Related Experiment Video

Updated: Mar 24, 2026

Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies
13:24

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

12.4K

Mutation based treatment recommendations from next generation sequencing data: a comparison of web tools

Jaymin M Patel1, Joshua Knopf1, Eric Reiner2

  • 1Medical Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA.

Oncotarget
|March 17, 2016
PubMed

Insights

Interpreting cancer genome data for personalized therapy is challenging due to non-standardized tools. A study found significant variation in drug recommendations from different genomic data interpretation platforms, highlighting the need for improved standardization.

Area of Science:

  • Genomic medicine
  • Computational oncology
  • Translational oncology

Background:

  • Personalized cancer therapy relies on interpreting complex tumor genome data.
  • Current methods for deriving therapeutic conclusions from tumor profiling are not standardized.
  • Discrepancies exist between commercial and academic cancer genome data interpretation tools.

Purpose of the Study:

  • To compare drug and clinical trial recommendations from multiple web-based tools using targeted sequencing data from metastatic breast cancer.
  • To assess the concordance of therapeutic recommendations generated by different genomic data interpretation platforms.

Main Methods:

  • Targeted sequencing of 315 cancer genes was performed on 75 metastatic breast cancer biopsies.
  • Results were analyzed using four distinct web tools: Drug-Gene Interaction Database (DGidb), My Cancer Genome (MCG), Personalized Cancer Therapy (PCT), and cBioPortal.
  • Recommendations were compared against each other and the FoundationOne assay's own recommendations.

Main Results:

  • The identification of actionable genomic alterations varied significantly across the evaluated recommendation sources.
  • Only 33% of cases received concordant drug recommendations from four or more sources for at least one altered gene.
  • Substantial heterogeneity in therapeutic recommendations was observed among the different tools.

Conclusions:

  • There is a critical need for the development and standardization of robust software tools for interpreting cancer genomic data.
  • Current algorithms require enhancement, potentially through artificial intelligence, to improve accuracy and real-time status updates for therapeutic recommendations.
  • Standardization is essential for reliable clinical decision-making in precision oncology.
Keywords:
biomarkers and intervention studiesbreast cancermutation based treatment recommendationspersonalized medicinetumor profiling

More Related Videos

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease09:34

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Published on: April 4, 2018

35.0K
Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing11:02

Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing

Published on: October 18, 2013

20.0K

Related Concept Videos

Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
7.2K
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....
100.8K
Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
830
Combination Therapies and Personalized Medicine02:50

Combination Therapies and Personalized Medicine

Combining two or more treatment methods increases the life span of cancer patients while reducing damage to vital organs or tissue from the overuse of a single treatment. Combination therapy also targets different cancer-inducing pathways, thus reducing the chances of developing resistance to treatment.
The combination of the drug acetazolamide and sulforaphane is a good example of combination therapy to treat cancer. The cells in the interior of a large tumor often die due to the hypoxic and...
6.3K