ArticleThe pharmacogenomics journal2011
High-efficiency genotype analysis from formalin-fixed, paraffin-embedded tumor tissues.
Article in The pharmacogenomics journal, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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
12 citing papers in PubMed, 18 citations in OpenAlex.
- CYP2D6 genotype and tamoxifen response in postmenopausal women with endocrine-responsive breast cancer: the breast international group 1-98 trial.Journal of the National Cancer Institute · 2012Trial
- vcferr: Development, validation, and application of a single nucleotide polymorphism genotyping error simulation framework.F1000Research · 2022Article
- The association between two genetic polymorphisms inSaudi journal of biological sciences · 2022Article
- Osteonecrosis of the jaw risk factors in bisphosphonate-treated patients with metastatic cancer.Oral diseases · 2022Article
- Genetic variation in EPHA contributes to sensitivity to paclitaxel-induced peripheral neuropathy.British journal of clinical pharmacology · 2020Article
- Concordance of DNA methylation profiles between breast core biopsy and surgical excision specimens containing ductal carcinoma in situ (DCIS).Experimental and molecular pathology · 2017Article
- Genotyping concordance in DNA extracted from formalin-fixed paraffin embedded (FFPE) breast tumor and whole blood for pharmacogenetic analyses.Molecular oncology · 2015Article
- Genetic Testing and Tissue Banking for Personalized Oncology: Analytical and Institutional Factors.Seminars in oncology · 2015Review
- DNA and RNA analysis of blood and muscle from bodies with variable postmortem intervals.Forensic science, medicine, and pathology · 2014Article
- Inducible nitric oxide synthase drives mTOR pathway activation and proliferation of human melanoma by reversible nitrosylation of TSC2.Cancer research · 2014Article
- CYP2D6 and UGT2B7 genotype and risk of recurrence in tamoxifen-treated breast cancer patients.Journal of the National Cancer Institute · 2012Article
- High quality and quantity Genome-wide germline genotypes from FFPE normal tissue.BMC research notes · 2011Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
Abstract
Single-nucleotide polymorphisms (SNPs) can be assayed using DNA isolated from archival formalin-fixed, paraffin-embedded (FFPE) samples, making retrospective pharmacogenetic studies possible. In this study, we describe methods that significantly increase the number of SNP determinations possible using FFPE samples. Quantifying the amount of DNA amenable to PCR (amplification-quality DNA, AQ-DNA) allows a significant reduction in the amount of sample required for Taqman-based SNP assays. Optimizing AQ-DNA input increases PCR amplification efficiency and SNP determination accuracy. DNA was extracted from 39 FFPE tumor sections and matched tumor and stromal cores, which were of the type used to generate tissue microarrays. Sections and tumor cores yielded sufficient AQ-DNA for more than 1000 SNP determinations. Seven SNPs were assessed following individual assay optimization for minimal AQ-DNA. Genotypes from tumor cores for single SNPs were 92.3-100% concordant with those obtained from sections. Using these methods, the number of SNP genotypes that can be determined from single FFPE samples is greatly increased expanding the genetic association studies possible from limited archival specimens. The use of tumor cores is of particular importance as the harvesting of tumor cores has minimal impact on the utility of the donor blocks for other purposes.
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.