Sachenkova Lundström, Oxana; Verbiest, Max; Xia, Feifei; Ziaei Jam, Helyaneh; Zlobec, Inti; Anisimova, Maria; Gymrek, Melissa (2023). WebSTR: a population-wide database of short tandem repeat variation in humans. Journal of molecular biology, 435(20), p. 168260. Elsevier 10.1016/j.jmb.2023.168260
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Short tandem repeats (STRs) are consecutive repetitions of one to six nucleotide motifs. They are hypervariable due to the high prevalence of repeat unit insertions or deletions primarily caused by polymerase slippage during replication. Genetic variation at STRs has been shown to influence a range of traits in humans, including gene expression, cancer risk, and autism. Until recently STRs have been poorly studied since they pose significant challenges to bioinformatics analyses. Moreover, genome-wide analysis of STR variation in population-scale cohorts requires large amounts of data and computational resources. However, the recent advent of genome-wide analysis tools has resulted in multiple large genome-wide datasets of STR variation spanning nearly two million genomic loci in thousands of individuals from diverse populations. Here we present WebSTR, a database of genetic variation and other characteristics of genome-wide STRs across human populations. WebSTR is based on reference panels of more than 1.7 million human STRs created with state of the art repeat annotation methods and can easily be extended to include additional cohorts or species. It currently contains data based on STR genotypes for individuals from the 1000 Genomes Project, H3Africa, the Genotype-Tissue Expression (GTEx) Project and colorectal cancer patients from the TCGA dataset. WebSTR is implemented as a relational database with programmatic access available through an API and a web portal for browsing data. The web portal is publicly available at http://webstr.ucsd.edu.
Item Type: |
Journal Article (Original Article) |
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Division/Institute: |
04 Faculty of Medicine > Service Sector > Institute of Pathology |
UniBE Contributor: |
Zlobec, Inti |
Subjects: |
500 Science > 570 Life sciences; biology 600 Technology > 610 Medicine & health |
ISSN: |
1089-8638 |
Publisher: |
Elsevier |
Language: |
English |
Submitter: |
Pubmed Import |
Date Deposited: |
11 Sep 2023 14:53 |
Last Modified: |
28 Dec 2023 09:50 |
Publisher DOI: |
10.1016/j.jmb.2023.168260 |
PubMed ID: |
37678708 |
Uncontrolled Keywords: |
API WebSTR allele frequencies database disease-associated variants gene regulatory regions genome-wide association studies genotyping human genetic variation mutation rates next-generation sequencing reference panel short tandem repeats transcription factor binding sites web portal |
BORIS DOI: |
10.48350/186156 |
URI: |
https://boris.unibe.ch/id/eprint/186156 |
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