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Sonbol HS, AlRashidi AA. Cloning and Expression of Receptor of Egg Jelly Protein of Polycystic Kidney Disease 1 Gene in Human Receptor of Egg Jelly Protein. PHARMACOPHORE 2022. [DOI: 10.51847/vqghabllgj] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Yu C, Yang Y, Zou L, Hu Z, Li J, Liu Y, Ma Y, Ma M, Su D, Zhang S. Identification of novel mutations in Chinese Hans with autosomal dominant polycystic kidney disease. BMC MEDICAL GENETICS 2011; 12:164. [PMID: 22185115 PMCID: PMC3341574 DOI: 10.1186/1471-2350-12-164] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Accepted: 12/20/2011] [Indexed: 02/05/2023]
Abstract
BACKGROUND Autosomal dominant polycystic kidney disease (ADPKD) is the most common inherited renal disease with an incidence of 1 in 400 to 1000. The disease is genetically heterogeneous, with two genes identified: PKD1 (16p13.3) and PKD2 (4q21). Molecular diagnosis of the disease in at-risk individuals is complicated due to the structural complexity of PKD1 gene and the high diversity of the mutations. This study is the first systematic ADPKD mutation analysis of both PKD1 and PKD2 genes in Chinese patients using denaturing high-performance liquid chromatography (DHPLC). METHODS Both PKD1 and PKD2 genes were mutation screened in each proband from 65 families using DHPLC followed by DNA sequencing. Novel variations found in the probands were checked in their family members available and 100 unrelated normal controls. Then the pathogenic potential of the variations of unknown significance was examined by evolutionary comparison, effects of amino acid substitutions on protein structure, and effects of splice site alterations using online mutation prediction resources. RESULTS A total of 92 variations were identified, including 27 reported previously. Definitely pathogenic mutations (ten frameshift, ten nonsense, two splicing defects and one duplication) were identified in 28 families, and probably pathogenic mutations were found in an additional six families, giving a total detection level of 52.3% (34/65). About 69% (20/29) of the mutations are first reported with a recurrent mutation rate of 31%. CONCLUSIONS Mutation study of PKD1 and PKD2 genes in Chinese Hans with ADPKD may contribute to a better understanding of the genetic diversity between different ethnic groups and enrich the mutation database. Besides, evaluating the pathogenic potential of novel variations should also facilitate the clinical diagnosis and genetic counseling of the disease.
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Affiliation(s)
- Chaowen Yu
- Department of Medical Genetics, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, P. R. China
| | - Yuan Yang
- Department of Medical Genetics, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, P. R. China
| | - Lin Zou
- Center for Clinical Molecular Medicine, Children's Hospital, Chongqing Medical University, Chongqing, 400014, P. R. China
| | - Zhangxue Hu
- Department of Nephrology, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, P. R. China
| | - Jing Li
- Department of Nephrology, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, P. R. China
| | - Yunqiang Liu
- Department of Medical Genetics, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, P. R. China
| | - Yongxin Ma
- Department of Medical Genetics, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, P. R. China
| | - Mingyi Ma
- Department of Medical Genetics, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, P. R. China
| | - Dan Su
- Department of Medical Genetics, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, P. R. China
| | - Sizhong Zhang
- Department of Medical Genetics, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, P. R. China
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Bataille S, Berland Y, Fontes M, Burtey S. High Resolution Melt analysis for mutation screening in PKD1 and PKD2. BMC Nephrol 2011; 12:57. [PMID: 22008521 PMCID: PMC3206831 DOI: 10.1186/1471-2369-12-57] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2011] [Accepted: 10/18/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Autosomal dominant polycystic kidney disease (ADPKD) is the most common hereditary kidney disorder. It is characterized by focal development and progressive enlargement of renal cysts leading to end-stage renal disease. PKD1 and PKD2 have been implicated in ADPKD pathogenesis but genetic features and the size of PKD1 make genetic diagnosis tedious. METHODS We aim to prove that high resolution melt analysis (HRM), a recent technique in molecular biology, can facilitate molecular diagnosis of ADPKD. We screened for mutations in PKD1 and PKD2 with HRM in 37 unrelated patients with ADPKD. RESULTS We identified 440 sequence variants in the 37 patients. One hundred and thirty eight were different. We found 28 pathogenic mutations (25 in PKD1 and 3 in PKD2 ) within 28 different patients, which is a diagnosis rate of 75% consistent with literature mean direct sequencing diagnosis rate. We describe 52 new sequence variants in PKD1 and two in PKD2. CONCLUSION HRM analysis is a sensitive and specific method for molecular diagnosis of ADPKD. HRM analysis is also costless and time sparing. Thus, this method is efficient and might be used for mutation pre-screening in ADPKD genes.
