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Volumn 21, Issue 3, 2010, Pages 126-140

Multi-sample pooling and illumina genome analyzer sequencing methods to determine gene sequence variation for database development

Author keywords

Illumina; Massively parallel sequencing; Next generation sequencing; RET

Indexed keywords

GENOMIC DNA; NUCLEOTIDE;

EID: 77956637236     PISSN: 15240215     EISSN: 19434731     Source Type: Journal    
DOI: None     Document Type: Article
Times cited : (8)

References (25)
  • 1
    • 60749100685 scopus 로고    scopus 로고
    • SNP frequency estimation using massively parallel sequencing of pooled DNA
    • Ingman M, Gyllensten U. SNP frequency estimation using massively parallel sequencing of pooled DNA. Eur J Hum Genet 2009;17:383-386.
    • (2009) Eur J Hum Genet , vol.17 , pp. 383-386
    • Ingman, M.1    Gyllensten, U.2
  • 2
    • 53249132629 scopus 로고    scopus 로고
    • Identification of genetic variants using bar-coded multiplexed sequencing
    • Craig DW, Pearson JV, Szelinger S, et al. Identification of genetic variants using bar-coded multiplexed sequencing. Nat Methods 2008;5:887-893.
    • (2008) Nat Methods , vol.5 , pp. 887-893
    • Craig, D.W.1    Pearson, J.V.2    Szelinger, S.3
  • 3
    • 56149096455 scopus 로고    scopus 로고
    • Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology
    • Cronn R, Liston A, Parks M, Gernandt DS, Shen R, Mockler T. Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology. Nucleic Acids Res 2008;36:e122.
    • (2008) Nucleic Acids Res , vol.36
    • Cronn, R.1    Liston, A.2    Parks, M.3    Gernandt, D.S.4    Shen, R.5    Mockler, T.6
  • 4
    • 63949086651 scopus 로고    scopus 로고
    • Quantification of rare allelic variants from pooled genomic DNA
    • Druley TE, Vallania FL, Wegner DJ, et al. Quantification of rare allelic variants from pooled genomic DNA. Nat Methods 2009;6:263-265.
    • (2009) Nat Methods , vol.6 , pp. 263-265
    • Druley, T.E.1    Vallania, F.L.2    Wegner, D.J.3
  • 5
    • 67650047735 scopus 로고    scopus 로고
    • DNA Sudoku - Harnessing high-throughput sequencing for multiplexed specimen analysis
    • Erlich Y, Chang K, Gordon A, et al. DNA Sudoku - harnessing high-throughput sequencing for multiplexed specimen analysis. Genome Res 2009;19:1243-1253.
    • (2009) Genome Res , vol.19 , pp. 1243-1253
    • Erlich, Y.1    Chang, K.2    Gordon, A.3
  • 6
    • 71749099456 scopus 로고    scopus 로고
    • Deep sequencing to reveal new variants in pooled DNA samples
    • Out AA, van Minderhout IJ, Goeman JJ, et al. Deep sequencing to reveal new variants in pooled DNA samples. Hum Mutat 2009;30:1703-1712.
    • (2009) Hum Mutat , vol.30 , pp. 1703-1712
    • Out, A.A.1    Van Minderhout, I.J.2    Goeman, J.J.3
  • 7
    • 40149098690 scopus 로고    scopus 로고
    • SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries
    • Van Tassell CP, Smith TP, Matukumalli LK, et al. SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries. Nat Methods 2008;5:247-252.
    • (2008) Nat Methods , vol.5 , pp. 247-252
    • Van Tassell, C.P.1    Smith, T.P.2    Matukumalli, L.K.3
  • 8
    • 68549098191 scopus 로고    scopus 로고
    • Detecting SNPs and estimating allele frequencies in clonal bacterial populations by sequencing pooled DNA
    • Holt KE, Teo YY, Li H, et al. Detecting SNPs and estimating allele frequencies in clonal bacterial populations by sequencing pooled DNA. Bioinformatics 2009;25:2074-2075.
    • (2009) Bioinformatics , vol.25 , pp. 2074-2075
    • Holt, K.E.1    Teo, Y.Y.2    Li, H.3
  • 9
    • 69949122158 scopus 로고    scopus 로고
    • VarScan: Variant detection in massively parallel sequencing of individual and pooled samples
    • Koboldt DC, Chen K, Wylie T, et al. VarScan: variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics 2009;25:2283-2285.
    • (2009) Bioinformatics , vol.25 , pp. 2283-2285
    • Koboldt, D.C.1    Chen, K.2    Wylie, T.3
  • 10
    • 67650034261 scopus 로고    scopus 로고
    • Overlapping pools for high-throughput targeted resequencing
    • Prabhu S, Pe'er I. Overlapping pools for high-throughput targeted resequencing. Genome Res 2009;19:1254-1261.
    • (2009) Genome Res , vol.19 , pp. 1254-1261
    • Prabhu, S.1    Pe'er, I.2
  • 11
    • 77950657866 scopus 로고    scopus 로고
    • Accurate detection and genotyping of SNPs utilizing population sequencing data
    • Bansal V, Harismendy O, Tewhey R, et al. Accurate detection and genotyping of SNPs utilizing population sequencing data. Genome Res 2010;20:537-545.
    • (2010) Genome Res , vol.20 , pp. 537-545
    • Bansal, V.1    Harismendy, O.2    Tewhey, R.3
  • 12
    • 34948901347 scopus 로고    scopus 로고
    • Mutation database for the galactose-1-phosphate uridyltransferase (GALT) gene
    • DOI 10.1002/humu.20544
    • Calderon FR, Phansalkar AR, Crockett DK, Miller M, Mao R. Mutation database for the galactose-1-phosphate uridyltransferase (GALT) gene. Hum Mutat 2007;28:939-943. (Pubitemid 47519385)
