1
|
Maggi J, Koller S, Feil S, Bachmann-Gagescu R, Gerth-Kahlert C, Berger W. Limited Added Diagnostic Value of Whole Genome Sequencing in Genetic Testing of Inherited Retinal Diseases in a Swiss Patient Cohort. Int J Mol Sci 2024; 25:6540. [PMID: 38928247 PMCID: PMC11203445 DOI: 10.3390/ijms25126540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024] Open
Abstract
The purpose of this study was to assess the added diagnostic value of whole genome sequencing (WGS) for patients with inherited retinal diseases (IRDs) who remained undiagnosed after whole exome sequencing (WES). WGS was performed for index patients in 66 families. The datasets were analyzed according to GATK's guidelines. Additionally, DeepVariant was complemented by GATK's workflow, and a novel structural variant pipeline was developed. Overall, a molecular diagnosis was established in 19/66 (28.8%) index patients. Pathogenic deletions and one deep-intronic variant contributed to the diagnostic yield in 4/19 and 1/19 index patients, respectively. The remaining diagnoses (14/19) were attributed to exonic variants that were missed during WES analysis due to bioinformatic limitations, newly described loci, or unclear pathogenicity. The added diagnostic value of WGS equals 5/66 (9.6%) for our cohort, which is comparable to previous studies. This figure would decrease further to 1/66 (1.5%) with a standardized and reliable copy number variant workflow during WES analysis. Given the higher costs and limited added value, the implementation of WGS as a first-tier assay for inherited eye disorders in a diagnostic laboratory remains untimely. Instead, progress in bioinformatic tools and communication between diagnostic and clinical teams have the potential to ameliorate diagnostic yields.
Collapse
Affiliation(s)
- Jordi Maggi
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland; (J.M.); (S.K.); (S.F.)
| | - Samuel Koller
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland; (J.M.); (S.K.); (S.F.)
| | - Silke Feil
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland; (J.M.); (S.K.); (S.F.)
| | | | - Christina Gerth-Kahlert
- Department of Ophthalmology, University Hospital Zurich and University of Zurich, 8091 Zurich, Switzerland;
| | - Wolfgang Berger
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland; (J.M.); (S.K.); (S.F.)
- Zurich Center for Integrative Human Physiology (ZIHP), University of Zurich, 8057 Zurich, Switzerland
- Neuroscience Center Zurich (ZNZ), University and ETH Zurich, 8057 Zurich, Switzerland
| |
Collapse
|
2
|
Severino-Freire M, Granier Tournier C, Chiaverini C, Audouze A, Morice-Picard F, Texier H, Dreyfus I, Bing-Lecointe AC, Mallet S, Bodemer C, Fischer J, Jonca N, Mazereeuw-Hautier J. French national protocol for the management of congenital ichthyosis. Ann Dermatol Venereol 2024; 151:103247. [PMID: 38513308 DOI: 10.1016/j.annder.2024.103247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 09/27/2023] [Indexed: 03/23/2024]
Abstract
Congenital ichthyoses (CI) comprise a heterogeneous group of monogenic genetic skin diseases characterized by diffuse scaling, often associated with skin inflammation. Diagnosis of the individual form of ichthyosis is complex and is guided by clinical expertise. CI usually has a major impact on quality of life (QOL) and thus requires lifelong treatment. To date, there are no curative therapies, although various symptomatic treatment options exist. The present protocol for the management of CI has been drawn up in accordance with the recommendations published in 2012 by the French National Authority for Health, based on a literature review, with the help and validation of members of the French network for rare skin diseases (FIMARAD). It provides a summary of evidence and expert-based recommendations and is intended to help clinicians with the management of these rare and often complex diseases.
Collapse
Affiliation(s)
- M Severino-Freire
- University Hospital Center of Toulouse, Reference Centre for Rare Skin Diseases, Department of Dermatology, Larrey Hospital, 24, Chemin de Pouvourville, TSA 30030 Toulouse Cedex 9, France
| | - C Granier Tournier
- University Hospital Center of Toulouse, Reference Centre for Rare Skin Diseases, Department of Dermatology, Larrey Hospital, 24, Chemin de Pouvourville, TSA 30030 Toulouse Cedex 9, France
| | - C Chiaverini
- University Hospital Center of Nice, Department of Dermatology, Archet 2 Hospital, CS 23079, 06202 Nice Cedex 3, France
| | - A Audouze
- Association Ichtyose France, 37 rue du Golf, 03700 Bellerive sur Allier, France
| | - F Morice-Picard
- Department of Dermatology, University Hospital Center of Bordeaux - Hôpital Saint André, 1 Rue Jean Burguet, 33075 Bordeaux Cedex, France
| | - H Texier
- University Hospital Center of Toulouse, Reference Centre for Rare Skin Diseases, Department of Dermatology, Larrey Hospital, 24, Chemin de Pouvourville, TSA 30030 Toulouse Cedex 9, France
| | - I Dreyfus
- University Hospital Center of Toulouse, Reference Centre for Rare Skin Diseases, Department of Dermatology, Larrey Hospital, 24, Chemin de Pouvourville, TSA 30030 Toulouse Cedex 9, France
| | - A-C Bing-Lecointe
- Hospital Annecy-Genevois site Annecy, 1 Avenue De L'hôpital, 74370 Annecy, France
| | - S Mallet
- Department of Dermatology, University Hospital Center of Marseille, 264 rue Saint-Pierre, 13005 Marseille, France
| | - C Bodemer
- Department of Dermatology, Reference Center for Genodermatoses and Rare Skin Diseases (MAGEC), Hôpital Necker-Enfants Malades, AP-HP, 149 Rue de Sèvres, 75743 Paris cedex 15, France
| | - J Fischer
- Institute of Human Genetics, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Breisacher Straße 153, 79110 Freiburg, Germany
| | - N Jonca
- University Hospital Center of Toulouse, Hôpital Purpan, Cell Biology and Cytology Laboratory, Institut Fédératif de Biologie, Toulouse F-31300, France
| | - J Mazereeuw-Hautier
- University Hospital Center of Toulouse, Reference Centre for Rare Skin Diseases, Department of Dermatology, Larrey Hospital, 24, Chemin de Pouvourville, TSA 30030 Toulouse Cedex 9, France.
