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Fioretti T, Martora F, De Maggio I, Ambrosio A, Piscopo C, Vallone S, Amato F, Passaro D, Acquaviva F, Gaudiello F, Di Girolamo D, Maiolo V, Zarrilli F, Esposito S, Vitiello G, Auricchio L, Sammarco E, Brasi DD, Petillo R, Gambale A, Cattaneo F, Ammendola R, Nappa P, Esposito G. Comprehensive Molecular Analysis of Disease-Related Genes as First-Tier Test for Early Diagnosis, Classification, and Management of Patients Affected by Nonsyndromic Ichthyosis. Biomedicines 2024; 12:1112. [PMID: 38791074 PMCID: PMC11117922 DOI: 10.3390/biomedicines12051112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 05/07/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
Inherited ichthyoses are a group of clinically and genetically heterogeneous rare disorders of skin keratinization with overlapping phenotypes. The clinical picture and family history are crucial to formulating the diagnostic hypothesis, but only the identification of the genetic defect allows the correct classification. In the attempt to molecularly classify 17 unrelated Italian patients referred with congenital nonsyndromic ichthyosis, we performed massively parallel sequencing of over 50 ichthyosis-related genes. Genetic data of 300 Italian unaffected subjects were also analyzed to evaluate frequencies of putative disease-causing alleles in our population. For all patients, we identified the molecular cause of the disease. Eight patients were affected by autosomal recessive congenital ichthyosis associated with ALOX12B, NIPAL4, and TGM1 mutations. Three patients had biallelic loss-of-function variants in FLG, whereas 6/11 males were affected by X-linked ichthyosis. Among the 24 different disease-causing alleles we identified, 8 carried novel variants, including a synonymous TGM1 variant that resulted in a splicing defect. Moreover, we generated a priority list of the ichthyosis-related genes that showed a significant number of rare and novel variants in our population. In conclusion, our comprehensive molecular analysis resulted in an effective first-tier test for the early classification of ichthyosis patients. It also expands the genetic, mutational, and phenotypic spectra of inherited ichthyosis and provides new insight into the current understanding of etiologies and epidemiology of this group of rare disorders.
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Affiliation(s)
- Tiziana Fioretti
- CEINGE Advanced Biotechnologies Franco Salvatore, 80145 Naples, Italy; (T.F.); (A.A.); (S.V.); (F.A.); (F.Z.); (S.E.)
| | - Fabrizio Martora
- Section of Dermatology, Department of Clinical Medicine and Surgery, School of Medicine, University of Naples “Federico II”, 80131 Naples, Italy; (F.M.); (F.G.); (L.A.); (P.N.)
| | - Ilaria De Maggio
- Medical and Laboratory Genetics Unit, AORN A. Cardarelli, 80131 Naples, Italy; (I.D.M.); (C.P.); (R.P.)
| | - Adelaide Ambrosio
- CEINGE Advanced Biotechnologies Franco Salvatore, 80145 Naples, Italy; (T.F.); (A.A.); (S.V.); (F.A.); (F.Z.); (S.E.)
| | - Carmelo Piscopo
- Medical and Laboratory Genetics Unit, AORN A. Cardarelli, 80131 Naples, Italy; (I.D.M.); (C.P.); (R.P.)
| | - Sabrina Vallone
- CEINGE Advanced Biotechnologies Franco Salvatore, 80145 Naples, Italy; (T.F.); (A.A.); (S.V.); (F.A.); (F.Z.); (S.E.)
- Department of Molecular Medicine and Medical Biotechnologies, School of Medicine, University of Naples “Federico II”, 80131 Naples, Italy; (D.P.); (V.M.); (F.C.); (R.A.)
| | - Felice Amato
- CEINGE Advanced Biotechnologies Franco Salvatore, 80145 Naples, Italy; (T.F.); (A.A.); (S.V.); (F.A.); (F.Z.); (S.E.)
