Extended Data Table 1.
Deep sequencing, allele specific PCR and droplet PCR analyses of matched diagnostic and remission DNA from patients with NT5C2 mutations at relapse.
| Duplex Sequencing | |||||
|---|---|---|---|---|---|
|
| |||||
| Sample | Relapse Mutation | Average duplex depth | Allele load at diagnosis | ||
| T-ALL 11 | K359Q | 5009 | Not detected | ||
| T-ALL 22 | R238W | 6519 | Not detected | ||
| T-ALL 29 | R391 | 3728 | Not detected | ||
| T-ALL 30 | Q523* | 3512 | Not detected | ||
| T-ALL C4 | R367Q | 5863 | Not detected | ||
| T-ALL C5 | R238W | 3341 | Not detected | ||
| T-ALL C7 | R367Q | 5134 | Not detected | ||
| T-ALL C10 | R238W | 4299 | Not detected | ||
| T-ALL C11 | R367Q | 3086 | Not detected | ||
| T-ALL C14 | D407E | 3755 | Not detected | ||
| T-ALL C17 | R367Q | 3497 | Not detected | ||
| T-ALL C18 | R367Q | 3660 | Not detected | ||
| T-ALL C20 | R367Q | 3693 | Not detected | ||
| T-ALL N1 | R367Q | 3507 | Not detected | ||
| Allele Specific PCR | |||||
|
| |||||
| Sample | Detection threshold | Allele load at diagnosis | Allele load at remission | ||
|
| |||||
| T-ALL 4 | 1/1000 | Not detected | - | ||
| T-ALL 17 | 1/1000 | Not detected | Not detected | ||
| T-ALL 35 | 1/1000 | Not detected | - | ||
| T-ALL C4 | 1/1000 | Not detected | Not detected | ||
| T-ALL C7 | 1/1000 | Not detected | Not detected | ||
| T-ALL C11 | 1/1000 | Not detected | Not detected | ||
| T-ALL C17 | 1/1000 | Not detected | Not detected | ||
| T-ALL C18 | 1/1000 | Not detected | Not detected | ||
| T-ALL C20 | 1/1000 | Not detected | Not detected | ||
| Serial Patient Sample Droplet PCR | |||||
|
| |||||
| Sample | Sample Type | Days since diagnosis | Detection threshold (%) | Mutation | Mutant Allele Frequency (%) |
|
| |||||
| SJBALL192 | D | 0 | 0.005 | P414A | 0.00000 |
| SJBALL192 | R1 | 170 | 0.005 | P414A | 37.73843 |
| SJBALL192 | CR | 204 | 0.005 | P414A | 0.20425 |
| SJBALL192 | CR | 230 | 0.005 | P414A | 0.15196 |
| SJBALL192 | R2 | 280 | 0.005 | P414A | 0.00064 |
| SJBALL192 | D | 0 | 0.005 | R39Q | 0.00256 |
| SJBALL192 | R1 | 170 | 0.005 | R39Q | 0.00584 |
| SJBALL192 | CR | 230 | 0.005 | R39Q | 0.02241 |
| SJBALL192 | R2 | 280 | 0.005 | R39Q | 48.57407 |
| SJTALL001 | D | 0 | 0.005 | R39Q | 0.00238 |
| SJTALL001 | D | 0 | 0.005 | R39Q | 0.00307 |
| SJTALL001 | CR | 53 | 0.005 | R39Q | 0.00576 |
| SJTALL001 | CR | 53 | 0.005 | R39Q | 0.00762 |
| SJTALL001 | CR | 218 | 0.005 | R39Q | 0.00333 |
| SJTALL001 | CR | 218 | 0.005 | R39Q | 0.00579 |
| SJTALL001 | CR | 362 | 0.005 | R39Q | 0.01952 |
| SJTALL001 | R1 | 399 | 0.005 | R39Q | 3.70027 |
| SJTALL001 | R1 | 412 | 0.005 | R39Q | 3.57648 |
| SJTALL001 | CR | 434 | 0.005 | R39Q | 0.00931 |
| SJTALL001 | R2 | 751 | 0.005 | R39Q | 37.58709 |
| SJTALL001 | R2 | 751 | 0.005 | R39Q | 39.23768 |