ArticleBMC cancer2007
Automated array-CGH optimized for archival formalin-fixed, paraffin-embedded tumor material.
Article in BMC cancer, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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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.
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Who cites it
12 citing papers in PubMed.
- An aCGH classifier derived from BRCA1-mutated breast cancer and benefit of high-dose platinum-based chemotherapy in HER2-negative breast cancer patients.Annals of oncology : official journal of the European Society for Medical Oncology · 2011Trial
- Comparative study of whole genome amplification and next generation sequencing performance of single cancer cells.Oncotarget · 2017Article
- The Utilization of Formalin Fixed-Paraffin-Embedded Specimens in High Throughput Genomic Studies.International journal of genomics · 2017Review
- Robust BRCA1-like classification of copy number profiles of samples repeated across different datasets and platforms.Molecular oncology · 2015Article
- Genomic patterns resembling BRCA1- and BRCA2-mutated breast cancers predict benefit of intensified carboplatin-based chemotherapy.Breast cancer research : BCR · 2014Article
- Triple-negative breast cancer: BRCAness and concordance of clinical features with BRCA1-mutation carriers.British journal of cancer · 2013Article
- Significance of genomic instability in breast cancer in atomic bomb survivors: analysis of microarray-comparative genomic hybridization.Radiation oncology (London, England) · 2011Article
- Molecular alterations associated with liver metastases development in colorectal cancer patients.British journal of cancer · 2011Article
- 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
- Specific genomic aberrations in primary colorectal cancer are associated with liver metastases.BMC cancer · 2010Article
- BRCA1-mutated and basal-like breast cancers have similar aCGH profiles and a high incidence of protein truncating TP53 mutations.BMC cancer · 2010Article
- Pathogenicity of the BRCA1 missense variant M1775K is determined by the disruption of the BRCT phosphopeptide-binding pocket: a multi-modal approach.European journal of human genetics : EJHG · 2008Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundArray Comparative Genomic Hybridization (aCGH) is a rapidly evolving technology that still lacks complete standardization. Yet, it is of great importance to obtain robust and reproducible data to enable meaningful multiple hybridization comparisons. Special difficulties arise when aCGH is performed on archival formalin-fixed, paraffin-embedded (FFPE) tissue due to its variable DNA quality. Recently, we have developed an effective DNA quality test that predicts suitability of archival samples for BAC aCGH.
methodsIn this report, we first used DNA from a cancer cell-line (SKBR3) to optimize the aCGH protocol for automated hybridization, and subsequently optimized and validated the procedure for FFPE breast cancer samples. We aimed for highest throughput, accuracy, and reproducibility applicable to FFPE samples, which can also be important in future diagnostic use.
resultsOur protocol of automated array-CGH on archival FFPE ULS-labeled DNA showed very similar results compared with published data and our previous manual hybridization method.
conclusionThis report combines automated aCGH on unamplified archival FFPE DNA using non-enzymatic ULS labeling, and describes an optimized protocol for this combination resulting in improved quality and reproducibility.
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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.