List of candidate somatic mutations identified in the AML index patient
| Chromosome . | Position . | Gene . | R/V . | AA . | Tumor . | Normal . | P . | ||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| (F+R)/T . | % . | (F+R)/T . | % . | T err . | N err . | Germ. . | |||||
| Somatic mutations confirmed by Sanger sequencing | |||||||||||
| 3 | 174317684 | SPATA16 | C/T | V178I | (38 + 38)/182 | 42 | (0 + 2)/138 | 1 | 2.8 × 10−78 | .77 | 1.6 × 10−61 |
| 6 | 7529633 | DSP | C/T | P2380L | (33 + 19)/100 | 52 | (1 + 0)/91 | 1 | 1.6 × 10−60 | .84 | 3.5 × 10−51 |
| 2 | 25312132 | DNMT3A | G/A | P660S | (26 + 20)/95 | 48 | (0 + 0)/88 | 0 | 8.2 × 10−52 | 1 | 8.1 × 10−52 |
| 1 | 70488756 | SFRS11 | G/C | E413D | (29 + 18)/114 | 41 | (0 + 1)/117 | 1 | 1 × 10−48 | .91 | 5.8 × 10−42 |
| 5 | 21788048 | CDH12 | A/C | M647R | (11 + 18)/67 | 43 | (1 + 1)/81 | 2 | 2.0 × 10−31 | .48 | 5.4 × 10−22 |
| 11 | 56856812 | SSRP1 | G/A | R211C | (12 + 11)/49 | 47 | (0 + 0)/43 | 0 | 3.0 × 10−26 | 1 | 2.9 × 10−26 |
| X | 39818006 | BCOR | C/T | G513R | (6 + 13)/48 | 40 | (0 + 1)/40 | 3 | 3.5 × 10−20 | .55 | 5.3 × 10−14 |
| X | 21784900 | YY2 | C/T | S126L | (2 + 14)/39 | 41 | (0 + 0)/29 | 0 | 1.6 × 10−17 | 1 | 1.6 × 10−17 |
| 18 | 42814666 | TCEB3B | C/T | R323Q | (2 + 12)/29 | 48 | (0 + 0)/32 | 0 | 9.6 × 10−17 | 1 | 9.4 × 10−17 |
| X | 39808770 | BCOR | −/AT | R1089HfsX25 | (8 + 6)/35 | 40 | (0 + 0)/37 | 0 | 2.6 × 10−15 | 1 | 2.5 × 10−15 |
| 2 | 25315524 | DNMT3A | C/T | G607D | (6 + 1)/11 | 64 | (0 + 0)/10 | 0 | 3.9 × 10−10 | 1 | 3.9 × 10−10 |
| 7 | 6787044 | RSPH10B2 | G/A | G537S | (3 + 5)/39 | 21 | (0 + 0)/37 | 0 | 9.0 × 10−07 | .49 | 8.4 × 10−7 |
| 19 | 22155572 | ZNF676 | T/A | S263C | (15 + 35)/142 | 35 | (0 + 0)/139 | 0 | 1.3 × 10−47 | 1 | 1.3 × 10−47 |
| Candidate somatic mutations not confirmed by Sanger sequencing in the leukemic cell DNA | |||||||||||
| 2 | 86112970 | POLR1A | G/C | A1403G | (1 + 10)/56 | 20 | (0 + 1)/33 | 3 | 1.3 × 10−8 | .49 | 6.2 × 10−5 |
| 3 | 195336860 | HES1 | G/A | splice | (4 + 1)/9 | 56 | (0 + 0)/7 | 0 | 3.8 × 10−7 | 1 | 3.7 × 10−7 |
| 22 | 36351755 | GGA1 | A/C | T316P | (1 + 5)/16 | 38 | (0 + 0)/20 | 0 | 4.3 × 10−7 | 1 | 4.2 × 10−7 |
| Germline variant (present both in leukemic and normal cell DNA) | |||||||||||
| 1 | 208924107 | KCNH1 | −/GA | (8 + 2)/19 | 53 | (1 + 0)/13 | 8 | 8.0 × 10−13 | .23 | 2.0 × 10−6 | |
| Chromosome . | Position . | Gene . | R/V . | AA . | Tumor . | Normal . | P . | ||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| (F+R)/T . | % . | (F+R)/T . | % . | T err . | N err . | Germ. . | |||||
