Personalized cancer care requires molecular characterization of neoplasms. While the research community accepts frozen tissues as the gold standard analyte for molecular assays, the source of tissue for testing in clinical cancer care comes almost universally from formalin-fixed, paraffin-embedded tissue (FFPE). As newer technologies emerge for DNA characterization that requires higher molecular weight DNA, it was necessary to compare the quality of DNA in terms of DNA length between FFPE and cryopreserved samples. We hypothesized that cryopreserved samples would yield higher quantity and superior quality DNA compared to FFPE samples. We analyzed DNA metrics by performing a head-to-head comparison between FFPE and cryopreserved samples from 38 human tumors representing various cancer types. DNA quantity and purity were measured by UV spectrophotometry, and DNA from cryopreserved tissue demonstrated a 4.2-fold increase in DNA yield per mg of tissue (p-value < 0.001). DNA quality was measured on a fragment microelectrophoresis analyzer, and again, DNA from cryopreserved tissue demonstrated a 223% increase in the DNA quality number and a 9-fold increase in DNA fragments > 40,000 bp (p-value < 0.0001). DNA from the cryopreserved tissues was superior to the DNA from FFPE samples in terms of DNA yield and quality.

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.

Intratumoral heterogeneity is a defining feature of cancer, yet standard sequencing and reporting practices often overlook somatic variants present at low variant allele frequencies (VAFs), commonly below 5%. Increasing evidence indicates that these rare alleles can represent clinically meaningful subclones involved in tumor evolution, therapeutic resistance, minimal residual disease, and metastatic dissemination. However, detecting and interpreting low-VAF variants is technically and analytically challenging because background error rates, library artifacts, genomic context, and caller assumptions increasingly overlap with true signal as allele fraction decreases. In this review, we integrate biological and clinical evidence supporting the relevance of low-VAFs and evaluate constraints across sequencing strategies, including whole genome and whole exome approaches and deep targeted panels. We discuss why detectability depends strongly on variant class and genome architecture, with SNVs generally more tractable than indels and structural variants. We then summarize practical approaches that improve sensitivity and specificity beyond increasing depth, including proper tissue handling, molecular enrichment, unique molecular identifiers, duplex-consensus methods, advanced error modeling, and orthogonal validation. Finally, we highlight emerging single-cell, spatial, and multiomic technologies that resolve rare variants in a cellular context. Collectively, these advances support incorporating low-VAF detection into precision oncology frameworks.

Purpose of Review: Precision oncology increasingly depends on accurate molecular and functional characterization of tumor tissue across genomic, transcriptomic, proteomic, epigenetic, and live-cell applications. This review evaluates how commonly used tissue preservation methods, including formalin-fixed paraffin-embedded (FFPE), fresh, flash-frozen, and cryopreserved tissue, affect downstream analytical fidelity and translational utility. Recent Findings: Recent comparative studies demonstrate that FFPE remains effective for histopathology and a few established molecular assays but introduces nucleic acid fragmentation, crosslinking, deamination artifacts, protein modification, and loss of cellular viability. These effects can reduce sequencing efficiency, alter quantitative molecular measurements, and limit applications requiring intact proteins or viable cells. In contrast, flash-frozen and cryopreserved tissues generally provide greater molecular fidelity, while controlled-rate cryopreservation additionally preserves viable cellular populations for single-cell analysis, organoid development, functional precision medicine, tumor-infiltrating lymphocyte expansion, and CAR-T manufacturing. Emerging evidence also supports the use of cryopreserved living tumor biobanks for longitudinal and functional testing. Summary: No single preservation method is optimal for every application. FFPE remains essential for routine pathology, whereas flash freezing is well suited for high-fidelity molecular profiling and controlled-rate cryopreservation offers the broadest compatibility with both molecular and live-cell applications. Prospective biospecimen strategies that align tissue preservation with anticipated diagnostic, molecular, functional, and therapeutic uses may improve the reliability and clinical utility of precision oncology.