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Zhou D, Zhang D, Sun X, Li Z, Ni Y, Shan Z, Li H, Liu C, Zhang S, Liu Y, Zheng R, Pan F, Zhu Y, Shi Y, Lai M. A novel variant associated with HDL-C levels by modifying DAGLB expression levels: An annotation-based genome-wide association study. Eur J Hum Genet 2018; 26:838-847. [PMID: 29476167 DOI: 10.1038/s41431-018-0108-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 12/10/2017] [Accepted: 01/23/2018] [Indexed: 11/09/2022] Open
Abstract
Although numbers of genome-wide association studies (GWAS) have been performed for serum lipid levels, limited heritability has been explained. Studies showed that combining data from GWAS and expression quantitative trait loci (eQTLs) signals can both enhance the discovery of trait-associated SNPs and gain a better understanding of the mechanism. We performed an annotation-based, multistage genome-wide screening for serum-lipid-level-associated loci in totally 6863 Han Chinese. A serum high-density lipoprotein cholesterol (HDL-C) associated variant rs1880118 (hg19 chr7:g. 6435220G>C) was replicated (Pcombined = 1.4E-10). rs1880118 was associated with DAGLB (diacylglycerol lipase, beta) expression levels in subcutaneous adipose tissue (P = 5.9E-42) and explained 47.7% of the expression variance. After the replication, an active segment covering variants tagged by rs1880118 near 5' of DAGLB was annotated using histone modification and transcription factor binding signals. The luciferase report assay revealed that the segment containing the minor alleles showed increased transcriptional activity compared with segment contains the major alleles, which was consistent with the eQTL analyses. The expression-trait association tests indicated the association between the DAGLB and serum HDL-C levels using gene-based approaches called "TWAS" (P = 3.0E-8), "SMR" (P = 1.1E-4), and "Sherlock" (P = 1.6E-6). To summarize, we identified a novel HDL-C-associated variant which explained nearly half of the expression variance of DAGLB. Integrated analyses established a genotype-gene-phenotype three-way association and expanded our knowledge of DAGLB in lipid metabolism.
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Affiliation(s)
- Dan Zhou
- Department of Epidemiology & Biostatistics, Zhejiang University School of Public Health, Hangzhou, Zhejiang, 310058, China.,Department of Pathology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, China.,Key Laboratory of Disease Proteomics of Zhejiang Province, Hangzhou, Zhejiang, 310058, China
| | - Dandan Zhang
- Department of Pathology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, China.,Key Laboratory of Disease Proteomics of Zhejiang Province, Hangzhou, Zhejiang, 310058, China
| | - Xiaohui Sun
- Department of Epidemiology & Biostatistics, Zhejiang University School of Public Health, Hangzhou, Zhejiang, 310058, China
| | - Zhiqiang Li
- The Affiliated Hospital of Qingdao University & The Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, 266000, China.,Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education) Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Yaqin Ni
- Department of Epidemiology & Biostatistics, Zhejiang University School of Public Health, Hangzhou, Zhejiang, 310058, China
| | - Zhongyan Shan
- The Endocrine Institute and Liaoning Provincial Key Laboratory of Endocrine Diseases, Department of Endocrinology and Metabolism, The First Hospital of China Medical University, Shenyang, Liaoning, 110001, China
| | - Hong Li
- Department of Endocrinology, Sir Run Run Shaw Hospital Affiliated to School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310020, China
| | - Chengguo Liu
- Putuo District People's Hospital, Zhoushan, Zhejiang, 316100, China
| | - Shuai Zhang
- Department of Pathology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, China.,Key Laboratory of Disease Proteomics of Zhejiang Province, Hangzhou, Zhejiang, 310058, China
| | - Yi Liu
- Department of Epidemiology & Biostatistics, Zhejiang University School of Public Health, Hangzhou, Zhejiang, 310058, China
| | - Ruizhi Zheng
- Department of Epidemiology & Biostatistics, Zhejiang University School of Public Health, Hangzhou, Zhejiang, 310058, China
| | - Feixia Pan
- Department of Epidemiology & Biostatistics, Zhejiang University School of Public Health, Hangzhou, Zhejiang, 310058, China
| | - Yimin Zhu
- Department of Epidemiology & Biostatistics, Zhejiang University School of Public Health, Hangzhou, Zhejiang, 310058, China.
| | - Yongyong Shi
- The Affiliated Hospital of Qingdao University & The Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, 266000, China. .,Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education) Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, 200030, China. .,Department of Psychiatry, The First Teaching Hospital of Xinjiang Medical University, Urumqi, 830000, China.
| | - Maode Lai
- Department of Pathology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, China. .,Key Laboratory of Disease Proteomics of Zhejiang Province, Hangzhou, Zhejiang, 310058, China.
