Precision cancer genome testing needs proficiency testing involving all stakeholders.

Area of Science:

• Oncology
• Genomics
• Clinical Diagnostics

Background:

• Precision oncology relies on accurate analytical and clinical validity of genomic tests.
• Systematic proficiency testing (PT) for cancer genome testing is lacking in Japan.

Purpose of the Study:

• To assess the quality of next-generation sequencing (NGS) platforms and cancer genome testing in Japanese laboratories.
• To evaluate the feasibility of implementing a pilot PT program using patient samples.

Main Methods:

• Genomic DNA from 5 cancer patients' tissues and blood was distributed to 15 participating laboratories.
• Laboratories performed cancer genome testing using their routine NGS platforms.
• Performance was evaluated based on the accurate identification of known pathogenic variants.

Main Results:

• Most laboratories accurately identified pathogenic variants, with exceptions for closely located KRAS variants and EGFR delins.
• The EGFR L858R variant was consistently identified with similar allele frequencies across labs.
• High DNA integrity correlated with reliable NGS depth and results.

Conclusions:

• This pilot PT provided insights into the current state of cancer genome testing in Japan.
• Establishing local PT programs with stakeholder involvement is essential for improving domestic cancer genome testing quality.
• Enhanced quality assurance is vital for the successful implementation of precision oncology.