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Microtia in Cornelia de Lange syndrome: a case from Democratic Republic of the Congo. Clin Dysmorphol 2016; 25:178-80. [DOI: 10.1097/mcd.0000000000000129] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Goldenberg A, Riccardi F, Tessier A, Pfundt R, Busa T, Cacciagli P, Capri Y, Coutton C, Delahaye-Duriez A, Frebourg T, Gatinois V, Guerrot AM, Genevieve D, Lecoquierre F, Jacquette A, Khau Van Kien P, Leheup B, Marlin S, Verloes A, Michaud V, Nadeau G, Mignot C, Parent P, Rossi M, Toutain A, Schaefer E, Thauvin-Robinet C, Van Maldergem L, Thevenon J, Satre V, Perrin L, Vincent-Delorme C, Sorlin A, Missirian C, Villard L, Mancini J, Saugier-Veber P, Philip N. Clinical and molecular findings in 39 patients with KBG syndrome caused by deletion or mutation of ANKRD11. Am J Med Genet A 2016; 170:2847-2859. [PMID: 27605097 DOI: 10.1002/ajmg.a.37878] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 07/19/2016] [Indexed: 12/28/2022]
Abstract
KBG syndrome, due to ANKRD11 alteration is characterized by developmental delay, short stature, dysmorphic facial features, and skeletal anomalies. We report a clinical and molecular study of 39 patients affected by KBG syndrome. Among them, 19 were diagnosed after the detection of a 16q24.3 deletion encompassing the ANKRD11 gene by array CGH. In the 20 remaining patients, the clinical suspicion was confirmed by the identification of an ANKRD11 mutation by direct sequencing. We present arguments to modulate the previously reported diagnostic criteria. Macrodontia should no longer be considered a mandatory feature. KBG syndrome is compatible with autonomous life in adulthood. Autism is less frequent than previously reported. We also describe new clinical findings with a potential impact on the follow-up of patients, such as precocious puberty and a case of malignancy. Most deletions remove the 5'end or the entire coding region but never extend toward 16q telomere suggesting that distal 16q deletion could be lethal. Although ANKRD11 appears to be a major gene associated with intellectual disability, KBG syndrome remains under-diagnosed. NGS-based approaches for sequencing will improve the detection of point mutations in this gene. Broad knowledge of the clinical phenotype is essential for a correct interpretation of the molecular results. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Alice Goldenberg
- Service de génétique, CHU de Rouen et Inserm U1079, Université de Rouen, Centre Normand de Génomique Médicale et Médecine Personnalisée, Rouen, France.
| | - Florence Riccardi
- Département de génétique médicale, Hôpital de la Timone-Enfant, Assistance publique hôpitaux de Marseille, Marseille, France
| | - Aude Tessier
- Service de génétique, CHU de Rouen et Inserm U1079, Université de Rouen, Centre Normand de Génomique Médicale et Médecine Personnalisée, Rouen, France
| | - Rolph Pfundt
- Afdeling Genetica, Radboud universitair medisch centrum, Nijmegen, Holland
| | - Tiffany Busa
- Département de génétique médicale, Hôpital de la Timone-Enfant, Assistance publique hôpitaux de Marseille, Marseille, France
| | | | - Yline Capri
- Unité fonctionnelle de génétique clinique, CHU Robert Debré, Paris, France
| | - Charles Coutton
- Unité fonctionnelle de génétique chromosomique, Hôpital Couple-Enfant, CHU de Grenoble, Université de Grenoble Alpes, INSERM 1209, CNRS UMR 5309, Grenoble, France
| | - Andree Delahaye-Duriez
- Laboratoire d'histologie-embryologie-cytogénétique-BDR, Hôpital Jean Verdier, CHU de Paris Seine-Saint-Denis, APHP et Université Paris 13, Sorbonne Paris Cité, Bondy, France
| | - Thierry Frebourg
- Service de génétique, CHU de Rouen et Inserm U1079, Université de Rouen, Centre Normand de Génomique Médicale et Médecine Personnalisée, Rouen, France
| | - Vincent Gatinois
- Laboratoire de génétique des maladies rares et auto-inflammatoires, Hôpital Arnaud de Villeneuve, CHRU de Montpellier, Montpellier, France
| | - Anne-Marie Guerrot
- Service de génétique, CHU de Rouen et Inserm U1079, Université de Rouen, Centre Normand de Génomique Médicale et Médecine Personnalisée, Rouen, France
| | - David Genevieve
- Département de génétique médicale, Hôpital Arnaud de Villeneuve, CHRU de Montpellier, Montpellier, France
| | - Francois Lecoquierre
- Service de génétique, CHU de Rouen et Inserm U1079, Université de Rouen, Centre Normand de Génomique Médicale et Médecine Personnalisée, Rouen, France
| | - Aurélia Jacquette
- APHP, Département de Génétique, Centre de référence déficiences intellectuelles de Causes Rares, GRC UPMC "déficiences intellectuelles et autisme", Groupe Hospitalier Pitié Salpêtrière, Paris, France
| | - Philippe Khau Van Kien
- Unité fonctionnelle de génétique médicale et cytogénétique, Hôpital Caremeau, CHU de Nîmes, Nîmes, France
| | - Bruno Leheup
- Service de génétique clinique, Hôpital de Brabois, CHU de Nancy, Nancy, France
| | - Sandrine Marlin
- Service de génétique, Hôpital Necker-Enfants Malades, Paris, France
| | - Alain Verloes
- Unité fonctionnelle de génétique clinique, CHU Robert Debré, Paris, France
| | - Vincent Michaud
- Service de génétique médicale, GH Pellegrin, CHU de Bordeaux, Bordeaux, France
| | - Gwenael Nadeau
- Unité fonctionnelle de cytogénétique, CH de Valence, Valence, France
| | - Cyril Mignot
- APHP, Département de Génétique, Centre de référence déficiences intellectuelles de Causes Rares, GRC UPMC "déficiences intellectuelles et autisme", Groupe Hospitalier Pitié Salpêtrière, Paris, France
| | - Philippe Parent
- Département de pédiatrie et génétique médicale, Hôpital Morvan, CHRU de Brest, Brest, France
| | - Massimiliano Rossi
- Service de génétique, Hôpital Femme-Mère-Enfant, GH Est, CHU de Lyon, Lyon, France
| | - Annick Toutain
- Service de génétique, Hôpital Bretonneau, CHRU de Tours, Tours, France
| | - Elise Schaefer
- Service de génétique médicale, Hôpital de Hautepierre, CHU de Strasbourg, Strasbourg, France
| | | | - Lionel Van Maldergem
- Centre de génétique humaine, Hôpital Saint-Jacques, CHRU de Besançon, Besançon, France
| | - Julien Thevenon
- Centre de génétique, Hôpital François Mitterrand, CHU Dijon Bourgogne, Dijon, France
| | - Véronique Satre
- Unité fonctionnelle de génétique chromosomique, Hôpital Couple-Enfant, CHU de Grenoble, Université de Grenoble Alpes, INSERM 1209, CNRS UMR 5309, Grenoble, France
| | - Laurence Perrin
- Unité fonctionnelle de génétique clinique, CHU Robert Debré, Paris, France
| | | | - Arthur Sorlin
- Service de génétique clinique, Hôpital de Brabois, CHU de Nancy, Nancy, France
| | - Chantal Missirian
- Département de génétique médicale, Hôpital de la Timone-Enfant, Assistance publique hôpitaux de Marseille, Marseille, France
| | | | - Julien Mancini
- Aix Marseille Université, Inserm, IRD, UMR_S912, SESSTIM, Marseille, France.,APHM, Hôpital de la Timone, BiosTIC, Marseille, France
| | - Pascale Saugier-Veber
- Service de génétique, CHU de Rouen et Inserm U1079, Université de Rouen, Centre Normand de Génomique Médicale et Médecine Personnalisée, Rouen, France
| | - Nicole Philip
- Département de génétique médicale, Hôpital de la Timone-Enfant, Assistance publique hôpitaux de Marseille, Marseille, France.,Aix Marseille Université, INSERM, GMGF, Marseille, France
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103
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Janek KC, Smith DF, Kline AD, Benke JR, Chen ML, Kimball A, Ishman SL. Improvement in hearing loss over time in Cornelia de Lange syndrome. Int J Pediatr Otorhinolaryngol 2016; 87:203-7. [PMID: 27368472 DOI: 10.1016/j.ijporl.2016.06.032] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 06/07/2016] [Accepted: 06/08/2016] [Indexed: 11/29/2022]
Abstract
OBJECTIVES Patients with Cornelia de Lange Syndrome (CdLS) are reported to have conductive (CHL) and sensorineural hearing loss (SNHL), but there is little information pertaining to the progression of hearing loss over time. The goal of this study was to examine the prevalence of CHL and SNHL in adults and children with CdLS and look for changes in SNHL over time. METHODS Retrospective chart review of patients with CdLS presenting to a CdLS clinic was conducted. Also, a written survey of clinical concerns was collected from additional patients/families seen in the clinic and through the Cornelia de Lange Foundation. RESULTS Seventy-eight patients (50% female) were included in the chart review. Mean age was 16.8 ± 11.4 years (range-0.6-50 years) and mean age at diagnosis of hearing loss was 4.6 ± 10.6 years (n = 26). Five patients (6.4%) had severe to profound SNHL that improved with time, including 2 who had complete normalization of audiogram results. Thirty-five families/patients completed the clinical survey, and 45.5% of the families reported a noticeable improvement of hearing over time. CONCLUSIONS Conductive hearing loss and SNHL are common in CdLS. More than 50% of the patients seen in an adult CdLS clinic reported improvement in hearing loss over time, and a subset of patients had an improvement in SNHL. In light of these findings, we recommend longitudinal evaluations of hearing loss in these patients with both auditory brainstem response and otoacoustic emissions testing if SNHL is identified.