- Department of Molecular Medicine and Medical Biotechnologies, School of Medicine, University of Naples “Federico II”, 80131 Naples, Italy; (D.P.); (V.M.); (F.C.); (R.A.)
| | - Diego Passaro
- Department of Molecular Medicine and Medical Biotechnologies, School of Medicine, University of Naples “Federico II”, 80131 Naples, Italy; (D.P.); (V.M.); (F.C.); (R.A.)
| | - Fabio Acquaviva
- Medical Genetics Unit, Department of General and Emergency Paediatrics, AORN Santobono-Pausilipon, 80122 Naples, Italy; (F.A.); (D.D.B.)
| | - Francesca Gaudiello
- Section of Dermatology, Department of Clinical Medicine and Surgery, School of Medicine, University of Naples “Federico II”, 80131 Naples, Italy; (F.M.); (F.G.); (L.A.); (P.N.)
| | - Daniela Di Girolamo
- Department of Biology, University of Naples “Federico II”, 80126 Naples, Italy;
| | - Valeria Maiolo
- Department of Molecular Medicine and Medical Biotechnologies, School of Medicine, University of Naples “Federico II”, 80131 Naples, Italy; (D.P.); (V.M.); (F.C.); (R.A.)
| | - Federica Zarrilli
- CEINGE Advanced Biotechnologies Franco Salvatore, 80145 Naples, Italy; (T.F.); (A.A.); (S.V.); (F.A.); (F.Z.); (S.E.)
- Department of Molecular Medicine and Medical Biotechnologies, School of Medicine, University of Naples “Federico II”, 80131 Naples, Italy; (D.P.); (V.M.); (F.C.); (R.A.)
| | - Speranza Esposito
- CEINGE Advanced Biotechnologies Franco Salvatore, 80145 Naples, Italy; (T.F.); (A.A.); (S.V.); (F.A.); (F.Z.); (S.E.)
- Department of Molecular Medicine and Medical Biotechnologies, School of Medicine, University of Naples “Federico II”, 80131 Naples, Italy; (D.P.); (V.M.); (F.C.); (R.A.)
| | - Giuseppina Vitiello
- Medical Genetics Unit, Integrated Care Department of Laboratory and Transfusion Medicine, Federico II Hospital, 80131 Naples, Italy; (G.V.); (A.G.)
| | - Luigi Auricchio
- Section of Dermatology, Department of Clinical Medicine and Surgery, School of Medicine, University of Naples “Federico II”, 80131 Naples, Italy; (F.M.); (F.G.); (L.A.); (P.N.)
| | - Elena Sammarco
- Pediatric Dermatology Unit, Department of Dermo-Immuno-Rheumatology Paediatrics, AORN Santobono-Pausilipon, 80122 Naples, Italy;
| | - Daniele De Brasi
- Medical Genetics Unit, Department of General and Emergency Paediatrics, AORN Santobono-Pausilipon, 80122 Naples, Italy; (F.A.); (D.D.B.)
| | - Roberta Petillo
- Medical and Laboratory Genetics Unit, AORN A. Cardarelli, 80131 Naples, Italy; (I.D.M.); (C.P.); (R.P.)
| | - Antonella Gambale
- Medical Genetics Unit, Integrated Care Department of Laboratory and Transfusion Medicine, Federico II Hospital, 80131 Naples, Italy; (G.V.); (A.G.)
| | - Fabio Cattaneo
- Department of Molecular Medicine and Medical Biotechnologies, School of Medicine, University of Naples “Federico II”, 80131 Naples, Italy; (D.P.); (V.M.); (F.C.); (R.A.)
| | - Rosario Ammendola
- Department of Molecular Medicine and Medical Biotechnologies, School of Medicine, University of Naples “Federico II”, 80131 Naples, Italy; (D.P.); (V.M.); (F.C.); (R.A.)
| | - Paola Nappa
- Section of Dermatology, Department of Clinical Medicine and Surgery, School of Medicine, University of Naples “Federico II”, 80131 Naples, Italy; (F.M.); (F.G.); (L.A.); (P.N.)
| | - Gabriella Esposito
- CEINGE Advanced Biotechnologies Franco Salvatore, 80145 Naples, Italy; (T.F.); (A.A.); (S.V.); (F.A.); (F.Z.); (S.E.)
