ArticleInternational journal of molecular sciences2016
A Comparison of Fresh Frozen vs. Formalin-Fixed, Paraffin-Embedded Specimens of Canine Mammary Tumors via Branched-DNA Assay.
Article in International journal of molecular sciences, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers, 2 of them syntheses that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
28 citing papers in PubMed, 2 syntheses or guidelines pooled it, 39 citations in OpenAlex.
- Role of the intestinal microbiome in colorectal cancer surgery outcomes.World journal of surgical oncology · 2019Pooled it
- Pooled it
- DNA Quantity and Quality Comparisons between Cryopreserved and FFPE Tumors from Matched Pan-Cancer Samples.Current oncology (Toronto, Ont.) · 2024Article
- Utility of bronchoscopically obtained frozen cytology pellets for next-generation sequencing.BMC cancer · 2024Article
- C-Myc protein expression indicates unfavorable clinical outcome in surgically resected small cell lung cancer.World journal of surgical oncology · 2024Article
- Infrared spectroscopic laser scanning confocal microscopy for whole-slide chemical imaging.Nature communications · 2023Article
- HER2 Overexpression and Cytogenetical Patterns in Canine Mammary Carcinomas.Veterinary sciences · 2022Article
- Article
- A generative adversarial approach to facilitate archival-quality histopathologic diagnoses from frozen tissue sections.Laboratory investigation; a journal of technical methods and pathology · 2022Article
- Spatial transcriptomics using combinatorial fluorescence spectral and lifetime encoding, imaging and analysis.Nature communications · 2022Article
- Analysis of Genetic Alterations in Ocular Adnexal Mucosa-Associated Lymphoid Tissue Lymphoma With Whole-Exome Sequencing.Frontiers in oncology · 2022Article
- Gene Expression Studies in Formalin-Fixed Paraffin-Embedded Samples of Cutaneous Cancer: The Need for Reference Genes.Current issues in molecular biology · 2021Article
- Evidencing the presence of merkel cell polyomavirus in papillary thyroid cancer.Scientific reports · 2021Article
- Suitability of transbronchial brushing cytology specimens for next-generation sequencing in peripheral lung cancer.Cancer science · 2021Article
- MIXnorm: normalizing RNA-seq data from formalin-fixed paraffin-embedded samples.Bioinformatics (Oxford, England) · 2020Article
- Human papilloma virus (HPV) profiles in breast cancer: future management.Annals of translational medicine · 2020Review
- Long non-coding RNA transcriptome of uncharacterized samples can be accurately imputed using protein-coding genes.Briefings in bioinformatics · 2020Article
- The functions and mechanisms of prefoldin complex and prefoldin-subunits.Cell & bioscience · 2020Review
- The new horizon of liquid biopsy in sarcoma: the potential utility of circulating tumor nucleic acids.Journal of Cancer · 2020Review
- RCRnorm: An integrated system of random-coefficient hierarchical regression models for normalizing NanoString nCounter data.The annals of applied statistics · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Mammary neoplasms are the tumors most affecting female dogs and women. Formalin-fixed, paraffin-embedded (FFPE) tissues are an invaluable source of archived biological material. Fresh frozen (FF) tissue is considered ideal for gene expression analysis. However, strategies based on FFPE material offer several advantages. Branched-DNA assays permit a reliable and fast workflow when analyzing gene expression. The aim of this study was to assess the comparability of the branched-DNA assay when analyzing certain gene expression patterns between FF and FFPE samples in canine mammary tumors. RNA was isolated from 109 FFPE samples and from 93 FF samples of different canine mammary tissues. Sixteen (16) target genes (Tp53; Myc; HMGA1; Pik3ca; Mcl1; MAPK3; FOXO3; PTEN; GATA4; PFDN5; HMGB1; MAPK1; BRCA2; BRCA1; HMGA2; and Her2) were analyzed via branched-DNA assay (b-DNA). ACTB, GAPDH, and HPRT1 were used as data normalizers. Overall, the relative gene expression of the two different origins of samples showed an agreement of 63%. Still, care should be taken, as FFPE specimens showed lower expression of the analyzed targets when compared to FF samples. The fact that the gene expression in FFPE proved to be lower than in FF specimens is likely to have been caused by the effect of storage time. ACTB had the best performance as a data normalizer.
Indexed as
Identifiers
What OpenQuestion holds
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.