Fig. 1: Overview of mammalian methylation array design process.
From: A mammalian methylation array for profiling methylation levels at conserved sequences
a Toy example of a multiple sequence alignment at a CpG site being considered by the CMAPS algorithm. The orange coloring highlights the CpG being targeted. Positions, where other species have alignment that matches the human sequence, are in dark blue; positions, where other species have alignment that does not match the human sequence, are in neon yellow; positions, where other species have no alignment, are in gray. b Flowchart detailing the selection of probes on the array by the CMAPS algorithm. A small fraction of probes designed were dropped during the manufacturing process. The number of selected CpGs in different sets were determined by biological considerations (e.g., sufficient numbers of Type I probes to capture CpG rich regions), statistical considerations (sufficient numbers of Type I probes for normalization methods), and costs of the resulting array (fewer than 40 K CpGs resulted in tolerable costs and Type II probes being more cost-effective than Type I probes).
