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Defining a tandem repeat catalog and variation clusters for genome-wide analyses and population databases
Ben Weisburd1, Egor Dolzhenko2, Mark F Bennett3
1Program in Medical and Population Genetics, Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
A new tandem repeat (TR) catalog addresses inconsistencies in genomic analysis by providing a unified, annotated resource. This catalog distinguishes between isolated repeats and variation clusters for improved genotyping and sequence-level studies.
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 vary significantly in size and locus definitions, risking data fragmentation.
- Divergent catalogs can lead to confusion and incompatibility across population genetics resources.
Purpose of the Study:
- To compare existing TR catalogs and identify features of a comprehensive genome-wide catalog.
- To present a new, richly annotated TR catalog for genome-wide and population analyses.
- To stratify TRs into distinct types for tailored analytical approaches.
Main Methods:
- Comparison of existing tandem repeat catalogs.
- Development of a new, annotated genome-wide TR catalog.
- Algorithm leveraging long-read HiFi sequencing data to stratify TRs.
- Annotation and sharing of TR catalog, variation clusters, and annotations via the TRExplorer portal.
Main Results:
- A new, comprehensive, and richly annotated TR catalog has been developed.
- TRs are stratified into isolated repeats and variation clusters using long-read sequencing data.
- The TRExplorer portal provides access to the catalog and associated data for analysis support.
Conclusions:
- A unified TR catalog is essential to mitigate fragmentation and incompatibility in genomic studies.
- The new catalog and stratification method enhance the analysis of TR variation in population datasets.
- The TRExplorer portal facilitates the selection and interpretation of TR loci in genetic analyses.
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