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RNA-seq

RNA-seq

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...

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Related Experiment Video

Updated: May 27, 2025

Large-Scale SARS-CoV-2 Testing Utilizing Saliva and Transposition Sample Pooling

Large-Scale SARS-CoV-2 Testing Utilizing Saliva and Transposition Sample Pooling

Published on: June 23, 2022

Evaluation of sample pooling for gene sequencing of SARS-CoV-2: a simulation study.

Heng Chen¹, Yue Cheng¹, Xun He¹

¹Chengdu Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Chengdu, 610047, China.

Journal of Infection in Developing Countries

|February 20, 2025

Summary

Pooled sequencing offers a cost-effective method for monitoring severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants, aiding in public health surveillance for coronavirus disease 2019 (COVID-19). This approach enhances genomic surveillance efficiency.

Keywords:

SARS-CoV-2 gene sequencing sample pooling simulation study

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Last Updated: May 27, 2025

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Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Published on: June 23, 2012

Area of Science:

Genomics
Virology
Bioinformatics

Background:

Coronavirus disease 2019 (COVID-19) surveillance is crucial for public health.
Next-generation sequencing (NGS) is vital for monitoring viral evolution but is expensive.
Cost-effective methods are needed for continuous genomic surveillance of SARS-CoV-2.

Purpose of the Study:

To evaluate pooled sequencing as a cost-effective strategy for SARS-CoV-2 variant monitoring.
To assess the efficacy of different pooling strategies in recovering original sample genotypes.
To determine the feasibility of pooled sequencing for large-scale genomic surveillance.

Main Methods:

A simulation study was performed using 72 sets of SARS-CoV-2 sequencing data.
Seventy simulated pooled samples were created using five distinct pooling strategies.
A bioinformatics tool based on Freyja analyzed variant composition, with results evaluated using R software.

Main Results:

Pooled sequencing largely recovered the original sample genotypes, with minor discrepancies in top results.
Variability in genotype identification efficiency was noted across pooling strategies for top results.
Low-quality original samples showed reduced accuracy in identification.

Conclusions:

Pooled sequencing combined with streamlined genotyping is a viable, cost-effective approach for SARS-CoV-2 surveillance.
This method supports efficient genomic surveillance for COVID-19.
Further optimization may improve accuracy for low-quality samples.