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Related Concept Videos

Next-generation Sequencing03:00

Next-generation Sequencing

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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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RNA-seq03:21

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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: Apr 21, 2026

Oncogenic Gene Fusion Detection Using Anchored Multiplex Polymerase Chain Reaction Followed by Next Generation Sequencing
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Oncogenic Gene Fusion Detection Using Anchored Multiplex Polymerase Chain Reaction Followed by Next Generation Sequencing

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Anchored multiplex PCR for targeted next-generation sequencing.

Zongli Zheng1, Matthew Liebers2, Boryana Zhelyazkova2

  • 11] Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA. [2] Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.

Nature Medicine
|November 11, 2014
PubMed
Summary
This summary is machine-generated.

Anchored multiplex PCR (AMP) is a new method for next-generation sequencing that works with limited DNA from FFPE samples. This rapid assay accurately detects various genetic alterations and identifies novel gene fusions in cancer research.

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Area of Science:

  • Molecular Biology
  • Genomics
  • Oncology

Background:

  • Formalin-fixed paraffin-embedded (FFPE) specimens are crucial for clinical diagnostics but often yield low amounts of nucleic acids.
  • Accurate detection of diverse genetic alterations, including gene rearrangements, is vital for cancer diagnosis and targeted therapy.

Purpose of the Study:

  • To introduce and validate Anchored Multiplex PCR (AMP), a novel target enrichment method for next-generation sequencing (NGS).
  • To assess AMP's compatibility with low-input DNA from FFPE samples.
  • To demonstrate AMP's utility in detecting gene rearrangements, single nucleotide variants, insertions, deletions, and copy number changes, and its application in identifying novel therapeutic targets.

Main Methods:

  • Development of Anchored Multiplex PCR (AMP) for NGS target enrichment.
  • Application of AMP to low-input DNA from FFPE specimens.
  • Validation of an AMP-based gene rearrangement panel using 319 FFPE samples.
  • Analysis of 986 clinical FFPE samples to identify novel gene fusions.

Main Results:

  • AMP demonstrated high sensitivity and specificity (100%) in detecting gene rearrangements compared to reference assays.
  • The method successfully identified multiple novel, therapeutically relevant gene fusions in various cancers, including glioblastoma, lung cancer, cholangiocarcinoma, and thyroid carcinoma.
  • AMP proved effective for detecting single nucleotide variants, insertions, deletions, and copy number changes.

Conclusions:

  • Anchored Multiplex PCR (AMP) is a rapid, scalable, and efficient NGS target enrichment method suitable for low-input FFPE samples.
  • AMP serves as a robust clinical assay and a powerful discovery tool for identifying clinically significant genetic alterations and novel therapeutic targets in oncology.
  • The method facilitates comprehensive genomic profiling from archival FFPE tissues, advancing both research and clinical applications.