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Breaking the waves: improved detection of copy number variation from microarray-based comparative genomic hybridization
John C Marioni, Natalie P Thorne, Armand Valsesia, Tomas Fitzgerald, Richard Redon, Heike Fiegler, T Daniel Andrews, Barbara E Stranger, Andrew G Lynch, Emmanouil T Dermitzakis, Nigel P Carter, Simon Tavaré, Matthew E Hurles
Genome Biol. 2007; 8(10): R228. Published online 2007 October 25. doi: 10.1186/gb-2007-8-10-r228
PMCID:
PMC2246302
Abstract Full Text PDF–29M Supplementary Material

Is Cited by the Following 35 Articles in this Archive:

Genetic Association Studies of Copy-Number Variation: Should Assignment of Copy Number States Precede Testing?
Patrick Breheny, Prabhakar Chalise, Anthony Batzler, Liewei Wang, Brooke L. Fridley
PLoS One. 2012; 7(4): e34262. Published online 2012 April 6. doi: 10.1371/journal.pone.0034262
PMCID:
PMC3320903
Abstract Full Text PDF–313K
Reducing system noise in copy number data using principal components of self-self hybridizations
Yoon-ha Lee, Michael Ronemus, Jude Kendall, B. Lakshmi, Anthony Leotta, Dan Levy, Diane Esposito, Vladimir Grubor, Kenny Ye, Michael Wigler, Boris Yamrom
Proc Natl Acad Sci U S A. 2012 January 17; 109(3): E103-E110. Published online 2011 December 29. doi: 10.1073/pnas.1106233109
Includes additional comments & authors
PMCID:
PMC3271883
Abstract Full Text PDF–4.3M Supplementary Material
Reducing system noise in copy number data using principal components of self-self hybridizations
Yoon-ha Lee, Michael Ronemus, Jude Kendall, B. Lakshmi, Anthony Leotta, Dan Levy, Diane Esposito, Vladimir Grubor, Kenny Ye, Michael Wigler, Boris Yamrom
Proc Natl Acad Sci U S A. 2012 January 17; 109(3): E103-E110. Published online 2011 December 29. doi: 10.1073/pnas.1106233109
Includes additional comments & authors
PMCID:
PMC3271883
Abstract Full Text PDF–4.3M Supplementary Material
Characterising chromosome rearrangements: recent technical advances in molecular cytogenetics
S Le Scouarnec, S M Gribble
Heredity (Edinb) 2012 January; 108(1): 75–85. Published online 2011 November 16. doi: 10.1038/hdy.2011.100
PMCID:
PMC3238113
Abstract Full Text PDF–798K Supplementary Material
A novel signal processing approach for the detection of copy number variations in the human genome
Catherine Stamoulis, Rebecca A. Betensky
Bioinformatics. 2011 September 1; 27(17): 2338–2345. Published online 2011 July 12. doi: 10.1093/bioinformatics/btr402
PMCID:
PMC3157926
Free in PMC on 2012/09/01
CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing
Alexej Abyzov, Alexander E. Urban, Michael Snyder, Mark Gerstein
Genome Res. 2011 June; 21(6): 974–984. doi: 10.1101/gr.114876.110
PMCID:
PMC3106330
Abstract Full Text PDF–927K
Software comparison for evaluating genomic copy number variation for Affymetrix 6.0 SNP array platform
Jeanette E Eckel-Passow, Elizabeth J Atkinson, Sooraj Maharjan, Sharon LR Kardia, Mariza de Andrade
BMC Bioinformatics. 2011; 12: 220. Published online 2011 May 31. doi: 10.1186/1471-2105-12-220
PMCID:
PMC3146450
Abstract Full Text PDF–1.4M Supplementary Material
Assessment of genome integrity with array CGH in cattle transgenic cell lines produced by homologous recombination and somatic cell cloning
George E Liu, Yali Hou, James M Robl, Yoshimi Kuroiwa, Zhongde Wang
