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Updated: Feb 3, 2026

A Novel Bayesian Change-point Algorithm for Genome-wide Analysis of Diverse ChIPseq Data Types
Published on: December 10, 2012
Exploratory genome-wide analysis suggests potential associations of PPP1R12B, FSTL5, G5K3B, and GFRA2 loci with a
Ribanna A M Braga1, Livia Alvarenga2, Marlene N Aldin3
1University of São Paulo, Postgraduate Program in Cardiology, Heart Institute (InCor), Faculty of Medicine of the University of São Paulo (FMUSP), São Paulo, Brazil (Drs Braga and Damasceno).
Background:
The size, composition, and functionality of high-density lipoprotein cholesterol (HDL-C) are potential biomarkers for predicting atherosclerosis, representing a major advance in the prevention and treatment of cardiovascular diseases.
Objective:
This study aims to explore HDL-C concentrations and a derived HDL functionality score (HFS), and to investigate suggestive genetic associations in a representative Brazilian population.
Methods:
This is an observational cross-sectional study. Plasma lipid profiles were analyzed using an automated system. The Lipoprint System determined HDL particle sizes. HFS was calculated using a composite based on the large HDL particle concentration combined with relevant cardiovascular data from demographic and clinical parameters. After DNA extraction, genotyping, and quality control, information on 330,656 single-nucleotide polymorphisms (SNPs) was available for genome-wide association studies (GWAS) of HFS.
Results:
Among 345 participants, HDL functionality was impaired in 38%. Those with low functionality exhibited higher average waist circumference, systolic blood pressure, and glucose, as well as lower HDL-C concentrations, compared with those with high HDL functionality (P < .05). GWAS revealed suggestive associations for 5 SNPs and HFS, including rs11730709, rs78565063, and rs11786395 (P < 1 × 10-5), as well as rs12734338 and rs36019094 (P < 1 ×10-8). Additional regression analyses showed that SNPs rs12734338 and rs36019094 were positively associated with HFS, while rs11730709 showed an inverse association. Furthermore, rs12734338 increased the prevalence of low HFS by 41%, whereas rs11730709 reduced it by 34%.
Conclusion:
These findings suggest potential genetic loci associated with the HFS, creating an opportunity for further investigations. Replication in larger and independent cohorts is warranted to confirm and extend these observations.
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