1
|
Ma THT, Luong TLA, Hoang TL, Nguyen TTH, Vu TH, Tran VK, Nguyen DB, Trieu TS, Nguyen HH, Nong VH, Nguyen DT. Novel and very rare causative variants in the COL7A1 gene of Vietnamese patients with recessive dystrophic epidermolysis bullosa revealed by whole-exome sequencing. Mol Genet Genomic Med 2021; 9:e1748. [PMID: 34286919 PMCID: PMC8404230 DOI: 10.1002/mgg3.1748] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/27/2021] [Accepted: 07/03/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Dystrophic epidermolysis bullosa (DEB) is a rare inherited disorder characterized by skin fragility leading to trauma-induced subepidermal blisters and healing with scarring. DEB is caused by mutations in COL7A1, the gene encoding for type VII collagen (COLVII). The DEB inheritance trait is divided into dominant dystrophic epidermolysis bullosa (DDEB) and recessive dystrophic epidermolysis bullosa (RDEB). METHODS Whole-exome sequencing (WES) was performed for identifying mutations in six affected individuals of five Vietnamese families. RESULTS Three novel variants in total of eight variants were found in five families. The first novel variant causing glycine substitution (c.8279G>A, p.G2760E), the remaining two novel variants resulted in splice site affecting (c.4518+2delT and c.5821-2A>G). Functional analysis indicated that the splice site at c.4518+2delT resulted in a skipping of exon 43, leading to an in-frame deletion of 12 amino acids. CONCLUSION Our finding expands the spectrum of COL7A1 mutations and reports altered splicing at c.4518+2delT during the processing of the pre-mRNA. This study provides an additional scientific basis for diagnosis, genetic counseling, and prognosis purposes of EB patients.
Collapse
Affiliation(s)
- Thi Huyen Thuong Ma
- Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi, Vietnam.,Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | | | | | - Thi Thanh Hoa Nguyen
- Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Thi Ha Vu
- Hanoi Medical University, Hanoi, Vietnam
| | | | | | | | - Hai Ha Nguyen
- Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi, Vietnam.,Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Van Hai Nong
- Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi, Vietnam.,Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Dang Ton Nguyen
- Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi, Vietnam.,Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| |
Collapse
|
2
|
Khan FF, Khan N, Rehman S, Ejaz A, Ali U, Erfan M, Ahmed ZM, Naeem M. Identification and Computational Analysis of Novel Pathogenic Variants in Pakistani Families with Diverse Epidermolysis Bullosa Phenotypes. Biomolecules 2021; 11:620. [PMID: 33921969 PMCID: PMC8143555 DOI: 10.3390/biom11050620] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/12/2021] [Accepted: 04/15/2021] [Indexed: 12/17/2022] Open
Abstract
Epidermolysis bullosa (EB) includes a group of rare gesnodermatoses that result in blistering and erosions of the skin and mucous membranes. Genetically, pathogenic variants in around 20 genes are known to alter the structural and functional integrity of intraepidermal adhesion and dermo-epidermal anchorage, leading to four different types of EB. Here we report the underlying genetic causes of EB phenotypes segregating in seven large consanguineous families, recruited from different regions of Pakistan. Whole exome sequencing, followed by segregation analysis of candidate variants through Sanger sequencing, identified eight pathogenic variants, including three novel (ITGB4: c.1285G>T, and c.3373G>A; PLEC: c.1828A>G) and five previously reported variants (COL7A1: c.6209G>A, and c.1573C>T; FERMT1: c.676insC; LAMA3: c.151insG; LAMB3: c.1705C>T). All identified variants were either absent or had very low frequencies in the control databases. Our in-silico analyses and 3-dimensional (3D) molecular modeling support the deleterious impact of these variants on the encoded proteins. Intriguingly, we report the first case of a recessively inherited form of rare EBS-Ogna associated with a homozygous variant in the PLEC gene. Our study highlights the clinical and genetic diversity of EB in the Pakistani population and expands the mutation spectrum of EB; it could also be useful for prenatal diagnosis and genetic counseling of the affected families.
