Estimation and assessment of raw copy numbers at the single locus level

Bioinformatics

Volumn 24, Issue 6, 2008, Pages 759-767

  Bengtsson, H ^a   Irizarry, R ^b   Carvalho, B ^b   Speed, T P ^a,c  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b JOHNS HOPKINS UNIVERSITY   (United States)

^c WALTER AND ELIZA HALL INSTITUTE OF MEDICAL RESEARCH   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

OLIGONUCLEOTIDE;

ALLELE; ARTICLE; CONTROLLED STUDY; CROSS HYBRIDIZATION; DIPLOIDY; GENE EXPRESSION; GENE LOCUS; GENE SEQUENCE; GENETIC ALGORITHM; HAPLOTYPE MAP; INTERMETHOD COMPARISON; MATHEMATICAL COMPUTING; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; SIGNAL NOISE RATIO; SINGLE NUCLEOTIDE POLYMORPHISM; X CHROMOSOME;

EID: 40749162839     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btn016     Document Type: Article

References (23)

1. Affymetrix (2007) CNAT 4.0: Copy number and loss of heterozygosity estimation algorithms for the GeneChip human mapping 10/50/100/250/500K array set. Technical report, Affymetrix.
2. Affymetrix Inc (2007) Affymetrix Genotyping Console 2.0 - User Manual Affymetrix Inc.
3. Altshuler,D. et al. (2005) A haplotype-map of the human genome. Nature, 437, 1299-1320.
4. Bengtsson,H. (2004) Low-level analysis of microarray data. PhD Thesis, Centre for Mathematical Sciences, Division of Mathematical Statistics, Lund University.
5. Bengtsson,H., and Hössjer,O. (2006) Methodological study of affine transformations of gene expression data with proposed robust non-parametric multi-dimensional normalization method. BMC Bioinformatics, 7, 100.
6. Bengtsson,H. et al. (2004) Calibration and assessment of channel-specific biases in microarray data with extended dynamical range. BMC Bioinfo., 5, 177.
7. Bolstad,B. et al. (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics, 19, 185-93.
8. Bolstad,B.M. (2004) Low-level analysis of high-density oligonucleotide array data: Background, normalization and summarization PhD Thesis, University of California, Berkeley.
9. Bolstad,B. (2007) affyPLM: Methods for fitting probe-level models. http://bmbolstad.com.
10. Carvalho,B. et al. (2007) Exploration, normalization, and genotype calls of high density oligonucleotide SNP array data. Biostatistics 8, 485-499.
11. Iafrate,A.J. et al. (2004) Detection of large-scale variation in the human genome. Nature Genet, 36, 949-951.
12. Irizarry,R.A. et al. (2003) Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res., 31, e15.
13. Ishikawa,S. et al. (2005) Allelic dosage analysis with genotyping microarrays. Biochem. Biophys. Res. Commun., 333, 1309-1314.
14. Li,C. and Wong,W. (2001) Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc. Natl. Acad. Sci. USA, 98, 31-6. dchip.
15. Nannya,Y. et al. (2005) A robust algorithm for copy number detection using high-density oligonucleotide single nucleotide polymorphism genotyping arrays. Cancer Res., 65, 6071-6079.
16. Peiffer,D.A. et al. (2006) High-resolution genomic profiling of chromosomal aberrations using Intinium whole-genome genotyping. Genome Res., 16, 1136-1148.
17. R Development Core Team (2007) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria ISBN 3-900051-07-0.
18. Redon,R. et al. (2006) Global variation in copy number in the human genome Nature, 444, 444-454.
19. Sebat,J. et al. (2004) Large-scale copy number polymorphism in the human genome. Science 305, 525-8.
20. The International HapMap Consortium (2003) The International HapMap Project. Nature, 426, 789-796.
21. Ting,J. et al. (2006) Analysis and visualization of chromosomal abnormalities in SNP data with SNPscan. BMC Bioinfo., 7, 25.
22. Wirapati,P. and Speed,T. (2001) Fitting polyhedrial cones and simplices to multivariate data points. Draft.
23. Zhou,L. and Rocke,D.M. (2005) An expression index for Affymetrix GeneChips based on the generalized logarithm. Bioinformatics, 21, 3983-3989.