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

Staaf, Johan LU ; Vallon-Christersson, Johan LU ; Lindgren, David LU ; Juliusson, Gunnar LU ; Rosenquist, Richard; Höglund, Mattias LU ; Borg, Åke LU and Ringnér, Markus LU (2008) In BMC Bioinformatics 9.
Abstract
BACKGROUND: Illumina Infinium whole genome genotyping (WGG) arrays are increasingly being applied in cancer genomics to study gene copy number alterations and allele-specific aberrations such as loss-of-heterozygosity (LOH). Methods developed for normalization of WGG arrays have mostly focused on diploid, normal samples. However, for cancer samples genomic aberrations may confound normalization and data interpretation. Therefore, we examined the effects of the conventionally used normalization method for Illumina Infinium arrays when applied to cancer samples. RESULTS: We demonstrate an asymmetry in the detection of the two alleles for each SNP, which deleteriously influences both allelic proportions and copy number estimates. The... (More)
BACKGROUND: Illumina Infinium whole genome genotyping (WGG) arrays are increasingly being applied in cancer genomics to study gene copy number alterations and allele-specific aberrations such as loss-of-heterozygosity (LOH). Methods developed for normalization of WGG arrays have mostly focused on diploid, normal samples. However, for cancer samples genomic aberrations may confound normalization and data interpretation. Therefore, we examined the effects of the conventionally used normalization method for Illumina Infinium arrays when applied to cancer samples. RESULTS: We demonstrate an asymmetry in the detection of the two alleles for each SNP, which deleteriously influences both allelic proportions and copy number estimates. The asymmetry is caused by a remaining bias between the two dyes used in the Infinium II assay after using the normalization method in Illumina's proprietary software (BeadStudio). We propose a quantile normalization strategy for correction of this dye bias. We tested the normalization strategy using 535 individual hybridizations from 10 data sets from the analysis of cancer genomes and normal blood samples generated on Illumina Infinium II 300 k version 1 and 2, 370 k and 550 k BeadChips. We show that the proposed normalization strategy successfully removes asymmetry in estimates of both allelic proportions and copy numbers. Additionally, the normalization strategy reduces the technical variation for copy number estimates while retaining the response to copy number alterations. CONCLUSION: The proposed normalization strategy represents a valuable tool that improves the quality of data obtained from Illumina Infinium arrays, in particular when used for LOH and copy number variation studies. (Less)
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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
BMC Bioinformatics
volume
9
publisher
BioMed Central
external identifiers
  • WOS:000260489200002
  • PMID:18831757
  • Scopus:54949156063
ISSN
1471-2105
DOI
10.1186/1471-2105-9-409
project
CREATE Health
language
English
LU publication?
yes
id
bdad6745-a610-4565-97e2-76c617d483b9 (old id 1262617)
alternative location
http://www.ncbi.nlm.nih.gov/pubmed/18831757?dopt=Abstract
date added to LUP
2008-11-06 12:00:20
date last changed
2016-10-13 04:25:11
@misc{bdad6745-a610-4565-97e2-76c617d483b9,
  abstract     = {BACKGROUND: Illumina Infinium whole genome genotyping (WGG) arrays are increasingly being applied in cancer genomics to study gene copy number alterations and allele-specific aberrations such as loss-of-heterozygosity (LOH). Methods developed for normalization of WGG arrays have mostly focused on diploid, normal samples. However, for cancer samples genomic aberrations may confound normalization and data interpretation. Therefore, we examined the effects of the conventionally used normalization method for Illumina Infinium arrays when applied to cancer samples. RESULTS: We demonstrate an asymmetry in the detection of the two alleles for each SNP, which deleteriously influences both allelic proportions and copy number estimates. The asymmetry is caused by a remaining bias between the two dyes used in the Infinium II assay after using the normalization method in Illumina's proprietary software (BeadStudio). We propose a quantile normalization strategy for correction of this dye bias. We tested the normalization strategy using 535 individual hybridizations from 10 data sets from the analysis of cancer genomes and normal blood samples generated on Illumina Infinium II 300 k version 1 and 2, 370 k and 550 k BeadChips. We show that the proposed normalization strategy successfully removes asymmetry in estimates of both allelic proportions and copy numbers. Additionally, the normalization strategy reduces the technical variation for copy number estimates while retaining the response to copy number alterations. CONCLUSION: The proposed normalization strategy represents a valuable tool that improves the quality of data obtained from Illumina Infinium arrays, in particular when used for LOH and copy number variation studies.},
  author       = {Staaf, Johan and Vallon-Christersson, Johan and Lindgren, David and Juliusson, Gunnar and Rosenquist, Richard and Höglund, Mattias and Borg, Åke and Ringnér, Markus},
  issn         = {1471-2105},
  language     = {eng},
  publisher    = {ARRAY(0x9d1b338)},
  series       = {BMC Bioinformatics},
  title        = {Normalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios.},
  url          = {http://dx.doi.org/10.1186/1471-2105-9-409},
  volume       = {9},
  year         = {2008},
}