Abstract
To implement precision oncology, analytical validity as well as clinical validity and utility are important. However, proficiency testing (PT) to assess validity has not yet been systematically performed in Japan. To investigate the quality of next-generation sequencing (NGS) platforms and cancer genome testing prevalent in laboratories, we performed pilot PT using patient samples. We prepared genomic DNA from the cancer tissue and peripheral blood of 5 cancer patients and distributed these to 15 laboratories. Most participating laboratories successfully identified the pathogenic variants, except for two closely located KRAS variants and 25 bp delins in EGFR. Conversely, the EGFR L858R variant was successfully identified, and the allele frequency was similar for all the laboratories. A high DNA integrity number led to excellent depth and reliable NGS results. By conducting this pilot study using patient samples, we were able to obtain a glimpse of the current status of cancer genome testing at participating laboratories. To enhance domestic cancer genome testing, it is important to conduct local PT and to involve the parties concerned as organizers and participants.
Highlights
Not analyzed is very complex because it comprises nucleic acid extraction, library preparation and sequencing chemistry, and bioinformatics pipelines
The major variants reported by the laboratories and variant allele frequency (VAF) concordance with the coefficient of variation (CV) for five patient samples are shown in Supplementary Figs. 1, 2, 3, 5 and 6
The sample from Patient No 1 was analyzed by ten laboratories, and all of them reported the KRAS p.Gly13Asp (NM_033360.2: c.38G>A) missense variant with similar VAF to the droplet digital PCR result
Summary
Not analyzed is very complex because it comprises nucleic acid extraction, library preparation and sequencing chemistry, and bioinformatics pipelines. PT for cancer genome testing using NGS has been implemented in other countries using several types of testing specimens, primarily cell line-based samples and human genome DNA with spiked synthetic mutated DNA1–10. Such PT has not been systematically performed in Japan. We have attempted to implement PT in patient samples to investigate the quality of NGS platforms and cancer genome testing usually used in laboratories. The purpose of this pilot PT is to ascertain the current quality status of cancer gene panel testing in Japan and disseminate the findings to stakeholders, including the participating laboratories, concerned academic societies, and policymakers
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