Table 1.
Summary characteristics of retinoblastoma and peripheral blood DNA samples tested in this study CpGs counted as methylated includes any CpG with at least partial methylation (>10% per allele). (PB=peripheral blood). 1011 (homo c.1363C>T), 1012 (homo c.1814+1291T>G), 1013 (homo c.844G>T), 1014 (homo c.1215+1G>A), 1015 (c.2663+1G>A/c.-?1814+?del). *DNA methylation boundary location where CpGs are methylated up to and including boundary site with weak or no methylation downstream. Specimens PB=peripheral blood, T=tumour
| Sample ID | DNA sample origin |
13q14 locus zygosity |
RB1 promoter status |
CpGs (n=38) methylated (c.-1183-c.-259) |
CTCF CpGs (n=8) methylated (c.-240-c.-208) |
CP CpGs (n=7) methylated (c.-203-c.-170) |
CpGs (n=40) methylated (c.-167-c.+77) |
RB1 coding exon status |
DNA Methylation boundary CpGs* |
Heritable Status |
|---|---|---|---|---|---|---|---|---|---|---|
| M22508 | T | homo | c.-197_-196delinsTT | 21/38 | 0/8 | 0/8 | 0/40 | RB+/+ | c.-516 | germline |
| 3208 | T | homo | c.-198G>A | 21/38 | 0/8 | 0/8 | 0/40 | RB+/+ | c.-516 | germline |
| 3532 | T | homo | c.-198G>A | 23/38 | 0/8 | 0/8 | 0/40 | RB+/+ | c.-481 | germline |
| 1706 | T | homo | c.-212G>T | 36/38 | 7/8 | 4/7 | 4/40 | RB+/+ | c.-190 | germline |
| 1323 | PB | hetero | Pr+/+ | 7/38 | 0/8 | 0/8 | 0/40 | RB+/+ | c.-978 | normal |
| 1456 | PB | hetero | Pr+/+ | 7/38 | 0/8 | 0/8 | 0/40 | RB+/+ | c.-978 | normal |
| 1789 | PB | hetero | Pr+/+ | 7/38 | 0/8 | 0/8 | 0/40 | RB+/+ | c.-978 | normal |
| 1876 | PB | hetero | Pr+/+ | 7/38 | 0/8 | 0/8 | 0/40 | RB+/+ | c.-978 | normal |
| 1987 | PB | hetero | Pr+/+ | 7/38 | 0/8 | 0/8 | 0/40 | RB+/+ | c.-978 | normal |
| 1011 | T | Homo | Pr+/+ | 0/38 | 0/8 | 0/8 | 0/40 | RB−/- | c.-1365 | sporadic |
| 1012 | T | homo | Pr+/+ | 0/38 | 0/8 | 0/8 | 0/40 | RB−/- | c.-1365 | germline |
| 1013 | T | homo | Pr+/+ | 0/38 | 0/8 | 0/8 | 0/40 | RB−/- | c.-1365 | sporadic |
| 1014 | T | homo | Pr+/+ | 0/38 | 0/8 | 0/8 | 0/40 | RB−/- | c.-1365 | sporadic |
| 1015 | T | hetero | Pr+/+ | 0/38 | 0/8 | 0/8 | 0/40 | RB−/- | c.-1365 | sporadic |
| M22507 | PB | hetero | Pr+/c.-197_-196delinsTT | 7/38 | 0/8 | 0/8 | 0/40 | RB+/+ | c.-978 | germline |
| 3208 | PB | hetero | Pr+/c.-198G>A | 7/38 | 0/8 | 0/8 | 0/40 | RB+/+ | c.-978 | germline |
| 3532 | PB | hetero | Pr+/c.-198G>A | 7/38 | 0/8 | 0/8 | 0/40 | RB+/+ | c.-978 | germline |
| 1706 | PB | hetero | Pr+/c.-212G>T | 7/38 | 0/8 | 0/8 | 0/40 | RB+/+ | c.-978 | germline |
| 664 | PB | hetero | Pr+/c.-189G>T | 8/38 | 0/8 | 0/8 | 0/40 | RB+/+ | c.-978 | germline |
| 2149 | PB | hetero | Pr+/c.-197G>A | 10/38 | 0/8 | 0/8 | 0/40 | RB+/+ | c.-978 | germline |
| M5616 | PB | hetero | Pr+/c.-198G>A | 8/38 | 0/8 | 0/8 | 0/40 | RB+/+ | c.-978 | germline |
| M25851 | PB | hetero | Pr+/c.-239G>T | 8/38 | 0/8 | 0/8 | 0/40 | RB+/+ | c.-978 | germline |
| D16.31062 | PB | hetero | Pr+/c.-198G>T | 7/38 | 0/8 | 0/8 | 0/40 | RB+/+ | c.-978 | germline |
| 1342 | PB | hetero | Pr+/c.-206_-189del | 23/38 | 0/8 | 0/8 | 0/40 | RB+/+ | c.-481 | germline |
| 4220 | PB | hetero | Pr+/c.-212G>T | 7/38 | 0/8 | 0/8 | 0/40 | RB+/+ | c.-978 | germline |