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Feizabadi MH, Alerasool M, Eslahi A, Esmaeilzadeh E, Mehrjardi MYV, Saket M, Farokhi S, Fattahi Z, Khorshid HRK, Mojarrad M. Characterizing Homozygous Variants in Bardet-Biedl Syndrome-Associated Genes Within Iranian Families: Unveiling a Founder Variant in BBS2, c.471G>A. Biochem Genet 2024:10.1007/s10528-023-10637-w. [PMID: 38407766 DOI: 10.1007/s10528-023-10637-w] [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: 10/14/2023] [Accepted: 12/12/2023] [Indexed: 02/27/2024]
Abstract
Bardet-Biedl syndrome (BBS) is a rare inherited ciliopathy disorder characterized by a broad spectrum of clinical symptoms such as retinal dystrophy, obesity, polydactyly, genitourinary and kidney anomalies, learning disability, and hypogonadism. The understanding of the variants involved in BBS-causing genes remains incomplete, highlighting the need for further research to develop a molecular diagnostic strategy for this syndrome. Singleton whole-exome sequencing (WES) was performed on sixteen patients. Our study revealed (1) nine patients carried eight homozygous pathogenic variants with four of them being novel (2) Specifically, a synonymous splicing variant (c.471G > A) in BBS2 gene in six patients with Baloch ethnicity. The identification of runs of homozygosity (ROH) calling was performed using the BCFtools/RoH software on WES data of patients harboring c.471G > A variant. The presence of shared homozygous regions containing the identified variant was confirmed in these patients. In-silico analysis predicted the effect of the c.471G > A variants on BBS2 mRNA splicing. This variant results in disrupted wild-type donor site and intron retention in the mature mRNA. (3) And a deletion of exons 14 to 17 in the BBS1 gene was identified in one patient by Copy-Number Variation (CNV) analysis using the ExomeDepth pipeline. Our results identified the founder variant c.471G > A in the BBS2 gene in the Baloch ethnicity of the Iranian population. This finding can guide the diagnostic approach of this syndrome in future studies.
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Affiliation(s)
| | - Masoome Alerasool
- Genetic Foundation of Khorasan Razavi, Mashhad, Iran
- Faculty of Medicine, Department of Medical Genetics, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Atieh Eslahi
- Faculty of Medicine, Department of Medical Genetics, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | | | - Mitra Saket
- RP Eye Patients Supporting Institute, Tehran, Iran
| | - Shima Farokhi
- Faculty of Medicine, Department of Medical Genetics, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Zohreh Fattahi
- Genetics Research Centre, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | | | - Majid Mojarrad
- Faculty of Medicine, Department of Medical Genetics, Mashhad University of Medical Sciences, Mashhad, Iran.
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2
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Hassan S, Khan QA, Saravanan P, Iram S, Rohail S, Belay NF, Afzal M, Hadi FA, Pande H. Megaloblastic Anemia in Bardet-Biedl Syndrome: A Rare Case Report. CLINICAL MEDICINE INSIGHTS-CASE REPORTS 2023; 16:11795476231193896. [PMID: 37588947 PMCID: PMC10426295 DOI: 10.1177/11795476231193896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 07/05/2023] [Indexed: 08/18/2023]
Abstract
Background Bardet-Biedl syndrome (BBS) also known as Laurence-Moon-Bardet-Biedl syndrome one of the rarely reported genetic disorder characterized by an intellectual disability, limb, kidney abnormalities, obesity, and Rod-cone dystrophy. Other associated condition includes diabetes mellitus, hypertension, hypogonadism, facial dysmorphism, and congenital heart defects. This case highlights megaloblastic anemia associated with BBS. Case presentation A 16-year-old female patient who had a moon face, truncal obesity, polydactyly, low IQ, and visual impairment presented with the complaint of shortness of breath and easy fatiguability. She had bilateral retinal pigmentosa in her eyes and her laboratory evaluation and bone marrow biopsy revealed megaloblastic anemia secondary to vitamin B12 deficiency. She received injectable vitamin B12, folate, and red cell contrate transfusion. Her symptoms improved and she was discharged with oral medication. Conclusion Megaloblastic anemia in BBS is rarely reported, further research is needed to find the exact cause that is necessary for proper management and better outcome.
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Affiliation(s)
| | | | | | | | - Samia Rohail
- Karachi Medical and Dental College, Karachi, Pakistan
| | - Naod F Belay
- Michigan State University, East Lansing, MI, USA
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3
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Novel Mutations in the MKKS, BBS7, and ALMS1 Genes in Iranian Children with Clinically Suspected Bardet–Biedl Syndrome. Case Rep Ophthalmol Med 2022; 2022:6110775. [PMID: 35912300 PMCID: PMC9334124 DOI: 10.1155/2022/6110775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 07/07/2022] [Indexed: 11/18/2022] Open
Abstract
Bardet–Biedl syndrome is a rare autosomal recessive form of syndromic obesity which is characterized by retinal degeneration, obesity, polydactyly, cognitive impairment, and renal and urogenital anomalies. In this study, we used whole-exome sequencing (WES) to investigate the underlying mutations in four Iranian children from consanguineous families with a clinical diagnosis of Bardet–Biedl syndrome (BBS). In three out of four children, we identified one previously reported frameshifting variant in the BBS12 gene (c.265-266delTT, p.L89fs) and two novel nonsense variants in MKKS (c.1196T>G, p.L399X) and BBS7 genes (c.1636C>T, p.Q546X). In the other child, no mutations were detected in known genes for BBS. However, we identified a novel variant in the ALMS1 gene (c.10996delC, p.Q3666fs) indicative of Alström syndrome. All variants were interpreted as pathogenic according to American College of Medical Genetics and Genomics (ACMG) guidelines and confirmed through Sanger sequencing. In conclusion, our results not only expand the spectrum of mutations in BBS and ALMS1 genes but also accentuate the importance of genetic testing for differentiating BBS from Alström syndrome.