    • (2007) Human Mutation , vol.28 , Issue.10 , pp. 939-943
    • Calderon, F.R.O.1    Phansalkar, A.R.2    Crockett, D.K.3    Miller, M.4    Mao, R.5
  • 13
    • 63749097657 scopus 로고    scopus 로고
    • Multiple endocrine neoplasia type 2 RET protooncogene database: Repository of MEN2-associated RET sequence variation and reference for genotype/phenotype correlations
    • Margraf RL, Crockett DK, Krautscheid PM, et al. Multiple endocrine neoplasia type 2 RET protooncogene database: repository of MEN2-associated RET sequence variation and reference for genotype/phenotype correlations. Hum Mutat 2009;30:548-556.
    • (2009) Hum Mutat , vol.30 , pp. 548-556
    • Margraf, R.L.1    Crockett, D.K.2    Krautscheid, P.M.3
  • 14
    • 4644256817 scopus 로고    scopus 로고
    • The relationship between specific RET proto-oncogene mutations and disease phenotype in multiple endocrine neoplasia type 2. International RET mutation consortium analysis
    • Eng C, Clayton D, Schuffenecker I, et al. The relationship between specific RET proto-oncogene mutations and disease phenotype in multiple endocrine neoplasia type 2. International RET mutation consortium analysis. JAMA 1996;276:1575-1579.
    • (1996) JAMA , vol.276 , pp. 1575-1579
    • Eng, C.1    Clayton, D.2    Schuffenecker, I.3
  • 15
    • 52649157765 scopus 로고    scopus 로고
    • Substantial biases in ultra-short read data sets from high-throughput DNA sequencing
    • Dohm JC, Lottaz C, Borodina T, Himmelbauer H. Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res 2008;36:e105.
    • (2008) Nucleic Acids Res , vol.36
    • Dohm, J.C.1    Lottaz, C.2    Borodina, T.3    Himmelbauer, H.4
  • 16
    • 67749130797 scopus 로고    scopus 로고
    • Medullary thyroid cancer: Management guidelines of the American Thyroid Association
    • Kloos RT, Eng C, Evans DB, et al. Medullary thyroid cancer: management guidelines of the American Thyroid Association. Thyroid 2009;19:565-612.
    • (2009) Thyroid , vol.19 , pp. 565-612
    • Kloos, R.T.1    Eng, C.2    Evans, D.B.3
  • 17
    • 0033990048 scopus 로고    scopus 로고
    • Primer3 on the www for general users and for biologist programmers
    • Rozen S, Skaletsky H. Primer3 on the www for general users and for biologist programmers. Methods Mol Biol 2000;132:365-386.
    • (2000) Methods Mol Biol , vol.132 , pp. 365-386
    • Rozen, S.1    Skaletsky, H.2
  • 18
    • 57049122389 scopus 로고    scopus 로고
    • A large genome center's improvements to the Illumina sequencing system
    • Quail MA, Kozarewa I, Smith F, et al. A large genome center's improvements to the Illumina sequencing system. Nat Methods 2008;5:1005-1010.
    • (2008) Nat Methods , vol.5 , pp. 1005-1010
    • Quail, M.A.1    Kozarewa, I.2    Smith, F.3
  • 19
    • 66449114324 scopus 로고    scopus 로고
    • SNP detection for massively parallel whole-genome resequencing
    • Li R, Li Y, Fang X, Yang H, Wang J, Kristiansen K. SNP detection for massively parallel whole-genome resequencing. Genome Res 2009;19:1124-1132.
    • (2009) Genome Res , vol.19 , pp. 1124-1132
    • Li, R.1    Li, Y.2    Fang, X.3    Yang, H.4    Wang, J.5    Kristiansen, K.6
  • 20
    • 65449144325 scopus 로고    scopus 로고
    • Evaluation of next generation sequencing platforms for population targeted sequencing studies
    • Harismendy O, Ng PC, Strausberg RL, et al. Evaluation of next generation sequencing platforms for population targeted sequencing studies. Genome Biol 2009;10:R32.
    • (2009) Genome Biol , vol.10
    • Harismendy, O.1    Ng, P.C.2    Strausberg, R.L.3
  • 21
    • 65449154418 scopus 로고    scopus 로고
    • Method for improving sequence coverage uniformity of targeted genomic intervals amplified by LR-PCR using Illumina GA sequencing-by-synthesis technology
    • Harismendy O, Frazer K. Method for improving sequence coverage uniformity of targeted genomic intervals amplified by LR-PCR using Illumina GA sequencing-by-synthesis technology. Biotechniques 2009;46:229-231.
    • (2009) Biotechniques , vol.46 , pp. 229-231
    • Harismendy, O.1    Frazer, K.2
  • 22
    • 55549089660 scopus 로고    scopus 로고
    • Accurate whole human genome sequencing using reversible terminator chemistry
    • Bentley DR, Balasubramanian S, Swerdlow HP, et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 2008;456:53-59.
    • (2008) Nature , vol.456 , pp. 53-59
    • Bentley, D.R.1    Balasubramanian, S.2    Swerdlow, H.P.3
  • 25
    • 55549097836 scopus 로고    scopus 로고
    • Mapping short DNA sequencing reads and calling variants using mapping quality scores
    • Li H, Ruan J, Durbin R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 2008;18:1851-1858.
    • (2008) Genome Res , vol.18 , pp. 1851-1858
    • Li, H.1    Ruan, J.2    Durbin, R.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.