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Guo X, Shi T, Lin M, Liu B, Pan Y. Two Novel Frameshift Mutations in the GLI3 Gene Underlie Non-Syndromic Polydactyly in Chinese Families. Genet Test Mol Biomarkers 2023; 27:299-305. [PMID: 37768332 DOI: 10.1089/gtmb.2023.0022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/29/2023] Open
Abstract
Objective: Polydactyly is characterized by multiple distinct heterogeneous phenotypes, the etiologies of which involve several genes. This study aimed to explore the genetic defects and further clarify the molecular mechanism of polydactyly in several Chinese families. Methods: Three families with diverse phenotypes of non-syndromic polydactyly were analyzed: two were cases of familial disease, whereas one was sporadic. PCR and Sanger sequencing were used to screen for pathogenic mutations in two known disease-associated genes, GLI3 and HOXD13, while bioinformatic analyses predicted the pathogenicity of the identified variants. Reverse transcription PCR was used to analyze the splicing effect of an intronic variant. Results: Two novel heterozygous frameshift mutations (c.4478delG/p.S1493Tfs*18; c.846_c.847insC/p.R283Qfs*21) were identified in the GLI3 gene from two of the pedigrees. Both c.4478delG and c.846_c.847insC were later confirmed in affected and unaffected members and normal controls, to truncate and disrupt the integrity of the GLI3 protein, reduce its level of expression, and disrupt its biological function through nonsense-mediated mRNA decay (NMD). In addition, a deep intron mutation (c.125-47 C>A) was detected in the GLI3 gene from the sporadic case, however, both bioinformatics analysis (HSF, splice AI, and CBS) and RT-PCR indicated that the variant c.125-47 C>A had minimal if any impact on splicing of the GLI3 gene. Conclusion: Two newly identified heterozygous frameshift mutations in the GLI3 gene were detected in two families with non-syndromic polydactyly, further extending the mutational spectrum of the GLI3 gene in non-syndromic polydactyly. Moreover, our study further expanded the phenotypic spectrum of non-syndromic polydactyly.
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Affiliation(s)
- Xiaoyan Guo
- Department of Laboratory Medicine, Fuzhou Second Hospital, Fuzhou, P.R. China
- Department of Laboratory Medicine, Fuzhou Second Hospital of Xiamen University, School of Medicine, Xiamen University, Fuzhou, P.R. China
- Department of Laboratory Medicine, The Third Clinical Medical College, Fujian Medical University, Fuzhou, P.R. China
| | - Tengfei Shi
- Department of Laboratory Medicine, Fuzhou Second Hospital, Fuzhou, P.R. China
| | - Mingrui Lin
- Intensive Care Unit, The Affiliated People's Hospital of Fujian Traditional Medical University, Fuzhou, P.R. China
| | - Boling Liu
- Department of Orthopaedics, Fuzhou Second Hospital, Fuzhou, P.R. China
| | - Yuancheng Pan
- Department of Orthopaedics, Fuzhou Second Hospital, Fuzhou, P.R. China
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Baas M, Burger EB, van den Ouweland AM, Hovius SE, de Klein A, van Nieuwenhoven CA, Galjaard RJH. Variant type and position predict two distinct limb phenotypes in patients with GLI3-mediated polydactyly syndromes. J Med Genet 2020; 58:362-368. [PMID: 32591344 PMCID: PMC8142428 DOI: 10.1136/jmedgenet-2020-106948] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 05/11/2020] [Accepted: 05/13/2020] [Indexed: 01/06/2023]
Abstract
