Defining a tandem repeat catalog and variation clusters for genome-wide analyses
Biorxiv : the Preprint Server for Biology
|November 24, 2025
Summary
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.
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.
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