| |
Collapse
|
3
|
Chegini M, Eslami M, Motavaf M, Memarsadeghi O, Hoseini A, Torab E, Hoseininasab F, Amiri H, Ramandi S, Mostofinezhad N, Keivani F, Ghaffari SR, Rafati M. Whole exome sequencing identifies novel pathogenic variants in TGM1 and ALOX12B in patients with hereditary ichthyosis. Arch Dermatol Res 2023; 316:24. [PMID: 38060040 DOI: 10.1007/s00403-023-02775-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 10/25/2023] [Accepted: 11/09/2023] [Indexed: 12/08/2023]
Abstract
BACKGROUND Hereditary ichthyosis is a clinically and genetically heterogeneous disorder associated with more than 50 genes with TGM1, ALOX12B, and ALOXE3 being the most prevalent. Establishing an accurate diagnosis is important for effective genetic counseling and optimal patient management. OBJECTIVE We studied the diagnostic value of whole exome sequencing (WES) in a small case series with hereditary ichthyosis. METHODS During a 1-year period, index cases of 5 unrelated families clinically diagnosed with hereditary ichthyosis went through WES, followed by extensive segregation analysis. Prenatal diagnosis (PND) was conducted where indicated. RESULTS We identified 4 homozygous variants-2 in TGM1 (c.655A > G and c.797A > G) and 2 in ALOX12B (c.527 + 2 T > G and c.1654G > T)-alongside a heterozygous variant in TGM1 (c.428G > A) in 5 families. The variants were all pathogenic/likely pathogenic according to the ACMG classification and segregation analysis, except for c.797A > G in TGM1 which remained a variant of unknown clinical significance. Four variants were novel. All families were referred either during pregnancy or before reproductive planning; 4 benefited from WES as it identified the mutation in the probands and enabled carrier detection in at-risk relatives; PND was conducted in 2 families. CONCLUSION Our findings further support WES is a powerful tool for the comprehensive, accurate, and rapid molecular diagnosis of hereditary ichthyosis and can offer opportunities for reproductive planning, carrier screening and prenatal diagnosis to at-risk families.
Collapse
Affiliation(s)
- Mitra Chegini
- Department of Genetics, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
- Applied Biotechnology Research Center, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Maryam Eslami
- Department of Genetics, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
- Applied Biotechnology Research Center, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Mahsa Motavaf
- Functional Neurosurgery Research Center, Shohada Tajrish Neurosurgical Comprehensive Center of Excellence, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Omid Memarsadeghi
- Applied Biotechnology Research Center, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Azadeh Hoseini
- Department of Genomics, Fetal Health Research Center, Hope Generation Foundation, Tehran, Iran
| | - Elnaz Torab
- Department of Genomics, Fetal Health Research Center, Hope Generation Foundation, Tehran, Iran
| | - Fatemeh Hoseininasab
- Department of Reproductive Genetics, Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Hosna Amiri
- Department of Genomics, Fetal Health Research Center, Hope Generation Foundation, Tehran, Iran
| | - Somayeh Ramandi
- Department of Genomics, Fetal Health Research Center, Hope Generation Foundation, Tehran, Iran
| | - Niusha Mostofinezhad
- Department of Genomics, Fetal Health Research Center, Hope Generation Foundation, Tehran, Iran
| | - Fatane Keivani
- Department of Genomics, Fetal Health Research Center, Hope Generation Foundation, Tehran, Iran
| | - Saeed Reza Ghaffari
- Department of Genomics, Fetal Health Research Center, Hope Generation Foundation, Tehran, Iran.
- Department of Reproductive Genetics, Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran.
- Department of Genomics, Gene Clinic, Tehran, Iran.
| | - Maryam Rafati
- Department of Genomics, Fetal Health Research Center, Hope Generation Foundation, Tehran, Iran.
- Department of Reproductive Genetics, Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran.
| |
Collapse
|
4
|
Theil AF, Häckes D, Lans H. TFIIH central activity in nucleotide excision repair to prevent disease. DNA Repair (Amst) 2023; 132:103568. [PMID: 37977600 DOI: 10.1016/j.dnarep.2023.103568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 08/22/2023] [Accepted: 09/03/2023] [Indexed: 11/19/2023]
Abstract
The heterodecameric transcription factor IIH (TFIIH) functions in multiple cellular processes, foremost in nucleotide excision repair (NER) and transcription initiation by RNA polymerase II. TFIIH is essential for life and hereditary mutations in TFIIH cause the devastating human syndromes xeroderma pigmentosum, Cockayne syndrome or trichothiodystrophy, or combinations of these. In NER, TFIIH binds to DNA after DNA damage is detected and, using its translocase and helicase subunits XPB and XPD, opens up the DNA and checks for the presence of DNA damage. This central activity leads to dual incision and removal of the DNA strand containing the damage, after which the resulting DNA gap is restored. In this review, we discuss new structural and mechanistic insights into the central function of TFIIH in NER. Moreover, we provide an elaborate overview of all currently known patients and diseases associated with inherited TFIIH mutations and describe how our understanding of TFIIH function in NER and transcription can explain the different disease features caused by TFIIH deficiency.
Collapse
Affiliation(s)
- Arjan F Theil
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - David Häckes
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Hannes Lans
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD Rotterdam, the Netherlands.
| |
Collapse
|
5
|
King AD, Deirawan H, Klein PA, Dasgeb B, Dumur CI, Mehregan DR. Next-generation sequencing in dermatology. Front Med (Lausanne) 2023; 10:1218404. [PMID: 37841001 PMCID: PMC10570430 DOI: 10.3389/fmed.2023.1218404] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 09/04/2023] [Indexed: 10/17/2023] Open
Abstract
Over the past decade, Next-Generation Sequencing (NGS) has advanced our understanding, diagnosis, and management of several areas within dermatology. NGS has emerged as a powerful tool for diagnosing genetic diseases of the skin, improving upon traditional PCR-based techniques limited by significant genetic heterogeneity associated with these disorders. Epidermolysis bullosa and ichthyosis are two of the most extensively studied genetic diseases of the skin, with a well-characterized spectrum of genetic changes occurring in these conditions. NGS has also played a critical role in expanding the mutational landscape of cutaneous squamous cell carcinoma, enhancing our understanding of its molecular pathogenesis. Similarly, genetic testing has greatly benefited melanoma diagnosis and treatment, primarily due to the high prevalence of BRAF hot spot mutations and other well-characterized genetic alterations. Additionally, NGS provides a valuable tool for measuring tumor mutational burden, which can aid in management of melanoma. Lastly, NGS demonstrates promise in improving the sensitivity of diagnosing cutaneous T-cell lymphoma. This article provides a comprehensive summary of NGS applications in the diagnosis and management of genodermatoses, cutaneous squamous cell carcinoma, melanoma, and cutaneous T-cell lymphoma, highlighting the impact of NGS on the field of dermatology.
