As fusion detection NGS techniques are adopted by clinical labs, assay performance comparison is urgently needed. We compared four fusion-detection assay platforms on a pilot cohort of 24 prostate cancer samples: (1) Oncomine Comprehensive panel v3; (2) AmpliSeq comprehensive panel v3; (3) The solid tumor panel of FusionPlex; and (4) The human oncology panel of QIAseq. The assays were compared for the detection of different types of fusion based on whether the partner gene or the breakpoints are known. All assays detected fusion with known gene partners and known breakpoint, represented by TMPRSS2-ERG. A fusion with known partners but unknown breakpoint, TMPRSS2-ETV4, was reported by OCAv3 and FusionPlex, but not by AICv3 because the specific breakpoint was not in the manifest, nor by QIAseq since the panel did not target the exact exons involved. For fusion with unknown partners, FusionPlex identified the largest number of ETV1 fusions because it had the highest exon coverage for ETV1. Among these, SNRPN-ETV1 and MALAT1-ETV1, were novel findings. To determine reportability of low-level calls of highly prevalent fusions, such as TMPRSS2-ERG, we propose the use of percent fusion reads over total number of reads per sample instead of the fusion read count.

随着融合检测NGS技术被临床实验室采用，迫切需要进行检测性能比较。我们在 24 个前列腺癌样本的试点队列中比较了四个融合检测分析平台：(1) Oncomine Comprehensive panel v3；(2) AmpliSeq综合面板v3；(3) FusionPlex实体瘤panel；(4) QIAseq的人类肿瘤学小组。根据伴侣基因或断点是否已知，比较了检测不同类型融合的测定。所有测定都检测到与已知基因伴侣和已知断点的融合，以TMPRSS2-ERG为代表。与已知伙伴但未知断点的融合，TMPRSS2-ETV4，由 OCAv3 和 FusionPlex 报告，但不是由 AICv3 报告，因为特定断点不在清单中，也不是由 QIAseq 报告，因为面板没有针对所涉及的确切外显子。对于与未知伙伴的融合，FusionPlex 确定了最多的ETV1融合，因为它对 ETV1 具有最高的外显子覆盖率。其中，SNRPN - ETV1和MALAT1 - ETV1是新发现。为了确定高度流行融合的低级别调用的可报告性，例如TMPRSS2-ERG，我们建议使用百分比融合读数而不是每个样本的读数总数，而不是融合读数计数。