Using variant databases for variant prioritization and to detect erroneous genotype-phenotype associations.

ABSTRACT:

Background

In the search for novel causal mutations, public and/or private variant databases are nearly always used to facilitate the search as they result in a massive reduction of putative variants in one step. Practically, variant filtering is often done by either using all variants from the variant database (called the absence-approach, i.e. it is assumed that disease-causing variants do not reside in variant databases) or by using the subset of variants with an allelic frequency > 1% (called the 1%-approach). We investigate the validity of these two approaches in terms of false negatives (the true disease-causing variant does not pass all filters) and false positives (a harmless mutation passes all filters and is erroneously retained in the list of putative disease-causing var

SUBMITTER: Broeckx BJG 

PROVIDER: S-EPMC5710091 | biostudies-literature | 2017 Dec

REPOSITORIES: biostudies-literature