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Lecoquierre F, Quenez O, Fourneaux S, Coutant S, Vezain M, Rolain M, Drouot N, Boland A, Olaso R, Meyer V, Deleuze JF, Dabbagh D, Gilles I, Gayet C, Saugier-Veber P, Goldenberg A, Guerrot AM, Nicolas G. High diagnostic potential of short and long read genome sequencing with transcriptome analysis in exome-negative developmental disorders. Hum Genet 2023; 142:773-783. [PMID: 37076692 DOI: 10.1007/s00439-023-02553-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 04/05/2023] [Indexed: 04/21/2023]
Abstract
Exome sequencing (ES) has become the method of choice for diagnosing rare diseases, while the availability of short-read genome sequencing (SR-GS) in a medical setting is increasing. In addition, new sequencing technologies, such as long-read genome sequencing (LR-GS) and transcriptome sequencing, are being increasingly used. However, the contribution of these techniques compared to widely used ES is not well established, particularly in regards to the analysis of non-coding regions. In a pilot study of five probands affected by an undiagnosed neurodevelopmental disorder, we performed trio-based short-read GS and long-read GS as well as case-only peripheral blood transcriptome sequencing. We identified three new genetic diagnoses, none of which affected the coding regions. More specifically, LR-GS identified a balanced inversion in NSD1, highlighting a rare mechanism of Sotos syndrome. SR-GS identified a homozygous deep intronic variant of KLHL7 resulting in a neoexon inclusion, and a de novo mosaic intronic 22-bp deletion in KMT2D, leading to the diagnosis of Perching and Kabuki syndromes, respectively. All three variants had a significant effect on the transcriptome, which showed decreased gene expression, mono-allelic expression and splicing defects, respectively, further validating the effect of these variants. Overall, in undiagnosed patients, the combination of short and long read GS allowed the detection of cryptic variations not or barely detectable by ES, making it a highly sensitive method at the cost of more complex bioinformatics approaches. Transcriptome sequencing is a valuable complement for the functional validation of variations, particularly in the non-coding genome.
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Affiliation(s)
- François Lecoquierre
- Univ Rouen Normandie, Inserm U12045 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU-G4 Génomique, F-76000, Rouen, France.
| | - Olivier Quenez
- Univ Rouen Normandie, Inserm U12045 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Steeve Fourneaux
- Univ Rouen Normandie, Inserm U12045 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Sophie Coutant
- Univ Rouen Normandie, Inserm U12045 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Myriam Vezain
- Univ Rouen Normandie, Inserm U12045 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Marion Rolain
- Univ Rouen Normandie, Inserm U12045 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Nathalie Drouot
- Univ Rouen Normandie, Inserm U12045 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Anne Boland
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057, Evry, France
| | - Robert Olaso
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057, Evry, France
| | - Vincent Meyer
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057, Evry, France
| | - Jean-François Deleuze
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057, Evry, France
| | - Dana Dabbagh
- Department of Pediatrics, Elbeuf Hospital, Elbeuf, France
| | | | - Claire Gayet
- Department of Pediatrics, CHU Rouen, F-76000, Rouen, France
| | - Pascale Saugier-Veber
- Univ Rouen Normandie, Inserm U12045 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Alice Goldenberg
- Univ Rouen Normandie, Inserm U12045 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Anne-Marie Guerrot
- Univ Rouen Normandie, Inserm U12045 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Gaël Nicolas
- Univ Rouen Normandie, Inserm U12045 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU-G4 Génomique, F-76000, Rouen, France.
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Makay P, Mubungu G, Mupuala A, Bluske K, Brown C, Schmidt SA, Ngole M, Fuanani P, Perry DL, Lukusa P, Devriendt K, Taft RJ, Lumaka A. PERCHING syndrome: Clinical presentation in the first African patient confirmed by clinical whole genome sequencing. Am J Med Genet A 2022; 188:2825-2831. [PMID: 35670385 DOI: 10.1002/ajmg.a.62855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 04/17/2022] [Accepted: 05/12/2022] [Indexed: 01/25/2023]
Abstract
PERCHING syndrome is a rare multisystem developmental disorder caused by autosomal recessive (AR) variants (truncating and missense) in the Kelch-like family member 7 gene (KLHL7). We report the first phenotypic and molecular description of PERCHING syndrome in a patient from Central Africa. The patient presented multiple dysmorphic features in addition to neurological, respiratory, gastroenteric, and dysautonomic disorders. Clinical Whole Genome Sequencing in the proband and his mother identified two novel heterozygous variants in the KLHL7 gene, including a maternally inherited intronic variant (NM_001031710.2:c.793 + 5G > C) classified as Variant of Uncertain Significance and a frameshift stop gain variant (NM_001031710.2:c.944delG; p.Ser315ThrfsTer23) of unknown inheritance classified as likely pathogenic. Although the diagnosis was only evoked after genomic testing, the review of published patients suggests that this disease could be clinically recognizable and maybe considered as an encephalopathy. Our report will allow expanding the phenotypic and molecular spectrum of Perching syndrome.