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Affiliation(s)
- Kevin C Janek
- College of Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - David F Smith
- Division of Pediatric Otolaryngology - Head and Neck Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Antonie D Kline
- Harvey Institute of Human Genetics, Greater Baltimore Medical Center, Baltimore, MD, USA
| | - James R Benke
- Lake Erie College of Osteopathic Medicine, Erie, PA, USA
| | - Mei-Ling Chen
- Department of Audiology, St. Agnes Hospital, Baltimore, MD, USA
| | - Amy Kimball
- Harvey Institute of Human Genetics, Greater Baltimore Medical Center, Baltimore, MD, USA
| | - Stacey L Ishman
- Division of Pediatric Otolaryngology - Head and Neck Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Department of Otolaryngology - Head and Neck Surgery, University of Cincinnati College of Medicine, Cincinnati, OH, USA; Department of Pulmonary Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
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Cereda A, Mariani M, Rebora P, Sajeva A, Ajmone PF, Gervasini C, Russo S, Kullmann G, Valsecchi G, Selicorni A. A new prognostic index of severity of intellectual disabilities in Cornelia de Lange syndrome. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2016; 172:179-89. [PMID: 27148700 DOI: 10.1002/ajmg.c.31494] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Cornelia de Lange syndrome is a well-known multiple congenital anomalies/intellectual disability syndrome with genetic heterogeneity and wide clinical variability, regarding the severity of both the intellectual disabilities and the physical features, not completely explained by the genotype-phenotype correlations known to date. The aim of the study was the identification of prognostic features, ascertainable precociously in the patient's life, of a better intellectual outcome and the development of a new prognostic index of severity of intellectual disability in CdLS patients. In 66 italian CdLS patients aged 8 years or more, we evaluated the association of the degree of intellectual disability with various clinical parameters ascertainable before 6 months of life and with the molecular data by the application of cumulative regression logistic model. Based on these results and on the previously known genotype-phenotype correlations, we selected seven parameters to be used in a multivariate cumulative regression logistic model to develop a prognostic index of severity of intellectual disability. The probability of a mild ID increases with the reducing final score less than two, the probability of a severe ID increases with the increasing final score more than three. This prognostic index allows to define, precociously in the life of a baby, the probability of a better or worse intellectual outcome in CdLS patients. © 2016 Wiley Periodicals, Inc.
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Moretto A, Scaravilli V, Ciceri V, Bosatra M, Giannatelli F, Ateniese B, Mariani M, Cereda A, Sosio S, Zanella A, Pesenti A, Selicorni A. Sedation and general anesthesia for patients with Cornelia De Lange syndrome: A case series. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2016; 172:222-8. [PMID: 27145336 DOI: 10.1002/ajmg.c.31493] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Cornelia De Lange syndrome (CdLS) is a rare congenital disease characterized by typical facial dysmorphism, developmental disability, and limb deficiency defects. Various congenital malformations and medical complications have been described with gastroesophageal reflux as the major one. CdLS patients often require multiple high-risk anesthetic procedures. At San Gerardo Hospital (Monza, Italy) the management of CdLS patients is routinely organized through a standard protocol and a dedicated pediatric anesthesia team has been implemented. We report on a retrospective descriptive analysis of the anesthetic records of the CdLS patients admitted to San Gerardo Hospital from January 2010 to December 2015. We retrieved: demographics, genetic profiles, type of procedures, anesthetic approaches, anesthetics usage and complications. Data are reported as median (interquartile range) values. Twenty-seven patients (11 female), with age 12 (7-15) years old, weight 24 (14-35) kg, and severity score of 25 (18-32) were included. NIBPL mutations were the most frequently represented. We analyzed 58 procedures (30 esophagogastroduodenoscopies, 8 evoked auditory potential tests, 5 radiodiagnostics, 5 catheters positioning, 4 bronchoscopies) managed by sedation (36) and general anesthesia (6). Each patient underwent one (1-2) anesthetic procedure. Propofol (59%), sevoflurane (31%), fentanyl (24%), and ketamine (10%) were used. Three out of six endotracheal intubations were difficult. The only documented intraoperative complications were three episodes of desaturation (oxygen saturation <90%) occurring during sedations and were managed without the need for an invasive control of the airways. Implementation of a specific management protocol and a dedicated allowed to provide anesthesia to CdLS patients without the occurrence of major complications. © 2016 Wiley Periodicals, Inc.
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106
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Daly AF, Yuan B, Fina F, Caberg JH, Trivellin G, Rostomyan L, de Herder WW, Naves LA, Metzger D, Cuny T, Rabl W, Shah N, Jaffrain-Rea ML, Zatelli MC, Faucz FR, Castermans E, Nanni-Metellus I, Lodish M, Muhammad A, Palmeira L, Potorac I, Mantovani G, Neggers SJ, Klein M, Barlier A, Liu P, Ouafik L, Bours V, Lupski JR, Stratakis CA, Beckers A. Somatic mosaicism underlies X-linked acrogigantism syndrome in sporadic male subjects. Endocr Relat Cancer 2016; 23:221-33. [PMID: 26935837 PMCID: PMC4877443 DOI: 10.1530/erc-16-0082] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 03/01/2016] [Indexed: 12/15/2022]
Abstract
Somatic mosaicism has been implicated as a causative mechanism in a number of genetic and genomic disorders. X-linked acrogigantism (XLAG) syndrome is a recently characterized genomic form of pediatric gigantism due to aggressive pituitary tumors that is caused by submicroscopic chromosome Xq26.3 duplications that include GPR101 We studied XLAG syndrome patients (n= 18) to determine if somatic mosaicism contributed to the genomic pathophysiology. Eighteen subjects with XLAG syndrome caused by Xq26.3 duplications were identified using high-definition array comparative genomic hybridization (HD-aCGH). We noted that males with XLAG had a decreased log2ratio (LR) compared with expected values, suggesting potential mosaicism, whereas females showed no such decrease. Compared with familial male XLAG cases, sporadic males had more marked evidence for mosaicism, with levels of Xq26.3 duplication between 16.1 and 53.8%. These characteristics were replicated using a novel, personalized breakpoint junction-specific quantification droplet digital polymerase chain reaction (ddPCR) technique. Using a separate ddPCR technique, we studied the feasibility of identifying XLAG syndrome cases in a distinct patient population of 64 unrelated subjects with acromegaly/gigantism, and identified one female gigantism patient who had had increased copy number variation (CNV) threshold for GPR101 that was subsequently diagnosed as having XLAG syndrome on HD-aCGH. Employing a combination of HD-aCGH and novel ddPCR approaches, we have demonstrated, for the first time, that XLAG syndrome can be caused by variable degrees of somatic mosaicism for duplications at chromosome Xq26.3. Somatic mosaicism was shown to occur in sporadic males but not in females with XLAG syndrome, although the clinical characteristics of the disease were similarly severe in both sexes.
