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Garg B, Tomar N, Biswas A, Mehta N, Malhotra R. Understanding Musculoskeletal Disorders Through Next-Generation Sequencing. JBJS Rev 2022; 10:01874474-202204000-00001. [PMID: 35383688 DOI: 10.2106/jbjs.rvw.21.00165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
» An insight into musculoskeletal disorders through advancements in next-generation sequencing (NGS) promises to maximize benefits and improve outcomes through improved genetic diagnosis. » The primary use of whole exome sequencing (WES) for musculoskeletal disorders is to identify functionally relevant variants. » The current evidence has shown the superiority of NGS over conventional genotyping for identifying novel and rare genetic variants in patients with musculoskeletal disorders, due to its high throughput and low cost. » Genes identified in patients with scoliosis, osteoporosis, osteoarthritis, and osteogenesis imperfecta using NGS technologies are listed for further reference.
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Affiliation(s)
- Bhavuk Garg
- Department of Orthopaedics, All India Institute of Medical Sciences, New Delhi, India
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Phenotypic Variation in Vietnamese Osteogenesis Imperfecta Patients Sharing a Recessive P3H1 Pathogenic Variant. Genes (Basel) 2022; 13:genes13030407. [PMID: 35327962 PMCID: PMC8950175 DOI: 10.3390/genes13030407] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 02/14/2022] [Accepted: 02/21/2022] [Indexed: 02/04/2023] Open
Abstract
Osteogenesis imperfecta (OI) is a syndromic disorder of bone fragility with high variation in its clinical presentation. Equally variable is molecular aetiology; recessive forms are caused by approximately 20 different genes, many of which are directly implicated in collagen type I biosynthesis. Biallelic variants in prolyl 3-hydroxylase 1 (P3H1) are known to cause severe OI by affecting the competence of the prolyl 3-hydroxylation—cartilage associated protein—peptidyl-prolyl cis-trans isomerase B (P3H1-CRTAP-CyPB) complex, which acts on the Pro986 residue of collagen type I α 1 (COL1A1) and Pro707 collagen type I α 2 (COL1A2) chains. The investigation of an OI cohort of 146 patients in Vietnam identified 14 families with P3H1 variants. The c.1170+5G>C variant was found to be very prevalent (12/14) and accounted for 10.3% of the Vietnamese OI cohort. New P3H1 variants were also identified in this population. Interestingly, the c.1170+5G>C variants were found in families with the severe clinical Sillence types 2 and 3 but also the milder types 1 and 4. This is the first time that OI type 1 is reported in patients with P3H1 variants expanding the clinical spectrum. Patients with a homozygous c.1170+5G>C variant shared severe progressively deforming OI type 3: bowed long bones, deformities of ribcage, long phalanges and hands, bluish sclera, brachycephaly, and early intrauterine fractures. Although it remains unclear if the c.1170+5G>C variant constitutes a founder mutation in the Vietnamese population, its prevalence makes it valuable for the molecular diagnosis of OI in patients of the Kinh ethnicity. Our study provides insight into the clinical and genetic variation of P3H1-related OI in the Vietnamese population.
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Silva GCV, Borsatto T, Schwartz IVD, Sperb-Ludwig F. Characterization of the 3'UTR of the BTD gene and identification of regulatory elements and microRNAs. Genet Mol Biol 2022; 45:e20200432. [PMID: 35167647 PMCID: PMC8846296 DOI: 10.1590/1678-4685-gmb-2020-0432] [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: 11/20/2020] [Accepted: 08/22/2021] [Indexed: 12/05/2022] Open
Abstract
Reduced biotinidase activity is associated with a spectrum of deficiency ranging
from total deficiency to heterozygous levels, a finding that is not always
explained by the pathogenic variants observed in the BTD gene.
