Deep amplicon results from 13 subclinical cases
| Sample ID . | Mutation in ARMS-PCR screening . | Genomic coordinates . | Deep sequencing somatic variant result . | Percent of mutant variant reads . | Percent of next “noise” variant read . | Coverage . | Diagnosis . |
|---|---|---|---|---|---|---|---|
| UPN92 | D661Y | chrl7:40474420 | Positive | 1.8 | 0.002 | 2318 | MDS |
| UPN10 | D661Y | chrl7:40474420 | Positive | 13.2 | 0.002 | 5271 | MDS |
| UPN28 | DG61Y | chrl7:40474420 | Positive | 0.5 | 0.01 | 2585 | AA |
| UPN11 | D661Y | chrl7:40474419 | Positive | 5.4 | 0.01 | 7413 | MDS |
| UPN2 | D661Y | chrl7:40474420 | Positive | 0.9 | 0.002 | 17 200 | AA |
| UPN1 | Y640F | chrl7:40474482 | Positive | 1.7 | 0.003 | 9032 | AA |
| UPN3 | Y640F | chr17:40474482 | Positive | 0.3 | 0.0004 | 2352 | AA |
| UPN22 | Y640F | chrl7:40474482 | Negative | 0.00008 | 0.003 | 12 306 | MDS |
| UPN52 | D661Y | chrl7:40474420 | Negative | 0.6 | 1.3 | 14 680 | MDS |
| UPN57 | Y640F | chrl7:40474482 | Negative | 0 | 0 | 1335 | AA |
| UPN72 | Y640F | chrl7:404744S2 | Negative | 0 | 0.002 | 17 562 | AA |
| UPN60 | D661Y | chrl7:40474420 | Negative | 0.6 | 1.4 | 23 012 | AA |
| UPN32 | D661Y | chrl7:40474420 | Negative | 0.6 | 1.4 | 5620 | AA |
| Sample ID . | Mutation in ARMS-PCR screening . | Genomic coordinates . | Deep sequencing somatic variant result . | Percent of mutant variant reads . | Percent of next “noise” variant read . | Coverage . | Diagnosis . |
|---|---|---|---|---|---|---|---|
| UPN92 | D661Y | chrl7:40474420 | Positive | 1.8 | 0.002 | 2318 | MDS |
| UPN10 | D661Y | chrl7:40474420 | Positive | 13.2 | 0.002 | 5271 | MDS |
| UPN28 | DG61Y | chrl7:40474420 | Positive | 0.5 | 0.01 | 2585 | AA |
| UPN11 | D661Y | chrl7:40474419 | Positive | 5.4 | 0.01 | 7413 | MDS |
| UPN2 | D661Y | chrl7:40474420 | Positive | 0.9 | 0.002 | 17 200 | AA |
| UPN1 | Y640F | chrl7:40474482 | Positive | 1.7 | 0.003 | 9032 | AA |
| UPN3 | Y640F | chr17:40474482 | Positive | 0.3 | 0.0004 | 2352 | AA |
| UPN22 | Y640F | chrl7:40474482 | Negative | 0.00008 | 0.003 | 12 306 | MDS |
| UPN52 | D661Y | chrl7:40474420 | Negative | 0.6 | 1.3 | 14 680 | MDS |
| UPN57 | Y640F | chrl7:40474482 | Negative | 0 | 0 | 1335 | AA |
| UPN72 | Y640F | chrl7:404744S2 | Negative | 0 | 0.002 | 17 562 | AA |
| UPN60 | D661Y | chrl7:40474420 | Negative | 0.6 | 1.4 | 23 012 | AA |
| UPN32 | D661Y | chrl7:40474420 | Negative | 0.6 | 1.4 | 5620 | AA |
Six cases were considered ARMS-PCR false positives because either no variant reads were found or the number of reads was under the set detection threshold as defined by the noise level (multiple bases calls). The percentage of next “noise” variant reads corresponds to the base calls considered background errors (different from the reference or the known somatic mutated variant). Coverage indicates the numbers of reads generated in every case.