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Affiliation(s)
- Adrian F Daly
- Department of Endocrinology, Centre Hospitalier Universitaire de Liege, University of Liege, Liege, Belgium
| | - Bo Yuan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TexasUSA
| | - Frederic Fina
- Assistance Publique Hôpitaux de Marseille (AP-HM), Hôpital Nord, Service de Transfert d'Oncologie Biologique, Marseille, France Laboratoire de Biologie Médicale, and Aix-Marseille UniversitéInserm, CRO2 UMR_S 911, Marseille, France
| | - Jean-Hubert Caberg
- Department of Human Genetics, Centre Hospitalier Universitaire de Liege, University of Liege, Liege, Belgium
| | - Giampaolo Trivellin
- Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Liliya Rostomyan
- Department of Endocrinology, Centre Hospitalier Universitaire de Liege, University of Liege, Liege, Belgium
| | - Wouter W de Herder
- Section of Endocrinology, Department of Medicine, Erasmus University Medical Center Rotterdam and Pituitary Center Rotterdam, Rotterdam, The Netherlands
| | - Luciana A Naves
- Department of Endocrinology, University of Brasilia, Brasilia, Brazil
| | - Daniel Metzger
- Endocrinology and Diabetes Unit, BC Children's Hospital, Vancouver, British Columbia, Canada
| | - Thomas Cuny
- Department of Endocrinology, University Hospital, Nancy, France
| | - Wolfgang Rabl
- Kinderklinik, Technische Universität München, Munich, Germany
| | - Nalini Shah
- Department of Endocrinology, KEM Hospital, Mumbai, India
| | - Marie-Lise Jaffrain-Rea
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila and Neuromed Institute, IRCCS, Pozzilli, Italy
| | - Maria Chiara Zatelli
- Section of Endocrinology, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Fabio R Faucz
- Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Emilie Castermans
- Department of Human Genetics, Centre Hospitalier Universitaire de Liege, University of Liege, Liege, Belgium
| | - Isabelle Nanni-Metellus
- Assistance Publique Hôpitaux de Marseille (AP-HM), Hôpital Nord, Service de Transfert d'Oncologie Biologique, Marseille, France
| | - Maya Lodish
- Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Ammar Muhammad
- Section of Endocrinology, Department of Medicine, Erasmus University Medical Center Rotterdam and Pituitary Center Rotterdam, Rotterdam, The Netherlands
| | - Leonor Palmeira
- Department of Endocrinology, Centre Hospitalier Universitaire de Liege, University of Liege, Liege, Belgium
| | - Iulia Potorac
- Department of Endocrinology, Centre Hospitalier Universitaire de Liege, University of Liege, Liege, Belgium Department of Human GeneticsCentre Hospitalier Universitaire de Liege, University of Liege, Liege, Belgium
| | - Giovanna Mantovani
- Endocrinology and Diabetology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Sebastian J Neggers
- Section of Endocrinology, Department of Medicine, Erasmus University Medical Center Rotterdam and Pituitary Center Rotterdam, Rotterdam, The Netherlands
| | - Marc Klein
- Department of Endocrinology, University Hospital, Nancy, France
| | - Anne Barlier
- Laboratory of Molecular Biology, APHM, Hopital la Conception, Aix Marseille Universite, Marseilles, France CRNSCRN2M-UMR 7286, Marseille, France
| | - Pengfei Liu
- Assistance Publique Hôpitaux de Marseille (AP-HM), Hôpital Nord, Service de Transfert d'Oncologie Biologique, Marseille, France
| | - L'Houcine Ouafik
- Laboratoire de Biologie Médicale, and Aix-Marseille Université, Inserm, CRO2 UMR_S 911, Marseille, France
| | - Vincent Bours
- Department of Human Genetics, Centre Hospitalier Universitaire de Liege, University of Liege, Liege, Belgium
| | - James R Lupski
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Constantine A Stratakis
- Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Albert Beckers
- Department of Endocrinology, Centre Hospitalier Universitaire de Liege, University of Liege, Liege, Belgium
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Mosaic CREBBP mutation causes overlapping clinical features of Rubinstein-Taybi and Filippi syndromes. Eur J Hum Genet 2016; 24:1363-6. [PMID: 26956253 DOI: 10.1038/ejhg.2016.14] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 12/28/2015] [Accepted: 01/03/2016] [Indexed: 12/30/2022] Open
Abstract
Rubinstein-Taybi syndrome (RTS, OMIM 180849) and Filippi syndrome (FLPIS, OMIM 272440) are both rare syndromes, with multiple congenital anomalies and intellectual deficit (MCA/ID). We present a patient with intellectual deficit, short stature, bilateral syndactyly of hands and feet, broad thumbs, ocular abnormalities, and dysmorphic facial features. These clinical features suggest both RTS and FLPIS. Initial DNA analysis of DNA isolated from blood did not identify variants to confirm either of these syndrome diagnoses. Whole-exome sequencing identified a homozygous variant in C9orf173, which was novel at the time of analysis. Further Sanger sequencing analysis of FLPIS cases tested negative for CKAP2L variants did not, however, reveal any further variants. Subsequent analysis using DNA isolated from buccal mucosa revealed a mosaic variant in CREBBP. This report highlights the importance of excluding mosaic variants in patients with a strong but atypical clinical presentation of a MCA/ID syndrome if no disease-causing variants can be detected in DNA isolated from blood samples. As the striking syndactyly observed in the present case is typical for FLPIS, we suggest CREBBP analysis in saliva samples for FLPIS syndrome cases in which no causal CKAP2L variant is detected.
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108
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Jansen S, Kleefstra T, Willemsen MH, de Vries P, Pfundt R, Hehir-Kwa JY, Gilissen C, Veltman JA, de Vries BBA, Vissers LELM. De novo loss-of-function mutations in X-linked SMC1A cause severe ID and therapy-resistant epilepsy in females: expanding the phenotypic spectrum. Clin Genet 2016; 90:413-419. [PMID: 26752331 DOI: 10.1111/cge.12729] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 01/04/2016] [Accepted: 01/04/2016] [Indexed: 12/30/2022]
Abstract
De novo missense mutations and in-frame coding deletions in the X-linked gene SMC1A (structural maintenance of chromosomes 1A), encoding part of the cohesin complex, are known to cause Cornelia de Lange syndrome in both males and females. For a long time, loss-of-function (LoF) mutations in SMC1A were considered incompatible with life, as such mutations had not been reported in neither male nor female patients. However, recently, the authors and others reported LoF mutations in females with intellectual disability (ID) and epilepsy. Here we present the detailed phenotype of two females with de novo LoF mutations in SMC1A, including a de novo mutation of single base deletion [c.2364del, p.(Asn788Lysfs*10)], predicted to result in a frameshift, and a de novo deletion of exon 16, resulting in an out-of-frame mRNA splice product [p.(Leu808Argfs*6)]. By combining our patients with the other recently reported females carrying SMC1A LoF mutations, we ascertained a phenotypic spectrum of (severe) ID, therapy-resistant epilepsy, absence/delay of speech, hypotonia and small hands and feet. Our data show the existence of a novel phenotypic entity - distinct from CdLS - and caused by de novo SMC1A LoF mutations.
