyen, Marketa Vlckova, Lindsay Rhodes, Gregory M. Cooper, Darina Prchalova, Thomas Courtin, Øystein L. Holla, David Kronn, Akemi J. Tanaka, E. Martina Bebin, Tara Funari, Miroslava Hancarova, Ennio Del Giudice, Nicolas Guex, Astrid Eisenkölbl, Dawn L. Earl, Toshiki Takenouchi, Ursula Gruber-Sedlmayr, Sedlácek Z, Sofia Douzgou, Heidelis A. Seebacher, Gerarda Cappuccio, Jasmin Blatterer, Anna Mikhaleva, Dian Donnai, Wendy K. Chung, Else Merckoll, Natasha J Brown, Elizabeth A. Sellars, Stefan Mundlos, Susan M. Hiatt, Giuliana Giannuzzi, Sinje Geuer, Giuseppina Vitiello, Séverine Lorrain, Alexandre Reymond, David J. Amor, Nicolas Chatron, Julien Delafontaine, Martine Doco, Kristian Tveten, Cecilie F. Rustad, Sylvain Pradervand, Delphine Héron, Alfredo Brusco, Elena L. Dadali, Nicola Brunetti-Pierri, Boris Keren, Yuri A. Zarate, Crystle Lee, Joel Charrow, Binnaz Yalcin, Heidi Taska-Tench, Elin Tønne, Tomoko Uehara, Alexander Lavrov, Jennifer Norman, Norine Voisin, Anna C.E. Hurst, Victoria R. Sanders, Ganka Douglas, Diana Johnson, Kenjiro Kosaki, Université de Lausanne = University of Lausanne (UNIL), Cooper Medical School of Rowan University [Camden] (CMSRU), Manchester University NHS Foundation Trust (MFT), University of Manchester [Manchester], HudsonAlpha Institute for Biotechnology [Huntsville, AL], Oslo University Hospital [Oslo], Victorian Clinical Genetics Services [Melbourne, VIC, Australia] (VCGS), Murdoch Children's Research Institute (MCRI), University of Melbourne, Seattle Children’s Hospital, Groupe de Recherche Clinique : Déficience Intellectuelle et Autisme [ CHU Pitié-Salpêtrière AP-HP] (GRC : DIA), Université Pierre et Marie Curie - Paris 6 (UPMC)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Research Centre for Medical Genetics [Moscow, Russia] (RCMG), Max Planck Institute for Molecular Genetics (MPIMG), Max-Planck-Gesellschaft, Medical University of Graz, Sheffield Children's NHS Foundation Trust, University of Arkansas at Little Rock, Charles University [Prague] (CU), University Hospital Motol [Prague], University of Alabama at Birmingham [ Birmingham] (UAB), Università degli studi di Torino = University of Turin (UNITO), Azienda Ospedalerio - Universitaria Città della Salute e della Scienza di Torino = University Hospital Città della Salute e della Scienza di Torino, University of Naples Federico II = Università degli studi di Napoli Federico II, Ann & Robert H. Lurie Children's Hospital of Chicago, Swiss Institute of Bioinformatics [Lausanne] (SIB), Hémostase et Remodelage Vasculaire Post-Ischémie (HERVI - EA 3801), Université de Reims Champagne-Ardenne (URCA), GeneDx [Gaithersburg, MD, USA], Johannes Kepler University Linz [Linz] (JKU), Telemark Hospital Trust [Skien, Norway], New York Medical College (NYMC), Integris Pediatric Neurology [Oklahoma City, OK, USA] (IPN), Institute for Maternal and Child Health - IRCCS 'Burlo Garofolo' [Trieste], Keio University School of Medicine [Tokyo, Japan], Columbia University [New York], Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Manchester Centre for Genomic Medicine [Manchester, UK] (MCGM), St Mary's Hospital Manchester-Manchester Academic Health Science Centre (MAHSC), University of Manchester [Manchester]-University of Manchester [Manchester]-Manchester University NHS Foundation Trust (MFT)-Faculty of Biology, Medicine and Health [Manchester, UK], Charité - UniversitätsMedizin = Charité - University Hospital [Berlin], Dupuis, Christine, Voisin, N., Schnur, R. E., Douzgou, S., Hiatt, S. M., Rustad, C. F., Brown, N. J., Earl, D. L., Keren, B., Levchenko, O., Geuer, S., Verheyen, S., Johnson, D., Zarate, Y. A., Hancarova, M., Amor, D. J., Bebin, E. M., Blatterer, J., Brusco, A., Cappuccio, G., Charrow, J., Chatron, N., Cooper, G. M., Courtin, T., Dadali, E., Delafontaine, J., Del Giudice, E., Doco, M., Douglas, G., Eisenkolbl, A., Funari, T., Giannuzzi, G., Gruber-Sedlmayr, U., Guex, N., Heron, D., Holla, O. L., Hurst, A. C. E., Juusola, J., Kronn, D., Lavrov, A., Lee, C., Lorrain, S., Merckoll, E., Mikhaleva, A., Norman, J., Pradervand, S., Prchalova, D., Rhodes, L., Sanders, V. R., Sedlacek, Z., Seebacher, H. A., Sellars, E. A., Sirchia, F., Takenouchi, T., Tanaka, A. J., Taska-Tench, H., Tonne, E., Tveten, K., Vitiello, G., Vlckova, M., Uehara, T., Nava, C., Yalcin, B., Kosaki, K., Donnai, D., Mundlos, S., Brunetti Pierri, N., Chung, W. K., and Reymond, A.

Subjects
Male, Models, Molecular, Hypertrichosis, [SDV]Life Sciences [q-bio], Mesomelic Dysplasia, Transcriptome, Mice, Gene Frequency, Missense mutation, Child, Zebrafish, Genetics (clinical), Genetics, Brain Diseases, 0303 health sciences, biology, Protein Stability, 030305 genetics & heredity, AFF3, AFF4, horseshoe kidney, intellectual disability, mesomelic dysplasia, Nuclear Proteins, Syndrome, Phenotype, Ubiquitin ligase, [SDV] Life Sciences [q-bio], Child, Preschool, Female, Transcriptional Elongation Factors, Adolescent, Mutation, Missense, Osteochondrodysplasias, Article, Evolution, Molecular, Young Adult, 03 medical and health sciences, medicine, Animals, Humans, Amino Acid Sequence, Fused Kidney, 030304 developmental biology, Epilepsy, Infant, Horseshoe kidney, biology.organism_classification, medicine.disease, biology.protein
Abstract

International audience; The ALF transcription factor paralogs, AFF1, AFF2, AFF3, and AFF4, are components of the transcriptional super elongation complex that regulates expression of genes involved in neurogenesis and development. We describe an autosomal dominant disorder associated with de novo missense variants in the degron of AFF3, a nine amino acid sequence important for its binding to ubiquitin ligase, or with de novo deletions of this region. The sixteen affected individuals we identified, along with two previously reported individuals, present with a recognizable pattern of anomalies, which we named KINSSHIP syndrome (KI for horseshoe kidney, NS for Nievergelt/Savarirayan type of mesomelic dysplasia, S for seizures, H for hypertrichosis, I for intellectual disability, and P for pulmonary involvement), partially overlapping the AFF4-associated CHOPS syndrome. Whereas homozygous Aff3 knockout mice display skeletal anomalies, kidney defects, brain malformations, and neurological anomalies, knockin animals modeling one of the microdeletions and the most common of the missense variants identified in affected individuals presented with lower mesomelic limb deformities like KINSSHIP-affected individuals and early lethality, respectively. Overexpression of AFF3 in zebrafish resulted in body axis anomalies, providing some support for the pathological effect of increased amount of AFF3. The only partial phenotypic overlap of AFF3-and AFF4-associated syndromes and the previously published transcriptome analyses of ALF transcription factors suggest that these factors are not redundant and each contributes uniquely to proper development.

