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Literature DB >> 17267432

CGHcall: calling aberrations for array CGH tumor profiles.

Mark A van de Wiel¹, Kyung In Kim, Sjoerd J Vosse, Wessel N van Wieringen, Saskia M Wilting, Bauke Ylstra.

Abstract

UNLABELLED: CGHcall achieves high calling accuracy for array CGH data by effective use of breakpoint information from segmentation and by inclusion of several biological concepts that are ignored by existing algorithms. The algorithm is validated for simulated and verified real array CGH data. By incorporating more than three classes, CGHcall improves detection of single copy gains and amplifications. Moreover, it allows effective inclusion of chromosome arm information. AVAILABILITY: An R-package (GUI), a manual and an example data set are available at http://www.few.vu.nl/~mavdwiel/CGHcall.html. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Entities: Disease

Mesh：

Substances：
DNA, Neoplasm

Year: 2007 PMID： 17267432 DOI： 10.1093/bioinformatics/btm030

Source DB: PubMed Journal: Bioinformatics ISSN： 1367-4803 Impact factor: 6.937

Keyword Cloud
Cited

103 in total

1. Chromosomal copy number alterations and HPV integration in cervical precancer and invasive cancer.

Authors: Clara Bodelon; Svetlana Vinokurova; Joshua N Sampson; Johan A den Boon; Joan L Walker; Mark A Horswill; Keegan Korthauer; Mark Schiffman; Mark E Sherman; Rosemary E Zuna; Jason Mitchell; Xijun Zhang; Joseph F Boland; Anil K Chaturvedi; S Terence Dunn; Michael A Newton; Paul Ahlquist; Sophia S Wang; Nicolas Wentzensen
Journal: Carcinogenesis Date: 2015-12-09 Impact factor: 4.944

2. DDX3X Suppresses the Susceptibility of Hindbrain Lineages to Medulloblastoma.

Authors: Deanna M Patmore; Amir Jassim; Erica Nathan; Reuben J Gilbertson; Daniel Tahan; Nadin Hoffmann; Yiai Tong; Kyle S Smith; Thirumala-Devi Kanneganti; Hiromichi Suzuki; Michael D Taylor; Paul Northcott; Richard J Gilbertson
Journal: Dev Cell Date: 2020-06-17 Impact factor: 12.270

3. Evolution of DNA repair defects during malignant progression of low-grade gliomas after temozolomide treatment.

Authors: Hinke F van Thuijl; Tali Mazor; Brett E Johnson; Shaun D Fouse; Koki Aihara; Chibo Hong; Annika Malmström; Martin Hallbeck; Jan J Heimans; Jenneke J Kloezeman; Marie Stenmark-Askmalm; Martine L M Lamfers; Nobuhito Saito; Hiroyuki Aburatani; Akitake Mukasa; Mitchell S Berger; Peter Söderkvist; Barry S Taylor; Annette M Molinaro; Pieter Wesseling; Jaap C Reijneveld; Susan M Chang; Bauke Ylstra; Joseph F Costello
Journal: Acta Neuropathol Date: 2015-02-28 Impact factor: 17.088

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Authors: Hyungwon Choi; Zhaohui S Qin; Debashis Ghosh
Journal: J Comput Biol Date: 2010-02 Impact factor: 1.479

5. Targeted Inhibition of the Dual Specificity Phosphatases DUSP1 and DUSP6 Suppress MPNST Growth via JNK.

Authors: Annmarie Ramkissoon; Katherine E Chaney; David Milewski; Kyle B Williams; Rory L Williams; Kwangmin Choi; Adam Miller; Tanya V Kalin; Joseph G Pressey; Sara Szabo; Mohammad Azam; David A Largaespada; Nancy Ratner
Journal: Clin Cancer Res Date: 2019-04-01 Impact factor: 12.531

6. Losses of chromosome 5q and 14q are associated with favorable clinical outcome of patients with gastric cancer.

Authors: Tineke E Buffart; Beatriz Carvalho; Nicole C T van Grieken; Wessel N van Wieringen; Marianne Tijssen; Elma Meershoek-Klein Kranenbarg; Henk M W Verheul; Heike I Grabsch; Bauke Ylstra; Cornelis J H van de Velde; Gerrit A Meijer
Journal: Oncologist Date: 2012-04-24

CGHcall: calling aberrations for array CGH tumor profiles.

1. Chromosomal copy number alterations and HPV integration in cervical precancer and invasive cancer.

2. DDX3X Suppresses the Susceptibility of Hindbrain Lineages to Medulloblastoma.

3. Evolution of DNA repair defects during malignant progression of low-grade gliomas after temozolomide treatment.

4. A double-layered mixture model for the joint analysis of DNA copy number and gene expression data.

5. Targeted Inhibition of the Dual Specificity Phosphatases DUSP1 and DUSP6 Suppress MPNST Growth via JNK.

6. Losses of chromosome 5q and 14q are associated with favorable clinical outcome of patients with gastric cancer.

7. Array comparative genomic hybridization identifies novel potential therapeutic targets in cholangiocarcinoma.

8. Use of autocorrelation scanning in DNA copy number analysis.

9. aCGH.Spline--an R package for aCGH dye bias normalization.

10. Normalized, segmented or called aCGH data?