- Department of Molecular Medicine and Medical Biotechnologies, School of Medicine, University of Naples “Federico II”, 80131 Naples, Italy; (D.P.); (V.M.); (F.C.); (R.A.)
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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.
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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.
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Park JS, Saeidian AH, Youssefian L, Kondratuk KE, Pride HB, Vahidnezhad H, Uitto J. Inherited ichthyosis as a paradigm of rare skin disorders: Genomic medicine, pathogenesis, and management. J Am Acad Dermatol 2023; 89:1215-1226. [PMID: 35963288 DOI: 10.1016/j.jaad.2022.08.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 08/02/2022] [Accepted: 08/05/2022] [Indexed: 11/26/2022]
Abstract
Great advances have been made in the field of heritable skin disorders using next-generation sequencing (NGS) technologies (ie, whole-genome sequencing, whole-exome sequencing, whole-transcriptome sequencing, and disease-targeted multigene panels). When NGS first became available, the cost and lack of access to these technologies were limiting factors; however, with decreasing sequencing costs and the expanding knowledge base of genetic skin diseases, fundamental awareness of NGS has become prudent. The heritable ichthyoses comprise a genotypically and phenotypically heterogeneous group of monogenic keratinization disorders characterized by persistent scaling, with at least 55 distinct genes currently implicated in causing nonsyndromic and syndromic forms of the disease. By providing a simplified overview of available NGS techniques and applying them in the context of ichthyosis, one of the most common genodermatoses, we hope to encourage dermatologists to offer, when appropriate, genetic testing earlier in patients with unsolved presentations. With the aid of NGS, dermatologists can provide diagnostic certainty in cases of suspected genodermatoses and offer potentially life-changing genome-guided and targeted therapies as they become available.
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Affiliation(s)
- Jason S Park
- Department of Dermatology and Cutaneous Biology, Thomas Jefferson University, Philadelphia, Pennsylvania; Geisinger Commonwealth School of Medicine, Scranton, Pennsylvania; Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Amir Hossein Saeidian
- Department of Dermatology and Cutaneous Biology, Thomas Jefferson University, Philadelphia, Pennsylvania; Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Leila Youssefian
- Department of Dermatology and Cutaneous Biology, Thomas Jefferson University, Philadelphia, Pennsylvania; Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania
| | | | - Howard B Pride
- Department of Dermatology, Geisinger Medical Center, Danville, Pennsylvania
| | - Hassan Vahidnezhad
- Department of Dermatology and Cutaneous Biology, Thomas Jefferson University, Philadelphia, Pennsylvania; Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania.
| | - Jouni Uitto
- Department of Dermatology and Cutaneous Biology, Thomas Jefferson University, Philadelphia, Pennsylvania; Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania.
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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: 0] [Impact Index Per Article: 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.
