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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. 
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Updated: Mar 9, 2026

Detection of Rare Mutations in CtDNA Using Next Generation Sequencing
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INDELseek: detection of complex insertions and deletions from next-generation sequencing data.

Chun Hang Au1, Anskar Y H Leung2, Ava Kwong3,4,5

  • 1Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong SAR.

BMC Genomics
|January 7, 2017
PubMed
Summary

INDELseek accurately detects complex insertions and deletions (indels) in next-generation sequencing (NGS) data, outperforming other tools. This advancement is crucial for identifying disease-driving mutations in genomics studies.

Keywords:
BioinformaticsComplex indelNext-generation sequencingVariant calling

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Complex insertions and deletions (indels) are frequently missed by current variant callers in next-generation sequencing (NGS) data.
  • This underdetection impacts the identification of somatic and germline mutations in critical disease-associated genes.

Purpose of the Study:

  • To introduce INDELseek, an open-source tool for accurate complex indel detection in NGS data.
  • To evaluate INDELseek's performance against established variant callers and in clinical samples.

Main Methods:

  • INDELseek analyzes each NGS read alignment holistically, unlike position-based pileup methods.
  • Benchmarking was performed using the NA12878 genome reference material and clinical samples with known mutations.

Main Results:

  • INDELseek achieved 100% sensitivity in detecting complex indels, surpassing GATK and SAMtools (0% sensitivity).
  • It successfully identified known germline (BRCA1, BRCA2) and somatic (CALR, JAK2) complex indels.
  • In silico simulations demonstrated high sensitivity (93.7-96.2%) across thousands of genes.

Conclusions:

  • INDELseek is a highly accurate and adaptable tool for complex indel detection in NGS data.
  • It enhances the comprehensive analysis of genetic variations in genomics research.