Table 2. Summary of the mutations identified in positive control samples.
| Patient | Diagnosis | Known Gene mutated | Nucleotide change* | Amino acid change* | Zygosity | Read depth | Allele frequency | ||
|---|---|---|---|---|---|---|---|---|---|
| 1000G | ESP6500 | ExAC | |||||||
| 1 | SAVI | TMEM173 | 463G>A | V155M | Het | 250 | - | - | - |
| 2 | FHL2 | PRF1 | 1034C>G | P345R | Het | 250 | - | - | - |
| c.50delT | L17fs | Het | 218 | 0.0008 | 0.001 | - | |||
| 3 | FHL3 | UNC13D | 1090delC | S363RfsX1 | Het | 210 | - | - | - |
| c.118-308C>T (intronic) | n/a | Het | 99 | 0.28 | - | - | |||
| 4 | FHL3 | UNC13D | c.2831-13 G>A (Intronic) | n/a | Het |
242 | - | - | - |
| 2436_2437insTTGA | N813delinsLN | Het | 236 | - | - | - | |||
| 5 | XLP1 | SH2D1A | Gene deletion | n/a | - | - | - | - | - |
| 6 | ALPS | CASP10 | A1216T | I406L | Het | 250 | 0.0048 | 0.0026 | 0.0049 |
| 7 | FHL5 | STXBP2 | c.1247-1G>C | n/a | Hom | 230 | - | 0.0002 | 0.0003 |
| 8 | FHL2 | PRF1 | c.C272T | A91V | Het | 227 | 0.02 | 0.034 | 0.0311 |
| 9 | Familial SLE | PRKCD | c.G1294T | G432W | Hom | 250 | - | - | - |
| 10 | FHL4 | STX11 | Gene deletion | n/a | - | - | - | - | - |
| 11 | DADA2 | CECR1 | C752T | P251L | Het | 177 | 0.0002 | 0.0001 | 0.00003 |
| -12233delC (5UTR) | n/a | Het | 247 | 0.07 | - | - | |||
| 12 | DADA2 | CECR1 | c.T2C | M1T | Het | 248 | - | - | 0.00002 |
| c.144delG | G48Fs | Het | 246 | - | - | 0.0002 | |||
| 13 | XLP1 | SH2D1A | Exon 2 deletion | n/a | - | - | - | - | - |
| 14 | TRAPS | TNFRSF1A Mosaic [7%] | 255_278del | 85_93del | Het | 163 | - | - | - |
| 15 | CAPS | NLRP3 Mosaic [20%] | C1698A | F566L | Het | 243 | - | - | - |
| 16 | CAPS | NLRP3 Mosaic [3%] | G1699A | E567K | Het | 426 | - | - | - |
| 17 | AGS | TREX1 | c.859_876del | p.287_292del | Hom | 233 | - | - | - |
| 18 | PAPA | PSTPIP1 | c.G748A | E250K | Het | 298 | - | - | - |
| 19 | CAPS | NLRP3 | c.G2336T | G779V | Het | 151 | - | - | - |
| 20 | Amyloidosis | TTR | delGAinsTT | E74L | Het | 286 | - | - | - |
| 21 | Blau | NOD2 | G1534T | D512Y | Het | 249 | - | - | - |
| 22 | ALPS | FAS | 569-2A>C | n/a | Het | 55 | - | - | - |
Patients 1–16 were used in a formal blinded initial validation analysis for VIP1. Patients 17–22 were subsequently included in future runs and where thus not included in the blinded validation analysis.
*Since each gene may have multiple splicing isoforms, the variants were annotated according to the RefSeq transcript in S1 and S2 Tables. Het = heterozygote, Hom = homozygote, n/a = not available,— = not known. SAVI (STING-associated vasculopathy with onset in infancy), FHL (Familial haemophagocytic lymphohistiocytosis), XLP1 (X-linked lymphoproliferative disease type 1), ALPS (Autoimmune lymphoproliferative syndrome), SLE (Systemic lupus erythematosus), DADA2 (Deficiency of Adenosine Deaminase type 2), TRAPS (Tumour Necrosis Factor Receptor Associated Periodic Syndrome), AGS (Aicardi–Goutières syndrome), PAPA (pyogenic arthritis, pyoderma gangrenosum and acne), CAPS (Cryopyrin-Associated Period Syndrome).