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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
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5
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Zagoras T, Inci R, Kantere D, Holmström P, Broström J, Gillstedt M, Polesie S, Peltonen S. Incidence and Prevalence of 73 Different Genodermatoses: A Nationwide Study in Sweden. Acta Derm Venereol 2023; 103:adv12404. [PMID: 37615526 PMCID: PMC10464823 DOI: 10.2340/actadv.v103.12404] [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: 05/02/2023] [Accepted: 07/11/2023] [Indexed: 08/25/2023] Open
Abstract
This retrospective registry-based cohort study aimed to estimate the incidence and prevalence of genodermatoses in the Swedish population and to analyse associated healthcare usage. Patients diagnosed with genodermatoses were identified from the patient registry of Sahlgrenska University Hospital (Gothenburg, Sweden) between 2016 and 2020. Clinical data from medical records were used to verify diagnoses recorded in the National Patient Registry (NPR). The NPR was then searched for International Classification of Diseases, Tenth Revision (ICD-10) codes Q80-82 and Q84 from 2001 to 2020. The local cohort included 298 patients with 36 unique genodermatosis diagnoses. Verification of these diagnoses in the NPR showed positive predictive values of over 90%. The NPR search yielded 13,318 patients with 73 unique diagnoses, including ichthyoses (n = 3,341; 25%), porokeratosis (n = 2,277; 17%), palmoplantar keratodermas (n = 1,754; 13%), the epidermolysis bullosa group (n = 1011; 7%); Darier disease (n = 770; 6%), Hailey-Hailey disease (n = 477; 4%) and Gorlin syndrome (n = 402; 3%). The incidence and prevalence of each diagnosis were calculated based on the nationwide cohort and are reported. A total of 149,538 outpatient visits were registered, a mean of 4.6 visits per patient. This study provides a valuable resource for the epidemiology of genodermatoses by reporting on the incidence and prevalence of 73 different genodermatoses.
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Affiliation(s)
- Theofanis Zagoras
- Department of Dermatology and Venereology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Region Västra Götaland, Sahlgrenska University Hospital, Department of Clinical Genetics and Genomics, Gothenburg, Sweden
| | - Rahime Inci
- Department of Dermatology and Venereology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Region Västra Götaland, Sahlgrenska University Hospital, Department of Dermatology and Venereology, Gothenburg, Sweden
| | - Despoina Kantere
- Department of Dermatology and Venereology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Region Västra Götaland, Sahlgrenska University Hospital, Department of Dermatology and Venereology, Gothenburg, Sweden
| | - Peter Holmström
- Department of Dermatology and Venereology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Jenny Broström
- Department of Dermatology and Venereology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Martin Gillstedt
- Department of Dermatology and Venereology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Region Västra Götaland, Sahlgrenska University Hospital, Department of Dermatology and Venereology, Gothenburg, Sweden
| | - Sam Polesie
- Department of Dermatology and Venereology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Region Västra Götaland, Sahlgrenska University Hospital, Department of Dermatology and Venereology, Gothenburg, Sweden
| | - Sirkku Peltonen
- Department of Dermatology and Venereology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Region Västra Götaland, Sahlgrenska University Hospital, Department of Dermatology and Venereology, Gothenburg, Sweden
- Department of Dermatology and Allergology, University of Helsinki, Helsinki, Finland
- Skin and Allergy Hospital, Helsinki University Hospital, Helsinki, Finland.
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Xintong Z, Kexin Z, Junwen W, Ziyi W, Na L, Hong G. Whole-exome sequencing enables rapid and prenatal diagnosis of inherited skin disorders. BMC Med Genomics 2023; 16:193. [PMID: 37605172 PMCID: PMC10440863 DOI: 10.1186/s12920-023-01628-2] [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: 08/21/2022] [Accepted: 08/07/2023] [Indexed: 08/23/2023] Open
Abstract
BACKGROUND Genodermatoses are a broad group of disorders with specific or non-specific skin-based phenotypes, most of which are monogenic disorders. However, it's a great challenge to make a precise molecular diagnosis because of the clinical heterogeneity. The genetic and clinical heterogeneity brings great challenges for diagnosis in dermatology. The whole exome sequencing (WES) not only expedites the discovery of the genetic variations, but also contributes to genetic counselling and prenatal diagnosis. MATERIALS AND METHODS Followed by the initial clinical and pathological diagnosis, genetic variations were identified by WES. The pathogenicity of the copy number variations (CNVs) and single-nucleotide variants (SNVs) were evaluated according to ACMG guidelines. Candidate pathogenic SNVs were confirmed by Sanger sequencing in the proband and the family members. RESULTS Totally 25 cases were recruited. Nine novel variations, including c.5546G > C and c.1457delC in NF1, c.6110G > T in COL7A1, c.2127delG in TSC1, c.1445 C > A and c.1265G > A in TYR, Xp22.31 deletion in STS, c.908 C > T in ATP2A2, c.1371insC in IKBKG, and nine known ones were identified in 16 cases (64%). Prenatal diagnosis was applied in 6 pregnant women by amniocentesis, two of whom carried positive findings. CONCLUSIONS Our findings highlighted the value of WES as a first-tier genetic test in determining the molecular diagnosis. We also discovered the distribution of genodermatoses in this district, which provided a novel clinical dataset for dermatologists.