Collapse
Affiliation(s)
- Fehmida F. Khan
- Medical Genetics Research Laboratory, Department of Biotechnology, Quaid-i-Azam University, Islamabad 45320, Pakistan; (F.F.K.); (N.K.)
| | - Naima Khan
- Medical Genetics Research Laboratory, Department of Biotechnology, Quaid-i-Azam University, Islamabad 45320, Pakistan; (F.F.K.); (N.K.)
| | - Sakina Rehman
- Laboratory of Neurogenetics and Translational Research, University of Maryland School of Medicine, Baltimore, MD 21201, USA;
| | - Amir Ejaz
- Army Medical College, Rawalpindi 46000, Pakistan;
| | - Uzma Ali
- Department of Dermatology, Capital Hospital, Islamabad 44000, Pakistan;
| | - Muhammad Erfan
- Department of Dermatology, Federal Government Polyclinic Hospital, Islamabad 44000, Pakistan;
| | - Zubair M. Ahmed
- Laboratory of Neurogenetics and Translational Research, University of Maryland School of Medicine, Baltimore, MD 21201, USA;
| | - Muhammad Naeem
- Medical Genetics Research Laboratory, Department of Biotechnology, Quaid-i-Azam University, Islamabad 45320, Pakistan; (F.F.K.); (N.K.)
| |
Collapse
|
3
|
Yang N, Ma Y, Yao H, Chang Q, Zhang V, Liang Z, Cai X. Novel biallelic variants in COL7A1 cause recessive dystrophic epidermolysis bullosa. Mol Genet Genomic Med 2020; 8:e1347. [PMID: 32537942 PMCID: PMC7434731 DOI: 10.1002/mgg3.1347] [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: 02/21/2020] [Revised: 05/18/2020] [Accepted: 05/19/2020] [Indexed: 12/17/2022] Open
Abstract
Background Autosomal recessive dystrophic epidermolysis bullosa (RDEB) is an incurable and severe inherited skin disorder characterized by recurrent blistering at the sublamina densa beneath the cutaneous basement membrane. It is caused by biallelic loss‐of‐function mutation in the gene encoding type VII collagen (COL7A1). This study aimed to identify the causative variants of a Chinese RDEB patient and further provide prenatal diagnosis for the ongoing risk pregnancy of the proband's mother. Methods Clinical exome sequencing (CES) has been performed and an in‐house pipeline was used to conduct a phenotype‐driven data analysis. A minigene assay was used to verify the pathogenicity of a novel splice site variant in the COL7A1. Results Here we report two compound heterozygous variants in COL7A1, c.3867delT (p.G1290Efs*35) and c.5532+4_5532+5delAG, identified in a RDEB patient by CES. The minigene assay confirmed that thec.5532+4_5532+5delAGchange was a noncanonic splice site variant leading to in an in‐frame deletion of exon 64. Prenatal diagnosis indicated that the present pregnancy of the patient's mother was not affected. Conclusion Our study expands the mutation spectrum of COL7A1 and demonstrated that CES and minigene assays were efficient tools for RDEB molecular diagnoses.
