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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
BMC Bioinformatics. 2008; 9: 409. Published online 2008 October 2. doi: 10.1186/1471-2105-9-409
PMCID:
PMC2572624
Abstract Full Text PDF–3.0M Supplementary Material

Is Cited by the Following 16 Articles in this Archive:

Identity by Descent Mapping of Founder Mutations in Cancer Using High-Resolution Tumor SNP Data
Eric Letouzé, Aliou Sow, Fabien Petel, Roberto Rosati, Bonald C. Figueiredo, Nelly Burnichon, Anne-Paule Gimenez-Roqueplo, Enzo Lalli, Aurélien de Reyniès
PLoS One. 2012; 7(5): e35897. Published online 2012 May 2. doi: 10.1371/journal.pone.0035897
PMCID:
PMC3342326
Abstract Full Text PDF–1.2M Supplementary Material
Allele-specific disparity in breast cancer
Fatemeh Kaveh, Hege Edvardsen, Anne-Lise Børresen-Dale, Vessela N Kristensen, Hiroko K Solvang
BMC Med Genomics. 2011; 4: 85. Published online 2011 December 21. doi: 10.1186/1755-8794-4-85
PMCID:
PMC3337547
Abstract Full Text PDF–723K Supplementary Material
Batch effect correction for genome-wide methylation data with Illumina Infinium platform
Zhifu Sun, High Seng Chai, Yanhong Wu, Wendy M White, Krishna V Donkena, Christopher J Klein, Vesna D Garovic, Terry M Therneau, Jean-Pierre A Kocher
BMC Med Genomics. 2011; 4: 84. Published online 2011 December 16. doi: 10.1186/1755-8794-4-84
PMCID:
PMC3265417
Abstract Full Text PDF–1.5M Supplementary Material
Landscape of somatic allelic imbalances and copy number alterations in HER2-amplified breast cancer
Johan Staaf, Göran Jönsson, Markus Ringnér, Bo Baldetorp, Åke Borg
Breast Cancer Res. 2011; 13(6): R129. Published online 2011 December 14. doi: 10.1186/bcr3075
PMCID:
PMC3326571
Abstract Full Text PDF–845K Supplementary Material
Identification, utilisation and mapping of novel transcriptome-based markers from blackcurrant (Ribes nigrum)
Joanne R Russell, Micha Bayer, Clare Booth, Linda Cardle, Christine A Hackett, Pete E Hedley, Linzi Jorgensen, Jenny A Morris, Rex M Brennan
BMC Plant Biol. 2011; 11: 147. Published online 2011 October 28. doi: 10.1186/1471-2229-11-147
PMCID:
PMC3217869
Abstract Full Text PDF–376K Supplementary Material
Clonal Evolution through Loss of Chromosomes and Subsequent Polyploidization in Chondrosarcoma
Linda Olsson, Kajsa Paulsson, Judith V. M. G. Bovée, Karolin H. Nord
PLoS One. 2011; 6(9): e24977. Published online 2011 September 20. doi: 10.1371/journal.pone.0024977
Correction in:
PLoS One. 2011; 6(10): 10.1371/annotation/8f845569-8244-416b-b15e-89562177ce32.
