Table 2.
Variances between institutional and central laboratories
| Gene | Tissue type |
Mutation present or absent (VAF % ∗) |
VUS, SS, and other comments specific to the mutation identified | ||
|---|---|---|---|---|---|
| Institution | Central | Institution | Central | ||
| FLT3 | |||||
| 1 | BM | BM | A | P (14.41) | FLT3 N676K, not ITD or TKD, not pathogenic and not in OSU panel |
| 2 | PB | PB | A | P (3.66) | FLT3 S543F, mutation not clearly pathogenic, not in OSU design |
| IDH1 | |||||
| 1 | PB | PB | A | P (49.71) | IDH1 F32V, VUS |
| IDH2 | |||||
| 1 | BM | BM | P (40.3) | A | IDH2 R172_H173delinsSA, complex indel |
| 2 | BM | BM | A | P (2.29) | IDH2 R140W, observed but below cutoff (2%) at OHSU laboratory |
| DMNT3A | |||||
| 1 | PB | PB | A | P (44.20) | DNMT3A SS 855+1G>A, SS calls are excluded in OSU panel |
| 2 | BM | BM | A | P (50.00) | DNMT3A G156E, VUS |
| 3 | PB | PB | A | P (44.26) | DNMT3A SS 2478+1G>A, SS calls are excluded in OSU panel |
| 4 | BM | BM | P (20.2) | A | DNMT3A R379C, VUS, low tumor purity at central laboratory |
| TET2 | |||||
| 1 | BM | BM | P (49.6) | A | TET2 S1039L, benign SNP |
| 2 | BM | BM | A | P (82.78) | TET2 SS 4044+1G>A, SS calls are excluded in OSU panel |
| 3 | BM | BM | P (47.0) | A | TET2 I1873T, reported as a somatic pathogenic variant |
| 4 | BM | BM | P (45.0, 49.0) | A | TET2 I1873T, reported as a somatic pathogenic variant (45%); R814C is likely germ line variant (49%) |
| WT1 | |||||
| 1 | BM | BM | A | P (4.20) | WT1 A382fs, VUS |
| 2 | PB | PB | A | P (53.56) | WT1 A5V, benign SNP |
| 3 | BM | BM | A | P (52.82) | WT1 G6OR, area not covered on OSU panel |
| 4 | BM | PB | P (3.00) | A | WT1 R462Q, tissue mismatch |
| TP53 | |||||
| 1 | BM | BM | A | P (10.37) | TP53 P153fs, likely artifact owing to large insertion |
| 2 | PB | PB | A | P (46.6) | TP53 R205Q, VUS |
| 3 | PB | PB | P (2.3) | A | TP53 C124R, below cutoff at central laboratory |
| 4 | PB | PB | A | P (3.44) | TP53 L194R, below cutoff at institution laboratory (OSU) |
| 5 | BM | BM | P (10.8) | A | TP53 G245S, suboptimal tumor purity and sample quality at central laboratory |
| 6 | PB | PB | A | P (69.55) | TP53 C215G, area not covered on OSU panel |
| 7 | BM | BM | A | P (49.85) | TP53 T125T, detected by local laboratory (OHSU) but filtered as a synonymous variant. |
A, absent; SS, splice site; P, present.
†VAF % cutoff value for OSU is 2.0 and for FMI is 2.0.
∗
Assume absent of mutation is equivalent to 0.00 VAF % unless otherwise specified.