Egor Dolzhenko

Tandem repeat variation shapes immune cell type-specific gene expression

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

LRP2: A proteogenomics pipeline for long-read informed protein isoform analysis and discovery

LRP2 is a proteogenomics pipeline that integrates long-read RNA sequencing and mass spectrometry to detect novel protein isoforms and improve their translation inference.

Isocall enables scalable transcript identification from long-read RNA-sequencing data

Isocall is a scalable method for joint transcript identification from long-read RNA-seq data, showing high precision and handling large datasets efficiently.

Hunting for microsatellite instability in long-read data with Owl

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

Enrichment of Repeat Expansions in FGF14 Associated with Amyotrophic Lateral Sclerosis

The paper identifies FGF14 GAA repeat expansions in ALS patients, showing enrichment compared to controls and suggesting a broader pathogenic role in motor neuron disease.

Aardvark: Sifting through differences in a mound of variants

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

A family portrait of the genomic factors shaping tandem repeat mutagenesis

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.

Resolution of the D4Z4 repeat responsible for facioscapulohumeral muscular dystrophy with HiFi sequencing

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.

A computational model for quantifying instability of tandem repeats across the genome

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.

A Tandem Repeat Atlas for the Genome of Inbred Mouse Strains: A Genetic Variation Resource

The paper creates a tandem repeat atlas for 39 inbred mouse strains using long-read sequencing, showing TRs are abundant but differ from human TRs in expansion and transposable element association.

The Platinum Pedigree: A long-read benchmark for genetic variants

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.

A familial, telomere-to-telomere reference for human de novo mutation and recombination from a four-generation pedigree

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: a dynamic resource detailing population-level and locus-specific insights at tandem repeat disease loci

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.

Genome-wide profiling of highly similar paralogous genes using HiFi sequencing

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

HiFi long-read genomes for difficult-to-detect clinically relevant variants

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.

A Murine Database of Structural Variants Enables the Genetic Architecture of a Spontaneous Murine Lymphoma to be Characterized

The paper creates a database of structural variants in 40 inbred mouse strains and identifies an SV linked to lymphoma susceptibility in SJL mice.

Population-scale variability at short tandem repeat loci reveals pathogenicity signature

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.

Huntington's disease phenocopy syndromes revisited: a clinical comparison and next-generation sequencing exploration

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.

Defining a tandem repeat catalog and variation clusters for genome-wide analyses

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: accurate detection of de novo tandem repeat mutations

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

A common flanking variant is associated with enhanced meiotic stability of the FGF14-SCA27B locus

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

RExPRT: a machine learning tool to predict pathogenicity of tandem repeat loci

RExPRT predicts pathogenicity of tandem repeat expansions with high precision, identifying ~30,000 likely pathogenic TRs in the reference genome.

Benchmarking of small and large variants across tandem repeats

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

A deep population reference panel of tandem repeat variation

The paper creates a deep population reference panel of tandem repeat variation using whole genome sequencing and develops a method to genotype over 1.7 million TR loci, identifying novel eQTL signals and a phased haplotype panel for imputation.

Resolving the unsolved: Comprehensive assessment of tandem repeats at scale

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.

A phenome-wide association study of methylated GC-rich repeats identifies a GCC repeat expansion in AFF3 as a significant cause of intellectual disability

The paper identifies a GCC repeat expansion in AFF3 as a significant cause of intellectual disability through a phenome-wide association study using DNA methylation profiling and UK Biobank data.

An intronic GAA repeat expansion in FGF14 causes autosomal dominant adult-onset ataxia (SCA50, ATX-FGF14)

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.

A genome-wide atlas of recurrent repeat expansions in human cancer

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

REViewer: Haplotype-resolved visualization of read alignments in and around tandem repeats

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

STRipy: a graphical application for enhanced genotyping of pathogenic short tandem repeats in sequencing data

STRipy simplifies STR genotyping in HTS data by providing a user-friendly tool that targets all known disease-causing STRs and handles long alleles.