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Affiliation(s)
- Zhu Xintong
- Department of Medical Genetics, College of Basic Medical Science, Army Medical University, 30# Gaotanyan St., Shapingba District, Chongqing, 400038, P.R. China
| | - Zhang Kexin
- Department of Dermatology, Southwest Hospital, Army Medical University, 30# Gaotanyan St., Shapingba District, Chongqing, 400038, P.R. China
| | - Wang Junwen
- Department of Medical Genetics, College of Basic Medical Science, Army Medical University, 30# Gaotanyan St., Shapingba District, Chongqing, 400038, P.R. China
| | - Wang Ziyi
- Department of Medical Genetics, College of Basic Medical Science, Army Medical University, 30# Gaotanyan St., Shapingba District, Chongqing, 400038, P.R. China
| | - Luo Na
- Department of Dermatology, Southwest Hospital, Army Medical University, 30# Gaotanyan St., Shapingba District, Chongqing, 400038, P.R. China.
| | - Guo Hong
- Department of Medical Genetics, College of Basic Medical Science, Army Medical University, 30# Gaotanyan St., Shapingba District, Chongqing, 400038, P.R. China.
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Rayinda T, Trisnowati N, Danarti R. Current challenges of genodermatosis in a limited-resource country: An Indonesian perspective. Int J Dermatol 2023; 62:e109-e111. [PMID: 36331132 DOI: 10.1111/ijd.16490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 10/08/2022] [Accepted: 10/20/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Tuntas Rayinda
- Department of Dermatology and Venereology, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia.,Department of Dermatology and Venereology, Dr Sardjito General Hospital, Yogyakarta, Indonesia
| | - Niken Trisnowati
- Department of Dermatology and Venereology, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia.,Department of Dermatology and Venereology, Dr Sardjito General Hospital, Yogyakarta, Indonesia
| | - Retno Danarti
- Department of Dermatology and Venereology, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia.,Department of Dermatology and Venereology, Dr Sardjito General Hospital, Yogyakarta, Indonesia
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8
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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.
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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
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9
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Overview of familial syndromes with increased skin malignancies. Arch Dermatol Res 2022; 315:707-727. [PMID: 36342513 DOI: 10.1007/s00403-022-02447-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 10/21/2022] [Indexed: 11/09/2022]
Abstract
The vast majority of skin cancers can be classified into two main types: melanoma and keratinocyte carcinomas. The most common keratinocyte carcinomas include basal cell carcinoma (BCC) and squamous cell carcinoma (SCC). Multiple familial syndromes have been identified that can increase the risk of developing SCC, BCC, and/or melanoma. The major syndromes include oculocutaneous albinism for SCC, basal cell nevus syndrome for BCC, familial atypical multiple mole-melanoma syndrome, and hereditary breast and ovarian cancer syndrome for melanoma. In addition, familial syndromes that can predispose individuals to all three major skin cancers include xeroderma pigmentosum and Li-Fraumeni syndrome. This review highlights the epidemiology, risk factors, pathogenesis, and etiology of the major and minor syndromes to better identify and manage these conditions. Current investigational trials in genomic medicine are making their way in revolutionizing the clinical diagnosis of these familial syndromes for earlier preventative measures and improvement of long-term prognosis in these patients.
