Array Comparative Genomic Hybridization Analysis of Colorectal Cancer Cell Lines and Primary Carcinomas

@article{Douglas2004ArrayCG,
  title={Array Comparative Genomic Hybridization Analysis of Colorectal Cancer Cell Lines and Primary Carcinomas},
  author={Eleanor J Douglas and Heike Fiegler and Andrew J. Rowan and Sarah Halford and David C. Bicknell and Walter F. Bodmer and Ian P. M. Tomlinson and Nigel P. Carter},
  journal={Cancer Research},
  year={2004},
  volume={64},
  pages={4817 - 4825}
}
Array comparative genomic hybridization, with a genome-wide resolution of ∼1 Mb, has been used to investigate copy number changes in 48 colorectal cancer (CRC) cell lines and 37 primary CRCs. The samples were divided for analysis according to the type of genomic instability that they exhibit, microsatellite instability (MSI) or chromosomal instability (CIN). Consistent copy number changes were identified, including gain of chromosomes 20, 13, and 8q and smaller regions of amplification such as… 

Figures and Tables from this paper

Deletion at chromosome band 20p12.1 in colorectal cancer revealed by high resolution array comparative genomic hybridization
TLDR
Two noncoding RNA genes located in the region, BA318C17.1 and DJ974N19.1, were investigated by mutation analysis and real‐time PCR in colorectal cancer cell lines and reduced expression of both genes was detected, suggesting that the abrogation of these genes may play a role in colOREctal tumorigenesis.
Integrative genomics reveals mechanisms of copy number alterations responsible for transcriptional deregulation in colorectal cancer
TLDR
A preponderance of chromosome breakpoints at sites of copy number variants (CNVs) in the CRC cell lines is revealed, a novel mechanism of DNA breakage in cancer.
Copy-Number Alterations in the Colorectal Cancer Genome
TLDR
The landscape of SCNA in CRC has been revealed and the biologic rationale and significance for this spectrum of recurrent structural alterations in the genomes of these cancers is fully appreciated.
A Genome-Wide Study of Cytogenetic Changes in Colorectal Cancer Using SNP Microarrays: Opportunities for Future Personalized Treatment
TLDR
This study shows the application of high density SNP arrays for cytogenetic study in CRC and its potential utility for personalized treatment, and identified relevant drugs, targeted to the genes located in these regions with CN changes, approved or in trials for other cancers and common diseases.
Genome-wide differences between microsatellite stable and unstable colorectal tumors.
Genomic copy number changes are frequently found in cancers and they have been demonstrated to contribute to carcinogenesis; and it is widely accepted that tumors with microsatellite instability
Association between genomic alterations and metastatic behavior of colorectal cancer identified by array‐based comparative genomic hybridization
TLDR
DNA copy number profiles may be predictive of the metastatic behavior of CRCs and an inverse relationship between chromosomal instability and aberrant methylation and a positive association between genomic losses and distant metastasis and between genomic gains and lymph node metastasis are suggested.
Analysis of ovarian cancer cell lines using array‐based comparative genomic hybridization
TLDR
Evidence was found for two types of ovarian cancer, one typically near‐triploid and characterized by a generally higher frequency of chromosomal changes (especially losses of 4p, 4q, 13q, 15q, 16p, 16q, 18p and 18q), and the other typically near-diploid/tetraploidand with fewer changes overall, but with relatively high frequencies of 9p loss, 9q gain, and 20p gain.
Combined array-comparative genomic hybridization and single-nucleotide polymorphism-loss of heterozygosity analysis reveals complex changes and multiple forms of chromosomal instability in colorectal cancers.
TLDR
Investigation of colorectal cancer cell lines using array-comparative genomic hybridization for copy number changes and single-copy number polymorphism (SNP) microarrays for allelic loss suggests that CIN is not synonymous with copy number change and some cancers have a specific tendency to whole-chromosome deletion and regain or to mitotic recombination.
...
...

References

SHOWING 1-10 OF 67 REFERENCES
Comparative genomic hybridization reveals a specific pattern of chromosomal gains and losses during the genesis of colorectal tumors
TLDR
It is observed that crude aneuploidy and increased proliferative activity are early events in colorectal carcinogenesis, followed by TP53 overexpression and the acquisition of recurrent chromosomal gains and losses during the progression from high‐grade adenomas to invasive carcinomas.
Chromosome arm 20q gains and other genomic alterations in colorectal cancer metastatic to liver, as analyzed by comparative genomic hybridization and fluorescence in situ hybridization
TLDR
The authors' CGH data indicate that colorectal metastases show chromosomal changes similar to those that have been reported for primary tumors, particularly for chromosomes 14 and 15.
High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays
TLDR
The implementation of array CGH is demonstrated to be able to measure copy number with high precision in the human genome, and to analyse clinical specimens by obtaining new information on chromosome 20 aberrations in breast cancer.
Chromosomal aberrations in colorectal cancers and liver metastases analyzed by comparative genomic hybridization
TLDR
The pattern of genetic changes seen in metastatic tumors, with frequent gains at 8q23‐24 and 20q and loss at 18q12‐23, suggests the progression of colorectal cancer.
Optimizing comparative genomic hybridization for analysis of DNA sequence copy number changes in solid tumors
TLDR
Recent optimized procedures for CGH are described, including DNA labeling, hybridization, fluorescence microscopy, digital image analysis, data interpretation, and quality control, emphasizing those steps that are most critical.
Minimal sizes of deletions detected by comparative genomic hybridization
TLDR
Comparative genomic hybridization (CGH) analyses on five DNA samples derived from B‐cell leukemias with 11q deletions, the sizes of which ranged from 3 Mbp to 14–18 Mbp, found that there was complete agreement between the two image analysis systems.
Spectral karyotyping suggests additional subsets of colorectal cancers characterized by pattern of chromosome rearrangement
TLDR
Ch Chromosome rearrangement was investigated in 17 colorectal carcinoma-derived cell lines and showed coexistence in one tumor of two kinds of genomic instability, to be expected if the underlying defects are selected for in tumor evolution.
Evaluation of candidate tumour suppressor genes on chromosome 18 in colorectal cancers
TLDR
A rigorous strategy for mapping and evaluating allelic deletions in sporadic tumours is presented and applied to the evaluation of chromosome 18 in colorectal cancers, finding a minimally lost region on chromosome 18q21, which contains at least two candidate tumour suppressor genes, DPC4 and DCC.
Chromosomal gains and losses in primary colorectal carcinomas detected by CGH and their associations with tumour DNA ploidy, genotypes and phenotypes
TLDR
The study is consistent with the idea that these two groups of tumours evolve along separate genetic pathways and that gross genomic instability is associated with TP53 gene aberrations and that genomic instability and possible growth advantages in diploid tumours do not result from acquisition of gross chromosomal aberration but rather from selection for other types of mutations.
Chromosomal imbalances in the colorectal carcinomas with microsatellite instability.
...
...