Low tumour content was the only independent predictor of genomic profiling failure in a 371-request audit

Design

Retrospective single-institution audit of consecutive requests

Population

371 FoundationOne CDx requests at a cancer genomic medicine hospital in Japan

Primary outcome

Assay quality outcome (cancelled, suspended, Qualified, Pass) and its predictors

Effect

Pass 86.2% and Qualified 13.8% of 297 returned results; low tumour content the only independent predictor of failure

Comprehensive genomic profiling with the FoundationOne CDx assay needs formalin-fixed, paraffin-embedded tissue with enough tumour area and DNA. This audit covered 371 consecutive requests at a designated cancer genomic medicine hospital in Japan, with pathologist checks of tumour surface area, section number and remaining tissue before submission.

Of the 371 requests, 52 (14.0%) were cancelled before submission, mostly because of too little tissue or a clinical decision. Of 319 submitted, 22 (6.9%) were temporarily suspended. Among 297 with returned results, 256 (86.2%) passed and 41 (13.8%) were only Qualified. In Qualified cases, tumour mutational burden was evaluable in 31.7% and microsatellite instability in 19.5%. In multivariable analysis, lower tumour content was the only independent predictor of quality-control failure.

For laboratories, the actionable step is to review pre-submission checks: tumour area, estimated content and whether macrodissection or a better block would help. The study is retrospective, from one institution, with no external validation.

• Of 371 requests, 14.0% were cancelled before submission.
• Of returned results, 13.8% were Qualified; TMB and MSI were often not evaluable in those.
• Low tumour content was the only independent predictor of failure.
• Consider selecting the block with the highest tumour content and macrodissecting where needed.
• Agree a pre-submission checklist with oncology and the genomics team.

Why it matters

Most failures trace to the sample the pathologist selects, which is within the laboratory's control.

Don't overread it

This is a retrospective single-centre audit with no external validation.

The statistics, in plain English

A Qualified result means the assay ran but fell short of full quality criteria, so some biomarkers may be unreliable. Being an audit of one centre, the percentages describe this hospital's workflow and may differ elsewhere.

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