While promising, circulating tumor DNA (ctDNA) from plasma is not yet ready for guiding local treatment decisions in bladder cancer. Data from studies like RETAIN show it is insufficient for identifying patients with residual disease confined to the bladder, limiting its utility in bladder-sparing protocols.

While liquid biopsies are a valuable, less invasive tool, a negative result is inconclusive for ruling out actionable mutations in NSCLC. It may simply mean the tumor isn't shedding enough DNA. Therefore, a negative liquid biopsy should never be the final word; it must be followed by a tissue biopsy to ensure patients don't miss out on targeted therapies.

To maximize the chances of successful biomarker identification from a liquid biopsy, especially when tissue is scant, the blood sample must be drawn before initiating any chemotherapy. This pre-treatment timing is critical for improving the diagnostic yield of blood-based next-generation sequencing (NGS) testing.

Clinicians ordering "NGS for lung" often misunderstand that Next-Generation Sequencing alone does not cover all actionable biomarkers, such as PD-L1 or HER2. This requires pathologists to interpret the clinician's intent and order a more comprehensive and appropriate test panel.

While Next-Gen Sequencing (NGS) provides genetic data, IHC directly measures the protein, is faster, cheaper, and requires less tissue. This makes it more scalable for routine clinical use, especially with small biopsy samples. High-level IHC loss correlates well with genetic loss seen on NGS.

For post-progression biopsies, which are often small and contain necrotic tissue, institutions may prioritize DNA-based NGS panels. This strategy is based on the rationale that most resistance mechanisms are genetic mutations detectable by DNA sequencing, reserving RNA panels primarily for identifying less common fusion events.

LOH (Loss of Heterozygosity) scores offer a functional assessment of a tumor's DNA repair capability. They are computationally derived to detect a 'scar' of characteristic genomic changes, like copy number alterations, that accumulate when a tumor cannot repair DNA double-strand breaks, going beyond single-gene mutation analysis.

The panel suggests AKT inhibitor trials in prostate cancer have been disappointing due to suboptimal biomarker selection (e.g., PTEN IHC). A similar drug in breast cancer showed significant survival benefit when using a more precise NGS-based strategy, indicating a potential path forward if the right patient population is identified genetically.

Key resistance biomarkers in prostate cancer, such as AR alterations, are acquired over time. This means that a biomarker test performed at initial diagnosis in the hormone-sensitive stage (MHSPC) is not sufficient for guiding therapy decisions in the castrate-resistant (CRPC) setting.