Haplotype analysis. The sequenced amplicons were interrogated using the available SNPs (UCSC database). When a heterozygous SNP was observed, sequence reads were separated accordingly to the SNP genotype and unsupervised cluster analysis performed on the allelic CpG methylation pattern. Allelic DNA methylation profiles at the MEG3-DMR: the diagnostic (A) and complete remission (B) stages of a patient with APL; (C) healthy donor. D) Allelic DNA-methylation profile at the IG-DMR, healthy donor. Each column represents a CpG site and each row the methylation pattern of a single sequence read. Blue, methylated; yellow not methylated.