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

doi:10.1186/1471-2105-9-409

BMC Bioinformatics

Volume 9

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Staaf J
Vallon-Christersson J
Lindgren D
Juliusson G
Rosenquist R
Höglund M
Borg Å
Ringnér M

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Staaf J
Vallon-Christersson J
Lindgren D
Juliusson G
Rosenquist R
Höglund M
Borg Å
Ringnér M
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Methodology article

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

Johan Staaf¹^,2 , Johan Vallon-Christersson¹^,2 , David Lindgren¹ , Gunnar Juliusson³ , Richard Rosenquist⁴ , Mattias Höglund¹ , Åke Borg¹^,2^,3 and Markus Ringnér¹^,2

¹Department of Oncology, Clinical Sciences, Lund University, SE-22185 Lund, Sweden

²CREATE Health Strategic Centre for Clinical Cancer Research, Lund University, SE-22184 Lund, Sweden

³Lund Strategic Research Center for Stem Cell Biology and Cell Therapy, Lund University, SE-22184 Lund, Sweden

⁴Department of Genetics and Pathology, Uppsala University, SE-75185 Uppsala, Sweden

author email corresponding author email

BMC Bioinformatics 2008, 9:409doi:10.1186/1471-2105-9-409


Published:	2 October 2008

Additional files

Additional file 1:

Supplementary figures. This file contains supplementary figures on the effect of BAF asymmetry on downstream analysis, a comparison of CN estimates before and after tQN, and a comparison of BAF asymmetry for regions of allelic imbalance before and after tQN.

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