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Article: AluScan: A method for genome-wide scanning of sequence and structure variations in the human genome

TitleAluScan: A method for genome-wide scanning of sequence and structure variations in the human genome
Authors
Issue Date2011
PublisherBioMed Central Ltd. The Journal's web site is located at http://www.biomedcentral.com/bmcgenomics/
Citation
Bmc Genomics, 2011, v. 12 How to Cite?
AbstractBackground: To complement next-generation sequencing technologies, there is a pressing need for efficient pre-sequencing capture methods with reduced costs and DNA requirement. The Alu family of short interspersed nucleotide elements is the most abundant type of transposable elements in the human genome and a recognized source of genome instability. With over one million Alu elements distributed throughout the genome, they are well positioned to facilitate genome-wide sequence amplification and capture of regions likely to harbor genetic variation hotspots of biological relevance.Results: Here we report on the use of inter-Alu PCR with an enhanced range of amplicons in conjunction with next-generation sequencing to generate an Alu-anchored scan, or 'AluScan', of DNA sequences between Alu transposons, where Alu consensus sequence-based 'H-type' PCR primers that elongate outward from the head of an Alu element are combined with 'T-type' primers elongating from the poly-A containing tail to achieve huge amplicon range. To illustrate the method, glioma DNA was compared with white blood cell control DNA of the same patient by means of AluScan. The over 10 Mb sequences obtained, derived from more than 8,000 genes spread over all the chromosomes, revealed a highly reproducible capture of genomic sequences enriched in genic sequences and cancer candidate gene regions. Requiring only sub-micrograms of sample DNA, the power of AluScan as a discovery tool for genetic variations was demonstrated by the identification of 357 instances of loss of heterozygosity, 341 somatic indels, 274 somatic SNVs, and seven potential somatic SNV hotspots between control and glioma DNA.Conclusions: AluScan, implemented with just a small number of H-type and T-type inter-Alu PCR primers, provides an effective capture of a diversity of genome-wide sequences for analysis. The method, by enabling an examination of gene-enriched regions containing exons, introns, and intergenic sequences with modest capture and sequencing costs, computation workload and DNA sample requirement is particularly well suited for accelerating the discovery of somatic mutations, as well as analysis of disease-predisposing germline polymorphisms, by making possible the comparative genome-wide scanning of DNA sequences from large human cohorts. © 2011 Mei et al; licensee BioMed Central Ltd.
Persistent Identifierhttp://hdl.handle.net/10722/144581
ISSN
2014 Impact Factor: 3.986
2013 SCImago Journal Rankings: 2.139
PubMed Central ID
ISI Accession Number ID
Funding AgencyGrant Number
Innovation and Technology Fund of Hong Kong SARITS/085/10
Hong Kong University of Science and TechnologyVPRDO09/10.SC08
SRFI11SC06
Funding Information:

We are grateful to the Innovation and Technology Fund of Hong Kong SAR (Grant ITS/085/10) and Hong Kong University of Science and Technology (Grant VPRDO09/10.SC08 and Special Research Fund Initiative SRFI11SC06) for financial support.

References

 

