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Related Concept Videos

Ribosome Profiling02:24

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...
RNA-seq03:21

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 microarray-based...
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
Alternative RNA Splicing02:18

Alternative RNA Splicing

Alternative RNA splicing is the regulated splicing of exons and introns to produce different mature mRNAs from a single pre-mRNA. Unlike in constitutive splicing where a single gene produces a single type of mRNA, alternative splicing allows an organism to produce multiple proteins from a single gene and plays an important role in protein diversity.
There are five types of alternative RNA splicing that vary in the ways the pre-mRNA segments are removed or retained in the mature mRNA. The first...
Organization of Genes02:07

Organization of Genes

Overview

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Updated: May 23, 2026

A Strategy to Identify de Novo Mutations in Common Disorders such as Autism and Schizophrenia
05:51

A Strategy to Identify de Novo Mutations in Common Disorders such as Autism and Schizophrenia

Published on: June 15, 2011

Exome versus transcriptome sequencing in identifying coding region variants.

Chee-Seng Ku1, Mengchu Wu, David N Cooper

  • 1Cancer Science Institute of Singapore, #12-01, MD6, Centre for Translational Medicine, NUS Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, 117599, Singapore. g0700040@nus.edu.sg

Expert Review of Molecular Diagnostics
|April 4, 2012
PubMed
Summary
This summary is machine-generated.

Next-generation sequencing offers various methods for detecting genetic variation. Transcriptome sequencing emerges as a cost-effective alternative to whole-exome sequencing for identifying protein-coding variants.

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Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay (EMSA) and DNA-affinity Precipitation Assay (DAPA)
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Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay (EMSA) and DNA-affinity Precipitation Assay (DAPA)

Published on: August 21, 2016

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
08:35

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Published on: June 24, 2021

Related Experiment Videos

Last Updated: May 23, 2026

A Strategy to Identify de Novo Mutations in Common Disorders such as Autism and Schizophrenia
05:51

A Strategy to Identify de Novo Mutations in Common Disorders such as Autism and Schizophrenia

Published on: June 15, 2011

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay (EMSA) and DNA-affinity Precipitation Assay (DAPA)
11:35

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay (EMSA) and DNA-affinity Precipitation Assay (DAPA)

Published on: August 21, 2016

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
08:35

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Published on: June 24, 2021

Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Next-generation sequencing (NGS) technologies have transformed human genetic variation studies.
  • Whole-genome sequencing (WGS) is comprehensive but costly and struggles with noncoding regions.
  • Whole-exome sequencing (WES) excels at identifying disease-causing mutations but requires costly enrichment.

Purpose of the Study:

  • To compare the utility of WGS, WES, and transcriptome sequencing (RNA-seq) for variant detection in protein-coding regions.
  • To evaluate the advantages and limitations of each sequencing approach for genetic variation analysis.

Main Methods:

  • Comparative analysis of WGS, WES, and RNA-seq methodologies.
  • Focus on variant detection within gene coding regions (exons).
  • Discussion of technical requirements, costs, and interpretability of variants.

Main Results:

  • WGS provides genome-wide coverage but is expensive and less interpretable for noncoding variants.
  • WES is effective for identifying mutations in Mendelian disorders, cancers, and neurodevelopmental disorders.
  • RNA-seq offers a cost-effective alternative to WES for detecting variants in coding regions, bypassing enrichment steps.

Conclusions:

  • RNA-seq presents a viable alternative to WES for variant detection in protein-coding regions.
  • The choice of sequencing strategy depends on research goals, sample size, and cost considerations.
  • Further evaluation is needed to fully understand the scope and limitations of RNA-seq for variant discovery.