DNA bioinformatic search and methylation analysis by qMSP
It's likely that they accomplished this by using the UCSC Table Browser to:


Find the loci of the two isoforms you mention
Finding CpG islands (Group = Regulation, Track = CpG Islands) near those transcription start sites
Design primers using Applied Biosystem's software


Alternatively, they list the exact primers used in Table 1.

They don't detail exactly how they did it, so if you have specific questions it might be worth it to email the corresponding author