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

AC English, E Dolzhenko, H Ziaei Jam… - Nature …, 2024 - nature.com
Tandem repeats (TRs) are highly polymorphic in the human genome, have thousands of
associated molecular traits and are linked to over 60 disease phenotypes. However, they …

Benchmarking of small and large variants across tandem repeats

A English, E Dolzhenko, H Ziaei-Jam, ND Olson… - bioRxiv, 2023 - biorxiv.org
Tandem repeats (TRs) are highly polymorphic in the human genome, have thousands of
associated molecular traits, and are linked to over 60 disease phenotypes. However, their …

Characterization and visualization of tandem repeats at genome scale

E Dolzhenko, A English, H Dashnow… - Nature …, 2024 - nature.com
Tandem repeat (TR) variation is associated with gene expression changes and numerous
rare monogenic diseases. Although long-read sequencing provides accurate full-length …

A deep population reference panel of tandem repeat variation

H Ziaei Jam, Y Li, R DeVito, N Mousavi, N Ma… - Nature …, 2023 - nature.com
Tandem repeats (TRs) represent one of the largest sources of genetic variation in humans
and are implicated in a range of phenotypes. Here we present a deep characterization of TR …

A landscape of complex tandem repeats within individual human genomes

K Ichikawa, R Kawahara, T Asano… - Nature …, 2023 - nature.com
Markedly expanded tandem repeats (TRs) have been correlated with~ 60 diseases. TR
diversity has been considered a clue toward understanding missing heritability. However …

TRTools: a toolkit for genome-wide analysis of tandem repeats

N Mousavi, J Margoliash, N Pusarla, S Saini… - …, 2021 - academic.oup.com
A rich set of tools have recently been developed for performing genome-wide genotyping of
tandem repeats (TRs). However, standardized tools for downstream analysis of these results …

Resolving the unsolved: comprehensive assessment of tandem repeats at scale

E Dolzhenko, A English, H Dashnow… - bioRxiv, 2023 - biorxiv.org
Tandem repeat (TR) variation is associated with gene expression changes and over 50 rare
monogenic diseases. Recent advances in sequencing have enabled accurate, long reads …

A genome-wide spectrum of tandem repeat expansions in 338,963 humans

Y Cui, W Ye, JS Li, JJ Li, E Vilain, T Sallam, W Li - Cell, 2024 - cell.com
Summary The Genome Aggregation Database (gnomAD), widely recognized as the gold-
standard reference map of human genetic variation, has largely overlooked tandem repeat …

Detecting and annotating genetic variations using the HugeSeq pipeline

HYK Lam, C Pan, MJ Clark, P Lacroute, R Chen… - Nature …, 2012 - nature.com
indexed for rapid and random access using SAMtools. Because most variant detections are
intrachromosomal, the detection process can be carried out on each chromosomal BAM …

Statistical approaches to detecting and analyzing tandem repeats in genomic sequences

M Anisimova, J Pečerska, E Schaper - Frontiers in bioengineering …, 2015 - frontiersin.org
Tandem repeats (TRs) are frequently observed in genomes across all domains of life.
Evidence suggests that some TRs are crucial for proteins with fundamental biological …