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Affiliation(s)
- Prince Makay
- Centre for Human Genetics, Faculty of Medicine, University of Kinshasa, Kinshasa, Democratic Republic of the Congo.,Department of Pediatrics, Faculty of Medicine, University of Kinshasa, Kinshasa, Democratic Republic of the Congo.,Centre for Human Genetics, University Hospital, University of Leuven, Leuven, Belgium
| | - Gerrye Mubungu
- Centre for Human Genetics, Faculty of Medicine, University of Kinshasa, Kinshasa, Democratic Republic of the Congo.,Department of Pediatrics, Faculty of Medicine, University of Kinshasa, Kinshasa, Democratic Republic of the Congo.,Centre for Human Genetics, University Hospital, University of Leuven, Leuven, Belgium
| | - Aimée Mupuala
- Department of Pediatrics, Faculty of Medicine, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | | | | | | | - Mamy Ngole
- Centre for Human Genetics, Faculty of Medicine, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Patrick Fuanani
- Centre for Human Genetics, Faculty of Medicine, University of Kinshasa, Kinshasa, Democratic Republic of the Congo.,Department of Pediatrics, Faculty of Medicine, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | | | - Prosper Lukusa
- Centre for Human Genetics, Faculty of Medicine, University of Kinshasa, Kinshasa, Democratic Republic of the Congo.,Department of Pediatrics, Faculty of Medicine, University of Kinshasa, Kinshasa, Democratic Republic of the Congo.,Centre for Human Genetics, University Hospital, University of Leuven, Leuven, Belgium
| | - Koenraad Devriendt
- Centre for Human Genetics, University Hospital, University of Leuven, Leuven, Belgium
| | | | - Aimé Lumaka
- Centre for Human Genetics, Faculty of Medicine, University of Kinshasa, Kinshasa, Democratic Republic of the Congo.,Department of Pediatrics, Faculty of Medicine, University of Kinshasa, Kinshasa, Democratic Republic of the Congo.,Laboratoire de Génétique Humaine, GIGA-Research Institute, University of Liège, Liège, Belgium
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Yılmaz Gulec E, Turgut GT, Gezdırıcı A, Karaman V, Ozturk FN, Avcı S, Kalaycı T, Senturk L, Ayaz A, Kayserılı H, Uyguner OZ, Altunoğlu U. Clinical and molecular genetic findings of Crisponi / cold-induced sweating syndrome (CS/CISS) spectrum in patients from Turkey. Clin Genet 2022; 102:201-217. [PMID: 35699517 DOI: 10.1111/cge.14177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 11/29/2022]
Abstract
Crisponi / cold-induced sweating syndrome (CS/CISS) is a rare autosomal recessive disorder characterized by episodic hyperthermia, arthrogryposis, impaired feeding ability, and respiratory distress. The classic CS/CISS is mainly associated with CRLF1 and, rarely, CLCF1. PERCHING syndrome, previously known as CS/CISS type-3 associated with biallelic pathogenic variants in KLHL7, is notable for its few overlapping manifestations. This study presents genotype-phenotype relationships in CS/CISS-like spectrum associated with CRLF1 and KLHL7. Clinical findings of 19 patients from 14 families and four patients from three families were found in association with six different CRLF1 and three different KLHL7 variants, respectively. c.167 T > C and c.713delC of the CRLF1 gene and the c.642G > C of the KLHL7 were novel. The c.708_709delCCinsT allele of CRLF1 was identified in 10 families from the Mardin province of Turkey, underlining that an ancestral haplotype has become widespread. CRLF1-associated phenotypes revealed novel manifestations such as prenatal oligohydramnios, benign external hydrocephalus, previously unreported dysmorphic features emerging with advancing age, severe palmoplantar keratoderma and facial erythema, hypopigmented macules and streaks, and recurrent cardiac arrests. KLHL7 variants presented with glabellar nevus flammeus, blepharophimosis, microcephaly, thin corpus callosum, and cleft palate. Abnormalities of sweating, observed in one patient reported herein, is known to be very rare among KLHL7-related phenotypes. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Elif Yılmaz Gulec
- Department of Medical Genetics, Health Sciences University, Istanbul Kanuni Sultan Suleyman Research and Training Hospital, Istanbul, Turkey.,Department of Medical Genetics, Istanbul Medeniyet University Medical School, Istanbul Goztepe Prof Dr Suleyman Yalcin City Hospital, Istanbul, Turkey
| | - Gozde Tutku Turgut
- Department of Medical Genetics, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey
| | - Alper Gezdırıcı
- Department of Medical Genetics, Health Sciences University, Istanbul Kanuni Sultan Suleyman Research and Training Hospital, Istanbul, Turkey.,Department of Medical Genetics, Basaksehir Cam and Sakura City Hospital, Istanbul, Turkey
