PMC:6037202 / 10779-12694 JSONTXT

{"project":"2_test","denotations":[{"id":"29909963-27535533-2051604","span":{"begin":651,"end":653},"obj":"27535533"},{"id":"29909963-26432245-2051605","span":{"begin":699,"end":701},"obj":"26432245"},{"id":"29909963-26582918-2051606","span":{"begin":908,"end":910},"obj":"26582918"},{"id":"29909963-12754702-2051607","span":{"begin":1196,"end":1198},"obj":"12754702"},{"id":"29909963-24487276-2051608","span":{"begin":1405,"end":1407},"obj":"24487276"}],"text":"In order to identify clinically relevant variants, we subjected the resulting data to a range of filters (Figure S1). First, variants were removed if they failed to satisfy the quality criteria of a genotype quality (GQ) ≥ 30 (a Phred-scaled probability that the called genotype is incorrect), read depth (DP) ≥ 10 (at least ten reads covering the variant base[s]), variant allele fraction (VAF) ≥ 33%, and filter PASS (quality criteria applied by the Isaac variant caller in the NIHR BioResource Rare Disease Project). Second, variants were excluded if they had an allele frequency above 0.01 in either the Exome Aggregation Consortium (ExAC) Browser18 (all populations) or the 1000 Genomes Project19 (all populations). Third, variants were retained for further review if the predicted consequence was among a list of SO terms indicating protein truncation, if there was evidence of pathogenicity in ClinVar20 (at least two-star evidence of pathogenic or likely pathogenic [P/LP] effect corresponding to multiple submissions with no conflicts as to the assertion of clinical significance), or if the variant was assigned a disease mutation (DM) status in the Human Gene Mutation Database (HGMD).21 In order to consider a subset of non-truncating variants that are predicted to be pathogenic by in silico tools but do not appear in public databases, we also retained variants exceeding a Phred-scaled CADD22 score threshold of 34 for further review. CADD was selected for this purpose given that it incorporates a range of tools and consequently a number of lines of evidence. The threshold was chosen as the median of scores assigned to other variants (affecting any gene) deemed pathogenic according to the criteria described below. Therefore, as a second variant filtering process, variants were identified for retention solely on the basis of CADD scores after variants retained for other reasons were assessed."}