Neurodegenerative diseases represent a large group of neurological disorders with heterogeneous clinical and pathological presentations—often affecting a specific subset of cells in particular anatomical regions. These complex and often overlapping features presents a challenge in identifying the cause behind the vulnerability of these cell populations and anatomical area. However, with recent advancements in omics technology, the complexity of the mammalian brain is being rapidly teased out. Two of these technologies offer a unique perspective and deeper resolution to study the heterogeneity in the brain: long-read sequencing and single-cell microfluidics. In this dissertation, I demonstrate the use of one or both technologies to further characterize the heterogeneity in human brain and its relationship to various neurodegenerative diseases. My initial work identifies a novel genomic structural variant in the gene SNCA, a causal gene in Parkinson’s disease (PD) and other synucleinopathies. These intron-less sequences are known as gencDNAs (genomic cDNA) and are found in human cortical neurons of both PD and age-matched controls in a mosaic manner. Furthermore, it is unveiled that a small subset of copies contains point mutations in loci reported to cause monogenic PD, if mutated in its native counterpart, when using long-read amplicon sequencing. Though much is unknown about of SNCA gencDNAs, it is hypothesized to be created due to a reverse transcription event and re-inserted back into the genome. My subsequent work combines both single-cell RNA sequencing and long-read sequencing to examine and compare the transcriptome of various neurodegenerative diseases in the frontal cortex at a single cell resolution. Despite being a synucleinopathy, dementia with Lewy bodies (DLB) has more transcriptomic similarities to Alzheimer’s disease (AD) than with PD. While profiling the isoforms of selected genes within these diseases, a vast number of novel isoforms are also identified, with some specific to a particular cell type, such as NRGN. Finally, some major isoform switching is observed in at a cell type resolution, even in genes that were not differentially expressed in our short-read RNA-seq data, such as BIN1 in DLB oligodendrocyte and CLU in AD and DLB excitatory neurons. This dissertation further illuminates the heterogeneity in the human brain at a genomic and transcriptomic layer in the context of various neurodegeneration using long-read sequencing and single cell microfluidics.