Published
2021
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7. Targeted long-read sequencing resolves complex structural variants and identifies missing disease-causing variants

Author

Ting Wang, Karynne E. Patterson, Penny M Chow, Alexandra P. Lewis, Bonkowski Es, Adam Mp, Katherine M. Munson, Catherine R Paschal, Deborah A. Nickerson, Won Hee Lee, Audrey Squire, Dipple Km, Fuerte Epa, Angela Sun, Dan Doherty, Loucks H, Christina Lam, Ian A. Glass, Danny E. Miller, Dawn L. Earl, Rando Allikmets, Jenny Thies, Chang I, Beckman E, Arvis Sulovari, Evan E. Eichler, Jessica X. Chong, Perlman Sj, Nelson Z, Kendra Hoekzema, Robin L. Bennett, Anne V. Hing, Timothy J. Cherry, Megan C. Sikes, Michael J. Bamshad, Heather C Mefford, and James T. Bennett

Subjects
Candidate gene, symbols.namesake, Mutation (genetic algorithm), Mendelian inheritance, symbols, Computational biology, Nanopore sequencing, Copy-number variation, Biology, Gene, Phenotype, Sequence (medicine)
Abstract

BACKGROUNDDespite widespread availability of clinical genetic testing, many individuals with suspected genetic conditions do not have a precise diagnosis. This limits their opportunity to take advantage of state-of-the-art treatments. In such instances, testing sometimes reveals difficult-to-evaluate complex structural differences, candidate variants that do not fully explain the phenotype, single pathogenic variants in recessive disorders, or no variants in specific genes of interest. Thus, there is a need for better tools to identify a precise genetic diagnosis in individuals when conventional testing approaches have been exhausted.METHODSTargeted long-read sequencing (T-LRS) was performed on 33 individuals using Read Until on the Oxford Nanopore platform. This method allowed us to computationally target up to 100 Mbp of sequence per experiment, resulting in an average of 20x coverage of target regions, a 500% increase over background. We analyzed patient DNA for pathogenic substitutions, structural variants, and methylation differences using a single data source.RESULTSThe effectiveness of T-LRS was validated by detecting all genomic aberrations, including single-nucleotide variants, copy number changes, repeat expansions, and methylation differences, previously identified by prior clinical testing. In 6/7 individuals who had complex structural rearrangements, T-LRS enabled more precise resolution of the mutation, which led, in one case, to a change in clinical management. In nine individuals with suspected Mendelian conditions who lacked a precise genetic diagnosis, T-LRS identified pathogenic or likely pathogenic variants in five and variants of uncertain significance in two others.CONCLUSIONST-LRS can accurately predict pathogenic copy number variants and triplet repeat expansions, resolve complex rearrangements, and identify single-nucleotide variants not detected by other technologies, including short-read sequencing. T-LRS represents an efficient and cost-effective strategy to evaluate high-priority candidate genes and regions or to further evaluate complex clinical testing results. The application of T-LRS will likely increase the diagnostic rate of rare disorders.

Published
2020
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8. A Recurrent De Novo Heterozygous COG4 Substitution Leads to Saul-Wilson Syndrome, Disrupted Vesicular Trafficking, and Altered Proteoglycan Glycosylation

Author

Gen Nishimura, Tito Onyekweli, David A. Parry, Bernardo Blanco-Sánchez, Dawn L. Earl, Ganka Douglas, Clare V. Logan, Carlos Ferreira, Bobby G. Ng, Jeremy Wegner, Marte Gjøl Haug, Zöe Powis, Benjamin D. Solomon, Megan T. Cho, Ellen Macnamara, Lynne A. Wolfe, Ann Nordgren, Anna Hammarsjö, Melissa Gabriel, Zhi-Jie Xia, Angela L. Duker, Fulya Taylan, Kelly Radtke, Mariya Kozenko, Daniel R. Carvalho, Prashant Sharma, Hudson H. Freeze, Monte Westerfield, Kazuhiro Aoki, Michael B. Bober, Luis Rohena, Alvaro H Serrano Russi, Jennifer B. Phillips, Coleman T. Turgeon, Aurélie Clément, Giedre Grigelioniene, Tara E. Weixel, John A. Phillips, Rizwan Hamid, May Christine V. Malicdan, David H. Adams, George E. Tiller, Mariska Davids, Cynthia J. Tifft, Kimiyo Raymond, Andrew P. Jackson, Emma Tham, Hanne B Hove, Lauren Brick, Jakob Ek, Heiko Bratke, William G. Wilson, Michael Tiemeyer, and William A. Gahl

Subjects
Adult, Male, 0301 basic medicine, Heterozygote, Glycosylation, Decorin, Vesicular Transport Proteins, Golgi Apparatus, 030105 genetics & heredity, Endoplasmic Reticulum, Cell Line, Animals, Genetically Modified, Extracellular matrix, 03 medical and health sciences, symbols.namesake, chemistry.chemical_compound, Genetics, medicine, Animals, Humans, Child, Zebrafish, Genetics (clinical), biology, Infant, Heterozygote advantage, Fibroblasts, Golgi apparatus, medicine.disease, Molecular biology, Extracellular Matrix, Vesicular transport protein, Protein Transport, 030104 developmental biology, Amino Acid Substitution, Proteoglycan, chemistry, Child, Preschool, Fragile X Syndrome, biology.protein, symbols, Female, Proteoglycans, Primordial dwarfism
Abstract

The conserved oligomeric Golgi (COG) complex is involved in intracellular vesicular transport, and is composed of eight subunits distributed in two lobes, lobe A (COG1-4) and lobe B (COG5-8). We describe fourteen individuals with Saul-Wilson syndrome, a rare form of primordial dwarfism with characteristic facial and radiographic features. All affected subjects harbored heterozygous de novo variants in COG4, giving rise to the same recurrent amino acid substitution (p.Gly516Arg). Affected individuals' fibroblasts, whose COG4 mRNA and protein were not decreased, exhibited delayed anterograde vesicular trafficking from the ER to the Golgi and accelerated retrograde vesicular recycling from the Golgi to the ER. This altered steady-state equilibrium led to a decrease in Golgi volume, as well as morphologic abnormalities with collapse of the Golgi stacks. Despite these abnormalities of the Golgi apparatus, protein glycosylation in sera and fibroblasts from affected subjects was not notably altered, but decorin, a proteoglycan secreted into the extracellular matrix, showed altered Golgi-dependent glycosylation. In summary, we define a specific heterozygous COG4 substitution as the molecular basis of Saul-Wilson syndrome, a rare skeletal dysplasia distinct from biallelic COG4-CDG.

Published
2018
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9. NFIB Haploinsufficiency Is Associated with Intellectual Disability and Macrocephaly