| | - Volkan Karaman
- Department of Medical Genetics, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey
| | - Fatma Nihal Ozturk
- Department of Medical Genetics, Istanbul Sultangazi Haseki Training and Research Hospital, Istanbul, Turkey
| | - Sahin Avcı
- Department of Medical Genetics, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey.,Department of Medical Genetics, Koc University Medical Faculty, Istanbul, Turkey
| | - Tugba Kalaycı
- Department of Medical Genetics, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey
| | - Leyli Senturk
- Department of Medical Genetics, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey.,Department of Medical Genetics, Istanbul Bagcilar Training and Research Hospital, Istanbul, Turkey
| | - Akif Ayaz
- Department of Medical Genetics, Health Sciences University, Istanbul Kanuni Sultan Suleyman Research and Training Hospital, Istanbul, Turkey.,Department of Medical Genetics, Istanbul Medipol University Medical School, Istanbul, Turkey
| | - Hulya Kayserılı
- Department of Medical Genetics, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey.,Department of Medical Genetics, Koc University Medical Faculty, Istanbul, Turkey
| | - Oya Zehra Uyguner
- Department of Medical Genetics, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey
| | - Umut Altunoğlu
- Department of Medical Genetics, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey.,Department of Medical Genetics, Koc University Medical Faculty, Istanbul, Turkey
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Latypova X, Creadore SG, Dahan-Oliel N, Gustafson AG, Wei-Hung Hwang S, Bedard T, Shazand K, van Bosse HJP, Giampietro PF, Dieterich K. A Genomic Approach to Delineating the Occurrence of Scoliosis in Arthrogryposis Multiplex Congenita. Genes (Basel) 2021; 12:genes12071052. [PMID: 34356068 PMCID: PMC8305424 DOI: 10.3390/genes12071052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/28/2021] [Accepted: 06/29/2021] [Indexed: 12/15/2022] Open
Abstract
Arthrogryposis multiplex congenita (AMC) describes a group of conditions characterized by the presence of non-progressive congenital contractures in multiple body areas. Scoliosis, defined as a coronal plane spine curvature of ≥10 degrees as measured radiographically, has been reported to occur in approximately 20% of children with AMC. To identify genes that are associated with both scoliosis as a clinical outcome and AMC, we first queried the DECIPHER database for copy number variations (CNVs). Upon query, we identified only two patients with both AMC and scoliosis (AMC-SC). The first patient contained CNVs in three genes (FBN2, MGF10, and PITX1), while the second case had a CNV in ZC4H2. Looking into small variants, using a combination of Human Phenotype Ontogeny and literature searching, 908 genes linked with scoliosis and 444 genes linked with AMC were identified. From these lists, 227 genes were associated with AMC-SC. Ingenuity Pathway Analysis (IPA) was performed on the final gene list to gain insight into the functional interactions of genes and various categories. To summarize, this group of genes encompasses a diverse group of cellular functions including transcription regulation, transmembrane receptor, growth factor, and ion channels. These results provide a focal point for further research using genomics and animal models to facilitate the identification of prognostic factors and therapeutic targets for AMC.
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Affiliation(s)
- Xenia Latypova
- Grenoble Institut Neurosciences, Université Grenoble Alpes, Inserm, U1216, CHU Grenoble Alpes, 38000 Grenoble, France;
| | | | - Noémi Dahan-Oliel
- Shriners Hospitals for Children, Montreal, QC H4A 0A9, Canada;
- School of Physical & Occupational Therapy, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC H3G 2M1, Canada
| | | | - Steven Wei-Hung Hwang
- Shriners Hospitals for Children, Philadelphia, PA 19140, USA; (S.W.-H.H.); (H.J.P.v.B.)
| | - Tanya Bedard
- Alberta Congenital Anomalies Surveillance System, Alberta Health Services, Edmonton, AB T5J 3E4, Canada;
| | - Kamran Shazand
- Shriners Hospitals for Children Headquarters, Tampa, FL 33607, USA; (S.G.C.); (A.G.G.); (K.S.)
| | | | - Philip F. Giampietro
- Department of Pediatrics, University of Illinois-Chicago, Chicago, IL 60607, USA
- Correspondence: (P.F.G.); (K.D.)
| | - Klaus Dieterich
- Institut of Advanced Biosciences, Université Grenoble Alpes, Inserm, U1209, CHU Grenoble Alpes, 38000 Grenoble, France
- Correspondence: (P.F.G.); (K.D.)
