Table 1.
Single cell genotyping of acquired mutations and deletions in PD3958a and PD3971a.
Variant allele fraction is reported for next-generation sequencing data. Adjusted estimate of total cell fraction reporting the variant using next-generation sequencing data copy number profiles and derived estimates of aberrant (normal) cell fraction. Single cell data reports the proportion and confidence intervals of single cells (ETV6-RUNX1 +ve) reporting the variant of interest. All ETV6-RUNX1 −ve cells were wild type for all the remaining variants genotyped.
| Type | Variant | Chr | Pos | WT | Mt | Variant allele fraction | Copy number adjusted estimated cell fraction | Single cell data (normal cells excluded) |
|---|---|---|---|---|---|---|---|---|
| PD3958a | ||||||||
|
| ||||||||
| Deletion | Del11p12* | 100% (96.6-100) | ||||||
| Deletion | Del21q22* | 41.7% (33.5-50.4) | ||||||
| Deletion | Del12q13 | 55.3% (46.7-63.7) | ||||||
| Substitution | CCDC110_p.Q432E | 4 | 186380447 | G | C | 45.30% | 76.14%(72.78-79.6) | 100% (96.6-100) |
| Substitution | CYLC1_p.N205Y | X | 83128329 | A | T | 95.20% | 100% | 100% (96.6-100) |
| Substitution | SLC3A1_p.S168L | 2 | 44507927 | C | T | 52% | 100% | 100% (96.6-100) |
|
| ||||||||
| PD3971a | ||||||||
|
| ||||||||
| Deletion | Del1q31* | 100% (96.4-100) | ||||||
| Deletion | Del12p13* | 19.2% (13.05-27.27) | ||||||
| Substitution | ARHGAP6_p.M362K | X | 11204544 | A | T | 12.70% | 29.2%(22.9-35.6) | 39% (33-50.5) |
| Substitution | C1orf101_p.G789S | 1 | 244769058 | G | A | 14.10% | 32% (19-47) | 39% (33-50.5) |
| Substitution | DNAH2_p.R1797* | 17 | 7681635 | C | T | 13% | 29.8%(24-35.8) | 39% (33-50.5) |
| Substitution | GPR156_p.S652A | 3 | 119886370 | A | C | 42.40% | 97.4%(87.1-100) | 100% (96.4-100) |
*
Indicate deletions with an RSS signature. For SV coordinates please refer to Supplementary Table 4.