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Affiliation(s)
- Stanislas Bataille
- EA 4263 Thérapie des Maladies Génétiques, Faculté de Médecine, Université de la Méditerranée, Boulevard Jean Moulin 13005 Marseille, France
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A non-synonymous mutation in the canine Pkd1 gene is associated with autosomal dominant polycystic kidney disease in Bull Terriers. PLoS One 2011; 6:e22455. [PMID: 21818326 PMCID: PMC3144903 DOI: 10.1371/journal.pone.0022455] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Accepted: 06/28/2011] [Indexed: 01/03/2023] Open
Abstract
Polycystic Kidney Disease is an autosomal dominant disease common in some lines of Bull Terriers (BTPKD). The disease is linked to the canine orthologue of human PKD1 gene, Pkd1, located on CFA06, but no disease-associated mutation has been reported. This study sequenced genomic DNA from two Bull Terriers with BTPKD and two without the disease. A non-synonymous G>A transition mutation in exon 29 of Pkd1 was identified. A TaqMan® SNP Genotyping Assay was designed and demonstrated the heterozygous detection of the mutation in 47 Bull Terriers with BTPKD, but not in 102 Bull Terriers over one year of age and without BTPKD. This missense mutation replaces a glutamic acid residue with a lysine residue in the predicted protein, Polycystin 1. This region of Polycystin 1 is highly conserved between species, and is located in the first cytoplasmic loop of the predicted protein structure, close to the PLAT domain and the second transmembrane region. Thus, this change could alter Polycystin 1 binding or localization. Analytic programs PolyPhen 2, Align GVGD and SIFT predict this mutation to be pathogenic. Thus, BTPKD is associated with a missense mutation in Pkd1, and the application of this mutation specific assay could reduce disease transmission by allowing diagnosis of disease in young animals prior to breeding.
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Kirsch S, Pasantes J, Wolf A, Bogdanova N, Münch C, Pennekamp P, Krawczak M, Dworniczak B, Schempp W. Chromosomal evolution of the PKD1 gene family in primates. BMC Evol Biol 2008; 8:263. [PMID: 18822117 PMCID: PMC2564946 DOI: 10.1186/1471-2148-8-263] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2007] [Accepted: 09/26/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The autosomal dominant polycystic kidney disease (ADPKD) is mostly caused by mutations in the PKD1 (polycystic kidney disease 1) gene located in 16p13.3. Moreover, there are six pseudogenes of PKD1 that are located proximal to the master gene in 16p13.1. In contrast, no pseudogene could be detected in the mouse genome, only a single copy gene on chromosome 17. The question arises how the human situation originated phylogenetically. To address this question we applied comparative FISH-mapping of a human PKD1-containing genomic BAC clone and a PKD1-cDNA clone to chromosomes of a variety of primate species and the dog as a non-primate outgroup species. RESULTS Comparative FISH with the PKD1-cDNA clone clearly shows that in all primate species studied distinct single signals map in subtelomeric chromosomal positions orthologous to the short arm of human chromosome 16 harbouring the master PKD1 gene. Only in human and African great apes, but not in orangutan, FISH with both BAC and cDNA clones reveals additional signal clusters located proximal of and clearly separated from the PKD1 master genes indicating the chromosomal position of PKD1 pseudogenes in 16p of these species, respectively. Indeed, this is in accordance with sequencing data in human, chimpanzee and orangutan. Apart from the master PKD1 gene, six pseudogenes are identified in both, human and chimpanzee, while only a single-copy gene is present in the whole-genome sequence of orangutan. The phylogenetic reconstruction of the PKD1-tree reveals that all human pseudogenes are closely related to the human PKD1 gene, and all chimpanzee pseudogenes are closely related to the chimpanzee PKD1 gene. However, our statistical analyses provide strong indication that gene conversion events may have occurred within the PKD1 family members of human and chimpanzee, respectively. CONCLUSION PKD1 must have undergone amplification very recently in hominid evolution. Duplicative transposition of the PKD1 gene and further amplification and evolution of the PKD1 pseudogenes may have arisen in a common ancestor of Homo, Pan and Gorilla approximately 8 MYA. Reticulate evolutionary processes such as gene conversion and non-allelic homologous recombination (NAHR) may have resulted in concerted evolution of PKD1 family members in human and chimpanzee and, thus, simulate an independent evolution of the PKD1 pseudogenes from their master PKD1 genes in human and chimpanzee.
