Extended Data Table 2. Identified somatic structural variations in ASCs.
| Copy Number Variants | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Sample | Tissue | Chr | Start | Stop | Size | Type | No. genes | Fragile site | Microhomology | Genes at breakpoint | LINE/SINE |
| ASC 14-a | Liver | 3 | 94,491,729 | 95,651,811 | 1,160,082 | gain | 5 | - | 5 bp | -|- | L1MC1|- |
| ASC 14-a | Liver | 3 | 111,726,406 | 113,471,637 | 1,745,231 | gain | 46 | - | 2 bp | TAGLN3|ATP6V1A | L1MC1|L1M5 |
| ASC 16-a | Liver | 9 | 50,763,759 | 141,213,431 | 90,449,672 | gain | 1,472 | - | NA | NA | NA |
| ASC 18-e | Liver | 7 | 132,751,706 | 133,009,202 | 257,496 | gain | 2 | - | 0 bp | CHCHD3|EXOC4 | MIR|L1PA6 |
| ASC 18-d | Liver | 5 | 59,125,105 | 59,718,364 | 593,259 | loss | 1 | - | 0 bp | PDE4D|PDE4D | -|L1PA6 |
| ASC 8-a | Small intestine | 5 | 3,815,936 | 3,908,819 | 92,883 | loss | 0 | - | 2 bp | -|- | -|- |
| ASC 11-a | Small intestine | 2 | 205,420,067 | 205,511,877 | 91,810 | loss | 1 | FRA2I | 1 bp | PARD3B|PARD3B | AluSx|L1ME3B |
| ASC 13-a | Small intestine | 11 | 63,974,352 | 66,222,668 | 2,248,316 | loss | 163 | - | 3 bp | FERMT3|- | -|L1M4b |
| ASC 13-b | Small intestine | 1 | 5,878,566 | 6,321,750 | 443,184 | loss | 13 | FRA1A | 1 bp | -|- | THE1B|- |
| ASC 1-c | Colon | 3 | 60,700,662 | 61,199,328 | 498,666 | loss | 4 | FRA3B | 1 bp | FHIT|FHIT | L1PA3|L1PA3 |
| ASC 3-c | Colon | 13 | 0 | 115,169,878 | 115,169,878 | gain | 1,217 | - | NA | NA | NA |
| ASC 4-b&e | Colon | 14 | 102,805,595 | 104,172,376 | 1,366,781 | loss | 57 | - | NA | NA | NA |
| ASC 4-b&e | Colon | 17 | 2,429,169 | 2,572,747 | 143,578 | loss | 5 | - | CTTG ins | -|PAFAH1B1 | AluJo|AluSq |
| ASC 4-b&e | Colon | 17 | 2,634,433 | 2,927,007 | 292,574 | loss | 4 | - | NA | NA | NA |
| Unbalanced Translocations | |||||||||||
| Sample | Tissue | Chr (1) | Position (1) | Chr (2) | Position (2) | Type | No. genes | Fragile site | Microhomology | Genes at breakpoint | LINE/SINE |
| ASC 4-b&e | Colon | 14 | 102,805,595 | 17 | 2,634,145 | translocation | NA | - | 4 bp | ZNF839|- | -|- |
| ASC 4-b&e | Colon | 14 | 104,172,376 | 18 | 18,518,987 | translocation | NA | - | 0 bp | XRCC3|- | -|ALR Alpha |
| ASC 4-b&e | Colon | 17 | 2,927,007 | 18 | 18,518,987 | translocation | NA | - | 0 bp | RAF1GAP2|- | L1PA8|ALR Alpha |
No. genes, number of genes overlapping the event; fragile site, common fragile sites overlapping the event; microhomology, number of bases of microhomology observed at breakpoints; genes at breakpoint, gene bodies affected by the breakpoint; LINE/SINE elements, observed elements within 100 bp of the breakpoint.