Allelic expression imbalance in articular cartilage and subchondral bone refined genome-wide association signals in osteoarthritis
Authors' conclusion
By prioritizing proxy transcript SNPs that mark AEI in cartilage and/or subchondral bone at loci harbouring GWAS signals, we present an unbiased approach to identify the most likely functional OA risk-SNP and gene.
Study context
- Population
- Osteoarthritis (OA) patients: articular cartilage and subchondral bone samples; genes in the 100 genome-wide association studies (GWAS) catalog OA risk regions expressed in cartilage or bone65 cartilage, 24 subchondral bone samples
- Outcome
- Transcript SNPs subject to AEI at OA risk loci (meta-φ vs null hypothesis median φ = 0.49)
Methodological detailsRNA sequencing, allelic expression imbalance analysis, meta-analysis of φ per SNP
- RNA sequencing
- Allelic expression imbalance analysis
- Meta-analysis of φ per SNP
Main finding
As reported in the abstract
Transcript SNPs subject to AEI
- Transcript single nucleotide polymorphisms (SNPs) subject to allelic expression imbalance (AEI) in 29 genes (28 in cartilage, 2 in subchondral bone)
- 30
- Transcript SNPs in genes not previously reported in GWAS catalog
- 10
- MALAT1 (lincRNA) meta-φ
- 0.54
- MALAT1 FDR
- 1.7×10-4
- ILF3-DT (lincRNA) meta-φ
- 0.6
- ILF3-DT FDR
- 1.75×10-5
Further findings
- Drugs interacting with seven genes displaying AEI
- 12
- Of which already approved
- 7
Original publication
Allelic expression imbalance in articular cartilage and subchondral bone refined genome-wide association signals in osteoarthritis. Rheumatology (Oxford). Published 30 August 2022. doi:10.
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