Table 1. CFs of SNV- and CNA-based growth clones.
| Patient | Growth clone | No. SNVs | Chrom | Position | TCN | CF | ||||
|---|---|---|---|---|---|---|---|---|---|---|
| TU | S1 | S2 | X1 | X2 | ||||||
| P1 | Mbp | % | % | % | % | % | ||||
| main | 194.680 | na | na | na | 105 | 100 | 100 | 100 | 100 | |
| P1-q1 | 2.937 | na | na | na | 40 | 45 | 0 | 45 | 65 | |
| P1-q2 | 18.158 | na | na | na | 0 | 5 | 0 | 15 | 60 | |
| P1-q3 | 5.640 | na | na | na | 15 | 20 | 95 | 20 | 25 | |
| P1-q4 | 226 | na | na | na | 35 | 40 | 0 | 30 | 0 | |
| P1-q5 | 15.353 | na | na | na | 0 | 0 | 90 | 0 | 0 | |
| P1-c1 | na | X | 1-155 | 1n | 0 | 10 | 0 | 40 | 10 | |
| P2 | ||||||||||
| main | 14.875 | na | na | na | 95 | 100 | 100 | 100 | 100 | |
| P2-q1 | 796 | na | na | na | 0 | 10 | 10 | 45 | 90 | |
| P2-q2 | 1.174 | na | na | na | 0 | 0 | 0 | 0 | 60 | |
| P2-q3 | 3.106 | na | na | na | 0 | 15 | 20 | 10 | 0 | |
| P2-c1 raw | na | 5 | 63-69 | 3 n | 0 | 70 | 40 | 30 | 10 | |
| P2-c1 raw | na | 5 | 71-180.5 | 3 n | 0 | 70 | 40 | 30 | 10 | |
| P2-c1 raw | na | 7 | 62-70.5 | 3 n | 10 | 60 | 40 | 20 | 0 | |
| P2-c1 raw | na | 7 | 70.5-88.5 | 3 n | 0 | 70 | 40 | 30 | 0 | |
| P2-c1 combined | na | 5 and 7 | na | na | 0 | 70 | 40 | 30 | ≤10 | |
| P2-c2 raw | na | 7 | 90.5-117.5 | 3 n | 100 | 60 | 50 | 30 | 0 | |
| P2-c2 raw | na | 7 | 117.5-159 | 4 n | 100 | 60 | 40 | 30 | 0 | |
| P2-c2 combined | na | 7 | na | na | 100 | 60 | 40-50 | 30 | 0 | |
| P2-c3 raw | na | 18 | 26.5-36.5 | 1 n | 100 | 10 | 10 | 40 | 80 | |
| P2-c3 raw | na | 18 | 38.5-43 | 1 n | 100 | 20 | 20 | 50 | 90 | |
| P2-c3 raw | na | 18 | 48.5-78 | 1 n | 100 | 10 | 10 | 40 | 90 | |
| P2-c3 combined | na | 18 | na | na | 100 | 10 | 10 | 40 | 90 | |
| P2-c4 raw | na | 3 | 95-102.5 | 4 n | 0 | 10 | 0 | 10 | 60 | |
| P2-c4 raw | na | 3 | 105-175.5 | 4 n | 0 | 0 | 0 | 10 | 60 | |
| P2-c4 raw | na | 3 | 175.5-198 | 5 n | 0 | 0 | 0 | 0 | 70 | |
| P2-c4 combined | na | 3 | na | na | 0 | 0 | 0 | 10 | 60 | |
| P2-c5 | na | 8 | 68-131.5 | 5 n | 40 | 0 | 0 | 0 | 0 | |
| P2-c6 | na | 22 | 17.5-20 | 3 n | 50 | 0 | 0 | 0 | 0 | |
| P3 | ||||||||||
| main | 13.625 | na | 13.625 | na | 100 | 100 | 100 | 100 | 100 | |
| P3-q1 | 608 | na | 608 | na | 0 | 10 | 0 | 15 | 85 | |
| P3-q2 | 343 | na | 343 | na | 0 | 55 | 95 | 55 | 10 | |
| P3-q3 | 390 | na | 390 | na | 0 | 0 | 65 | 0 | 0 | |
| P3-c1 raw | na | 3 | 1-7 | 4 n | 30 | 0 | 0 | 0 | 0 | |
| P3-c1 raw | na | 3 | 13-29 | 4 n | 20 | 0 | 0 | 0 | 0 | |
| P3-c1 raw | na | 3 | 29.5-33.5 | 4 n | 20 | 0 | 0 | 0 | 0 | |
| P3-c1 raw | na | 3 | 52.5-61 | 4 n | 30 | 0 | 0 | 0 | 0 | |
| P3-c1 combined | na | 3 | na | na | 20-30 | 0 | 0 | 0 | 0 | |
| P3-c2 | na | 3 | 7-13 | 4 n | 50 | 0 | 0 | 0 | 0 | |
| P3-c3 raw | na | 3 | 40.5-51.4 | 4 n | 30 | 10 | 0 | 10 | 10 | |
| P3-c3 raw | na | 3 | 66.5-75.5 | 4 n | 30 | 0 | 0 | 10 | 10 | |
| P3-c3 combined | na | 3 | na | na | 30 | ≤10 | 0 | 10 | 10 | |
| P3-c4 | na | 3 | 61-66.5 | 4 n | 70 | 70 | 90 | 50 | 20 | |
| P3-c5 | na | 16 | 53.5-56 | 2 n | 100 | 30 | 0 | 10 | 0 | |
| P3-c6 | na | 10 | 75-79 | 3 n | 10 | 0 | 60 | 0 | 0 | |
All noninteger CNA segments included are ≥2.5 Mbp, harbor maximal one noninteger allele, and have a minimum deviation of 30% from both contributing copy numbers in at least one sample (TU, S1, S2, X1, or X2). Breakpoints were rounded to the nearest 0.5 Mbp. Individual “raw” CNA segments were “combined” to CNA-based growth clones. Cellular fractions of raw CNA segments and CNA-based growth clones were rounded to the nearest 10%, cellular fractions of SNV-based growth clones to the neatest 5%. All experiments were performed independently with tumor material from three patients with CRC. c, CNA-based growth clone; na, not applicable; q, SNV-based growth clone.