Wouter De Coster from the VIB Center for Molecular Neurology in Belgium presented a session for the Oxford Nanopore Community Meeting 2020 entitled “Allele-specific methylation in human brains.” De Coster is a bioinformatician and started with a quote from Sydney Brenner: “Progress in science depends on new techniques, new discoveries and new ideas, probably in that order.” I appreciate that quote! De Coster’s project focuses on frontotemporal dementia that often causes language or behavioral impairment with an onset typically after sixty-five years. With PromethION sequencing, they found a large inversion in one gene of interest. They conducted ONT PromethION genome sequencing for numerous individuals and controls. After optimizing, they obtain 80 Gbases and 25 coverage. They optimized their shearing strategy because, De Coster noted, there is a tradeoff between yield, shearing, and read length. Most of their sequences are ~20 kb. Structural variants were detected along with modification and parental haplotypes. The most common nucleotide modifications include 5-methylcytosine. De Coster also called for better models for 5hmC detection. To find haplotype-specific methylation, they begin by phasing reads into haplotypes, determine methylation per CpG per reads, count methylated and unmethylated CpGs per locus… De Coster developed Methplotlib to browse for nucleotide modifications and uses nanocompore, nanopolish, and bedgraph. The plots are color coded by the probability of having a likely modification. The visualization tools seem really useful, and De Coster called for community input. This tools may be useful for numerous samples, maybe beyond human genomes.
