Skip Navigation


Bioinformatics Advance Access originally published online on June 16, 2004
Bioinformatics 2004 20(18):3636-3637; doi:10.1093/bioinformatics/bth355
This Article
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow FREE Full Text (Screen PDF)
Right arrow All Versions of this Article:
20/18/3636    most recent
bth355v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Jong, K.
Right arrow Articles by Ylstra, B.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Jong, K.
Right arrow Articles by Ylstra, B.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Bioinformatics vol. 20 issue 18 © Oxford University Press 2004; all rights reserved.

Applications Note

Breakpoint identification and smoothing of array comparative genomic hybridization data

Kees Jong 1,*, Elena Marchiori 1, Gerrit Meijer 2, A. v. d. Vaart 1 and Bauke Ylstra 2

1 Faculty of Sciences and 2 VU University Medical Center, Vrije Universiteit, De Boelelaan 1117, Amsterdam 1081HV, The Netherlands

Received on October 10, 2003; revised on May 11, 2004; accepted on June 7, 2004
Advance Access Publication June 17, 2004

Summary: We describe a tool, called aCGH-Smooth, for the automated identification of breakpoints and smoothing of microarray comparative genomic hybridization (array CGH) data. aCGH-Smooth is written in visual C++, has a user-friendly interface including a visualization of the results and user-defined parameters adapting the performance of data smoothing and breakpoint recognition. aCGH-Smooth can handle array-CGH data generated by all array-CGH platforms: BAC, PAC, cosmid, cDNA and oligo CGH arrays. The tool has been successfully applied to real-life data.

Availability: aCGH-Smooth is free for researchers at academic and non-profit institutions at http://www.few.vu.nl/~vumarray/

Contact: cjong{at}few.vu.nl

* To whom correspondence should be addressed.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Proc. Natl. Acad. Sci. USAHome page
S. Aviel-Ronen, B. P. Coe, S. K. Lau, G. da Cunha Santos, C.-Q. Zhu, D. Strumpf, I. Jurisica, W. L. Lam, and M.-S. Tsao
Genomic markers for malignant progression in pulmonary adenocarcinoma with bronchioloalveolar features
PNAS, July 22, 2008; 105(29): 10155 - 10160.
[Abstract] [Full Text] [PDF]

Home page
 BloodHome page
M. S. Hasemann, I. Damgaard, M. B. Schuster, K. Theilgaard-Monch, A. B. Sorensen, A. Mrsic, T. Krugers, B. Ylstra, F. S. Pedersen, C. Nerlov, et al.
Mutation of C/EBP{alpha} predisposes to the development of myeloid leukemia in a retroviral insertional mutagenesis screen
Blood, April 15, 2008; 111(8): 4309 - 4321.
[Abstract] [Full Text] [PDF]

Home page
 CarcinogenesisHome page
S. Derks, C. Postma, B. Carvalho, S. M. van den Bosch, P. T.M. Moerkerk, J. G. Herman, M. P. Weijenberg, A. P. de Bruine, G. A. Meijer, and M. van Engeland
Integrated analysis of chromosomal, microsatellite and epigenetic instability in colorectal cancer identifies specific associations between promoter methylation of pivotal tumour suppressor and DNA repair genes and specific chromosomal alterations
Carcinogenesis, February 1, 2008; 29(2): 434 - 439.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
Y. Li and J. Zhu
Analysis of array CGH data for cancer studies using fused quantile regression
Bioinformatics, September 15, 2007; 23(18): 2470 - 2476.
[Abstract] [Full Text] [PDF]

Home page
 J HeredHome page
R. Thomas, S. E. Duke, S. K. Bloom, T. E. Breen, A. C. Young, E. Feiste, E. L. Seiser, P.-C. Tsai, C. F. Langford, P. Ellis, et al.
A Cytogenetically Characterized, Genome-Anchored 10-Mb BAC Set and CGH Array for the Domestic Dog
J. Hered., August 16, 2007; (2007) esm053v1.
[Abstract] [Full Text] [PDF]

Home page
 BiostatisticsHome page
B. Xing, C. M. T. Greenwood, and S. B. Bull
A hierarchical clustering method for estimating copy number variation
Biostat., July 1, 2007; 8(3): 632 - 653.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
S. P. Shah, W. L. Lam, R. T. Ng, and K. P. Murphy
Modeling recurrent DNA copy number alterations in array CGH data
Bioinformatics, July 1, 2007; 23(13): i450 - i458.
[Abstract] [Full Text] [PDF]

