Nature Search

Analysis and benchmarking of small and large genomic variants across tandem repeats

A truth-set catalog of human tandem repeats allows benchmarking of variant analysis tools.

Adam C. English
Egor Dolzhenko
Fritz J. Sedlazeck
Research26 Apr 2024
Nature Biotechnology

Volume: 43, P: 431-442
Genome-wide profiling of highly similar paralogous genes using HiFi sequencing

Here, the authors present Paraphase, a HiFi-based informatics method that resolves highly similar genes located in segmental duplications. They apply Paraphase to 316 paralogous genes and summarize extensive genetic diversity across populations.

Xiao Chen
Daniel Baker
Michael A. Eberle
ResearchOpen Access08 Mar 2025
Nature Communications

Volume: 16, P: 1-13
Human de novo mutation rates from a four-generation pedigree reference

Analysis of more than 95% of each diploid human genome of a four-generation, twenty-eight-member family using five complementary short-read and long-read sequencing technologies provides a truth set to understand the most fundamental processes underlying human genetic variation.

David Porubsky
Harriet Dashnow
Evan E. Eichler
ResearchOpen Access23 Apr 2025
Nature

P: 1-10
Characterization and visualization of tandem repeats at genome scale

A set of tools maps tandem repeats across complete genomes.

Egor Dolzhenko
Adam English
Michael A. Eberle
Research02 Jan 2024
Nature Biotechnology

Volume: 42, P: 1606-1614
A common flanking variant is associated with enhanced stability of the FGF14-SCA27B repeat locus

Analysis of the FGF14-SCA27B repeat locus identifies a common 5′-flanking insertion that represents the major allele, is present exclusively on nonpathogenic alleles, enhances repeat stability and increases chromatin accessibility.

David Pellerin
Giulia F. Del Gobbo
Matt C. Danzi
Research27 Jun 2024
Nature Genetics

Volume: 56, P: 1366-1370
A phenome-wide association study of methylated GC-rich repeats identifies a GCC repeat expansion in AFF3 associated with intellectual disability

Phenome-wide analysis in the UK Biobank identifies GC-rich tandem repeat expansions associated with a range of traits, including a GCC expansion in AFF3 contributing to intellectual disability.

Bharati Jadhav
Paras Garg
Andrew J. Sharp
Research23 Sept 2024
Nature Genetics

Volume: 56, P: 2322-2332
Repeat expansions confer WRN dependence in microsatellite-unstable cancers

In cells with microsatellite instability, expanded TA-dinucleotide repeats form cruciform structures that stall replication forks and cause chromosome shattering in the absence of the WRN helicase.

Niek van Wietmarschen
Sriram Sridharan
André Nussenzweig
Research30 Sept 2020
Nature

Volume: 586, P: 292-298
Recurrent repeat expansions in human cancer genomes

An atlas explores the landscape of recurrent repeat expansions in human cancer genomes.

Graham S. Erwin
Gamze Gürsoy
Michael P. Snyder
ResearchOpen Access14 Dec 2022
Nature

Volume: 613, P: 96-102
A deep population reference panel of tandem repeat variation

Tandem repeats (TRs) comprise some of the most polymorphic regions of the human genome but are difficult to study. Here, the authors develop an ensemble-based genotyping method and characterize 1.7 million TRs across 3,550 humans from diverse populations.

Helyaneh Ziaei Jam
Yang Li
Melissa Gymrek
ResearchOpen Access23 Oct 2023
Nature Communications

Volume: 14, P: 1-15
Common and rare variant association analyses in amyotrophic lateral sclerosis identify 15 risk loci with distinct genetic architectures and neuron-specific biology

A cross-ancestry genome-wide association meta-analysis of amyotrophic lateral sclerosis (ALS) including 29,612 patients with ALS and 122,656 controls identifies 15 risk loci with distinct genetic architectures and neuron-specific biology.

Wouter van Rheenen
Rick A. A. van der Spek
Jan H. Veldink
ResearchOpen Access06 Dec 2021
Nature Genetics

Volume: 53, P: 1636-1648
Genome-wide detection of tandem DNA repeats that are expanded in autism

Genome-wide analysis of tandem DNA repeats in the genomes of individuals with autism spectrum disorder and control participants reveals a strong contribution of tandem repeat expansions to the genetic aetiology and phenotypic complexity of autism spectrum disorder.

Brett Trost
Worrawat Engchuan
Ryan K. C. Yuen
Research27 Jul 2020
Nature

Volume: 586, P: 80-86
Large scale in silico characterization of repeat expansion variation in human genomes

Sarah Fazal
Matt C. Danzi
Stephan Zuchner
ResearchOpen Access08 Sept 2020
Scientific Data

Volume: 7, P: 1-14
Sequence composition changes in short tandem repeats: heterogeneity, detection, mechanisms and clinical implications

This Review highlights the diversity in sequence composition of disease-related short tandem repeats. The authors discuss how to detect non-canonical motifs in repeat sequences from sequencing data and review the molecular and clinical consequences of sequence composition changes.

Indhu-Shree Rajan-Babu
Egor Dolzhenko
Jan M. Friedman
Reviews11 Mar 2024
Nature Reviews Genetics

Volume: 25, P: 476-499
Characterizing a complex CT-rich haplotype in intron 4 of SNCA using large-scale targeted amplicon long-read sequencing

Pilar Alvarez Jerez
Kensuke Daida
Kimberley J. Billingsley
ResearchOpen Access26 Jul 2024
npj Parkinson's Disease

Volume: 10, P: 1-8
Author Correction: Common and rare variant association analyses in amyotrophic lateral sclerosis identify 15 risk loci with distinct genetic architectures and neuron-specific biology

Wouter van Rheenen
Rick A. A. van der Spek
Jan H. Veldink
Amendments and CorrectionsOpen Access31 Jan 2022
Nature Genetics

Volume: 54, P: 361
Copy-number variants in clinical genome sequencing: deployment and interpretation for rare and undiagnosed disease

Andrew M. Gross
Subramanian S. Ajay
Ryan J. Taft
ResearchOpen Access08 Oct 2018
Genetics in Medicine

Volume: 21, P: 1121-1130

Search

Analysis and benchmarking of small and large genomic variants across tandem repeats

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

Human de novo mutation rates from a four-generation pedigree reference

Characterization and visualization of tandem repeats at genome scale

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

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

Repeat expansions confer WRN dependence in microsatellite-unstable cancers

Recurrent repeat expansions in human cancer genomes

A deep population reference panel of tandem repeat variation

Common and rare variant association analyses in amyotrophic lateral sclerosis identify 15 risk loci with distinct genetic architectures and neuron-specific biology

Genome-wide detection of tandem DNA repeats that are expanded in autism

Large scale in silico characterization of repeat expansion variation in human genomes

Sequence composition changes in short tandem repeats: heterogeneity, detection, mechanisms and clinical implications

Characterizing a complex CT-rich haplotype in intron 4 of SNCA using large-scale targeted amplicon long-read sequencing

Author Correction: Common and rare variant association analyses in amyotrophic lateral sclerosis identify 15 risk loci with distinct genetic architectures and neuron-specific biology

Copy-number variants in clinical genome sequencing: deployment and interpretation for rare and undiagnosed disease

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