Tandem repeats (TRs) occupy a significant portion of the human genome and are a source of polymorphisms due to variations in sizes and motif compositions. Some of these variations have been associated with various neuropathological disorders, highlighting the clinical importance of assessing the motif structure of TRs. Moreover, assessing the TR motif variation can offer valuable insights into evolutionary dynamics and population structure. Previously, characterizations of TRs were limited by short-read sequencing technology, which lacks the ability to accurately capture the full TR sequences. As long-read sequencing becomes more accessible and can capture the full complexity of TRs, there is now also a need for tools to characterize and analyze TRs using long-read data across multiple samples. In this study, we present MotifScope, a novel algorithm for the characterization and visualization of TRs based on a de novo k-mer approach for motif discovery. Comparative analysis against established tools reveals that MotifScope can identify a greater number of motifs and more accurately represent the underlying repeat sequences. Moreover, MotifScope has been specifically designed to enable motif composition comparisons across assemblies of different individuals, as well as across long-read sequencing reads within an individual, through combined motif discovery and sequence alignment. We showcase potential applications of MotifScope in diverse fields, including population genetics, clinical settings, and forensic analyses.@en

Background
The TMEM106B protein is critical for proper functioning of the endolysomal system, which is utilised by all cells to traffic and degrade molecular cargo. Genome-wide association studies identified a haplotype in the TMEM106B gene that is associated with increased risk for Alzheimer’s disease (AD), amyotrophic lateral sclerosis (ALS), and frontotemporal lobar degeneration with TAR DNA binding protein inclusions (FTLD-TDP). However, the causal variant that drives the association has thus far remained elusive.

Methods
We generated long-read whole-genome sequencing data of 256 individuals, primarily from Dutch descent. We characterized SNPs and larger structural variants in the TMEM106B locus using de novo genome assembly.

Results
We identified an insertion of an AluYb8 retrotransposon in the 3’ UTR of TMEM106B gene, that was in complete linkage with the TMEM106B risk-SNP. AluYb8 retrotransposons have the propensity to propagate through our genomes by utilising a ‘copy-paste’ mechanism, and once integrated can disrupt transcription and translation of nearby genes. However, propagation of retrotransposons can be suppressed by methylation of the insert and its surrounding regions. Indeed, we observed that the risk haplotype with the AluYb8 insertion, but not the protective haplotype, accumulated CpG islands over evolutionary time. Notably, we observed similar retrotransposon insertions in the 3’ UTR of TMEM106B orthologs in non-primate species. This suggests a survival advantage, which may be explained by recent findings that TMEM106B is an entry-receptor for specific viruses in lung-tissue, such that SINE-mediated downregulation of TMEM106B may limit viral infection-load across species.

Conclusions
We speculate that AluYb8-mediated downregulation of TMEM106B may be protective at younger ages in lung tissues, but that at advanced ages its downregulation in the brain may contribute to increased risk of neurodegenerative diseases. Furthermore, next to the supression of AluYb8 activation by DNA methylation, it may also be suppressed by TDP-43, in its role in post-translational RNA-processing. This leads us to further speculate that age-related demethylation and age-related dysregulation of TDP-43 may result in a negative feedback loop that ultimately reduces the endolysosomal activity in cells. We argue that such a mechanism would explain why increased age is among the strongest risk factors of neurodegenerative diseases.@en

Background
Genome-Wide Association Studies (GWAS) have identified 86 SNPs associated with Alzheimer’s disease (AD). GWAS-SNPs are markers of genetic variation in linkage disequilibrium (LD), which may drive the association with AD. One major class of genetic variation are Structural Variants (SVs), which can regulate transcription and translation of nearby genes. Here, we explored the interplay between large SVs (>50 bp) and AD-associated SNPs.

Method
We performed long-read whole-genome sequencing of 214 individuals representing the extreme ends of the cognitive spectrum: N = 93 AD patients (age 67.2∓8.5), and N = 121 cognitively healthy centenarians (age 101.2∓1.8). We identified SVs using sniffles2 genome-wide, further characterised them through (local) de novo assembly, and annotated tandem repeats (TR) and transposable elements (TE). Next, we estimated LD between SVs and 86 AD-associated GWAS-SNPs, Finally, we compared SNP frequencies and SV sizes between AD cases and centenarians using logistic regression models.

Result
Across all 214 individuals, we found >27,404 SVs (>50 bp), with a Minor Allele Frequency (MAF) ≥ 5%. Most SVs were TRs (63%), followed by TEs (37%). We found that 37 AD GWAS-SNPs paired with 90 SVs in low to strong LD (R2 > 0.1), 56 of which involved SNP-TR pairs (62%) and 34 involved SNP-TE pairs (38%). In six AD loci, the SVs associated more strongly with AD risk than the leading GWAS-SNP (p < 0.05). This includes ADAM10, CTSH, SLC2A4RG, CD2AP, SPI1, and IDUA, which were encompassed by complex haplotypes harbouring multiple TRs and TEs.

Conclusion
Our findings provide the first support for SVs as candidate-drivers of the association between respective GWAS loci with AD risk. Hence, SVs may lead to increased effect sizes.@en