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

ABSTRACT:

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 qua

SUBMITTER: Isago H 

PROVIDER: S-EPMC10884978 | biostudies-literature | 2024 Mar

REPOSITORIES: biostudies-literature