메뉴 건너뛰기




Volumn 37, Issue 17, 2009, Pages

Hybridization modeling of oligonucleotide snp arrays for accurate DNA copy number estimation

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ALLELE; ARTICLE; BASE MISPAIRING; BINDING AFFINITY; CELL LINE; CONTROLLED STUDY; DNA BINDING; DNA HYBRIDIZATION; DNA SEQUENCE; ENERGY; GENE LOCUS; GENE REPLICATION; GENOTYPE; HAPLOTYPE MAP; NUCLEIC ACID PROBE; PRIORITY JOURNAL; PROBE INTENSITY COMPOSITE REPRESENTATION; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 73149105510     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp559     Document Type: Article
Times cited : (11)

References (31)
  • 1
    • 84969213492 scopus 로고    scopus 로고
    • Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls
    • Wellcome Trust Case-Control Consortium.
    • Wellcome Trust Case-Control Consortium. (2007) Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature, 447, 661-678.
    • (2007) Nature , vol.447 , pp. 661-678
  • 6
    • 73149122153 scopus 로고    scopus 로고
    • Affymetrix. BRLMM: an improved genotying calling method for the GeneChip Human Mapping 500K Array Set. White Paper
    • Affymetrix. (2006) BRLMM: an improved genotying calling method for the GeneChip Human Mapping 500K Array Set. White Paper.
    • (2006)
  • 9
    • 22244453416 scopus 로고    scopus 로고
    • A robust algorithm for copy number detection using high-density oligonucleotide single nucleotide polymorphism genotyping arrays
    • Nannya, Y., Sanada, M., Nakazaki, K., Hosoya, N., Wang, L., Hangaishi, A., Kurokawa, M., Chiba, S., Bailey, D.K., Kennedy, G.C. et al. (2005) A robust algorithm for copy number detection using high-density oligonucleotide single nucleotide polymorphism genotyping arrays. Cancer Res., 65, 6071-6079.
    • (2005) Cancer Res. , vol.65 , pp. 6071-6079
    • Nannya, Y.1    Sanada, M.2    Nakazaki, K.3    Hosoya, N.4    Wang, L.5    Hangaishi, A.6    Kurokawa, M.7    Chiba, S.8    Bailey, D.K.9    Kennedy, G.C.10
  • 13
    • 33747864545 scopus 로고    scopus 로고
    • GEL: a novel genotype calling algorithm using empirical likelihood
    • Nicolae, D.L., Wu, X., Miyake, K. and Cox, N.J. (2006) GEL: a novel genotype calling algorithm using empirical likelihood. Bioinformatics, 22, 1942-1947.
    • (2006) Bioinformatics , vol.22 , pp. 1942-1947
    • Nicolae, D.L.1    Wu, X.2    Miyake, K.3    Cox, N.J.4
  • 14
    • 30344454706 scopus 로고    scopus 로고
    • A genotype calling algorithm for Affymetrix SNP arrays
    • Rabbee, N. and Speed, T.P. (2006) A genotype calling algorithm for Affymetrix SNP arrays. Bioinformatics, 22, 7-12.
    • (2006) Bioinformatics , vol.22 , pp. 7-12
    • Rabbee, N.1    Speed, T.P.2
  • 15
    • 34147131753 scopus 로고    scopus 로고
    • PLASQ: a generalized linear model-based procedure to determine allelic dosage in cancer cells from SNP array data
    • LaFramboise, T., Harrington, D. and Weir, B.A. (2007) PLASQ: a generalized linear model-based procedure to determine allelic dosage in cancer cells from SNP array data. Biostatistics, 8, 323-336.
    • (2007) Biostatistics , vol.8 , pp. 323-336
    • LaFramboise, T.1    Harrington, D.2    Weir, B.A.3
  • 16
    • 34547830829 scopus 로고    scopus 로고
    • A multi-array multi-SNP genotyping algorithm for Affymetrix SNP microarrays
    • Xiao, Y., Segal, M.R., Yang, Y.H. and Yeh, R.F. (2007) A multi-array multi-SNP genotyping algorithm for Affymetrix SNP microarrays. Bioinformatics, 23, 1459-1467.
    • (2007) Bioinformatics , vol.23 , pp. 1459-1467
    • Xiao, Y.1    Segal, M.R.2    Yang, Y.H.3    Yeh, R.F.4
  • 17
    • 34147136617 scopus 로고    scopus 로고
    • Exploration, normalization, and genotype calls of high-density oligonucleotide SNP array data
    • Carvalho, B., Bengtsson, H., Speed, T.P. and Irizarry, R.A. (2007) Exploration, normalization, and genotype calls of high-density oligonucleotide SNP array data. Biostatistics, 8, 485-499.
