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High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

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

Ben Weisburd, Egor Dolzhenko, Mark F Bennett

Biorxiv : the Preprint Server for Biology

|November 24, 2025

Summary

This summary is machine-generated.

This study introduces the TRExplorer catalog v1.0, a new resource for tandem repeat (TR) genotyping. It addresses inconsistencies in existing TR catalogs and offers a comprehensive, annotated dataset for both short-read and long-read analyses.

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High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

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Area of Science:

Genomics
Bioinformatics
Population Genetics

Background:

Tandem repeat (TR) catalogs are crucial for repeat genotyping, defining genomic locations and motifs.
Existing TR catalogs often disagree on locus boundaries, hindering cross-study comparisons and data reuse.
Developing public databases of TR variation risks fragmentation due to divergent locus definitions.

Purpose of the Study:

To compare existing tandem repeat catalogs and identify desirable features for a comprehensive genome-wide catalog.
To present a new, richly annotated TR catalog (TRExplorer v1.0) for large-scale analyses and population databases.
To introduce a novel algorithm for defining variation clusters using long-read sequencing data.

Main Methods:

Comparative analysis of existing tandem repeat catalogs.
Development and annotation of the TRExplorer catalog v1.0, including STRs and VNTRs.
Application of a novel algorithm utilizing long-read HiFi sequencing data to identify and define variation clusters.

Main Results:

The TRExplorer catalog v1.0 contains 4.9 million TR loci, including novel polymorphic loci absent from previous catalogs.
TRs are stratified into isolated repeats for copy number analysis and variation clusters for sequence-level analysis.
At least 25,000 complex variation clusters were identified in the human genome, often containing multiple TRs within polymorphic regions.

Conclusions:

The TRExplorer catalog v1.0 provides a standardized, comprehensive resource for TR genotyping across diverse sequencing technologies.
The novel variation cluster definition method enables more accurate analysis of complex polymorphic regions.
The trexplorer.broadinstitute.org portal facilitates access and utilization of the catalog and variation cluster data.