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Nasser F, Kohl S, Kurtenbach A, Kempf M, Biskup S, Zuleger T, Haack TB, Weisschuh N, Stingl K, Zrenner E. Ophthalmic and Genetic Features of Bardet Biedl Syndrome in a German Cohort. Genes (Basel) 2022; 13:genes13071218. [PMID: 35886001 PMCID: PMC9322102 DOI: 10.3390/genes13071218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 06/29/2022] [Accepted: 07/02/2022] [Indexed: 12/04/2022] Open
Abstract
The aim of this study was to characterize the ophthalmic and genetic features of Bardet Biedl (BBS) syndrome in a cohort of patients from a German specialized ophthalmic care center. Sixty-one patients, aged 5−56 years, underwent a detailed ophthalmic examination including visual acuity and color vision testing, electroretinography (ERG), visually evoked potential recording (VEP), fundus examination, and spectral domain optical coherence tomography (SD-OCT). Adaptive optics flood illumination ophthalmoscopy was performed in five patients. All patients had received diagnostic genetic testing and were selected upon the presence of apparent biallelic variants in known BBS-associated genes. All patients had retinal dystrophy with morphologic changes of the retina. Visual acuity decreased from ~0.2 (decimal) at age 5 to blindness 0 at 50 years. Visual field examination could be performed in only half of the patients and showed a concentric constriction with remaining islands of function in the periphery. ERG recordings were mostly extinguished whereas VEP recordings were reduced in about half of the patients. The cohort of patients showed 51 different likely biallelic mutations—of which 11 are novel—in 12 different BBS-associated genes. The most common associated genes were BBS10 (32.8%) and BBS1 (24.6%), and by far the most commonly observed variants were BBS10 c.271dup;p.C91Lfs*5 (21 alleles) and BBS1 c.1169T>G;p.M390R (18 alleles). The phenotype associated with the different BBS-associated genes and genotypes in our cohort is heterogeneous, with diverse features without genotype−phenotype correlation. The results confirm and expand our knowledge of this rare disease.
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Affiliation(s)
- Fadi Nasser
- Centre for Ophthalmology, University of Tübingen, 72076 Tuebingen, Germany; (S.K.); (A.K.); (M.K.); (N.W.); (K.S.); (E.Z.)
- Department of Ophthalmology, University of Leipzig, 04103 Leipzig, Germany
- Correspondence:
| | - Susanne Kohl
- Centre for Ophthalmology, University of Tübingen, 72076 Tuebingen, Germany; (S.K.); (A.K.); (M.K.); (N.W.); (K.S.); (E.Z.)
| | - Anne Kurtenbach
- Centre for Ophthalmology, University of Tübingen, 72076 Tuebingen, Germany; (S.K.); (A.K.); (M.K.); (N.W.); (K.S.); (E.Z.)
| | - Melanie Kempf
- Centre for Ophthalmology, University of Tübingen, 72076 Tuebingen, Germany; (S.K.); (A.K.); (M.K.); (N.W.); (K.S.); (E.Z.)
- Center for Rare Eye Diseases, University of Tübingen, 72076 Tuebingen, Germany
| | | | - Theresia Zuleger
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tuebingen, Germany; (T.Z.); (T.B.H.)
| | - Tobias B. Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tuebingen, Germany; (T.Z.); (T.B.H.)
| | - Nicole Weisschuh
- Centre for Ophthalmology, University of Tübingen, 72076 Tuebingen, Germany; (S.K.); (A.K.); (M.K.); (N.W.); (K.S.); (E.Z.)
| | - Katarina Stingl
- Centre for Ophthalmology, University of Tübingen, 72076 Tuebingen, Germany; (S.K.); (A.K.); (M.K.); (N.W.); (K.S.); (E.Z.)
- Center for Rare Eye Diseases, University of Tübingen, 72076 Tuebingen, Germany
| | - Eberhart Zrenner
- Centre for Ophthalmology, University of Tübingen, 72076 Tuebingen, Germany; (S.K.); (A.K.); (M.K.); (N.W.); (K.S.); (E.Z.)
- Werner Reichardt Centre for Integrative Neuroscience (CIN), University of Tübingen, 72076 Tuebingen, Germany
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Yan K, Sun Y, Yang Y, Liu B, Dong M. Case Report: Identification Pathogenic Abnormal Splicing of BBS1 Causing Bardet-Biedl Syndrome Type I (BBS1) due to Missense Mutation. Front Genet 2022; 13:849562. [PMID: 35692835 PMCID: PMC9186647 DOI: 10.3389/fgene.2022.849562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
Conventionally, protein features affected by missense mutation was attributed to destroy an important domain with amino acid alternation, and it was difficult to clearly specify the pathogenicity of a novel missense mutation. Nevertheless, the associations between missense mutations and abnormal splicing are nowadays increasingly reported. Rarely, some missense mutations, locating at the non-canonical splicing sites, are observed to damage the splicing process. In this study, a couple has three adverse pregnancy history that the affected fetus presented typical polydactyly, renal abnormalities, and cerebral ventriculomegaly. To identify its genetic etiology, whole-exome sequencing (WES) was performed and a missense mutation c.1339G > A was identified, which was located at the non-canonical splicing sites of the BBS1 gene. Then, reverse transcription polymerase chain reaction was carried out and demonstrated extra 115bp originating from intron 13 cut into cDNA, which generated a predicted premature termination codon (PTC) in the BBS1 protein. Further expression analysis by using real-time reverse-transcribed PCR confirmed the occurrence of nonsense-mediated decay (NMD). Therefore, the pathogenicity of the missense mutation c.1339G > A was explicit and our study helped to extend the spectrum of pathogenic mutations in Bardet–Biedl syndrome type I.
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Affiliation(s)
- Kai Yan
- Department of Reproductive Genetics, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou, China
| | - Yixi Sun
- Department of Reproductive Genetics, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou, China
| | - Yanmei Yang
- Department of Reproductive Genetics, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou, China
| | - Bei Liu
- Department of Reproductive Genetics, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou, China
| | - Minyue Dong
- Department of Reproductive Genetics, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou, China
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6
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Rehman AU, Sepahi N, Bedoni N, Ravesh Z, Salmaninejad A, Cancellieri F, Peter VG, Quinodoz M, Mojarrad M, Pasdar A, Asad AG, Ghalamkari S, Piran M, Piran M, Superti-Furga A, Rivolta C. Whole exome sequencing in 17 consanguineous Iranian pedigrees expands the mutational spectrum of inherited retinal dystrophies. Sci Rep 2021; 11:19332. [PMID: 34588515 PMCID: PMC8481312 DOI: 10.1038/s41598-021-98677-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 09/06/2021] [Indexed: 11/24/2022] Open
Abstract
Inherited retinal dystrophies (IRDs) constitute one of the most heterogeneous groups of Mendelian human disorders. Using autozygome-guided next-generation sequencing methods in 17 consanguineous pedigrees of Iranian descent with isolated or syndromic IRD, we identified 17 distinct genomic variants in 11 previously-reported disease genes. Consistent with a recessive inheritance pattern, as suggested by pedigrees, variants discovered in our study were exclusively bi-allelic and mostly in a homozygous state (in 15 families out of 17, or 88%). Out of the 17 variants identified, 5 (29%) were never reported before. Interestingly, two mutations (GUCY2D:c.564dup, p.Ala189ArgfsTer130 and TULP1:c.1199G > A, p.Arg400Gln) were also identified in four separate pedigrees (two pedigrees each). In addition to expanding the mutational spectrum of IRDs, our findings confirm that the traditional practice of endogamy in the Iranian population is a prime cause for the appearance of IRDs.
