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 |