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Updated: Mar 8, 2026

Comparative Lesions Analysis Through a Targeted Sequencing Approach
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Published on: November 5, 2019

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Performance comparison of NextSeq and Ion Proton platforms for molecular diagnosis of clinical oncology

Fei Cao1, Lianju Gao2, Longgang Wei2

  • 1Department of Gastrointestinal Medical Oncology, The Affiliated Tumor Hospital of Harbin Medical University, Harbin - China.

Tumori
|January 28, 2017
PubMed
Abstract

Insights

Illumina NextSeq and Ion Proton platforms show high concordance for detecting cancer mutations in FFPE tissues. Both are suitable for clinical mutation detection, with Ion Proton identifying 89% of SNVs above 5% MAF found by NextSeq.

Area of Science:

  • Genomics and Bioinformatics
  • Cancer Research
  • Molecular Diagnostics

Background:

  • Personalized and precision medicine rely on accurate genetic mutation detection for tailored cancer treatment.
  • Formalin-fixed paraffin-embedded (FFPE) tissues are crucial for retrospective studies and clinical diagnostics.
  • Limited comparative data exists for major next-generation sequencing (NGS) platforms like Illumina NextSeq and Ion Torrent Ion Proton using FFPE samples.

Purpose of the Study:

  • To benchmark and compare the performance of Illumina NextSeq and Ion Torrent Ion Proton platforms for mutation detection in FFPE samples.
  • To evaluate sequencing metrics including coverage depth, read length, and variant detection accuracy between the two platforms.

Main Methods:

  • Benchmarking NGS platform performance using FFPE samples from 23 cancer patients.
  • Analyzing sequencing data for average coverage depth, read length, and variant detection.
  • Comparing variant calls, specifically single nucleotide variants (SNVs) and small insertions/deletions (indels).

Main Results:

  • Both NextSeq and Ion Proton demonstrated high coverage (>99%) on target regions.
  • Ion Proton identified 89% of SNVs (>=5% MAF) detected by NextSeq in common regions, with high MAF correlation (R2=0.973).
  • Concordance for small insertions and deletions reached 100% between the platforms; improved coverage depth is recommended for NextSeq to detect lower MAF mutations (5%-10%).

Conclusions:

  • Both evaluated NGS pipelines generate usable sequence data with high concordance.
  • The Illumina NextSeq and Ion Torrent Ion Proton platforms are suitable for clinical mutation detection in FFPE samples.
  • Comparative analysis provides valuable insights for selecting NGS platforms in precision oncology.

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