Concordance of PAM50 molecular subtyping between oligonucleotide microarray and NanoString nCounter assay for Taiwanese breast cancer

Five molecular subtypes have been identified according to intrinsic genes transcription. Microarrays have been adopted for molecular subtyping in addition to the original NanoString nCounter assay. This study aimed to evaluate subtyping consistency among Taiwanese breast cancers. Our study showed that fundamental discrepancy exists between distinct gene expression measuring approaches, and cross platform equivalence should not be overemphasized with too much extrapolation. A total of 109 Taiwanese breast cancers (24 with adjacent normal breast) were assayed with Affymetrix microarrays and 96 were assayed with NanoString Codeset BCeCSig, which also investigated academic PAM50. Sixty-one patients were assayed for both platforms. Subtyping was called for each patient with the nearest centroid.