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Affiliation(s)
- S Jansen
- Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, the Netherlands
| | - T Kleefstra
- Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, the Netherlands
| | - M H Willemsen
- Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, the Netherlands
| | - P de Vries
- Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, the Netherlands
| | - R Pfundt
- Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, the Netherlands
| | - J Y Hehir-Kwa
- Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, the Netherlands
| | - C Gilissen
- Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, the Netherlands
| | - J A Veltman
- Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, the Netherlands.,Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - B B A de Vries
- Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, the Netherlands.
| | - L E L M Vissers
- Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, the Netherlands
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Nizon M, Henry M, Michot C, Baumann C, Bazin A, Bessières B, Blesson S, Cordier-Alex MP, David A, Delahaye-Duriez A, Delezoïde AL, Dieux-Coeslier A, Doco-Fenzy M, Faivre L, Goldenberg A, Layet V, Loget P, Marlin S, Martinovic J, Odent S, Pasquier L, Plessis G, Prieur F, Putoux A, Rio M, Testard H, Bonnefont JP, Cormier-Daire V. A series of 38 novel germline and somatic mutations of NIPBL in Cornelia de Lange syndrome. Clin Genet 2016; 89:584-9. [PMID: 26701315 DOI: 10.1111/cge.12720] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Revised: 12/17/2015] [Accepted: 12/21/2015] [Indexed: 01/15/2023]
Abstract
Cornelia de Lange syndrome is a multisystemic developmental disorder mainly related to de novo heterozygous NIPBL mutation. Recently, NIPBL somatic mosaicism has been highlighted through buccal cell DNA study in some patients with a negative molecular analysis on leukocyte DNA. Here, we present a series of 38 patients with a Cornelia de Lange syndrome related to a heterozygous NIPBL mutation identified by Sanger sequencing. The diagnosis was based on the following criteria: (i) intrauterine growth retardation and postnatal short stature, (ii) feeding difficulties and/or gastro-oesophageal reflux, (iii) microcephaly, (iv) intellectual disability, and (v) characteristic facial features. We identified 37 novel NIPBL mutations including 34 in leukocytes and 3 in buccal cells only. All mutations shown to have arisen de novo when parent blood samples were available. The present series confirms the difficulty in predicting the phenotype according to the NIPBL mutation. Until now, somatic mosaicism has been observed for 20 cases which do not seem to be consistently associated with a milder phenotype. Besides, several reports support a postzygotic event for those cases. Considering these elements, we recommend a first-line buccal cell DNA analysis in order to improve gene testing sensitivity in Cornelia de Lange syndrome and genetic counselling.
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Affiliation(s)
- M Nizon
- Département de Génétique, Université Paris Descartes-Sorbonne Paris Cité, INSERM UMR1163, Institut IMAGINE, Hôpital Necker-Enfants Malades, Paris, France
| | - M Henry
- Département de Génétique, Université Paris Descartes-Sorbonne Paris Cité, INSERM UMR1163, Institut IMAGINE, Hôpital Necker-Enfants Malades, Paris, France
| | - C Michot
- Département de Génétique, Université Paris Descartes-Sorbonne Paris Cité, INSERM UMR1163, Institut IMAGINE, Hôpital Necker-Enfants Malades, Paris, France
| | - C Baumann
- Département de Génétique, CHU Robert Debré, Paris, France
| | - A Bazin
- Département de Génétique, CH René Dubos, Pontoise, France
| | - B Bessières
- Département de Génétique, Université Paris Descartes-Sorbonne Paris Cité, INSERM UMR1163, Institut IMAGINE, Hôpital Necker-Enfants Malades, Paris, France
| | - S Blesson
- Service de Génétique, CHRU Tours, Hôpital Bretonneau, Tours, France
| | - M-P Cordier-Alex
- Service de Génétique Clinique, Hospices Civils de Lyon, Bron, France
| | - A David
- Service de Génétique Médicale, CHU, Nantes, France
| | - A Delahaye-Duriez
- Service de Génétique, CHU Paris Seine-Saint-Denis, Hôpital Jean Verdier, Bondy, France
| | - A-L Delezoïde
- Département de Génétique, CHU Robert Debré, Paris, France
| | - A Dieux-Coeslier
- Service de Génétique Clinique, CHRU de Lille, Hôpital Jeanne de Flandre, Lille, France
| | - M Doco-Fenzy
- Service de Génétique, CHU de Reims, Hôpital Maison Blanche, Reims, France
| | - L Faivre
- Centre de Génétique, CHU de Dijon, Dijon, France
| | | | - V Layet
- Service de Génétique Médicale, GH du Havre, Hôpital Jacques Monod, Le Havre, France
| | - P Loget
- Service d'anatomie et cytologie pathologiques, Hôpital Pontchaillou, Université de Rennes 1, CHU, Rennes, France
| | - S Marlin
- Département de Génétique, Université Paris Descartes-Sorbonne Paris Cité, INSERM UMR1163, Institut IMAGINE, Hôpital Necker-Enfants Malades, Paris, France
| | - J Martinovic
- Département de Génétique, Université Paris Descartes-Sorbonne Paris Cité, INSERM UMR1163, Institut IMAGINE, Hôpital Necker-Enfants Malades, Paris, France
| | - S Odent
- Service de Génétique Clinique, CHU Rennes, Hôpital Sud, Rennes, France
| | - L Pasquier
- Service de Génétique Clinique, CHU Rennes, Hôpital Sud, Rennes, France
| | - G Plessis
- Service de Génétique Médicale, CHU Clémenceau, Caen, France
| | - F Prieur
- Service de Génétique Clinique, CHU de Saint-Etienne, Hôpital Nord, Saint-Priest-en-Jarez, France
| | - A Putoux
- Service de Génétique Clinique, Hospices Civils de Lyon, Bron, France
| | - M Rio
- Département de Génétique, Université Paris Descartes-Sorbonne Paris Cité, INSERM UMR1163, Institut IMAGINE, Hôpital Necker-Enfants Malades, Paris, France
| | - H Testard
- Département de Pédiatrie, CHU Grenoble, Grenoble, France
| | - J-P Bonnefont
- Département de Génétique, Université Paris Descartes-Sorbonne Paris Cité, INSERM UMR1163, Institut IMAGINE, Hôpital Necker-Enfants Malades, Paris, France
| | - V Cormier-Daire
- Département de Génétique, Université Paris Descartes-Sorbonne Paris Cité, INSERM UMR1163, Institut IMAGINE, Hôpital Necker-Enfants Malades, Paris, France
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110
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Identification and Functional Characterization of Two Intronic NIPBL Mutations in Two Patients with Cornelia de Lange Syndrome. BIOMED RESEARCH INTERNATIONAL 2016; 2016:8742939. [PMID: 26925417 PMCID: PMC4746300 DOI: 10.1155/2016/8742939] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2015] [Accepted: 11/16/2015] [Indexed: 12/03/2022]
Abstract
Cornelia de Lange syndrome (CdLS) is a rare genetically heterogeneous disorder with a high phenotypic variability including mental retardation, developmental delay, and limb malformations. The genetic causes in about 30% of patients with CdLS are still unknown. We report on the functional characterization of two intronic NIPBL mutations in two patients with CdLS that do not affect a conserved splice-donor or acceptor site. Interestingly, mRNA analyses showed aberrantly spliced transcripts missing exon 28 or 37, suggesting the loss of the branch site by the c.5329-15A>G transition and a disruption of the polypyrimidine by the c.6344del(-13)_(-8) deletion. While the loss of exon 28 retains the reading frame of the NIBPL transcript resulting in a shortened protein, the loss of exon 37 shifts the reading frame with the consequence of a premature stop of translation. Subsequent quantitative PCR analysis demonstrated a 30% decrease of the total NIPBL mRNA levels associated with the frameshift transcript. Consistent with our results, this patient shows a more severe phenotype compared to the patient with the aberrant transcript that retains its reading frame. Thus, intronic variants identified by sequencing analysis in CdLS diagnostics should carefully be examined before excluding them as nonrelevant to disease.
