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Article: A DNA pooling-based case-control study of myopia candidate genes COL11A1, COL18A1, FBN1, and PLOD1 in a Chinese population

TitleA DNA pooling-based case-control study of myopia candidate genes COL11A1, COL18A1, FBN1, and PLOD1 in a Chinese population
Authors
Issue Date2011
PublisherMolecular Vision. The Journal's web site is located at http://www.molvis.org/molvis/
Citation
Molecular Vision, 2011, v. 17, p. 810-821 How to Cite?
AbstractPurpose: We examined the relationship between high myopia and common polymorphisms in four candidate genes: collagen, type XI, alpha 1 (COL11A1); collagen, type XVIII, alpha 1 (COL18A1); fibrillin 1 (FBN1); and procollagenlysine 1,2-oxoglutarate 5-dioxygenase 1 (PLOD1). These genes were selected because rare pathogenic mutations in these genes cause disease syndromes that have myopia, usually high myopia, as one of the common presenting features. Methods: This study recruited 600 unrelated Han Chinese subjects including 300 cases with high myopia (spherical equivalent or SE≤-8.00 diopters) and 300 controls (SE within ±1.00 diopter). A total of 66 tag single nucleotide polymorphisms (SNPs) were selected for study from these four candidate genes. The study adopted a DNA pooling strategy with an initial screen of DNA pools to identify putatively positive SNPs and then confirmed the "positive" SNPs by genotyping individual samples forming the original DNA pools. DNA pools were each constructed by mixing equal amounts of DNA from 50 individuals with the same phenotype status. Six case pools were prepared from 300 cases and six control pools from 300 controls. Allele frequencies of DNA pools were estimated by analyzing the primer-extended products with denaturing high performance liquid chromatography and compared between case pools and control pools with nested ANOVA. Results: In the first stage, 60 SNPs from the 4 candidate genes were successfully screened using the DNA pooling approach. Of these, 6 SNPs showed a statistical significant difference in estimated allele frequencies between case pools and controls at p<0.10. In the second stage, these "positive" SNPs were followed up by individual genotyping, but failed to be confirmed via standard single-marker and haplotype analyses. Conclusions: Common polymorphisms in these four candidate genes (COL11A1, COL18A1, FBN1 and PLOD1) were unlikely to play important roles in the genetic susceptibility to high myopia. © 2011 Molecular Vision.
Persistent Identifierhttp://hdl.handle.net/10722/137520
ISSN
2015 Impact Factor: 2.11
2015 SCImago Journal Rankings: 1.037
PubMed Central ID
ISI Accession Number ID
References

 

DC FieldValueLanguage
dc.contributor.authorYip, SPen_HK
dc.contributor.authorLeung, KHen_HK
dc.contributor.authorFung, WYen_HK
dc.contributor.authorNg, PWen_HK
dc.contributor.authorSham, PCen_HK
dc.contributor.authorYap, MKHen_HK
dc.date.accessioned2011-08-26T14:26:55Z-
dc.date.available2011-08-26T14:26:55Z-
dc.date.issued2011en_HK
dc.identifier.citationMolecular Vision, 2011, v. 17, p. 810-821en_HK
dc.identifier.issn1090-0535en_HK
dc.identifier.urihttp://hdl.handle.net/10722/137520-
dc.description.abstractPurpose: We examined the relationship between high myopia and common polymorphisms in four candidate genes: collagen, type XI, alpha 1 (COL11A1); collagen, type XVIII, alpha 1 (COL18A1); fibrillin 1 (FBN1); and procollagenlysine 1,2-oxoglutarate 5-dioxygenase 1 (PLOD1). These genes were selected because rare pathogenic mutations in these genes cause disease syndromes that have myopia, usually high myopia, as one of the common presenting features. Methods: This study recruited 600 unrelated Han Chinese subjects including 300 cases with high myopia (spherical equivalent or SE≤-8.00 diopters) and 300 controls (SE within ±1.00 diopter). A total of 66 tag single nucleotide polymorphisms (SNPs) were selected for study from these four candidate genes. The study adopted a DNA pooling strategy with an initial screen of DNA pools to identify putatively positive SNPs and then confirmed the "positive" SNPs by genotyping individual samples forming the original DNA pools. DNA pools were each constructed by mixing equal amounts of DNA from 50 individuals with the same phenotype status. Six case pools were prepared from 300 cases and six control pools from 300 controls. Allele frequencies of DNA pools were estimated by analyzing the primer-extended products with denaturing high performance liquid chromatography and compared between case pools and control pools with nested ANOVA. Results: In the first stage, 60 SNPs from the 4 candidate genes were successfully screened using the DNA pooling approach. Of these, 6 SNPs showed a statistical significant difference in estimated allele frequencies between case pools and controls at p<0.10. In the second stage, these "positive" SNPs were followed up by individual genotyping, but failed to be confirmed via standard single-marker and haplotype analyses. Conclusions: Common polymorphisms in these four candidate genes (COL11A1, COL18A1, FBN1 and PLOD1) were unlikely to play important roles in the genetic susceptibility to high myopia. © 2011 Molecular Vision.en_HK
dc.languageengen_US
dc.publisherMolecular Vision. The Journal's web site is located at http://www.molvis.org/molvis/en_HK
dc.relation.ispartofMolecular Visionen_HK
dc.subject.meshCollagen Type XI - genetics - metabolism-
dc.subject.meshCollagen Type XVIII - genetics - metabolism-
dc.subject.meshMicrofilament Proteins - genetics - metabolism-
dc.subject.meshMyopia - genetics - pathology-
dc.subject.meshProcollagen-Lysine, 2-Oxoglutarate 5-Dioxygenase - genetics - metabolism-
dc.titleA DNA pooling-based case-control study of myopia candidate genes COL11A1, COL18A1, FBN1, and PLOD1 in a Chinese populationen_HK
dc.typeArticleen_HK
dc.identifier.emailSham, PC: pcsham@hku.hken_HK
dc.identifier.authoritySham, PC=rp00459en_HK
dc.description.naturelink_to_OA_fulltext-
dc.identifier.pmid21527992-
dc.identifier.pmcidPMC3081793-
dc.identifier.scopuseid_2-s2.0-79955618723en_HK
dc.identifier.hkuros189866en_US
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-79955618723&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume17en_HK
dc.identifier.spage810en_HK
dc.identifier.epage821en_HK
dc.identifier.isiWOS:000288947800002-
dc.publisher.placeUnited Statesen_HK
dc.identifier.scopusauthoridYip, SP=7102133673en_HK
dc.identifier.scopusauthoridLeung, KH=36946027000en_HK
dc.identifier.scopusauthoridFung, WY=25958608900en_HK
dc.identifier.scopusauthoridNg, PW=16199988300en_HK
dc.identifier.scopusauthoridSham, PC=34573429300en_HK
dc.identifier.scopusauthoridYap, MKH=7006673734en_HK

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