Collapse
Affiliation(s)
- Andrew D. King
- Department of Dermatology, Wayne State University School of Medicine, Detroit, MI, United States
| | - Hany Deirawan
- Department of Dermatology, Wayne State University School of Medicine, Detroit, MI, United States
| | | | - Bahar Dasgeb
- Department of Surgical Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, United States
| | - Catherine I. Dumur
- Bernhardt Laboratories, Sonic Healthcare Anatomic Pathology Division, Jacksonville, FL, United States
| | - Darius R. Mehregan
- Department of Dermatology, Wayne State University School of Medicine, Detroit, MI, United States
| |
Collapse
|
6
|
Salik D, Richert B, Smits G. Clinical and molecular diagnosis of genodermatoses: Review and perspectives. J Eur Acad Dermatol Venereol 2023; 37:488-500. [PMID: 36502512 DOI: 10.1111/jdv.18769] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 11/08/2022] [Indexed: 11/23/2022]
Abstract
Genodermatoses are a complex and heterogeneous group of genetic skin disorders characterized by variable expression and clinical and genetic heterogeneity, rendering their diagnosis challenging. DNA-based techniques, like whole-exome sequencing, can establish a diagnosis in 50% of cases. RNA-sequencing is emerging as an attractive tool that can obtain information regarding gene expression while integrating functional genomic data with regard to the interpretation of variants. This increases the diagnostic rate by an additional 10-15%. In the present review, we detail the clinical steps involved in the diagnosis of genodermatoses, as well as the current DNA-based technologies available to clinicians. Herein, the intention is to facilitate a better understanding of the possibilities and limitations of these diagnostic technologies. In addition, this review could guide dermatologists through new emerging techniques, such as RNA-sequencing and its applications to familiarizing them with future techniques. Currently, this multi-omics approach is likely the best strategy designed to promote the diagnosis of patients with genodermatoses and discover new skin disease genes that could result in novel targeted therapies.
Collapse
Affiliation(s)
- Deborah Salik
- Department of Dermatology, CHU Saint-Pierre, CHU Brugmann and Hôpital Universitaire des Enfants Reine Fabiola, Université Libre de Bruxelles, Brussels, Belgium
| | - Bertrand Richert
- Department of Dermatology, CHU Saint-Pierre, CHU Brugmann and Hôpital Universitaire des Enfants Reine Fabiola, Université Libre de Bruxelles, Brussels, Belgium
| | - Guillaume Smits
- Department of Genetics, Hôpital Erasme, ULB Center of Human Genetics, Université Libre de Bruxelles (ULB), Brussels, Belgium.,Department of Genetics, Hôpital Universitaire des Enfants Reine Fabiola, ULB Center of Human Genetics Université Libre de Bruxelles (ULB), Brussels, Belgium.,Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles, Brussels, Belgium
| |
Collapse
|
7
|
PNPLA1-Mediated Acylceramide Biosynthesis and Autosomal Recessive Congenital Ichthyosis. Metabolites 2022; 12:metabo12080685. [PMID: 35893253 PMCID: PMC9332298 DOI: 10.3390/metabo12080685] [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: 06/10/2022] [Revised: 07/14/2022] [Accepted: 07/21/2022] [Indexed: 02/01/2023] Open
Abstract
The stratum corneum of the epidermis acts as a life-sustaining permeability barrier. Unique heterogeneous ceramides, especially ω-O-acylceramides, are key components for the formation of stable lamellar membrane structures in the stratum corneum and are essential for a vital epidermal permeability barrier. Several enzymes involved in acylceramide synthesis have been demonstrated to be associated with ichthyosis. The function of patatin-like phospholipase domain-containing protein 1 (PNPLA1) was a mystery until the finding that PNPLA1 gene mutations were involved in autosomal-recessive congenital ichthyosis (ARCI) patients, both humans and dogs. PNPLA1 plays an essential role in the biosynthesis of acylceramide as a CoA-independent transacylase. PNPLA1 gene mutations cause decreased acylceramide levels and impaired skin barrier function. More and more mutations in PNPLA1 genes have been identified in recent years. Herein, we describe the structural and functional specificity of PNPLA1, highlight its critical roles in acylceramide synthesis and skin barrier maintenance, and summarize the PNPLA1 mutations currently identified in ARCI patients.
Collapse
|
8
|
Hamama I, Patel W, Razak A. A Late-Preterm Infant with Ichthyosis, Pancytopenia, and Recurrent Sepsis. Neoreviews 2021; 22:e843-e846. [PMID: 34850146 DOI: 10.1542/neo.22-12-e843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Ibrahim Hamama
- Division of Neonatology, Department of Pediatrics, Princess Nourah Bint Abdulrahman University, King Abdullah bin Abdulaziz University Hospital, Riyadh, Saudi Arabia
| | - Waseemoddin Patel
- Division of Neonatology, Department of Pediatrics, Princess Nourah Bint Abdulrahman University, King Abdullah bin Abdulaziz University Hospital, Riyadh, Saudi Arabia
| | - Abdul Razak
- Division of Neonatology, Department of Pediatrics, Princess Nourah Bint Abdulrahman University, King Abdullah bin Abdulaziz University Hospital, Riyadh, Saudi Arabia
| |
Collapse
|
9
|
Charfeddine C, Laroussi N, Mkaouar R, Jouini R, Khayat O, Redissi A, Mosbah A, Dallali H, Chedly Debbiche A, Zaouak A, Fenniche S, Abdelhak S, Hammami-Ghorbel H. Expanding the clinical phenotype associated with NIPAL4 mutation: Study of a Tunisian consanguineous family with erythrokeratodermia variabilis-Like Autosomal Recessive Congenital Ichthyosis. PLoS One 2021; 16:e0258777. [PMID: 34669720 PMCID: PMC8528321 DOI: 10.1371/journal.pone.0258777] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 10/05/2021] [Indexed: 11/19/2022] Open
Abstract
Erythrokeratodermia variabilis (EKV) is a rare disorder of cornification usually associated with dominant mutations in the GJB3 and GJB4 genes encoding connexins (Cx)31 and 30.3. Genetic heterogeneity of EKV has already been suggested. We investigated at the clinical and genetic level a consanguineous Tunisian family with 2 sisters presenting an autosomal recessive form of EKV to better characterize this disease. Mutational analysis initially screened the connexin genes and Whole-exome sequencing (WES) was performed to identify the molecular aetiology of the particular EKV phenotype in the proband. Migratory shaped erythematous areas are the initial presenting sign followed by relatively stable hyperkeratotic plaques are the two predominates characteristics in both patients. However, remarkable variability of morphological and dominating features of the disease were observed between patients. In particular, the younger sister (proband) exhibited ichthyosiform-like appearance suggesting Autosomal Recessive Congenital Ichthyosis (ARCI) condition. No causative mutations were detected in the GJB3 and GJB4 genes. WES results revealed a novel missense homozygous mutation in NIPAL4 gene (c.835C>G, p.Pro279Ala) in both patients. This variant is predicted to be likely pathogenic. In addition, in silico analysis of the mutated 3D domain structure predicted that this variant would result in NIPA4 protein destabilization and Mg2+ transport perturbation, pointing out the potential role of NIPAL4 gene in the development and maintenance of the barrier function of the epidermis. Taken togheter, these results expand the clinical phenotype associated with NIPAL4 mutation and reinforce our hypothesis of NIPAL4 as the main candidate gene for the EKV-like ARCI phenotype.