Genome Integr. 2011; 2: 6. Published online 2011 May 23. doi: 10.1186/2041-9414-2-6
PMCID:
PMC3123262
Abstract Full Text PDF–361K
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
aCGH.Spline—an R package for aCGH dye bias normalization
Tomas W. Fitzgerald, Lee D. Larcombe, Solena Le Scouarnec, Stephen Clayton, Diana Rajan, Nigel P. Carter, Richard Redon
Bioinformatics. 2011 May 1; 27(9): 1195–1200. Published online 2011 February 25. doi: 10.1093/bioinformatics/btr107
PMCID:
PMC3077069
Abstract Full Text PDF–600K Supplementary Material
Genomic characteristics of cattle copy number variations
Yali Hou, George E Liu, Derek M Bickhart, Maria Francesca Cardone, Kai Wang, Eui-soo Kim, Lakshmi K Matukumalli, Mario Ventura, Jiuzhou Song, Paul M VanRaden, Tad S Sonstegard, Curt P Van Tassell
BMC Genomics. 2011; 12: 127. Published online 2011 February 23. doi: 10.1186/1471-2164-12-127
PMCID:
PMC3053260
Abstract Full Text PDF–540K Supplementary Material
Bayesian estimation of genomic copy number with single nucleotide polymorphism genotyping arrays
Beibei Guo, Alejandro Villagran, Marina Vannucci, Jian Wang, Caleb Davis, Tsz-Kwong Man, Ching Lau, Rudy Guerra
BMC Res Notes. 2010; 3: 350. Published online 2010 December 30. doi: 10.1186/1756-0500-3-350
PMCID:
PMC3023756
Abstract Full Text PDF–2.4M Supplementary Material
DiNAMIC: a method to identify recurrent DNA copy number aberrations in tumors
Vonn Walter, Andrew B. Nobel, Fred A. Wright
Bioinformatics. 2011 March 1; 27(5): 678–685. Published online 2010 December 23. doi: 10.1093/bioinformatics/btq717
PMCID:
PMC3042182
Abstract Full Text PDF–567K Supplementary Material
Novel common copy number variation for early onset extreme obesity on chromosome 11q11 identified by a genome-wide analysis
Ivonne Jarick, Carla I.G. Vogel, Susann Scherag, Helmut Schäfer, Johannes Hebebrand, Anke Hinney, André Scherag
Hum Mol Genet. 2011 February 15; 20(4): 840–852. Published online 2010 December 2. doi: 10.1093/hmg/ddq518
PMCID:
PMC3024044
Abstract Full Text PDF–358K Supplementary Material
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
Accurate genome-scale percentage DNA methylation estimates from microarray data
Martin J. Aryee, Zhijin Wu, Christine Ladd-Acosta, Brian Herb, Andrew P. Feinberg, Srinivasan Yegnasubramanian, Rafael A. Irizarry
Biostatistics. 2011 April; 12(2): 197–210. Published online 2010 September 21. doi: 10.1093/biostatistics/kxq055
PMCID:
PMC3062148
Abstract Full Text PDF–354K Supplementary Material
Fine-Scale Survey of X Chromosome Copy Number Variants and Indels Underlying Intellectual Disability
Annabel C. Whibley, Vincent Plagnol, Patrick S. Tarpey, Fatima Abidi, Tod Fullston, Maja K. Choma, Catherine A. Boucher, Lorraine Shepherd, Lionel Willatt, Georgina Parkin, Raffaella Smith, P. Andrew Futreal, Marie Shaw, Jackie Boyle, Andrea Licata, Cindy Skinner, Roger E. Stevenson, Gillian Turner, Michael Field, Anna Hackett, Charles E. Schwartz, Jozef Gecz, Michael R. Stratton, F. Lucy Raymond
Am J Hum Genet. 2010 August 13; 87(2): 173–188. doi: 10.1016/j.ajhg.2010.06.017
PMCID:
PMC2917707
Abstract Full Text PDF–372K Supplementary Material
Computational Analysis of Whole-Genome Differential Allelic Expression Data in Human
James R. Wagner, Bing Ge, Dmitry Pokholok, Kevin L. Gunderson, Tomi Pastinen, Mathieu Blanchette
