Table 1.
Recurrent Focal CNAs in Major SGCs
| SNP ID | Chromosome | Cytoband | Position | ACC (%) |
MEC (%) |
SDC (%) |
Gene | |||
|---|---|---|---|---|---|---|---|---|---|---|
| G | L | G | L | G | L | |||||
| 2131660 | 1 | p36.33 | 1145994 | 11 | 0 | 10 | 10 | 10 | 0 | TP73 |
| 1988527 | 6 | q27 | 168176083 | 16 | 16 | 0 | 20 | 5 | 5 | FGFR1OP |
| 1822252 | 7 | p22.1 | 5642226 | 5 | 0 | 5 | 15 | 10 | 5 | RNF216 |
| 1996220 | 9 | p21.3 | 21763222 | 0 | 5 | 5 | 10 | 0 | 10 | CDKN2A |
| 2191519 | 9 | p21.3 | 22115503 | 0 | 5 | 0 | 5 | 0 | 20 | CDKN2A |
| 2185617 | 10 | q11.22 | 47062478 | 11 | 5 | 10 | 15 | 10 | 0 | ANAX8 |
| 1822332 | 13 | q31.1 | 83036907 | 5 | 5 | 0 | 5 | 5 | 0 | SLITRK1 |
| 1942128 | 14 | q11.2 | 19417144 | 32 | 32 | 35 | 45 | 40 | 50 | APEX1 |
| 4204773 | 15 | q11.2 | 19163125 | 21 | 37 | 45 | 25 | 35 | 25 | POTEB |
| 1943770 | 15 | q11.2 | 19912458 | 32 | 32 | 40 | 25 | 45 | 20 | OR4N4 |
| 2249545 | 16 | p13.2 | 7092171 | 5 | 0 | 5 | 5 | 0 | 0 | A2BP1 |
| 1822964 | 16 | p11.2 | 34307201 | 16 | 5 | 5 | 25 | 10 | 0 | TP53TG3 |
| 2200283 | 17 | p13.3 | 285707 | 0 | 0 | 0 | 0 | 15 | 10 | RPH3AL |
| 2264661 | 17 | q12 | 31489488 | 11 | 11 | 5 | 10 | 20 | 10 | CCL3L1 |
| 2005155 | 17 | q12 | 34949761 | 0 | 0 | 0 | 0 | 25 | 0 | ERBB2 |
| 2029077 | 17 | q21.31 | 41602401 | 16 | 26 | 50 | 40 | 20 | 35 | MAPT |
| 4222078 | 18 | p11.32 | 1738722 | 5 | 5 | 5 | 0 | 5 | 5 | None |
| 4240882 | 20 | p12.1 | 14798101 | 0 | 5 | 0 | 5 | 0 | 5 | MACROD2 |
| 1919387 | 22 | q11.21 | 18703211 | 0 | 5 | 0 | 20 | 5 | 0 | GGT2 |
| 2192475 | 22 | q11.22 | 20825481 | 0 | 11 | 15 | 0 | 0 | 5 | VPREB1 |
| 4207761 | X | p22.33 | 2581725 | 26 | 0 | 10 | 0 | 15 | 0 | CD99 |
| 2170987 | X | q22.3 | 103915401 | 5 | 5 | 0 | 0 | 0 | 0 | IL1RAPL2 |
The genomic loci were identified from SNP probe positions in which the variance focal CNA profile peaked across samples. Loci with more than three significant focal CNAs are listed. A complete list can be found in Supplemental Table S2.
G, gain; L, loss.