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Metadata Updated: July 18, 2022

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).

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Metadata Created Date July 18, 2022
Metadata Updated Date July 18, 2022

Metadata Source

Harvested from EPA ScienceHub

Additional Metadata

Resource Type Dataset
Metadata Created Date July 18, 2022
Metadata Updated Date July 18, 2022
Publisher U.S. EPA Office of Research and Development (ORD)
Data Last Modified 2021-02-17
Public Access Level public
Bureau Code 020:00
Schema Version
Harvest Object Id 6fcd372a-3784-4f9e-a2f2-f6cf1fe06d9e
Harvest Source Id 04b59eaf-ae53-4066-93db-80f2ed0df446
Harvest Source Title EPA ScienceHub
Program Code 020:000
Publisher Hierarchy U.S. Government > U.S. Environmental Protection Agency > U.S. EPA Office of Research and Development (ORD)
Related Documents,
Source Datajson Identifier True
Source Hash 74654f1a29eb924dc5763749e2c261bb9f461d1c
Source Schema Version 1.1

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