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Updated: Oct 18, 2026
Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies
Published on: April 11, 2016
Quantifying the diagnostic time gap in precision oncology: A retrospective analysis of potential time savings from
Kevin Tran1, Eveline Chen1, W Fraser Symmans1,2
1Department of Translational Molecular Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America.
Background:
Next-generation sequencing (NGS) turnaround times (TAT) exceed two weeks and can delay the initiation of targeted therapy. Rapid cartridge-based platforms such as Idylla deliver single-gene or fusion results from minimal cytology material within hours, but time savings have not been systematically quantified.
Methods:
Forty-two cases of non-small cell lung carcinoma, thyroid carcinoma, melanoma, and mammary analogue secretory carcinoma of the salivary gland that underwent both Idylla testing (KRAS, EGFR, BRAF, and GeneFusion assays) and orthogonal NGS at a single academic center were reviewed. NGS TAT was calculated from specimen collection to report release, and Idylla results were modeled as available one day after collection. The primary outcome was per-case time savings (NGS TAT minus one day); treatment timelines were reconstructed from the medical record. Analyses were descriptive; no inferential testing was performed. A sensitivity analysis varied the modeled Idylla TAT from 1 to 3 days, and an adjusted estimate assigned no time saving to the two cartridge results that were not actionable on the day of collection.
Results:
The median NGS TAT across all 42 cases was 20.0 days (IQR, 17.0-23.8; range, 8-51). Against the modeled 1-day Idylla TAT, the median time savings was 19.0 days per case (IQR, 16.0-22.8; range, 7-50), totaling 858 patient-days. Assigning no time saving to those two cases gave a median of 18.0 days and 817 patient-days. No patient received therapy that was subsequently contradicted by the sequencing result. In thirteen patients, the sequencing interval alone exceeded three weeks, and in seven, no systemic therapy was underway while the result was awaited.
Conclusions:
Same-day cartridge-based testing from cytology and small biopsy specimens could provide actionable results a median of 19 days earlier than standard NGS. Whether this translates into earlier treatment initiation was not assessed and requires prospective evaluation.
