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Zhu X, Shen X, Jiang X, Wei K, He T, Ma Y, Liu J, Hu X. Nonlinear expression and visualization of nonmetric relationships in genetic diseases and microbiome data. BMC Bioinformatics 2018; 19:505. [PMID: 30577738 PMCID: PMC6302369 DOI: 10.1186/s12859-018-2537-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Background The traditional methods of visualizing high-dimensional data objects in low-dimensional metric spaces are subject to the basic limitations of metric space. These limitations result in multidimensional scaling that fails to faithfully represent non-metric similarity data. Results Multiple maps t-SNE (mm-tSNE) has drawn much attention due to the construction of multiple mappings in low-dimensional space to visualize the non-metric pairwise similarity to eliminate the limitations of a single metric map. mm-tSNE regularization combines the intrinsic geometry between data points in a high-dimensional space. The weight of data points on each map is used as the regularization parameter of the manifold, so the weights of similar data points on the same map are also as close as possible. However, these methods use standard momentum methods to calculate parameters of gradient at each iteration, which may lead to erroneous gradient search directions so that the target loss function fails to achieve a better local minimum. In this article, we use a Nesterov momentum method to learn the target loss function and correct each gradient update by looking back at the previous gradient in the candidate search direction. By using indirect second-order information, the algorithm obtains faster convergence than the original algorithm. To further evaluate our approach from a comparative perspective, we conducted experiments on several datasets including social network data, phenotype similarity data, and microbiomic data. Conclusions The experimental results show that the proposed method achieves better results than several versions of mm-tSNE based on three evaluation indicators including the neighborhood preservation ratio (NPR), error rate and time complexity.
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Affiliation(s)
- Xianchao Zhu
- School of Computer, Central China Normal University, Wuhan, China
| | - Xianjun Shen
- School of Computer, Central China Normal University, Wuhan, China.
| | - Xingpeng Jiang
- School of Computer, Central China Normal University, Wuhan, China
| | - Kaiping Wei
- School of Computer, Central China Normal University, Wuhan, China
| | - Tingting He
- School of Computer, Central China Normal University, Wuhan, China
| | - Yuanyuan Ma
- School of Computer, Central China Normal University, Wuhan, China
| | - Jiaqi Liu
- School of Computer, Central China Normal University, Wuhan, China
| | - Xiaohua Hu
- School of Computer, Central China Normal University, Wuhan, China.,College of Computing and Informatics, Drexel University, Philadelphia, PA, 19104, USA
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Chopra A, Mitra D, Kandpal R, Agarwal R. Rare Variant of Ankyloblepharon-ectodermal Defect-cleft Lip/Cleft Palate Syndrome: Curly Hair-ankyloblepharon-nail Disease Syndrome. Int J Trichology 2018; 10:17-20. [PMID: 29440852 PMCID: PMC5803846 DOI: 10.4103/ijt.ijt_55_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Ankyloblepharon-ectodermal defect-cleft lip/cleft palate (AEC) syndrome is one of the variants of ectodermal dysplasia. It is an autosomal dominant disorder comprising of ankyloblepharon, ectodermal dysplasia, and cleft palate or cleft lip. In 1976, it wasfirst described by Hay and Wells, therefore also known as Hay–Wells syndrome. The characteristic feature of this syndrome is “ankyloblepharon filiforme adnatum”, which refers to the partial thickness fusion of the eyelid margins. The “curly hair-ankyloblepharon-nail disease (CHAND) syndrome” is a clinical variant of AEC syndrome. We report a rare case of a 7-year-old girl child who presented with history of abnormal dentition, 20 nail dystrophy, and light-colored, sparse curly hairs since birth. Parents gave history that at the time of birth, her both eyelids were fused partially, which was surgically corrected by an ophthalmologist at 1 month of age. There was no history of hypohidrosis or anhidrosis, heat intolerance, cleft lip or cleft palate. Microscopy of the hair shaft found “bubbly hair” morphology. This case is unique as it is a rare presentation, and awareness should be there for this constellation of findings so that the systemic associations can be investigated. “Bubble hair” morphology on microscopy is a unique feature in this rare autosomal recessive condition.
