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Related Concept Videos

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Related Experiment Video

Updated: Jun 23, 2025

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Characterizing the Relationship between Expression Quantitative Trait Loci (eQTLs), DNA Methylation Quantitative

Peh Joo Ho1,2,3, Alexis Khng1, Benita Kiat-Tee Tan4,5,6

  • 1Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore 138672, Singapore.

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|June 19, 2024
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Summary

A new polygenic risk score (PRS) using functional variants for breast cancer risk did not improve prediction compared to the established GWAS PRS. The established GWAS PRS demonstrated superior discriminatory ability for identifying breast cancer cases.

Keywords:
KCNN4SMRbreast cancer riskeQTLgenetic risk scoremQTLmethylation

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Area of Science:

  • Genetics
  • Cancer Research
  • Epidemiology

Background:

  • Polygenic risk scores (PRS) are crucial for assessing genetic predisposition to complex diseases.
  • Identifying functional genetic variants can potentially refine PRS for improved disease risk prediction.
  • Breast cancer remains a significant global health concern, necessitating advancements in risk stratification.

Purpose of the Study:

  • To evaluate a novel PRS derived from functional genetic variants for breast cancer risk.
  • To compare the predictive performance of this functional PRS against a standard 313-variant genome-wide association study (GWAS) PRS.
  • To determine if incorporating functional variants enhances breast cancer risk prediction accuracy.

Main Methods:

  • Summary data-based Mendelian randomization (SMR) and heterogeneity in dependent instruments (HEIDI) were employed to identify risk variants linked to gene expression and methylation.
  • A functional PRS was constructed using SMR-identified variants.
  • The functional PRS and a 313-variant GWAS PRS were compared in case-control and prospective cohorts.

Main Results:

  • 149 variants showed pleiotropic associations with breast cancer risk.
  • The functional PRS exhibited lower discriminatory ability (AUC: 0.540) than the GWAS PRS (AUC: 0.609).
  • Combining functional and GWAS PRS variants did not surpass the predictive performance of the GWAS PRS alone.

Conclusions:

  • Potentially functional variants associated with breast cancer risk were identified.
  • The inclusion of these functional variants did not significantly improve the predictive accuracy of the established GWAS PRS.
  • The standard GWAS PRS remains a more effective tool for breast cancer risk prediction in this context.