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Background <p>Clinically relevant ALK alterations are identified across routine comprehensive genomic profiling (CGP), but their observed frequency may vary according to testing context. Because ALK-directed treatment is primarily linked to fusion/rearrangement events, we sought to define a nationwide benchmark for interpreting ALK fusion/rearrangement findings across routine CGP settings in Japan.</p> Methods <p>We performed a retrospective descriptive analysis of anonymized aggregated Center for Cancer Genomics and Advanced Therapeutics data through March 31, 2025. Case-level observed frequencies within the CGP-tested cohort were evaluated across 97,343 cases, five CGP assays, 12 organ groups, and pooled tissue-based versus liquid-based settings. A supplementary fusion-only sensitivity analysis evaluated definitional dependence.</p> Results <p>The overall case-level observed ALK fusion/rearrangement frequency within the CGP-tested cohort was 0.329% (320/97,343; 95% CI 0.294–0.367). Observed frequencies ranged from 0.152% for NCC Oncopanel to 0.598% for FoundationOne Liquid CDx (<i>P</i> &lt; 0.001). When pooled by specimen context, observed frequency was 0.280% in tissue-based CGP and 0.561% in liquid-based CGP (<i>P</i> &lt; 0.001). Thoracic tumors showed the highest observed frequency (1.988%), whereas liver tumors showed no positive cases. In the fusion-only sensitivity analysis, the overall frequency decreased to 0.234%, with a larger reduction in pooled liquid-based CGP than in pooled tissue-based CGP, reflecting reporting-category and context dependence rather than lower analytical sensitivity, while the broad directional pattern was preserved.</p> Conclusion <p>This nationwide C-CAT analysis provides an implementation-oriented CGP-cohort benchmark for panel-aware and specimen-context-aware interpretation of observed ALK findings; these case-level frequencies should not be interpreted as population prevalence.</p>

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Observed ALK fusion/rearrangement frequency across comprehensive genomic profiling platforms in Japanese routine oncology practice

  • 期刊论文

  • 发表日期：

    2026年7月27日

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  • Shinya Kajiura,
  • Naohiko Nakamura,
  • Ryuji Hayashi

摘要

Background

Clinically relevant ALK alterations are identified across routine comprehensive genomic profiling (CGP), but their observed frequency may vary according to testing context. Because ALK-directed treatment is primarily linked to fusion/rearrangement events, we sought to define a nationwide benchmark for interpreting ALK fusion/rearrangement findings across routine CGP settings in Japan.

Methods

We performed a retrospective descriptive analysis of anonymized aggregated Center for Cancer Genomics and Advanced Therapeutics data through March 31, 2025. Case-level observed frequencies within the CGP-tested cohort were evaluated across 97,343 cases, five CGP assays, 12 organ groups, and pooled tissue-based versus liquid-based settings. A supplementary fusion-only sensitivity analysis evaluated definitional dependence.

Results

The overall case-level observed ALK fusion/rearrangement frequency within the CGP-tested cohort was 0.329% (320/97,343; 95% CI 0.294–0.367). Observed frequencies ranged from 0.152% for NCC Oncopanel to 0.598% for FoundationOne Liquid CDx (P < 0.001). When pooled by specimen context, observed frequency was 0.280% in tissue-based CGP and 0.561% in liquid-based CGP (P < 0.001). Thoracic tumors showed the highest observed frequency (1.988%), whereas liver tumors showed no positive cases. In the fusion-only sensitivity analysis, the overall frequency decreased to 0.234%, with a larger reduction in pooled liquid-based CGP than in pooled tissue-based CGP, reflecting reporting-category and context dependence rather than lower analytical sensitivity, while the broad directional pattern was preserved.

Conclusion

This nationwide C-CAT analysis provides an implementation-oriented CGP-cohort benchmark for panel-aware and specimen-context-aware interpretation of observed ALK findings; these case-level frequencies should not be interpreted as population prevalence.