Sung-Su Kim, Hyun-Jeung Choi, Jin Ju Kim, M. Sun Kim, In-Seon Lee, Bohyun Byun, Lina Jia, Myung Ryurl Oh, Youngho Moon, Sarah Park, Joon-Seok Choi, Seoung Wan Chae, Byung-Ho Nam, Jin-Soo Kim, Jihun Kim, Byung Soh Min, Jae Seok Lee, Jae-Kyung Won, Soo Youn Cho, Yoon-La Choi,Young Kee Shin

Published : January 11, 2018

Journal: Nature

In clinical translational research and molecular in vitro diagnostics, a major challenge in the detection of genetic mutations is overcoming artefactual results caused by the low-quality of formalin-fixed paraffin-embedded tissue (FFPET)-derived DNA (FFPET-DNA). Here, we propose the use of an ‘internal quality control (iQC) index’ as a criterion for judging the minimum quality of DNA for PCR-based analyses. In a pre-clinical study comparing the results from droplet digital PCR-based EGFR mutation test (ddEGFR test) and qPCR-based EGFR mutation test (cobas EGFR test), iQC index ≥ 0.5 (iQC copies ≥ 500, using 3.3 ng of FFPET-DNA [1,000 genome equivalents]) was established, indicating that more than half of the input DNA was amplifiable. Using this criterion, we conducted a retrospective comparative clinical study of the ddEGFR and cobas EGFR tests for the detection of EGFR mutations in non-small cell lung cancer (NSCLC) FFPET-DNA samples. Compared with the cobas EGFR test, the ddEGFR test exhibited superior analytical performance and equivalent or higher clinical performance. Furthermore, iQC index is a reliable indicator of the quality of FFPET-DNA and could be used to prevent incorrect diagnoses arising from low-quality samples.

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