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RSDB: A rare skin disease database to link drugs with potential drug targets for rare skin diseases. Sci Data 2022; 9:521. [PMID: 36028515 PMCID: PMC9418253 DOI: 10.1038/s41597-022-01654-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 08/19/2022] [Indexed: 11/09/2022] Open
Abstract
Rare skin diseases include more than 800 diseases affecting more than 6.8 million patients worldwide. However, only 100 drugs have been developed for treating rare skin diseases in the past 38 years. To investigate potential treatments through drug repurposing for rare skin diseases, it is necessary to have a well-organized database to link all known disease causes, mechanisms, and related information to accelerate the process. Drug repurposing provides less expensive and faster potential options to develop treatments for known diseases. In this work, we designed and constructed a rare skin disease database (RSDB) as a disease-centered information depository to facilitate repurposing drug candidates for rare skin diseases. We collected and integrated associated genes, chemicals, and phenotypes into a network connected by pairwise relationships between different components for rare skin diseases. The RSDB covers 891 rare skin diseases defined by the Orphanet and GARD databases. The organized network for each rare skin disease comprises associated genes, phenotypes, and chemicals with the corresponding connections. The RSDB is available at https://rsdb.cmdm.tw .
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Lee YR, Lin YC, Chang YH, Huang HY, Hong YK, Aala WJF, Tu WT, Tsai MC, Chou YY, Hsu CK. Genetic Diagnosis of Rubinstein–Taybi Syndrome With Multiplex Ligation-Dependent Probe Amplification (MLPA) and Whole-Exome Sequencing (WES): Case Series With a Novel CREBBP Variant. Front Genet 2022; 13:848879. [PMID: 35464843 PMCID: PMC9024331 DOI: 10.3389/fgene.2022.848879] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 03/15/2022] [Indexed: 11/13/2022] Open
Abstract
Rubinstein–Taybi Syndrome (RSTS) is a rare congenital disease with distinctive facial features, broadening of the thumbs and halluces, and developmental delay. RSTS is caused by de novo genetic alterations in CREBBP and the homologous EP300 genes. In this study, we established a genetic diagnostic protocol by integrating multiplex ligation-dependent probe amplification (MLPA) and whole-exome sequencing (WES). Five patients clinically diagnosed with RSTS were enrolled for genetic testing. Germline DNA was extracted from the peripheral blood of the patients and their families. One patient (case 1) was identified as harboring a large heterozygous deletion in the 16p13.3 region, spanning the CREBBP gene. Three patients (Cases 2–4) harbored different CREBBP variants (c.2608C>T:p.Gln870Ter,c.4404_4405del:p.Thr1468fs,c.3649C>T:p.Gln1217Ter). No causative variants were identified for the fifth RSTS patient (case 5). Here, we propose a molecular diagnostic protocol that identified causative genetic alterations in 4/5 of the patients, yielding a molecular diagnostic rate of 80%. Given the rarity of RSTS, more research is needed to explore its pathogenesis and mechanism.