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111
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Parenti I, Gervasini C, Pozojevic J, Wendt KS, Watrin E, Azzollini J, Braunholz D, Buiting K, Cereda A, Engels H, Garavelli L, Glazar R, Graffmann B, Larizza L, Lüdecke HJ, Mariani M, Masciadri M, Pié J, Ramos FJ, Russo S, Selicorni A, Stefanova M, Strom TM, Werner R, Wierzba J, Zampino G, Gillessen-Kaesbach G, Wieczorek D, Kaiser FJ. Expanding the clinical spectrum of the 'HDAC8-phenotype' - implications for molecular diagnostics, counseling and risk prediction. Clin Genet 2016; 89:564-73. [PMID: 26671848 DOI: 10.1111/cge.12717] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 11/30/2015] [Accepted: 12/12/2015] [Indexed: 01/25/2023]
Abstract
Cornelia de Lange syndrome (CdLS) is a clinically heterogeneous disorder characterized by typical facial dysmorphism, cognitive impairment and multiple congenital anomalies. Approximately 75% of patients carry a variant in one of the five cohesin-related genes NIPBL, SMC1A, SMC3, RAD21 and HDAC8. Herein we report on the clinical and molecular characterization of 11 patients carrying 10 distinct variants in HDAC8. Given the high number of variants identified so far, we advise sequencing of HDAC8 as an indispensable part of the routine molecular diagnostic for patients with CdLS or CdLS-overlapping features. The phenotype of our patients is very broad, whereas males tend to be more severely affected than females, who instead often present with less canonical CdLS features. The extensive clinical variability observed in the heterozygous females might be at least partially associated with a completely skewed X-inactivation, observed in seven out of eight female patients. Our cohort also includes two affected siblings whose unaffected mother was found to be mosaic for the causative mutation inherited to both affected children. This further supports the urgent need for an integration of highly sensitive sequencing technology to allow an appropriate molecular diagnostic, genetic counseling and risk prediction.
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Affiliation(s)
- I Parenti
- Sektion für Funktionelle Genetik am Institut für Humangenetik Lübeck, Universität zu Lübeck, Lübeck, Germany.,Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - C Gervasini
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - J Pozojevic
- Sektion für Funktionelle Genetik am Institut für Humangenetik Lübeck, Universität zu Lübeck, Lübeck, Germany
| | - K S Wendt
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands
| | - E Watrin
- Faculté de Médecine, Institut de Génétique et Développement de Rennes, UMR6290-CNRS, Rennes, France
| | - J Azzollini
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - D Braunholz
- Sektion für Funktionelle Genetik am Institut für Humangenetik Lübeck, Universität zu Lübeck, Lübeck, Germany
| | - K Buiting
- Institut für Humangenetik, Universitätsklinikum Düsseldorf, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - A Cereda
- U.O.S. Genetica Clinica Pediatrica, Clinica Pediatrica Fondazione MBBM, A.O. S.Gerardo, Monza, Italy
| | - H Engels
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - L Garavelli
- Clinical Genetics Unit, Department of Obstetrics and Pediatrics, IRCCS S. Maria Nuova Hospital, Reggio Emilia, Italy
| | - R Glazar
- The Center for Medical Genetics GENESIS Poznan, Poland
| | - B Graffmann
- Department of Pediatrics, University Hospital Linköping, Linköping, Sweden
| | - L Larizza
- Laboratory of Medical Cytogenetics and Molecular Genetics, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - H J Lüdecke
- Institut für Humangenetik, Universitätsklinikum Düsseldorf, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - M Mariani
- U.O.S. Genetica Clinica Pediatrica, Clinica Pediatrica Fondazione MBBM, A.O. S.Gerardo, Monza, Italy
| | - M Masciadri
- Laboratory of Medical Cytogenetics and Molecular Genetics, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - J Pié
- Unit of Clinical Genetics and Functional Genomics, Departments of Pharmacology-Physiology and Pediatrics, Medical School, University of Zaragoza, CIBERER-GCV and ISS-Aragon, Zaragoza, Spain
| | - F J Ramos
- Unit of Clinical Genetics and Functional Genomics, Departments of Pharmacology-Physiology and Pediatrics, Medical School, University of Zaragoza, CIBERER-GCV and ISS-Aragon, Zaragoza, Spain.,Unidad de Genetica Clınica, Servicio de Pediatrıa, Hospital Clınico Universitario "Lozano Blesa", CIBERER-GCV and ISS-Aragon, Zaragoza, Spain
| | - S Russo
- Laboratory of Medical Cytogenetics and Molecular Genetics, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - A Selicorni
- U.O.S. Genetica Clinica Pediatrica, Clinica Pediatrica Fondazione MBBM, A.O. S.Gerardo, Monza, Italy
| | - M Stefanova
- Department of Clinical Genetics, University Hospital Linköping, Linköping, Sweden
| | - T M Strom
- Institute of Human Genetics, Technische Universität München, Munich, Germany.,Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - R Werner
- Division of Experimental Paediatric Endocrinology and Diabetes, Department of Paediatrics and Adolescent Medicine, University of Lübeck, Lübeck, Germany
| | - J Wierzba
- Department and Clinic of Pediatrics, Hematooncology, Oncology and Endocrinology, Medical University of Gdańsk, Gdańsk, Poland.,Department of General Nursing, Medical University of Gdańsk, Gdańsk, Poland
| | - G Zampino
- Birth Defects Unit, Department of Pediatrics, Università Cattolica del Sacro Cuore, Rome, Italy
| | | | - D Wieczorek
- Institut für Humangenetik, Universitätsklinikum Düsseldorf, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - F J Kaiser
- Sektion für Funktionelle Genetik am Institut für Humangenetik Lübeck, Universität zu Lübeck, Lübeck, Germany
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112
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Goldstein JH, Tim-aroon T, Shieh J, Merrill M, Deeb KK, Zhang S, Bass NE, Bedoyan JK. Novel SMC1A frameshift mutations in children with developmental delay and epilepsy. Eur J Med Genet 2015; 58:562-8. [DOI: 10.1016/j.ejmg.2015.09.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2015] [Revised: 09/10/2015] [Accepted: 09/15/2015] [Indexed: 11/26/2022]
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113
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Pezzani L, Milani D, Tadini G. Intellectual Disability: When the Hypertrichosis Is a Clue. J Pediatr Genet 2015; 4:154-8. [PMID: 27617126 DOI: 10.1055/s-0035-1564442] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 06/17/2015] [Indexed: 01/18/2023]
Abstract
The skin and the central and peripheral nervous system both derive from the ectoderm ridge. Therefore, several syndromes characterized by the presence of intellectual disability (ID) can be associated with specific congenital cutaneous manifestations. In this review, we list some of the most frequent diseases characterized by the presence of ID associated with hirsutism, which might be an incentive for the clinicians to pay attention to the ectodermal annexes in patients with ID.
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Affiliation(s)
- Lidia Pezzani
- Pathology Unit, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
| | - Donatella Milani
- Pediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
| | - Gianluca Tadini
- Pediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy; Unit of Dermatology, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
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114
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Lebrun N, Lebon S, Jeannet PY, Jacquemont S, Billuart P, Bienvenu T. Early-onset encephalopathy with epilepsy associated with a novel splice site mutation in SMC1A. Am J Med Genet A 2015; 167A:3076-81. [PMID: 26358754 DOI: 10.1002/ajmg.a.37364] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 08/28/2015] [Indexed: 11/07/2022]
Abstract
We report on the clinical and molecular characterization of a female patient with early-onset epileptic encephalopathy, who was found to carry a de novo novel splice site mutation in SMC1A. This girl shared some morphologic and anthropometric traits described in patients with clinical diagnosis of Cornelia de Lange syndrome and with SMC1A mutation but also has severe encephalopathy with early-onset epilepsy. In addition, she had midline hand stereotypies and scoliosis leading to the misdiagnosis of a Rett overlap syndrome. Molecular studies found a novel de novo splice site mutation (c.1911 + 1G > T) in SMC1A. This novel splice mutation was associated with an aberrantly processed mRNA that included intron 11 of the gene. Moreover, quantitative approach by RT-PCR showed a severe reduction of the SMC1A transcript suggesting that this aberrant transcript may be unstable and degraded. Taken together, our data suggest that the phenotype may be due to a loss-of-function of SMC1A in this patient. Our findings suggest that loss-of-function mutations of SMC1A may be associated with early-onset encephalopathy with epilepsy.
