Michael A. Eberle

Owl quantifies microsatellite instability from long-read data, identifying MSI-high genomes and motif-specific patterns in cancer samples.

Aardvark benchmarks genomic variant calling accuracy by comparing haplotype sequences with a basepair score, supporting multiple variant types and outperforming hap.py.

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 introduces Kivvi, a tool to genotype D4Z4 repeats using HiFi sequencing, enabling accurate detection of FSHD-related alleles and revealing genetic diversity across populations.

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.

Portello improves variant calling accuracy in rare-disease whole genome sequencing by aligning de novo assembly contigs to a reference genome, reducing basecall errors and enabling better interpretation of complex loci.

SVTopo visualizes complex structural variants using high-accuracy long reads, providing clear figures to understand multi-breakpoint events in human genomes.

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.

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.

Sawfish improves long-read structural variant calling accuracy by modeling local haplotypes, outperforming existing tools in benchmark tests and joint-genotyping analyses.

The paper develops Paraphase, a HiFi-based method to resolve highly similar paralogous genes, revealing genetic diversity and de novo events in segmental duplications.

The paper demonstrates that HiFi long-read sequencing can detect 93% of clinically relevant variants challenging to identify with short-read sequencing, using 30x coverage and showing potential for cost-effective diagnostic implementation.

The paper uses long-read sequencing data to analyze STR variability across 2,645 individuals, identifying disease-associated STR loci with elevated allelic variability and introducing the PLVI metric.

StarPhase diplotypes 21 pharmacogenes using long-read sequencing with high accuracy, updating 26.2% of existing diplotypes and highlighting gaps in pharmacogenomic databases.

The paper introduces a CN caller for KIV-2 repeats using short reads, showing high accuracy and demonstrating its correlation with Lp(a) levels and population-specific CN distributions.

This study estimates the prevalence of HD phenocopy syndromes, finds clinical distinctions are difficult, and uses whole-genome sequencing to identify one ATXN1 expansion in a subcohort.

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.

This study evaluates the diagnostic yield of long-read sequencing in pediatric sensorineural hearing loss, finding it detects structural variants missed by short-read sequencing.

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 identifies a common flanking variant linked to increased meiotic stability at the FGF14-SCA27B repeat locus.

The paper introduces a targeted sequencing framework, TADGP, that accurately calls variants in complex medically relevant genes at lower cost than HiFi-WGS, enabling scalable analysis of dark genomic regions.

The paper develops a whole genome sequencing method to detect RFC1 repeat expansions, improving diagnostic rates and simplifying the workflow for cerebellar ataxia diagnosis.

The paper benchmarks small and large variants in tandem repeats across 86 samples, creating a benchmark dataset and comparison method for TR variant calling.

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.

HiPhase jointly phases small and structural variants from HiFi sequencing, achieving improved phase block NG50 and gene phasing rates.

The paper develops Paraphase, a method using long-read sequencing to accurately determine SMN1 and SMN2 haplotypes and copy numbers, improving silent carrier detection in spinal muscular atrophy.

This study identifies a novel intronic GAA repeat expansion in FGF14 as a cause of autosomal dominant adult-onset ataxia, with (GAA)>335 being fully penetrant and (GAA)>250 likely pathogenic.

The paper identifies recurrent repeat expansions in cancer genomes, showing their association with gene regulation and demonstrating their therapeutic targeting potential.

REViewer visualizes sequencing data around long repeat expansions by reconstructing haplotypes and aligning reads, improving the assessment of repeat genotype calls and detecting interruptions.

The paper presents two methods to accurately detect GBA variants and reciprocal recombinants, showing higher GBA variant frequency in Lewy body dementia compared to Parkinson's disease.