Table 2.
ddPCR assays and limit of detection on genomic tumor DNA.
| UPN | Target | Target Position GRCh38/hg38 | Amplicon Size | LoD | FPR |
|---|---|---|---|---|---|
| (bp) | (pg) | Events/Well | |||
| 1 | der(11)t(11;17)(p11.2;q23.1) | chr11:46,349,051 | 98 | 100 | 0 |
| 5q23.2 tandem duplication (SNCAIP) | chr5:122,518,910 | 100 | 100 | 0 | |
| 9 | CTNNB1 c.100G>A, p.Gly34Arg * | chr3:41,224,612 | 62 | 100 | 0.17 |
| CSNK2B c.419G>T, p.Cys140Phe | chr6:31,669,370 | 64 | 100 | 0 | |
| 1p21.1 intergenic tandem duplication | chr1:105,150,201 | 89 | 100 | 0 | |
| 13 | CTNNB1 c.101G>A, p.Gly34Glu * | chr3:41,224,613 | 64 | 100 | 0.58 |
| PIK3CA c.3140A>G, p.His1047Arg | chr3:179,234,297 | 80 | 100 | 0 | |
| 15 | FOSL2 c.383G>A, p.Arg128His | chr2:28,408,787 | 62 | 10 | 0 |
| 19q12 tandem duplication (ZNF536) | chr19:30,403,430 | 116 | 100 | 0 | |
| 5q13.3 tandem duplication (HEXB) | chr5:74,152,786 | 91 | 100 | 0 | |
| 19 | MAX c.179G>A, p.Arg60Gln | chr14:65,078,029 | 69 | 100 | 0.25 |
| PTCH1 c.2287dup, p.Val763GlyfsTer27 | chr9:95,467,388 | 63 | 100 | 0.25 | |
| 21 | B4GALT1 c.421_428dup p.Glu144CysfsTer2 | chr9:33,135,408 | 64 | 10 | 0 |
| 10q22.2 amp (SAMD8) | chr10:73,926,074 | 87 | 10 | 0 | |
| 22 | KDM5D c.1642G>C, p.Asp548His | chrY:19,720,946 | 64 | 100 | 0 |
| 7q21.2 amp (CDK6) | chr7:92,501,482 | 92 | 10 | 0 | |
| 24 | PRMT7 c.224C>T, p.Thr75Met | chr16:68,324,774 | 62 | 10 | 0.5 |
| 27 | KMT2D c.13825C>T, p.Gln4609Ter | chr12:49,030,615 | 98 | 100 | 0.6 |
| OFD1 c.1411+1G>A | chrX:13,756,768 | 65 | 10 | 0.25 | |
| 31 | KMT2D c.7933C>T, p.Arg2645Ter | chr12:49,039,837 | 68 | 100 | 0.75 |
| SMO c.1247_1248delinsAA, p.Gly416Glu * | chr7:129,206,570 | 61 | 100 | 1.58 | |
| 35 | CTNNB1, c.101G>A, p.Gly34Glu * | chr3:41,224,613 | 64 | 100 | 0.17 |
| 13q14.2 tandem duplication (CAB39L) | chr13:49,304,384 | 112 | 100 | 0 | |
| 43 | KDM6A c.4129C>T, p.Gln1377Ter * | chrX:45,110,202 | 68 | 100 | 0.08 |
| Xp22.11 tandem duplication (KLHL15) | chrX:24,005,865 | 90 | 100 | 0 |
Target sequences used for final ddPCR assays. Point mutations detected with clinical Sanger sequencing marked with an asterisk. UNP, unique patient number; GRCh38, Genome Reference Consortium Human Build 38; LoD, limit of detection; FPR, false positive rate; amp, amplification.