ArticleLaboratory investigation; a journal of technical methods and pathology2006
Application of array CGH on archival formalin-fixed paraffin-embedded tissues including small numbers of microdissected cells.
Article in Laboratory investigation; a journal of technical methods and pathology, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
32 citing papers in PubMed, 82 citations in OpenAlex.
- Autologous mesenchymal stem cells for the treatment of secondary progressive multiple sclerosis: an open-label phase 2a proof-of-concept study.The Lancet. Neurology · 2012Trial
- Chromosomal copy number alterations are associated with tumor response to chemoradiation in locally advanced rectal cancer.Genes, chromosomes & cancer · 2011Trial
- Genomic aberrations associated with outcome in anaplastic oligodendroglial tumors treated within the EORTC phase III trial 26951.Journal of neuro-oncology · 2011Trial
- Array comparative genomic hybridisation in haematological malignancies: A comprehensive review.African journal of laboratory medicine · 2026Review
- Formalin Fixation, Delay to Fixation, and Time in Fixative Adversely Impact Copy Number Variation Analysis by aCGH.Biopreservation and biobanking · 2023Article
- Enriched transcriptome analysis of laser capture microdissected populations of single cells to investigate intracellular heterogeneity in immunostained FFPE sections.Computational and structural biotechnology journal · 2021Article
- Flow cytometric sorting coupled with exon capture sequencing identifies somatic mutations in archival lymphoma tissues.Laboratory investigation; a journal of technical methods and pathology · 2017Article
- The Utilization of Formalin Fixed-Paraffin-Embedded Specimens in High Throughput Genomic Studies.International journal of genomics · 2017Review
- Patterns of Chromosomal Aberrations in Solid Tumors.Recent results in cancer research. Fortschritte der Krebsforschung. Progres dans les recherches sur le cancer · 2015Review
- Progress and opportunities in molecular pathological epidemiology of colorectal premalignant lesions.The American journal of gastroenterology · 2014Review
- Recurrent genomic alterations in sequential progressive leukoplakia and oral cancer: drivers of oral tumorigenesis?Human molecular genetics · 2014Article
- Detection limits of DNA copy number alterations in heterogeneous cell populations.Cellular oncology (Dordrecht, Netherlands) · 2013Article
- Genomic differences in benign and malignant follicular thyroid tumours using 1-Mb array-comparative genomic hybridisation.European archives of oto-rhino-laryngology : official journal of the European Federation of Oto-Rhino-Laryngological Societies (EUFOS) : affiliated with the German Society for Oto-Rhino-Laryngology - Head and Neck Surgery · 2013Article
- Identification of a novel population in high-grade oligodendroglial tumors not deleted on 1p/19q using array CGH.Journal of neuro-oncology · 2012Article
- A new whole genome amplification method for studying clonal evolution patterns in malignant colorectal polyps.Genes, chromosomes & cancer · 2012Article
- DNA fragmentation simulation method (FSM) and fragment size matching improve aCGH performance of FFPE tissues.PloS one · 2012Article
- Effective DNA/RNA co-extraction for analysis of microRNAs, mRNAs, and genomic DNA from formalin-fixed paraffin-embedded specimens.PloS one · 2012Article
- High-efficiency genotype analysis from formalin-fixed, paraffin-embedded tumor tissues.The pharmacogenomics journal · 2011Article
- Genomic changes in gliomas detected using single nucleotide polymorphism array in formalin-fixed, paraffin-embedded tissue: superior results compared with microsatellite analysis.The Journal of molecular diagnostics : JMD · 2011Article
- Primary central nervous system lymphomas: a validation study of array-based comparative genomic hybridization in formalin-fixed paraffin-embedded tumor specimens.Clinical cancer research : an official journal of the American Association for Cancer Research · 2011Article
Corrections and comments
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
Abstract
Array-based comparative genomic hybridisation (aCGH) has diverse applications in cancer gene discovery and translational research. Currently, aCGH is performed primarily using high molecular weight DNA samples and its application to formalin-fixed and paraffin-embedded (FFPE) tissues remains to be established. To explore how aCGH can be reliably applied to archival FFPE tissues and whether it is possible to apply aCGH to small numbers of cells microdissected from FFPE tissue sections, we have systematically performed aCGH on 15 pairs of matched frozen and FFPE astrocytic tumour tissues using a well-established in-house human 1 Mb BAC/PAC genomic array. By spiking tumour DNA with normal DNA, we demonstrated that at least 70% of tumour DNA was required for reliable aCGH analysis. Using aCGH data from frozen tissue as a reference, it was found that only FFPE astrocytic tumour tissues that supported PCR amplification of >300 bp DNA fragment provided high quality, reproducible aCGH data. The presence of necrosis in a tissue specimen had an adverse effect on the quality of aCGH, while fixation in formalin for up to 96 h of fresh tissue did not appear to affect the quality of the result. As little as 10-20 ng DNA from frozen or FFPE tissues could be readily used for aCGH analysis following whole genome amplification (WGA). Furthermore, as few as 2000 microdissected cells from haematoxylin-stained slides of archival FFPE tissues could be successfully used for aCGH investigations when WGA was used. By careful assessment of DNA integrity and review of histology, to exclude necrosis and select specimens with a high proportion of tumour cells, it is feasible to preselect archival FFPE tissues adequate for aCGH analysis. With the help of microdissection and WGA, it is also possible to apply aCGH to histologically defined lesions, such as carcinoma in situ.
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Registered trials
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.