ArticleThe Journal of molecular diagnostics : JMD2005
Array-based comparative genomic hybridization from formalin-fixed, paraffin-embedded breast tumors.
Article in The Journal of molecular diagnostics : JMD, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
22 citing papers in PubMed.
- Predicting links between tumor samples and genes using 2-Layered graph based diffusion approach.BMC bioinformatics · 2019Article
- Understanding preanalytical variables and their effects on clinical biomarkers of oncology and immunotherapy.Seminars in cancer biology · 2018Review
- The Utilization of Formalin Fixed-Paraffin-Embedded Specimens in High Throughput Genomic Studies.International journal of genomics · 2017Review
- Recurrent genomic alterations in sequential progressive leukoplakia and oral cancer: drivers of oral tumorigenesis?Human molecular genetics · 2014Article
- Chromosomal and genetic imbalances in Chinese patients with rhabdomyosarcoma detected by high-resolution array comparative genomic hybridization.International journal of clinical and experimental pathology · 2014Article
- Isolation and genomic analysis of circulating tumor cells from castration resistant metastatic prostate cancer.BMC cancer · 2012Article
- DNA fragmentation simulation method (FSM) and fragment size matching improve aCGH performance of FFPE tissues.PloS one · 2012Article
- Comparison of whole genome amplification methods for analysis of DNA extracted from microdissected early breast lesions in formalin-fixed paraffin-embedded tissue.ISRN oncology · 2012Article
- Genome-wide comparison of paired fresh frozen and formalin-fixed paraffin-embedded gliomas by custom BAC and oligonucleotide array comparative genomic hybridization: facilitating analysis of archival gliomas.Acta neuropathologica · 2011Article
- Genomic alterations of primary tumor and blood in invasive ductal carcinoma of breast.World journal of surgical oncology · 2010Article
- Prognostic and predictive biomarkers in resected colon cancer: current status and future perspectives for integrating genomics into biomarker discovery.The oncologist · 2010Review
- Whole genome amplification for array comparative genomic hybridization using DNA extracted from formalin-fixed, paraffin-embedded histological sections.The Journal of molecular diagnostics : JMD · 2009Article
- Copy-number analysis of topoisomerase and thymidylate synthase genes in frozen and FFPE DNAs of colorectal cancers.Pharmacogenomics · 2008Article
- Genomewide scan for loss of heterozygosity and chromosomal amplification in breast carcinoma using single-nucleotide polymorphism arrays.Cancer genetics and cytogenetics · 2008Article
- Matrix-comparative genomic hybridization from multicenter formalin-fixed paraffin-embedded colorectal cancer tissue blocks.BMC cancer · 2007Article
- Automated array-CGH optimized for archival formalin-fixed, paraffin-embedded tumor material.BMC cancer · 2007Article
- Microarray-based comparative genomic hybridisation of breast cancer patients receiving neoadjuvant chemotherapy.British journal of cancer · 2007Article
- Glioma test array for use with formalin-fixed, paraffin-embedded tissue: array comparative genomic hybridization correlates with loss of heterozygosity and fluorescence in situ hybridization.The Journal of molecular diagnostics : JMD · 2006Article
- A multiplex PCR predictor for aCGH success of FFPE samples.British journal of cancer · 2006Article
- Array-CGH and breast cancer.Breast cancer research : BCR · 2006Review
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
Identification of prognostic and predictive genomic markers requires long-term clinical follow-up of patients. Extraction of high-quality DNA from archived formalin-fixed, paraffin-embedded material is essential for such studies. Of particular importance is a robust reproducible method of whole genome amplification for small tissue samples. This is especially true for high-resolution analytical approaches because different genomic regions and sequences may amplify differentially. We have tested a number of protocols for DNA amplification for array-based comparative genomic hybridization (CGH), in which relative copy number of the entire genome is measured at 1 to 2 mb resolution. Both random-primed amplification and degenerate oligonucleotide-primed amplification approaches were tested using varying amounts of fresh and paraffin-extracted normal and breast tumor input DNAs. We found that random-primed amplification was clearly superior to degenerate oligonucleotide-primed amplification for array-based CGH. The best quality and reproducibility strongly depended on accurate determination of the amount of input DNA using a quantitative polymerase chain reaction-based method. Reproducible and high-quality results were attained using 50 ng of input DNA, and some samples yielded quality results with as little as 5 ng input DNA. We conclude that random-primed amplification of DNA isolated from paraffin sections is a robust and reproducible approach for array-based CGH analysis of archival tumor samples.
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