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Affiliation(s)
- Atta Ur Rehman
- Division of Genetic Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Neda Sepahi
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | - Nicola Bedoni
- Division of Genetic Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Zeinab Ravesh
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Arash Salmaninejad
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Francesca Cancellieri
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Virginie G Peter
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK.,Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Institute of Experimental Pathology, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Mathieu Quinodoz
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK.,Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Majid Mojarrad
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Alireza Pasdar
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Medical Genetics Research Centre, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Division of Applied Medicine, Medical School, University of Aberdeen, Aberdeen, UK
| | - Ali Ghanbari Asad
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | | | - Mehran Piran
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | - Mehrdad Piran
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | - Andrea Superti-Furga
- Division of Genetic Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Carlo Rivolta
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK. .,Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland. .,Department of Ophthalmology, University of Basel, Basel, Switzerland.
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7
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Xie C, Habif JC, Uytingco CR, Ukhanov K, Zhang L, de Celis C, Sheffield VC, Martens JR. Gene therapy rescues olfactory perception in a clinically relevant ciliopathy model of Bardet-Biedl syndrome. FASEB J 2021; 35:e21766. [PMID: 34383976 DOI: 10.1096/fj.202100627r] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 06/02/2021] [Accepted: 06/14/2021] [Indexed: 11/11/2022]
Abstract
Bardet-Biedl syndrome (BBS) is a hereditary genetic disorder that results in numerous clinical manifestations including olfactory dysfunction. Of at least 21 BBS-related genes that can carry multiple mutations, a pathogenic mutation, BBS1M390R, is the single most common mutation of clinically diagnosed BBS outcomes. While the deletion of BBS-related genes in mice can cause variable penetrance in different organ systems, the impact of the Bbs1M390R mutation in the olfactory system remains unclear. Using a clinically relevant knock-in mouse model homozygous for Bbs1M390R, we investigated the impact of the mutation on the olfactory system and tested the potential of viral-mediated, wildtype gene replacement therapy to rescue smell loss. The cilia of olfactory sensory neurons (OSNs) in Bbs1M390R/M390R mice were significantly shorter and fewer than those of wild-type mice. Also, both peripheral cellular odor detection and synaptic-dependent activity in the olfactory bulb were significantly decreased in the mutant mice. Furthermore, to gain insight into the degree to which perceptual features are impaired in the mutant mice, we used whole-body plethysmography to quantitatively measure odor-evoked sniffing. The Bbs1M390R/M390R mice showed significantly higher odor detection thresholds (reduced odor sensitivity) compared to wild-type mice; however, their odor discrimination acuity was still well maintained. Importantly, adenoviral expression of Bbs1 in OSNs restored cilia length and re-established both peripheral odorant detection and odor perception. Together, our findings further expand our understanding for the development of gene therapeutic treatment for congenital ciliopathies in the olfactory system.
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Affiliation(s)
- Chao Xie
- Department of Pharmacology and Therapeutics, University of Florida College of Medicine, Gainesville, FL, USA.,Center for Smell and Taste, University of Florida College of Medicine, Gainesville, FL, USA
| | - Julien C Habif
- Department of Pharmacology and Therapeutics, University of Florida College of Medicine, Gainesville, FL, USA.,Center for Smell and Taste, University of Florida College of Medicine, Gainesville, FL, USA
| | - Cedric R Uytingco
- Department of Pharmacology and Therapeutics, University of Florida College of Medicine, Gainesville, FL, USA.,Center for Smell and Taste, University of Florida College of Medicine, Gainesville, FL, USA
| | - Kirill Ukhanov
- Department of Pharmacology and Therapeutics, University of Florida College of Medicine, Gainesville, FL, USA.,Center for Smell and Taste, University of Florida College of Medicine, Gainesville, FL, USA
| | - Lian Zhang
- Department of Pharmacology and Therapeutics, University of Florida College of Medicine, Gainesville, FL, USA.,Center for Smell and Taste, University of Florida College of Medicine, Gainesville, FL, USA
| | - Carlos de Celis
- Department of Pharmacology and Therapeutics, University of Florida College of Medicine, Gainesville, FL, USA.,Center for Smell and Taste, University of Florida College of Medicine, Gainesville, FL, USA
| | - Val C Sheffield
- Division of Medical Genetics and Genomics, Department of Pediatrics, University of Iowa, Iowa City, IA, USA.,Department of Ophthalmology and Vision Research, University of Iowa, Iowa City, IA, USA
| | - Jeffrey R Martens
- Department of Pharmacology and Therapeutics, University of Florida College of Medicine, Gainesville, FL, USA.,Center for Smell and Taste, University of Florida College of Medicine, Gainesville, FL, USA
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8
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Najafi K, Mehrjoo Z, Ardalani F, Ghaderi-Sohi S, Kariminejad A, Kariminejad R, Najmabadi H. Identifying the causes of recurrent pregnancy loss in consanguineous couples using whole exome sequencing on the products of miscarriage with no chromosomal abnormalities. Sci Rep 2021; 11:6952. [PMID: 33772059 PMCID: PMC7997959 DOI: 10.1038/s41598-021-86309-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 03/08/2021] [Indexed: 12/26/2022] Open
Abstract
Recurrent miscarriages occur in about 5% of couples trying to conceive. In the past decade, the products of miscarriage have been studied using array comparative genomic hybridization (a-CGH). Within the last decade, an association has been proposed between miscarriages and single or multigenic changes, introducing the possibility of detecting other underlying genetic factors by whole exome sequencing (WES). We performed a-CGH on the products of miscarriage from 1625 Iranian women in consanguineous or non-consanguineous marriages. WES was carried out on DNA extracted from the products of miscarriage from 20 Iranian women in consanguineous marriages and with earlier normal genetic testing. Using a-CGH, a statistically significant difference was detected between the frequency of imbalances in related vs. unrelated couples (P < 0.001). WES positively identified relevant alterations in 11 genes in 65% of cases. In 45% of cases, we were able to classify these variants as pathogenic or likely pathogenic, according to the American College of Medical Genetics and Genomics guidelines, while in the remainder, the variants were classified as of unknown significance. To the best of our knowledge, our study is the first to employ WES on the products of miscarriage in consanguineous families with recurrent miscarriages regardless of the presence of fetal abnormalities. We propose that WES can be helpful in making a diagnosis of lethal disorders in consanguineous couples after prior genetic testing.