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Al-Barry MA, Albalawi AM, Sayf MA, Badawi A, Afzal S, Latif M, Samman MI, Basit S. Sequence analysis of four vitamin D family genes (VDR, CYP24A1, CYP27B1 and CYP2R1) in Vogt-Koyanagi-Harada (VKH) patients: identification of a potentially pathogenic variant in CYP2R1. BMC Ophthalmol 2016; 16:172. [PMID: 27716192 PMCID: PMC5050582 DOI: 10.1186/s12886-016-0354-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 09/27/2016] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND VKH is a rare autoimmune disease. Decreased level of vitamin D has recently been found to be involved in the pathogenesis of Vogt-Koyanagi-Harada (VKH) disease. This study was designed to screen the vitamin D pathway genes for pathogenic mutations, if any, in VKH patients. METHODS Genomic DNA was extracted from blood samples collected from patients with VKH disease and healthy controls. Entire coding region, exon-intron junctions of four genes were sequenced in DNA from 39 Saudi VKH patients and 50 ethnically matched healthy individuals. All patients and controls were unrelated. RESULTS Vitamin D levels in VKH patients were found either insufficient (21-29 ng/mL) or deficient (<20 ng/mL). Sequencing analysis of the VDR, CYP24A1, CYP27B1 and CYP2R1 detected twelve nucleotide changes in these genes in our cohort of 39 patients; 4 of which were non-coding, 6 were synonymous coding and 2 were non-synonymous coding sequence changes. All synonymous coding variants were benign polymorphisms with no apparent clinical significance. A non-synonymous coding sequence variant (c.2 T > C; p.1Met?) found in VDR is an initiation coding change and was detected in control individuals as well, while another variant (c.852G > A; p.284 M > I) found in CYP2R1 is predicted to be disease causing by mutationtaster software. This potentially pathogenic variant was found in 17 out of 39 VKH patients. CONCLUSIONS Screening of four Vitamin D pathway genes in 39 VKH patients shows that a potentially pathogenic sequence variant in CYP2R1 may cause VKH in a subset of patients. These findings support the previous observation that low vitamin D levels might play a role in VKH pathogenesis and mutations in genes involved in vitamin D anabolism and catabolism might be of importance in VKH pathobiology.
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Affiliation(s)
- Ma'an Abdullah Al-Barry
- College of Medicine, Taibah University Almadinah Almunawarah, Medina, Kingdom of Saudi Arabia.,Magribi Hospital, Almadinah Almunawarah, Medina, Kingdom of Saudi Arabia
| | - Alia M Albalawi
- Center for Genetics and Inherited Diseases, Taibah University Almadinah Almunawarah, Medina, 30001, Kingdom of Saudi Arabia
| | - Mohammed Abu Sayf
- College of Medicine, Taibah University Almadinah Almunawarah, Medina, Kingdom of Saudi Arabia
| | - Abdulrahman Badawi
- College of Medicine, Taibah University Almadinah Almunawarah, Medina, Kingdom of Saudi Arabia
| | - Sibtain Afzal
- Prince Naif Center for Immunology Research, College of Medicine, King Saud University, Riyadh, 11472, Saudi Arabia
| | - Muhammad Latif
- Center for Genetics and Inherited Diseases, Taibah University Almadinah Almunawarah, Medina, 30001, Kingdom of Saudi Arabia
| | - Mohammed I Samman
- Center for Genetics and Inherited Diseases, Taibah University Almadinah Almunawarah, Medina, 30001, Kingdom of Saudi Arabia
| | - Sulman Basit
- Center for Genetics and Inherited Diseases, Taibah University Almadinah Almunawarah, Medina, 30001, Kingdom of Saudi Arabia.
