ArticleMolecular oncology2015
Genotyping concordance in DNA extracted from formalin-fixed paraffin embedded (FFPE) breast tumor and whole blood for pharmacogenetic analyses.
Article in Molecular oncology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers, 1 of them a synthesis 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
21 citing papers in PubMed, 1 synthesis or guideline pooled it, 32 citations in OpenAlex.
- Cytochrome P-450 2D6 (CYP2D6) Genotype and Breast Cancer Recurrence in Tamoxifen-Treated Patients: Evaluating the Importance of Loss of Heterozygosity.American journal of epidemiology · 2017Pooled it
- Article
- Article
- Genetic variants and social benefit receipt in premenopausal women with breast cancer treated with docetaxel: a Danish population-based cohort study.Breast cancer research and treatment · 2025Article
- Predictive and prognostic value of excision repair cross-complementing group 1 in patients with advanced gastric cancer.BJC reports · 2024Article
- Promoter-Specific Variants in NeuroD1 and H3K4me3 Coincident Regions and Clinical Outcomes of Small Cell Lung Cancer.Journal of Korean medical science · 2023Article
- Sequencing of genes of drug response in tumor DNA and implications for precision medicine in cancer patients.The pharmacogenomics journal · 2023Article
- The impact of single nucleotide polymorphisms on return-to-work after taxane-based chemotherapy in breast cancer.Cancer chemotherapy and pharmacology · 2023Article
- Successful restoration of archived ovine formalin fixed paraffin-embedded tissue DNA and single nucleotide polymorphism analysis.Veterinary research communications · 2023Article
- Single-nucleotide polymorphisms and the effectiveness of taxane-based chemotherapy in premenopausal breast cancer: a population-based cohort study in Denmark.Breast cancer research and treatment · 2022Article
- Defining Clinical Utility of Germline Indicators of Toxicity Risk: A Perspective.Journal of clinical oncology : official journal of the American Society of Clinical Oncology · 2022Article
- Osteonecrosis of the jaw risk factors in bisphosphonate-treated patients with metastatic cancer.Oral diseases · 2022Article
- vcferr: Development, validation, and application of a single nucleotide polymorphism genotyping error simulation framework.F1000Research · 2022Article
- Article
- Male and female breast cancer: the two faces of the same genetic susceptibility coin.Breast cancer research and treatment · 2021Article
- Comparison of different methods for repairing damaged DNA from buffered and unbuffered formalin-fixed tissues.International journal of legal medicine · 2018Article
- Article
- Polymorphisms in drug-metabolizing enzymes and steady-state exemestane concentration in postmenopausal patients with breast cancer.The pharmacogenomics journal · 2017Article
- Article
- PSCA rs2294008 polymorphism contributes to the decreased risk for cervical cancer in a Chinese population.Scientific reports · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors at 4 institutions in 1 country.
Funding
Abstract
backgroundCancer pharmacogenetic studies use archival tumor samples as a DNA source when germline DNA is unavailable. Genotyping DNA from formalin-fixed paraffin embedded tumors (FFPE-T) may be inaccurate due to FFPE storage, genetic aberrations, and/or insufficient DNA extraction. Our objective was to assess the extent and source of genotyping inaccuracy from FFPE-T DNA and demonstrate analytical validity of FFPE-T genotyping of candidate single nucleotide polymorphisms (SNPs) for pharmacogenetic analyses.
methodsCancer pharmacogenetics SNPs were genotyped by Sequenom MassARRAYs in DNA harvested from matched FFPE-T, FFPE lymph node (FFPE-LN), and whole blood leukocyte samples obtained from breast cancer patients. No- and discordant-call rates were calculated for each tissue type and SNP. Analytical validity was defined as any SNP with <5% discordance between FFPE-T and blood and <10% discordance plus no-calls.
resultsMatched samples from 114 patients were genotyped for 247 SNPs. No-call rate in FFPE-T was greater than FFPE-LN and blood (4.3% vs. 3.0% vs. 0.5%, p < 0.001). Discordant-call rate between FFPE-T and blood was very low, but greater than that between FFPE-LN and blood (1.1% vs. 0.3%, p < 0.001). Samples with heterozygous genotypes were more likely to be no- or discordantly-called in either tissue (p < 0.001). Analytical validity of FFPE-T genotyping was demonstrated for 218 (88%) SNPs.
conclusionsNo- and discordant-call rates were below concerning thresholds, confirming that most SNPs can be accurately genotyped from FFPE-T on our Sequenom platform. FFPE-T is a viable DNA source for prospective-retrospective pharmacogenetic analyses of clinical trial cohorts.
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.