Skip to main content

Table 3 The results of applying filtering steps over all the variant files (including those with no relevant variant detected)

From: Comprehensive gene panels provide advantages over clinical exome sequencing for Mendelian diseases

Panel Input Functional sites Public Pop. DBs SGP Pop. DB Quality Zygosity
Cardiovascular 746 338 76 26 9 2
Deafness 828 257 63 50 17 6
Dermatology 1113 271 71 41 17 5
Dysmorphology/Dysplasia 1529 369 80 43 15 2
Endocrinology 1129 326 61 42 19 5
Gastroenterology 362 190 60 20 6 1
Hematology 1474 324 79 39 18 3
Inborn Errors of Metabolism 1955 571 94 54 24 4
Neurology 2885 718 158 87 29 4
PID 633 309 111 22 6 1
Pulmonology 723 230 74 39 21 3
Renal 507 132 35 21 7 1
Vision 906 341 75 51 17 3
Total (averages) 1138 337 80 41 16 3
  1. The table entries are the average number of variants per panel after applying the respective filter in the column title. The column titled ‘Input’ is the input without applying any filter. The column titled ‘Functional sites’ is for the step of filtering intronic, UTR, synonymous variants. The column titled ‘Public Pop. DBs’ is for the step of filtering variants based on the 1000 Genomes Project database. The column titled ‘SGP Pop. DBs’ is for the step of filtering variants based on the in-house database. The column titled ‘Quality’ is for the step of filtering based on the quality criteria. The column titled ‘Zygosity’ is for the step of excluding non-homozygous variants