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Affiliation(s)
- Ajay Chopra
- Department of Dermatology, Base Hospital Delhi Cantt, New Delhi, India
| | - Debdeep Mitra
- Department of Dermatology, Base Hospital Delhi Cantt, New Delhi, India
| | - Renu Kandpal
- Department of Dermatology, Base Hospital Delhi Cantt, New Delhi, India
| | - Reetu Agarwal
- Department of Dermatology, Base Hospital Delhi Cantt, New Delhi, India
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Busa T, Jeraiby M, Clémenson A, Manouvrier S, Granados V, Philip N, Touraine R. Confirmation that RIPK4
mutations cause not only Bartsocas-Papas syndrome but also CHAND syndrome. Am J Med Genet A 2017; 173:3114-3117. [DOI: 10.1002/ajmg.a.38475] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 08/03/2017] [Accepted: 08/21/2017] [Indexed: 12/12/2022]
Affiliation(s)
- Tiffany Busa
- Unité de génétique clinique, APHM; CHU Timone-Enfants; Marseille France
| | - Mohammed Jeraiby
- Service de Génétique Clinique, Chromosomique et Moléculaire; CHU-Hôpital Nord; Saint Etienne France
| | - Alix Clémenson
- Service d'Anatomie et Cytologie Pathologiques; CHU-Hôpital Nord; Saint Etienne France
| | - Sylvie Manouvrier
- Service de Génétique médicale; Hôpital Jeanne de Flandre; CHRU de Lille; Lille France
| | - Viviana Granados
- Service de Génétique Clinique, Chromosomique et Moléculaire; CHU-Hôpital Nord; Saint Etienne France
| | - Nicole Philip
- Unité de génétique clinique, APHM; CHU Timone-Enfants; Marseille France
| | - Renaud Touraine
- Service de Génétique Clinique, Chromosomique et Moléculaire; CHU-Hôpital Nord; Saint Etienne France
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Gollasch B, Basmanav FB, Nanda A, Fritz G, Mahmoudi H, Thiele H, Wehner M, Wolf S, Altmüller J, Nürnberg P, Frank J, Betz RC. Identification of a novel mutation inRIPK4in a kindred with phenotypic features of Bartsocas-Papas and CHAND syndromes. Am J Med Genet A 2015; 167A:2555-62. [DOI: 10.1002/ajmg.a.37233] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 06/15/2015] [Indexed: 12/15/2022]
Affiliation(s)
| | | | - Arti Nanda
- Genetic Skin Diseases Clinic; As'ad Al-Hamad Dermatology Center; Al-Sabah Hospital Kuwait
| | - Günter Fritz
- Department of Neuropathology; Neurozentrum; University of Freiburg; Freiburg Germany
| | | | - Holger Thiele
- Cologne Center for Genomics (CCG); University of Cologne; Cologne Germany
| | - Maria Wehner
- Institute of Human Genetics; University of Bonn; Bonn Germany
| | - Sabrina Wolf
- Institute of Human Genetics; University of Bonn; Bonn Germany
| | - Janine Altmüller
- Cologne Center for Genomics (CCG); University of Cologne; Cologne Germany
- Institute of Human Genetics; University of Cologne; Cologne Germany
| | - Peter Nürnberg
- Cologne Center for Genomics (CCG); University of Cologne; Cologne Germany
- Cluster of Excellence on Cellular Stress Responses in Aging-Associated Diseases (CECAD); University of Cologne; Cologne Germany
- Center for Molecular Medicine Cologne (CMMC); University of Cologne; Cologne Germany
| | - Jorge Frank
- Division of Dermatogenetics and Skin Cancer Center; Department of Dermatology; University of Düsseldorf; Düsseldorf Germany
| | - Regina C. Betz
- Institute of Human Genetics; University of Bonn; Bonn Germany
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5
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Abstract
Hay-Wells syndrome is a rare form of ectodermal dysplasia initially described by Hay and Wells in 1976. It is an autosomal dominant disorder with varying forms of expression featuring congenital abnormalities of the skin, hair, teeth, nails and sweat glands. The present report describes the case of a 17-year old white boy, the son of nonconsanguineous parents, who presented ankyloblepharon filiforme adnatum, ectodermal dysplasia and a cleft palate at birth, which are considered cardinal signs of this syndrome by most authors. We also highlight the importance of implementing multidisciplinary follow-up of these patients.