Collapse
Affiliation(s)
- Cherine Charfeddine
- University Tunis El Manar, Institut Pasteur de Tunis, Biomedical Genomics and Oncogenetics Laboratory, LR20IPT05, Tunis, Tunisia
- Université de la Manouba, Institut de Biotechnologie de Sidi Thabet, Ariana, Tunisia
- * E-mail:
| | - Nadia Laroussi
- University Tunis El Manar, Institut Pasteur de Tunis, Biomedical Genomics and Oncogenetics Laboratory, LR20IPT05, Tunis, Tunisia
| | - Rahma Mkaouar
- University Tunis El Manar, Institut Pasteur de Tunis, Biomedical Genomics and Oncogenetics Laboratory, LR20IPT05, Tunis, Tunisia
| | - Raja Jouini
- Department of Pathology, Habib Thameur Hospital, Tunis, Tunisia
| | - Olfa Khayat
- Department of Pathology, Habib Thameur Hospital, Tunis, Tunisia
| | - Aladin Redissi
- BVBGR-LR11ES31, ISBST, Université de la Manouba, Institut de Biotechnologie de Sidi Thabet, Ariana, Tunisia
| | - Amor Mosbah
- BVBGR-LR11ES31, ISBST, Université de la Manouba, Institut de Biotechnologie de Sidi Thabet, Ariana, Tunisia
| | - Hamza Dallali
- University Tunis El Manar, Institut Pasteur de Tunis, Biomedical Genomics and Oncogenetics Laboratory, LR20IPT05, Tunis, Tunisia
| | | | - Anissa Zaouak
- Department of Dermatology, Genodermatosis and Cancers Laboratory LR12SP03, Habib Thameur Hospital, Tunis, Tunisia
| | - Sami Fenniche
- Department of Dermatology, Genodermatosis and Cancers Laboratory LR12SP03, Habib Thameur Hospital, Tunis, Tunisia
| | - Sonia Abdelhak
- University Tunis El Manar, Institut Pasteur de Tunis, Biomedical Genomics and Oncogenetics Laboratory, LR20IPT05, Tunis, Tunisia
| | - Houda Hammami-Ghorbel
- Department of Dermatology, Genodermatosis and Cancers Laboratory LR12SP03, Habib Thameur Hospital, Tunis, Tunisia
| |
Collapse
|
10
|
Zhuang J, Zhang N, Fu W, Yao J, Li Y, Zeng S, Wang Y, Xie Y, Jiang Y. Cytogenetic and molecular analysis of distal 4q duplication with distinctive phenotype using single-nucleotide polymorphism array. Mol Cytogenet 2021; 14:46. [PMID: 34587985 PMCID: PMC8482616 DOI: 10.1186/s13039-021-00568-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 08/31/2021] [Indexed: 11/30/2022] Open
Abstract
Aims There is little knowledge about partial trisomy 4q and the genotype–phenotype correlation. In this study, we presented the detail of two Chinese families with partial distal 4q duplication in an attempt to clarify the correlation between the genotype and the phenotype. Methods Two pedigrees with distal 4q duplication were enrolled in this study. Karyotype analysis and single-nucleotide polymorphism (SNP) array detection were performed for prenatal diagnosis. Fluorescence in situ hybridization analysis. (FISH) was conducted to verify the copy number variants. Results Two families with partial trisomy 4q were identified. The fetus in pedigree 1 exhibited multiple ultrasound anomalies including intrauterine growth restriction and an atrioventricular septal defect who had a duplication of 4q28.3-qter associate with 6p25.2-p25.3 deletion, which resulted from balanced translocation carried by his father t(4;6)(q28.3;p25.2). The fetus in pedigree 2 had a distal 4q28.3-qter duplication combined with monosomy of Xp21.3-p22.3, and the karyotype was described as 46,X,der(X)t(X;4)(p21.3;q28.3)mat, which originally inherited from the pregnant woman who exhibited a mild clinical phenotype limited to short stature. Conclusions In our study, we for the first time identified the partial trisomy 4q associate with 6p or Xp deletion. In addition, our finding further strengthens that mild clinical phenotype in 4q duplication case may be due to the spreading of X inactivation to the autosomal in derivation of chromosome X.
Collapse
Affiliation(s)
- Jianlong Zhuang
- Prenatal Diagnosis Center, Quanzhou Women's and Children's Hospital, Quanzhou, 362000, Fujian, People's Republic of China
| | - Na Zhang
- Prenatal Diagnosis Center, Quanzhou Women's and Children's Hospital, Quanzhou, 362000, Fujian, People's Republic of China
| | - Wanyu Fu
- Prenatal Diagnosis Center, Quanzhou Women's and Children's Hospital, Quanzhou, 362000, Fujian, People's Republic of China
| | - Jianfeng Yao
- Department of Women Healthcare, Quanzhou Women's and Children's Hospital, Quanzhou, 362000, Fujian, People's Republic of China
| | - Yanqing Li
- Prenatal Diagnosis Center, Quanzhou Women's and Children's Hospital, Quanzhou, 362000, Fujian, People's Republic of China
| | - Shuhong Zeng
- Prenatal Diagnosis Center, Quanzhou Women's and Children's Hospital, Quanzhou, 362000, Fujian, People's Republic of China
| | - Yuanbai Wang
- Prenatal Diagnosis Center, Quanzhou Women's and Children's Hospital, Quanzhou, 362000, Fujian, People's Republic of China
| | - Yingjun Xie
- Department of Obstetrics and Gynecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, Guangdong, People's Republic of China.
| | - Yuying Jiang
- Prenatal Diagnosis Center, Quanzhou Women's and Children's Hospital, Quanzhou, 362000, Fujian, People's Republic of China.
| |
Collapse
|
11
|
Xie W, Zhou H, Zhou L, Gong Y, Lin J, Chen Y. Clinical features and genetic analysis of two Chinese families with X-linked ichthyosis. J Int Med Res 2021; 48:300060520962292. [PMID: 33026262 PMCID: PMC7545777 DOI: 10.1177/0300060520962292] [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] [Indexed: 11/20/2022] Open
Abstract
Objective Recessive X-linked ichthyosis (RXLI) caused by deficiency of the steroid sulfatase gene (STS) has a reported prevalence of 1/2000 to 1/6000. The present study aimed to characterize the phenotypes and genotypes of two Chinese families with RXLI. Methods The patients were referred to the Family Planning Research Institute of Hunan Province for genetic counseling. Their skin phenotypes were photographed, and venous blood was drawn and used for chromosomal microarray analysis (CMA). Results The skin phenotype of the proband from the first family was characterized by generalized skin dryness and scaling, with noticeable dark brown, polygonal scales on his trunk and extensor surfaces of his extremities. The proband from the second family had an atypical phenotype showing mild skin dryness over his entire body, slight scaling on his abdomen, and small skin fissures on his arms and legs. No mental disability or developmental anomaly was noted in either proband. CMA revealed that both probands carried a 1.4-Mb deletion on chromosome Xp22.31 involving four Online Mendelian Inheritance in Man-listed genes including STS. Conclusions Our findings add knowledge to the genotype and phenotype spectrum of RXLI, which may be helpful in genetic counseling and prenatal diagnosis.
