ArticleOncotarget2015
Targeted or whole genome sequencing of formalin fixed tissue samples: potential applications in cancer genomics.
Article in Oncotarget, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
What it found
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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.
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Who cites it
38 citing papers in PubMed, 69 citations in OpenAlex.
- Tutorial for variant interrogation in tumor samples.PLoS computational biology · 2026Article
- Enabling whole genome sequencing analysis from FFPE specimens in clinical oncology.Nature communications · 2025Article
- Cryopreserved Tissue Biospecimens Offer Superior Quality for Whole-Genome Sequencing of Various Cancers Compared to Paired Formalin-Fixed Paraffin-Embedded Tissues.International journal of molecular sciences · 2025Article
- Assessing the suitability of formalin-fixed paraffin-embedded (FFPE) tissue for genome-wide association studies (GWAS).BMC research notes · 2025Article
- Genomic Analysis Reveals Racial and Age-Related Differences in the Somatic Landscape of Breast Cancer and the Association with Socioeconomic Factors.Cancer research · 2025Article
- Prognostic markers in oesophageal and gastric cancer review. Are they ready for clinical practice?ESMO gastrointestinal oncology · 2024Review
- From Genomic Exploration to Personalized Treatment: Next-Generation Sequencing in Oncology.Current issues in molecular biology · 2024Review
- snPATHO-seq, a versatile FFPE single-nucleus RNA sequencing method to unlock pathology archives.Communications biology · 2024Article
- Exploratory genomic analysis of high-grade neuroendocrine neoplasms across diverse primary sites.Endocrine-related cancer · 2022Article
- A complete reference genome improves analysis of human genetic variation.Science (New York, N.Y.) · 2022Article
- Article
- Cross-Site Concordance Evaluation of Tumor DNA and RNA Sequencing Platforms for the CIMAC-CIDC Network.Clinical cancer research : an official journal of the American Association for Cancer Research · 2021Article
- Evaluation of clinical formalin-fixed paraffin-embedded tissue quality for targeted-bisulfite sequencing.Pathology international · 2021Article
- Mutational profiling of micro-dissected pre-malignant lesions from archived specimens.BMC medical genomics · 2020Article
- Novel insights into the mixed germ cell-sex cord stromal tumor of the testis: detection of chromosomal aneuploidy and further morphological evidence supporting the neoplastic nature of the germ cell component.Virchows Archiv : an international journal of pathology · 2020Article
- Why Formalin-fixed, Paraffin-embedded Biospecimens Must Be Used in Genomic Medicine: An Evidence-based Review and Conclusion.The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society · 2020Article
- Comparison of commercially available whole-genome sequencing kits for variant detection in circulating cell-free DNA.Scientific reports · 2020Article
- Article
- Characterization of FFPE-induced bacterial DNA damage and development of a repair method.Biology methods & protocols · 2020Article
- Regulatory variants: from detection to predicting impact.Briefings in bioinformatics · 2019Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors at 3 institutions in 2 countries.
Funding
Abstract
Current genomic studies are limited by the poor availability of fresh-frozen tissue samples. Although formalin-fixed diagnostic samples are in abundance, they are seldom used in current genomic studies because of the concern of formalin-fixation artifacts. Better characterization of these artifacts will allow the use of archived clinical specimens in translational and clinical research studies. To provide a systematic analysis of formalin-fixation artifacts on Illumina sequencing, we generated 26 DNA sequencing data sets from 13 pairs of matched formalin-fixed paraffin-embedded (FFPE) and fresh-frozen (FF) tissue samples. The results indicate high rate of concordant calls between matched FF/FFPE pairs at reference and variant positions in three commonly used sequencing approaches (whole genome, whole exome, and targeted exon sequencing). Global mismatch rates and C · G > T · A substitutions were comparable between matched FF/FFPE samples, and discordant rates were low (<0.26%) in all samples. Finally, low-pass whole genome sequencing produces similar pattern of copy number alterations between FF/FFPE pairs. The results from our studies suggest the potential use of diagnostic FFPE samples for cancer genomic studies to characterize and catalog variations in cancer genomes.
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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.