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Genome-wide Association Studies-GWAS

Genome-wide Association Studies-GWAS

Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...

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Updated: Jun 28, 2026

Changes in Mammary Gland Morphology and Breast Cancer Risk in Rats

Changes in Mammary Gland Morphology and Breast Cancer Risk in Rats

Published on: October 16, 2010

Cell-type aware transcriptome-wide association study of mammographic density phenotypes.

Adriana Sistig¹, Joseph H Rothstein^2,3,4, Sinan Zhu⁵

¹Department of Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA.

Medrxiv : the Preprint Server for Health Sciences

|December 8, 2025

Summary

This summary is machine-generated.

This study used cell-type-aware transcriptome-wide association studies (TWAS) to identify novel genes associated with mammographic density (MD) and breast cancer risk. The new method found more genes than standard TWAS, including THBS2-AS1, linked to increased breast cancer risk.

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Area of Science:

Genetics
Genomics
Breast Cancer Research

Background:

Mammographic density (MD) is highly heritable and a strong breast cancer risk factor.
Genome-wide association studies (GWAS) have identified genetic variants for MD, but explain limited heritability.
Transcriptome-wide association studies (TWAS) can identify genes linked to MD via genetically regulated gene expression (GReX), but bulk tissue analysis can obscure cell-type-specific effects.

Purpose of the Study:

To conduct TWAS for MD phenotypes using standard and a novel cell-type-aware framework.
To identify novel genes associated with MD and breast cancer risk.
To improve the understanding of the genetic architecture of MD and its relationship with breast cancer.

Main Methods:

A study population of 24,158 European ancestry women was analyzed.
Mammographic density phenotypes (dense area, nondense area, percent density) were measured.
Standard TWAS and a cell-type-aware TWAS (MiXcan2) were used to assess GReX associations with MD phenotypes.

Main Results:

A total of 20 genes at 16 loci were significantly associated with MD phenotypes.
Six novel genes at six loci, including THBS2-AS1, were identified.
THBS2-AS1 was associated with decreased nondense area, increased percent density, and increased breast cancer risk.

Conclusions:

Cell-type-aware TWAS identified novel genes for MD and breast cancer risk.
The study highlights the importance of considering cell-type heterogeneity in genetic analyses of complex traits.
This approach provides insights into the biological basis of dense versus nondense breast tissue and breast cancer susceptibility.