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Affiliation(s)
- Stefan Kirsch
- Institut für Humangenetik und Anthropologie, Universität Freiburg, Breisacher Str. 33, 79106 Freiburg, Germany
| | - Juanjo Pasantes
- Institut für Humangenetik und Anthropologie, Universität Freiburg, Breisacher Str. 33, 79106 Freiburg, Germany
- Department of Biochemistry, Genetics & Immunology, University of Vigo, E-36200 Vigo, Spain
| | - Andreas Wolf
- Institut für Medizinische Informatik und Statistik, Universität Kiel, Brunswiker Str. 10, 24105 Kiel, Germany
| | - Nadia Bogdanova
- Institut für Humangenetik, Universität Münster, Vesaliusweg 12-14, 48129 Münster, Germany
| | - Claudia Münch
- Institut für Humangenetik und Anthropologie, Universität Freiburg, Breisacher Str. 33, 79106 Freiburg, Germany
| | - Petra Pennekamp
- Institut für Humangenetik, Universität Münster, Vesaliusweg 12-14, 48129 Münster, Germany
| | - Michael Krawczak
- Institut für Medizinische Informatik und Statistik, Universität Kiel, Brunswiker Str. 10, 24105 Kiel, Germany
| | - Bernd Dworniczak
- Institut für Humangenetik, Universität Münster, Vesaliusweg 12-14, 48129 Münster, Germany
| | - Werner Schempp
- Institut für Humangenetik und Anthropologie, Universität Freiburg, Breisacher Str. 33, 79106 Freiburg, Germany
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Symmons O, Váradi A, Arányi T. How segmental duplications shape our genome: recent evolution of ABCC6 and PKD1 Mendelian disease genes. Mol Biol Evol 2008; 25:2601-13. [PMID: 18791038 DOI: 10.1093/molbev/msn202] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The completion of the Human Genome Project has brought the understanding that our genome contains an unexpectedly large proportion of segmental duplications. This poses the challenge of elucidating the consequences of recent duplications on physiology. We have conducted an in-depth study of a subset of segmental duplications on chromosome 16. We focused on PKD1 and ABCC6 duplications because mutations affecting these genes are responsible for the Mendelian disorders autosomal dominant polycystic kidney disease and pseudoxanthoma elasticum, respectively. We establish that duplications of PKD1 and ABCC6 are associated to low-copy repeat 16a and show that such duplications have occurred several times independently in different primate species. We demonstrate that partial duplication of PKD1 and ABCC6 has numerous consequences: the pseudogenes give rise to new transcripts and mediate gene conversion, which not only results in disease-causing mutations but also serves as a reservoir for sequence variation. The duplicated segments are also involved in submicroscopic and microscopic genomic rearrangements, contributing to structural variation in human and chromosomal break points in the gibbon. In conclusion, our data shed light on the recent and ongoing evolution of chromosome 16 mediated by segmental duplication and deepen our understanding of the history of two Mendelian disorder genes.