Introduction Pathogenic DNA variants in the GLI-Kruppel family member 3 (GLI3) gene are known to cause multiple syndromes: for example, Greig syndrome, preaxial polydactyly-type 4 (PPD4) and Pallister-Hall syndrome. Out of these, Pallister-Hall is a different entity, but the distinction between Greig syndrome and PPD4 is less evident. Using latent class analysis (LCA), our study aimed to investigate the correlation between reported limb anomalies and the reported GLI3 variants in these GLI3-mediated polydactyly syndromes. We identified two subclasses of limb anomalies that relate to the underlying variant. Methods Both local and published cases were included for analysis. The presence of individual limb phenotypes was dichotomised and an exploratory LCA was performed. Distribution of phenotypes and genotypes over the classes were explored and subsequently the key predictors of latent class membership were correlated to the different clustered genotypes. Results 297 cases were identified with 127 different variants in the GLI3 gene. A two-class model was fitted revealing two subgroups of patients with anterior versus posterior anomalies. Posterior anomalies were observed in cases with truncating variants in the activator domain (postaxial polydactyly; hand, OR: 12.7; foot, OR: 33.9). Multivariate analysis supports these results (Beta: 1.467, p=0.013 and Beta: 2.548, p<0.001, respectively). Corpus callosum agenesis was significantly correlated to these variants (OR: 8.8, p<0.001). Conclusion There are two distinct phenotypes within the GLI3-mediated polydactyly population: anteriorly and posteriorly orientated. Variants that likely produce haploinsufficiency are associated with anterior phenotypes. Posterior phenotypes are associated with truncating variants in the activator domain. Patients with these truncating variants have a greater risk for corpus callosum anomalies.
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Affiliation(s)
- Martijn Baas
- Plastic, Reconstructive and Hand Surgery, Erasmus MC, Rotterdam, The Netherlands
| | - Elise Bette Burger
- Plastic, Reconstructive and Hand Surgery, Erasmus MC, Rotterdam, The Netherlands
| | | | - Steven Er Hovius
- Plastic, Reconstructive and Hand Surgery, Radboud University Nijmegen, Nijmegen, Gelderland, The Netherlands.,Hand and Wrist Centre, Xpert Clinic, Eindhoven, The Netherlands
| | - Annelies de Klein
- Clinical Genetics, Erasmus MC, Rotterdam, Zuid-Holland, The Netherlands
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Abstract
BACKGROUND GLI3 encodes a transcription factor in the sonic hedgehog signaling pathway, which is essential in regulating the human limb bud development, especially on the anteroposterior axis. Mutations in GLI3 have been confirmed to be associated with various human congenital malformations, including Greig cephalopolysyndactyly syndrome, Pallister-Hall syndrome, and isolated polydactyly. A robust gene-phenotype relationship between GLI3 and Greig cephalopolysyndactyly syndrome and Pallister-Hall syndrome has been well elucidated, and less is known about GLI3 mutation-caused isolated polydactyly. This study intended to perform a mutation analysis of GLl3 in a family with isolated polydactyly. METHODS A 3-generation Chinese family with 19 members was recruited in this study, of which the proband and her mother were affected with polydactyly. The whole-exon sequencing was performed to find mutations, and Sanger sequencing was performed to validate the mutations. RESULTS We found a novel heterozygous frameshift mutation of GLI3 (c.1180C > TT, p.P394fs18x) in the proband of a Chinese family with isolated postaxial polydactyly. No mutation was detected in the proband's father or another 2 patients with sporadic preaxial polydactyly. CONCLUSIONS By systematically reviewing the gene-phenotype relationship, we found that GLI3 p.P394fs18x mutation might be specific for isolated postaxial polydactyly.
