Table 2.
Summary of next generation sequencing (NGS), droplet digital PCR (ddPCR), and single molecule molecular inversion probe (smMIP) results for tissue samples from the Boston Children’s Hospital CLOVES, KTS, isolated LM, and FAVA cohorts. NGS, employing either whole exome sequencing (WES) or targeted capture sequencing of 26 genes (TCS), results are reported as mutant alleles/total alleles sequenced. ddPCR was performed for 5 specific mutations and a minimum of 2000 amplimer-containing droplets was analyzed for each ddPCR assay. The percent mutant allele is reported for the ddPCR assay; for example LM12, which had 0.8% mutant alleles, generated 41 droplets that fluoresced positive for the mutant probe among 4005 total amplimer-containing droplets. smMIP results are reported as mutant alleles/total alleles sequenced. Samples for which no mutant alleles were identified by NGS, ddPCR, or smMIP are indicated with a “-,” whereas samples not studied with a technique are left blank. Occasional large differences in mutant allele frequencies from the same study participant may be the consequence of DNA being extracted from different tissues sections for the NGS, ddPCR, and smMIP experiments. Participant for which DNA was extracted from fresh frozen tissue are identified in bold, while participants for which DNA was extracted from paraffin embedded tissue are listed using standard font. Some individuals with CLOVES syndrome (asterisked) had WES and TCS data published previously 4 and are included in this table as positive controls.
| CLOVES | KTS | LM | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Pt. | Var. | NGS | ddPCR | smMIP | Pt. | Var. | NGS | ddPCR | smMIP | Pt. | Var. | NGS | ddPCR | smMIP |
| CL1* | H1047R | 5/24(TCS) | 17 | KT1 | - | - | - | - | LM1 | E542K | 1/31(WES)¶ | 8.5 | ||
| CL2* | H1047R | 13/64(TCS) | 20 | KT2 | E545K | - | 6.2 | LM2 | H1047R | 3/35(WES)¶ | 2.5 | |||
| CL3* | E542K | 1/11(WES)¶ | 8.4 | KT3 | E545G | - | - | 28/825 | LM3 | C420R | 9/58(WES) | 7.9 | ||
| CL4* | E542K | 2/16(WES)¶ | KT4 | H1047L | 4/84(TCS) | 4.7 | LM4 | E545K | 2/36(WES)¶ | 9.8 | ||||
| CL5* | C420R | 12/40(WES) | 15 | KT5 | E545K | - | 12 | LM5 | H1047R | - | 6.2 | |||
| CL6* | C420R | 8/44(WES) | 25 | KT6 | E545K | - | 7.4 | LM6 | H1047L | - | 5.4 | |||
| CL7 | H1047R | - | 3.3 | KT7 | E545K | - | 14 | LM7 | E542K | 1/58(WES)¶ | 2.8 | |||
| CL8 | - | - | - | - | KT8 | H1047R | - | 8.0 | LM8 | H1047R | 6.6 | |||
| CL9 | E545K | - | 8.0 | KT9 | E545K | - | 7.4 | LM9 | E542K | 4.9 | ||||
| CL10 | E545K | 10/180(TCS) | 9.4 | KT10 | H1047R | 2/58(TCS) | 8.0 | LM10 | - | - | ||||
| CL11 | H1047R | - | 14 | KT11 | H1047R | 2/44(TCS) | 7.4 | LM11 | H1047L | 6.0 | ||||
| CL12 | H1047R | 19/73(TCS) | 32 | KT12 | H1047R | - | 2.7 | LM12 | E545K | 0.8 | ||||
| CL13 | H1047R | - | ? | KT13 | E542K | 2/48(TCS) | 5.0 | LM13 | H1047L | 10 | ||||
| CL14 | E545K | 4/86(TCS) | 5.6 | KT14 | H1047R | - | 16 | LM14 | H1047R | 4.2 | ||||
| CL15 | E545K | 5/68(TCS) | 10 | KT15 | E545K | - | 5.5 | LM15 | H1047R | 8.4 | ||||
| CL16 | H1047L | 4/43(TCS) | 16 | KT16 | E545K | 8.2 | LM16 | E542K | 4.4 | |||||
| CL17 | C420R | - | 9.4 | KT17 | H1047R | 8.9 | LM17 | E545K | 2.8 | |||||
| CL18 | E545K | 62/228(TCS) | 27 | KT18 | E542K | 10 | ||||||||
| CL19 | E545K | - | 11 | KT19 | E545K | 8.7 | ||||||||
| CL20 | E542K | - | 8.9 | 88/903 | KT20 | E545K | 13 | FAVA | ||||||
| CL21 | T1025A | - | - | 8/275 | KT21 | E542K | 3.7 | Pt. | Var. | NGS | ddPCR | smMIP | ||
| CL22 | E545K | - | 4.3 | F1 | - | - | - | - | ||||||
| CL23 | H1047L | 48/149(TCS) | 24 | F2 | E545K | 2/30(WES)¶ | 8.9 | |||||||
| CL24 | C420R | - | 10 | F3 | Q546K | 4/53(WES) | 6.9# | |||||||
| CL25 | C420R | - | 25 | F4 | - | - | - | |||||||
| CL26 | C420R | 135/527(TCS) | 20 | F5 | E542K | 1/31(WES)¶ | 8.4 | |||||||
| CL27 | E542K | 1.2 | F6 | - | - | - | - | |||||||
| CL28 | E542K | 9.8 | F7 | H1047R | 26/238(WES) | 20 | ||||||||
| CL29 | N345K | - | 314/837 | F8 | E545K | - | 5.0 | |||||||
| CL30 | H450R! | - | 11/459 | |||||||||||
| CL31 | E542K | 5.0 | 110/1362 | |||||||||||
| CL32 | - | - | ||||||||||||
| CL33 | E545K | 9.2 | ||||||||||||
indicate samples that would have been missed by our NGS filtering strategy due to insufficient number of reads containing the mutation.
indicates sample for which the p.E545K ddPCR assay indicated an alternate mutation.