    • (2007) Biostatistics , vol.8 , pp. 485-499
    • Carvalho, B.1    Bengtsson, H.2    Speed, T.P.3    Irizarry, R.A.4
  • 18
    • 40749162839 scopus 로고    scopus 로고
    • Estimation and assessment of raw copy numbers at the single locus level
    • Bengtsson, H., Irizarry, R., Carvalho, B. and Speed, T.P. (2008) Estimation and assessment of raw copy numbers at the single locus level. Bioinformatics, 24, 759-767.
    • (2008) Bioinformatics , vol.24 , pp. 759-767
    • Bengtsson, H.1    Irizarry, R.2    Carvalho, B.3    Speed, T.P.4
  • 19
    • 33847413173 scopus 로고    scopus 로고
    • Free energy of DNA duplex formation on short oligonucleotide microarrays
    • Zhang, L., Wu, C., Carta, R. and Zhao, H. (2007) Free energy of DNA duplex formation on short oligonucleotide microarrays. Nucleic Acids Res., 35, e18.
    • (2007) Nucleic Acids Res. , vol.35
    • Zhang, L.1    Wu, C.2    Carta, R.3    Zhao, H.4
  • 20
    • 0038729666 scopus 로고    scopus 로고
    • A model of molecular interactions on short oligonucleotide microarrays
    • Zhang, L., Miles, M.F. and Aldape, K.D. (2003) A model of molecular interactions on short oligonucleotide microarrays. Nat. Biotechnol., 21, 818-821.
    • (2003) Nat. Biotechnol. , vol.21 , pp. 818-821
    • Zhang, L.1    Miles, M.F.2    Aldape, K.D.3
  • 21
    • 33744542889 scopus 로고    scopus 로고
    • Relationship between gene expression and observed intensities in DNA microarrays-a modeling study
    • Held, G.A., Grinstein, G. and Tu, Y. (2006) Relationship between gene expression and observed intensities in DNA microarrays-a modeling study. Nucleic Acids Res., 34, e70.
    • (2006) Nucleic Acids Res. , vol.34
    • Held, G.A.1    Grinstein, G.2    Tu, Y.3
  • 22
    • 0037934649 scopus 로고    scopus 로고
    • Modeling of DNA microarray data by using physical properties of hybridization
    • Held, G.A., Grinstein, G. and Tu, Y. (2003) Modeling of DNA microarray data by using physical properties of hybridization. Proc. Natl Acad. Sci. USA, 100, 7575-7580.
    • (2003) Proc. Natl Acad. Sci. USA , vol.100 , pp. 7575-7580
    • Held, G.A.1    Grinstein, G.2    Tu, Y.3
  • 24
    • 0037316303 scopus 로고    scopus 로고
    • A comparison of normalization methods for high density oligonu-cleotide array data based on variance and bias
    • Bolstad, B.M., Irizarry, R.A., Astrand, M. and Speed, T.P. (2003) A comparison of normalization methods for high density oligonu-cleotide array data based on variance and bias. Bioinformatics, 19, 185-193.
    • (2003) Bioinformatics , vol.19 , pp. 185-193
    • Bolstad, B.M.1    Irizarry, R.A.2    Astrand, M.3    Speed, T.P.4
  • 25
    • 57249116888 scopus 로고    scopus 로고
    • Cross-hybridization modeling on Affymetrix exon arrays
    • Kapur, K., Jiang, H., Xing, Y. and Wong, W.H. (2008) Cross-hybridization modeling on Affymetrix exon arrays. Bioinformatics, 24, 2887-2893.
    • (2008) Bioinformatics , vol.24 , pp. 2887-2893
    • Kapur, K.1    Jiang, H.2    Xing, Y.3    Wong, W.H.4
  • 27
    • 0035793042 scopus 로고    scopus 로고
    • Model-based analysis of oligonu-cleotide arrays: expression index computation and outlier detection
    • Li, C. and Wong, W.H. (2001) Model-based analysis of oligonu-cleotide arrays: expression index computation and outlier detection. Proc. Natl Acad. Sci. USA, 98, 31-36.
    • (2001) Proc. Natl Acad. Sci. USA , vol.98 , pp. 31-36
    • Li, C.1    Wong, W.H.2
  • 29
    • 34347339520 scopus 로고    scopus 로고
    • Methods and strategies for analyzing copy number variation using DNA microarrays
    • Carter, N.P. (2007) Methods and strategies for analyzing copy number variation using DNA microarrays. Nat. Genet., 39, S16-S21.
    • (2007) Nat. Genet. , vol.39
    • Carter, N.P.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.