Harriet Dashnow

The paper identifies immune cell type-specific gene expression regulated by tandem repeats using multi-omics data from large cohorts.

This paper benchmarks 7 TR genotyping tools using Nanopore long-read data, finding that no single tool is best across all metrics, and that sequence-level accuracy is crucial for clinical and population studies.

The paper introduces criTRia, a framework to evaluate TR locus-disease relationships, curating 65 loci and identifying inconsistencies in existing gene-level classifications.

This study identifies genomic factors influencing tandem repeat mutagenesis using long-read sequencing in a large family, finding that de novo mutations are more common at longer, uninterrupted, and heterozygous loci.

The paper develops TRoLR, a pipeline using long-read sequencing to detect and prioritize pathogenic tandem repeat expansions in diverse populations, identifying known and novel expansions with clinical relevance.

The paper introduces a computational model to quantify tandem repeat instability using long-read sequencing data and applies it to identify unstable alleles in 256 HPRC cell lines.

This study examines how interruptions at short tandem repeats (STRs) affect mutability and functional importance, finding that coding STRs with purifying selection have higher synonymous interruptions, while noncoding regulatory STRs have fewer interruptions.

This study uses long-read sequencing to reveal extensive somatic mosaicism in FMR1 repeats and methylation in FXTAS brain tissue, identifying expansions and contractions beyond traditional methods' resolution.

The paper creates a long-read benchmark for genetic variants using a large pedigree, improving variant calling performance and introducing new truth sets for tandem repeats and structural variants.

ATaRVa improves TR genotyping accuracy and efficiency using long-read sequencing, excels in low coverage datasets, and includes motif decomposition and methylation profiling.

The paper uses a four-generation family to systematically assess de novo mutations and recombination, finding high mutation rates and paternal bias, along with a detailed recombination map.

STRchive provides a dynamic resource for interpreting TR variants at disease loci, showing most TR diseases affect children and pathogenic genotypes exist in gnomAD without known disease prevalence.

The paper uses long-read sequencing on 100 samples from the 1000 Genomes Project to identify structural variants and improve understanding of human genetic variation.

The paper introduces a new TR catalog, TRExplorer v1.0, containing 4.86 million loci, designed for both short-read and long-read analyses and includes variation clusters identified using long-read HiFi data.

TRGT-denovo accurately detects de novo tandem repeat mutations in family trios, reducing false positives and improving precision compared to genotype-based methods.

The paper introduces TRGT, a tool for tandem repeat genotyping, and a database of 937,122 TRs across 100 genomes, achieving high concordance and detecting repeat expansions, methylation, and mosaicism.

STRling detects short tandem repeat expansions at known and novel loci using k-mer counting, achieving high sensitivity and base pair accuracy.

The paper establishes variant filtering guidelines for rare disease studies and estimates candidate variant yields for different inheritance modes using slivar software.

This paper introduces a pooled-parent exome sequencing strategy to prioritize de novo variants in genetic disease, showing it effectively filters variants while reducing costs.

STRetch detects pathogenic short tandem repeat expansions in whole genome sequencing data, revealing novel disease-causing STRs with low false discovery rate.

Cpipe is a variant detection pipeline designed for clinical genomics, offering fast, reproducible, and customizable analysis for diagnostic settings.