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Oh JK, Lima de Carvalho JR, Sun YJ, Ragi S, Yang J, Levi SR, Ryu J, Bassuk AG, Mahajan VB, Tsang SH. Novel mutations in the 3-box motif of the BACK domain of KLHL7 associated with nonsyndromic autosomal dominant retinitis pigmentosa. Orphanet J Rare Dis 2019; 14:295. [PMID: 31856884 PMCID: PMC6924004 DOI: 10.1186/s13023-019-1275-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 12/05/2019] [Indexed: 02/03/2023] Open
Abstract
Background Mutations in the Kelch-like protein 7 (KLHL7) represent a recently described and, to date, poorly characterized etiology of inherited retinal dystrophy. Dominant mutations in KLHL7 are a cause of isolated, non-syndromic retinitis pigmentosa (RP). In contrast, recessive loss-of-function mutations are known to cause Crisponi or Bohring-Opitz like cold induced sweating syndrome-3 (BOS-3). In this study, the phenotype and progression of five unrelated patients with KLHL7 mediated autosomal dominant RP (adRP) are characterized. Clinical evaluation of these patients involved a complete ophthalmic exam, full-field electroretinography (ffERG), and imaging, including fundus photography, spectral domain optical coherence tomography (SD-OCT), short wavelength fundus autofluorescence (SW-AF), and near-infrared fundus autofluorescence (NIR-AF). Molecular diagnoses were performed using whole-exome sequencing or gene panel testing. Disease progression was monitored in three patients with available data for a mean follow up time of 4.5 ± 2.9 years. Protein modeling was performed for all variants found in this study in addition to those documented in the literature for recessive loss-of-function alleles causing Crisponi or Bohring-Opitz like cold-induced sweating syndrome. Results Genetic testing in three patients identified two novel variants within the 3-box motif of the BACK domain: c.472 T > C:p.(Cys158Arg) and c.433A > T:p.(Asn145Tyr). Clinical imaging demonstrated hyperautofluorescent ring formation on both SW-AF and NIR-AF in three patients, with diffuse peripheral and peripapillary atrophy seen in all but one case. SD-OCT demonstrated a phenotypic spectrum, from parafoveal atrophy of the outer retina with foveal sparing to widespread retinal thinning and loss of photoreceptors. Incidence of cystoid macular edema was high with four of five patients affected. Protein modeling of dominant alleles versus recessive loss-of-function alleles showed dominant alleles localized to the BTB and BACK domains while recessive alleles were found in the Kelch domain. Conclusions We report the phenotype in five patients with KLHL7 mediated adRP, two novel coding variants, and imaging biomarkers using SW-AF and NIR-AF. These findings may influence future gene-based therapies for adRP and pave the way for mechanistic studies that elucidate the pathogenesis of KLHL7-mediated RP.
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Affiliation(s)
- Jin Kyun Oh
- Department of Ophthalmology, Columbia University Medical Center, New York, NY, USA.,State University of New York at Downstate Medical Center, Brooklyn, NY, USA
| | - Jose Ronaldo Lima de Carvalho
- Department of Ophthalmology, Columbia University Medical Center, New York, NY, USA.,Department of Ophthalmology, Empresa Brasileira de Servicos Hospitalares (EBSERH) - Hospital das Clinicas de Pernambuco (HCPE), Federal University of Pernambuco (UFPE), Recife, Brazil.,Department of Ophthalmology, Federal University of São Paulo (UNIFESP), São Paulo, Brazil
| | - Young Joo Sun
- Omics Laboratory, Byers Eye Institute, Stanford University, Palo Alto, CA, USA
| | - Sara Ragi
- Department of Ophthalmology, Columbia University Medical Center, New York, NY, USA
| | - Jing Yang
- Omics Laboratory, Byers Eye Institute, Stanford University, Palo Alto, CA, USA
| | - Sarah R Levi
- Department of Ophthalmology, Columbia University Medical Center, New York, NY, USA
| | - Joseph Ryu
- Department of Ophthalmology, Columbia University Medical Center, New York, NY, USA
| | - Alexander G Bassuk
- Department of Pediatrics, University of Iowa, Iowa City, USA.,Department of Neurology, University of Iowa, Iowa City, USA
| | - Vinit B Mahajan
- Omics Laboratory, Byers Eye Institute, Stanford University, Palo Alto, CA, USA.,Veterans Affairs Palo Alto Health Care System, Palo Alto, CA, USA
| | - Stephen H Tsang
- Department of Ophthalmology, Columbia University Medical Center, New York, NY, USA. .,Department of Pathology & Cell Biology, and Columbia Stem Cell Initiative, Columbia University Medical Center, 635 West 165th Street, Box 212, New York, NY, 10032, USA.
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