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Article: AluScan: A method for genome-wide scanning of sequence and structure variations in the human genome
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TitleAluScan: A method for genome-wide scanning of sequence and structure variations in the human genome
 
AuthorsMei, L5
Ding, X5
Tsang, SY5
Pun, FW5
Ng, SK5
Yang, J5
Zhao, C5
Li, D6
Wan, W6 2
Yu, CH3 5
Tan, TC3 5
Poon, WS5 4
Leung, GK5 1
Ng, HK5 4
Zhang, L6 2
Xue, H5 2 5
 
Issue Date2011
 
PublisherBioMed Central Ltd. The Journal's web site is located at http://www.biomedcentral.com/bmcgenomics/
 
CitationBmc Genomics, 2011, v. 12 [How to Cite?]
DOI: http://dx.doi.org/10.1186/1471-2164-12-564
 
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.
 
ISSN1471-2164
2012 Impact Factor: 4.397
2012 SCImago Journal Rankings: 1.772
 
DOIhttp://dx.doi.org/10.1186/1471-2164-12-564
 
PubMed Central IDPMC3228862
 
ISI Accession Number IDWOS:000297808000001
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.

 
ReferencesReferences in Scopus
 
DC FieldValue
dc.contributor.authorMei, L
 
dc.contributor.authorDing, X
 
dc.contributor.authorTsang, SY
 
dc.contributor.authorPun, FW
 
dc.contributor.authorNg, SK
 
dc.contributor.authorYang, J
 
dc.contributor.authorZhao, C
 
dc.contributor.authorLi, D
 
dc.contributor.authorWan, W
 
dc.contributor.authorYu, CH
 
dc.contributor.authorTan, TC
 
dc.contributor.authorPoon, WS
 
dc.contributor.authorLeung, GK
 
dc.contributor.authorNg, HK
 
dc.contributor.authorZhang, L
 
dc.contributor.authorXue, H
 
dc.date.accessioned2012-02-03T06:15:01Z
 
dc.date.available2012-02-03T06:15:01Z
 
dc.date.issued2011
 
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.
 
dc.description.naturepublished_or_final_version
 
dc.identifier.citationBmc Genomics, 2011, v. 12 [How to Cite?]
DOI: http://dx.doi.org/10.1186/1471-2164-12-564
 
dc.identifier.citeulike10036281
 
dc.identifier.doihttp://dx.doi.org/10.1186/1471-2164-12-564
 
dc.identifier.hkuros198205
 
dc.identifier.isiWOS:000297808000001
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.

 
dc.identifier.issn1471-2164
2012 Impact Factor: 4.397
2012 SCImago Journal Rankings: 1.772
 
dc.identifier.pmcidPMC3228862
 
dc.identifier.pmid22087792
 
dc.identifier.scopuseid_2-s2.0-81155151513
 
dc.identifier.urihttp://hdl.handle.net/10722/144581
 
dc.identifier.volume12
 
dc.languageeng
 
dc.publisherBioMed Central Ltd. The Journal's web site is located at http://www.biomedcentral.com/bmcgenomics/
 
dc.publisher.placeUnited Kingdom
 
dc.relation.ispartofBMC Genomics
 
dc.relation.referencesReferences in Scopus
 
dc.rightsBMC Genomics. Copyright © BioMed Central Ltd.
 
dc.titleAluScan: A method for genome-wide scanning of sequence and structure variations in the human genome
 
dc.typeArticle
 
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<description.abstract>Background: 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 &apos;AluScan&apos;, of DNA sequences between Alu transposons, where Alu consensus sequence-based &apos;H-type&apos; PCR primers that elongate outward from the head of an Alu element are combined with &apos;T-type&apos; 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. &#169; 2011 Mei et al; licensee BioMed Central Ltd.</description.abstract>
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Author Affiliations
  1. The University of Hong Kong Li Ka Shing Faculty of Medicine
  2. Chinese Cancer Genome Consortium
  3. Queen Elizabeth Hospital Hong Kong
  4. Prince of Wales Hospital Hong Kong
  5. Hong Kong University of Science and Technology
  6. Capital Medical University China