PLoS Comput Biol. 2010 July; 6(7): e1000849. Published online 2010 July 8. doi: 10.1371/journal.pcbi.1000849
PMCID:
PMC2900287
Abstract Full Text PDF–811K Supplementary Material
Waved aCGH: to smooth or not to smooth
F. Leprêtre, C. Villenet, S. Quief, O. Nibourel, C. Jacquemin, X. Troussard, F. Jardin, F. Gibson, J. P. Kerckaert, C. Roumier, M. Figeac
Nucleic Acids Res. 2010 April; 38(7): e94. Published online 2010 April. doi: 10.1093/nar/gkp1215
PMCID:
PMC2853126
Abstract Full Text PDF–6.6M
A novel highly-penetrant form of obesity due to microdeletions on chromosome 16p11.2
R. G. Walters, S. Jacquemont, A. Valsesia, A. J. de Smith, D. Martinet, J. Andersson, M. Falchi, F. Chen, J. Andrieux, S. Lobbens, B. Delobel, F. Stutzmann, J. S. El-Sayed Moustafa, J.-C. Chèvre, C. Lecoeur, V. Vatin, S. Bouquillon, J. L. Buxton, O. Boute, M. Holder-Espinasse, J.-M. Cuisset, M.-P. Lemaitre, A.-E. Ambresin, A. Brioshi, M. Gaillard, V. Giusti, F. Fellmann, A. Ferrarini, N. Hadjikhani, D. Campion, A. Guilmatre, A. Goldenberg, N. Calmels, J.-L. Mandel, C. Le Caignec, A. David, B. Isidor, M.-P. Cordier, S. Dupuis-Girod, A. Labalme, D. Sanlaville, M. Béri-Deixheimer, P. Jonveaux, B. Leheup, K. Õunap, E. G. Bochukova, E. Henning, J. Keogh, R. J. Ellis, K. D. MacDermot, C. Vincent-Delorme, G. Plessis, R. Touraine, A. Philippe, V. Malan, M. Mathieu-Dramard, J. Chiesa, B. Blaumeiser, R. F. Kooy, R. Caiazzo, M. Pigeyre, B. Balkau, R. Sladek, S. Bergmann, V. Mooser, D. Waterworth, A. Reymond, P. Vollenweider, G. Waeber, A. Kurg, P. Palta, T. Esko, A. Metspalu, M. Nelis, P. Elliott, A.-L. Hartikainen, M. I. McCarthy, L. Peltonen, L. Carlsson, P. Jacobson, L. Sjöström, N. Huang, M. E. Hurles, S. O’Rahilly, I. S. Farooqi, K. Männik, M.-R. Jarvelin, F. Pattou, D. Meyre, A. J. Walley, L. J. M. Coin, A. I. F. Blakemore, P. Froguel, J. S. Beckmann
Nature. Author manuscript; available in PMC 2010 August 4.
Published in final edited form as: Nature. 2010 February 4; 463(7281): 671–675. doi: 10.1038/nature08727
PMCID:
PMC2880448
Full Text PDF–376K Supplementary Material
CMDS: a population-based method for identifying recurrent DNA copy number aberrations in cancer from high-resolution data
Qunyuan Zhang, Li Ding, David E. Larson, Daniel C. Koboldt, Michael D. McLellan, Ken Chen, Xiaoqi Shi, Aldi Kraja, Elaine R. Mardis, Richard K. Wilson, Ingrid B. Borecki, Michael A. Province
Bioinformatics. 2010 February 15; 26(4): 464–469. Published online 2009 December 23. doi: 10.1093/bioinformatics/btp708
PMCID:
PMC2852218
Abstract Full Text PDF–441K Supplementary Material
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
Cancer gene discovery in mouse and man
Jenny Mattison, Louise van der Weyden, Tim Hubbard, David J. Adams
Biochim Biophys Acta. 2009 December; 1796(2-2): 140–161. doi: 10.1016/j.bbcan.2009.03.001
PMCID:
PMC2756404
Abstract Full Text
Reduced TFAP2A function causes variable optic fissure closure and retinal defects and sensitizes eye development to mutations in other morphogenetic regulators
Gaia Gestri, Robert J. Osborne, Alexander W. Wyatt, Dianne Gerrelli, Susan Gribble, Helen Stewart, Alan Fryer, David J. Bunyan, Katrina Prescott, J. Richard O. Collin, Tomas Fitzgerald, David Robinson, Nigel P. Carter, Stephen W. Wilson, Nicola K. Ragge
Hum Genet. Author manuscript; available in PMC 2011 April 28.
