Improving and estimating Y chromosome loss in blood and brain tissues using high-throughput sequencing

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To our knowledge age-related loss of chromosome Y (LOY) in circulating leukocytes is the most common somatic genetic aberration. Many recent epidemiology studies have found robust associations between LOY in leukocytes and age-related diseases such as blood and solid tumour cancers, Alzheimer’s disease, and macular degeneration. Despite these associations, the prevalence and mechanisms of LOY in non-hematopoietic cell-types are not well characterized. In response, the need for bioinformatic methods to analyse Y chromosome ploidy across multiple genomic/transcriptomic datatypes has escalated. In the past, the Y chromosome was commonly removed from genomic analyses for several reasons including low gene count, haploidy, lack of biological interest and short-read mapping difficulties. Resultingly, methods for investigating chromosome Y specific trends using next-generation sequencing have suffered and require improvement. The main objective of this thesis was two-fold. First, to improve methods of Y chromosome aneuploidy detection using whole genome sequencing and single-nuclei RNA sequencing. Second, to use these improved methods to provide estimates of loss of Y (LOY) in brain tissue – which had not previously been established in humans. Using genomic characteristics such as mappability, GC content, and read alignment filtering I was able to improve LOY detection in both WGS and single-nuclei RNA-seq. Given high sequence similarity between the X and Y chromosome, strict mappability filtering improves, and smooths read depth estimates of Y chromosome aneuploidy. Using these methods we estimate that of the elderly male population represented in this cohort (median age = 87.5), LOY was found in 13.8% (11/123) of blood samples, 0% (0/159) in prefrontal cortex and 0% (0/78) cerebellum samples. Despite this, we found a significant association between age and reduced Y ploidy in the dorsolateral prefrontal cortex (R=-0.35, p=3.9x10-⁵), suggesting low-frequency LOY may be occurring in the cortex. In single-nuclei data from the dorsolateral prefrontal cortex we found 8.6% of cells lacked a Y chromosome. LOY was enriched in the glial cells, and particularly the microglia where 33% of male cells were affected. Although further evidence is required, LOY within the frontal cortex (and specifically the microglia) may represent an understudied factor in cognitive decline and neurodegeneration.

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