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Affiliation(s)
- Nicolas Lebrun
- Inserm, Institut Cochin, Paris, France.,Cnrs, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Sébastien Lebon
- Department of Pediatrics, Pediatric Neurology and Neurorehabilitation Unit, Lausanne University Hospital, Switzerland
| | - Pierre-Yves Jeannet
- Department of Pediatrics, Pediatric Neurology and Neurorehabilitation Unit, Lausanne University Hospital, Switzerland
| | - Sébastien Jacquemont
- Département de Pédiatrie, Faculté de médecine, Université de Montréal, CHU Sainte Justine, Montreal, Canada
| | - Pierre Billuart
- Inserm, Institut Cochin, Paris, France.,Cnrs, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Thierry Bienvenu
- Inserm, Institut Cochin, Paris, France.,Cnrs, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France.,Assistance Publique - Hôpitaux de Paris, Groupe Universitaire Paris Centre, Site Cochin, Laboratoire de Biochimie et Génétique Moléculaire, Paris, France
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115
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Shim U, Kim HN, Lee H, Oh JY, Sung YA, Kim HL. Pathway Analysis Based on a Genome-Wide Association Study of Polycystic Ovary Syndrome. PLoS One 2015; 10:e0136609. [PMID: 26308735 PMCID: PMC4550465 DOI: 10.1371/journal.pone.0136609] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 08/06/2015] [Indexed: 12/20/2022] Open
Abstract
Background Polycystic ovary syndrome (PCOS) is one of the most common endocrine disorders in women of reproductive age, and it is affected by both environmental and genetic factors. Although the genetic component of PCOS is evident, studies aiming to identify susceptibility genes have shown controversial results. This study conducted a pathway-based analysis using a dataset obtained through a genome-wide association study (GWAS) to elucidate the biological pathways that contribute to PCOS susceptibility and the associated genes. Methods We used GWAS data on 636,797 autosomal single nucleotide polymorphisms (SNPs) from 1,221 individuals (432 PCOS patients and 789 controls) for analysis. A pathway analysis was conducted using meta-analysis gene-set enrichment of variant associations (MAGENTA). Top-ranking pathways or gene sets associated with PCOS were identified, and significant genes within the pathways were analyzed. Results The pathway analysis of the GWAS dataset identified significant pathways related to oocyte meiosis and the regulation of insulin secretion by acetylcholine and free fatty acids (all nominal gene-set enrichment analysis (GSEA) P-values < 0.05). In addition, INS, GNAQ, STXBP1, PLCB3, PLCB2, SMC3 and PLCZ1 were significant genes observed within the biological pathways (all gene P-values < 0.05). Conclusions By applying MAGENTA pathway analysis to PCOS GWAS data, we identified significant pathways and candidate genes involved in PCOS. Our findings may provide new leads for understanding the mechanisms underlying the development of PCOS.
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Affiliation(s)
- Unjin Shim
- Department of Internal Medicine, Seoul Seonam Hospital, Ewha Womans University Medical Center, Seoul, Korea
| | - Han-Na Kim
- Department of Biochemistry, Ewha Womans University School of Medicine, Seoul, Korea
| | - Hyejin Lee
- Department of Internal Medicine, Ewha Womans University School of Medicine, Seoul, Korea
| | - Jee-Young Oh
- Department of Internal Medicine, Ewha Womans University School of Medicine, Seoul, Korea
| | - Yeon-Ah Sung
- Department of Internal Medicine, Ewha Womans University School of Medicine, Seoul, Korea
- * E-mail: (YAS); (HLK)
| | - Hyung-Lae Kim
- Department of Biochemistry, Ewha Womans University School of Medicine, Seoul, Korea
- * E-mail: (YAS); (HLK)
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116
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Patwardhan A, Harris J, Leng N, Bartha G, Church DM, Luo S, Haudenschild C, Pratt M, Zook J, Salit M, Tirch J, Morra M, Chervitz S, Li M, Clark M, Garcia S, Chandratillake G, Kirk S, Ashley E, Snyder M, Altman R, Bustamante C, Butte AJ, West J, Chen R. Achieving high-sensitivity for clinical applications using augmented exome sequencing. Genome Med 2015; 7:71. [PMID: 26269718 PMCID: PMC4534066 DOI: 10.1186/s13073-015-0197-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 07/09/2015] [Indexed: 12/25/2022] Open
Abstract
Background Whole exome sequencing is increasingly used for the clinical evaluation of genetic disease, yet the variation of coverage and sensitivity over medically relevant parts of the genome remains poorly understood. Several sequencing-based assays continue to provide coverage that is inadequate for clinical assessment. Methods Using sequence data obtained from the NA12878 reference sample and pre-defined lists of medically-relevant protein-coding and noncoding sequences, we compared the breadth and depth of coverage obtained among four commercial exome capture platforms and whole genome sequencing. In addition, we evaluated the performance of an augmented exome strategy, ACE, that extends coverage in medically relevant regions and enhances coverage in areas that are challenging to sequence. Leveraging reference call-sets, we also examined the effects of improved coverage on variant detection sensitivity. Results We observed coverage shortfalls with each of the conventional exome-capture and whole-genome platforms across several medically interpretable genes. These gaps included areas of the genome required for reporting recently established secondary findings (ACMG) and known disease-associated loci. The augmented exome strategy recovered many of these gaps, resulting in improved coverage in these areas. At clinically-relevant coverage levels (100 % bases covered at ≥20×), ACE improved coverage among genes in the medically interpretable genome (>90 % covered relative to 10-78 % with other platforms), the set of ACMG secondary finding genes (91 % covered relative to 4-75 % with other platforms) and a subset of variants known to be associated with human disease (99 % covered relative to 52-95 % with other platforms). Improved coverage translated into improvements in sensitivity, with ACE variant detection sensitivities (>97.5 % SNVs, >92.5 % InDels) exceeding that observed with conventional whole-exome and whole-genome platforms. Conclusions Clinicians should consider analytical performance when making clinical assessments, given that even a few missed variants can lead to reporting false negative results. An augmented exome strategy provides a level of coverage not achievable with other platforms, thus addressing concerns regarding the lack of sensitivity in clinically important regions. In clinical applications where comprehensive coverage of medically interpretable areas of the genome requires higher localized sequencing depth, an augmented exome approach offers both cost and performance advantages over other sequencing-based tests. Electronic supplementary material The online version of this article (doi:10.1186/s13073-015-0197-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anil Patwardhan
- Personalis, Inc, 1330 O'Brien Drive, Menlo Park, California 94025 USA
