Open Access Highly Accessed Research

Large-scale analysis of chromosomal aberrations in cancer karyotypes reveals two distinct paths to aneuploidy

Michal Ozery-Flato12, Chaim Linhart1, Luba Trakhtenbrot34, Shai Izraeli356 and Ron Shamir1*

Author Affiliations

1 The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, 69978, Israel

2 Machine Learning and Data Mining Group, IBM Haifa Research Lab, Mount Carmel, Haifa, 31905, Israel

3 Chaim Sheba Cancer Research Center, Sheba Medical Center, Tel Hashomer, Ramat Gan, 52620, Israel

4 Institute of Hematology, Sheba Medical Center, Tel Hashomer, Ramat Gan, 52620, Israel

5 Department of Pediatric Hemato-Oncology, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Ramat Gan, 52620, Israel

6 Sackler School of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel

For all author emails, please log on.

Genome Biology 2011, 12:R61  doi:10.1186/gb-2011-12-6-r61

Published: 29 June 2011

Additional files

Additional file 1:

Table S1. Chromosomal events allowed in the reconstruction algorithm.

Format: DOC Size: 38KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 2:

Figure S1. Event frequencies.

Format: TIFF Size: 36KB Download file

Open Data

Additional file 3:

Figure S2. Highly co-occurring aberration pairs. Highly co-occurring aberrations (P < 0.05 after Bonferroni correction) are connected by lines. Aberrations that are involved only in expected links are not shown. See Additional file 1 for aberration name abbreviations. (a) Lymphoid disorders, (b) non-lymphoid hematological disorders, (c) solid tumors, (d) carcinomas, (e) all karyotypes. Results were obtained on a dataset that includes partially defined and selected karyotypes (83% of the Mitelman Database). Legend is as in Figure 2 for (a-d), and for (e) with the addition of light red and light green colors corresponding to partial deletions and partial duplications, respectively.

Format: JPEG Size: 487KB Download file

Open Data

Additional file 4:

Figure S3. Tumor classes with similar common aberrations. (a) Tumor class pairs with significantly high numbers of common aberrations are connected by lines (FDR 5%). Aberrations assigned to tumor classes are: (a1) significantly correlated at FDR 5%, (a2) correlated with P-value < 0.05 (uncorrected). (b) Hierarchical clustering of classes based on class similarity in sharing common aberrations. Results were obtained with a dataset that includes partially defined and selected karyotypes (83% of the Mitelman Database). Legend is as in Figure 3.

Format: JPEG Size: 428KB Download file

Open Data

Additional file 5:

Text S1. Description of the algorithm for reconstructing aberrations from karyotypes.

Format: DOC Size: 67KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data