Author

Sonal Mahida, Elliott H. Sherr, Elodie Lacaze, William B. Dobyns, Kosuke Izumi, Hilde Peeters, Marielle Alders, Catherine Nowak, Dawn L. Earl, Richard M. Gronostajski, Ryan J. Dean, Megan T. Cho, Anouck Schneider, Siren Berland, Patricia Blanchet, Laurence Faivre, Martin Zenker, Ina Schanze, Caitlin J. Bridges, Daniela T. Pilz, Sangamitra Boppudi, Ilse Wieland, Jens Bunt, Avni Santani, Jessica Douglas, Elaine H. Zackai, Muriel Holder-Espinasse, Linda J. Richards, Jean Baptiste Rivière, Tania Attié-Bitach, Timothy J. Edwards, Vincent Gatinois, Jacques Puechberty, Jonathan W. C. Lim, Ghayda Mirzaa, Sian Morgan, Phillis Lakeman, Steven Boogert, Samuel Huth, Marion Gérard, Denny Schanze, Florence Petit, Xiaonan Zhao, Eyal Reinstein, David Geneviève, Bronwyn Kerr, Dian Donnai, Constance Smith-Hicks, Brieana Fregeau, Amsterdam Reproduction & Development (AR&D), ACS - Pulmonary hypertension & thrombosis, Human Genetics, Otto-von-Guericke-Universität Magdeburg = Otto-von-Guericke University [Magdeburg] (OVGU), Queensland Brain Institute, University of Queensland [Brisbane], University of Amsterdam [Amsterdam] (UvA), Cellules Souches, Plasticité Cellulaire, Médecine Régénératrice et Immunothérapies (IRMB), Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Département de génétique médicale, maladies rares et médecine personnalisée [CHRU Montpellier], Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Embryology and genetics of human malformation (Equipe Inserm U1163), Imagine - Institut des maladies génétiques (IMAGINE - U1163), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Haukeland University Hospital, University of Bergen (UiB), GeneDx [Gaithersburg, MD, USA], University of Washington [Seattle], Seattle Children’s Hospital, University of Manchester [Manchester], Boston Children's Hospital, Harvard Medical School [Boston] (HMS), Centre de génétique - Centre de référence des maladies rares, anomalies du développement et syndromes malformatifs (CHU de Dijon), Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), Equipe GAD (LNC - U1231), Lipides - Nutrition - Cancer [Dijon - U1231] (LNC), Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, FHU TRANSLAD (CHU de Dijon), University of California [San Francisco] (UC San Francisco), University of California (UC), Unité fonctionnelle de génétique clinique, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Robert Debré-Université Paris Diderot - Paris 7 (UPD7), Service de Génétique [CHU Caen], Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-CHU Caen, Normandie Université (NU)-Tumorothèque de Caen Basse-Normandie (TCBN)-Tumorothèque de Caen Basse-Normandie (TCBN), CHU Lille, Children’s Hospital of Philadelphia (CHOP ), Département de génétique (groupe hospitalier le Havre), Groupe Hospitalier du Havre, Kennedy Krieger Institute [Baltimore], University Hospital of Wales (UHW), University Hospitals Leuven [Leuven], University of Glasgow, Sackler Faculty of Medicine, Tel Aviv University (TAU), Perelman School of Medicine, University of Pennsylvania, This work was supported by grants from the National Healthand Medical Research Council Australia (GNT1100443 to L.J.R.), the French Ministry of Health (PHRC national 2008/2008-A00515-50), Regional Council of Burgundy/Dijon University hospital (PARI 2012), The Genesis Foundation for Children, the US National Institutes of Health under NINDS grants(1R01NS092772 and 234567890 to W.B.D., 1R01NS058721 toW.B.D. and E.H.S., and K08NS092898 to G.M.M.), and Jordan’s Guardian Angels (G.M.M.). J.W.C.L. was supported by an International Postgraduate Research Scholarship and UQ Centennial Scholarship. R.M.G. was supported by NYSTEM grants (C026714,C026429, and C030133). R.J.D. was supported by Brain Injured Children’s Aftercare Recovery Endeavours (BICARE) Fellowship.L.J.R. was supported by an NHMRC Principal Research Fellowship(GNT1005751). M.Z. was supported by a grant from the GermanMinistry of Education and Research (BMBF) (GeNeRARe01GM1519A). We acknowledge the Linkage Infrastructure, Equipment and Facilities (LIEF) grant (LE100100074) awarded to the Queensland Brain Institute for the Slide Scanner and the facilities of the National Imaging Facility (NIF) at the Centre for Advanced Imaging, University of Queensland, used in the animal experiments., European Project: 270259,EC:FP7:ICT,FP7-ICT-2009-6,TBICARE(2011), Institute of Human Genetics (University Hospital Magdeburg), University Hospital of the Otto von Guericke University of Magdeburg, Department of Clinical Genetics, Academic Medical Centre, Amsterdam, Institut de recherche en santé, environnement et travail (Irset), Université d'Angers (UA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), University of Bergen (UIB), Seattle Children's Research Institute, Department of Neurology (University of California : San Francisco), University of California [San Francisco] (UCSF), University of California-University of California, Department of Medical Genetics, HMNC Brain Health, Seattle Children’s Hospital [Seattle, WA, USA], Centre Régional de Lutte contre le cancer - Centre Georges-François Leclerc (CRLCC - CGFL), Département de génétique médicale, maladies rares et médecine personnalisée [CHRU de Montpellier], Université de Lorraine (UL), Service de Génétique clinique, Hôpital Jeanne de Flandre [Lille]-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Department of Pediatrics (Perelman School of Medicine), University of Pennsylvania [Philadelphia], Regional Genetic Service, St Mary's Hospital, Manchester, Department of Clinical Genetics (Academic Medical Center, University of Amsterdam), VU University Medical Center [Amsterdam], Department of Pediatrics [Seattle, WA, USA] (Division of Genetic Medicine), University of Washington [Seattle]-Seattle Children’s Hospital [Seattle, WA, USA], Institute of Medical Genetics (University Hospital of Wales), University Hospital of Wales, Center for Human Genetics, University Hospitals Leuven, Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer (JPArc - U837 Inserm), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Lille 2 - Faculté de Médecine -Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), West of Scotland Genetics Service (Queen Elizabeth University Hospital), University Hospital Birmingham Queen Elizabeth, Institut de génétique humaine (IGH), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Medical Genetics Institute, Meir Medical Center, Génétique des Anomalies du Développement (GAD), Université de Bourgogne (UB)-IFR100 - Structure fédérative de recherche Santé-STIC, Department of Pathology and Laboratory Medicine [Philadelphia, PA, USA], University of Pennsylvania [Philadelphia]-Perelman School of Medicine, Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, School of Computer Science and Technology, Northwestern Polytechnical University [Xi'an] (NPU), Department of Biochemistry and Developmental Genomics Group, University at Buffalo [SUNY] (SUNY Buffalo), State University of New York (SUNY)-State University of New York (SUNY)-Center of Excellence in Bioinformatics and Life Sciences, Institute of Human Genetics, University Hospital Magdeburg, université de Bourgogne, LNC, Evidence based Diagnostic and Treatment Planning Solution for Traumatic Brain Injuries - TBICARE - - EC:FP7:ICT2011-02-01 - 2014-07-31 - 270259 - VALID, Otto-von-Guericke University [Magdeburg] (OVGU), Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), University of California, Université Paris Diderot - Paris 7 (UPD7)-Hôpital Robert Debré-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), University Hospital of Wales [Cardiff, UK], and Tel Aviv University [Tel Aviv]

Subjects
Male, 0301 basic medicine, chromosome 9p23, Medical and Health Sciences, Corpus Callosum, Cohort Studies, Mice, 2.1 Biological and endogenous factors, Megalencephaly, Aetiology, Child, Agenesis of the corpus callosum, Genetics (clinical), Pediatric, Genetics & Heredity, Cerebral Cortex, Mice, Knockout, Genetics, Single Nucleotide, nuclear factor I, Biological Sciences, NFIB, NFIX, developmental delay, Mental Health, Codon, Nonsense, NFIA, intellectual disability, Child, Preschool, chromosome 9p22.3, Neurological, Speech delay, Female, medicine.symptom, Haploinsufficiency, Adult, Adolescent, Knockout, Intellectual and Developmental Disabilities (IDD), [SDV.GEN.GH] Life Sciences [q-bio]/Genetics/Human genetics, Biology, macrocephaly, Polymorphism, Single Nucleotide, Article, Young Adult, 03 medical and health sciences, Rare Diseases, Behavioral and Social Science, medicine, megalencephaly, Animals, Humans, Polymorphism, Codon, Preschool, Neurosciences, Macrocephaly, medicine.disease, Brain Disorders, haploinsufficiency, NFI Transcription Factors, 030104 developmental biology, Nonsense, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, biology.protein, agenesis of the corpus callosum
Abstract

