Summary of the final on-trial sample swap between Leeds and Cardiff, run in May 2017
| Sample ID | Cardiff pyrosequencing (VAF) | Cardiff NGS (VAF) | Leeds NGS (VAF) |
| Sample 1 | BRAF c.1798_1799delGTinsAA (~50%) | BRAF c.1798_1799delGTinsAA (48%) | BRAF c.1798G>A BRAF c.1799T>A (49%)* |
| Sample 2 | BRAF c.1798_1799delGTinsAA (~66%) | BRAF c.1798_1799delGTinsAA (66%) | BRAF c.1798G>A BRAF c.1799T>A (65%)* |
| Sample 3 | KRAS c.35G>A (25%) PIK3CA c.3140A>G (37%) | KRAS c.35G>A (15%) PIK3CA c.3140A>G (22%) TP53 c.215C>G (67%) TP53 c.475G>C (28%) | KRAS c.35G>A (12%) PIK3CA c.3140A>G (17%) TP53 c.215C>G (66%) TP53 c.475G>C (27%) |
| Sample 4 | KRAS c.35G>T (31%) | KRAS c.35G>T (21%) | KRAS c.35G>T (17%) |
| Sample 5 | Pyrosequencing not performed on this sample† | TP53 c.215C>T (99%) TP53 c.380C>T (25%) TP53 c.701A>G (14%) TP53 c.994–1G>T (6%) | TP53 c.215C>T (99%) TP53 c.380C>T (15%) TP53 c.701A>G (29%) TP53 c.994–1G>T (10%) |
| Sample ID | Leeds pyrosequencing (VAF) | Leeds NGS result (VAF) | Cardiff NGS result (VAF) |
| Sample 6 | KRAS c.34G>T (52%) PIK3CA c.1633G>A (48%) | KRAS c.34G>T (39%) PIK3CA c.1633G>A (43%) | NGS failed due to low coverage |
| Sample 7 | KRAS c.35G>A (45%) | KRAS c.35G>A (30%) TP53 c.797G>A (32%) | KRAS c.35G>A (35%) TP53 c.797G>A (41%) |
| Sample 8 | KRAS c.436G>A (30%) PIK3CA c.1634A>C (13%) | NGS failed due to low coverage | NGS failed due to low coverage |
| Sample 9 | KRAS c.35G>A (33%) | KRAS c.35G>A (29%) TP53 c.637C>T (60%) TP53 c.215C>G (100%) | KRAS c.35G>A (22%) TP53 c.637C>T (56%) TP53 c.215C>G (100%) |
| Sample 10 | KRAS c.34G>T (38%) | KRAS c.34G>T (28%) PIK3CA c.363C>T (47%) TP53 c.637C>T (60%) | KRAS c.34G>T (30%) PIK3CA c.363C>T (46%) TP53 c.637C>T (62%) |
*These two adjacent mutations can also be called as a single mutation, as was the case in Cardiff.
†No pyrosequencing was undertaken on this sample, as it was not a FOCUS4 patient sample, and local testing in Cardiff had switched to NGS, for routine diagnostic testing. The TP53 mutations detected by NGS are outside the scope of the pyrosequencing assay panel, so not detected by the latter assay.
NGS, next-generation sequencing; VAF, variant allele frequency.