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Jan A, Basit S, Wakil SM, Ramzan K, Ahmad W. A novel homozygous variant in the dsp gene underlies the first case of non-syndromic form of alopecia. Arch Dermatol Res 2015; 307:793-801. [DOI: 10.1007/s00403-015-1590-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Revised: 05/31/2015] [Accepted: 06/29/2015] [Indexed: 02/04/2023]
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Basit S, Khan S, Ahmad W. Genetics of human isolated hereditary hair loss disorders. Clin Genet 2014; 88:203-12. [DOI: 10.1111/cge.12531] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2014] [Revised: 09/22/2014] [Accepted: 10/23/2014] [Indexed: 12/25/2022]
Affiliation(s)
- S. Basit
- Center for Genetics and Inherited Diseases; Taibah University; Almadinah Almunawwarah Saudi Arabia
| | - S. Khan
- Department of Biotechnology and Genetic Engineering; Kohat University of Science and Technology; Khyber Pakhtunkhwa Pakistan
| | - W. Ahmad
- Department of Biochemistry, Faculty of Biological Sciences; Quaid-i-Azam University; Islamabad Pakistan
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Ullah A, Raza SI, Ali RH, Naveed AK, Jan A, Rizvi SDA, Satti R, Ahmad W. A novel deletion mutation in theDSG4gene underlies autosomal recessive hypotrichosis with variable phenotype in two unrelated consanguineous families. Clin Exp Dermatol 2014; 40:78-84. [DOI: 10.1111/ced.12457] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/03/2014] [Indexed: 11/28/2022]
Affiliation(s)
- A. Ullah
- Department of Biochemistry; Faculty of Biological Sciences; Quaid-i-Azam University; Islamabad Pakistan
| | - S. I. Raza
- Department of Biochemistry; Faculty of Biological Sciences; Quaid-i-Azam University; Islamabad Pakistan
- Army Medical College; National University of Science and Technology (NUST); Islamabad Pakistan
| | - R. H. Ali
- Department of Biochemistry; Faculty of Biological Sciences; Quaid-i-Azam University; Islamabad Pakistan
| | - A. K. Naveed
- Army Medical College; National University of Science and Technology (NUST); Islamabad Pakistan
| | - A. Jan
- Department of Biochemistry; Faculty of Biological Sciences; Quaid-i-Azam University; Islamabad Pakistan
| | - S. D. A. Rizvi
- Army Medical College; National University of Science and Technology (NUST); Islamabad Pakistan
| | - R. Satti
- Department of Biochemistry; Faculty of Biological Sciences; Quaid-i-Azam University; Islamabad Pakistan
| | - W. Ahmad
- Department of Biochemistry; Faculty of Biological Sciences; Quaid-i-Azam University; Islamabad Pakistan
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Basit S, Malibari O, Al Balwi AM, Abdusamad F, Abu Ismail F. A founder splice site mutation underlies glycogen storage disease type 3 in consanguineous Saudi families. Ann Saudi Med 2014; 34:390-5. [PMID: 25827695 PMCID: PMC6074555 DOI: 10.5144/0256-4947.2014.390] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND AND OBJECTIVES Glycogen storage disease type 3 (GSD III) is an autosomal recessive disorder caused by genetic mutations in the gene AGL. AGL encodes amylo-a-1, 6-glucosidase, 4-a-glucanotransferase, a glycogen debranching enzyme. GSD III is characterized by fasting hypoglycemia, hepatomegaly, growth retardation, progressive myopathy, and cardiomyopathy due to storage of abnormally structured glycogen in both skeletal and cardiac muscles and/or liver. The aim of this study is to detect mutations underlying GSD III in Saudi patients. DESIGN AND SETTINGS A cross-sectional clinical genetic study of 5 Saudi consanguineous families examined at the metabolic clinic of the Madinah Maternity and Children Hospital. PATIENTS AND METHODS We present a biochemical and molecular analysis of 5 consanguineous Saudi families with GSD III. DNA was isolated from the peripheral blood of 31 individuals, including 12 patients, and the AGL gene was sequenced bidirectionally. DNA sequences were compared with the AGL reference sequence from the ensemble genome browser. RESULTS Genotyping and sequence analysis identified a homozygous intronic splice acceptor site mutation (IVS32-12A > G) in 4 families perfectly segregating with the phenotype. Complementary (c)DNA sequence analysis of the AGL gene revealed an 11-bp sequence insertion between exon 32 and exon 33 due to the creation of a new 3' splice site. The predicted mutant enzyme was truncated by 112 carboxyl-terminal amino acids as a result of premature termination. CONCLUSION Haplotype analysis revealed that the mutation arises as a result of founder effect, not an independent event. This is the first report of a genetic mutation in the AGL gene from Saudi Arabia. Screening for this mutation can improve genetic counseling and prenatal diagnosis of GSD III in Saudi Arabia.