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6
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Simeonsson RJ. Classifying functional manifestations of ectodermal dysplasias. Am J Med Genet A 2009; 149A:2014-9. [DOI: 10.1002/ajmg.a.32991] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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7
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Garcia Bartels N, Neumann LM, Mleczko A, Rubach K, Peters H, Rossi R, Sterry W, Blume-Peytavi U. Hay-Wells syndrome in a child with mutation in the TP73L gene. J Dtsch Dermatol Ges 2007; 5:919-23. [PMID: 17910675 DOI: 10.1111/j.1610-0387.2007.06379.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hay-Wells syndrome is a rare form of ectodermal dysplasia, also known as AEC syndrome (Ankyloblepharon filiforme adnatum, Ectodermal effects, Cleft lip/palate). It is inherited in an autosomal dominant fashion with variable expression, featuring congenital abnormalities of skin, hair, teeth, nail, eccrine and mucous glands. We present a three-month-old boy, born to unaffected parents, with typical clinical findings of AEC syndrome. In this boy, a mutation Ile537Thr (c.1610C>T) in the sterile alpha motive (SAM) domain of the TP73L (p63) gene was detected. Because of the broad spectrum of related syndromes such as Rapp-Hodgkin syndrome, Bowen-Armstrong syndrome, CHAND syndrome and epidermolysis bullosa hereditaria, the diagnosis of AEC should be base don both clinical findings and genetic analysis.
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Cabiling DS, Yan AC, McDonald-McGinn DM, Zackai EH, Kirschner RE. Cleft lip and palate repair in Hay-Wells/ankyloblepharon-ectodermal dysplasia-clefting syndrome. Cleft Palate Craniofac J 2007; 44:335-9. [PMID: 17477760 DOI: 10.1597/06-065] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Hay-Wells/ankyloblepharon-ectodermal dysplasia-clefting syndrome is a rare autosomal dominant disorder characterized by ankyloblepharon, ectodermal dysplasia, and cleft lip and/or cleft palate. Mutations in the p63 gene recently have been shown to be etiologic in the majority of cases of ankyloblepharon-ectodermal dysplasia-clefting syndrome. To date, there have been no reports to document wound healing after cleft lip and/or palate repair in ankyloblepharon-ectodermal dysplasia-clefting patients. We describe two patients with ankyloblepharon-ectodermal dysplasia-clefting syndrome and provide a review of the literature. There have been no reported instances of wound healing complications in affected patients. Seventeen percent (3/18) of reported patients required revisions or repair of oronasal fistulae. Cleft lip and palate repair can be performed safely in patients with Hay-Wells syndrome.
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Affiliation(s)
- David S Cabiling
- Department of Surgery and Division of Plastic Surgery at The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104-4318, USA
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Rinne T, Hamel B, van Bokhoven H, Brunner HG. Pattern of p63 mutations and their phenotypes--update. Am J Med Genet A 2006; 140:1396-406. [PMID: 16691622 DOI: 10.1002/ajmg.a.31271] [Citation(s) in RCA: 120] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Heterozygous mutations in the transcription factor gene p63 cause at least six different syndromes with various combinations of ectodermal dysplasia, orofacial clefting and limb malformations. Here we will present an update of mutations in the p63 gene together with a comprehensive overview of the associated clinical features in 227 patients. These data confirm the previously recognized genotype-phenotype associations. Moreover, we report that there is a large degree of clinical variability in each of the p63-associated disorders. This is illustrated by the different phenotypes that are seen for the five-hotspot mutations that explain almost 90% of all EEC syndrome patients.
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Affiliation(s)
- Tuula Rinne
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, 6500 HB Nijmegen, The Netherlands
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Steele JA, Hansen H, Arn P, Kwong PC. Spectrum of phenotypic manifestations from a single point mutation of the p63 gene, including new cutaneous and immunologic findings. Pediatr Dermatol 2005; 22:415-9. [PMID: 16190990 DOI: 10.1111/j.1525-1470.2005.00105.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mutations in the p63 gene have been identified in five human disorders characterized by varying degrees of limb anomalies, ectodermal dysplasia, and facial clefts. We report a new point mutation in the p63 gene in a family in which the mother was initially diagnosed with Rapp-Hodgkin syndrome and her two offspring manifested ankyloblepharon, ectodermal defects, cleft lip and palate, syndrome. These three patients are the first to be reported with this particular mutation, which consists of a change from glycine to aspartic acid at position 506 on exon 14. The clinical spectrum observed in the three family members highlights the wide range of phenotypic variations that result from a single point mutation in the p63 gene. The mother lacks certain features classically associated with AEC, dermatitis of the scalp in particular. Severe erosive dermatitis of the scalp developed in both offspring, along with previously undescribed poikilodermatous skin changes and a deficiency of CD4 T lymphocytes. The new and varied phenotypic features noted in these patients emphasize the spectrum of disease caused by mutations in the p63 gene and raise the possibility of a role for it in maintaining immunocompetence.