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Affiliation(s)
- Kimia Najafi
- Genetic Research Center, National Reference Laboratory for Prenatal Diagnosis, University of Social Welfare and Rehabilitation Sciences, Koodakyar Avenue, Daneshjoo Blvd, Evin, Tehran, 1985713834, Iran
- Kariminejad-Najmabadi Pathology and Genetics Center, #2, West Side of Sanat Sq.-Metro Station, Shahrak Gharb, Tehran, 1466713713, Iran
| | - Zohreh Mehrjoo
- Genetic Research Center, National Reference Laboratory for Prenatal Diagnosis, University of Social Welfare and Rehabilitation Sciences, Koodakyar Avenue, Daneshjoo Blvd, Evin, Tehran, 1985713834, Iran
| | - Fariba Ardalani
- Genetic Research Center, National Reference Laboratory for Prenatal Diagnosis, University of Social Welfare and Rehabilitation Sciences, Koodakyar Avenue, Daneshjoo Blvd, Evin, Tehran, 1985713834, Iran
| | - Siavash Ghaderi-Sohi
- Kariminejad-Najmabadi Pathology and Genetics Center, #2, West Side of Sanat Sq.-Metro Station, Shahrak Gharb, Tehran, 1466713713, Iran
| | - Ariana Kariminejad
- Kariminejad-Najmabadi Pathology and Genetics Center, #2, West Side of Sanat Sq.-Metro Station, Shahrak Gharb, Tehran, 1466713713, Iran
| | - Roxana Kariminejad
- Kariminejad-Najmabadi Pathology and Genetics Center, #2, West Side of Sanat Sq.-Metro Station, Shahrak Gharb, Tehran, 1466713713, Iran
| | - Hossein Najmabadi
- Genetic Research Center, National Reference Laboratory for Prenatal Diagnosis, University of Social Welfare and Rehabilitation Sciences, Koodakyar Avenue, Daneshjoo Blvd, Evin, Tehran, 1985713834, Iran.
- Kariminejad-Najmabadi Pathology and Genetics Center, #2, West Side of Sanat Sq.-Metro Station, Shahrak Gharb, Tehran, 1466713713, Iran.
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9
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Al Alawi I, Al Riyami M, Barroso-Gil M, Powell L, Olinger E, Al Salmi I, Sayer JA. The diagnostic yield of whole exome sequencing as a first approach in consanguineous Omani renal ciliopathy syndrome patients. F1000Res 2021; 10:207. [PMID: 34354814 PMCID: PMC8290205 DOI: 10.12688/f1000research.40338.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/01/2021] [Indexed: 02/05/2023] Open
Abstract
Background: Whole exome sequencing (WES) is becoming part of routine clinical and diagnostic practice. In the investigation of inherited cystic kidney disease and renal ciliopathy syndromes, WES has been extensively applied in research studies as well as for diagnostic utility to detect various novel genes and variants. The yield of WES critically depends on the characteristics of the patient population. Methods: In this study, we selected 8 unrelated Omani children, presenting with renal ciliopathy syndromes with a positive family history and originating from consanguineous families. We performed WES in affected children to determine the genetic cause of disease and to test the yield of this approach, coupled with homozygosity mapping, in this highly selected population. DNA library construction and WES was carried out using SureSelect Human All Exon V6 Enrichment Kit and Illumina HiSeq platform. For variants filtering and annotation Qiagen Variant Ingenuity tool was used. Nexus copy number software from BioDiscovery was used for evaluation of copy number variants and whole gene deletions. Patient and parental DNA was used to confirm mutations and the segregation of alleles using Sanger sequencing. Results: Genetic analysis identified 4 potential causative homozygous variants each confirmed by Sanger sequencing in 4 clinically relevant ciliopathy syndrome genes, ( TMEM231, TMEM138, WDR19 and BBS9), leading to an overall diagnostic yield of 50%. Conclusions: WES coupled with homozygosity mapping provided a diagnostic yield of 50% in this selected population. This genetic approach needs to be embedded into clinical practise to allow confirmation of clinical diagnosis, to inform genetic screening as well as family planning decisions. Half of the patients remain without diagnosis highlighting the technical and interpretational hurdles that need to be overcome in the future.
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Affiliation(s)
- Intisar Al Alawi
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, Tyne and Wear, NE13BZ, UK
- National Genetic Center, Ministry of Health, Muscat, Oman
| | - Mohammed Al Riyami
- Pediatric Nephrology Unit, Department of Child Health, Royal Hospital, Ministry of Health, Muscat, Oman
| | - Miguel Barroso-Gil
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, Tyne and Wear, NE13BZ, UK
| | - Laura Powell
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, Tyne and Wear, NE13BZ, UK
| | - Eric Olinger
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, Tyne and Wear, NE13BZ, UK
| | - Issa Al Salmi
- Renal Medicine Department, Royal Hospital, Ministry of Health, Muscat, Oman
- Oman Medical Speciality Board, Muscat, Oman
| | - John A. Sayer
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, Tyne and Wear, NE13BZ, UK
- Oman Medical Speciality Board, Muscat, Oman
- Newcastle Biomedical Research Centre, NIHR, Newcastle upon Tyne, Tyne and Wear, NE45PL, UK
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10
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Al Alawi I, Al Riyami M, Barroso-Gil M, Powell L, Olinger E, Al Salmi I, Sayer JA. The diagnostic yield of whole exome sequencing as a first approach in consanguineous Omani renal ciliopathy syndrome patients. F1000Res 2021; 10:207. [PMID: 34354814 PMCID: PMC8290205 DOI: 10.12688/f1000research.40338.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/17/2021] [Indexed: 02/05/2023] Open
Abstract
Background: Whole exome sequencing (WES) is becoming part of routine clinical and diagnostic practice. In the investigation of inherited cystic kidney disease and renal ciliopathy syndromes, WES has been extensively applied in research studies as well as for diagnostic utility to detect various novel genes and variants. The yield of WES critically depends on the characteristics of the patient population. Methods: In this study, we selected 8 unrelated Omani children, presenting with renal ciliopathy syndromes with a positive family history and originating from consanguineous families. We performed WES in affected children to determine the genetic cause of disease and to test the yield of this approach, coupled with homozygosity mapping, in this highly selected population. DNA library construction and WES was carried out using SureSelect Human All Exon V6 Enrichment Kit and Illumina HiSeq platform. For variants filtering and annotation Qiagen Variant Ingenuity tool was used. Nexus copy number software from BioDiscovery was used for evaluation of copy number variants and whole gene deletions. Patient and parental DNA was used to confirm mutations and the segregation of alleles using Sanger sequencing. Results: Genetic analysis identified 4 potential causative homozygous variants each confirmed by Sanger sequencing in 4 clinically relevant ciliopathy syndrome genes, ( TMEM231, TMEM138, WDR19 and BBS9), leading to an overall diagnostic yield of 50%. Conclusions: WES coupled with homozygosity mapping provided a diagnostic yield of 50% in this selected population. This genetic approach needs to be embedded into clinical practise to allow confirmation of clinical diagnosis, to inform genetic screening as well as family planning decisions. Half of the patients remain without diagnosis highlighting the technical and interpretational hurdles that need to be overcome in the future.
