Cancer genome diagnostics

Cancer is the second most common cause of death in the world, with the number of patients increasing every year. Its formation is the result of increasing life expectancy (more accumulated mutations) and exposure to ubiquitous mutagenic factors. Hence, research on the formation, diagnosis and treatment of tumors is of such great importance.

In the light of today’s scientific findings, we know that cancer is a genetic disease resulting from the accumulation of errors in genetic information, i.e. in our DNA. As a result of these changes, cells are formed that begin to divide in an uncontrolled manner, lose their proper tissue organization and stop fulfilling their functions. Their constant unregulated growth leads to the formation of a tumor.

WHAT IS THE DIFFERENCE OF A GENETIC VARIANT AND A MUTATION?

The occurrence of errors in the sequence of DNA is not always harmful and lies at the root of the genetic variability of organisms – it is thanks to them that biological evolution is possible. We call such errors genetic variants.

Unfortunately, some variants may have a negative impact on the further functioning of the cell or the function of proteins. It was customary to call them mutations (in Latin, mutatio – change). Currently, due to numerous controversies and misconceptions related to the term “mutation”, the guidelines of the American College of Medical Genetics and Genomics (ACMG) assume the use of a 5-point scale for determining the pathogenicity of genetic variants:

  1. pathogenic
  2. likely pathogenic
  3. of unknown significance
  4. likely benign
  5. benign

Only those considered pathogenic and likely pathogenic are currently considered clinically significant variants.

Genetic variants may arise spontaneously, e.g. as a result of errors in the replication process or a malfunction of DNA repair mechanisms. They can also be caused by environmental factors such as cigarette smoke, sunlight (UV radiation) or chemicals. Some of them have been with us for millions of years – it is thanks to them that we differ in e.g. hair color, body shape and other features that make us different from each other.

TYPES OF CHANGES IN DNA

There are two types of changes within DNA.

Changes occurring within one gene

      • point mutations – replacement of one nitrogen base with another
      • insertions – insertion of one or more pairs of nucleotides
      • deletions – the loss of one or more pairs of nucleotides
          • They can also be found in intergenic regions and splice sites (located at the intron-exon junctions).
          They have a huge impact on the expression of a given gene or may cause the protein encoded by a given gene to be malfunctioning or even not produced.

Changes taking place at the chromosomal level

    • chromosomal aberrations (deficiencies, duplications, inversions, translocations, etc.,
    • changes in the number of chromosome copies (trisomes, monosomes, polyploidy, fusions, etc.).

WHAT ENVIRONMENTAL FACTORS CONTRIBUTE TO CANCER?

GERMLINE VARIANTS - 'INHERITED'

If the DNA changes in the gametes, it will be passed onto the offspring. The inherited genetic variant will be present in all cells of the newly formed organism. These variants are passed down from generation to generation and are called germline variants. The vast majority of them are benign and not harmful to the functioning of the orgasism, but a small number may be responsible for the development of rare genetic diseases and thus predispose the person to the development of cancer.

It is assumed that 5-10% of cancers are caused by such pathogenic germline variants (especially in the APC, BRCA1 / 2, MSH2 / 6, TP53 genes).

The predisposition to cancer itself does not mean, however, that the disease will certainly occur, but it signals the need for more frequent and targeted diagnostics in order to detect possible changes still in the precancerous stage. 

To limit further changes, it is necessary to avoid exposure to environmental factors that increase the likelihood of cancer, such as smoking, poor diet or an unhealthy lifestyle.

Genetic tests should be especially undergone by people with a family history of cancer. This is particularly crucial in situations where several family members were diagnosed, the disease appeared in relatives at a relatively young age and some unique features of the disease were found, e.g. breast cancer in men, bilateral involvement of paired organs or synchronous tumors (two independent tumors in one organ).

There is a tendency to define environmental factors very generally as “unhealthy lifestyle.” Some factors do indeed include our poor habits, such as smoking, drinking alcohol, a bad diet or lack of exercise.

Others depend on external factors related to the outside environment, for example the increasing pollution, smog or exhaust fumes in the air. In addition, in the case of skin cancers, long-term exposure to sunlight (and more precisely to ultraviolet radiation) poses a significant risk, against which we can protect ourselves using sunscreen.

SOMATIC VARIANTS - 'ACQUIRED'

The vast majority of pathogenic variants leading to tumor formation are not hereditary but are caused by a random error during cell division or by other internal or external factors.

Variants that are present in only one cell of our body are called somatic. They are formed continuously throughout life and are usually harmless.

Our body defends itself against these mutations by finding the places where an error occurred and repairing it, or redirecting the damaged cell to the path of apoptosis, i.e. programmed death. However, when the presence of a variant (mutation) disrupts an important gene responsible for DNA repair or cell cycle regulation, then these important protective systems can be disabled.

Such a cell will accumulate successive somatic variants (both benign and pathogenic), dividing faster and faster. Subsequent genes will be turned off or unregulated until the final transformation of such a cell into a cancer cell. It will continue to multiply, causing the tumor to grow and in some cases also invade surrounding tissue. The consequence of these changes at an advanced stage may be distant metastases.

There is a tendency to define environmental factors very generally as “unhealthy lifestyle.” Some factors do indeed include our poor habits, such as smoking, drinking alcohol, a bad diet or lack of exercise.

Others depend on external factors related to the outside environment, for example the increasing pollution, smog or exhaust fumes in the air. In addition, in the case of skin cancers, long-term exposure to sunlight (and more precisely to ultraviolet radiation) poses a significant risk, against which we can protect ourselves using sunscreen.

MUTATION DIAGNOSIS

The most modern diagnostic method that enables the detection of genetic variants and other changes in the genetic material is the Whole Genome Sequencing technique (WGS). It allows for the analysis of the entire genome sequence – all genes, introns, intergenic and regulatory regions in one diagnostic test.

WGS is used both to assess the probability of developing a disease in the case of hereditary genetic mutations (pathogenic germline variants), as well as allowing for a precise analysis of the tumor’s development and the selection of personalized treatment (analysis of somatic variants) in cases where the disease has already developed.

In the case of detection of germline variants, the test material is a blood sample. Due to the presence of altered genetic material in gametes, it is passed on to every cell in the child’s body.

It is much more difficult to analyze the genetic material in the case of somatic variants because they are present only in certain tissues of the body, are not hereditary and accumulate over the course of life. In these cases, we use two samples from a given patient for testing, one of which is a tumor sample taken during surgery or biopsy, and the other is the patient’s peripheral blood (the control sample).

After isolating the genetic material, the DNA from both samples is sequenced and compared in order to find changes present only in the tumor’s genetic material. Thanks to such an analysis, we can accurately determine the location of the genetic change in the patient’s chromosomes and thus select the appropriate, personalized type of treatment, which significantly increases the effectiveness of the therapy.