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. 2006 Dec 27:7:324.
doi: 10.1186/1471-2164-7-324.

SIGMA: a system for integrative genomic microarray analysis of cancer genomes

Raj Chari  1 , William W Lockwood, Bradley P Coe, Anna Chu, Devon Macey, Andrew Thomson, Jonathan J Davies, Calum MacAulay, Wan L Lam
Affiliations

SIGMA: a system for integrative genomic microarray analysis of cancer genomes

Raj Chari et al. BMC Genomics. .

Abstract

Background: The prevalence of high resolution profiling of genomes has created a need for the integrative analysis of information generated from multiple methodologies and platforms. Although the majority of data in the public domain are gene expression profiles, and expression analysis software are available, the increase of array CGH studies has enabled integration of high throughput genomic and gene expression datasets. However, tools for direct mining and analysis of array CGH data are limited. Hence, there is a great need for analytical and display software tailored to cross platform integrative analysis of cancer genomes.

Results: We have created a user-friendly java application to facilitate sophisticated visualization and analysis such as cross-tumor and cross-platform comparisons. To demonstrate the utility of this software, we assembled array CGH data representing Affymetrix SNP chip, Stanford cDNA arrays and whole genome tiling path array platforms for cross comparison. This cancer genome database contains 267 profiles from commonly used cancer cell lines representing 14 different tissue types.

Conclusion: In this study we have developed an application for the visualization and analysis of data from high resolution array CGH platforms that can be adapted for analysis of multiple types of high throughput genomic datasets. Furthermore, we invite researchers using array CGH technology to deposit both their raw and processed data, as this will be a continually expanding database of cancer genomes. This publicly available resource, the System for Integrative Genomic Microarray Analysis (SIGMA) of cancer genomes, can be accessed at http://sigma.bccrc.ca.

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Figures

Figure 1
Figure 1
(A) Schematic of the basic architecture of SIGMA. Java WebStart technology was utilized to develop the main user interface to the database, ensuring users will be running the latest version of the program. The application is connected to the MySQL database through a JDBC driver provided by MySQL, over an Apache Web Server. (B) Outline of the various functionalities of SIGMA, with the five main types of visualization and analysis along with their associated uses.
Figure 2
Figure 2
(A) Whole genome karyogram of the H2087 lung adenocarcinoma cell line profiled on the SMRT array using the May 2004 genomic build. For each chromosome, there is a ratio plot associated with plotting the log2 ratio of the genomic element vs. the position of the element on the chromosome. The log2 ratio of the data point is calculated against a normal reference where positive ratios represent increased content and negative ratios represent decreased content in the tumor compared to the normal. (B) The first level of zoom to view a particular chromosome, in this case, chromosome 8. (C) 32X zoom into the amplicon at chromosome band 8q24.21. (D) The ability to link out to biological databases such as NCBI MIM, UCSC Genome Browser, NCBI Gene and NCBI PubMed with a gene of interest.
Figure 3
Figure 3
Serial view of 8 samples representing 8 different tumor types, demonstrating the breadth of data available. From left to right: HL60, HT29, HCC2279, HCC1143, HBL2, PC3, HeLa and A2058. (A) Chromosome 8, highlighting the amplification of the MYC oncogene, which appears to be amplified in all 8 tumor types. (B) Chromosome 7, highlighting the EGFR locus, where it appears that the lung cancer line (HCC2279) and the breast cancer line (HCC1143) harbor the amplification of this gene. Vertical lines denote log2 signal ratios from -1 to +1 with copy number increases to the right and decreases to the left of 0. Each black dot represents a single BAC clone.
Figure 4
Figure 4
(A) Visualization of chromosome 17 of the breast cancer cell line MCF7 across multiple array CGH platforms using the May 2004 genomic build. The four platforms are labeled above each ratio plot. The architecture of the chromosome is consistent across all four platforms, with the altered region highlighted in yellow seen clearly across 3 of the 4 platforms. (B) Visualization of chromosome 16 of the same breast cancer cell line, illustrating decreased density of markers in 3 of the 4 array platforms, with the SMRT array providing greater coverage to a region centromeric to band 16p13.11.
Figure 5
Figure 5
Integration of genomic and epigenetic profiles of the H1395 lung cancer cell line. (A) The genomic profile of H1395 is represented by a moving average spline of the data points. (B) Similarly, the epigenetic profile represents a residual plot of the tumor cell line subtracting the matching blood lymphocyte profile (BL1395), with a moving average spline representing the data points. The moving average was done at 1 MB intervals at increments of 200 kb for both profiles. Specifically, chromosomal region 1q21.3 is highlighted illustrating a region of both copy number increase and hypomethylation.
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References

    1. Lockwood WW, Chari R, Chi B, Lam WL. Recent advances in array comparative genomic hybridization technologies and their applications in human genetics. Eur J Hum Genet. 2006;14:139–148. doi: 10.1038/sj.ejhg.5201531. - DOI - PubMed
    1. Davies JJ, Wilson IM, Lam WL. Array CGH technologies and their applications to cancer genomes. Chromosome Res. 2005;13:237–248. doi: 10.1007/s10577-005-2168-x. - DOI - PubMed
    1. Pinkel D, Albertson DG. Array comparative genomic hybridization and its applications in cancer. Nat Genet. 2005;37 Suppl:S11–7. doi: 10.1038/ng1569. - DOI - PubMed
    1. Barrett T, Suzek TO, Troup DB, Wilhite SE, Ngau WC, Ledoux P, Rudnev D, Lash AE, Fujibuchi W, Edgar R. NCBI GEO: mining millions of expression profiles--database and tools. Nucleic Acids Res. 2005;33:D562–6. doi: 10.1093/nar/gki022. - DOI - PMC - PubMed
    1. Parkinson H, Sarkans U, Shojatalab M, Abeygunawardena N, Contrino S, Coulson R, Farne A, Lara GG, Holloway E, Kapushesky M, Lilja P, Mukherjee G, Oezcimen A, Rayner T, Rocca-Serra P, Sharma A, Sansone S, Brazma A. ArrayExpress--a public repository for microarray gene expression data at the EBI. Nucleic Acids Res. 2005;33:D553–5. doi: 10.1093/nar/gki056. - DOI - PMC - PubMed

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