ArticlePloS one2012
Deep clonal profiling of formalin fixed paraffin embedded clinical samples.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 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
33 citing papers in PubMed.
- Tracking the Evolution of Cutaneous Melanoma by Multiparameter Flow Sorting and Genomic Profiling.International journal of molecular sciences · 2025Article
- Single nucleus DNA sequencing of flow sorted archived frozen and formalin fixed paraffin embedded solid tumors.BMC genomics · 2024Article
- Genomic landscape of diploid and aneuploid microsatellite stable early onset colorectal cancer.Scientific reports · 2024Article
- Single-Nucleus RNA-Seq: Open the Era of Great Navigation for FFPE Tissue.International journal of molecular sciences · 2023Review
- Formalin Fixation, Delay to Fixation, and Time in Fixative Adversely Impact Copy Number Variation Analysis by aCGH.Biopreservation and biobanking · 2023Article
- Enhancing Tumor Content through Tumor Macrodissection.Journal of visualized experiments : JoVE · 2022Article
- Genomic and Epigenomic Landscaping Defines New Therapeutic Targets for Adenosquamous Carcinoma of the Pancreas.Cancer research · 2020Article
- Unique genomic and neoepitope landscapes across tumors: a study across time, tissues, and space within a single lynch syndrome patient.Scientific reports · 2020Article
- Article
- Clonal analyses of refractory testicular germ cell tumors.PloS one · 2019Article
- Methods of measurement for tumor mutational burden in tumor tissue.Translational lung cancer research · 2018Review
- Novel cell enrichment technique for robust genetic analysis of archival classical Hodgkin lymphoma tissues.Laboratory investigation; a journal of technical methods and pathology · 2018Article
- Biotinylated amplicon sequencing: A method for preserving DNA samples of limited quantity.Practical laboratory medicine · 2018Article
- The association of genomic lesions and PD-1/PD-L1 expression in resected triple-negative breast cancers.Breast cancer research : BCR · 2018Article
- Shallow whole genome sequencing for robust copy number profiling of formalin-fixed paraffin-embedded breast cancers.Experimental and molecular pathology · 2018Article
- A phase 2 trial of personalized cytotoxic therapy based on tumor immunohistochemistry in previously treated metastatic pancreatic cancer patients.Journal of gastrointestinal oncology · 2017Article
- Bioinformatory-assisted analysis of next-generation sequencing data for precision medicine in pancreatic cancer.Molecular oncology · 2017Article
- Clinical study of genomic drivers in pancreatic ductal adenocarcinoma.British journal of cancer · 2017Article
- The Utilization of Formalin Fixed-Paraffin-Embedded Specimens in High Throughput Genomic Studies.International journal of genomics · 2017Review
- Performance comparison of two commercial human whole-exome capture systems on formalin-fixed paraffin-embedded lung adenocarcinoma samples.BMC cancer · 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
19 authors.
Funding
Abstract
Formalin fixed paraffin embedded (FFPE) tissues are a vast resource of annotated clinical samples. As such, they represent highly desirable and informative materials for the application of high definition genomics for improved patient management and to advance the development of personalized therapeutics. However, a limitation of FFPE tissues is the variable quality of DNA extracted for analyses. Furthermore, admixtures of non-tumor and polyclonal neoplastic cell populations limit the number of biopsies that can be studied and make it difficult to define cancer genomes in patient samples. To exploit these valuable tissues we applied flow cytometry-based methods to isolate pure populations of tumor cell nuclei from FFPE tissues and developed a methodology compatible with oligonucleotide array CGH and whole exome sequencing analyses. These were used to profile a variety of tumors (breast, brain, bladder, ovarian and pancreas) including the genomes and exomes of matching fresh frozen and FFPE pancreatic adenocarcinoma samples.
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.