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Genome-wide Association Studies-GWAS

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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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Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq

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scTWAS Atlas: an integrative knowledgebase of single-cell transcriptome-wide association studies.

Jialin Mai^1,2,3, Qiheng Qian^1,2,3, Hao Gao^1,2,3

¹National Genomics Data Center, China National Center for Bioinformation, Beijing 100101, China.

Nucleic Acids Research

|October 18, 2024

Summary

scTWAS Atlas is a new database for single-cell transcriptome-wide association studies (scTWAS), offering precise gene-trait associations. It integrates scTWAS and sc-eQTL data to explore cellular genetic regulation and human health insights.

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Area of Science:

Genomics
Bioinformatics
Cell Biology

Background:

Traditional transcriptome-wide association studies (TWAS) face challenges in interpreting cell-type heterogeneity.
Single-cell TWAS (scTWAS) offers higher precision for gene-trait associations at the cellular level.
A need exists for integrated database platforms to manage advancing scTWAS data.

Purpose of the Study:

To introduce scTWAS Atlas, a comprehensive database for scTWAS information.
To provide a platform for exploring genetic regulatory mechanisms at the cellular level.
To facilitate the understanding of cell-type-specific roles in biological processes and human health.

Main Methods:

Literature curation and data analysis to compile scTWAS information.
Development of an interactive knowledge graph integrating single-cell expression quantitative trait loci (sc-eQTL) and scTWAS associations.
Implementation of user-friendly interfaces for browsing, searching, and downloading data.

Main Results:

The database currently contains 2,765,211 associations across 34 traits, 30 cell types, 9 cell conditions, and 16,470 genes.
An interactive knowledge graph visualizes multi-omics regulatory networks at the cellular level.
Cross-cell-type analysis capabilities highlight cell-type-specific and shared TWAS genes.

Conclusions:

scTWAS Atlas is a valuable resource for advancing scTWAS research.
The database aids in dissecting genetic regulation within specific cell types.
It offers novel insights into the cellular basis of human health and disease.