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Affiliation(s)
- Intisar Al Alawi
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, Tyne and Wear, NE13BZ, UK
- National Genetic Center, Ministry of Health, Muscat, Oman
| | - Mohammed Al Riyami
- Pediatric Nephrology Unit, Department of Child Health, Royal Hospital, Ministry of Health, Muscat, Oman
| | - Miguel Barroso-Gil
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, Tyne and Wear, NE13BZ, UK
| | - Laura Powell
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, Tyne and Wear, NE13BZ, UK
| | - Eric Olinger
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, Tyne and Wear, NE13BZ, UK
| | - Issa Al Salmi
- Renal Medicine Department, Royal Hospital, Ministry of Health, Muscat, Oman
- Oman Medical Speciality Board, Muscat, Oman
| | - John A. Sayer
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, Tyne and Wear, NE13BZ, UK
- Oman Medical Speciality Board, Muscat, Oman
- Newcastle Biomedical Research Centre, NIHR, Newcastle upon Tyne, Tyne and Wear, NE45PL, UK
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11
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BBS4 Is Essential for Nuclear Transport of Transcription Factors Mediating Neuronal ER Stress Response. Mol Neurobiol 2020; 58:78-91. [PMID: 32894499 DOI: 10.1007/s12035-020-02104-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 08/27/2020] [Indexed: 11/09/2022]
Abstract
Bardet-Biedl syndrome (BBS) is an autosomal recessive syndrome presenting with retinal dystrophy, cognitive impairment, and obesity. BBS is characterized by elevated endoplasmic reticulum (ER) stress in the early stages of adipocyte and retinal development. BBS expression in the CNS and indications of hippocampal dysgenesis suggest neural development abnormalities. However, the role of BBS in ER stress in neuronal cells has not yet been studied. Therefore, we aimed at studying the role of BBS4 in neuronal development under normal and ER stress conditions. ER stress and unfolded protein response (UPR) were studied in BBS4-silenced (SiBBS4) SH-SY5Y cells during differentiation under normal and stress states, using molecular and biochemical markers. ER stress was demonstrated at early neural differentiation, with significantly augmented expression of UPR markers corresponding to BBS4 expression. In the undifferentiated state, BBS4 silencing resulted in significantly reduced ER-stress markers' expression under normal and ER-stress states. Independent of ER stress, SiBBS4 cells demonstrated significant reduction in activated phospho-IRE1α. Under BBS4 silencing, both sXBP-1 and activated ATF6α p50 failed to translocate to the nucleus. Transcript levels of apoptosis markers were upregulated under BBS4 depletion and ER-stress induction, corresponding to decreased viability. BBS4 depletion in neuronal cells results in reduced sensitivity to ER stress during differentiation and under ER-stress induction, partly due to failure in translocation of ER-transcription factors (TF) sXBP-1 and ATF6α p50 to the nucleus. Hence, BBS4 is essential for nuclear transport under ER-stress response in neuronal cells during early differentiation. Our studies shed light on molecular mechanisms through which BBS4 malfunction alters neuronal ER stress response.
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Niederlova V, Modrak M, Tsyklauri O, Huranova M, Stepanek O. Meta-analysis of genotype-phenotype associations in Bardet-Biedl syndrome uncovers differences among causative genes. Hum Mutat 2019; 40:2068-2087. [PMID: 31283077 DOI: 10.1002/humu.23862] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 06/17/2019] [Accepted: 07/03/2019] [Indexed: 12/16/2022]
Abstract
Bardet-Biedl syndrome (BBS) is a recessive genetic disease causing multiple organ anomalies. Most patients carry mutations in genes encoding for the subunits of the BBSome, an octameric ciliary transport complex, or accessory proteins involved in the BBSome assembly or function. BBS proteins have been extensively studied using in vitro, cellular, and animal models. However, the molecular functions of particular BBS proteins and the etiology of the BBS symptoms are still largely elusive. In this study, we applied a meta-analysis approach to study the genotype-phenotype association in humans using our database of all reported BBS patients. The analysis revealed that the identity of the causative gene and the character of the mutation partially predict the clinical outcome of the disease. Besides their potential use for clinical prognosis, our analysis revealed functional differences of particular BBS genes in humans. Core BBSome subunits BBS2, BBS7, and BBS9 manifest as more critical for the function and development of kidneys than peripheral subunits BBS1, BBS4, and BBS8/TTC8, suggesting that incomplete BBSome retains residual function at least in the kidney.
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Affiliation(s)
- Veronika Niederlova
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Martin Modrak
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Oksana Tsyklauri
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Martina Huranova
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Ondrej Stepanek
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
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13
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Novel splicing variant c. 208+2T>C in BBS5 segregates with Bardet-Biedl syndrome in an Iranian family by targeted exome sequencing. Biosci Rep 2019; 39:BSR20181544. [PMID: 30850397 PMCID: PMC6438871 DOI: 10.1042/bsr20181544] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 02/20/2019] [Accepted: 03/01/2019] [Indexed: 01/13/2023] Open
Abstract
Bardet–Biedl syndrome (BBS) is a rare genetically heterogeneous ciliopathy which accompanies retinitis pigmentosa (RP). However, the BBS5 mutation remains unclear in Iranians with BBS. The purpose of study is to evaluate genetic analyses of a BBS Iranian family using targetted exome sequencing (TES). A male 11-year-old proband and three related family members were recruited. Biochemical tests, electrocardiography and visual acuity testing, such as funduscopic, fundus photography (FP), optical coherence tomography (OCT), and standard electroretinography, were conducted. Molecular analysis and high-throughput DNA sequence analysis were performed. The proband was diagnosed with possible BBS based on the presence of three primary features and two secondary features. The TES analysis of the proband with BBS resulted in the identification of a novel, homozygous splicing variant c. 208+2T>C of the BBS5 gene (NM_152384.2) in this Iranian BBS family. This variant was confirmed and was completely co-segregated with the disease in this family by Sanger sequencing. Thus, we report a novel, homozygous splicing site variant c.208+2T>C in the BBS5 gene for the first time in the Iranian family.