DC FieldValueLanguage
dc.contributor.authorMei, Len_HK
dc.contributor.authorDing, Xen_HK
dc.contributor.authorTsang, SYen_HK
dc.contributor.authorPun, FWen_HK
dc.contributor.authorNg, SKen_HK
dc.contributor.authorYang, Jen_HK
dc.contributor.authorZhao, Cen_HK
dc.contributor.authorLi, Den_HK
dc.contributor.authorWan, Wen_HK
dc.contributor.authorYu, CHen_HK
dc.contributor.authorTan, TCen_HK
dc.contributor.authorPoon, WSen_HK
dc.contributor.authorLeung, GKen_HK
dc.contributor.authorNg, HKen_HK
dc.contributor.authorZhang, Len_HK
dc.contributor.authorXue, Hen_HK
dc.date.accessioned2012-02-03T06:15:01Z-
dc.date.available2012-02-03T06:15:01Z-
dc.date.issued2011en_HK
dc.identifier.citationBmc Genomics, 2011, v. 12en_HK
dc.identifier.issn1471-2164en_HK
dc.identifier.urihttp://hdl.handle.net/10722/144581-
dc.description.abstractBackground: To complement next-generation sequencing technologies, there is a pressing need for efficient pre-sequencing capture methods with reduced costs and DNA requirement. The Alu family of short interspersed nucleotide elements is the most abundant type of transposable elements in the human genome and a recognized source of genome instability. With over one million Alu elements distributed throughout the genome, they are well positioned to facilitate genome-wide sequence amplification and capture of regions likely to harbor genetic variation hotspots of biological relevance.Results: Here we report on the use of inter-Alu PCR with an enhanced range of amplicons in conjunction with next-generation sequencing to generate an Alu-anchored scan, or 'AluScan', of DNA sequences between Alu transposons, where Alu consensus sequence-based 'H-type' PCR primers that elongate outward from the head of an Alu element are combined with 'T-type' primers elongating from the poly-A containing tail to achieve huge amplicon range. To illustrate the method, glioma DNA was compared with white blood cell control DNA of the same patient by means of AluScan. The over 10 Mb sequences obtained, derived from more than 8,000 genes spread over all the chromosomes, revealed a highly reproducible capture of genomic sequences enriched in genic sequences and cancer candidate gene regions. Requiring only sub-micrograms of sample DNA, the power of AluScan as a discovery tool for genetic variations was demonstrated by the identification of 357 instances of loss of heterozygosity, 341 somatic indels, 274 somatic SNVs, and seven potential somatic SNV hotspots between control and glioma DNA.Conclusions: AluScan, implemented with just a small number of H-type and T-type inter-Alu PCR primers, provides an effective capture of a diversity of genome-wide sequences for analysis. The method, by enabling an examination of gene-enriched regions containing exons, introns, and intergenic sequences with modest capture and sequencing costs, computation workload and DNA sample requirement is particularly well suited for accelerating the discovery of somatic mutations, as well as analysis of disease-predisposing germline polymorphisms, by making possible the comparative genome-wide scanning of DNA sequences from large human cohorts. © 2011 Mei et al; licensee BioMed Central Ltd.en_HK
dc.languageengen_US
dc.publisherBioMed Central Ltd. The Journal's web site is located at http://www.biomedcentral.com/bmcgenomics/en_HK
dc.relation.ispartofBMC Genomicsen_HK
dc.rightsBMC Genomics. Copyright © BioMed Central Ltd.en_US
dc.titleAluScan: A method for genome-wide scanning of sequence and structure variations in the human genomeen_HK
dc.typeArticleen_HK
dc.identifier.emailLeung, GK: gilberto@hkucc.hku.hken_HK
dc.identifier.authorityLeung, GK=rp00522en_HK
dc.description.naturepublished_or_final_version-
dc.identifier.doi10.1186/1471-2164-12-564en_HK
dc.identifier.pmid22087792-
dc.identifier.pmcidPMC3228862-
dc.identifier.scopuseid_2-s2.0-81155151513en_HK
dc.identifier.hkuros198205en_US
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-81155151513&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume12en_HK
dc.identifier.isiWOS:000297808000001-
dc.publisher.placeUnited Kingdomen_HK
dc.identifier.scopusauthoridMei, L=35332267900en_HK
dc.identifier.scopusauthoridDing, X=54412134300en_HK
dc.identifier.scopusauthoridTsang, SY=7102255989en_HK
dc.identifier.scopusauthoridPun, FW=15124087400en_HK
dc.identifier.scopusauthoridNg, SK=16310300600en_HK
dc.identifier.scopusauthoridYang, J=54413413500en_HK
dc.identifier.scopusauthoridZhao, C=7403564096en_HK
dc.identifier.scopusauthoridLi, D=54412616600en_HK
dc.identifier.scopusauthoridWan, W=24726509900en_HK
dc.identifier.scopusauthoridYu, CH=54413473600en_HK
dc.identifier.scopusauthoridTan, TC=7402022442en_HK
dc.identifier.scopusauthoridPoon, WS=7103025507en_HK
dc.identifier.scopusauthoridLeung, GK=35965118200en_HK
dc.identifier.scopusauthoridNg, HK=7401619354en_HK
dc.identifier.scopusauthoridZhang, L=36092139000en_HK
dc.identifier.scopusauthoridXue, H=37041779000en_HK
dc.identifier.citeulike10036281-

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