Table 2.
Example of SNV detection results within the MYC CpG island (Table 1) for 2 COAD patients after being processed as indicated in Figure 1. Y, Yes; N, No. For the complete set for this report, see the SOM file entitled, “Samy et al. SOM Fig. 1D, Preliminary Excel Files.” rs3824120 is further characterized in Table 3 rs4645948 and rs4645955 did not meet the standard of the alternate allele appearing at least 12 times in one of the cancer datasets.
| TCGA-A6-6141 | ||||||||
|---|---|---|---|---|---|---|---|---|
| Chromosome Position | Variant (second nucleotide) | Reads Matching Reference | Reads Matching Variant | Context | Originally CpG? | Creates a CpG? | Eliminates a CpG? | SNP |
| 8:128747953 | G/T | 23 | 24 | CGG | Y | N | Y | rs3824120 |
| 8:128748494 | C/G | 18 | 24 | TCC | N | N | N | N |
| 8:128748498 | C/T | 23 | 19 | GCG | Y | N | Y | rs4645948 |
| 8:128749023 | G/T | 25 | 30 | GGT | N | N | N | N |
| 8:128749923 | G/A | 5 | 9 | CGG | Y | N | Y | rs4645955 |
| 8:128749934 | T/G | 13 | 4 | GTG | N | N | N | N |
| 8:128750139 | T/A | 19 | 17 | TTT | N | N | N | N |
| TCGA-CA-6718 | ||||||||
| Chromosome Position | Variant (second nucleotide) | Reads Matching Reference | Reads Matching Variant | Context | Originally CpG? | Creates a CpG? | Destroys a CpG? | SNP |
| 8:128748680 | C/T | 41 | 36 | GCC | N | N | N | N |
| 8:128748977 | G/T | 58 | 22 | TGA | N | N | N | N |