| | - Jason Harris
- Personalis, Inc, 1330 O'Brien Drive, Menlo Park, California 94025 USA
| | - Nan Leng
- Personalis, Inc, 1330 O'Brien Drive, Menlo Park, California 94025 USA
| | - Gabor Bartha
- Personalis, Inc, 1330 O'Brien Drive, Menlo Park, California 94025 USA
| | - Deanna M Church
- Personalis, Inc, 1330 O'Brien Drive, Menlo Park, California 94025 USA
| | - Shujun Luo
- Personalis, Inc, 1330 O'Brien Drive, Menlo Park, California 94025 USA
| | | | - Mark Pratt
- Personalis, Inc, 1330 O'Brien Drive, Menlo Park, California 94025 USA
| | - Justin Zook
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, Maryland USA
| | - Marc Salit
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, Maryland USA
| | - Jeanie Tirch
- Personalis, Inc, 1330 O'Brien Drive, Menlo Park, California 94025 USA
| | - Massimo Morra
- Personalis, Inc, 1330 O'Brien Drive, Menlo Park, California 94025 USA
| | - Stephen Chervitz
- Personalis, Inc, 1330 O'Brien Drive, Menlo Park, California 94025 USA
| | - Ming Li
- Personalis, Inc, 1330 O'Brien Drive, Menlo Park, California 94025 USA
| | - Michael Clark
- Personalis, Inc, 1330 O'Brien Drive, Menlo Park, California 94025 USA
| | - Sarah Garcia
- Personalis, Inc, 1330 O'Brien Drive, Menlo Park, California 94025 USA
| | | | - Scott Kirk
- Personalis, Inc, 1330 O'Brien Drive, Menlo Park, California 94025 USA
| | - Euan Ashley
- Personalis, Inc, 1330 O'Brien Drive, Menlo Park, California 94025 USA ; Center for Inherited Cardiovascular Disease, Stanford University School of Medicine, Stanford, California 94305 USA
| | - Michael Snyder
- Personalis, Inc, 1330 O'Brien Drive, Menlo Park, California 94025 USA ; Department of Genetics, Stanford University School of Medicine, Stanford, California 94305 USA
| | - Russ Altman
- Personalis, Inc, 1330 O'Brien Drive, Menlo Park, California 94025 USA ; Departments of Bioengineering & Genetics, Stanford University, Stanford, California 94305 USA
| | - Carlos Bustamante
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305 USA
| | - Atul J Butte
- Personalis, Inc, 1330 O'Brien Drive, Menlo Park, California 94025 USA ; Institute for Computational Health Sciences, University of California, San Francisco, California 94158 USA
| | - John West
- Personalis, Inc, 1330 O'Brien Drive, Menlo Park, California 94025 USA
| | - Richard Chen
- Personalis, Inc, 1330 O'Brien Drive, Menlo Park, California 94025 USA
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117
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Boyle MI, Tümer Z. Response to Dylan Mordaunt and Alisha McLauchlan. Clin Genet 2015; 88:99-100. [DOI: 10.1111/cge.12587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 03/16/2015] [Indexed: 11/29/2022]
Affiliation(s)
- M. I. Boyle
- Center for Applied Human Molecular Genetics; The Kennedy Center; Copenhagen Denmark
| | - Z. Tümer
- Center for Applied Human Molecular Genetics; The Kennedy Center; Copenhagen Denmark
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118
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119
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Phenotype and genotype in 103 patients with tricho-rhino-phalangeal syndrome. Eur J Med Genet 2015; 58:279-92. [DOI: 10.1016/j.ejmg.2015.03.002] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 03/08/2015] [Indexed: 11/21/2022]
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120
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Cornelia de Lange Syndrome: A Variable Disorder of Cohesin Pathology. CURRENT GENETIC MEDICINE REPORTS 2015. [DOI: 10.1007/s40142-015-0065-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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121
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Somatic mosaicism: implications for disease and transmission genetics. Trends Genet 2015; 31:382-92. [PMID: 25910407 DOI: 10.1016/j.tig.2015.03.013] [Citation(s) in RCA: 190] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 03/17/2015] [Accepted: 03/18/2015] [Indexed: 11/21/2022]
Abstract
Nearly all of the genetic material among cells within an organism is identical. However, single-nucleotide variants (SNVs), small insertions/deletions (indels), copy-number variants (CNVs), and other structural variants (SVs) continually accumulate as cells divide during development. This process results in an organism composed of countless cells, each with its own unique personal genome. Thus, every human is undoubtedly mosaic. Mosaic mutations can go unnoticed, underlie genetic disease or normal human variation, and may be transmitted to the next generation as constitutional variants. We review the influence of the developmental timing of mutations, the mechanisms by which they arise, methods for detecting mosaic variants, and the risk of passing these mutations on to the next generation.
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Gil-Rodríguez MC, Deardorff MA, Ansari M, Tan CA, Parenti I, Baquero-Montoya C, Ousager LB, Puisac B, Hernández-Marcos M, Teresa-Rodrigo ME, Marcos-Alcalde I, Wesselink JJ, Lusa-Bernal S, Bijlsma EK, Braunholz D, Bueno-Martinez I, Clark D, Cooper NS, Curry CJ, Fisher R, Fryer A, Ganesh J, Gervasini C, Gillessen-Kaesbach G, Guo Y, Hakonarson H, Hopkin RJ, Kaur M, Keating BJ, Kibaek M, Kinning E, Kleefstra T, Kline AD, Kuchinskaya E, Larizza L, Li YR, Liu X, Mariani M, Picker JD, Pié Á, Pozojevic J, Queralt E, Richer J, Roeder E, Sinha A, Scott RH, So J, Wusik KA, Wilson L, Zhang J, Gómez-Puertas P, Casale CH, Ström L, Selicorni A, Ramos FJ, Jackson LG, Krantz ID, Das S, Hennekam RCM, Kaiser FJ, FitzPatrick DR, Pié J. De novo heterozygous mutations in SMC3 cause a range of Cornelia de Lange syndrome-overlapping phenotypes. Hum Mutat 2015; 36:454-62. [PMID: 25655089 DOI: 10.1002/humu.22761] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 01/21/2015] [Accepted: 01/28/2015] [Indexed: 11/09/2022]
Abstract
Cornelia de Lange syndrome (CdLS) is characterized by facial dysmorphism, growth failure, intellectual disability, limb malformations, and multiple organ involvement. Mutations in five genes, encoding subunits of the cohesin complex (SMC1A, SMC3, RAD21) and its regulators (NIPBL, HDAC8), account for at least 70% of patients with CdLS or CdLS-like phenotypes. To date, only the clinical features from a single CdLS patient with SMC3 mutation has been published. Here, we report the efforts of an international research and clinical collaboration to provide clinical comparison of 16 patients with CdLS-like features caused by mutations in SMC3. Modeling of the mutation effects on protein structure suggests a dominant-negative effect on the multimeric cohesin complex. When compared with typical CdLS, many SMC3-associated phenotypes are also characterized by postnatal microcephaly but with a less distinctive craniofacial appearance, a milder prenatal growth retardation that worsens in childhood, few congenital heart defects, and an absence of limb deficiencies. While most mutations are unique, two unrelated affected individuals shared the same mutation but presented with different phenotypes. This work confirms that de novo SMC3 mutations account for ∼ 1%-2% of CdLS-like phenotypes.