Collapse
Affiliation(s)
- Neng Yang
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Laboratory of Molecular Developmental Biology, School of Life Sciences, Southwest University, Chongqing, China.,Department of Gynecology & Obstetrics, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Yongyi Ma
- Department of Gynecology & Obstetrics, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Hong Yao
- Department of Gynecology & Obstetrics, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Qing Chang
- Department of Gynecology & Obstetrics, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Victor Zhang
- Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX, USA.,AmCare Genomics Lab, Guangzhou, China
| | - Zhiqing Liang
- Department of Gynecology & Obstetrics, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Xiongwei Cai
- Department of Gynecology & Obstetrics, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| |
Collapse
|
4
|
Sivasubbu S, Scaria V. Genomics of rare genetic diseases-experiences from India. Hum Genomics 2019; 14:52. [PMID: 31554517 PMCID: PMC6760067 DOI: 10.1186/s40246-019-0215-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 06/26/2019] [Indexed: 12/15/2022] Open
Abstract
Home to a culturally heterogeneous population, India is also a melting pot of genetic diversity. The population architecture characterized by multiple endogamous groups with specific marriage patterns, including the widely prevalent practice of consanguinity, not only makes the Indian population distinct from rest of the world but also provides a unique advantage and niche to understand genetic diseases. Centuries of genetic isolation of population groups have amplified the founder effects, contributing to high prevalence of recessive alleles, which translates into genetic diseases, including rare genetic diseases in India.Rare genetic diseases are becoming a public health concern in India because a large population size of close to a billion people would essentially translate to a huge disease burden for even the rarest of the rare diseases. Genomics-based approaches have been demonstrated to accelerate the diagnosis of rare genetic diseases and reduce the socio-economic burden. The Genomics for Understanding Rare Diseases: India Alliance Network (GUaRDIAN) stands for providing genomic solutions for rare diseases in India. The consortium aims to establish a unique collaborative framework in health care planning, implementation, and delivery in the specific area of rare genetic diseases. It is a nation-wide collaborative research initiative catering to rare diseases across multiple cohorts, with over 240 clinician/scientist collaborators across 70 major medical/research centers. Within the GUaRDIAN framework, clinicians refer rare disease patients, generate whole genome or exome datasets followed by computational analysis of the data for identifying the causal pathogenic variations. The outcomes of GUaRDIAN are being translated as community services through a suitable platform providing low-cost diagnostic assays in India. In addition to GUaRDIAN, several genomic investigations for diseased and healthy population are being undertaken in the country to solve the rare disease dilemma.In summary, rare diseases contribute to a significant disease burden in India. Genomics-based solutions can enable accelerated diagnosis and management of rare diseases. We discuss how a collaborative research initiative such as GUaRDIAN can provide a nation-wide framework to cater to the rare disease community of India.
Collapse
Affiliation(s)
| | - Sridhar Sivasubbu
- CSIR Institute of Genomics and Integrative Biology, Delhi, 110025, India.
| | - Vinod Scaria
- CSIR Institute of Genomics and Integrative Biology, Delhi, 110025, India.
| |
Collapse
|
5
|
Tsai K, Lin T, Chen H, Chen W, Chen Y. Picosecond laser treatment for drug‐induced melanonychia. J Eur Acad Dermatol Venereol 2019; 33:e428. [PMID: 31220366 DOI: 10.1111/jdv.15750] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 05/30/2019] [Accepted: 06/13/2019] [Indexed: 12/26/2022]
Affiliation(s)
- K.‐S. Tsai
- Department of Applied Cosmetology Hungkuang University Taichung Taiwan
- Departments of Dermatology, Pathology, Obstetrics and Gynecology, Urology, and Medical Research China Medical University Hospital Taichung Taiwan
| | - T.‐Y. Lin
- Departments of Dermatology, Pathology, Obstetrics and Gynecology, Urology, and Medical Research China Medical University Hospital Taichung Taiwan
| | - H.‐Y. Chen
- Departments of Dermatology, Pathology, Obstetrics and Gynecology, Urology, and Medical Research China Medical University Hospital Taichung Taiwan
- Graduate Institute of Integrated Medicine, College of Chinese Medicine China Medical University Taichung Taiwan
| | - W.‐C. Chen
- Departments of Dermatology, Pathology, Obstetrics and Gynecology, Urology, and Medical Research China Medical University Hospital Taichung Taiwan
- Graduate Institute of Integrated Medicine, College of Chinese Medicine China Medical University Taichung Taiwan
| | - Y.‐H. Chen
- Departments of Dermatology, Pathology, Obstetrics and Gynecology, Urology, and Medical Research China Medical University Hospital Taichung Taiwan
- Graduate Institute of Integrated Medicine, College of Chinese Medicine China Medical University Taichung Taiwan
- Department of Psychology, College of Medical and Health Science Asia University Taichung Taiwan
| |
Collapse
|