The nuclear factor I (NFI) family of transcription factors play an important role in normal development of multiple organs. Three NFI family members are highly expressed in the brain, and deletions or sequence variants in two of these, NFIA and NFIX, have been associated with intellectual disability (ID) and brain malformations. NFIB, however, has not previously been implicated in human disease. Here, we present a cohort of 18 individuals with mild ID and behavioral issues who are haploinsufficient for NFIB. Ten individuals harbored overlapping microdeletions of the chromosomal 9p23-p22.2 region, ranging in size from 225 kb to 4.3 Mb. Five additional subjects had point sequence variations creating a premature termination codon, and three subjects harbored single-nucleotide variations resulting in an inactive protein as determined using an in vitro reporter assay. All individuals presented with additional variable neurodevelopmental phenotypes, including muscular hypotonia, motor and speech delay, attention deficit disorder, autism spectrum disorder, and behavioral abnormalities. While structural brain anomalies, including dysgenesis of corpus callosum, were variable, individuals most frequently presented with macrocephaly. To determine whether macrocephaly could be a functional consequence of NFIB disruption, we analyzed a cortex-specific Nfib conditional knockout mouse model, which is postnatally viable. Utilizing magnetic resonance imaging and histology, we demonstrate that Nfib conditional knockout mice have enlargement of the cerebral cortex but preservation of overall brain structure and interhemispheric connectivity. Based on our findings, we propose that haploinsufficiency of NFIB causes ID with macrocephaly. ispartof: AMERICAN JOURNAL OF HUMAN GENETICS vol:103 issue:5 pages:752-768 ispartof: location:United States status: published

Published
2018
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10. Variants in the degron ofAFF3cause a multi-system disorder with mesomelic dysplasia, horseshoe kidney and developmental and epileptic encephalopathy

Author

David Kronn, Akemi J. Tanaka, Stefan Mundlos, Jennifer Norman, Crystle Lee, Delphine Héron, Elena L. Dadali, Anna Mikhaleva, Tomoko Uehara, Alexander Lavrov, Kenjiro Kosaki, Cecilie F. Rustad, Victoria R. Sanders, Heidi Taska-Tench, Ganka Douglas, Boris Keren, Nicolas Chatron, Ennio Del Giudice, E. Martina Bebin, Julien Delafontaine, Wendy K. Chung, Susan M. Hiatt, Olga Levchenko, Nicolas Guex, Jane Juusola, Tara Funari, Rhonda E. Schnur, Caroline Nava, Giuliana Giannuzzi, Binnaz Yalcin, Gregory M. Cooper, Dawn L. Earl, Sofia Douzgou, Kristian Tveten, Anna C.E. Hurst, Gerarda Cappuccio, Joel Charrow, Sinje Geuer, Alexandre Reymond, David J. Amor, Elin Tønne, Norine Voisin, Natasha J Brown, Alfredo Brusco, Dian Donnai, Giuseppina Vitiello, Sylvain Pradervand, Nicola Brunetti-Pierri, Else Merckoll, Fabio Sirchia, Toshiki Takenouchi, and Øystein L. Holla

Subjects
Genetics, Hypertrichosis, 0303 health sciences, Mesomelic Dysplasia, Horseshoe kidney, Biology, biology.organism_classification, medicine.disease, Phenotype, Transcriptome, 03 medical and health sciences, 0302 clinical medicine, medicine, Missense mutation, Degron, Zebrafish, 030217 neurology & neurosurgery, 030304 developmental biology
Abstract

The ALF transcription factor paralogs,AFF1, AFF2, AFF3andAFF4, are components of the transcriptional super elongation complex that regulates expression of genes involved in neurogenesis and development. We describe a new autosomal dominant disorder associated withde novomissense variants in the degron of AFF3, a nine amino acid sequence important for its degradation. Consistent with a causative role ofAFF3variants, the mutated AFF3 proteins show reduced clearance. Ten affected individuals were identified, and present with a recognizable pattern of anomalies, which we named KINSSHIP syndrome (KI for horseshoeKIdney, NS forNievergelt/Savarirayan type of mesomelic dysplasia, S forSeizures, H forHypertrichosis, I forIntellectual disability and P forPulmonary involvement), partially overlapping theAFF4associated CHOPS syndrome. An eleventh individual with a microdeletion encompassing only the transactivation domain and degron motif ofAFF3exhibited overlapping clinical features. A zebrafish overexpression model that shows body axis anomalies provides further support for the pathological effect of increased amount of AFF3 protein.Whereas homozygousAff3knockout mice display skeletal anomalies, kidney defects, brain malformation and neurological anomalies, knock-in animals modeling the microdeletion and the missense variants identified in affected individuals presented with lower mesomelic limb deformities and early lethality, respectively.Transcriptome analyses as well as the partial phenotypic overlap of syndromes associated withAFF3andAFF4variants suggest that ALF transcription factors are not redundant in contrast to what was previously suggested

Published
2019
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11. Five children with deletions of 1p34.3 encompassing AGO1 and AGO3

Author

Ghayda M. Mirzaa, Bertrand Isidor, Tiziana Filippi, Lynette S. Penney, Giovanni Mazzotta, Emilio Donti, Dawn L. Earl, Bianca Maas, Laura Bernardini, Mari Tokita, Cédric Le Caignec, Agatino Battaglia, Nicola Dikow, Penny M Chow, and Paolo Prontera

Subjects
Male, Adolescent, Developmental Disabilities, Piwi-interacting RNA, Haploinsufficiency, Biology, Article, RNA interference, microRNA, Gene expression, Genetics, Humans, Eukaryotic Initiation Factors, Child, Gene, Genetics (clinical), Syndrome, Argonaute, Chromosomes, Human, Pair 1, Child, Preschool, Argonaute Proteins, Chromosomal region, Muscle Hypotonia, Female, Chromosome Deletion
Abstract

Small RNAs (miRNA, siRNA, and piRNA) regulate gene expression through targeted destruction or translational repression of specific messenger RNA in a fundamental biological process called RNA interference (RNAi). The Argonaute proteins, which derive from a highly conserved family of genes found in almost all eukaryotes, are critical mediators of this process. Four AGO genes are present in humans, three of which (AGO 1, 3, and 4) reside in a cluster on chromosome 1p35p34. The effects of germline AGO variants or dosage alterations in humans are not known, however, prior studies have implicated dysregulation of the RNAi mechanism in the pathogenesis of several neurodevelopmental disorders. We describe five patients with hypotonia, poor feeding, and developmental delay who were found to have microdeletions of chromosomal region 1p34.3 encompassing the AGO1 and AGO3 genes. We postulate that haploinsufficiency of AGO1 and AGO3 leading to impaired RNAi may be responsible for the neurocognitive deficits present in these patients. However, additional studies with rigorous phenotypic characterization of larger cohorts of affected individuals and systematic investigation of the underlying molecular defects will be necessary to confirm this.

