| Title: | Optimizing UK biobank cloud-based research analysis platform to fine-map coronary artery disease loci in whole genome sequencing data |
| Journal: | Scientific Reports |
| Published: | 25 Mar 2025 |
| Pubmed: | https://pubmed.ncbi.nlm.nih.gov/40133599/ |
| DOI: | https://doi.org/10.1038/s41598-025-95286-2 |
Publication 15857
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Abstract
We conducted the first comprehensive association analysis of a coronary artery disease (CAD) cohort within the recently released UK Biobank (UKB) whole genome sequencing dataset. We employed fine mapping tool PolyFun and pinpoint rs10757274 as the most likely causal SNV within the 9p21.3 CAD risk locus. Notably, we show that machine-learning (ML) approaches, REGENIE and VariantSpark, exhibited greater sensitivity compared to traditional single-SNV logistic regression, uncovering rs28451064 a known risk locus in 21q22.11. Our findings underscore the utility of leveraging advanced computational techniques and cloud-based resources for mega-biobank analyses. Aligning with the paradigm shift of bringing compute to data, we demonstrate a 44% cost reduction and 94% speedup through compute architecture optimisation on UK Biobank's Research Analysis Platform using our RAPpoet approach. We discuss three considerations for researchers implementing novel workflows for datasets hosted on cloud-platforms, to pave the way for harnessing mega-biobank-sized data through scalable, cost-effective cloud computing solutions.</p>
13 Keywords
- Biological Specimen Banks
- Cloud Computing
- Coronary Artery Disease
- Female
- Genetic Predisposition to Disease
- Genome-Wide Association Study
- Humans
- Machine Learning
- Male
- Polymorphism, Single Nucleotide
- UK Biobank
- United Kingdom
- Whole Genome Sequencing
9 Authors
- Letitia M.F. Sng
- Anubhav Kaphle
- Mitchell J. O'Brien
- Brendan Hosking
- Roc Reguant
- Johan Verjans
- Yatish Jain
- Natalie A. Twine
- Denis C. Bauer
1 Application
| Application ID | Title |
|---|---|
| 27483 | Quantifying the relationship between brain and body health using advanced MR imaging |
Enabling scientific discoveries that improve human health