The investigation of miRNAs, regulatory elements and variants in the 3’UTR
region may present relevance in understanding the genotype-phenotype
association. The aims of the study were to characterize the regulatory elements
of the 3’UTR of the BTD gene and identify variants and miRNAs
which may explain the discrepancies observed between genotype and biochemical
phenotype. We evaluated 92 individuals with reduced biotinidase activity (level
of heterozygotes = 33, borderline = 35, partial DB = 20 or total DB= 4) with
previously determined BTD genotype. The 3’UTR of the
BTD gene was Sanger sequenced. In silico
analysis was performed to identify miRNAs and regulatory elements. No variants
were found in the 3’UTR. We found 97 possible miRNAs associated with the
BTD gene, 49 predicted miRNAs involved in the alanine,
biotin, citrate and pyruvate metabolic pathways and 5 genes involved in biotin
metabolism. Six AU-rich elements were found. Our data suggest variants in the
3'UTR of BTD do not explain the genotype-phenotype
discrepancies found in Brazilian individuals with reduced biotinidase.
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Affiliation(s)
- Gerda Cristal Villalba Silva
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil.,Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório BRAIN, Porto Alegre, RS, Brazil
| | - Taciane Borsatto
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório BRAIN, Porto Alegre, RS, Brazil.,Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
| | - Ida Vanessa Doederlein Schwartz
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil.,Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório BRAIN, Porto Alegre, RS, Brazil.,Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil.,Universidade Federal do Rio Grande do Sul, Departamento de Genética, Porto Alegre, RS, Brazil
| | - Fernanda Sperb-Ludwig
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil.,Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório BRAIN, Porto Alegre, RS, Brazil
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Tsai MC, Chou YY, Li CY, Wang YC, Yu HW, Chen CH, Chen PC. New Structural and Single Nucleotide Mutations in Type I and Type II Collagens in Taiwanese Children With Type I and Type II Collagenopathies. Front Genet 2021; 12:594285. [PMID: 34394176 PMCID: PMC8355745 DOI: 10.3389/fgene.2021.594285] [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: 08/13/2020] [Accepted: 06/22/2021] [Indexed: 11/21/2022] Open
Abstract
Collagenopathy is a rare genetic condition characterized by abnormality in either collagen structure or metabolism. Variations in its clinical presentations highlight diversity in the genetic causes and potential existence of concurrent mutations. Through whole exome sequencing (WES) complemented with multiplex ligation-dependent probe amplification, we identified the genetic etiologies for six cases with osteogenesis imperfecta (OI) in COL1A1 (p.T1298N, p.Q1280Pfs∗51, and p.G557Vfs∗23) and COL1A2 (c.1-1677_133-441del) as well as three cases with spondyloepiphyseal dysplasia congenita in COL2A1 (p.G1041S, p.G654S, and p.G441A). Co-occurrence of COL1A1 and WNT1 mutations was found in a patient with a mild OI phenotype but severe osteoporosis. These findings extended the pathogenic variant spectrum of COL1A1, COL1A2, and COL2A1 for type I and type II collagenopathies. Although WES provides a fast and accurate method to identify the genetic causes in most of the patients with type I and type II collagenopathies, its limitation of detecting CNVs because of variable capturing uniformity should be kept in mind when interpreting the results. Taken together, we demonstrate that multiple genetic characterizing technologies can provide an accurate and efficient molecular diagnostic of new genetic variants in disease-causing genes that are compatible with clinical phenotypes.
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Affiliation(s)
- Meng-Che Tsai
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Depatment of Pediatrics, College of Medicine, National Cheng Kung University Hospital, National Cheng Kung University, Tainan, Taiwan
| | - Yen-Yin Chou
- Depatment of Pediatrics, College of Medicine, National Cheng Kung University Hospital, National Cheng Kung University, Tainan, Taiwan
| | - Chia-Yi Li
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yi-Chieh Wang
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Hui-Wen Yu
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chia-Hsiang Chen
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Peng-Chieh Chen
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Research Center of Clinical Medicine, College of Medicine, National Cheng Kung University Hospital, National Cheng Kung University, Tainan, Taiwan
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