Published
2014
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12. The genomic landscape of balanced cytogenetic abnormalities associated with human congenital anomalies

Author

Bert Callewaert, Robert J. Hopkin, David A. Koolen, Hennie T. Brüggenwirth, Dezso David, Heather L. Ferguson, Helen Cox, Claire Redin, Joseph V. Thakuria, Ryan L. Collins, Mary-Alice Abbott, Michael E. Talkowski, Sjors Middelkamp, Michael J. Macera, Salmo Raskin, William J. Rhead, Heather Fisher, Han G. Brunner, Emmanuelle Lemyre, Margo Grady, Elyse Mitchell, Tarja Mononen, Sofia L. Alcaraz-Estrada, Cristin Griffis, Emily Moe, Samantha L.P. Schilit, Matthew J. Waterman, Colby Chiang, Aggie W. M. Nieuwint, Ivo Renkens, Joan F. Atkin, Jessie C. Jacobsen, Shehla Mohammed, Ernie M.H.F. Bongers, Maria de la Concepcion A Yerena-de Vega, Wigard P. Kloosterman, Jiddeke M. van de Kamp, Ton van Essen, Liya R Mikami, Tom Cushing, Conny M. A. van Ravenswaaij-Arts, Melita Irving, Kwame Anyane-Yeboa, Diane Masser-Frye, Catarina M. Seabra, Daniela Giachino, Bert B.A. de Vries, Brynn Levy, Caroline Antolik, Tina M. Bartell, Erika Aberg, Edwin Cuppen, Pamela Gerrol, Shahrin Pereira, Megan Mortenson, Raul Eduardo Pina Aguilar, Zehra Ordulu, Jennelle C. Hodge, Nicole de Leeuw, Troy J. Gliem, Michael W. McClellan, Sarah Vergult, Julia Tagoe, Giulia Pregno, Sandhya Parkash, David R. FitzPatrick, Giorgia Mandrile, Catharina M L Volker-Touw, Joseph T. Glessner, Danielle Perrin, Haibo Li, Peter M. Kroisel, Rhett Adley, Jodi D. Hoffman, Dorothy Warburton, Lauren Margolin, David J. Harris, Omar A. Abdul-Rahman, Ineke van der Burgt, Benjamin Currall, Monika Weisz Hubshman, Marjolijn C.J. Jongmans, Roberto T. Zori, William Lawless, Cynthia Lim, Andrea Hanson-Kahn, Vamsee Pillalamarri, Ken Corning, Tamara Mason, Yu An, Pino J. Poddighe, Susan P. Pauker, Cinthya J Zepeda Mendoza, Fowzan S. Alkuraya, Mira Irons, Sandra Janssens, Ranad Shaheen, Kathleen A. Leppig, Erica Spiegel, Chester W. Brown, Cynthia C. Morton, Filip Roelens, Ron Hochstenbach, Tamison Jewett, James F. Gusella, John P. Johnson, Brett H. Graham, Björn Menten, Annelies Dheedene, Rosamund Hill, Eva H. Brilstra, Alex V. Levin, Carlo Marcelis, Anna Wilson, A. Micheil Innes, Matthew A. Deardorff, Marc D'Hooghe, Elizabeth Beyer, Katy Phelan, Jayla Ruliera, Carrie Hanscom, Mark A. Hayden, Debra Rita, Edward J. Lose, Poornima Manavalan, Jerome Korzelius, Susan Wiley, Harrison Brand, Matthew R. Stone, Diane Lucente, Markus J. van Roosmalen, Tammy Kammin, Rebecca Sparkes, Patrick Rump, Stephen G. Kahler, Graciela Moya, Bregje W.M. van Bon, Blair Stevens, Eric C. Liao, Karen W. Gripp, Yves Lacassie, Dawn L. Earl, Erik C. Thorland, Linda M. Reis, Andrea L. Gropman, Jonathan A. Bernstein, Ian Blumenthal, Mary-Anne Anderson, Hong Li, Erasmus MC other, Klinische Genetica, RS: GROW - R4 - Reproductive and Perinatal Medicine, MUMC+: DA Klinische Genetica (5), Human genetics, AGEM - Endocrinology, metabolism and nutrition, AGEM - Inborn errors of metabolism, Amsterdam Neuroscience - Complex Trait Genetics, and Clinical Cognitive Neuropsychiatry Research Program (CCNP)

Subjects
0301 basic medicine, Male, INTELLECTUAL DISABILITY, Autism, Genome-wide association study, 030105 genetics & heredity, OF-FUNCTION MUTATIONS, balanced chromosomal abnormalities (BCAs), MEF2C, Genetics, Gene Rearrangement, Cytogenetic Abnormalities, Chromothripsis, DEVELOPMENTAL DELAY, Inversion, karyotypes, Microdeletion syndrome, Doenças Genómicas, Structural Variation, Medical genetics, Female, Topologically Associated Domain (TAD), Rare cancers Radboud Institute for Health Sciences [Radboudumc 9], Genetic Markers, medicine.medical_specialty, Human Congenital Anomalies, MICRODELETION SYNDROME, Translocation, Genomics, Biology, Article, Congenital Abnormalities, Structural variation, 03 medical and health sciences, Cytogenetics, Intellectual Disability, medicine, Journal Article, Humans, Genetic Predisposition to Disease, Chromosome Aberrations, Whole-genome sequencing, Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], CHROMOSOME REARRANGEMENTS, karyotypes, balanced chromosomal abnormalities (BCAs), Whole-genome sequencing, AUTISM SPECTRUM DISORDER, CANCER GENOMES, Gene rearrangement, Balanced Chromosomal Abnormality, Doenças Genéticas, STRUCTURAL VARIATION, 030104 developmental biology, Congenital Anomaly, SEVERE MENTAL-RETARDATION, DE-NOVO MUTATIONS, Genome-Wide Association Study
Abstract

Despite the clinical significance of balanced chromosomal abnormalities (BCAs), their characterization has largely been restricted to cytogenetic resolution. We explored the landscape of BCAs at nucleotide resolution in 273 subjects with a spectrum of congenital anomalies. Whole-genome sequencing revised 93% of karyotypes and demonstrated complexity that was cryptic to karyotyping in 21% of BCAs, highlighting the limitations of conventional cytogenetic approaches. At least 33.9% of BCAs resulted in gene disruption that likely contributed to the developmental phenotype, 5.2% were associated with pathogenic genomic imbalances, and 7.3% disrupted topologically associated domains (TADs) encompassing known syndromic loci. Remarkably, BCA breakpoints in eight subjects altered a single TAD encompassing MEF2C, a known driver of 5q14.3 microdeletion syndrome, resulting in decreased MEF2C expression. We propose that sequence-level resolution dramatically improves prediction of clinical outcomes for balanced rearrangements and provides insight into new pathogenic mechanisms, such as altered regulation due to changes in chromosome topology. info:eu-repo/semantics/publishedVersion

Published
2017
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13. Mutations in ECEL1 Cause Distal Arthrogryposis Type 5D

Author

Sarju G. Mehta, Margaret J. McMillin, Sujatha Jagadeesh, Stephen P. Robertson, Heather C Mefford, Jacqueline T. Hecht, Jay Shendure, Gloria R. Gogola, Dorothy K. Grange, Dawn L. Earl, Anita E. Beck, Deborah A. Nickerson, Michael J. Bamshad, James M. Swanson, Heidi I. S. Gildersleeve, Elaine M. Faustman, David J. Harris, Kathryn M. Shively, Jennifer E. Below, and Jason Pinner

Subjects
Male, Genetic Linkage, Consanguinity, Biology, medicine.disease_cause, Neuromuscular junction, 03 medical and health sciences, Ptosis, Genetic linkage, Report, medicine, Genetics, Humans, Genetics(clinical), Gene, Genetics (clinical), 030304 developmental biology, Arthrogryposis, 0303 health sciences, Mutation, 030305 genetics & heredity, Metalloendopeptidases, Sequence Analysis, DNA, 3. Good health, medicine.anatomical_structure, Female, Congenital contracture, medicine.symptom
Abstract

Distal arthrogryposis (DA) syndromes are the most common of the heritable congenital-contracture disorders, and ∼50% of cases are caused by mutations in genes that encode contractile proteins of skeletal myofibers. DA type 5D (DA5D) is a rare, autosomal-recessive DA previously defined by us and is characterized by congenital contractures of the hands and feet, along with distinctive facial features, including ptosis. We used linkage analysis and whole-genome sequencing of a multiplex consanguineous family to identify in endothelin-converting enzyme-like 1 (ECEL1) mutations that result in DA5D. Evaluation of a total of seven families affected by DA5D revealed in five families ECEL1 mutations that explain ∼70% of cases overall. ECEL1 encodes a neuronal endopeptidase and is expressed in the brain and peripheral nerves. Mice deficient in Ecel1 exhibit perturbed terminal branching of motor neurons to the endplate of skeletal muscles, resulting in poor formation of the neuromuscular junction. Our results distinguish a second developmental pathway that causes congenital-contracture syndromes.

