Normalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios

BMC Bioinformatics

Volumn 9, Issue , 2008, Pages

  Staaf, Johan ^a   Vallon Christersson, Johan ^a   Lindgren, David ^a   Juliusson, Gunnar ^a   Rosenquist, Richard ^b   Höglund, Mattias ^a   Borg, Åke ^a   Ringnér, Markus ^a  

^a LUND UNIVERSITY   (Sweden)

^b UPPSALA UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

CANCER GENOMICS; COPY NUMBER VARIATIONS; COPY-NUMBER ALTERATIONS; DATA INTERPRETATION; GENE COPY NUMBER; NORMALIZATION METHODS; NORMALIZATION STRATEGIES; PROPRIETARY SOFTWARE;

DATA PROCESSING; DISEASES; DNA SEQUENCES; ESTIMATION;

GENES;

DYE; DNA;

ARTICLE; BLOOD SAMPLING; COMPUTER PROGRAM; CONTROLLED STUDY; GENE NUMBER; GENETIC ALGORITHM; GENETIC DATABASE; GENETIC LINKAGE; GENETIC VARIABILITY; GENOMIC IN SITU HYBRIDIZATION; HETEROZYGOSITY LOSS; HUMAN; MICROARRAY ANALYSIS; NORMALIZATION METHOD; NUCLEOTIDE SEQUENCE; QUALITATIVE ANALYSIS; SAMPLING ERROR; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL ANALYSIS; ALLELIC IMBALANCE; ARTIFACT; DNA MICROARRAY; GENE DOSAGE; GENE EXPRESSION PROFILING; GENETICS; GENOMICS; HUMAN GENOME; IMAGE SUBTRACTION; METHODOLOGY; NEOPLASM; STANDARD;

ALLELIC IMBALANCE; ARTIFACTS; DNA, NEOPLASM; GENE DOSAGE; GENE EXPRESSION PROFILING; GENOME, HUMAN; GENOMICS; HUMANS; NEOPLASMS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, SINGLE NUCLEOTIDE; REFERENCE STANDARDS; RESEARCH DESIGN; SUBTRACTION TECHNIQUE;

EID: 54949156063     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-409     Document Type: Article

References (33)