| Somatic mutations confirmed by Sanger sequencing | |||||||||||
| 3 | 174317684 | SPATA16 | C/T | V178I | (38 + 38)/182 | 42 | (0 + 2)/138 | 1 | 2.8 × 10−78 | .77 | 1.6 × 10−61 |
| 6 | 7529633 | DSP | C/T | P2380L | (33 + 19)/100 | 52 | (1 + 0)/91 | 1 | 1.6 × 10−60 | .84 | 3.5 × 10−51 |
| 2 | 25312132 | DNMT3A | G/A | P660S | (26 + 20)/95 | 48 | (0 + 0)/88 | 0 | 8.2 × 10−52 | 1 | 8.1 × 10−52 |
| 1 | 70488756 | SFRS11 | G/C | E413D | (29 + 18)/114 | 41 | (0 + 1)/117 | 1 | 1 × 10−48 | .91 | 5.8 × 10−42 |
| 5 | 21788048 | CDH12 | A/C | M647R | (11 + 18)/67 | 43 | (1 + 1)/81 | 2 | 2.0 × 10−31 | .48 | 5.4 × 10−22 |
| 11 | 56856812 | SSRP1 | G/A | R211C | (12 + 11)/49 | 47 | (0 + 0)/43 | 0 | 3.0 × 10−26 | 1 | 2.9 × 10−26 |
| X | 39818006 | BCOR | C/T | G513R | (6 + 13)/48 | 40 | (0 + 1)/40 | 3 | 3.5 × 10−20 | .55 | 5.3 × 10−14 |
| X | 21784900 | YY2 | C/T | S126L | (2 + 14)/39 | 41 | (0 + 0)/29 | 0 | 1.6 × 10−17 | 1 | 1.6 × 10−17 |
| 18 | 42814666 | TCEB3B | C/T | R323Q | (2 + 12)/29 | 48 | (0 + 0)/32 | 0 | 9.6 × 10−17 | 1 | 9.4 × 10−17 |
| X | 39808770 | BCOR | −/AT | R1089HfsX25 | (8 + 6)/35 | 40 | (0 + 0)/37 | 0 | 2.6 × 10−15 | 1 | 2.5 × 10−15 |
| 2 | 25315524 | DNMT3A | C/T | G607D | (6 + 1)/11 | 64 | (0 + 0)/10 | 0 | 3.9 × 10−10 | 1 | 3.9 × 10−10 |
| 7 | 6787044 | RSPH10B2 | G/A | G537S | (3 + 5)/39 | 21 | (0 + 0)/37 | 0 | 9.0 × 10−07 | .49 | 8.4 × 10−7 |
| 19 | 22155572 | ZNF676 | T/A | S263C | (15 + 35)/142 | 35 | (0 + 0)/139 | 0 | 1.3 × 10−47 | 1 | 1.3 × 10−47 |
| Candidate somatic mutations not confirmed by Sanger sequencing in the leukemic cell DNA | |||||||||||
| 2 | 86112970 | POLR1A | G/C | A1403G | (1 + 10)/56 | 20 | (0 + 1)/33 | 3 | 1.3 × 10−8 | .49 | 6.2 × 10−5 |
| 3 | 195336860 | HES1 | G/A | splice | (4 + 1)/9 | 56 | (0 + 0)/7 | 0 | 3.8 × 10−7 | 1 | 3.7 × 10−7 |
| 22 | 36351755 | GGA1 | A/C | T316P | (1 + 5)/16 | 38 | (0 + 0)/20 | 0 | 4.3 × 10−7 | 1 | 4.2 × 10−7 |
| Germline variant (present both in leukemic and normal cell DNA) | |||||||||||
| 1 | 208924107 | KCNH1 | −/GA | (8 + 2)/19 | 53 | (1 + 0)/13 | 8 | 8.0 × 10−13 | .23 | 2.0 × 10−6 | |
F, R and T indicate the number of variant reads observed in the forward strand (F) or in the reverse strand (R) and the number of total reads (T) covering that position; R/V, reference/variant nucleotide; P, p-value associated to the probability that the variant is detected due to a sequencing error in the tumor (T err), a sequencing error in the normal (N err), and a germline variant (Germ.).