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Affiliation(s)
- Orsolya Symmons
- Institute of Enzymology, Hungarian Academy of Sciences, Budapest, Hungary
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Garcia-Gonzalez MA, Jones JG, Allen SK, Palatucci CM, Batish SD, Seltzer WK, Lan Z, Allen E, Qian F, Lens XM, Pei Y, Germino GG, Watnick TJ. Evaluating the clinical utility of a molecular genetic test for polycystic kidney disease. Mol Genet Metab 2007; 92:160-7. [PMID: 17574468 PMCID: PMC2085355 DOI: 10.1016/j.ymgme.2007.05.004] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2007] [Accepted: 05/02/2007] [Indexed: 10/23/2022]
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) is estimated to affect 1/600-1/1000 individuals worldwide. The disease is characterized by age dependent renal cyst formation that results in kidney failure during adulthood. Although ultrasound imaging may be an adequate diagnostic tool in at risk individuals older than 30, this modality may not be sufficiently sensitive in younger individuals or for those from PKD2 families who have milder disease. DNA based assays may be indicated in certain clinical situations where imaging cannot provide a definitive clinical diagnosis. The goal of this study was to evaluate the utility of direct DNA analysis in a test sample of 82 individuals who were judged to have polycystic kidney disease by standard clinical criteria. The samples were analyzed using a commercially available assay that employs sequencing of both genes responsible for the disorder. Definite disease causing mutations were identified in 34 (approximately 42%) study participants. An additional 30 (approximately 37%) subjects had either in frame insertions/deletions, non-canonical splice site alterations or a combination of missense changes that were also judged likely to be pathogenic. We noted striking sequence variability in the PKD1 gene, with a mean of 13.1 variants per participant (range 0-60). Our results and analysis highlight the complexity of assessing the pathogenicity of missense variants particularly when individuals have multiple amino acid substitutions. We conclude that a significant fraction of ADPKD mutations are caused by amino acid substitutions that need to be interpreted carefully when utilized in clinical decision-making.
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Affiliation(s)
- Miguel A. Garcia-Gonzalez
- Johns Hopkins University School of Medicine, Department of Medicine, Division of Nephrology, Baltimore, MD
- Laboratorio de Investigación en Nefroloxía, Complexo Hospitalario Universitario de Santiago, Santiago de Compostela, Spain
| | | | - Susan K. Allen
- Athena Diagnostics, Inc. 377 Plantation St. Worcester, MA
| | | | - Sat D. Batish
- Athena Diagnostics, Inc. 377 Plantation St. Worcester, MA
| | | | - Zheng Lan
- Johns Hopkins University School of Medicine, Department of Medicine, Division of Nephrology, Baltimore, MD
| | - Erica Allen
- Johns Hopkins University School of Medicine, Department of Medicine, Division of Nephrology, Baltimore, MD
| | - Feng Qian
- Johns Hopkins University School of Medicine, Department of Medicine, Division of Nephrology, Baltimore, MD
| | - Xose M. Lens
- Laboratorio de Investigación en Nefroloxía, Complexo Hospitalario Universitario de Santiago, Santiago de Compostela, Spain
| | - York Pei
- Division of Nephrology, Department of Medicine, Toronto General Hospital and University of Toronto, Toronto, Ontario M5G2C4, Canada
| | - Gregory G. Germino
- Johns Hopkins University School of Medicine, Department of Medicine, Division of Nephrology, Baltimore, MD
| | - Terry J. Watnick
- Johns Hopkins University School of Medicine, Department of Medicine, Division of Nephrology, Baltimore, MD
- *Corresponding Author: Terry Watnick, M. D., Division of Nephrology, Johns Hopkins School of Medicine, 720 Rutland Avenue, Ross 954, Baltimore, MD21205, Phone: 410-614-7590, Fax: 410-614-5129,
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Taske NL, Williamson MP, Makoff A, Bate L, Curtis D, Kerr M, Kjeldsen MJ, Pang KA, Sundqvist A, Friis ML, Chadwick D, Richens A, Covanis A, Santos M, Arzimanoglou A, Panayiotopoulos CP, Whitehouse WP, Rees M, Gardiner RM. Evaluation of the positional candidate gene CHRNA7 at the juvenile myoclonic epilepsy locus (EJM2) on chromosome 15q13-14. Epilepsy Res 2002; 49:157-72. [PMID: 12049804 DOI: 10.1016/s0920-1211(02)00027-x] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