Collapse
Affiliation(s)
- Wanqin Xie
- NHC Key Laboratory of Birth Defects for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan, China.,Key Laboratory of Genetics and Birth Health, Family Planning Research Institute of Hunan Province, Changsha, Hunan, China
| | - Haiyan Zhou
- NHC Key Laboratory of Birth Defects for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan, China.,Key Laboratory of Genetics and Birth Health, Family Planning Research Institute of Hunan Province, Changsha, Hunan, China
| | - Lin Zhou
- NHC Key Laboratory of Birth Defects for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan, China.,Key Laboratory of Genetics and Birth Health, Family Planning Research Institute of Hunan Province, Changsha, Hunan, China
| | - Yun Gong
- NHC Key Laboratory of Birth Defects for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan, China.,Key Laboratory of Genetics and Birth Health, Family Planning Research Institute of Hunan Province, Changsha, Hunan, China
| | - Jiwu Lin
- NHC Key Laboratory of Birth Defects for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan, China.,Key Laboratory of Genetics and Birth Health, Family Planning Research Institute of Hunan Province, Changsha, Hunan, China
| | - Yong Chen
- NHC Key Laboratory of Birth Defects for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan, China.,Key Laboratory of Genetics and Birth Health, Family Planning Research Institute of Hunan Province, Changsha, Hunan, China
| |
Collapse
|
12
|
Zhuang J, Chen C, Jiang Y, Luo Q, Zeng S, Lv C, Wang Y, Fu W. Application of the BACs-on-Beads assay for the prenatal diagnosis of chromosomal abnormalities in Quanzhou, China. BMC Pregnancy Childbirth 2021; 21:94. [PMID: 33509128 PMCID: PMC7844892 DOI: 10.1186/s12884-021-03589-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 01/22/2021] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND An increasing number of techniques have been used for prenatal diagnosis of genetic abnormalities. Our initial objective was to explore the value of the BACs-on-Beads (BoBs) assay for the prenatal diagnosis of aneuploidies and microdeletion/microduplication syndromes in Quanzhou, Southeast China. METHODS A total of 1409 pregnant women with high-risk factors for chromosomal abnormalities admitted to Quanzhou Women's and Children's Hospital were enrolled in this study. BoBs assays and karyotype analyses were conducted for all subjects. Subsequently, chromosome microarray analysis (CMA) or fluorescence in situ hybridization (FISH) was performed to validate the findings. RESULTS In this study, karyotype analysis and BoBs assay failed in 4 cases, and 2 cases, respectively. A total of 1403 cases were successfully analyzed, with success rates of 99.72% (1405/1409) and 99.85% (1407/1409) for karyotype analysis and Bobs assay, respectively. BoBs assay rapidly detected chromosomal aneuploidies in line with the karyotyping data. Additionally, 23 cases of microdeletions/microduplications were detected by BoBs assay but missed by karyotyping, including 22q11.2 microdeletions/microduplications, 5p15.32p15.33 microdeletion, Xp22.31 microdeletions/microduplications, Xq27.3 microdeletion, and Yp11.2 and Yq11.22q11.222 microduplication. In comparison with karyotyping, fewer mosaicisms were identified by BoBs assay. A high detection rate of chromosomal abnormalities was observed in the high-risk group during noninvasive prenatal testing (NIPT) (41.72%) and the abnormal ultrasound group (13.43%). CONCLUSIONS BoBs assay can be used for the rapid and efficient prenatal diagnosis of common aneuploidies and microdeletion/microduplication syndromes. Moreover, the combined use of BoBs assay and karyotyping in prenatal diagnosis may allow for a more effective detection of chromosomal abnormalities.
Collapse
Affiliation(s)
- Jianlong Zhuang
- Prenatal Diagnosis Center, Quanzhou Women's and Children's Hospital, Quanzhou, Fujian, 362000, People's Republic of China
| | - Chunnuan Chen
- Department of Neurosurgery, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian, 362000, People's Republic of China
| | - Yuying Jiang
- Prenatal Diagnosis Center, Quanzhou Women's and Children's Hospital, Quanzhou, Fujian, 362000, People's Republic of China
| | - Qi Luo
- Department of Public Health for Women and Children, Quanzhou Women's and Children's Hospital, Quanzhou, Fujian, 362000, People's Republic of China
| | - Shuhong Zeng
- Prenatal Diagnosis Center, Quanzhou Women's and Children's Hospital, Quanzhou, Fujian, 362000, People's Republic of China
| | - Chunling Lv
- Zhejiang Biosan Technology Co., Ltd, Hangzhou, Zhejiang, 310000, People's Republic of China
| | - Yuanbai Wang
- Prenatal Diagnosis Center, Quanzhou Women's and Children's Hospital, Quanzhou, Fujian, 362000, People's Republic of China.
| | - Wanyu Fu
- Prenatal Diagnosis Center, Quanzhou Women's and Children's Hospital, Quanzhou, Fujian, 362000, People's Republic of China.
