Data set | Ogden (exome variants in hg19 coordinate) | Miller (genome variants in hg18 coordinate) | |||
Variants reduction strategy | Default | Custom | Default | Custom | Custom |
Input variants | 1479 | 1479 | 4702187 | 4702187 | 4702187 |
Identify missense, nonsense and splicing variants | 136 | 136 | 12410 | 12410 | 12410 |
Identify variants from conserved regions | – | – | – | 5395 | – |
Remove variants in segmental duplications regions | – | – | – | 5135 | – |
Remove variants observed in user-supplied controls | – | 16* | – | – | – |
Remove variants observed in the 1000 Genomes Project with MAF>1% | 19 | 3 | 2275 | 1116 | 2275 |
Remove variants observed in the NHLBI-ESP 5400 exomes with MAF>1% | 14 | 3 | 1256 | 740 | 1256 |
Remove variants in dbSNP (excluding clinically associated SNPs) | 1 | 1 | 516 | 313 | 516 |
Remove variants with SIFT score >0.05 | – | 1 | – | – | 395 |
Remove variants with PolyPhen2 score <0.85 | – | 1 | – | – | 351 |
Final list of candidate genes based on disease model | 1 | 1 | 24 | 10 | 14 |
Correct causal gene identified? | Yes | Yes | Yes | Yes | No |
↵* Two unaffected male family members were used as controls.
SNP, single nucleotide polymorphism.