Published
2013
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14. Role of Pediatric Geneticists in Craniofacial Teams: The Identification of Craniofacial Conditions with Cancer Predisposition

Author

Tara L. Wenger, Dawn L. Earl, Pedro A. Sanchez-Lara, and Penny Chow

Subjects
0301 basic medicine, Male, Pediatrics, medicine.medical_specialty, Adolescent, Dentistry, 030105 genetics & heredity, Risk Assessment, Craniofacial Abnormalities, 03 medical and health sciences, 0302 clinical medicine, Risk Factors, Neoplasms, Physicians, medicine, Humans, Genetic Predisposition to Disease, Genetic Testing, Neurofibromatosis type 2, Craniofacial, Child, Cancer predisposition, business.industry, Infant, Newborn, Infant, Geneticist, medicine.disease, Child, Preschool, Pediatrics, Perinatology and Child Health, Identification (biology), Female, business, 030217 neurology & neurosurgery
Abstract

Journal of Pediatrics, The - In Press.Proof corrected by the author Available online since jeudi 9 juin 2016

Published
2016

15. Polymicrogyria and deletion 22q11.2 syndrome: Window to the etiology of a common cortical malformation

Author

Donna M. McDonald-McGinn, Clare Taylor, Peter M. Bingham, Marie T. McDonald, Jean-Pierre Lin, Renzo Guerrini, Cathy A. Stevens, Neil Stoodley, Daniela T. Pilz, R. Curtis Rogers, David A. Lynch, Roger F. Massey, Marc D. Tischkowitz, Deepak Gill, Richard J. Leventer, Shehla Mohammed, Elaine H. Zackai, Nathaniel H. Robin, William B. Dobyns, Kevin Collins, Naomi T Katz, Miranda Splitt, Virginia Kimonis, Dawn L. Earl, and Tiziana Granata

Subjects
Male, Cerebellum, Pathology, medicine.medical_specialty, Velopharyngeal Insufficiency, Chromosomes, Human, Pair 22, Biology, Genetics, medicine, Polymicrogyria, Humans, Agenesis of the corpus callosum, Cerebellar hypoplasia, Genetics (clinical), Cerebral Cortex, Pachygyria, Sequela, Syndrome, medicine.disease, Perisylvian polymicrogyria, Magnetic Resonance Imaging, Hypoplasia, medicine.anatomical_structure, Female, Chromosome Deletion, Tomography, X-Ray Computed
Abstract

Several brain malformations have been described in rare patients with the deletion 22q11.2 syndrome (DEL22q11) including agenesis of the corpus callosum, pachygyria or polymicrogyria (PMG), cerebellar anomalies and meningomyelocele, with PMG reported most frequently. In view of our interest in the causes of PMG, we reviewed clinical data including brain-imaging studies on 21 patients with PMG associated with deletion 22q11.2 and another 11 from the literature. We found that the cortical malformation consists of perisylvian PMG of variable severity and frequent asymmetry with a striking predisposition for the right hemisphere (P = 0.008). This and other observations suggest that the PMG may be a sequela of abnormal embryonic vascular development rather than a primary brain malformation. We also noted mild cerebellar hypoplasia or mega-cisterna magna in 8 of 24 patients. Although this was not the focus of the present study, mild cerebellar anomalies are probably the most common brain malformation associated with DEL22q11.

Published
2006
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16. Deformational brachycephaly in supine-sleeping infants

Author

Xiuqing Guo, Dawn L. Earl, Andy Halberg, Carlos Samayoa, John M. Graham, and Jeannie T. Kreutzman

Subjects
Male, medicine.medical_specialty, Pediatrics, Supine position, Abnormal head shape, Supine Position, Humans, Medicine, Longitudinal Studies, Plagiocephaly, Nonsynostotic, business.industry, Skull, Infant, Mean age, Sudden infant death syndrome, medicine.disease, Surgery, Treatment Outcome, Pediatrics, Perinatology and Child Health, Head position, Female, Head Protective Devices, Sleep, business, Brachycephaly, After treatment
Abstract

Objectives Medical dictionaries and anthropologic sources define brachycephaly as a cranial index (CI = width divided by length × 100%) greater than 81%. We examine the impact of supine sleeping on CI and compare orthotic treatment with repositioning. Study design We compared the effect of repositioning versus helmet therapy on CI in 193 infants referred for abnormal head shape. Results Eighty percent of the infants had a pretreatment CI > 81%. Their initial mean CI at mean age 5.3 months was 89%, and after treatment, their mean CI was 87% (±2 SE = 0.9%) at mean age 9.0 months. For 92 infants with an initial CI at or above 90%, their initial mean CI of 96.1% was reduced to a mean of 91.9%. Conclusions Post-treatment CI was 86% to 88%, CI in neonates delivered by cesarean section was 80%, and CI in supine-sleeping Asian children was 85% to 91%, versus 78% to 83% for prone-sleeping American children. Repositioning was less effective than cranial orthotic therapy in correcting severe brachycephaly. We recommend varying the head position when putting infants to sleep.

Published
2005
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17. Management of deformational plagiocephaly: Repositioning versus orthotic therapy

Author

John M. Graham, Jinrui Cui, Jeannie T. Kreutzman, Mayela Gomez, Dawn L. Earl, Xiuqing Guo, and Andy Halberg

Subjects
Male, medicine.medical_specialty, Eye Diseases, Treatment outcome, Orthotics, Supine Position, Humans, Medicine, Cranial vault asymmetry, Longitudinal Studies, Positional plagiocephaly, Plagiocephaly, Nonsynostotic, business.industry, Skull, Age Factors, Infant, Mean age, Sudden infant death syndrome, medicine.disease, Surgery, Treatment Outcome, Pediatrics, Perinatology and Child Health, Female, Head Protective Devices, Deformational plagiocephaly, Plagiocephaly, business
Abstract

Objectives We compare positioning with orthotic therapy in 298 consecutive infants referred for correction of head asymmetry. Study design We evaluated 176 infants treated with repositioning, 159 treated with helmets, and 37 treated with initial repositioning followed by helmet therapy when treatment failed. We compared reductions in diagonal difference (RDD) between repositioning and cranial orthotic therapy. Helmets were routinely used for infants older than 6 months with DD >1 cm. Results For infants treated with repositioning at a mean age of 4.8 months, the mean RDD was 0.55 cm (from an initial mean DD of 1.05 cm). For infants treated with cranial orthotics at a mean age of 6.6 months, the mean RDD was 0.71 cm (from an initial mean DD of 1.13 cm). Conclusions Infants treated with orthotics were older and required a longer length of treatment (4.2 vs 3.5 months). Infants treated with orthosis had a mean final DD closer to the DD in unaffected infants (0.3 ± 0.1 cm), orthotic therapy was more effective than repositioning (61% decrease versus 52% decrease in DD), and early orthosis was significantly more effective than later orthosis (65% decrease versus 51% decrease in DD).