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14
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Shen T, Gao JM, Shou T, Li L, Zhang JP, Zhao Q, Yan XM. Identification of a homozygous BBS7 frameshift mutation in two (related) Chinese Miao families with Bardet-Biedl Syndrome. J Chin Med Assoc 2019; 82:110-114. [PMID: 30839500 DOI: 10.1097/jcma.0000000000000011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Bardet-Biedl Syndrome (BBS) is a genetically heterogeneous autosomal recessive disorder with a wide spectrum of clinical features. To date, mutations in 21 different genes (BBS1-21) have been identified as causing isolated or complex BBS phenotypes. In this report, we present three Chinese Miao ethnic patients who were diagnosed with BBS on the basis of characteristic clinical features and investigated the exsome of these patients. METHODS To evaluate disease genes, the Agilent SureSelect system and Illumina HiSeq 2000 platform for whole exome enrichment and sequencing (WES) were used on the proband and her mother. Variants that fit a recessive model of inheritance only were compared and filtered using public databases. Variants detected by exome sequencing were validated by Sanger sequencing. A total of 981 phenotypically normal subjects were enrolled as control data set. RESULTS A frameshift homozygous germline mutation in BBS7 was detected by WES and identified by Sanger sequencing in affected individuals. This mutation was predicted to result in premature termination of exon5 (c.389_390delAC, p.Asn130ThrfsX3; RefSeq NM_176824.2) and lead to a 133 amino acid truncated protein. The inheritance patterns in the families are consistent with autosomal recessive inheritance, and no such homozygous mutation was found in the other 981 controls. CONCLUSION This mutation has not yet been described in any reported literature, and this is the first report on BBS7 mutation in Chinese Miao families with BBS phenotypes.
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Affiliation(s)
- Tao Shen
- Institute of Basic and Clinical Medicine, Key laboratory of Clinical Virology, Key Laboratory for Birth Defects and Genetic Diseases, the First People's Hospital of Yunnan Province, Kunming, Yunnan Province, China
| | - Jian-Mei Gao
- Institute of Basic and Clinical Medicine, Key laboratory of Clinical Virology, Key Laboratory for Birth Defects and Genetic Diseases, the First People's Hospital of Yunnan Province, Kunming, Yunnan Province, China
| | - Tao Shou
- Oncology Department, the First People's Hospital of Yunnan Province, Kunming, Yunnan Province, China
| | - Li Li
- Institute of Basic and Clinical Medicine, Key laboratory of Clinical Virology, Key Laboratory for Birth Defects and Genetic Diseases, the First People's Hospital of Yunnan Province, Kunming, Yunnan Province, China
| | - Jin-Ping Zhang
- Institute of Basic and Clinical Medicine, Key laboratory of Clinical Virology, Key Laboratory for Birth Defects and Genetic Diseases, the First People's Hospital of Yunnan Province, Kunming, Yunnan Province, China
| | - Qian Zhao
- Institute of Basic and Clinical Medicine, Key laboratory of Clinical Virology, Key Laboratory for Birth Defects and Genetic Diseases, the First People's Hospital of Yunnan Province, Kunming, Yunnan Province, China
| | - Xin-Min Yan
- Institute of Basic and Clinical Medicine, Key laboratory of Clinical Virology, Key Laboratory for Birth Defects and Genetic Diseases, the First People's Hospital of Yunnan Province, Kunming, Yunnan Province, China
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15
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Chandrasekar SP, Namboothiri S, Sen P, Sarangapani S. Screening for mutation hotspots in Bardet-Biedl syndrome patients from India. Indian J Med Res 2018; 147:177-182. [PMID: 29806606 PMCID: PMC5991121 DOI: 10.4103/ijmr.ijmr_1822_15] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Background & objectives: Bardet–Biedl syndrome (BBS) is a genetically heterogeneous autosomal recessive disorder characterized by multiple organ defects involving retina, kidney, liver and brain. Disease-causing mutations in BBS genes narrowed down by homozygosity mapping in small consanguineous and non-consanguineous pedigrees were reported in 80 per cent of the study population. This study was aimed to screen these genes (BBS3, BBS10) and specific exons of BBS genes (BBS1, BBS5, MKKS, BBS9, BBS11 and BBS12) for recurrent mutations in a selected sample of BBS patients. Methods: The recurrent mutations in BBS genes were screened in the BBS affected individuals by PCR based direct sequencing. The pathogenicity of the observed mutations were confirmed by co-segregation analysis, screening of healthy unrelated controls and in silico analysis. Results: In the 64 BBS patients (44 males, 20 females) were studied, mutations were predominant in BBS10 and ARL6 genes; the c.272T>C; p.(I91T) mutation in ARL6 gene was a recurrent mutation. One novel non-sense mutation c.425T>G; p(L142*) was obtained in BBS5 gene (family BSI-31). Interpretation & conclusions: BBS10 gene mutations clustered in exon 2 of the gene suggesting the exon as a probable hotspot for mutations in Indian population. A cost- and time-effective strategy for the molecular diagnosis of BBS was designed based on these results.
