PDF(Pubmed)
Abstract：
Comprehensive molecular profiling by next generation sequencing (NGS) has revolutionized tumor classification and biomarker evaluation. However, routine implementation is challenged by the scant nature of diagnostic material obtained through minimally invasive procedures. Here, we describe our long-term experience in profiling cytology samples with an in-depth assessment of the performance, quality metrics, biomarker identification capabilities, and potential pitfalls. We highlight the impact of several optimization strategies to maximize performance with 4,871 prospectively sequenced clinical cytology samples tested by MSK-IMPACT™. Special emphasis is given to the use of residual supernatant cell free DNA (ScfDNA) as a valuable source of tumor DNA. Overall, cytology samples were similar in performance to surgical samples in identifying clinically relevant genomic alterations, achieving success rates up to 93% with full optimization. While cell block (CB) samples had excellent performance overall, low-level cross-contamination was identified in a small proportion of cases (4.7%), a common pitfall intrinsic to the processing of paraffin blocks, suggesting that more stringent precautions and processing modifications should be considered in quality control initiatives. By contrast ScfDNA samples had negligible contamination. Finally, ScfDNA testing exclusively used as a rescue strategy delivered successful results in 71% of cases where tumor tissue from CB was depleted.
摘要：
通过下一代测序（NGS）进行的全面分子谱分析彻底改变了肿瘤分类和生物标志物评估。然而,常规实施受到通过微创手术获得的诊断材料匮乏的挑战。这里,我们描述了我们在分析细胞学样品方面的长期经验，并对性能进行了深入评估，质量指标，生物标志物识别能力，和潜在的陷阱。我们强调了几种优化策略的影响，以最大限度地提高通过MSK-IMPACT™测试的4,871个前瞻性测序的临床细胞学样品的性能。特别强调使用残留的上清液无细胞DNA（ScfDNA）作为有价值的肿瘤DNA来源。总的来说,细胞学样本在识别临床相关基因组改变方面的表现与手术样本相似。通过全面优化实现高达93%的成功率。虽然电池块（CB）样品具有优异的整体性能，在一小部分病例(4.7%)中发现了低水平交叉污染，石蜡块加工固有的一个常见缺陷，建议在质量控制举措中应考虑更严格的预防措施和加工修改。相比之下,ScfDNA样品具有可忽略的污染。最后,专门用作救援策略的ScfDNA测试在71％的CB肿瘤组织耗尽的病例中取得了成功的结果。
