Abstract 156P
Background
Sensitivity of Next-Generation Sequencing (NGS) methods to tissue sample quantity and quality is insufficiently reported in rare tumors. We conducted a retrospective study to estimate the NGS failure rate due to insufficient quantity or quality of material in rare tumors and to identify its predictors.
Methods
Patients with sarcomas, rare carcinomas, and rare melanomas who underwent NGS at SQCCCRC between January 2022 and October 2023 were eligible. Clinicopathological and NGS-related data were extracted from clinical charts and quantitatively described. We constructed a univariable logistic regression models with the outcome variable Insufficient quantity or quality of material, and the following explanatory variables: Assay [whole exome sequencing (WES) vs. targeted panel], Sampling method (surgery vs. biopsy), Source tissue (bone vs. soft tissue), and Storage time.
Results
We identified 102 NGS reports from 86 patients with sarcomas (73.3%), rare carcinomas (16.3%), and rare melanomas (10.5%). The median age was 40 years, interquartile range (IQR) = 23-61 years. Samples were obtained by biopsy (51%) and surgery (48%) from soft tissue (92.1%) or bone (7.9%) lesions. The median storage time was 2.5 months (IQR = 1.3 - 4.6). Targeted sequencing and WES were used in 39.2% and 60.8% of reports, respectively. Material quantity or quality was insufficient in 14.7% of tests and 4.7% of patients. Repeated testing was successful in 7 out of 8 patients. WES was significantly associated with higher probability of NGS failure due to low quantity or quality of material as compared to targeted panel (OR = 11.4, 95% confidence interval = 1.4 - 90.4, p = 0.022). No other variable significantly predicted NGS failure.
Conclusions
Our results suggest that the overall, the NGS failure rate due to sample quantity or quality issues is low. WES demands significantly higher sample quantity and quality compared to targeted panels. Retesting can often overcome quantity or quality issues.
Clinical trial identification
Editorial acknowledgement
Legal entity responsible for the study
The authors.
Funding
Has not received any funding.
Disclosure
All authors have declared no conflicts of interest.