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Updated: Sep 9, 2025

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A practical guide to identifying associations between tandem repeats and complex human traits using consensus

Ibra Lujumba1, Yagoub Adam2, Helyaneh Ziaei Jam3

  • 1The African Center of Excellence in Bioinformatics and Data Intensive Sciences, Makerere University, Kampala, Uganda.

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|September 1, 2025
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Summary

This protocol provides a method for accurate tandem repeat (TR) genotyping from whole-genome sequencing data. It enables robust analysis of TR variation for population genomics and TR-trait association studies.

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Area of Science:

  • Genomics
  • Human Genetics
  • Bioinformatics

Background:

  • Tandem repeats (TRs) are variable genomic regions associated with human phenotypes.
  • Accurate TR genotyping is crucial for understanding population variation and TR-trait associations.

Purpose of the Study:

  • To present a protocol for generating high-quality consensus TR genotypes for population genomics.
  • To detail methods for TR genotyping, quality control, and genotype integration.

Main Methods:

  • TR genotyping using HipSTR, GangSTR, adVNTR, and ExpansionHunter.
  • Quality control with TRTools and genotype integration with EnsembleTR.
  • Analysis of TR variation patterns, population-specific expansions, and TR-trait associations.

Main Results:

  • Demonstrated utility with 1000 Genomes Project data.
  • Replicated a previously identified TR length and gene expression association in African populations.
  • Provided a framework for TR analysis in complex trait identification.

Conclusions:

  • The protocol facilitates reliable TR genotyping for population genomics.
  • TR analysis is relevant for uncovering complex traits and understanding genomic variation.