ArticleBMC genomics2008
Comparison of the Agilent, ROMA/NimbleGen and Illumina platforms for classification of copy number alterations in human breast tumors.
Article in BMC genomics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
- Influence of DNA copy number and mRNA levels on the expression of breast cancer related proteins.Molecular oncology · 2013Trial
- CINmetrics: an R package for analyzing copy number aberrations as a measure of chromosomal instability.PeerJ · 2023Article
- Measuring DNA Copy Number Variation Using High-Density Methylation Microarrays.Journal of computational biology : a journal of computational molecular cell biology · 2019Article
- Phylogenetic Copy-Number Factorization of Multiple Tumor Samples.Journal of computational biology : a journal of computational molecular cell biology · 2018Article
- Identification of copy number variation in French dairy and beef breeds using next-generation sequencing.Genetics, selection, evolution : GSE · 2017Article
- Article
- Robust BRCA1-like classification of copy number profiles of samples repeated across different datasets and platforms.Molecular oncology · 2015Article
- The HER2 amplicon includes several genes required for the growth and survival of HER2 positive breast cancer cells - A data description.Genomics data · 2014Article
- High resolution copy number variation data in the NCI-60 cancer cell lines from whole genome microarrays accessible through CellMiner.PloS one · 2014Article
- Signatures of mutational processes in human cancer.Nature · 2013Article
- Comparability and reproducibility of biomedical data.Briefings in bioinformatics · 2013Review
- The HER2 amplicon includes several genes required for the growth and survival of HER2 positive breast cancer cells.Molecular oncology · 2013Article
- Genome-wide detection of copy number variations using high-density SNP genotyping platforms in Holsteins.BMC genomics · 2013Article
- Evaluation of calling algorithms for array-CGH.Frontiers in genetics · 2013Article
- Short copy number variations potentially associated with tonic immobility responses in newly hatched chicks.PloS one · 2013Article
- High levels of genomic aberrations in serous ovarian cancers are associated with better survival.PloS one · 2013Article
- Identifying in-trans process associated genes in breast cancer by integrated analysis of copy number and expression data.PloS one · 2013Article
- Effect of Combining Multiple CNV Defining Algorithms on the Reliability of CNV Calls from SNP Genotyping Data.Genomics & informatics · 2012Article
- The life history of 21 breast cancers.Cell · 2012Article
- Bayesian method to predict individual SNP genotypes from gene expression data.Nature genetics · 2012Article
Corrections and comments
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Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMicroarray Comparative Genomic Hybridization (array CGH) provides a means to examine DNA copy number aberrations. Various platforms, brands and underlying technologies are available, facing the user with many choices regarding platform sensitivity and number, localization, and density distribution of probes.
resultsWe evaluate three different platforms presenting different nature and arrangement of the probes: The Agilent Human Genome CGH Microarray 44 k, the ROMA/NimbleGen Representational Oligonucleotide Microarray 82 k, and the Illumina Human-1 Genotyping 109 k BeadChip, with Agilent being gene oriented, ROMA/NimbleGen being genome oriented, and Illumina being genotyping oriented. We investigated copy number changes in 20 human breast tumor samples representing different gene expression subclasses, using a suite of graphical and statistical methods designed to work across platforms. Despite substantial differences in the composition and spatial distribution of probes, the comparison revealed high overall concordance. Notably however, some short amplifications and deletions of potential biological importance were not detected by all platforms. Both correlation and cluster analysis indicate a somewhat higher similarity between ROMA/NimbleGen and Illumina than between Agilent and the other two platforms. The programs developed for the analysis are available from http://www.ifi.uio.no/bioinf/Projects/.
conclusionWe conclude that platforms based on different technology principles reveal similar aberration patterns, although we observed some unique amplification or deletion peaks at various locations, only detected by one of the platforms. The correct platform choice for a particular study is dependent on whether the appointed research intention is gene, genome, or genotype oriented.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.