False negatives in GBA1 sequencing due to polymerase dependent allelic imbalance.

ABSTRACT: A variant in the GBA1 gene is one of the most common genetic risk factors to develop Parkinson's disease (PD). Here the serendipitous finding is reported of a polymerase dependent allelic imbalance when using next generation sequencing, potentially resulting in false-negative results when the allele frequency falls below the variant calling threshold (by default commonly at 30%). The full GBA1 gene was sequenced using next generation sequencing on saliva derived DNA from PD patients. Four polymerase chain reaction conditions were varied in twelve samples, to investigate the effect on allelic imbalance: (1) the primers (n = 4); (2) the polymerase enzymes (n = 2); (3) the primer annealing temperature (T_a) specified for the used polymerase; and (4) the amount of DNA input. Initiall

SUBMITTER: den Heijer JM 

PROVIDER: S-EPMC7794395 | biostudies-literature | 2021 Jan

REPOSITORIES: biostudies-literature