# Cryopreserved Tissue Biospecimens Offer Superior Quality for Whole-Genome Sequencing of Various Cancers Compared to Paired Formalin-Fixed Paraffin-Embedded Tissues

## TL;DR

Cryopreserved cancer tissues provide better DNA quality for whole-genome sequencing than formalin-fixed paraffin-embedded tissues, leading to more accurate mutation detection.

## Contribution

Demonstrates that cryopreserved tissues yield superior sequencing quality and variant detection compared to FFPE in cancer genomics.

## Key findings

- Cryopreserved tissues had higher DNA concentration, DIN, and fragment size compared to FFPE.
- Cryopreserved samples showed higher mean read depth and better identification of oncogenic driver mutations.
- FFPE tissues had higher tumor mutation burden but lower concordance with cryopreserved variant calls.

## Abstract

Whole-genome sequencing (WGS) is integral to precision oncology, yet most cancer biospecimens used for WGS are formalin-fixed paraffin-embedded (FFPE) due to their widespread availability in clinical practice. However, FFPE processing can degrade DNA quality. This study compares WGS outcomes from matched cryopreserved (CP) and FFPE tumor samples, hypothesizing that CP tissues yield superior sequencing quality and variant detection. Fifty matched pairs of CP and FFPE tumor samples spanning multiple cancer types were obtained from a biobank. DNA was extracted, and WGS was performed. We assessed sequencing quality metrics and variant analysis between the two preservation methods. Presequencing metrics favored CP tissue, with a significantly higher gDNA concentration, DIN, and DNA fragment size. The WGS results showed that the CP samples had a higher mean read depth and larger insert size. Although the mapping percentages were similar, FFPE exhibited higher tumor mutation burden (13.7 vs. 6.4 mutations/Mb) and lower concordance with CP in variant calls (43.5% overlap). CP samples detected more structural variants and enabled the improved identification of oncogenic driver mutations. Cryopreserved tissues consistently outperform FFPE in terms of DNA quality and WGS metrics, enabling the more accurate detection of clinically relevant mutations. These findings support prioritizing CP sample preservation for genomic profiling in cancer care.