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Related Concept Videos

Next-generation Sequencing03:00

Next-generation Sequencing

The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.
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...
Sanger Sequencing01:57

Sanger Sequencing

DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
Genome Annotation and Assembly03:36

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

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...

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Related Experiment Video

Updated: May 29, 2026

Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing
11:02

Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing

Published on: October 18, 2013

Comparison of solution-based exome capture methods for next generation sequencing.

Anna-Maija Sulonen1, Pekka Ellonen, Henrikki Almusa

  • 1Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Biomedicum Helsinki 2U, Tukholmankatu 8, 00290 Helsinki, Finland.

Genome Biology
|September 30, 2011
PubMed
Summary
This summary is machine-generated.

NimbleGen exome capture kits demonstrated superior alignment to target regions compared to Agilent kits. While no kit captured all coding exons, NimbleGen offered more efficient exome coverage for next-generation sequencing.

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Last Updated: May 29, 2026

Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing
11:02

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Published on: October 18, 2013

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Published on: August 4, 2016

Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies
13:24

Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies

Published on: April 11, 2016

Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Targeted re-sequencing of the human genome is crucial for next-generation sequencing (NGS).
  • Solution-based exome capture kits from Agilent and Roche NimbleGen were systematically compared.
  • Standard DNA samples were processed using four capture methods and Illumina GAII sequencing.

Purpose of the Study:

  • To systematically compare the performance of Agilent and Roche NimbleGen exome capture kits.
  • To evaluate capture efficiency, alignment rates, and variant calling accuracy.
  • To identify factors affecting exome enrichment success.

Main Methods:

  • Development of a bioinformatics pipeline for data quality control, alignment, and variant analysis.
  • Comparative analysis of sequence data from Agilent and NimbleGen capture methods.
  • Assessment of genotype concordance with SNP arrays.

Main Results:

  • NimbleGen captures showed higher alignment percentages to target regions compared to Agilent.
  • High GC content negatively impacted capture success across all methods.
  • Genotype concordance with SNP arrays was similar across kits; 11× coverage ensured 99% accuracy for heterozygous calls.

Conclusions:

  • NimbleGen kits provided more accurate alignment to target regions.
  • The updated NimbleGen kit achieved efficient exome coverage (≥20×).
  • No tested kit fully captured all Consensus Coding Sequence annotated exons.