WHO/BS/2019.2368 Collaborative Study to evaluate the proposed WHO 1st IS for Cancer Genomes

Overview

With an ever-increasing number of clinically actionable genomic variants in cancer, there is an urgent need for the provision of reference standards to aid the definition of assay limit-ofdetection and for the harmonization of variant measurement in response to treatment. By using tumor cell lines carrying multiple rather than single actionable variants, the development of cancer genomic DNA (gDNA) standards may be accelerated. Furthermore, as additional variants within the cancer gDNA standards become clinically relevant, the data on such variants may be added to pre-existing WHO International Standards, thus enhancing their clinical utility. It is proposed that the candidate cancer gDNA standards presented here be the first in a series of cancer gDNA standards and that they will together act as calibrants for many clinically-relevant variants. The background of non-clinically relevant variants in these candidate cancer gDNAs standards may also have value in the validation of next-generation sequencing (NGS) assays. An international collaborative study assessed the suitability of three genomic gDNA materials as proposed WHO 1st International Standards for two cell line cancer genomes carrying a total of five clinically relevant markers, and a wild-type cell line genome. The three gDNA materials (18/118, 18/130, and 18/164) were derived from the following cell lines, respectively: HCT 15, a colon adenocarcinoma cell line (putatively carrying the PIK3CA p.E545 variant); MOLT-4, an acute T lymphoblastic leukemia cell line (putatively carrying the TP53 p.R306*, NRAS p.G12C, PTEN p.K267fs*9, and MAP2K1/MEK1 p.D67N variants); ATDB102, a wild-type cell line intended for use both as a common reference and to dilute the variant-positive standards. The study encompassed both NGS and digital polymerase chain reaction (dPCR) methods. In addition to characterizing the five clinically-relevant variants, the study also captured the presence of other variants in the three materials which may be useful in the broader validation of NGS pipelines, although not for calibration or diagnostic purposes.