Table 4.
Inter-assay concordance
| Sample | Variant | Run 1 | Run 2 | Run 3 | Run 4 | Avg | SD | %CV |
|---|---|---|---|---|---|---|---|---|
| FNAB | ||||||||
| SNV | ||||||||
| HL2 | BAP1 c.2188T>A p.Ter730Arg | 88.3 | 88.1 | 87.8 | 86.0 | 87.6 | 1.05 | 1.2 |
| GNA11 c.626A>T p.Gln209Leu | 46.7 | 52.2 | 48.5 | 50.3 | 49.4 | 2.37 | 4.8 | |
| HL3 | GNA11 c.626A>T p.Gln209Leu | 46.2 | 46.4 | 43.4 | 42.7 | 44.7 | 1.91 | 4.3 |
| EIF1AX c.26G>C p.Gly9Ala | 82.8 | 88.9 | 84.3 | 89.9 | 86.5 | 3.45 | 4.0 | |
| HL4 | BAP1 c.507C>G p.His169Gln | 83.5 | 82.4 | 84.2 | 84.5 | 83.6 | 0.93 | 1.1 |
| GNA11 c.626A>T p.Gln209Leu | 48.0 | 46.0 | 43.4 | 48.9 | 46.6 | 2.45 | 5.3 | |
| HL5 | GNA11 c.626A>T p.Gln209Leu | 47.2 | 45.7 | 46.8 | 45.5 | 46.3 | 0.81 | 1.8 |
| EIF1AX c.17-2A>G (splice site) | 92.0 | 90.0 | 88.5 | 91.3 | 90.4 | 1.56 | 1.7 | |
| HL6 | GNAQ c.626A>C p.Gln209Pro | 66.9 | 64.7 | 66.7 | 65.8 | 66.0 | 1.00 | 1.5 |
| EIF1AX c.17G>A p.Gly6Asp | 96.9 | 97.2 | 95.6 | 98.1 | 97.0 | 1.03 | 1.1 | |
| HL7 | GNA11 c.626A>T p.Gln209Leu | 43.6 | 45.7 | 42.1 | 46.6 | 44.5 | 2.02 | 4.5 |
| HL10 | CYSLTR2 c.386T>A p.Leu129Gln | 48.2 | 47.9 | 51.3 | 50.6 | 49.5 | 1.70 | 3.4 |
| SF3B1 c.1873C>T p.Arg625Cys | 47.5 | 46.8 | 52.7 | 47.5 | 48.6 | 2.75 | 5.6 | |
| HL12 | GNA11 c.547C>T p.Arg183Cys | 36.2 | 39.7 | 39.0 | 37.4 | 38.1 | 1.57 | 4.1 |
| SF3B1 c.1873C>T p.Arg625Cys | 35.6 | 37.2 | 39.9 | 36.6 | 37.3 | 1.83 | 4.9 | |
| HL13 | GNAQ c.626A>C p.Gln209Pro | 62.0 | 61.1 | 60.4 | 61.3 | 61.2 | 0.66 | 1.1 |
| HL15 | SF3B1 c.1874G>A p.Arg625His | 47.0 | 49.1 | 48.9 | 48.0 | 48.2 | 0.95 | 2.0 |
| GNAQ c.626A>T p.Gln209Leu | 42.9 | 45.9 | 47.9 | 46.5 | 45.8 | 2.11 | 4.6 | |
| HL8 | PLCB4 c.1516C>G p.Gln506Glu | 51.4 | 47.7 | 51.1 | 50.4 | 50.2 | 1.69 | 3.4 |
| GNA11 c.626A>T p.Gln209Leu | 39.2 | 40.2 | 37.3 | 39.2 | 39.0 | 1.21 | 3.1 | |
| HL16 | GNA11 c.626A>T p.Gln209Leu | 47.8 | 49.5 | 49.0 | 47.4 | 48.4 | 0.99 | 2.0 |
| INDEL | ||||||||
| HL7 | BAP1 c.898_899delAG p.Arg300fs | 78.4 | 74.0 | 77.2 | 76.2 | 76.5 | 1.86 | 2.4 |
| HL12 | BAP1 c.853delT p.Ser285fs | 58.6 | 58.5 | 54.2 | 55.3 | 56.6 | 2.25 | 4.0 |
| HL16 | BAP1 c.145delC p.Leu49fs | 92.8 | 93.1 | 92.7 | 92.5 | 92.8 | 0.25 | 0.3 |
| FFPE | ||||||||
| SNV | ||||||||
| FFPE27 | GNAQ c.626A>T p.Gln209Leu | 77.8 | 76.4 | 77.5 | 73.3 | 76.2 | 2.0 | 2.7 |
| FFPE31 | GNA11 c.626A>T p.Gln209Leu | 40.1 | 39.5 | 45.0 | 40.1 | 41.4 | 2.5 | 6.0 |
| FFPE32 | GNA11 c.626A>T p.Gln209Leu | 49.2 | 41.9 | 40.1 | 46.4 | 44.4 | 4.1 | 9.3 |
| FFPE33 | GNAQ c.626A>C p.Gln209Pro | 35.5 | 37.5 | 33.8 | 29.2 | 34.0 | 3.5 | 10.4 |
| FFPE35 | GNA11 c.626A>T p.Gln209Leu | 40.0 | 35.1 | 39.1 | 42.4 | 39.1 | 3.0 | 7.8 |
| INDEL | ||||||||
| FFPE27 | BAP1 c.1375_1387delCTCTCAATTCCTC p.Leu459fs | 82.6 | 86.2 | 82.5 | 80.6 | 83.0 | 2.4 | 2.9 |
| FFPE31 | BAP1 c.376delA p.Ser126fs | 61.4 | 65.6 | 59.7 | 63.0 | 62.4 | 2.5 | 4.0 |
| FFPE32 | BAP1 c.1753_1774delTCCATCAGACCAA p.Ser585fs | 81.0 | 85.5 | 85.8 | 87.9 | 85.0 | 2.9 | 3.4 |
| FFPE33 | BAP1 c.87_97delGGAAGGAGATCT | 93.7 | 95.6 | 95.0 | 94.8 | 94.8 | 0.8 | 0.8 |
| FFPE35 | BAP1 c.1055_1056delCC p.Pro352fs | 64.6 | 74.7 | 76.1 | 71.5 | 71.7 | 5.1 | 7.2 |
FFPE, formalin-fixed paraffin-embedded; FNAB, fine-needle aspiration biopsy; INDEL, insertions/deletions.