Comparison of clinical targeted next-generation sequence data from formalin-fixed and fresh-frozen tissue specimens

The Journal of Molecular Diagnostics : JMD
David H SpencerEric J Duncavage

Abstract

Next-generation sequencing (NGS) has emerged as a powerful technique for the detection of genetic variants in the clinical laboratory. NGS can be performed using DNA from FFPE tissue, but it is unknown whether such specimens are truly equivalent to unfixed tissue for NGS applications. To address this question, we performed hybridization-capture enrichment and multiplexed Illumina NGS for 27 cancer-related genes using DNA from 16 paired fresh-frozen and routine FFPE lung adenocarcinoma specimens and conducted extensive comparisons between the sequence data from each sample type. This analysis revealed small but detectable differences between FFPE and frozen samples. Compared with frozen samples, NGS data from FFPE samples had smaller library insert sizes, greater coverage variability, and an increase in C to T transitions that was most pronounced at CpG dinucleotides, suggesting interplay between DNA methylation and formalin-induced changes; however, the error rate, library complexity, enrichment performance, and coverage statistics were not significantly different. Comparison of base calls between paired samples demonstrated concordances of >99.99%, with 96.8% agreement in the single-nucleotide variants detected and >98% accura...Continue Reading

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Related Concepts

Specimen Collection
Single Nucleotide Polymorphism
High-Throughput Nucleotide Sequencing
DNA
Laboratory Procedures
Oncogenes
cytidylyl-3'-5'-guanosine
Adenocarcinoma of Lung (Disorder)
DNA Methylation
Size

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