Published
2005
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18. High Incidence of Noonan Syndrome Features Including Short Stature and Pulmonic Stenosis in Patients carrying NF1 Missense Mutations Affecting p.Arg1809: Genotype-Phenotype Correlation

Author

Angela E. Scheuerle, Ludwine Messiaen, Yunjia Chen, Kitiwan Rojnueangnit, Martin G. Bialer, Kathy A. Leppig, Anne Destree, Salmo Raskin, Mary Alice Abbott, Jennifer Ibrahim, Shay Ben-Shachar, Jordi Rosell, Elizabeth K. Schorry, Patricia Galvin-Parton, James H. Tonsgard, Tom Callens, Dawn L. Earl, Begona Ezquieta, Eniko K. Pivnick, Dennis Bartholomew, Sandra Janssens, Christian P. Schaaf, Meagan E. Cochran, Gary Bellus, Stephanie E Wallace, Isabel Llano-Rivas, Vinodh Narayanan, Angela Sharp, Anna Duat-Rodriguez, Helio Pedro, Ishwar C. Verma, Meredith Schultz, Ying Liu, Jing Xie, Dusica Babovic-Vuksanovic, Elizabeth Siqveland, Kathleen Claes, Bruce Blumberg, Vinod K. Misra, Meena Upadhyaya, Rhonda E. Schnur, Jonathan Zonana, Elaine H. Zackai, Eric Legius, Bruce R. Korf, Melissa Crenshaw, David P. Bick, Fanny Cortés, Joan F. Atkin, Alicia Gomes, Marie T. McDonald, Linda M. Randolph, Lina Basel, Conxi Lázaro, Margretta R. Seashore, Karen W. Gripp, Kurt Heyrman, Beth Keena, Marthanda Eswara, Moshe Frydman, Christopher P. Barnett, Yolanda Martin, Jennifer Mulbury, Luis F. Escobar, Amanda Tkachuk, Naama Orenstein, Kathy Gardner, Karen L. David, Karol Rubin, Charles A. Williams, Concepción Hernández-Chico, Cynthia M. Powell, and Ian M. Frayling

Subjects
Proband, Male, humanos, adolescente, medicine.disease_cause, Cohort Studies, enanismo, Missense mutation, estudios de cohortes, Child, mediana edad, Genetics (clinical), Research Articles, phenotype–genotype correlations, Genetics, Mutation, Neurofibromin 1, p.Arg1809, Noonan Syndrome, sustitución de aminoácidos, adulto, Middle Aged, estudios de asociación genética, Arg1809, adulto joven, Legius syndrome, Phenotype, OF-THE-LITERATURE, Child, Preschool, fenotipo, Female, medicine.symptom, STANDARDS, Research Article, Adult, congenital, hereditary, and neonatal diseases and abnormalities, VONRECKLINGHAUSEN NEUROFIBROMATOSIS, Adolescent, Pulmonic stenosis, Mutation, Missense, Dwarfism, Biology, Short stature, neurofibromatosis type 1, Young Adult, medicine, Humans, Neurofibromatosis, Codon, mutación, Genetic Association Studies, lactante, OPTIC PATHWAY TUMORS, Biology and Life Sciences, Infant, NEUROFIBROMATOSIS TYPE-1 PATIENTS, SOUTH EAST WALES, medicine.disease, GENE, DELETIONS, CARDIOVASCULAR MALFORMATIONS, Amino Acid Substitution, NF1, síndrome de Noonan, phenotype-genotype correlations, Noonan syndrome, neurofibromina 1, codón
Abstract

Neurofibromatosis type 1 (NF1) is one of the most frequent genetic disorders, affecting 1:3,000 worldwide. Identification of genotype-phenotype correlations is challenging because of the wide range clinical variability, the progressive nature of the disorder, and extreme diversity of the mutational spectrum. We report 136 individuals with a distinct phenotype carrying one of five different NF1 missense mutations affecting p.Arg1809. Patients presented with multiple cafe-au-lait macules (CALM) with or without freckling and Lisch nodules, but no externally visible plexiform neurofibromas or clear cutaneous neurofibromas were found. About 25% of the individuals had Noonan-like features. Pulmonic stenosis and short stature were significantly more prevalent compared with classic cohorts (P, We thank the patients, their family and their referral physicians for the information. We thank the genetics counselor students who helped to re-contact all referral physicians for confirming information. This work was supported though the Children's Tumor Foundation by the Isaac and Sadie Fuchs Genotype-Phenotype Study (to L.M.) and by internal funds from the Medical Genomics Laboratory at UAB.

Published
2015

19. Deletions involving genes WHSC1 and LETM1 may be necessary, but are not sufficient to cause Wolf–Hirschhorn Syndrome

Author

Erica F. Andersen, Dawn L. Earl, Peter Hammond, Michael Suttie, Sarah T. South, John C. Carey, and Deyanira Corzo

Subjects
Male, Candidate gene, Genome-wide association study, Hemizygosity, Biology, Bioinformatics, Article, Genetics, medicine, Image Processing, Computer-Assisted, Humans, Child, Wolf–Hirschhorn syndrome, Genetics (clinical), Sequence Deletion, Wolf-Hirschhorn Syndrome, Calcium-Binding Proteins, Genetic disorder, Membrane Proteins, Histone-Lysine N-Methyltransferase, medicine.disease, Phenotype, Repressor Proteins, Chromosome 4, Child, Preschool, Female, Chromosomes, Human, Pair 4, Haploinsufficiency, Genome-Wide Association Study
Abstract

Wolf–Hirschhorn syndrome (WHS) is a complex genetic disorder caused by the loss of genomic material from the short arm of chromosome 4. Genotype–phenotype correlation studies indicated that the loss of genes within 4p16.3 is necessary for expression of the core features of the phenotype. Within this region, haploinsufficiency of the genes WHSC1 and LETM1 is thought to be a major contributor to the pathogenesis of WHS. We present clinical findings for three patients with relatively small (

Published
2013

20. Whole-genome analysis reveals that mutations in inositol polyphosphate phosphatase-like 1 cause opsismodysplasia

Author

Mark J. Stephan, Jozef Hertecant, James M. Swanson, Sheila Unger, Michael J. Bamshad, Dawn L. Earl, Margaret J. McMillin, Deborah A. Nickerson, Daniel H. Cohn, Jay Shendure, Lihadh Al-Gazali, David Chitayat, Deborah Krakow, Joshua D. Smith, Elaine M. Faustman, Kathryn M. Shively, Jennifer E. Below, and Emily H. Turner

Subjects
Male, Biology, medicine.disease_cause, Osteochondrodysplasias, Short stature, Genome, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Genetic linkage, Report, medicine, Genetics, Humans, Inositol, Genetics(clinical), Child, Genetics (clinical), 030304 developmental biology, 0303 health sciences, Mutation, Genome, Human, Infant, Newborn, Infant, medicine.disease, Phosphoric Monoester Hydrolases, chemistry, Dysplasia, Child, Preschool, Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatases, Opsismodysplasia, Human genome, Female, medicine.symptom, 030217 neurology & neurosurgery
Abstract

Opsismodysplasia is a rare, autosomal-recessive skeletal dysplasia characterized by short stature, characteristic facial features, and in some cases severe renal phosphate wasting. We used linkage analysis and whole-genome sequencing of a consanguineous trio to discover that mutations in inositol polyphosphate phosphatase-like 1 (INPPL1) cause opsismodysplasia with or without renal phosphate wasting. Evaluation of 12 families with opsismodysplasia revealed that INPPL1 mutations explain ∼60% of cases overall, including both of the families in our cohort with more than one affected child and 50% of the simplex cases. © 2013 The American Society of Human Genetics.

