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

  • Johan Staaf
  • Johan Vallon-Christersson
  • David Lindgren
  • Gunnar Juliusson
  • Richard Rosenquist
  • Mattias Höglund
  • Åke Borg
  • Markus Ringnér
Publishing year: 2008
Language: English
Publication/Series: BMC Bioinformatics
Volume: 9
Document type: Journal article
Publisher: BioMed Central (BMC)
Additional info: The information about affiliations in this record was updated in December 2015. The record was previously connected to the following departments: Division of Clinical Genetics (013022003), Hematology/Transplantation (013022014), Oncology, MV (013035000)

Abstract english

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.


  • Bioinformatics and Systems Biology


  • ISSN: 1471-2105
Åke Borg
Åke Borg
E-mail: ake [dot] borg [at] med [dot] lu [dot] se

Principal investigator


+46 46 275 25 52

MV 404 C21B2




MV 404 C21C2


Project manager

Familial Breast Cancer


Principal investigator

LUCC - Lund University Cancer Centre