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Affiliation(s)
- Yu-Rong Lee
- Department of Dermatology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- School of Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yu-Chen Lin
- Department of Dermatology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- International Center of Wound Repair and Regeneration, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yi-Han Chang
- Department of Dermatology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Education Center, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Hsin-Yu Huang
- Department of Dermatology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yi-Kai Hong
- Department of Dermatology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- International Center of Wound Repair and Regeneration, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Wilson Jr F. Aala
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Wei-Ting Tu
- Department of Dermatology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Meng-Che Tsai
- Department of Pediatrics, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yen-Yin Chou
- Department of Pediatrics, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chao-Kai Hsu
- Department of Dermatology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- International Center of Wound Repair and Regeneration, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- *Correspondence: Chao-Kai Hsu,
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Has C. Molecular diagnostics in dermatology. J Dtsch Dermatol Ges 2022; 20:251-252. [PMID: 35304963 DOI: 10.1111/ddg.14760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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13
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Has C. Molekulare Diagnostik in der Dermatologie. J Dtsch Dermatol Ges 2022; 20:251-252. [PMID: 35304952 DOI: 10.1111/ddg.14760_g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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14
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Picchetta L, Caroselli S, Figliuzzi M, Cogo F, Zambon P, Costa M, Pergher I, Patassini C, Cortellessa F, Zuccarello D, Poli M, Capalbo A. Molecular tools for the genomic assessment of oocyte’s reproductive competence. J Assist Reprod Genet 2022; 39:847-860. [PMID: 35124783 PMCID: PMC9050973 DOI: 10.1007/s10815-022-02411-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 01/24/2022] [Indexed: 12/15/2022] Open
Abstract
The most important factor associated with oocytes' developmental competence has been widely identified as the presence of chromosomal abnormalities. However, growing application of genome-wide sequencing (GS) in population diagnostics has enabled the identification of multifactorial genetic predispositions to sub-lethal pathologies, including those affecting IVF outcomes and reproductive fitness. Indeed, GS analysis in families with history of isolated infertility has recently led to the discovery of new genes and variants involved in specific human infertility endophenotypes that impact the availability and the functionality of female gametes by altering unique mechanisms necessary for oocyte maturation and early embryo development. Ongoing advancements in analytical and bioinformatic pipelines for the study of the genetic determinants of oocyte competence may provide the biological evidence required not only for improving the diagnosis of isolated female infertility but also for the development of novel preventive and therapeutic approaches for reproductive failure. Here, we provide an updated discussion and review of the progresses made in preconception genomic medicine in the identification of genetic factors associated with oocyte availability, function, and competence.
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Onoufriadis A, McGrath JA. ESDR 50th Anniversary Lecture summary: The past and future of rare skin disease research/therapy. J Invest Dermatol 2022; 142:1010-1014. [DOI: 10.1016/j.jid.2021.11.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/16/2021] [Accepted: 11/18/2021] [Indexed: 10/19/2022]
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16
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[The skin microbiome as a natural protection factor : Insights from basic research]. Hautarzt 2021; 72:563-569. [PMID: 34115160 PMCID: PMC8193591 DOI: 10.1007/s00105-021-04831-3] [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] [Accepted: 05/06/2021] [Indexed: 11/12/2022]
Abstract
Hintergrund Eine neue Generation von Technologien deckt eine große Zahl von Mikroorganismen auf, die mit der Haut in einer engen und oft funktionellen Beziehung stehen. Störungen dieser Partnerschaft haben erhebliche Konsequenzen. Seit Jahrzehnten schreitet die Verarmung des Mikrobioms im Zuge eines modernen, globalisierten Lebensstils voran. Bei der Aufrechterhaltung der Gesundheit sind neben den genetischen Aspekten auch die auf der Haut und anderen Organen lebenden Mikroben zu berücksichtigen. Alle Epithelien einschließlich der Haut sind mit einer Vielzahl von Mikroben besiedelt. Fragestellung Betrachtet wird die Funktion des Mikrobioms in der Haut und anderen Organen. Material und Methode Es erfolgt eine Diskussion von Grundlagenarbeiten. Ergebnisse Das Mikrobiom der Haut ist für die Aufrechterhaltung der Gesundheit von großer Bedeutung. Schlussfolgerungen Wir brauchen das Verständnis unseres Körpers als multiorganismischer Metaorganismus, um intelligent auf die Herausforderungen einer sich immer rascher ändernden Umwelt reagieren zu können.