1. Pinkel D Albertson DG Comparative genomic hybridization Annu Rev Genomics Hum Genet 2005, 6:331-354. 10.1146/ annurev.genom.6.080604.162140 16124865
2. Rajagopalan H Lengauer C Aneuploidy and cancer Nature 2004, 432:338-341. 10.1038/nature03099 15549096
3. Matsuzaki H Dong S Loi H Di X Liu G Hubbell E Law J Berntsen T Chadha M Hui H Yang G Kennedy GC Webster TA Cawley S Walsh PS Jones KW Fodor SP Mei R Genotyping over 100,000 SNPs on a pair of oligonucleotide arrays Nat Methods 2004, 1:109-111. 10.1038/nmeth718 15782172
4. Gunderson KL Steemers FJ Lee G Mendoza LG Chee MS A genome-wide scalable SNP genotyping assay using microarray technology Nat Genet 2005, 37:549-554. 10.1038/ng1547 15838508
5. Peiffer DA Le JM Steemers FJ Chang W Jenniges T Garcia F Haden K Li J Shaw CA Belmont J Cheung SW Shen RM Barker DL Gunderson KL High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping Genome Res 2006, 16:1136-1148. 1557768 16899659 10.1101/gr.5402306
6. Affymetrix http://www.affymetrix.com
7. Illumina http://www.illumina.com
8. Steemers FJ Chang W Lee G Barker DL Shen R Gunderson KL Whole-genome genotyping with the single-base extension assay Nat Methods 2006, 3:31-33. 10.1038/nmeth842 16369550
9. Bolstad BM Irizarry RA Astrand M Speed TP A comparison of normalization methods for high density oligonucleotide array data based on variance and bias Bioinformatics 2003, 19:185-193. 10.1093/bioinformatics/ 19.2.185 12538238
10. Barnes M Freudenberg J Thompson S Aronow B Pavlidis P Experimental comparison and cross-validation of the Affymetrix and Illumina gene expression analysis platforms Nucleic Acids Res 2005, 33:5914-5923. 1258170 16237126 10.1093/nar/gki890
11. Carvalho B Bengtsson H Speed TP Irizarry RA Exploration, normalization, and genotype calls of high-density oligonucleotide SNP array data Biostatistics 2007, 8:485-499. 10.1093/biostatistics/kxl042 17189563
12. Dunning MJ Barbosa-Morais NL Lynch AG Tavare S Ritchie ME Statistical issues in the analysis of Illumina data BMC Bioinformatics 2008, 9:85. 2291044 18254947 10.1186/1471-2105-9-85
13. Oosting J Lips EH van Eijk R Eilers PH Szuhai K Wijmenga C Morreau H van Wezel T High-resolution copy number analysis of paraffin-embedded archival tissue using SNP BeadArrays Genome Res 2007, 17:368-376. 1800928 17267813 10.1101/gr.5686107
14. Yang YH Dudoit S Luu P Lin DM Peng V Ngai J Speed TP Normalization for cDNA microarray data: A robust composite method addressing single and multiple slide systematic variation Nucleic Acids Res 2002, 30:e15. 100354 11842121 10.1093/nar/30.4.e15
15. Quackenbush J Microarray data normalization and transformation Nat Genet 2002, 32(Suppl):496-501. 10.1038/ng1032 12454644
16. Smyth GK Speed T Normalization of cDNA microarray data Methods 2003, 31:265-273. 10.1016/S1046-2023(03)00155-5 14597310
17. Khojasteh M Lam WL Ward RK MacAulay C A stepwise framework for the normalization of array CGH data BMC Bioinformatics 2005, 6:274. 1310623 16297240 10.1186/1471-2105-6-274
18. Staaf J Jonsson G Ringner M Vallon-Christersson J Normalization of array-CGH data: Influence of copy number imbalances BMC Genomics 2007, 8:382. 2190775 17953745 10.1186/1471-2164-8-382
19. Neuvial P Hupe P Brito I Liva S Manie E Brennetot C Radvanyi F Aurias A Barillot E Spatial normalization of array-CGH data BMC Bioinformatics 2006, 7:264. 1523216 16716215 10.1186/1471-2105-7-264
20. Assie G LaFramboise T Platzer P Bertherat J Stratakis CA Eng C SNP arrays in heterogeneous tissue: Highly accurate collection of both germline and somatic genetic information from unpaired single tumor samples Am J Hum Genet 2008, 82:903-915. 10.1016/j.ajhg.2008.01.012 18355774
21. Lin M Wei LJ Sellers WR Lieberfarb M Wong WH Li C dChipSNP: Significance curve and clustering of SNP-array-based loss-of-heterozygosity data Bioinformatics 2004, 20:1233-1240. 10.1093/bioinformatics/bth069 14871870
22. Staaf J Lindgren D Vallon-Christersson J Isaksson A Goransson H Juliusson G Rosenquist R Hoglund M Borg A Ringner M Segmentation-based detection of allelic imbalance and loss-of-heterozygosity in cancer cells using whole genome SNP arrays Genome Biol 2008, 9:R136. 10.1186/ gb-2008-9-9-r136 18796136
23. Gunnarsson R Staaf J Jansson M Ottesen AM Goransson H Liljedahl U Ralfkiaer U Mansouri M Buhl AM Smedby KE Hjalgrim H Syvanen AC Borg A Isaksson A Jurlander J Juliusson G Rosenquist R Screening for copy-number alterations and loss of heterozygosity in chronic lymphocytic leukemia-A comparative study of four differently designed, high resolution microarray platforms Genes Chromosomes Cancer 2008, 47:697-711. 10.1002/gcc.20575 18484635
24. Wang K Li M Hadley D Liu R Glessner J Grant SF Hakonarson H Bucan M PennCNV: An integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data Genome Res 2007, 17:1665-1674. 2045149 17921354 10.1101/gr.6861907
25. Greshock J Feng B Nogueira C Ivanova E Perna I Nathanson K Protopopov A Weber BL Chin L A comparison of DNA copy number profiling platforms Cancer Res 2007, 67:10173-10180. 10.1158/0008-5472.CAN-07-2102 17968032
26. HapMap http://www.hapmap.org
27. PennCNV http://www.neurogenome.org/cnv/penncnv/
28. SCIBLU Genomics, Lund University, Sweden http://www.lth.se/sciblu
29. SNP Technology Platform in Uppsala, Sweden http://www.genotyping.se
30. The R project for statistical computing http://www.r-project.org
31. BioConductor http://www.bioconductor.org
32. Venkatraman ES Olshen AB A faster circular binary segmentation algorithm for the analysis of array CGH data Bioinformatics 2007, 23:657-663. 10.1093/bioinformatics/btl646 17234643
33. Gene Expression Omnibus http://www.ncbi.nlm.nih.gov/geo/