FFPE_DNA_MS_v12_20210211

Description

The primary goal of this study was to investigate the effects of whether organocatalyst (ORGΔ) treatment improves DNA-sequencing data by overcoming formalin-induced artifacts from clinical formalin-fixed paraffin-embedded (FFPE) samples. We isolated RNA and DNA ± ORGΔ from paired FFPE and frozen human renal and ovarian carcinoma specimens collected as part of the National Cancer Institute Biospecimen Pre-analytical Variables program. Tumor types were microscopically confirmed from adjacent tissue sections. Following extraction, DNA was fragmented and sequence differences were compared between frozen and FFPE sample pairs. Treatment with ORGΔ improved concurrent SNP calls in FFPE DNA compared to non-ORGΔ FFPE samples and enhanced confidence in SNP calls for all FFPE DNA samples, beyond that of matched frozen samples. In general, the concordant SNPs identified in paired frozen and FFPE DNA samples agreed for both genotype and homozygosity vs. heterozygosity of calls regardless of ORGΔ treatment. The increased confidence in ORGΔ FFPE DNA variant calls relative to the matched frozen DNA suggests a novel application of this method. With further optimization, this method may improve quality of DNA-sequencing data in frozen as well as FFPE tissue samples. These findings could have important implications for studies using FFPE samples, especially if adequate matched controls are not available. This dataset is associated with the following publication: Wehmas, L., C. Wood, P. Guan, M. Gosink, and S. Hester. Organocatalyst treatment improves variant calling and mutant detection in archival clinical samples. Scientific Data. Springer Nature, New York, NY, 12: 6509, (2022).

Resources

Name Format Description Link
53 FFPE_DNA_ms_Tables.xlsx https://pasteur.epa.gov/uploads/10.23719/1522621/FFPE_DNA_ms_Tables.xlsx
53 SNP_Count_Totals.xlsx https://pasteur.epa.gov/uploads/10.23719/1522621/SNP_Count_Totals.xlsx
53 SNP_Analyses_GQ_tissue_comp.xlsx https://pasteur.epa.gov/uploads/10.23719/1522621/SNP_Analyses_GQ_tissue_comp.xlsx
53 SNP%20Types%20Fig3.xlsx https://pasteur.epa.gov/uploads/10.23719/1522621/SNP%20Types%20Fig3.xlsx
53 DNA%20-%20SNP%20Quality%20by%20Group%20Fig2A.xlsx https://pasteur.epa.gov/uploads/10.23719/1522621/DNA%20-%20SNP%20Quality%20by%20Group%20Fig2A.xlsx
53 RNA%20-%20SNP%20Quality%20by%20Group%20Fig2B.xlsx https://pasteur.epa.gov/uploads/10.23719/1522621/RNA%20-%20SNP%20Quality%20by%20Group%20Fig2B.xlsx

Tags

  • archival
  • dna-seq
  • exome
  • human-tumors
  • single-nucleotide-polymorphism-snp

Topics

Categories