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

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TitleA fast modified protocol for random-access ultra-high density whole-genome scan: A tool for personalized genomic medicine, positional mapping, and cytogenetic analysis
AuthorsLau, KC1
Mak, CM2
Leung, KY4
Tsoi, TH3
Tang, HY3
Lee, P1
Lam, CW1
Issue Date2009
PublisherElsevier BV. The Journal's web site is located at http://www.elsevier.com/locate/cca
CitationClinica Chimica Acta, 2009, v. 406 n. 1-2, p. 31-35 [How to Cite?]
DOI: http://dx.doi.org/10.1016/j.cca.2009.05.005
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.
ISSN0009-8981
2011 Impact Factor: 2.535
2011 SCImago Journal Rankings: 0.189
DOIhttp://dx.doi.org/10.1016/j.cca.2009.05.005
ISI Accession Number IDWOS:000268923900007
ReferencesReferences in Scopus
DC Field
Value
dc.contributor.authorLau, KC
dc.contributor.authorMak, CM
dc.contributor.authorLeung, KY
dc.contributor.authorTsoi, TH
dc.contributor.authorTang, HY
dc.contributor.authorLee, P
dc.contributor.authorLam, CW
dc.date.accessioned2010-09-06T09:41:36Z
dc.date.available2010-09-06T09:41:36Z
dc.date.issued2009
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.
dc.description.natureLink_to_subscribed_fulltext
dc.identifier.citationClinica Chimica Acta, 2009, v. 406 n. 1-2, p. 31-35 [How to Cite?]
DOI: http://dx.doi.org/10.1016/j.cca.2009.05.005
dc.identifier.citeulike4794519
dc.identifier.doihttp://dx.doi.org/10.1016/j.cca.2009.05.005
dc.identifier.epage35
dc.identifier.hkuros167820
dc.identifier.isiWOS:000268923900007
dc.identifier.issn0009-8981
2011 Impact Factor: 2.535
2011 SCImago Journal Rankings: 0.189
dc.identifier.issue1-2
dc.identifier.openurl
dc.identifier.pmid19445911
dc.identifier.scopuseid_2-s2.0-67650257202
dc.identifier.spage31
dc.identifier.urihttp://hdl.handle.net/10722/88303
dc.identifier.volume406
dc.languageeng
dc.publisherElsevier BV. The Journal's web site is located at http://www.elsevier.com/locate/cca
dc.publisher.placeNetherlands
dc.relation.ispartofClinica Chimica Acta
dc.relation.referencesReferences in Scopus
dc.rightsClinica Chimica Acta. Copyright © Elsevier BV.
dc.subject.meshCarcinoma, Basal Cell - genetics
dc.subject.meshChromosome Mapping - methods
dc.subject.meshCytogenetic Analysis - methods
dc.subject.meshFemale
dc.subject.meshGenetics, Medical - methods
dc.subject.meshGenome, Human
dc.subject.meshGenome-Wide Association Study - methods
dc.subject.meshGenomics - methods
dc.subject.meshHomozygote
dc.subject.meshHumans
dc.subject.meshReproducibility of Results
dc.subject.meshSkin Neoplasms - genetics
dc.subject.meshTime Factors
dc.titleA fast modified protocol for random-access ultra-high density whole-genome scan: A tool for personalized genomic medicine, positional mapping, and cytogenetic analysis
dc.typeArticle
Author Affiliations
  1. The University of Hong Kong
  2. Princess Margaret Hospital Hong Kong
  3. Pamela Youde Nethersole Eastern Hospital
  4. Tsan Yuk Hospital