| 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 | |
| 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.