Home page
 Clin. Cancer Res.Home page
H. Vekony, B. Ylstra, S. M. Wilting, G. A. Meijer, M. A. van de Wiel, C. R. Leemans, I. van der Waal, and E. Bloemena
DNA Copy Number Gains at Loci of Growth Factors and Their Receptors in Salivary Gland Adenoid Cystic Carcinoma
Clin. Cancer Res., June 1, 2007; 13(11): 3133 - 3139.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J. Hu, J.-B. Gao, Y. Cao, E. Bottinger, and W. Zhang
Exploiting noise in array CGH data to improve detection of DNA copy number change
Nucleic Acids Res., March 12, 2007; 35(5): e35 - e35.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
J. Oosting, E. H. Lips, R. van Eijk, P. H.C. Eilers, K. Szuhai, C. Wijmenga, H. Morreau, and T. van Wezel
High-resolution copy number analysis of paraffin-embedded archival tissue using SNP BeadArrays
Genome Res., March 1, 2007; 17(3): 368 - 376.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
W. N. van Wieringen, J. A. M. Belien, S. J. Vosse, E. M. Achame, and B. Ylstra
ACE-it: a tool for genome-wide integration of gene dosage and RNA expression data
Bioinformatics, August 1, 2006; 22(15): 1919 - 1920.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
J. C. Marioni, N. P. Thorne, and S. Tavare
BioHMM: a heterogeneous hidden Markov model for segmenting array CGH data
Bioinformatics, May 1, 2006; 22(9): 1144 - 1146.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
P. Broet and S. Richardson
Detection of gene copy number changes in CGH microarrays using a spatially correlated mixture model
Bioinformatics, April 15, 2006; 22(8): 911 - 918.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
P. van den IJssel, M. Tijssen, S.-F. Chin, P. Eijk, B. Carvalho, E. Hopmans, H. Holstege, D. K. Bangarusamy, J. Jonkers, G. A. Meijer, et al.
Human and mouse oligonucleotide-based array CGH
Nucleic Acids Res., December 16, 2005; 33(22): e192 - e192.
[Abstract] [Full Text] [PDF]

Home page
 Cancer Res.Home page
M. A. van de Wiel, J. L. Costa, K. Smid, C. B.M. Oudejans, A. M. Bergman, G. A. Meijer, G. J. Peters, and B. Ylstra
Expression Microarray Analysis and Oligo Array Comparative Genomic Hybridization of Acquired Gemcitabine Resistance in Mouse Colon Reveals Selection for Chromosomal Aberrations
Cancer Res., November 15, 2005; 65(22): 10208 - 10213.
[Abstract] [Full Text] [PDF]

Home page
 Hum Mol GenetHome page
L. E.L.M. Vissers, J. A. Veltman, A. G. van Kessel, and H. G. Brunner
Identification of disease genes by whole genome CGH arrays
Hum. Mol. Genet., October 15, 2005; 14(suppl_2): R215 - R223.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J. Knijnenburg, M. van der Burg, P. Nilsson, H. K. P. van Amstel, H. Tanke, and K. Szuhai
Rapid detection of genomic imbalances using micro-arrays consisting of pooled BACs covering all human chromosome arms
Nucleic Acids Res., October 12, 2005; 33(18): e159 - e159.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
W. R. Lai, M. D. Johnson, R. Kucherlapati, and P. J. Park
Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data
Bioinformatics, October 1, 2005; 21(19): 3763 - 3770.
[Abstract] [Full Text] [PDF]

Home page
 Cancer Res.Home page
C. Baldwin, C. Garnis, L. Zhang, M. P. Rosin, and W. L. Lam
Multiple Microalterations Detected at High Frequency in Oral Cancer
Cancer Res., September 1, 2005; 65(17): 7561 - 7567.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
M. A. van de Wiel, S. J. Smeets, R. H. Brakenhoff, and B. Ylstra
CGHMultiArray: exact P-values for multi-array comparative genomic hybridization data
Bioinformatics, July 15, 2005; 21(14): 3193 - 3194.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
T. S. Price, R. Regan, R. Mott, A. Hedman, B. Honey, R. J. Daniels, L. Smith, A. Greenfield, A. Tiganescu, V. Buckle, et al.
SW-ARRAY: a dynamic programming solution for the identification of copy-number changes in genomic DNA using array comparative genome hybridization data
Nucleic Acids Res., June 16, 2005; 33(11): 3455 - 3464.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
S. Y. Kim, S. W. Nam, S. H. Lee, W. S. Park, N. J. Yoo, J. Y. Lee, and Y.-J. Chung
ArrayCyGHt: a web application for analysis and visualization of array-CGH data
Bioinformatics, May 15, 2005; 21(10): 2554 - 2555.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
S. Bilke, Q.-R. Chen, C. C. Whiteford, and J. Khan
Detection of low level genomic alterations by comparative genomic hybridization based on cDNA micro-arrays
Bioinformatics, April 1, 2005; 21(7): 1138 - 1145.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
P. H. C. Eilers and R. X. de Menezes
Quantile smoothing of array CGH data
Bioinformatics, April 1, 2005; 21(7): 1146 - 1153.
[Abstract] [Full Text] [PDF]


Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.