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A Brief Comparison of Molecular Methods in Oncology

Molecular genetic methods are primarily used in oncology for diagnosis clarification, disease prognosis, and for selection of the most effective therapy (including targeted cancer therapy)

Next-generation sequencing (NGS)

is the most advanced and promising method that allows performing whole genome, whole exome, and targeted sequencing. Sequencing multiple DNA fragments occurs in parallel, providing high information content at a relatively high speed. NGS can simultaneously assess the presence of various genetic abnormalities in DNA and RNA molecules, such as hotspot mutations (mutations with increased frequency in the population), single nucleotide variants (SNV), copy number variations (CNV), large insertions, deletions, and gene fusions.

Oncomine Focus Assay is an excellent example of an NGS assay used in cancer laboratory diagnostics.

Oncomine Focus Assay is a targeted next-generation sequencing (NGS), a multi-biomarker assay based on the Ion Torrent platform that detects variants across 52 cancer-relevant genes.

1000
different mutations detected with Oncomine Focus Assay

Advantages of the method

  • A universal method that is able to detect a wide range of mutations
  • Allows to perform diagnostics without prior hypothesis
  • Multiple candidate genes can be analyzed simultaneously
  • Only requires 10 ng of DNA or RNA
  • One of the most sensitive methods

Disadvantages of the method

  • High cost
  • The method is used to diagnose only solid tumors

Other molecular genetic methods used in oncology

FISH - fluorescent in situ hybridization

FISH (fluorescent in situ hybridization) - allows you to determine the exact location of the nucleotide sequences on the DNA or RNA, visualizing them with complementary fluorescent DNA probes. FISH detects chromosomal rearrangements (deletions, duplications, translocations, inversions). In oncology, it is most applicable to clarify the diagnosis and to determine tumor status when selecting therapy.

Detects chromosomal mutations: deletions, duplications, translocations, inversions

Advantages of the method

  • Fast results

Disadvantages of the method

  • Expedient to use when a mutation in a particular chromosome is suspected (cannot serve as a screening test)
  • Requires clarification of the diagnosis with other methods
  • Unable to detect balanced chromosomal rearrangements and point nucleotide variants (replacements, deletions, insertions)
  • False positive results are possible (1-5%)
  • High cost

arrayCGH - comparative genomic hybridization on microarrays

arrayCGH (comparative genomic hybridization on microarrays) is a method that detects unbalanced chromosomal rearrangements (deletions and duplications) of the entire genome. During the analysis, test and control DNA are labeled with different fluorescent dyes, mixed and hybridized on microarrays with DNA probes, quantitatively comparing the intensity of fluorescence.

Advantages of the method

  • Allows to analyze the presence of pathogenic variants in the whole genome simultaneously

Disadvantages of the method

  • Indicates only the presence of a variant and requires additional methods for clarification
  • Unable to detect balanced chromosomal rearrangements and point nucleotide variants (replacements, deletions, insertions)
  • High cost

PCR - Polymerase Chain Reaction

PCR (polymerase chain reaction) is a simple and effective laboratory diagnostic method that allows multiple copies of specific DNA or RNA fragments to be multiplied for qualitative or quantitative assessment of the fragment sought. In oncology, it can be used to detect single-nucleotide genetic variants (allele-specific PCR) or microRNA. More often, however, PCR is part of more sophisticated diagnostic methods, such as sequencing. In addition, PCR is widely used to detect the presence of potentially carcinogenic pathogens (HPV types 16 and 18, EBV infections, HBV and HCV, retroviruses, etc.).

Detects the presence of potentially carcinogenic pathogens HPV types 16 and 18, EBV infection, HBV and HCV, retroviruses, etc.

Advantages of the method

  • Relatively inexpensive
  • Accessible
  • Enables detection of potentially carcinogenic viral and bacterial DNA/RNA agents
  • Allows use of any biomaterial containing DNA or RNA

Disadvantages of the method

  • False positive results may occur
  • In diagnostic laboratories the analysis is usually limited to searching for the most common mutations in a given population
  • For best performance, it must be combined with other methods

A brief comparison of some of the characteristics of the methods described

NGS FISH aCGH PCR
Diagnosis of hereditary tumor syndromes Yes No Yes Yes
Tumor types Solid Solid and hematologic Solid and hematologic Solid and hematologic
Biomaterial used Tissue Blood, tissue, urine cell sediment Tissue, blood Any kind
Limitations

Not suitable for hematologic tumor types analysis

Number of mutations examined in a single approach is limited

Capable of detecting only large structural variations in the genome

High quality requirements for DNA samples provided

Tumor cell content must be greater than 50%

A limited number of specific mutations in a particular gene are examined in a single assay

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