| |
Collapse
|
13
|
González‐Del Carmen M, Montaño S, Reyes‐Hernández OD, Vizcaíno‐Dorado PA, Leyva‐García N, Morales‐Morfín JC, Diaz‐Beltran W, Quinto‐Santiago E, Cariño‐Calvo L, Magaña JJ, Leyva‐Gómez G, Cortés H. High prevalence of autosomal recessive congenital ichthyosis in a Mexican population caused by a new mutation in the
TGM1
gene: epidemiological evidence of a founder effect. Int J Dermatol 2020; 59:969-977. [DOI: 10.1111/ijd.14952] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 04/19/2020] [Accepted: 04/24/2020] [Indexed: 12/12/2022]
Affiliation(s)
| | - Sarita Montaño
- Laboratorio de Modelado Molecular y Bioinformática Facultad de Ciencias Químico‐Biológicas Universidad Autónoma de Sinaloa Culiacán Sinaloa México
| | - Octavio D. Reyes‐Hernández
- Laboratorio de Biología Molecular del Cáncer UMIEZ Facultad de Estudios Superiores Zaragoza Universidad Nacional Autónoma de México Ciudad de México México
| | - Pablo A. Vizcaíno‐Dorado
- Laboratorio de Medicina Genómica Departamento de Genética Instituto Nacional de Rehabilitación Luis Guillermo Ibarra Ibarra Ciudad de México México
| | - Norberto Leyva‐García
- Laboratorio de Medicina Genómica Departamento de Genética Instituto Nacional de Rehabilitación Luis Guillermo Ibarra Ibarra Ciudad de México México
| | - Juan C. Morales‐Morfín
- Laboratorio de Medicina Genómica Departamento de Genética Instituto Nacional de Rehabilitación Luis Guillermo Ibarra Ibarra Ciudad de México México
| | - Wendy Diaz‐Beltran
- Facultad de Medicina Universidad Veracruzana Ciudad Mendoza, Veracruz México
| | | | | | - Jonathan J. Magaña
- Laboratorio de Medicina Genómica Departamento de Genética Instituto Nacional de Rehabilitación Luis Guillermo Ibarra Ibarra Ciudad de México México
| | - Gerardo Leyva‐Gómez
- Departamento de Farmacia Facultad de Química Universidad Nacional Autónoma de México Ciudad de México México
| | - Hernán Cortés
- Laboratorio de Medicina Genómica Departamento de Genética Instituto Nacional de Rehabilitación Luis Guillermo Ibarra Ibarra Ciudad de México México
| |
Collapse
|
14
|
Esperón-Moldes U, Ginarte-Val M, Rodríguez-Pazos L, Fachal L, Martín-Santiago A, Vicente A, Jiménez-Gallo D, Guillén-Navarro E, Sampol LM, González-Enseñat MA, Vega A. Novel CYP4F22 mutations associated with autosomal recessive congenital ichthyosis (ARCI). Study of the CYP4F22 c.1303C>T founder mutation. PLoS One 2020; 15:e0229025. [PMID: 32069299 PMCID: PMC7028276 DOI: 10.1371/journal.pone.0229025] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Accepted: 01/28/2020] [Indexed: 11/18/2022] Open
Abstract
Mutations in CYP4F22 cause autosomal recessive congenital ichthyosis (ARCI). However, less than 10% of all ARCI patients carry a mutation in CYP4F22. In order to identify the molecular basis of ARCI among our patients (a cohort of ninety-two Spanish individuals) we performed a mutational analysis using direct Sanger sequencing in combination with a multigene targeted NGS panel. From these, eight ARCI families (three of them with Moroccan origin) were found to carry five different CYP4F22 mutations, of which two were novel. Computational analysis showed that the mutations found were present in highly conserved residues of the protein and may affect its structure and function. Seven of the eight families were carriers of a highly recurrent CYP4F22 variant, c.1303C>T; p.(His435Tyr). A 12Mb haplotype was reconstructed in all c.1303C>T carriers by genotyping ten microsatellite markers flanking the CYP4F22 gene. A prevalent 2.52Mb haplotype was observed among Spanish carrier patients suggesting a recent common ancestor. A smaller core haplotype of 1.2Mb was shared by Spanish and Moroccan families. Different approaches were applied to estimate the time to the most recent common ancestor (TMRCA) of carrier patients with Spanish origin. The age of the mutation was calculated by using DMLE and BDMC2. The algorithms estimated that the c.1303C>T variant arose approximately 2925 to 4925 years ago, while Spanish carrier families derived from a common ancestor who lived in the XIII century. The present study reports five CYP4F22 mutations, two of them novel, increasing the number of CYP4F22 mutations currently listed. Additionally, our results suggest that the recurrent c.1303C>T change has a founder effect in Spanish population and c.1303C>T carrier families originated from a single ancestor with probable African ancestry.
Collapse
Affiliation(s)
- Uxia Esperón-Moldes
- Fundación Pública Galega de Medicina Xenómica-SERGAS, Grupo de Medicina Xenómica-USC, CIBERER, IDIS, Santiago de Compostela, Spain
- Departamento de Ciencias Forenses, Anatomía Patolóxica, Xinecoloxía, Obstetricia e Pediatría, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Manuel Ginarte-Val
- Dermatology Service of Complexo Hospitalario Universitario de Santiago, Santiago de Compostela, Spain
| | | | - Laura Fachal
- Fundación Pública Galega de Medicina Xenómica-SERGAS, Grupo de Medicina Xenómica-USC, CIBERER, IDIS, Santiago de Compostela, Spain
| | - Ana Martín-Santiago
- Dermatology Service of Hospital Universitari Son Espases, Palma de Mallorca, Spain
| | - Asunción Vicente
- Dermatology Service of Hospital Sant Joan de Déu, Barcelona, Spain
| | | | | | | | | | - Ana Vega
- Fundación Pública Galega de Medicina Xenómica-SERGAS, Grupo de Medicina Xenómica-USC, CIBERER, IDIS, Santiago de Compostela, Spain
- * E-mail:
| |
Collapse
|
15
|
Cheng R, Liang J, Li Y, Zhang J, Ni C, Yu H, Kong X, Li M, Yao Z. Next-generation sequencing through multi-gene panel testing for diagnosis of hereditary ichthyosis in Chinese. Clin Genet 2020; 97:770-778. [PMID: 31953843 DOI: 10.1111/cge.13704] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 01/12/2020] [Accepted: 01/14/2020] [Indexed: 12/22/2022]
Abstract
Inherited ichthyoses are a heterogeneous group of rare disorders related to over 40 genes. To identify underlying molecular causes in inherited ichthyosis among Chinese and to correlate genotype and phenotype, 35 probands clinically diagnosed inherited ichthyosis, except ichthyosis vulgaris and X-linked ichthyosis, were included in our study. Molecular analysis was performed using next-generation sequencing (NGS) through multi-gene panel testing targeting all ichthyosis-related genes. Genetic variants causative for the ichthyosis were identified in 32 of 35 investigated patients. In all, 43 causative mutations across 12 genes were disclosed, including 16 novel variants. Thirteen keratinopathic ichthyosis, fourteen autosomal recessive congenital ichthyosis (ARCI) including one caused by mutations in SDR9C7, and five syndromic ichthyoses were confirmed. Four probands, with presumptive ARCI, turned out to be keratinopathic ichthyosis (2), neutral lipid storage disease (1), and Sjogren-Larsson syndrome (1), respectively. Next-generation technology has been demonstrated to be an effective tool in diagnosing inherited ichthyosis constituting a diverse group of cornification disorders. Our study further expands mutation spectrum and clinical phenotype associated with inherited ichthyosis in Chinese.