A previous study of 34 nuclear pedigrees segregating juvenile myoclonic epilepsy (JME) gave significant evidence of linkage with heterogeneity to marker loci on chromosome 15q13-14 close to the candidate gene CHRNA7 (Hum. Mol. Genet. 6 (1997) 1329). The aim of this work was to further evaluate the putative aetiological role of CHRNA7 in JME within the 34 families originally described, and to assess the contribution of this locus to a broader phenotype of idiopathic generalised epilepsy (IGE). Multipoint linkage analysis and intrafamilial association studies were performed with microsatellite markers that encompass both CHRNA7 and its partial duplication (CHRFAM7A). A maximum HLOD of 3.45 [alpha=0.58; (Zall=2.88, P=0.0008)] was observed 8 cM distal to D15S1360, a CHRNA7 intragenic marker. Significant exclusion lod scores were obtained across the region in 12 mixed phenotype JME/IGE families. Mutation screening of the CHRNA7 gene (and consequently exons 5-10 of CHRFAM7A) and its putative promoter sequence identified a total of 13 sequence variants across 23 of 34 JME-affected families. Two variants (c.1354G>A and c.1466C>T) are predicted to result in amino acid changes and one (IVS9+5G>A) is predicted to result in aberrant transcript splicing. However, none of the variants alone appeared either necessary or sufficient to cause JME in the families in which they occurred. In conclusion, linkage analyses continue to support the existence of a locus on chromosome 15q13-14 that confers susceptibility to JME but not to a broader IGE phenotype. Causal sequence variants in the positional candidate CHRNA7 have not been identified but the presence of multiple segmental duplications in this region raises the possibility of undetected disease-causing genomic rearrangements.
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Affiliation(s)
- Nichole L Taske
- Department of Paediatrics and Child Health, Royal Free and University College Medical School, University College London, Gower Street Campus, 5 University Street, London WC1E 6JJ, UK.
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McCluskey M, Schiavello T, Hunter M, Hantke J, Angelicheva D, Bogdanova N, Markoff A, Thomas M, Dworniczak B, Horst J, Kalaydjieva L. Mutation detection in the duplicated region of the polycystic kidney disease 1 (PKD1) gene in PKD1-linked Australian families. Hum Mutat 2002; 19:240-50. [PMID: 11857740 DOI: 10.1002/humu.10045] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Screening for disease-causing mutations in the duplicated region of the PKD1 gene was performed in 17 unrelated Australian individuals with PKD1-linked autosomal dominant polycystic kidney disease. Exons 2-21 and 23-34 were assayed using PKD1-specific PCR amplification and direct sequencing. We have identified 12 novel probably pathogenic DNA variants, including five truncating mutations (Q563X, c.5105delAT, c.5159delG, S2269X, c.9847delC), two in-frame deletions (c.7472del3, c.9292del39), and two splice-site mutations (IVS14+1G>C, IVS16+1G>T). Three of the mutations (G381C, Y2185D, G2785D) were predicted to lead to the replacement of conserved amino acid residues, with ensuing changes in protein conformation. Defects in the duplicated region of PKD1 thus account for 63% of our patients. Together with the previously detected mutations (Q4041X, R4227P) in the 3 region of the gene, the study has achieved an overall mutation detection rate of 74%. In addition, we have detected 31 variants (nine novel and 22 previously published) that did not segregate with the disease and were considered to be neutral polymorphisms. Three of the nine novel polymorphisms were missense mutations with a predicted effect on protein conformation, emphasizing the problems of interpretation in PKD1 mutation screening.
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Affiliation(s)
- Marie McCluskey
- Centre for Human Genetics, Edith Cowan University, Joondalup, Australia
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Afzal AR, Jeffery S. Amplification of a 13.5-kb region of the PKD1 gene containing the 2.5-kb polypyrimidine tract in intron 21 facilitates mutation detection in this gene. GENETIC TESTING 2001; 5:57-9. [PMID: 11336403 DOI: 10.1089/109065701750168761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Mutation detection in the PKD1 gene proved to be difficult because two-thirds of the gene is reiterated several times on chromosome 16. Long-range PCR has been used previously to overcome this limitation, but due to a 2.5-kb polypyrimidine tract in intron 21, the screening capacity of the PKD1 gene using this technique was hindered. Here we report the measures that we have used to overcome this limitation.
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Affiliation(s)
- A R Afzal
- Department of Medical Genetics, St. George's Hospital Medical School, London UK
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