Next‐generation sequencing of cytologic preparations: An analysis of quality metrics

作者：David H. Hwang, Elizabeth P. Garcia, Matthew D. Ducar, Edmund S. Cibas, Lynette Marie Sholl · 发表于：Cancer Cytopathology · 年份：2017 · DOI：10.1002/cncy.21897 · 被引用次数：79 · 研究领域：Cancer Genomics and Diagnostics、Genomic variations and chromosomal abnormalities、Lung Cancer Treatments and Mutations

BACKGROUND: Next-generation sequencing (NGS) fails for many small biopsies (BXs) because of a low overall DNA concentration or tumor percentage. Cytology smears and liquid-based preparations (LBPs), or smears/LBPs, often contain abundant tumor cells and may provide adequate material for molecular testing when other materials are insufficient. This study examined the performance of smears/LBPs on a clinical NGS assay. METHODS: This study retrospectively reviewed quality metrics from consecutive smear/LBP, core BX, and cell block (CB) cases run on a hybrid-capture NGS assay interrogating 309 cancer-related genes. The following quality metrics were compared: adequacy rate, initial DNA concentration, postshearing fragment size, post-library preparation fragment size, fragment size difference, insert size, total reads, passing-filter reads aligned, percent passing-filter unique reads aligned, mean target coverage, percentage of loci with >100× coverage, percent duplication rate, percent selected bases, and percent usable bases on bait. RESULTS: Twenty-three of 26 smears/LBPs (88%) were successfully sequenced, whereas 77 of 87 core BXs (89%) and 29 of 30 CBs (97%) were. The mean target coverage, median insert size, and percent usable bases were significantly higher in the smear/LBP category. The postshearing fragment size and the percent duplication were significantly lower for smears/LBPs. CONCLUSIONS: The adequacy rate of cytology smears/LBPs for NGS is comparable to that of core...