Published in final edited form as: Hum Genet. 2009 December; 126(6): 791–803. doi: 10.1007/s00439-009-0730-x
PMCID:
PMC3083835
Abstract Full Text PDF–1.4M
High resolution discovery and confirmation of copy number variants in 90 Yoruba Nigerians
Hajime Matsuzaki, Pei-Hua Wang, Jing Hu, Rich Rava, Glenn K Fu
Genome Biol. 2009; 10(11): R125. Published online 2009 November 9. doi: 10.1186/gb-2009-10-11-r125
PMCID:
PMC3091319
Abstract Full Text PDF–558K Supplementary Material
PICNIC: an algorithm to predict absolute allelic copy number variation with microarray cancer data
Chris D. Greenman, Graham Bignell, Adam Butler, Sarah Edkins, Jon Hinton, Dave Beare, Sajani Swamy, Thomas Santarius, Lina Chen, Sara Widaa, P. Andy Futreal, Michael R. Stratton
Biostatistics. 2010 January; 11(1): 164–175. Published online 2009 October 15. doi: 10.1093/biostatistics/kxp045
PMCID:
PMC2800165
Abstract Full Text PDF–531K Supplementary Material
Hybridization modeling of oligonucleotide SNP arrays for accurate DNA copy number estimation
Lin Wan, Kelian Sun, Qi Ding, Yuehua Cui, Ming Li, Yalu Wen, Robert C. Elston, Minping Qian, Wenjiang J Fu
Nucleic Acids Res. 2009 September; 37(17): e117. Published online 2009 September. doi: 10.1093/nar/gkp559
PMCID:
PMC2761258
Abstract Full Text PDF–2.1M Supplementary Material
A Genome-Wide Association Study Confirms VKORC1, CYP2C9, and CYP4F2 as Principal Genetic Determinants of Warfarin Dose
Fumihiko Takeuchi, Ralph McGinnis, Stephane Bourgeois, Chris Barnes, Niclas Eriksson, Nicole Soranzo, Pamela Whittaker, Venkatesh Ranganath, Vasudev Kumanduri, William McLaren, Lennart Holm, Jonatan Lindh, Anders Rane, Mia Wadelius, Panos Deloukas
PLoS Genet. 2009 March; 5(3): e1000433. Published online 2009 March 20. doi: 10.1371/journal.pgen.1000433
PMCID:
PMC2652833
Abstract Full Text PDF–203K Supplementary Material
Joint estimation of copy number variation and reference intensities on multiple DNA arrays using GADA
Roger Pique-Regi, Antonio Ortega, Shahab Asgharzadeh
Bioinformatics. 2009 May 15; 25(10): 1223–1230. Published online 2009 March 10. doi: 10.1093/bioinformatics/btp119
PMCID:
PMC2732310
Abstract Full Text PDF–550K Supplementary Material
Application of Signal Processing Techniques for Estimating Regions of Copy Number Variations in Human Meningioma DNA
Catherine Stamoulis, Rebecca A. Betensky, Gayatry Mohapatra, David N. Louis
Conf Proc IEEE Eng Med Biol Soc. Author manuscript; available in PMC 2010 January 1.
Published in final edited form as: Conf Proc IEEE Eng Med Biol Soc. 2009; 1: 6973–6976. doi: 10.1109/IEMBS.2009.5333851
PMCID:
PMC2796201
Abstract Full Text PDF–2.2M
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