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Affiliation(s)
- Sathya Priya Chandrasekar
- SN ONGC Department of Genetics & Molecular Biology, Vision Research Foundation, Chennai; School of Chemical & Biotechnology, SASTRA University, Thanjavur, India
| | - Sheela Namboothiri
- Department of Paediatric Genetics, Amrita Institute of Medical Sciences & Research Centre, Kochi, India
| | - Parveen Sen
- Department of Vitreo Retina Clinic, Medical Research Foundation, Chennai, India
| | - Sripriya Sarangapani
- SN ONGC Department of Genetics & Molecular Biology, Vision Research Foundation, Chennai, India
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16
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Nikkhah E, Safaralizadeh R, Mohammadiasl J, Tahmasebi Birgani M, Hosseinpour Feizi MA, Golchin N. Identification of A Novel Compound Heterozygous Mutation in BBS12 in An Iranian Family with Bardet-Biedl Syndrome Using Targeted Next Generation Sequencing. CELL JOURNAL 2018; 20:284-289. [PMID: 29633607 PMCID: PMC5893301 DOI: 10.22074/cellj.2018.5012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Accepted: 03/21/2017] [Indexed: 01/27/2023]
Abstract
Bardet-Biedl syndrome (BBS) is a pleiotropic and multisystemic disorder characterized by rod-cone dystrophy, polydactyly,
learning difficulties, renal abnormalities, obesity and hypogonadism. This disorder is genetically heterogeneous. Until
now, a total of nineteen genes have been identified for BBS whose mutations explain more than 80% of diagnosed
cases. Recently, the development of next generation sequencing (NGS) technology has accelerated mutation screening
of target genes, resulting in lower cost and less time consumption. Here, we screened the most common BBS genes
(BBS1-BBS13) using NGS in an Iranian family of a proposita displaying symptoms of BBS. Among the 18 mutations
identified in the proposita, one (BBS12 c.56T>G and BBS12 c.1156C>T) was novel. This compound heterozygosity
was confirmed by Sanger sequencing in the proposita and her parents. Although our data were presented as a case
report, however, we suggest a new probable genetic mechanism other than the conventional autosomal recessive
inheritance of BBS. Additionally, given that in some Iranian provinces, like Khuzestan, consanguineous marriages
are common, designing mutational panels for genetic diseases is strongly recommended, especially for those with an
autosomal recessive inheritance pattern.
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Affiliation(s)
- Emad Nikkhah
- Department of Animal Biology, Faculty of Natural Science, University of Tabriz, Tabriz, Iran
| | - Reza Safaralizadeh
- Department of Animal Biology, Faculty of Natural Science, University of Tabriz, Tabriz, Iran.
| | - Javad Mohammadiasl
- Department of Medical Genetics, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Maryam Tahmasebi Birgani
- Department of Medical Genetics, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
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17
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Falardeau F, Camurri MV, Campeau PM. Genomic approaches to diagnose rare bone disorders. Bone 2017; 102:5-14. [PMID: 27474525 DOI: 10.1016/j.bone.2016.07.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 07/24/2016] [Indexed: 02/01/2023]
Abstract
Skeletal dysplasias are Mendelian disorders with a prevalence of approximatively 1 in every 5000 individuals and can usually be diagnosed based on clinical and radiological findings. However, given that some diseases can be caused by several different genes, and that some genes can cause a variety of different phenotypes, achieving a molecular diagnosis can be challenging. We review here different approaches, from single gene sequencing to genomic approaches using next-generation sequencing, to reach a molecular diagnosis for skeletal dysplasias. We will further describe the overall advantages and limitations of first, second and third-generation sequencing, including single gene sequencing, whole-exome and genome sequencing (WES and WGS), multiple gene panel sequencing and single molecule sequencing. We also provide a brief overview of potential future applications of emerging technologies.
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Affiliation(s)
- Félix Falardeau
- CHU Sainte-Justine Research Center, Montreal, Canada; Division of Molecular and Cellular Biology, Department of Biology, University of Sherbrooke, Sherbrooke, Canada
| | | | - Philippe M Campeau
- CHU Sainte-Justine Research Center, Montreal, Canada; Division of Medical Genetics, Department of Pediatrics, University of Montreal, Montreal, Canada.
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18
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Kaur Y, de Souza RJ, Gibson WT, Meyre D. A systematic review of genetic syndromes with obesity. Obes Rev 2017; 18:603-634. [PMID: 28346723 DOI: 10.1111/obr.12531] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 02/01/2017] [Accepted: 02/02/2017] [Indexed: 11/29/2022]
Abstract
Syndromic monogenic obesity typically follows Mendelian patterns of inheritance and involves the co-presentation of other characteristics, such as mental retardation, dysmorphic features and organ-specific abnormalities. Previous reviews on obesity have reported 20 to 30 syndromes but no systematic review has yet been conducted on syndromic obesity. We searched seven databases using terms such as 'obesity', 'syndrome' and 'gene' to conduct a systematic review of literature on syndromic obesity. Our literature search identified 13,719 references. After abstract and full-text review, 119 relevant papers were eligible, and 42 papers were identified through additional searches. Our analysis of these 161 papers found that 79 obesity syndromes have been reported in literature. Of the 79 syndromes, 19 have been fully genetically elucidated, 11 have been partially elucidated, 27 have been mapped to a chromosomal region and for the remaining 22, neither the gene(s) nor the chromosomal location(s) have yet been identified. Interestingly, 54.4% of the syndromes have not been assigned a name, whereas 13.9% have more than one name. We report on organizational inconsistencies (e.g. naming discrepancies and syndrome classification) and provide suggestions for improvements. Overall, this review illustrates the need for increased clinical and genetic research on syndromes with obesity.
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Affiliation(s)
- Y Kaur
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Canada
| | - R J de Souza
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Canada
| | - W T Gibson
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada.,British Columbia Children's Hospital Research Institute, Vancouver, Canada
| | - D Meyre
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Canada.,Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Canada
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Abstract
Bardet-Biedl syndrome (BBS) is a rare autosomal recessive genetic disorder. It is characterized by heterogeneous clinical manifestations including primary features of the disease (rod-cone dystrophy, polydactyly, obesity, genital abnormalities, renal defects, and learning difficulties) and secondary BBS characteristics (developmental delay, speech deficit, brachydactyly or syndactyly, dental defects, ataxia or poor coordination, olfactory deficit, diabetes mellitus, congenital heart disease, etc.); most of these symptoms may not be present at birth but appear and progressively worsen during the first and second decades of life. At least 20 BBS genes have already been identified, and all of them are involved in primary cilia functioning. Genetic diagnosis of BBS is complicated due to lack of gene-specific disease symptoms; however, it is gradually becoming more accessible with the invention of multigene sequencing technologies. Clinical management of BBS is largely limited to a symptomatic treatment. Mouse experiments demonstrate that the most debilitating complication of BBS, blindness, can be rescued by topical gene therapy. There is a published case report describing the delay of BBS symptoms by nutritional compensation of the disease-related biochemical deficiencies. Progress in DNA testing technologies is likely to rapidly resolve all limitations in BBS diagnosis; however, much slower improvement is expected with regard to BBS treatment.