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Affiliation(s)
- Jennifer A Steele
- Department of Dermatology, Mayo Clinic, Jacksonville, Florida 32207, USA
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11
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Itin PH, Fistarol SK. Ectodermal dysplasias. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2005; 131C:45-51. [PMID: 15468153 DOI: 10.1002/ajmg.c.30033] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Ectodermal dysplasias are a large group of heritable conditions characterized by congenital defects of one or more ectodermal structures and their appendages: hair (hypotrichosis, partial, or total alopecia), nails (dystrophic, hypertrophic, abnormally keratinized), teeth (enamel defect or absent), and sweat glands (hypoplastic or aplastic). The ectodermal dysplasias, as a rule, are not pure "one-layer diseases." Mesodermal and, rarely, endodermal dysplasias coexist. Embryogenesis exhibits distinct tissue organizational fields and specific interactions among the germ layers that may lead to a wide range of ectodermal dysplasias when genes important for development are mutated or otherwise altered in expression. Of the approximately 200 different ectodermal dysplasias, about 30 have been studied at the molecular level with identification of the causative gene. Freire-Maia and Pinheiro used the clinical aspects for their classification, and Priolo integrated molecular genetic and clinical aspects for her scheme. Those two more historical classification schemes have the difficulty that, when applied strictly, several additional groups of diseases should be integrated within the term "ectodermal dysplasias," e.g. keratodermas with skin or hair alterations or the ichthyoses with associated features. Such consequent classification would lead to an endless list of diseases and would be useless for the practical work. Recent evidence implicates a genetic defect in different pathways orchestrating ectodermal organogenesis. Modern molecular genetics will increasingly elucidate the basic defects of the different syndromes and yield more insight into the regulatory mechanisms of embryology. In this way, a reclassification of ectodermal dysplasias will be possible according to the function of their involved mutated genes. Lamartine recently proposed a helpful classification according to the functions of the genes discovered in different types of ectodermal dysplasias. Accordingly, the present overview categorizes the various ectodermal dysplasias into four major functional subgroups: cell-cell communication and signaling, adhesion, transcription regulation, and development.
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Affiliation(s)
- Peter H Itin
- Department of Dermatology, Kantonsspital Aarau, Switzerland.
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12
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Síndrome AEC (Hay-Wells). ACTAS DERMO-SIFILIOGRAFICAS 2004. [DOI: 10.1016/s0001-7310(04)79208-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Sahin MT, Türel-Ermertcan A, Chan I, McGrath JA, Oztürkcan S. Ectodermal dysplasia showing clinical overlap between AEC, Rapp-Hodgkin and CHAND syndromes. Clin Exp Dermatol 2004; 29:486-8. [PMID: 15347331 DOI: 10.1111/j.1365-2230.2004.01584.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The ectodermal dysplasias represent a complex collection of congenital abnormalities of skin, hair, teeth, nail, and sweat gland development, many of which have overlapping clinical features. In this report, we describe a 7-year-old girl, born to clinically normal parents, with ankyloblepharon, cleft lip/palate and hair abnormalities, features resembling the autosomal dominant disorder, ankyloblepharon-ectodermal dysplasia-clefting (AEC) syndrome, which results from mutations in the sterile-alpha motif domain of the gene encoding the transcription factor, p63. However, direct sequencing of the p63 gene in this individual did not reveal any pathogenic sequence variants. Moreover, two of her paternal cousins were discovered to have similar congenital ectodermal anomalies, raising the alternative possibility of an autosomal recessive pattern of inheritance. Furthermore, all affected individuals lacked a history of erosive scalp dermatitis that is usually characteristic of AEC syndrome. Instead, the scalp hair was coarse and wiry. In addition, another atypical feature, hypohidrosis, was present. Collectively, the clinical features also resembled Rapp-Hodgkin syndrome, Bowen-Armstrong syndrome and CHAND syndrome, but did not appear to fit neatly with any one particular disorder. This case highlights the difficulties in trying to classify the ectodermal dysplasia syndromes on clinical features alone.
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Affiliation(s)
- M T Sahin
- Department of Dermatology, Celal Bayar University, Medical Faculty, Manisa, Turkey.
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Bertola DR, Kim CA, Albano LMJ, Scheffer H, Meijer R, van Bokhoven H. Molecular evidence that AEC syndrome and Rapp-Hodgkin syndrome are variable expression of a single genetic disorder. Clin Genet 2004; 66:79-80. [PMID: 15200513 DOI: 10.1111/j.0009-9163.2004.00278.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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