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Affiliation(s)
- Sulman Basit
- Sulman Basit PhD, Center for Genetics and Inherited Diseases, Taibah University Al Madinah Al Munawarah, Saudi Arabia, T: +966-535370209,
| | | | - Alia Mahmood Al Balwi
- Sulman Basit PhD, Center for Genetics and Inherited Diseases, Taibah University Al Madinah Al Munawarah, Saudi Arabia, T: +966-535370209,
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In silico analysis of missense mutations in LPAR6 reveals abnormal phospholipid signaling pathway leading to hypotrichosis. PLoS One 2014; 9:e104756. [PMID: 25119526 PMCID: PMC4132050 DOI: 10.1371/journal.pone.0104756] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 07/16/2014] [Indexed: 01/08/2023] Open
Abstract
Autosomal recessive hypotrichosis is a rare genetic irreversible hair loss disorder characterized by sparse scalp hair, sparse to absent eyebrows and eyelashes, and sparse axillary and body hair. The study, presented here, established genetic linkage in four families showing similar phenotypes to lysophosphatidic acid receptor 6 (LPAR6) gene on chromosome 13q14.11-q21.32. Subsequently, sequence analysis of the gene revealed two previously reported missense mutations including p.D63V in affected members of one and p.I188F in three other families. Molecular modeling and docking analysis was performed to investigate binding of a ligand oleoyl-L-alpha-lysophosphatidic acid (LPA) to modeled protein structures of normal and mutated (D63V, G146R, I188F, N248Y, S3T, L277P) LPAR6 receptors. The mutant receptors showed a complete shift in orientation of LPA at the binding site. In addition, hydropathy analysis revealed a significant change in the membrane spanning topology of LPAR6 helical segments. The present study further substantiated involvement of LPAR6-LPA signaling in the pathogenesis of hypotrichosis/woolly hair and provided additional insight into the molecular mechanism of hair development.
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Mohammed AES, Eguchi H, Wada S, Koyama N, Shimizu M, Otani K, Ohtaki M, Tanimoto K, Hiyama K, Gaber MS, Nishiyama M. TMEM158 and FBLP1 as novel marker genes of cisplatin sensitivity in non-small cell lung cancer cells. Exp Lung Res 2013; 38:463-74. [PMID: 23098063 DOI: 10.3109/01902148.2012.731625] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Even after development of molecular targeting therapies, platinum-based chemotherapy is still a standard care for treatment of locally advanced non-small cell lung cancer (NSCLC). So far, critical molecular markers capable to predict the therapeutic response in NSCLC patients remain undetermined. We here attempted to identify novel biomarker genes for cisplatin (CDDP) for a tailored therapy. Initial screening to explorer association of IC(50) values of CDDP obtained by MTT assay and gene expression levels measured with oligonucleotide microarray and real-time RT-PCR provided 6 candidate genes, namely, NUBPL, C9orf30, ZNF12, TMEM158, GSK3B, and FBLP1 using 9 lung cancer cells consisting of 3 small and 6 NSCLC cells. These 6 genes together with 5 reported biomarkers, i.e., GSTP1, ERCC1, BRCA1, FRAP1, and RRM1, were subjected to a linear regression analysis using 12 NSCLC cell lines including 6 additional NSCLC cells: only FBLP1 and TMEM158 genes showed positive associations with statistical significances (P = .016 and .026, respectively). The biological significance of these genes was explored by in vitro experiments: Knockdown experiments in PC-9/CDDP cells revealed that the reduced expression of TMEM158 significantly decreased the chemo-resistance against CDDP (P <.0001), while 2 transformants of PC-6 cells stably over-expressing FBLP1 resulted in an enhanced resistance to CDDP (P = .004 and P = .001). Furthermore, a stepwise multiple regression analysis demonstrated the best prediction formula could be fixed when we used expression data of TMEM158 and FBLP1 (R(2) = 0.755, P = .0018). TMEM158 and FBLP1 may be powerful predictive biomarkers for CDDP therapy in NSCLC.