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Ying Y, Lu L, Banerjee S, Xu L, Zhao Q, Wu H, Li R, Xu X, Yu H, Neculai D, Xi Y, Yang F, Qin J, Li C. KVarPredDB: a database for predicting pathogenicity of missense sequence variants of keratin genes associated with genodermatoses. Hum Genomics 2020; 14:45. [PMID: 33287903 PMCID: PMC7720490 DOI: 10.1186/s40246-020-00295-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 11/25/2020] [Indexed: 12/17/2022] Open
Abstract
Background Germline variants of ten keratin genes (K1, K2, K5, K6A, K6B, K9, K10, K14, K16, and K17) have been reported for causing different types of genodermatoses with an autosomal dominant mode of inheritance. Among all the variants of these ten keratin genes, most of them are missense variants. Unlike pathogenic and likely pathogenic variants, understanding the clinical importance of novel missense variants or variants of uncertain significance (VUS) is the biggest challenge for clinicians or medical geneticists. Functional characterization is the only way to understand the clinical association of novel missense variants or VUS but it is time consuming, costly, and depends on the availability of patient’s samples. Existing databases report the pathogenic variants of the keratin genes, but never emphasize the systematic effects of these variants on keratin protein structure and genotype-phenotype correlation. Results To address this need, we developed a comprehensive database KVarPredDB, which contains information of all ten keratin genes associated with genodermatoses. We integrated and curated 400 reported pathogenic missense variants as well as 4629 missense VUS. KVarPredDB predicts the pathogenicity of novel missense variants as well as to understand the severity of disease phenotype, based on four criteria; firstly, the difference in physico-chemical properties between the wild type and substituted amino acids; secondly, the loss of inter/intra-chain interactions; thirdly, evolutionary conservation of the wild type amino acids and lastly, the effect of the substituted amino acids in the heptad repeat. Molecular docking simulations based on resolved crystal structures were adopted to predict stability changes and get the binding energy to compare the wild type protein with the mutated one. We use this basic information to determine the structural and functional impact of novel missense variants on the keratin coiled-coil heterodimer. KVarPredDB was built under the integrative web application development framework SSM (SpringBoot, Spring MVC, MyBatis) and implemented in Java, Bootstrap, React-mutation-mapper, MySQL, Tomcat. The website can be accessed through http://bioinfo.zju.edu.cn/KVarPredDB. The genomic variants and analysis results are freely available under the Creative Commons license. Conclusions KVarPredDB provides an intuitive and user-friendly interface with computational analytical investigation for each missense variant of the keratin genes associated with genodermatoses.
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Affiliation(s)
- Yuyi Ying
- Department of Human Genetics, and Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Genetic & Developmental Disorders, Zhejiang University School of Medicine, Hangzhou, China
| | - Lu Lu
- Department of Human Genetics, and Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Genetic & Developmental Disorders, Zhejiang University School of Medicine, Hangzhou, China
| | - Santasree Banerjee
- Department of Genetics, College of Basic Medical Sciences, Jilin University, Changchun, 130021, Jilin, China
| | - Lizhen Xu
- Department of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou, China
| | - Qiang Zhao
- Department of Human Genetics, and Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Genetic & Developmental Disorders, Zhejiang University School of Medicine, Hangzhou, China
| | - Hao Wu
- Department of Human Genetics, and Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Genetic & Developmental Disorders, Zhejiang University School of Medicine, Hangzhou, China
| | - Ruiqi Li
- Chu Kochen Honors College, Undergraduate School of Zhejiang University, Hangzhou, China
| | - Xiao Xu
- Department of Human Genetics, and Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Genetic & Developmental Disorders, Zhejiang University School of Medicine, Hangzhou, China
| | - Hua Yu
- Department of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou, China
| | - Dante Neculai
- Department of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou, China
| | - Yongmei Xi
- Department of Human Genetics, and Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Genetic & Developmental Disorders, Zhejiang University School of Medicine, Hangzhou, China
| | - Fan Yang
- Department of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou, China
| | - Jiale Qin
- Department of Ultrasound, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Chen Li
- Department of Human Genetics, and Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China. .,Zhejiang Provincial Key Laboratory of Genetic & Developmental Disorders, Zhejiang University School of Medicine, Hangzhou, China.
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