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Article: A fast modified protocol for random-access ultra-high density whole-genome scan: A tool for personalized genomic medicine, positional mapping, and cytogenetic analysis

TitleA fast modified protocol for random-access ultra-high density whole-genome scan: A tool for personalized genomic medicine, positional mapping, and cytogenetic analysis
Authors
Issue Date2009
PublisherElsevier BV. The Journal's web site is located at http://www.elsevier.com/locate/cca
Citation
Clinica Chimica Acta, 2009, v. 406 n. 1-2, p. 31-35 How to Cite?
Abstract
Background: High density single nucleotide polymorphism (SNP) genotyping array is widely applied on genome-wide association study of common diseases. In these studies, a fixed batch-size of 48 or 96 samples allows high-throughput analysis. To enhance the clinical application of microarray analysis on personalized medicine, we describe a modified PCR purification protocol without batch-size limitation for whole-genome scan using ultra-high density SNP microarray. Methods: Enzyme-digested PCR products were purified with the use of magnetic beads. Separation of the magnetic particles applies magnetic stand devices instead of vacuum pumps. With no batch-size limitation, we genotyped 17 genomic samples and 3 whole genome amplified samples in order to examine the performance of the modified protocol. Results: Our method is simple and fast, provides sufficient amount and high quality PCR products for subsequent fragmentation and labeling procedures prior to GeneChip hybridization. We show that the purified DNA can be genotyped with good QC call rate of > 93% in average similar to standard protocol. With the use of the short protocol, we successfully identified the breakpoint localization of a ring chromosome in a female and located the disease gene in a consanguineous family affected by limb-girdle muscular dystrophy. Conclusion: By modifying a single step in the original protocol, we are able to speed up the overall genotyping analysis and change the batch-wise analysis to random-access analysis for ultra-high density whole-genome scan for personalized medicine, positional mapping, and cytogenetic analysis. © 2009 Elsevier B.V. All rights reserved.
Persistent Identifierhttp://hdl.handle.net/10722/88303
ISSN
2013 Impact Factor: 2.764
2013 SCImago Journal Rankings: 1.039
ISI Accession Number ID
References

 

Author Affiliations
  1. The University of Hong Kong
  2. Princess Margaret Hospital Hong Kong
  3. Pamela Youde Nethersole Eastern Hospital
  4. Tsan Yuk Hospital
DC FieldValueLanguage
dc.contributor.authorLau, KCen_HK
dc.contributor.authorMak, CMen_HK
dc.contributor.authorLeung, KYen_HK
dc.contributor.authorTsoi, THen_HK
dc.contributor.authorTang, HYen_HK
dc.contributor.authorLee, Pen_HK
dc.contributor.authorLam, CWen_HK
dc.date.accessioned2010-09-06T09:41:36Z-
dc.date.available2010-09-06T09:41:36Z-
dc.date.issued2009en_HK
dc.identifier.citationClinica Chimica Acta, 2009, v. 406 n. 1-2, p. 31-35en_HK
dc.identifier.issn0009-8981en_HK
dc.identifier.urihttp://hdl.handle.net/10722/88303-
dc.description.abstractBackground: High density single nucleotide polymorphism (SNP) genotyping array is widely applied on genome-wide association study of common diseases. In these studies, a fixed batch-size of 48 or 96 samples allows high-throughput analysis. To enhance the clinical application of microarray analysis on personalized medicine, we describe a modified PCR purification protocol without batch-size limitation for whole-genome scan using ultra-high density SNP microarray. Methods: Enzyme-digested PCR products were purified with the use of magnetic beads. Separation of the magnetic particles applies magnetic stand devices instead of vacuum pumps. With no batch-size limitation, we genotyped 17 genomic samples and 3 whole genome amplified samples in order to examine the performance of the modified protocol. Results: Our method is simple and fast, provides sufficient amount and high quality PCR products for subsequent fragmentation and labeling procedures prior to GeneChip hybridization. We show that the purified DNA can be genotyped with good QC call rate of > 93% in average similar to standard protocol. With the use of the short protocol, we successfully identified the breakpoint localization of a ring chromosome in a female and located the disease gene in a consanguineous family affected by limb-girdle muscular dystrophy. Conclusion: By modifying a single step in the original protocol, we are able to speed up the overall genotyping analysis and change the batch-wise analysis to random-access analysis for ultra-high density whole-genome scan for personalized medicine, positional mapping, and cytogenetic analysis. © 2009 Elsevier B.V. All rights reserved.en_HK
dc.languageengen_HK
dc.publisherElsevier BV. The Journal's web site is located at http://www.elsevier.com/locate/ccaen_HK
dc.relation.ispartofClinica Chimica Actaen_HK
dc.rightsClinica Chimica Acta. Copyright © Elsevier BV.en_HK
dc.subject.meshCarcinoma, Basal Cell - geneticsen_HK
dc.subject.meshChromosome Mapping - methodsen_HK
dc.subject.meshCytogenetic Analysis - methodsen_HK
dc.subject.meshFemaleen_HK
dc.subject.meshGenetics, Medical - methodsen_HK
dc.subject.meshGenome, Humanen_HK
dc.subject.meshGenome-Wide Association Study - methodsen_HK
dc.subject.meshGenomics - methodsen_HK
dc.subject.meshHomozygoteen_HK
dc.subject.meshHumansen_HK
dc.subject.meshReproducibility of Resultsen_HK
dc.subject.meshSkin Neoplasms - geneticsen_HK
dc.subject.meshTime Factorsen_HK
dc.titleA fast modified protocol for random-access ultra-high density whole-genome scan: A tool for personalized genomic medicine, positional mapping, and cytogenetic analysisen_HK
dc.typeArticleen_HK
dc.identifier.openurlhttp://library.hku.hk:4550/resserv?sid=HKU:IR&issn=0009-8981&volume=406&issue=1-2&spage=31&epage=35&date=2009&atitle=A+fast+modified+protocol+for+random-access+ultra-high+density+whole-genome+scan:+a+tool+for+personalized+genomic+medicine,+positional+mapping,+and+cytogenetic+analysisen_HK
dc.identifier.emailLam, CW:ching-wanlam@pathology.hku.hken_HK
dc.identifier.authorityLam, CW=rp00260en_HK
dc.description.naturelink_to_subscribed_fulltext-
dc.identifier.doi10.1016/j.cca.2009.05.005en_HK
dc.identifier.pmid19445911en_HK
dc.identifier.scopuseid_2-s2.0-67650257202en_HK
dc.identifier.hkuros167820en_HK
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-67650257202&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume406en_HK
dc.identifier.issue1-2en_HK
dc.identifier.spage31en_HK
dc.identifier.epage35en_HK
dc.identifier.isiWOS:000268923900007-
dc.publisher.placeNetherlandsen_HK
dc.identifier.citeulike4794519-

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