Table 1. Information on the CpG loci interrogated for each gene.
| Gene name | Chromo-somal location | Bona fide CpG island | # of Infinium probes and location relative to CpG island | Amplification and Sequencing Primers / Infinium Probes | CpGs read out of total number of CpGs in amplicon |
|---|---|---|---|---|---|
|
PBRM1 |
3p21 |
Yes |
1; outside |
F – TGGTGGTTGTAGTAATTTTTAGA R - GAGGGGTAAGGGAGGTGAG |
23/29 |
|
KDM6A |
Xp11 |
Yes |
1; outside |
F – GATAAAGTTGGTGTGTTGGTTT R – TAGTTTGATAGTRGAGGAGAG |
21/28 |
|
SETD2 |
3p21 |
Yes |
2; outside |
F – GGTTTATTGTTTYGGAGAGTTAT R - TGAGGGTGAGAGGGAGAGA |
|
|
BAP1 |
3p21 |
Yes |
1; outside |
assay #ADS1756FS1, EpigenDX |
7/7 |
| |
|
|
1; within |
F- GATGAATAAGGGTTGGTTGGAGT R – GTTTGTTTGATTATTATTTTTTTTTTTTG PSQ - TGGTTGGAGTTGGAGA |
3/6 |
|
KDM5C |
Xp11 |
Yes |
1; within |
cg04927982_CGTGCACCGCCGGTCCATCCGGAAAGACGATCCGGCAAACTAATTACAAT |
6 |
|
ARID1A |
1p36 |
Yes |
2; within |
cg11856093_CAGGCCAGGGCTTTGTTGTCCGCCATGTTGTTGGTGGAAGACGGCGGCCG |
4 |
| |
|
|
|
cg17385674_ACCCTCTTTGCAAGCCCGAAAGAATGACTGATCATTGTTCAGACGATTCG |
3 |
| MLL2 | 12q13 | No | 1 | cg13007988_CGGGGAGACCTGTTGGTGCCAAGAAAGAGATCTATATGCCTACTAAGTCT | 1 |
Gene name according to NCBI; chromosomal location according to NCBI; CpG island according to Takai and Jones criteria by CpG Island Searcher; number of probes in Infinium humanmethylation27 beadchip and position of probe relative to Takai and Jones CpG island; sequence of primers used and Infinium probes examined in our study, Y and R indicate degenerate T or C in forward and reverse primer respectively, primer sequences for the most 5′ area of BAP1 are proprietary and available as a commercial kit (Epigen DX, Hopkinton, MA, USA); number of CpG loci read from total number of CpG loci in amplicon due to loss of sequence read at the 5′ end of the bisulfite sequencing amplicon or the 3′ end of the pyrosequencing amplicon.