Collapse
Affiliation(s)
- Ruhong Cheng
- Department of Dermatology, Xinhua Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Institute of Dermatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jianying Liang
- Department of Dermatology, Xinhua Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Institute of Dermatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yue Li
- Department of Dermatology, Xinhua Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Institute of Dermatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jia Zhang
- Department of Dermatology, Xinhua Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Institute of Dermatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Cheng Ni
- Department of Dermatology, Xinhua Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Institute of Dermatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hong Yu
- Department of Dermatology, Xinhua Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Institute of Dermatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | | | - Ming Li
- Department of Dermatology, Xinhua Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Institute of Dermatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhirong Yao
- Department of Dermatology, Xinhua Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Institute of Dermatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| |
Collapse
|
16
|
Zhuang J, Wang Y, Zeng S, Lv C, Lin Y, Jiang Y. A prenatal diagnosis and genetics study of five pedigrees in the Chinese population with Xp22.31 microduplication. Mol Cytogenet 2019; 12:50. [PMID: 31857824 PMCID: PMC6907354 DOI: 10.1186/s13039-019-0461-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Accepted: 11/26/2019] [Indexed: 11/16/2022] Open
Abstract
Background Copy number variations (CNVs) can contribute to human phenotype, phenotypic diversity and disease susceptibility, while others may benign. In the current study, an attempt to investigate the pathogenicity of CNVs in chromosome Xp22.31 was explored. Methods G-banding and SNP-array techniques were used to analyze chromosome karyotypes and CNVs in fetuses. Parents associate with five different pedigrees possessing high risk factors in pregnancy were considered with such parameters as advanced age, high risk of serological screening and ultrasound abnormalities. Results The fetuses’ amniotic fluid karyotypes were 46, XX and those of their parents with the five pedigrees revealed no abnormalities. Here, we noticed a series of individuals with Xp22.31 duplications ranging from 534.6 kb to 1.6 Mb. It was detected through SNP array that the fetuses in Pedigree 1 and 2 had ~ 600 kb duplications in the Xp22.31 region of their X chromosomes which contained two OMIM genes, HDHD1 (OMIM: 306480) and part of STS (OMIM: 300747). The fetuses of Pedigrees 3, 4 and 5 had 1.6 Mb duplication in the same chromosome which contained four OMIM genes: HDHD1 (OMIM: 306480), STS (OMIM: 300747), PNPLA4 (OMIM: 300102) and VCX (OMIM: 300229). The duplications in the fetuses of Pedigrees 1 and 5 were inherited from the non-phenotypic parents. Pedigrees 3 and 4 refused to perform parental verification. Finally, four of the five pedigrees continue towards pregnancy with no abnormalities being observed during followed-ups. Conclusion Our study first showed duplications of Xp22.31 in Chinese population. Clinical and genetic investigation on five different pedigrees, we consider the duplication of these fragments as likely benign copy number variants (CNVs). We suggest that the duplications of Xp22.31 with recurrent duplication as a benign CNVs .
Collapse
Affiliation(s)
- Jianlong Zhuang
- Prenatal Diagnosis Center, Quanzhou Women's and Children's Hospital, Fujian Province, People's Republic of China
| | - Yuanbai Wang
- Prenatal Diagnosis Center, Quanzhou Women's and Children's Hospital, Fujian Province, People's Republic of China
| | - Shuhong Zeng
- Prenatal Diagnosis Center, Quanzhou Women's and Children's Hospital, Fujian Province, People's Republic of China
| | - Chunling Lv
- Zhejiang Biosan technology Co., Ltd, Zhejiang, People's Republic of China
| | - Yiming Lin
- Neonatal Disease Screening Center of Quanzhou, Quanzhou Women's and Children's Hospital, Fujian Province, People's Republic of China
| | - Yuying Jiang
- Prenatal Diagnosis Center, Quanzhou Women's and Children's Hospital, Fujian Province, People's Republic of China
| |
Collapse
|
17
|
Montalván-Suárez M, Esperón-Moldes US, Rodríguez-Pazos L, Ordóñez-Ugalde A, Moscoso F, Ugalde-Noritz N, Santomé L, Fachal L, Tettamanti-Miranda D, Ruiz JC, Ginarte M, Vega A. A novel ABCA12 pathologic variant identified in an Ecuadorian harlequin ichthyosis patient: A step forward in genotype-phenotype correlations. Mol Genet Genomic Med 2019; 7:e608. [PMID: 30916489 PMCID: PMC6503032 DOI: 10.1002/mgg3.608] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 01/10/2019] [Accepted: 01/24/2019] [Indexed: 11/22/2022] Open
Abstract
Background Autosomal recessive congenital ichthyoses (ARCI) have been associated with different phenotypes including: harlequin ichthyosis (HI), congenital ichthyosiform erythroderma (CIE), and lamellar ichthyosis (LI). While pathogenic variants in all ARCI genes are associated with LI and CIE phenotypes, the unique gene associated with HI is ABCA12. In HI, the most severe ARCI form, pathogenic variants in both ABCA12 gene alleles usually have a severe impact on protein function. The presence of at least one non‐truncating variant frequently causes a less severe congenital ichthyosis phenotype (LI and CIE). Methods We report the case of a 4‐year‐old Ecuadorian boy with a severe skin disease. Genetic diagnosis was performed by NGS. In silico predictions were performed using Alamut software v2.11. A review of the literature was carried out to identify all patients carrying ABCA12 splice‐site and missense variants, and to explore their genotype‐phenotype correlations. Results Genetic testing revealed a nonsense substitution, p.(Arg2204*), and a new missense variant, p.(Val1927Leu), in the ABCA12 gene. After performing in silico analysis and a comprehensive review of the literature, we conclude that p.(Val1927Leu) affects a well conserved residue which could either disturb the protein function or alter the splicing process, both alternatives could explain the severe phenotype of our patient. Conclusion This case expands the spectrum of ABCA12 reported disease‐causing variants which is important to unravel genotype‐phenotype correlations and highlights the importance of missense variants in the development of HI.
