ArticlePloS one2015
Comparison of Accuracy of Whole-Exome Sequencing with Formalin-Fixed Paraffin-Embedded and Fresh Frozen Tissue Samples.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 77 papers, 1 of them a synthesis that pooled it.
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Who cites it
77 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Guideline
- A Comparative Survey of Historical DNA Degradation From Vertebrate Museum Specimens: Unexpected Utility of Fluid-Preserved Specimens.Molecular ecology resources · 2026Article
- Genomic characterization of ER-positive primary tumors and corresponding relapses identifies potentially targetable alterations.NPJ breast cancer · 2026Article
- An alignment-free strategy for circulating tumor DNA detection and tumor fraction estimation from whole-genome sequencing data.PLoS computational biology · 2026Article
- Somatic mutational landscape in von Hippel-Lindau familial hemangioblastoma.Molecular oncology · 2026Article
- FFixR: a machine learning framework for accurate somatic mutation calling from FFPE RNA-seq data in cancer.Bioinformatics (Oxford, England) · 2026Article
- VariantMedium: sensitive and generalizable somatic point mutation calling with 3D DenseNets trained and evaluated on experimental data.Genome medicine · 2026Article
- Pre-Analytical and Analytical Challenges in Whole-Exome Sequencing of Formalin-Fixed Paraffin-Embedded Breast and Prostate Cancer Tissue: A Real-World Multicenter Study.Diagnostics (Basel, Switzerland) · 2026Article
- Understanding exceptional response: The role of MINDY1 SNP in CDK4/6 inhibitor therapy for ERHGG advances · 2026Article
- Enabling whole genome sequencing analysis from FFPE specimens in clinical oncology.Nature communications · 2025Article
- Article
- Assessing the suitability of formalin-fixed paraffin-embedded (FFPE) tissue for genome-wide association studies (GWAS).BMC research notes · 2025Article
- Fast and efficient method for parallel construction of targeted exome and methylome single-stranded DNA sequencing libraries.Scientific reports · 2025Article
- Exploring the influence of pre-analytical variables on gene expression measurements and relative expression orderings in cancer research.Scientific reports · 2025Article
- Extraction, Purification, and Next-Generation Sequencing (NGS) Analysis of DNA and RNA from Formalin-Fixed and Paraffin-Embedded (FFPE) Tissue.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Towards Reliable Methodology: Microbiome Analysis of Fresh Frozen vs. Formalin-Fixed Paraffin-Embedded Bladder Tissue Samples: A Feasibility Study.Microorganisms · 2024Article
- InDEL instability in two different tumoral tissues and its forensic significance.Forensic science, medicine, and pathology · 2024Article
- On the Boundary of Exploratory Genomics and Translation in Sequential Glioblastoma.International journal of molecular sciences · 2024Article
- Fusobacteria alterations are associated with colorectal cancer liver metastasis and a poor prognosis.Oncology letters · 2024Article
- Somatic mutations of esophageal adenocarcinoma: a comparison between Black and White patients.Scientific reports · 2024Article
17 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Formalin fixing with paraffin embedding (FFPE) has been a standard sample preparation method for decades, and archival FFPE samples are still very useful resources. Nonetheless, the use of FFPE samples in cancer genome analysis using next-generation sequencing, which is a powerful technique for the identification of genomic alterations at the nucleotide level, has been challenging due to poor DNA quality and artificial sequence alterations. In this study, we performed whole-exome sequencing of matched frozen samples and FFPE samples of tissues from 4 cancer patients and compared the next-generation sequencing data obtained from these samples. The major differences between data obtained from the 2 types of sample were the shorter insert size and artificial base alterations in the FFPE samples. A high proportion of short inserts in the FFPE samples resulted in overlapping paired reads, which could lead to overestimation of certain variants; >20% of the inserts in the FFPE samples were double sequenced. A large number of soft clipped reads was found in the sequencing data of the FFPE samples, and about 30% of total bases were soft clipped. The artificial base alterations, C>T and G>A, were observed in FFPE samples only, and the alteration rate ranged from 200 to 1,200 per 1M bases when sequencing errors were removed. Although high-confidence mutation calls in the FFPE samples were compatible to that in the frozen samples, caution should be exercised in terms of the artifacts, especially for low-confidence calls. Despite the clearly observed artifacts, archival FFPE samples can be a good resource for discovery or validation of biomarkers in cancer research based on whole-exome sequencing.
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