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Segmentation-based detection of allelic imbalance and loss-of-heterozygosity in cancer cells using whole genome SNP arrays
Johan Staaf, David Lindgren, Johan Vallon-Christersson, Anders Isaksson, Hanna Göransson, Gunnar Juliusson, Richard Rosenquist, Mattias Höglund, Åke Borg, Markus Ringnér
Genome Biol. 2008; 9(9): R136. Published online 2008 September 16. doi: 10.1186/gb-2008-9-9-r136
PMCID:
PMC2592714
Abstract Full Text PDF–2.9M Supplementary Material

Is Cited by the Following 25 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
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
Copy Number Alterations in Prostate Tumors and Disease Aggressiveness
Iona Cheng, Albert M. Levin, Yu Chuan Tai, Sarah Plummer, Gary K. Chen, Christine Neslund-Dudas, Graham Casey, Benjamin A. Rybicki, John S. Witte
Genes Chromosomes Cancer. Author manuscript; available in PMC 2013 January 1.
Published in final edited form as: Genes Chromosomes Cancer. 2012 January; 51(1): 66–76. Published online 2011 October 2. doi: 10.1002/gcc.20932
PMCID:
PMC3209417
Free in PMC on 2013/01/01
Lessons from a decade of integrating cancer copy number alterations with gene expression profiles
Norman Huang, Parantu K. Shah, Cheng Li
Brief Bioinform. 2012 May; 13(3): 305–316. Published online 2011 September 23. doi: 10.1093/bib/bbr056
PMCID:
PMC3357489
Free in PMC on 2013/05/01
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
Parent-specific copy number in paired tumor–normal studies using circular binary segmentation
Adam B. Olshen, Henrik Bengtsson, Pierre Neuvial, Paul T. Spellman, Richard A. Olshen, Venkatraman E. Seshan
Bioinformatics. 2011 August 1; 27(15): 2038–2046. Published online 2011 June 11. doi: 10.1093/bioinformatics/btr329
PMCID:
PMC3137217
Free in PMC on 2012/08/01
A fast and accurate method to detect allelic genomic imbalances underlying mosaic rearrangements using SNP array data
Juan R González, Benjamín Rodríguez-Santiago, Alejandro Cáceres, Roger Pique-Regi, Nathaniel Rothman, Stephen J Chanock, Lluís Armengol, Luis A Pérez-Jurado
BMC Bioinformatics. 2011; 12: 166. Published online 2011 May 17. doi: 10.1186/1471-2105-12-166
PMCID:
PMC3118168
Abstract Full Text PDF–2.8M Supplementary Material
SAQC: SNP Array Quality Control
Hsin-Chou Yang, Hsin-Chi Lin, Meijyh Kang, Chun-Houh Chen, Chien-Wei Lin, Ling-Hui Li, Jer-Yuarn Wu, Yuan-Tsong Chen, Wen-Harn Pan
BMC Bioinformatics. 2011; 12: 100. Published online 2011 April 18. doi: 10.1186/1471-2105-12-100
PMCID:
PMC3101186
Abstract Full Text PDF–1.4M 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
Estimation of Parent Specific DNA Copy Number in Tumors using High-Density Genotyping Arrays
Hao Chen, Haipeng Xing, Nancy R. Zhang
PLoS Comput Biol. 2011 January; 7(1): e1001060. Published online 2011 January 27. doi: 10.1371/journal.pcbi.1001060
PMCID:
PMC3029233
Abstract Full Text PDF–1.6M Supplementary Material
CNV-WebStore: Online CNV Analysis, Storage and Interpretation
Geert Vandeweyer, Edwin Reyniers, Wim Wuyts, Liesbeth Rooms, R Frank Kooy
BMC Bioinformatics. 2011; 12: 4. Published online 2011 January 5. doi: 10.1186/1471-2105-12-4
PMCID:
PMC3024943
Abstract Full Text PDF–626K Supplementary Material
