Interference of clonal hematopoiesis in cfDNA liquid biopsy testing and identification of actionable alterations in large diverse cohort of US veterans.

INTRODUCTION

Liquid biopsies using cell-free DNA (cfDNA) can identify actionable somatic alterations in prostate cancer (PCa). The presence of alterations related to clonal hematopoiesis (CH) can complicate interpretation of cfDNA results and lead to clinical inaction. We sought to determine alteration profiles identified by cfDNA testing in a large, racially diverse cohort of United States Veterans with metastatic PCa and quantify the extent of CH interference in the identification of actionable alterations.

METHODS

Next-generation sequencing of cfDNA biopsy specimens from US Veterans with metastatic PCa was performed using Foundation Medicine through the VA National Precision Oncology Program (NPOP) from August 2020 to January 2025. Actionable and non-actionable alteration rates were compared between tests with and without identification of a CH alteration. Tests with CH interference were then stratified by the presence of a PCa-related alteration (TMPRSS2, ERG, SPOP) and rates of actionable and non-actionable alterations were compared between these groups.

RESULTS

cfDNA alterations were identified in 2501/2657 (94.1%) cfDNA tests. CH interference was common, with 663/2657 (25%) tests identifying CH alterations only and 1615/2657 (60.8%) tests identifying CH and non-CH alterations concurrently. Accounting for tests in which no alteration was identified (156/2657; [5.9%]), only 223/2501 (8.4%) tests exhibited non-CH only alterations. Alteration rates in FDA-approved targetable genes were similar in samples with and without CH interference, except for CDK12 variants, which were more frequently identified in tests without CH interference (8.5% vs 3.8%, P < .01) and BRCA1 variants which were more frequently identified in tests with CH interference (2.0% vs 0%, P = .02). In samples with CH interference, alterations in PTEN, RB1, and TP53 were more likely and homologous recombination repair (HRR) alterations were less likely in samples with a PCa specific alteration versus those without (tumor suppressor gene 72% vs 51%, P < .0001; HRR 36% vs 56%, P < .0001).

CONCLUSIONS

CH interference was very common in cfDNA testing in metastatic PCa patients. The absence of a CH alteration or presence of a known PCa-related alteration does not reliably modify identification frequencies of actionable alterations. Robust CH inferential platforms or analysis of a matched lymphocyte sample with cfDNA may improve clinical differentiation of CH versus PCa-derived cfDNA results.