Kimberley Billingsley from the National Institutes of Health in the USA spoke at London Calling 2025 on “Decoding the genomics of neurodegenerative diseases with large-scale, long-read sequencing.” This session was an update from the CARD Applied Neurogenomics group. Billingsley divided the session into three topics: long-read sequencing, methylation, and RNA sequencing. Billingsley emphasized that current methods help resolve genetic variants and address gaps in neurodegenerative disease datasets. The research team has worked on establishing workflows. They use standardized protocols and the Hamilton NGS Star before sequencing on a PromethION 48. Basecalling with Dorado (SUP), QC, and a customized pipeline are run on the NIH HPC. Data analyses are performed using specialized scripts. By the end of 2025, the team will complete sequencing 3,000 human samples. Billingsley spoke about allele-specific methylation detection that can reveal haplotype-specific methylation. An example is the APOE locus. The team compared methylation data from long-read sequencing and methylation arrays. The ONT WGS frontal cortex control brains (n=332) and other cohort datasets were used. The research team created the ASM-LR tool to detect allele-specific DNA methylation data. These results identified novel phased QTL missed by unphased averaging. Billingsley explained that this tool and approach can help create better models. The long-read methylation data and GenoML were used to improve epigenetic clock determinations from diverse populations. Last, Billingsley spoke about optimizing the cDNA protocol for post-mortem brain tissue to yield high-quality long-read RNA sequencing data. The cDNA protocol was automated on the cDNA prep onto the Hamilton NGS Star. The approach can be scaled to prepare and sequence brain samples. Billingsley mentioned updates to the cDNA/RNA sequencing protocols that would be released by ONT.
