Statistical independence of the colocalized association signals for type 1 diabetes and RPS26 gene expression on chromosome 12q13
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Following the recent success of genome-wide association studies in uncovering disease-associated genetic variants, the next challenge is to understand how these variants affect downstream pathways. The most proximal trait to a disease-associated variant, most commonly a single nucleotide polymorphism (SNP), is differential gene expression due to the cis effect of SNP alleles on transcription, translation, and/or splicing gene expression quantitative trait loci (eQTL). Several genome-wide SNP-gene expression association studies have already provided convincing evidence of widespread association of eQTLs. As a consequence, some eQTL associations are found in the same genomic region as a disease variant, either as a coincidence or a causal relationship. Cis-regulation of RPS26 gene expression and a type 1 diabetes (T1D) susceptibility locus have been colocalized to the 12q13 genomic region. A recent study has also suggested RPS26 as the most likely susceptibility gene for T1D in this genomic region. However, it is still not clear whether this colocalization is the result of chance alone or if RPS26 expression is directly correlated with T1D susceptibility, and therefore, potentially causal. Here, we derive and apply a statistical test of this hypothesis. We conclude that RPS26 expression is unlikely to be the molecular trait responsible for T1D susceptibility at this locus, at least not in a direct, linear connection.
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The allele-score splitting approach can have low power compared to the inclusion of an interaction term in a 2SLS regression.
“It should be noted that this approach can have low power compared to the inclusion of an interaction term in a 2SLS regression.111”
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- Authors
- Plagnol, V., Smyth, D. J., Todd, J. A., & Clayton, D. G.
- Affiliations
- University of Cambridge (GB)
- Corresponding author
- Plagnol, Vincent
- Venue
- Biostatistics
- Publisher
- Oxford University Press (OUP)
- Published
- 2008-11-27
- Volume
- 10
- Issue
- 2
- Pages
- 327-334
- ISSN
- 1465-4644 (ISSN-L)
- 1468-4357
- PMC
- PMC2648905
- OpenAlex
- W2160717726
- Cited by
- 113
- References
- 14
- Citations by year
- 2026: 6 · 2025: 10 · 2024: 9 · 2023: 8 · 2022: 10 · 2021: 19 · 2020: 8 · 2019: 5 · 2018: 3 · 2016: 1 · 2015: 5 · 2014: 4 · 2013: 6 · 2012: 5
- FWCI
- 2.66
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- cc-by-nc
- Locations
- Biostatistics (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- UCL Discovery (University College London) (submittedVersion)
- Funders
- Wellcome Trust (061858, 079895)
- National Institute for Health and Care Research (NF-SI-0508-10275)
- Cambridge Institute for Medical Research, University of Cambridge (079895)
- NIHR Cambridge Biomedical Research Centre
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Diabetes and associated disorders
- Keywords
- type 1 diabetes, RPS26, expression quantitative trait loci, colocalization, cis-regulation, chromosome 12q13, single nucleotide polymorphisms, causal inference
- MeSH terms
- Chromosome Mapping, Chromosomes, Human, Pair 12, Diabetes Mellitus, Type 1, Humans, Models, Genetic, Ribosomal Proteins, Genetic Predisposition to Disease, Polymorphism, Single Nucleotide, Quantitative Trait Loci, Genome-Wide Association Study
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