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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.

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Related Experiment Video

Updated: May 19, 2026

Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry
05:53

Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry

Published on: June 21, 2018

Improving mapping and SNP-calling performance in multiplexed targeted next-generation sequencing.

Abdou Elsharawy1, Michael Forster, Nadine Schracke

  • 1Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany.

BMC Genomics
|August 24, 2012
PubMed
Summary
This summary is machine-generated.

Multiplexed targeted next-generation sequencing (tNGS) enables cost reduction. Evaluating analytical tools revealed a new two-step mapping approach significantly improves single nucleotide polymorphism (SNP) discovery efficiency in tNGS data.

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

Targeted DNA Methylation Analysis by Next-generation Sequencing
08:38

Targeted DNA Methylation Analysis by Next-generation Sequencing

Published on: February 24, 2015

Related Experiment Videos

Last Updated: May 19, 2026

Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry
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Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry

Published on: June 21, 2018

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

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Targeted DNA Methylation Analysis by Next-generation Sequencing
08:38

Targeted DNA Methylation Analysis by Next-generation Sequencing

Published on: February 24, 2015

Area of Science:

  • Genomics
  • Bioinformatics

Background:

  • Targeted next-generation sequencing (tNGS) offers custom-designed genomic region interrogation for variant detection.
  • Pooling barcoded libraries in tNGS reduces per-sample cost but impacts variant discovery quality.
  • The performance of analytical tools in multiplexed tNGS requires thorough evaluation for reliable variant discovery.

Purpose of the Study:

  • To evaluate the impact of different software tools and analytical approaches on single nucleotide polymorphism (SNP) discovery in multiplexed tNGS data.
  • To develop and validate a more efficient SNP discovery pipeline for multiplexed tNGS.

Main Methods:

  • Generated test models using sequence capture and NGS across three complexity stages (E. coli, multiplexed E. coli, multiplexed HapMap BRCA1/2).
  • Enriched barcoded NGS libraries, achieving reproducible coverage profiles across multiplexed samples.
  • Developed and tested a combined 'two-step' mapping pipeline (BWA, SAMtools) on public exome data.

Main Results:

  • Achieved reproducible coverage profiles (Pearson's r up to 0.99) and low strand bias (<10%) in multiplexed samples.
  • Demonstrated that SNP calling quality is significantly influenced by tool choice and mapping strategy.
  • The developed pipeline reduced run time by 12 hours per exome sample and detected ~5% more SNPs compared to conventional whole-genome mapping.

Conclusions:

  • Recommended a general 'two-step' mapping approach for enhanced SNP discovery in tNGS.
  • Highlighted the importance of inter-sample SNP concordance and read alignment inspection for confident results.
  • The new pipeline offers improved efficiency and potentially novel SNP discovery in tNGS.