Correlation between variant call accuracy and quality parameters in comprehensive cancer genomic profiling tests

Background

Comprehensive genomic profiling (CGP) tests have been widely utilized in clinical practice. In this test, the variant list automatically output from the data analysis pipeline often contains false-positive variants, although the correlation between the quality parameters and prevalence of false-positive variants remains unclear.

Methods

We analyzed 125 CGP tests performed in our laboratory. False-positive variants were manually detected via visual inspection. The quality parameters of both wet and dry processes were also analyzed.

Results

Among the 125 tests, 52 (41.6%) required more than one correction of the called variants, and 21 (16.8%) required multiple corrections. A significant correlation was detected between somatic false-positive variants and quality parameters in the wet (ΔΔCq, pre-capture library peak size, pre-capture library DNA amount, capture library peak size, and capture library concentration) and dry processes (total reads, mapping rates, duplication rates, mean depth, and depth coverage). Capture library concentration and mean depth were strong independent predictors of somatic false-positive variants.

Conclusions

We demonstrated a correlation between somatic false-positive variants and quality parameters in the CGP test. This study facilitates gaining a better understanding of CGP test quality management.