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Affiliation(s)
- Evgeny N Suspitsin
- N.N. Petrov Institute of Oncology, St. Petersburg, Russia; St. Petersburg Pediatric Medical University, St. Petersburg, Russia
| | - Evgeny N Imyanitov
- N.N. Petrov Institute of Oncology, St. Petersburg, Russia; St. Petersburg Pediatric Medical University, St. Petersburg, Russia; I.I. Mechnikov North-Western Medical University, St. Petersburg, Russia; St. Petersburg State University, St. Petersburg, Russia
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20
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Khan S, Muhammad N, Khan M, Kamal A, Rehman Z, Khan S. Genetics of human Bardet-Biedl syndrome, an updates. Clin Genet 2016; 90:3-15. [DOI: 10.1111/cge.12737] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Revised: 12/21/2015] [Accepted: 01/03/2016] [Indexed: 12/22/2022]
Affiliation(s)
- S.A. Khan
- Department of Biotechnology and Genetic Engineering; Kohat University of Science and Technology; Khyber Pakhtunkhwa Pakistan
| | - N. Muhammad
- Department of Biotechnology and Genetic Engineering; Kohat University of Science and Technology; Khyber Pakhtunkhwa Pakistan
| | - M.A. Khan
- Gomal Centre of Biochemistry and Biotechnology; Gomal University; Khyber Pakhtunkhwa Pakistan
- Genomic Core Facility; Interim Translational Research Institute; Doha Qatar
| | - A. Kamal
- Department of Biotechnology and Genetic Engineering; Kohat University of Science and Technology; Khyber Pakhtunkhwa Pakistan
| | - Z.U. Rehman
- Department of Biotechnology and Genetic Engineering; Kohat University of Science and Technology; Khyber Pakhtunkhwa Pakistan
| | - S. Khan
- Department of Biotechnology and Genetic Engineering; Kohat University of Science and Technology; Khyber Pakhtunkhwa Pakistan
- Genomic Core Facility; Interim Translational Research Institute; Doha Qatar
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21
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Polla DL, Cardoso MTO, Silva MCB, Cardoso ICC, Medina CTN, Araujo R, Fernandes CC, Reis AMM, de Andrade RV, Pereira RW, Pogue R. Use of Targeted Exome Sequencing for Molecular Diagnosis of Skeletal Disorders. PLoS One 2015; 10:e0138314. [PMID: 26380986 PMCID: PMC4575211 DOI: 10.1371/journal.pone.0138314] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 08/28/2015] [Indexed: 01/19/2023] Open
Abstract
Genetic disorders of the skeleton comprise a large group of more than 450 clinically distinct and genetically heterogeneous diseases associated with mutations in more than 300 genes. Achieving a definitive diagnosis is complicated due to the genetic heterogeneity of these disorders, their individual rarity and their diverse radiographic presentations. We used targeted exome sequencing and designed a 1.4Mb panel for simultaneous testing of more than 4,800 exons in 309 genes involved in skeletal disorders. DNA from 69 individuals from 66 families with a known or suspected clinical diagnosis of a skeletal disorder was analyzed. Of 36 cases with a specific clinical hypothesis with a known genetic basis, mutations were identified for eight cases (22%). Of 20 cases with a suspected skeletal disorder but without a specific diagnosis, four causative mutations were identified. Also included were 11 cases with a specific skeletal disorder but for which there was at the time no known associated gene. For these cases, one mutation was identified in a known skeletal disease genes, and re-evaluation of the clinical phenotype in this case changed the diagnoses from osteodysplasia syndrome to Apert syndrome. These results suggest that the NGS panel provides a fast, accurate and cost-effective molecular diagnostic tool for identifying mutations in a highly genetically heterogeneous set of disorders such as genetic skeletal disorders. The data also stress the importance of a thorough clinical evaluation before DNA sequencing. The strategy should be applicable to other groups of disorders in which the molecular basis is largely known.
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Affiliation(s)
- Daniel L. Polla
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
| | - Maria T. O. Cardoso
- Núcleo de Genética da Secretaria de Saúde do Distrito Federal, Brasília, Distrito Federal, Brazil
- Curso de Medicina, Universidade Católica de Brasília, Taguatinga, Distrito Federal, Brazil
| | - Mayara C. B. Silva
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
| | - Isabela C. C. Cardoso
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
| | - Cristina T. N. Medina
- Núcleo de Genética da Secretaria de Saúde do Distrito Federal, Brasília, Distrito Federal, Brazil
| | - Rosenelle Araujo
- Núcleo de Genética da Secretaria de Saúde do Distrito Federal, Brasília, Distrito Federal, Brazil
| | - Camila C. Fernandes
- Departamento de Tecnologia, Laboratório Multiusuário Centralizado para Sequenciamento de DNA em Larga Escala e Análise de Expressão Gênica, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Campus Jaboticabal, Jaboticabal, São Paulo, Brazil
| | - Alessandra M. M. Reis
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
| | - Rosangela V. de Andrade
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
| | - Rinaldo W. Pereira
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
| | - Robert Pogue
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
- * E-mail:
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Tollenaere MAX, Mailand N, Bekker-Jensen S. Centriolar satellites: key mediators of centrosome functions. Cell Mol Life Sci 2015; 72:11-23. [PMID: 25173771 PMCID: PMC11114028 DOI: 10.1007/s00018-014-1711-3] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 08/01/2014] [Accepted: 08/25/2014] [Indexed: 01/18/2023]
Abstract
Centriolar satellites are small, microscopically visible granules that cluster around centrosomes. These structures, which contain numerous proteins directly involved in centrosome maintenance, ciliogenesis, and neurogenesis, have traditionally been viewed as vehicles for protein trafficking towards the centrosome. However, the recent identification of several new centriolar satellite components suggests that this model offers only an incomplete picture of their cellular functions. While the mechanisms controlling centriolar satellite status and function are not yet understood in detail, emerging evidence points to these structures as important hubs for dynamic, multi-faceted regulation in response to a variety of cues. In this review, we summarize the current knowledge of the roles of centriolar satellites in regulating centrosome functions, ciliogenesis, and neurogenesis. We also highlight newly discovered regulatory mechanisms targeting centriolar satellites and their functional status, and we discuss how defects in centriolar satellite components are intimately linked to a wide spectrum of human diseases.
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Affiliation(s)
- Maxim A. X. Tollenaere
- Faculty of Health Sciences, Ubiquitin Signaling Group, The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark
| | - Niels Mailand
- Faculty of Health Sciences, Ubiquitin Signaling Group, The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark
| | - Simon Bekker-Jensen
- Faculty of Health Sciences, Ubiquitin Signaling Group, The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark
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