Table 2.
WES and WGS SKAT-O results and the internal replication in the other data set
| Discovery | Replication | ||||||||
|---|---|---|---|---|---|---|---|---|---|
| Gene | Gene position | Type | Pheno | N | Nvar | P | N | Nvar | P |
| Discovery study: WGS | |||||||||
| DEFT1P/ DEFT1P2 | 8:7006280-7008824 | PTV | VLDLPL XL | 187 | 1 | 1.3×10−6 | |||
| SBDS | 7:66987676-66995696 | PTV | apoC-III | 294 | 2 | 5.0×10−6 | |||
| RBM47 | 4:40423254-40629866 | PAV | apoC-III | 294 | 3 | 2.0×10−6 | 323 | 1 | 0.398 |
| TRMT5 | 14:60971448-60981690 | PAV | CHOL | 329 | 8 | 3.5×10−6 | 419 | 4 | 0.322 |
| VLDLPL XS | 329 | 8 | 5.9×10−6 | 419 | 4 | 0.015 | |||
| IDLFC | 329 | 8 | 6.8×10−6 | 419 | 4 | 0.019 | |||
| LDLC L | 329 | 8 | 9.3×10−6 | 419 | 4 | 0.436 | |||
| CCAR1 | 10:68721143-68792377 | PAV | VLDL XL | 329 | 2 | 7.4×10−6 | 419 | 3 | 0.555 |
| CYP3A43 | 7:99828012-99866106 | PAV | LDLCE M | 329 | 6 | 8.7×10−6 | 419 | 3 | 0.067 |
| LDLCE L | 329 | 6 | 8.7×10−6 | 419 | 3 | 0.038 | |||
| LDL M | 329 | 6 | 9.2×10−6 | 419 | 3 | 0.074 | |||
| DIPK1A | 1:92832728-92961522 | PAV | TG | 451 | 4 | 9.9×10−6 | 469 | 3 | 0.848 |
| Discovery study: WES | |||||||||
| PTGER3 | 1:70852352-71047808 | PTV | HDLFC M | 419 | 1 | 9.8×10−6 | 329 | 1 | 0.119 |
| AKAP3 | 12:4615507-4649047 | PAV | VLDLTG XXL | 304 | 5 | 6.0×10−7 | 245 | 5 | 0.766 |
| TTYH1 | 19:54415430-54436719 | PAV | HDLCE L | 419 | 3 | 5.7×10−6 | |||
| ATP4A | 19:35550192-35563658 | PAV | HDLTG XL | 419 | 3 | 8.1×10−6 | 329 | 3 | 0.810 |
All genes reaching a suggestive p-value <1×10−5 are shown. P-values <2.9×10−6 for PAVs, and p-values <10−5 for PTV burden were defined as statistically significant, highlighted in italics; in replication, p-values <0.05 are highlighted in italics
Discovery exome-wide analysis of either WGS or WES data, Replication for WGS, replication in WES data; for WES, replication in WGS data, Gene position chromosome number:start-end; if multiple gene isoforms exist, only one set of coordinates are given, Type burden of PAVs or PTVs, Nvar number of variants of the given variant type in the gene in discovery/ replication data, apoC-III serum apolipoprotein C-III, CHOL total cholesterol, TG triglycerides, HDLCE L cholesterol ester in large HDL, HDLFC M free cholesterol in medium HDL, HDLTG XL TG in extra-large HDL, IDLFC free cholesterol in IDL particles, LDL M total lipids in medium LDL, LDLC L cholesterol in large LDL, LDLCE M/L cholesterol esters in medium/large LDL, VLDL XL total lipids in extra-large VLDL, VLDLPL XS/XL phospholipid in extra small/extra-large VLDL, VLDLTG XXL TG in extremely large VLDL