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Affiliation(s)
- María Concepción Gil-Rodríguez
- Unit of Clinical Genetics and Functional Genomics, Departments of Pharmacology-Physiology and Pediatrics, Medical School, University of Zaragoza, CIBERER-GCV and ISS-Aragon, Zaragoza, Spain
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Parenti I, Gervasini C, Pozojevic J, Graul-Neumann L, Azzollini J, Braunholz D, Watrin E, Wendt K, Cereda A, Cittaro D, Gillessen-Kaesbach G, Lazarevic D, Mariani M, Russo S, Werner R, Krawitz P, Larizza L, Selicorni A, Kaiser F. Broadening of cohesinopathies: exome sequencing identifies mutations in ANKRD11
in two patients with Cornelia de Lange-overlapping phenotype. Clin Genet 2015; 89:74-81. [DOI: 10.1111/cge.12564] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 01/28/2015] [Accepted: 01/29/2015] [Indexed: 02/06/2023]
Affiliation(s)
- I. Parenti
- Medical Genetics, Department of Health Sciences; Università degli Studi di Milano; Milan Italy
- Sektion für Funktionelle Genetik am Institut für Humangenetik Lübeck; Universität zu Lübeck; Lübeck Germany
| | - C. Gervasini
- Medical Genetics, Department of Health Sciences; Università degli Studi di Milano; Milan Italy
| | - J. Pozojevic
- Sektion für Funktionelle Genetik am Institut für Humangenetik Lübeck; Universität zu Lübeck; Lübeck Germany
| | - L. Graul-Neumann
- Ambulantes Gesundheitszentrum der Charité Campus Virchow, Humangenetik; Universitätsmedizin Berlin; Berlin Germany
| | - J. Azzollini
- Medical Genetics, Department of Health Sciences; Università degli Studi di Milano; Milan Italy
| | - D. Braunholz
- Sektion für Funktionelle Genetik am Institut für Humangenetik Lübeck; Universität zu Lübeck; Lübeck Germany
| | - E. Watrin
- Institut de Génétique et Développement de Rennes, Faculté de Médecine; UMR6290-CNRS; Rennes France
| | - K.S. Wendt
- Department of Cell Biology; Erasmus MC; Rotterdam Netherlands
| | - A. Cereda
- A.O. S.Gerardo; U.O.S. Genetica Clinica Pediatrica, Clinica Pediatrica Fondazione MBBM; Monza Italy
| | - D. Cittaro
- Centre for Translational Genomics and Bioinformatics; San Raffaele Scientific Institute; Milan Italy
| | | | - D. Lazarevic
- Centre for Translational Genomics and Bioinformatics; San Raffaele Scientific Institute; Milan Italy
| | - M. Mariani
- A.O. S.Gerardo; U.O.S. Genetica Clinica Pediatrica, Clinica Pediatrica Fondazione MBBM; Monza Italy
| | - S. Russo
- Laboratory of Medical Cytogenetics and Molecular Genetics; IRCCS Istituto Auxologico Italiano; Milan Italy
| | - R. Werner
- Department of Paediatrics and Adolescent Medicine, Division of Experimental Paediatric Endocrinology and Diabetes; University of Lübeck; Lübeck Germany
| | - P. Krawitz
- Ambulantes Gesundheitszentrum der Charité Campus Virchow, Humangenetik; Universitätsmedizin Berlin; Berlin Germany
- Max Planck Institute for Molecular Genetics; Berlin Germany
| | - L. Larizza
- Medical Genetics, Department of Health Sciences; Università degli Studi di Milano; Milan Italy
- Laboratory of Medical Cytogenetics and Molecular Genetics; IRCCS Istituto Auxologico Italiano; Milan Italy
| | - A. Selicorni
- A.O. S.Gerardo; U.O.S. Genetica Clinica Pediatrica, Clinica Pediatrica Fondazione MBBM; Monza Italy
| | - F.J. Kaiser
- Sektion für Funktionelle Genetik am Institut für Humangenetik Lübeck; Universität zu Lübeck; Lübeck Germany
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124
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Yuan B, Pehlivan D, Karaca E, Patel N, Charng WL, Gambin T, Gonzaga-Jauregui C, Sutton VR, Yesil G, Bozdogan ST, Tos T, Koparir A, Koparir E, Beck CR, Gu S, Aslan H, Yuregir OO, Al Rubeaan K, Alnaqeb D, Alshammari MJ, Bayram Y, Atik MM, Aydin H, Geckinli BB, Seven M, Ulucan H, Fenercioglu E, Ozen M, Jhangiani S, Muzny DM, Boerwinkle E, Tuysuz B, Alkuraya FS, Gibbs RA, Lupski JR. Global transcriptional disturbances underlie Cornelia de Lange syndrome and related phenotypes. J Clin Invest 2015; 125:636-51. [PMID: 25574841 DOI: 10.1172/jci77435] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 12/09/2014] [Indexed: 01/05/2023] Open
Abstract
Cornelia de Lange syndrome (CdLS) is a genetically heterogeneous disorder that presents with extensive phenotypic variability, including facial dysmorphism, developmental delay/intellectual disability (DD/ID), abnormal extremities, and hirsutism. About 65% of patients harbor mutations in genes that encode subunits or regulators of the cohesin complex, including NIPBL, SMC1A, SMC3, RAD21, and HDAC8. Wiedemann-Steiner syndrome (WDSTS), which shares CdLS phenotypic features, is caused by mutations in lysine-specific methyltransferase 2A (KMT2A). Here, we performed whole-exome sequencing (WES) of 2 male siblings clinically diagnosed with WDSTS; this revealed a hemizygous, missense mutation in SMC1A that was predicted to be deleterious. Extensive clinical evaluation and WES of 32 Turkish patients clinically diagnosed with CdLS revealed the presence of a de novo heterozygous nonsense KMT2A mutation in 1 patient without characteristic WDSTS features. We also identified de novo heterozygous mutations in SMC3 or SMC1A that affected RNA splicing in 2 independent patients with combined CdLS and WDSTS features. Furthermore, in families from 2 separate world populations segregating an autosomal-recessive disorder with CdLS-like features, we identified homozygous mutations in TAF6, which encodes a core transcriptional regulatory pathway component. Together, our data, along with recent transcriptome studies, suggest that CdLS and related phenotypes may be "transcriptomopathies" rather than cohesinopathies.
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Ramos FJ, Puisac B, Baquero-Montoya C, Gil-Rodríguez MC, Bueno I, Deardorff MA, Hennekam RC, Kaiser FJ, Krantz ID, Musio A, Selicorni A, FitzPatrick DR, Pié J. Clinical utility gene card for: Cornelia de Lange syndrome. Eur J Hum Genet 2014; 23:ejhg2014270. [PMID: 25537356 DOI: 10.1038/ejhg.2014.270] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 11/01/2014] [Accepted: 11/16/2014] [Indexed: 11/09/2022] Open
Affiliation(s)
- Feliciano J Ramos
- Clinical Genetics Unit, Service of Paediatrics, University Hospital 'Lozano Blesa' Medical School, University of Zaragoza, CIBERER-GCV and IIS-Aragón, Zaragoza, Spain.,Unit of Clinical Genetics and Functional Genomics, Departments of Pharmacology-Physiology and Paediatrics Medical School, University of Zaragoza, CIBERER-GCV and IIS-Aragón, Zaragoza, Spain
| | - Beatriz Puisac
- Unit of Clinical Genetics and Functional Genomics, Departments of Pharmacology-Physiology and Paediatrics Medical School, University of Zaragoza, CIBERER-GCV and IIS-Aragón, Zaragoza, Spain
| | | | - Ma Concepción Gil-Rodríguez
- Unit of Clinical Genetics and Functional Genomics, Departments of Pharmacology-Physiology and Paediatrics Medical School, University of Zaragoza, CIBERER-GCV and IIS-Aragón, Zaragoza, Spain
| | - Inés Bueno
- Clinical Genetics Unit, Service of Paediatrics, University Hospital 'Lozano Blesa' Medical School, University of Zaragoza, CIBERER-GCV and IIS-Aragón, Zaragoza, Spain
| | - Matthew A Deardorff
- Department of Paediatrics, The Children's Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Raoul C Hennekam
- Department of Paediatrics, Academic Medical Centre, Amsterdam, The Netherlands
| | - Frank J Kaiser
- Sektion für Funktionelle Genetik am Institut für Humangenetik, Universität zu Lübeck, Lübeck, Germany
| | - Ian D Krantz
- Division of Human Genetics, The Children's Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Antonio Musio
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Pisa, Italy
| | - Angelo Selicorni
- Pediatric Genetic Clinic Unit, MBBM Foundation University of Milano Bicocca, San Gerardo Hospital, Monza, Italy
| | | | - Juan Pié
- Unit of Clinical Genetics and Functional Genomics, Departments of Pharmacology-Physiology and Paediatrics Medical School, University of Zaragoza, CIBERER-GCV and IIS-Aragón, Zaragoza, Spain
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126
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Boyle M, Jespersgaard C, Brøndum-Nielsen K, Bisgaard AM, Tümer Z. Cornelia de Lange syndrome. Clin Genet 2014; 88:1-12. [DOI: 10.1111/cge.12499] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 08/27/2014] [Accepted: 09/07/2014] [Indexed: 12/13/2022]
Affiliation(s)
- M.I. Boyle
- Applied Human Molecular Genetics, Kennedy Center, Department of Clinical Genetics, Rigshospitalet; University of Copenhagen; Glostrup Denmark
| | - C. Jespersgaard
- Applied Human Molecular Genetics, Kennedy Center, Department of Clinical Genetics, Rigshospitalet; University of Copenhagen; Glostrup Denmark
| | - K. Brøndum-Nielsen
- Applied Human Molecular Genetics, Kennedy Center, Department of Clinical Genetics, Rigshospitalet; University of Copenhagen; Glostrup Denmark
| | - A.-M. Bisgaard
- Applied Human Molecular Genetics, Kennedy Center, Department of Clinical Genetics, Rigshospitalet; University of Copenhagen; Glostrup Denmark
| | - Z. Tümer
- Applied Human Molecular Genetics, Kennedy Center, Department of Clinical Genetics, Rigshospitalet; University of Copenhagen; Glostrup Denmark
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