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Related Concept Videos

Cancer-Critical Genes II: Tumor Suppressor Genes01:05

Cancer-Critical Genes II: Tumor Suppressor Genes

Genes usually encode proteins necessary for the proper functioning of a healthy cell. Mutations can often cause changes to the gene expression pattern, thereby altering the phenotype.
When the function of certain critical genes, especially those involved in cell cycle regulation and cell growth signaling cascades, gets disrupted, it upsets the cell cycle progression. Such cells with unchecked cell cycles start proliferating uncontrollably and eventually develop into tumors.
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Cancer-Critical Genes I: Proto-oncogenes01:33

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Genes usually encode proteins necessary for the proper functioning of a healthy cell. Mutations can often cause changes to the gene expression pattern, thereby altering the phenotype.
When the function of certain critical genes, especially those involved in cell cycle regulation and cell growth signaling cascades, gets disrupted, it upsets the cell cycle progression. Such cells with unchecked cell cycles start proliferating uncontrollably and eventually develop into tumors.
Such genes that act...
Cancer-Critical Genes I: Proto-oncogenes01:33

Cancer-Critical Genes I: Proto-oncogenes

Genes usually encode proteins necessary for the proper functioning of a healthy cell. Mutations can often cause changes to the gene expression pattern, thereby altering the phenotype.
When the function of certain critical genes, especially those involved in cell cycle regulation and cell growth signaling cascades, gets disrupted, it upsets the cell cycle progression. Such cells with unchecked cell cycles start proliferating uncontrollably and eventually develop into tumors.
Such genes that act...

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Related Experiment Video

Updated: May 8, 2026

gDNA Enrichment by a Transposase-based Technology for NGS Analysis of the Whole Sequence of BRCA1, BRCA2, and 9 Genes Involved in DNA Damage Repair
08:15

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Published on: October 6, 2014

Streamlined ion torrent PGM-based diagnostics: BRCA1 and BRCA2 genes as a model.

Julien Tarabeux1, Bruno Zeitouni2, Virginie Moncoutier3

  • 11] Service de Génétique Oncologique, Institut Curie, Paris, France [2] INSERM U830, Centre de Recherche de l'Institut Curie, Paris, France.

European Journal of Human Genetics : EJHG
|August 15, 2013
PubMed
Summary

Next-generation sequencing (NGS) offers faster BRCA1/2 gene analysis for diagnostics. An Ion Torrent PGM platform with NextGene software improved mutation detection and reduced turnaround time for clinical testing.

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Area of Science:

  • Molecular Diagnostics
  • Genomic Sequencing
  • Clinical Laboratory Science

Background:

  • Diagnostic laboratories face throughput and turnaround time challenges with traditional Sanger sequencing.
  • Next-generation sequencing (NGS) platforms offer higher throughput but require different performance criteria for diagnostics.
  • BRCA1/2 gene sequencing is critical for hereditary cancer diagnostics but presents technical difficulties.

Purpose of the Study:

  • To develop and validate a routine diagnostic procedure for BRCA1/2 sequencing using Ion Torrent's Personal Genome Machine (PGM).
  • To compare the diagnostic performance of an in-house bioinformatics pipeline versus commercial NextGene software.
  • To assess the impact of the PGM-based procedure on turnaround time and identify large-scale rearrangements.

Main Methods:

  • Development of a PGM-based routine diagnostic procedure for BRCA1/2 sequencing.
  • Testing on a training set (62 samples) including complex cases (indels, rearrangements, homopolymers).
  • Blind validation on 77 samples in parallel with routine Sanger sequencing, comparing two bioinformatics solutions (in-house vs. NextGene).

Main Results:

  • NextGene software demonstrated higher sensitivity, detecting four previously unidentified single-nucleotide variations.
  • An average of 1.5 confirmatory Sanger sequences per patient were required for complete BRCA1/2 screening.
  • The PGM-based procedure reduced turnaround time to 10 working days for a series of 30 patients, with large-scale rearrangements identified via bioinformatics and fragment analysis.

Conclusions:

  • The developed Ion Torrent PGM-based procedure is effective for routine BRCA1/2 diagnostic sequencing, addressing challenges of throughput and turnaround time.
  • NextGene software offers improved sensitivity for variant detection in diagnostic settings.
  • The described pipeline is adaptable for diagnostic purposes by other users of the PGM platform.