Collapse
Affiliation(s)
- Martha Montalván-Suárez
- Sistema de Investigación y Desarrollo SINDE, Universidad Católica de Santiago de Guayaquil and Universidad de Guayaquil, Guayaquil, Ecuador
| | - Uxia Saraiva Esperón-Moldes
- Fundación Pública Galega de Medicina Xenómica-SERGAS, Grupo de Medicina Xenómica-USC, CIBERER, IDIS, Santiago de Compostela, Spain.,Departamento de Ciencias Forenses, Anatomía Patolóxica, Xinecoloxía, Obstetricia e Pediatría, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Laura Rodríguez-Pazos
- Servicio de Dermatología del Complejo Hospitalario Universitario de Vigo, Vigo, Spain
| | - Andrés Ordóñez-Ugalde
- Fundación Pública Galega de Medicina Xenómica-SERGAS, Grupo de Medicina Xenómica-USC, CIBERER, IDIS, Santiago de Compostela, Spain.,Laboratorio Biomolecular, Cuenca, Ecuador.,Unidad de Genética y Molecular del Hospital de Especialidades José Carrasco Arteaga, Cuenca, Ecuador
| | | | - Nora Ugalde-Noritz
- Unidad de Genética y Molecular del Hospital de Especialidades José Carrasco Arteaga, Cuenca, Ecuador
| | - Luis Santomé
- Fundación Pública Galega de Medicina Xenómica-SERGAS, Grupo de Medicina Xenómica-USC, CIBERER, IDIS, Santiago de Compostela, Spain
| | - Laura Fachal
- Fundación Pública Galega de Medicina Xenómica-SERGAS, Grupo de Medicina Xenómica-USC, CIBERER, IDIS, Santiago de Compostela, Spain
| | | | - Juan Carlos Ruiz
- Universidad Espíritu Santo and Hospital Luis Vernaza, Guayaquil, Ecuador.,Instituto de Biomedicina Universidad Católica de Santiago de Guayaquil and Centro de Investigación, Universidad Espíritu Santo, Guayaquil, Ecuador
| | - Manuel Ginarte
- Servicio de Dermatología del Complexo Hospitalario Universitario de Santiago, Facultad de Medicina, Santiago de Compostela, Spain
| | - Ana Vega
- Fundación Pública Galega de Medicina Xenómica-SERGAS, Grupo de Medicina Xenómica-USC, CIBERER, IDIS, Santiago de Compostela, Spain
| |
Collapse
|
18
|
Youssefian L, Vahidnezhad H, Saeidian AH, Touati A, Sotoudeh S, Mahmoudi H, Mansouri P, Daneshpazhooh M, Aghazadeh N, Hesari KK, Basiri M, Londin E, Kumar G, Zeinali S, Fortina P, Uitto J. Autosomal recessive congenital ichthyosis: Genomic landscape and phenotypic spectrum in a cohort of 125 consanguineous families. Hum Mutat 2019; 40:288-298. [PMID: 30578701 DOI: 10.1002/humu.23695] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 10/31/2018] [Accepted: 11/13/2018] [Indexed: 11/06/2022]
Abstract
Autosomal recessive congenital ichthyosis (ARCI), a phenotypically heterogeneous group of non-syndromic Mendelian disorders of keratinization, is caused by mutations in as many as 13 distinct genes. We examined a cohort of 125 consanguineous families with ARCI for underlying genetic mutations. The patients' DNA was analyzed with a gene-targeted next generation sequencing panel comprising 38 ichthyosis associated genes. The interpretations of results of genomic data were assisted by genome-wide homozygosity mapping and transcriptome sequencing. Sequence data analysis identified biallelic mutations in 106 families out of a total of 125 (85%), most of them (102, 96.2%) being homozygous, reflecting consanguinity in these families. Among the 85 distinct mutations in 10 different genes, 45 (53%) were previously unreported. Phenotype-genotype correlations allowed assignment of specific genes in the majority of the families to a specific subtype of ARCI, lamellar ichthyosis (LI) versus congenital ichthyosiform erythroderma (CIE). Interestingly, mutations in several genes could give rise to an overlapping phenotype consistent with either LI or CIE. Also, this is the third report for SDR9C7 and SULT2B1, and fourth report for CERS3 mutations. Direct comparison of our results with previously published regional cohorts highlights the global mutation landscape of ARCI, however, population specific differences were noted.
Collapse
Affiliation(s)
- Leila Youssefian
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, USA.,Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Genetics, Genomics and Cancer Biology PhD Program, Thomas Jefferson University, Philadelphia, PA, USA
| | - Hassan Vahidnezhad
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, USA.,Biotechnology Research Center, Department of Molecular Medicine, Pasteur Institute of Iran, Tehran, Iran
| | - Amir Hossein Saeidian
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, USA.,Genetics, Genomics and Cancer Biology PhD Program, Thomas Jefferson University, Philadelphia, PA, USA
| | - Andrew Touati
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, USA.,Drexel University College of Medicine, Philadelphia, PA, USA
| | - Soheila Sotoudeh
- Department of Dermatology, Children's Medical Center, Pediatric Center of Excellence, Tehran University of Medical Sciences, Tehran, Iran
| | - Hamidreza Mahmoudi
- Department of Dermatology, Razi Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Parvin Mansouri
- Skin and Stem Cell Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Daneshpazhooh
- Department of Dermatology, Razi Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Nessa Aghazadeh
- Department of Dermatology, Razi Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Kambiz Kamyab Hesari
- Pathology Department, Razi Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammadreza Basiri
- School of Medicine, Shahid Sadoughi University of Medical Sciences and Health Sciences, Yazd, Iran
| | - Eric Londin
- Computational Medicine Center, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Gaurav Kumar
- Sidney Kimmel Cancer Center, Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Sirous Zeinali
- Biotechnology Research Center, Department of Molecular Medicine, Pasteur Institute of Iran, Tehran, Iran.,Kawsar Human Genetics Research Center, Tehran, Iran
| | - Paolo Fortina
- Sidney Kimmel Cancer Center, Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA.,Department of Molecular Medicine, Sapienza University, Rome, Italy
| | - Jouni Uitto
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, USA.,Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, PA, USA
| |
Collapse
|
19
|
Pavone P, Corsello G, Marino S, Ruggieri M, Falsaperla R. Microcephaly/Trigonocephaly, Intellectual Disability, Autism Spectrum Disorder, and Atypical Dysmorphic Features in a Boy with Xp22.31 Duplication. Mol Syndromol 2018; 9:253-258. [PMID: 30733660 DOI: 10.1159/000493174] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/06/2018] [Indexed: 12/23/2022] Open
Abstract
The Xp22.31 segment of the short arm of the human X chromosome is a region of high instability with frequent rearrangement. The duplication of this region has been found in healthy people as well as in individuals with varying degrees of neurological impairment. The incidence has been reported in a range of 0.4-0.44% of the patients with neurological impairment. Moreover, there is evidence that Xp22.31 duplication may cause a common phenotype including developmental delay, intellectual disability, feeding difficulty, autistic spectrum disorders, hypotonia, seizures, and talipes. We report on a patient with microcephaly and trigonocephaly, moderate intellectual disability, speech and language delay, and poor social interaction in addition to minor but atypical dysmorphic features. This report provides further insight into the pathogenicity of the Xp22.31 duplication by extending knowledge of its clinical features. This case, in association with those reported in the literature, indicates that the Xp22.31 duplication may contribute to cause pathological phenotypes with minor facial dysmorphisms, microcephaly, and intellectual disability as main features.
Collapse
Affiliation(s)
- Piero Pavone
- Department of Clinical and Experimental Medicine, Section of Pediatrics and Child Neuropsychiatry, A.U.O. Policlinico-Vittorio Emanuele Catania, Catania, Italy
| | - Giovanni Corsello
- Department of Maternal and Child Health, University of Palermo, Palermo, Italy
| | - Silvia Marino
- University Hospital, A.U.O. Policlinico-Vittorio Emanuele Catania, Catania, Italy
| | - Martino Ruggieri
- Unit of Rare Diseases of the Nervous System, Section of Pediatrics and Child Neuropsychiatry, A.U.O. Policlinico-Vittorio Emanuele Catania, Catania, Italy
| | - Raffaele Falsaperla
- University Hospital, A.U.O. Policlinico-Vittorio Emanuele Catania, Catania, Italy
| |
Collapse
|