Published
2013
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21. Johnson-McMillin syndrome, a neuroectodermal syndrome with conductive hearing loss and microtia: report of a new case

Author

Shoji Yano, John M. Graham, Dawn L. Earl, and Daniela N. Schweitzer

Subjects
Ectodermal dysplasia, Microcephaly, Polydactyly, business.industry, Hearing loss, Developmental Disabilities, Neurocutaneous Syndromes, Microtia, Hearing Loss, Conductive, Infant, Newborn, Infant, Anatomy, Choanal stenosis, medicine.disease, Conductive hearing loss, Johnson–McMillin syndrome, otorhinolaryngologic diseases, medicine, Humans, Abnormalities, Multiple, Female, medicine.symptom, business, Genetics (clinical)
Abstract

In 1983, Johnson et al. described 16 related individuals with alopecia, anosmia or hyposmia, conductive hearing loss, microtia and/or atresia of the external auditory canal, and hypogonadotrophic hypogonadism inherited in an autosomal dominant pattern. Other less constant manifestations included facial asymmetry, mental retardation, congenital heart defect, cleft palate, and choanal stenosis. An isolated case was reported later (Johnston et al. [1987: Am J Med Genet 26: 925-927]) and thereafter an affected mother and son (Hennekam and Holtus [1993: Am J Med Genet 47: 714-716]). We describe an additional unrelated female patient with features resembling those of the previously reported cases. She presented with intrauterine growth deficiency, microcephaly, alopecia, bilateral microtia with canal atresia, conductive hearing loss, partial left facial palsy, posterior cleft palate, left choanal stenosis, tetralogy of Fallot, developmental delay, and right thumb polydactyly. Because the phenotypic abnormalities in this syndrome affect the brain, facial structures, ectoderm and its derivatives, outflow tract of the heart, and Rathke's pouch derivatives, this has suggested to previous authors etiologic involvement of the ectoderm and neuroectoderm of the first and second branchial arches, Rathke's pouch, and the diencephalon. Microtia with conductive hearing loss differentiates the condition from other ectodermal dysplasias. In the initial report, females appeared somewhat less affected than males, and there was male-to-male transmission. The mother of our patient manifests subtle features, which suggest she may be a mildly affected female. Additionally, there is a family history of early-onset alopecia in the maternal grandfather's relatives.

Published
2003

22. Syndromic ear anomalies and renal ultrasounds

Author

John M. Graham, Raymond Y. Wang, Robert O. Ruder, and Dawn L. Earl

Subjects
Male, medicine.medical_specialty, Population, Goldenhar syndrome, Deafness, Kidney, CHARGE syndrome, otorhinolaryngologic diseases, medicine, Prevalence, Humans, Abnormalities, Multiple, Ear, External, education, Child, Retrospective Studies, Ultrasonography, Cystic kidney, Branchio-oto-renal syndrome, education.field_of_study, business.industry, Infant, Newborn, medicine.disease, External ear malformation, Surgery, Pedigree, Bilateral Renal Agenesis, Anotia, Pediatrics, Perinatology and Child Health, Female, sense organs, business, Branchio-Oto-Renal Syndrome, Mandibulofacial Dysostosis
Abstract

Objective.Although many pediatricians pursue renal ultrasonography when patients are noted to have external ear malformations, there is much confusion over which specific ear malformations do and do not require imaging. The objective of this study was to delineate characteristics of a child with external ear malformations that suggest a greater risk of renal anomalies. We highlight several multiple congenital anomaly (MCA) syndromes that should be considered in a patient who has both ear and renal anomalies.Methods.Charts of patients who had ear anomalies and were seen for clinical genetics evaluations between 1981 and 2000 at Cedars-Sinai Medical Center in Los Angeles and Dartmouth-Hitchcock Medical Center in New Hampshire were reviewed retrospectively. Only patients who underwent renal ultrasound were included in the chart review. The literature was reviewed for the epidemiology of renal anomalies in the general population and in MCA syndromes with external ear anomalies. We defined a child as having an external ear anomaly when he or she had any of the following: preauricular pits and tags; microtia; anotia; or cup, lop, and other forms of dysplastic ears. A child was defined as having a renal anomaly if an ultrasound revealed any of the following: unilateral or bilateral renal agenesis; hypoplasia; crossed ectopia; horseshoe, pelvic, cystic kidney; hydronephrosis; duplicated ureters; megaureter; or vesicoureteric reflux.Results.Because clinical genetics assessments were made by the same clinician at both sites (J.M.G.), data were combined. A total of 42 patients with ear anomalies received renal ultrasound; 12 (29%) of them displayed renal anomalies. Of the 12 patients with renal anomalies, 11 (92%) also received a diagnosis of MCA syndrome. Eleven of 33 patients (33%) with MCA syndromes had renal anomalies, whereas 1 of 9 patients (11%) with isolated ear anomalies had renal anomalies. Specific disorders seen were CHARGE association, Townes-Brocks syndrome, branchio-oto-renal syndrome, Nager syndrome, and diabetic embryopathy.Conclusions.We conclude that ear malformations are associated with an increased frequency of clinically significant structural renal anomalies compared with the general population. This is due to the observation that auricular malformations often are associated with specific MCA syndromes that have high incidences of renal anomalies. These include CHARGE association, Townes-Brocks syndrome, branchio-oto-renal syndrome, Nager syndrome, Miller syndrome, and diabetic embryopathy. Patients with auricular anomalies should be assessed carefully for accompanying dysmorphic features, including facial asymmetry; colobomas of the lid, iris, and retina; choanal atresia; jaw hypoplasia; branchial cysts or sinuses; cardiac murmurs; distal limb anomalies; and imperforate or anteriorly placed anus. If any of these features are present, then a renal ultrasound is useful not only in discovering renal anomalies but also in the diagnosis and management of MCA syndromes themselves. A renal ultrasound should be performed in patients with isolated preauricular pits, cup ears, or any other ear anomaly accompanied by 1 or more of the following: other malformations or dysmorphic features, a family history of deafness, auricular and/or renal malformations, or a maternal history of gestational diabetes. In the absence of these findings, renal ultrasonography is not indicated.

Published
2001

23. Defining the clinical phenotype of Saul–Wilson syndrome

Author

William G. Wilson, Marte Gjøl Haug, Lynne A. Wolfe, Melissa Gabriel, Gen Nishimura, Seth I. Berger, William A. Gahl, Melissa A. Merideth, Heiko Bratke, Zhi-Jie Xia, John A. Phillips, Luis Rohena, Emma Tham, Carlos Ferreira, Giedre Grigelioniene, Daniel R. Carvalho, Michael B. Bober, Andrea Merker, Angela L. Duker, Mariya Kozenko, Hudson H. Freeze, Dawn L. Earl, Bobby G. Ng, George E. Tiller, Wadih M. Zein, Andrew P. Jackson, Alvaro H Serrano Russi, Rizwan Hamid, Laryssa A. Huryn, Hanne B Hove, and Lauren Brick

Subjects
Adult, Pediatrics, medicine.medical_specialty, Dwarfism, Disease, Neutropenia, Short stature, Article, 03 medical and health sciences, 0302 clinical medicine, medicine, Humans, Genetics (clinical), 030304 developmental biology, Saul-Wilson syndrome, Retrospective Studies, 0303 health sciences, business.industry, Dystrophy, medicine.disease, 3. Good health, Natural history, Phenotype, COG4, Cohort, Etiology, G516R, Female, medicine.symptom, business, Body mass index, 030217 neurology & neurosurgery
Abstract

Purpose: Four patients with Saul-Wilson syndrome were reported between 1982 and 1994, but no additional individuals were described until 2018, when the molecular etiology of the disease was elucidated. Hence, the clinical phenotype of the disease remains poorly defined. We address this shortcoming by providing a detailed characterization of its phenotype. Methods: Retrospective chart reviews were performed and primary radiographs assessed for all 14 individuals. Four individuals underwent detailed ophthalmologic examination by the same physician. Two individuals underwent gynecologic evaluation. Z-scores for height, weight, head circumference and BMI were calculated at different ages. Results: All patients exhibited short stature, with sharp decline from the mean within the first months of life, and a final height Z-score between −4 and −8.5 standard deviations. The facial and radiographic features evolved over time. Intermittent neutropenia was frequently observed. Novel findings included elevation of liver transaminases, skeletal fragility, rod-cone dystrophy, and cystic macular changes. Conclusion: Saul-Wilson syndrome presents a remarkably uniform phenotype, and the comprehensive description of our cohort allows for improved understanding of the long-term morbidity of the condition, establishment of follow-up recommendations for affected individuals, and documentation of the natural history into adulthood for comparison with treated patients, when therapeutics become available.

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