Journal Article (Review Article)

DKFZ-2025-01826

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png A practical guide to identifying associations between tandem repeats and complex human traits using consensus genotypes from multiple tools.

Lujumba, I. ; Adam, Y. ; Ziaei Jam, H. ; Isewon, I. ; Monnakgotla, N. ; Li, Y. ; Onyido, B. ; Fredrick, K. ; Adegoke, F. ; Emmanuel, J. ; Adeyemi, J. ; Ibitoye, O. ; Owusu-Ansah, S. ; Akanle, M. B. ; Joseph, H. ; Nsubuga, M. ; Galiwango, R. ; Okitwi, M. ; Magdalene, N. ; Walter, O. ; Mngadi, Z. ; Adebiyi, M. ; Oyelade, J. ; Nel, M. ; Jjingo, D. ; Gymrek, M. ; Adebiyi, E. F. (Last author)DKFZ*

2025
Nature Publishing Group Basingstoke

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Please use a persistent id in citations: doi:10.1038/s41596-025-01231-y

Abstract: Tandem repeats (TRs) are highly variable loci in the human genome that are linked to various human phenotypes. Accurate and reliable genotyping of TRs is important in understanding population TR variation dynamics and their effects in TR-trait association studies. In this protocol, we describe how to generate high-quality consensus TR genotypes for population genomics studies. In particular, we detail steps to: (i) perform TR genotyping from short-read whole-genome sequencing data by using the HipSTR, GangSTR, adVNTR and ExpansionHunter tools, (ii) perform quality control checks on TR genotypes by using TRTools and (iii) integrate TR genotypes from different tools by using EnsembleTR. We further discuss how to visualize and investigate TR variation patterns to identify population-specific expansions and perform TR-trait association analyses. We demonstrate the utility of these steps by analyzing a small dataset from the 1000 Genomes Project. In addition, we recapitulate a previously identified association between TR length and gene expression in the African population and provide a generalized discussion on TR analysis and its relevance to identifying complex traits. The expected time for installing the necessary software for each section is ~10 min. The expected run time on the user's desired dataset can vary from hours to days depending on factors such as the size of the data, input parameters and the capacity of the computing infrastructure.

Note: #LA:B330# / epub

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Contributing Institute(s):

1. Angewandte Bioinformatik (B330)

Research Program(s):

1. 312 - Funktionelle und strukturelle Genomforschung (POF4-312) (POF4-312)

Appears in the scientific report 2025

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Database coverage:
; Clarivate Analytics Master Journal List ; Current Contents - Life Sciences ; DEAL Nature ; Essential Science Indicators ; IF >= 10 ; JCR ; Nationallizenz ; SCOPUS ; Science Citation Index Expanded ; Web of Science Core Collection

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