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Rao C, Chen J, Peng Q, Mo Q, Xia X, Lu X. Mutational Screening of GLI3, SHH, and SHH ZRS in 78 Chinese Children with Nonsyndromic Polydactyly. Genet Test Mol Biomarkers 2018; 22:577-581. [PMID: 30235038 DOI: 10.1089/gtmb.2018.0096] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Polydactyly is one of the most common congenital limb abnormalities. Our objective was to identify the genetic causes of non-syndromic polydactyly in 78 Chinese children. MATERIALS AND METHODS Genomic DNA was isolated from 78 independent nonsyndromic polydactyly patients, of whom 71 had preaxial polydactyly (PPD), six had postaxial polydactyly (PAP), and one showed combined PPD1 and PAP-A/B. The coding areas and exon/intron boundaries of the GLI3 and SHH genes and the genomic region of SHH ZRS were amplified by polymerase chain reaction and sequenced. RESULTS The patient with combined PPD1 and PAP-A/B (subject DUO36) exhibited a heterozygous nonsense mutation in chr7: 42004164G>A (ENST00000395925, c.4507C>T, p.Gln1503Stop ) of the GLI3 gene that has not been previously recorded. We did not detect any mutations in GLI3, SHH, or SHH ZRS in the other 77 nonsyndromic polydactyly patients. CONCLUSION The novel mutation in GLI3 c.4507C>T is likely one of the causes of the PAP and PPD1 of subject DUO36. This important finding should facilitate the optimization of genetic testing for nonsyndromic polydactyly.
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Affiliation(s)
- Chunbao Rao
- 1 Department of Center for Scientific Research, Dongguan Children's Hospital , Dongguan, Guangdong, China
- 2 Department of Medical and Molecular Genetics, Dongguan Institute of Pediatrics , Dongguan, Guangdong, China
| | - Jiahui Chen
- 3 Department of Child Orthopaedics, Dongguan Children's Hospital , Dongguan, Guangdong, China
| | - Qi Peng
- 1 Department of Center for Scientific Research, Dongguan Children's Hospital , Dongguan, Guangdong, China
- 2 Department of Medical and Molecular Genetics, Dongguan Institute of Pediatrics , Dongguan, Guangdong, China
| | - Qineng Mo
- 3 Department of Child Orthopaedics, Dongguan Children's Hospital , Dongguan, Guangdong, China
| | - Xiansheng Xia
- 3 Department of Child Orthopaedics, Dongguan Children's Hospital , Dongguan, Guangdong, China
| | - Xiaomei Lu
- 1 Department of Center for Scientific Research, Dongguan Children's Hospital , Dongguan, Guangdong, China
- 2 Department of Medical and Molecular Genetics, Dongguan Institute of Pediatrics , Dongguan, Guangdong, China
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Complex postaxial polydactyly types A and B with camptodactyly, hypoplastic third toe, zygodactyly and other digit anomalies caused by a novel GLI3 mutation. Eur J Med Genet 2017; 60:268-274. [DOI: 10.1016/j.ejmg.2017.03.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 03/07/2017] [Accepted: 03/11/2017] [Indexed: 11/21/2022]
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Xiang Y, Jiang L, Wang B, Xu Y, Cai H, Fu Q. Mutational screening of GLI3, SHH, preZRS, and ZRS in 102 Chinese children with nonsyndromic polydactyly. Dev Dyn 2017; 246:392-402. [PMID: 28127823 DOI: 10.1002/dvdy.24488] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 01/06/2017] [Accepted: 01/16/2017] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Polydactyly is a group of congenital limb malformations that show high degree of phenotypic variability and genetic heterogeneity. RESULTS In the present study, four genomic regions (exons of GLI3, SHH, and noncoding sequences of preZRS and ZRS) involved in hedgehog (Hh) signaling pathway were sequenced for 102 unrelated Chinese children with nonsyndromic polydactyly. Two GLI3 variants (c.2844 G > G/A; c.1486C > C/T) and four preZRS variants (chr7:156585336 A>G; chr7:156585421 C>A; chr7: 156585247 G>C; chr7:156585420 A > C) were observed in 2(2.0%) and 6(5.9%) patients, respectively. These variants are not over-represented in the Chinese healthy population. All the 8 cases showed preaxial polydactyly in hands. Additionally, no specific patterns of malformation predicted mutations in other candidate genes or sequences. CONCLUSIONS This is the first report of the assessment of the frequency of GLI3/SHH/preZRS/ZRS in Chinese patients to show any higher possibility of mutations or variants for the 4 genes or sequences in China. Developmental Dynamics 246:392-402, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Ying Xiang
