PT - JOURNAL ARTICLE AU - Adriana Arneson AU - Amin Haghani AU - Michael J. Thompson AU - Matteo Pellegrini AU - Soo Bin Kwon AU - Ha Vu AU - Caesar Z. Li AU - Ake T. Lu AU - Bret Barnes AU - Kasper D. Hansen AU - Wanding Zhou AU - Charles E. Breeze AU - Jason Ernst AU - Steve Horvath TI - A mammalian methylation array for profiling methylation levels at conserved sequences AID - 10.1101/2021.01.07.425637 DP - 2021 Jan 01 TA - bioRxiv PG - 2021.01.07.425637 4099 - http://biorxiv.org/content/early/2021/01/08/2021.01.07.425637.short 4100 - http://biorxiv.org/content/early/2021/01/08/2021.01.07.425637.full AB - Infinium methylation arrays are widely used to robustly measure methylation of DNA in humans. However, such arrays are not available for the vast majority of non-human mammals. Moreover, even if species-specific arrays were available, probe differences between them would confound cross-species comparisons. To address these challenges, we developed the Mammalian Methylation Array, a single custom Infinium array that measures cytosine methylation levels of over 35 thousand CpG sites that are well conserved across species within the mammalian class. By design, the probes on the array tolerate cross-species mutations. To design the array, we developed the Conserved Methylation Array Probe Selector (CMAPS) algorithm, which takes as input a multi-species sequence alignment and probe design constraints. A greedy search algorithm was used to identify oligonucleotide sequences (probes) with high coverage across different mammalian species. We annotate the probes on the array with respect to genes in 159 different species and provide details on the sequence context including CpG island status and chromatin states. Our calibration experiments demonstrate the high fidelity of this array in humans, rats, and mice. The mammalian methylation array has several strengths: it applies to all mammalian species even those that have not yet been sequenced, it provides deep coverage of specific cytosines facilitating the development of highly robust epigenetic biomarkers, and it covers highly conserved CpGs which greatly increases the probability that biological insights gained in one species will readily translate to others. The mammalian methylation array is expected to find many applications in preclinical studies, comparative biology, and epigenetic studies of aging and development.Competing Interest StatementThe Regents of the University of California is the sole owner of a provisional patent application directed at this invention for which AA, JE and SH are named inventors. SH is a founder of the non-profit Epigenetic Clock Development Foundation, which plans to license several patents from his employer UC Regents, and distributes the mammalian methylation array. Bret Barnes is an employee for Illumina Inc which manufactures the mammalian methylation array. The other authors declare no conflicts of interest.