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Affiliation(s)
- Ahmed El Sayed Mohammed
- Translational Research Center, Saitama Medical University International Medical Center, Hidaka, Saitama, Japan
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Current progress in non-Edg family LPA receptor research. Biochim Biophys Acta Mol Cell Biol Lipids 2012; 1831:33-41. [PMID: 22902318 DOI: 10.1016/j.bbalip.2012.08.003] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Revised: 08/01/2012] [Accepted: 08/02/2012] [Indexed: 01/08/2023]
Abstract
Lysophosphatidic acid (LPA) is the simplest phospholipid yet possesses myriad biological functions. Until 2003, the functions of LPA were thought to be elicited exclusively by three subtypes of the endothelial differentiation gene (Edg) family of G protein-coupled receptors - LPA(1), LPA(2), and LPA(3). However, several biological functions of LPA could not be assigned to any of these receptors indicating the existence of one or more additional LPA receptor(s). More recently, the discovery of a second cluster of LPA receptors which includes LPA(4), LPA(5), and LPA(6) has paved the way for new avenues of LPA research. Analyses of these non-Edg family LPA receptors have begun to fill in gaps to understand biological functions of LPA such as platelet aggregation and vascular development that could not be ascribed to classical Edg family LPA receptors and are also unveiling new biological functions. Here we review recent progress in the non-Edg family LPA receptor research, with special emphasis on the pharmacology, signaling, and physiological roles of this family of receptors. This article is part of a Special Issue entitled Advances in Lysophospholipid Research.
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Yanagida K, Ishii S. Non-Edg family LPA receptors: the cutting edge of LPA research. J Biochem 2011; 150:223-32. [PMID: 21746769 DOI: 10.1093/jb/mvr087] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Lysophosphatidic acid (LPA) is a bioactive lipid mediator with diverse physiological and pathological actions on many types of cells. Originally, LPA was thought to elicit its biological functions through three subtypes of endothelial differentiation gene (Edg) family G protein-coupled receptors (LPA1, LPA2 and LPA3) until our group identified a fourth subtype, LPA4. The discovery of this receptor, which is structurally distinct from the Edg family LPA receptors, led to the identification of two additional LPA receptors, LPA5 and LPA6, homologous to LPA4. These 'non-Edg family' LPA receptors now provide a new framework for understanding the diverse functions of LPA, including vascular development, platelet activation and hair growth. In this review, we summarize the identification, intracellular signalling and biological functions of this novel cluster of LPA receptors.
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Affiliation(s)
- Keisuke Yanagida
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, The University of Tokyo, Tokyo 113-0033
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Wasif N, Naqvi SKUH, Basit S, Ali N, Ansar M, Ahmad W. Novel mutations in the keratin-74 (KRT74) gene underlie autosomal dominant woolly hair/hypotrichosis in Pakistani families. Hum Genet 2010; 129:419-24. [PMID: 21188418 DOI: 10.1007/s00439-010-0938-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2010] [Accepted: 12/19/2010] [Indexed: 10/18/2022]
Abstract
Autosomal dominant woolly hair (ADWH) is an inherited condition of tightly curled and twisted scalp hair. Recently, a mutation in human keratin-74 (KRT74) gene has been shown to cause this form of hereditary hair disorder. In the present study, we have described two families (A and B) having multiple individuals affected with autosomal dominant form of hair loss disorders. In family A, 10 individuals showed ADWH phenotype while in the family B, 14 individuals showed hypotrichosis of the scalp. Genotyping using polymorphic microsatellite markers showed linkage of both the families to type II keratin gene cluster on the chromosome 12q12-14.1. Mutation analysis of the KRT74 gene identified two novel mutations in the affected individuals of the families. The sequence analysis revealed a splice acceptor site mutation (c.IVS8-1G>A) in family A and a missense variant (c.1444G>A, p.Asp482Asn) in family B. Mutations identified in the present study extend the body of evidence implicating the KRT74 gene in the pathogenesis of autosomal dominant hair loss disorders.
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Affiliation(s)
- Naveed Wasif
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
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