- Department of Laboratory Medicine, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
| | - Limin Jiang
- Department of Laboratory Medicine, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
| | - Bo Wang
- Department of Laboratory Medicine, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
| | - Yunlan Xu
- Department of Pediatric Orthopedic, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
| | - Haiqing Cai
- Department of Pediatric Orthopedic, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
| | - Qihua Fu
- Department of Laboratory Medicine, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
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Wang Z, Wang J, Li Y, Geng J, Fu Q, Xu Y, Shen Y. Novel frame-shift mutations of GLI3 gene in non-syndromic postaxial polydactyly patients. Clin Chim Acta 2014; 433:195-9. [DOI: 10.1016/j.cca.2014.03.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Revised: 02/27/2014] [Accepted: 03/13/2014] [Indexed: 11/16/2022]
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Sethi SK, Goyal D, Khalil S, Yadav DK. Two Indian families with Greig cephalopolysyndactyly with non-syndromic phenotype. Eur J Pediatr 2013; 172:1131-5. [PMID: 23334564 DOI: 10.1007/s00431-013-1938-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Accepted: 01/09/2013] [Indexed: 11/25/2022]
Abstract
The Greig cephalopolysyndactyly syndrome (GCPS) is a rare, autosomal dominant, pleiotropic, multiple congenital anomaly syndrome. The typical findings include hypertelorism, macrocephaly with frontal bossing, and polysyndactyly. We present two families, with GCPS with a non-syndromic phenotype, without the characteristic craniofacial anomalies and with the presence of complex digital anomalies including various types of polydactyly and syndactyly of the fingers and toes. The cases were proven to be GCPS by mutational analysis of GL13 gene. Our patients support the fact that the phenotypic spectrum of GL13 mutations is broader than that encompassed by the usual clinical diagnostic criteria. Individuals with features of familial polysyndactyly should be screened for mutations in GL13 even if they do not fulfill clinical criteria.
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Affiliation(s)
- Sidharth Kumar Sethi
- Department of Pediatrics, PGIMER and Associated RML Hospital, New Delhi 110001, India.
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Cheng F, Zhang X, Zhang Y, Li C, Zeng C. Haplo2Ped: a tool using haplotypes as markers for linkage analysis. BMC Bioinformatics 2011; 12:350. [PMID: 21854652 PMCID: PMC3179971 DOI: 10.1186/1471-2105-12-350] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2011] [Accepted: 08/22/2011] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Generally, SNPs are abundant in the genome; however, they display low power in linkage analysis because of their limited heterozygosity. Haplotype markers, on the other hand, which are composed of many SNPs, greatly increase heterozygosity and have superiority in linkage statistics. RESULTS Here we developed Haplo2Ped to automatically transform SNP data into haplotype markers and then to compute the logarithm (base 10) of odds (LOD) scores of regional haplotypes that are homozygous within the disease co-segregation haploid group. The results are reported as a hypertext file and a 3D figure to help users to obtain the candidate linkage regions. The hypertext file contains parameters of the disease linked regions, candidate genes, and their links to public databases. The 3D figure clearly displays the linkage signals in each chromosome. We tested Haplo2Ped in a simulated SNP dataset and also applied it to data from a real study. It successfully and accurately located the causative genomic regions. Comparison of Haplo2Ped with other existing software for linkage analysis further indicated the high effectiveness of this software. CONCLUSIONS Haplo2Ped uses haplotype fragments as mapping markers in whole genome linkage analysis. The advantages of Haplo2Ped over other existing software include straightforward output files, increased accuracy and superior ability to deal with pedigrees showing incomplete penetrance. Haplo2Ped is freely available at: http://bighapmap.big.ac.cn/software.html.
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Affiliation(s)
- Feng Cheng
- Laboratory of Disease Genomics and Individualized Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, No.7 Beitucheng West Road, Beijing 100029, PR China
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