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Table 1 Stepwise breakdown of results obtained by TAPER™ using WES datasets for which the causal mutations have previously been identified

From: A new tool for prioritization of sequence variants from whole exome sequencing data

  Parkinson’s disease dataset 1 –FBOX7 (L34R) [12} Intellectual disability and microcephaly dataset 1 –SLC1A4 (E256K) [13} Ataxia and myoclonic epilepsy dataset 1 – KCNA2 (R297Q) [14} Parkinson’s disease dataset 2 - PARK2 (R275W and M432V)
  Individual_1 Individual_2 Individual_3 Individual_1 Individual_2 Individual_1 Individual_1 Individual_2 Individual_3
Total number of variants in VCF file 55 726 55 336 55 289 54 426 54 574 60 128 104 307 108 243 97 833
STEP 1: Total number of variants assigned to exonic regions by wANNOVAR 19 727 19 969 20 353 24 573 24 425 23 163 19 850 19 972 19 863
STEP 2: All synonymous and non-frameshifts removed 9 465 9 544 9 766 12 227 12 248 11 693 9 752 9 777 9 838
STEP 3: Remove all variants with a frequency >1 % in 1KGP 1 281 934 966 2 177 2 153 1 377 1 771 1 681 1 932
STEP 4: Remove all variants with a frequency >1 % in ESP6500 917 797 819 1 928 1 906 941 1 335 1 445 1 575
STEP 5: Remove all variants with negative GERP+++ scores 718 615 651 1 243 1 261 688 1 014 1 126 1 232
STEP 6: Remove all variants with FATHMM scores greater than 1.0 262 224 240 252 231 257 413 301 328
STEP 7: Variants linked to relevant diseases 252 221 236 241 221 239 398 262 292
Variant of interest in shortlist? Yes Yes Yes Yes Yes Yes Yes Yes Yes