Generation of trisomies in cancer cells by multipolar mitosis and incomplete cytokinesis
David Gisselsson, Yuesheng Jin, David Lindgren, Johan Persson, Lennart Gisselsson, Sandra Hanks, Daniel Sehic, Linda Holmquist Mengelbier, Ingrid Øra, Nazneen Rahman, Fredrik Mertens, Felix Mitelman, Nils Mandahl
Proc Natl Acad Sci U S A. 2010 November 23; 107(47): 20489–20493. Published online 2010 November 8. doi: 10.1073/pnas.1006829107
PMCID:
PMC2996656
Abstract Full Text PDF–1.1M 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
Allele-specific copy number analysis of tumors
Peter Van Loo, Silje H. Nordgard, Ole Christian Lingjærde, Hege G. Russnes, Inga H. Rye, Wei Sun, Victor J. Weigman, Peter Marynen, Anders Zetterberg, Bjørn Naume, Charles M. Perou, Anne-Lise Børresen-Dale, Vessela N. Kristensen
Proc Natl Acad Sci U S A. 2010 September 28; 107(39): 16910–16915. Published online 2010 September 13. doi: 10.1073/pnas.1009843107
PMCID:
PMC2947907
Abstract Full Text PDF–2.3M Supplementary Material
ANO1 amplification and expression in HNSCC with a high propensity for future distant metastasis and its functions in HNSCC cell lines
C Ayoub, C Wasylyk, Y Li, E Thomas, L Marisa, A Robé, M Roux, J Abecassis, A de Reyniès, B Wasylyk
Br J Cancer. 2010 August 24; 103(5): 715–726. Published online 2010 July 27. doi: 10.1038/sj.bjc.6605823
PMCID:
PMC2938263
Abstract Full Text PDF–920K Supplementary Material
Analysis of the copy number profiles of several tumor samples from the same patient reveals the successive steps in tumorigenesis
Eric Letouzé, Yves Allory, Marc A Bollet, François Radvanyi, Frédéric Guyon
Genome Biol. 2010; 11(7): R76. Published online 2010 July 22. doi: 10.1186/gb-2010-11-7-r76
PMCID:
PMC2926787
Abstract Full Text PDF–3.8M Supplementary Material
A new analysis tool for individual-level allele frequency for genomic studies
Hsin-Chou Yang, Hsin-Chi Lin, Mei-Chu Huang, Ling-Hui Li, Wen-Harn Pan, Jer-Yuarn Wu, Yuan-Tsong Chen
BMC Genomics. 2010; 11: 415. Published online 2010 July 5. doi: 10.1186/1471-2164-11-415
PMCID:
PMC2996943
Abstract Full Text PDF–2.4M Supplementary Material
An integrated Bayesian analysis of LOH and copy number data
Paola MV Rancoita, Marcus Hutter, Francesco Bertoni, Ivo Kwee
BMC Bioinformatics. 2010; 11: 321. Published online 2010 June 15. doi: 10.1186/1471-2105-11-321
PMCID:
PMC2912301
Abstract Full Text PDF–2.0M Supplementary Material
ACNE: a summarization method to estimate allele-specific copy numbers for Affymetrix SNP arrays
Maria Ortiz-Estevez, Henrik Bengtsson, Angel Rubio
Bioinformatics. 2010 August 1; 26(15): 1827–1833. Published online 2010 June 6. doi: 10.1093/bioinformatics/btq300
PMCID:
PMC2913655
Abstract Full Text PDF–2.8M 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
TumorBoost: Normalization of allele-specific tumor copy numbers from a single pair of tumor-normal genotyping microarrays
Henrik Bengtsson, Pierre Neuvial, Terence P Speed
BMC Bioinformatics. 2010; 11: 245. Published online 2010 May 12. doi: 10.1186/1471-2105-11-245
PMCID:
PMC2894037
Abstract Full Text PDF–1.7M 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
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
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
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