Related Experiment Video
Updated: Jul 20, 2025
10:34
Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
Published on: December 9, 2022
4.3K
Direct inference and control of genetic population structure from RNA sequencing data
Muhamad Fachrul1,2,3, Abhilasha Karkey4,5, Mila Shakya4,5
1Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia. fachrul.mhmd@gmail.com.
Communications Biology
|August 2, 2023
Summary
RNA sequencing (RNAseq) data can now estimate genetic population structure using the new RGStraP tool. This method effectively controls for population stratification in gene expression studies, improving data analysis.
Area of Science:
- Genomics
- Bioinformatics
- Population Genetics
Background:
- RNA sequencing (RNAseq) data is primarily used for gene expression analysis.
- Inferring genetic population structure from RNAseq data is an underexplored area.
- Population structure can confound gene expression analyses.
Purpose of the Study:
- To develop a computational tool (RGStraP) for estimating genetic principal components (RG-PCs) from RNAseq data.
- To evaluate the utility of RG-PCs for controlling population structure in gene expression studies.
Main Methods:
- Construction of the RGStraP computational tool.
- Estimation of RNAseq-based genetic principal components (RG-PCs).
- Comparison of RG-PCs with array-based genotypes.
- Application of RG-PCs as covariates in differential gene expression analysis.
Main Results:
- RG-PCs showed high genotype concordance and correlation with array-based genetic principal components.
- RG-PCs successfully captured subpopulation structures within datasets.
- Inclusion of RG-PCs reduced test statistic inflation in gene expression analyses.
Conclusions:
- Genetic population structure can be directly inferred from RNAseq data.
- RG-PCs provide a viable method to control for population stratification in transcriptomic studies.
- This approach enhances the accuracy of retrospective and future gene expression analyses.
Related Concept Videos
03:21RNA-seq
10.1K
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
10.1K
01:25What is Population Genetics?
58.1K
A population is composed of members of the same species that simultaneously live and interact in the same area. When individuals in a population breed, they pass down their genes to their offspring. Many of these genes are polymorphic, meaning that they occur in multiple variants. Such variations of a gene are referred to as alleles. The collective set of all the alleles within a population is known as the gene pool.
58.1K
02:54Evolutionary Relationships through Genome Comparisons
5.8K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
5.8K
01:23RNA Structure
71.6K
Overview
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...
71.6K
01:09Mutation, Gene Flow, and Genetic Drift
58.5K
In a population that is not at Hardy-Weinberg equilibrium, the frequency of alleles changes over time. Therefore, any deviations from the five conditions of Hardy-Weinberg equilibrium can alter the genetic variation of a given population. Conditions that change the genetic variability of a population include mutations, natural selection, non-random mating, gene flow, and genetic drift (small population size).
58.5K