PMCID:
PMC3176800
Abstract Full Text PDF–599K Supplementary Material Correction
Performance assessment of copy number microarray platforms using a spike-in experiment
Eitan Halper-Stromberg, Laurence Frelin, Ingo Ruczinski, Robert Scharpf, Chunfa Jie, Benilton Carvalho, Haiping Hao, Kurt Hetrick, Anne Jedlicka, Amanda Dziedzic, Kim Doheny, Alan F. Scott, Steve Baylin, Jonathan Pevsner, Forrest Spencer, Rafael A. Irizarry
Bioinformatics. 2011 April 15; 27(8): 1052–1060. Published online 2011 April 6. doi: 10.1093/bioinformatics/btr106
PMCID:
PMC3072561
Abstract Full Text PDF–2.1M Supplementary Material
GPHMM: an integrated hidden Markov model for identification of copy number alteration and loss of heterozygosity in complex tumor samples using whole genome SNP arrays
Ao Li, Zongzhi Liu, Kimberly Lezon-Geyda, Sudipa Sarkar, Donald Lannin, Vincent Schulz, Ian Krop, Eric Winer, Lyndsay Harris, David Tuck
Nucleic Acids Res. 2011 July; 39(12): 4928–4941. Published online 2011 March 11. doi: 10.1093/nar/gkr014
PMCID:
PMC3130254
Abstract Full Text PDF–9.7M Supplementary Material
Deletions of 16q in Wilms Tumors Localize to Blastemal-Anaplastic Cells and Are Associated with Reduced Expression of the IRXB Renal Tubulogenesis Gene Cluster
Linda Holmquist Mengelbier, Jenny Karlsson, David Lindgren, Ingrid Øra, Margareth Isaksson, Ildiko Frigyesi, Attila Frigyesi, Johannes Bras, Bengt Sandstedt, David Gisselsson
Am J Pathol. 2010 November; 177(5): 2609–2621. doi: 10.2353/ajpath.2010.100130
PMCID:
PMC2966816
Abstract Full Text PDF–1.1M
A statistical approach for detecting genomic aberrations in heterogeneous tumor samples from single nucleotide polymorphism genotyping data
Christopher Yau, Dmitri Mouradov, Robert N Jorissen, Stefano Colella, Ghazala Mirza, Graham Steers, Adrian Harris, Jiannis Ragoussis, Oliver Sieber, Christopher C Holmes
Genome Biol. 2010; 11(9): R92. Published online 2010 September 21. doi: 10.1186/gb-2010-11-9-r92
PMCID:
PMC2965384
Abstract Full Text PDF–1.5M Supplementary Material
MixHMM: Inferring Copy Number Variation and Allelic Imbalance Using SNP Arrays and Tumor Samples Mixed with Stromal Cells
Zongzhi Liu, Ao Li, Vincent Schulz, Min Chen, David Tuck
PLoS One. 2010; 5(6): e10909. Published online 2010 June 1. doi: 10.1371/journal.pone.0010909
PMCID:
PMC2879364
Abstract Full Text PDF–859K Supplementary Material
Data analysis issues for allele-specific expression using Illumina's GoldenGate assay
Matthew E Ritchie, Matthew S Forrest, Antigone S Dimas, Caroline Daelemans, Emmanouil T Dermitzakis, Panagiotis Deloukas, Simon Tavaré
BMC Bioinformatics. 2010; 11: 280. Published online 2010 May 26. doi: 10.1186/1471-2105-11-280
PMCID:
PMC2887809
Abstract Full Text PDF–1.3M
The pitfalls of platform comparison: DNA copy number array technologies assessed
Christina Curtis, Andy G Lynch, Mark J Dunning, Inmaculada Spiteri, John C Marioni, James Hadfield, Suet-Feung Chin, James D Brenton, Simon Tavaré, Carlos Caldas
BMC Genomics. 2009; 10: 588. Published online 2009 December 8. doi: 10.1186/1471-2164-10-588
PMCID:
PMC2797821
Abstract Full Text PDF–1.4M Supplementary Material
Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays
Tatiana Popova, Elodie Manié, Dominique Stoppa-Lyonnet, Guillem Rigaill, Emmanuel Barillot, Marc Henri Stern
Genome Biol. 2009; 10(11): R128. Published online 2009 November 11. doi: 10.1186/gb-2009-10-11-r128
PMCID:
PMC2810663
Abstract Full Text PDF–2.8M Supplementary Material
R/Bioconductor software for Illumina's Infinium whole-genome genotyping BeadChips
Matthew E. Ritchie, Benilton S. Carvalho, Kurt N. Hetrick, Simon Tavaré, Rafael A. Irizarry
Bioinformatics. 2009 October 1; 25(19): 2621–2623. Published online 2009 August 6. doi: 10.1093/bioinformatics/btp470
PMCID:
PMC2752620
Abstract Full Text PDF–216K
Integrated study of copy number states and genotype calls using high-density SNP arrays
Wei Sun, Fred A. Wright, Zhengzheng Tang, Silje H. Nordgard, Peter Van Loo, Tianwei Yu, Vessela N. Kristensen, Charles M. Perou
Nucleic Acids Res. 2009 September; 37(16): 5365–5377. Published online 2009 July 6. doi: 10.1093/nar/gkp493
PMCID:
PMC2935461
Abstract Full Text PDF–5.6M Supplementary Material
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