Why and How Do We Perform Genetic Testing and Mapping in Cancer? What Is Sequencing?

Cancer as a Genetic Disease

Cancer arises from changes in the genetic makeup of the body's cells. Each cancer type, and even the same cancer in different patients, may have different genetic characteristics. Understanding the genetic makeup of a patient's cancer therefore plays a key role in understanding how the disease will progress and which treatments may be most effective.

Genetic tests allow us to map a cancer's genetics. This map helps us understand which genetic mutations cancer cells carry, how those mutations arose and how they may change during treatment. Information obtained through methods called genetic sequencing helps patients receive more effective treatment and guides healthcare professionals.

Why Are Genetic Tests Important?

Genetic testing in cancer has several main purposes:

• Developing Targeted Therapies: Genetic mutations identified in cancer cells determine which treatments may be effective. For example, lung cancer patients with an EGFR mutation respond to treatments specific to that mutation.

• Monitoring Treatment Resistance: In some patients, cancer cells may develop resistance to treatment. Genetic analyses allow us to understand how this resistance develops and to develop alternative treatments.

• Early Diagnosis and Screening: Genetic tests may help detect cancer at an early stage. In particular, using MCED (Multi Cancer Early Detection, meaning early detection of multiple cancers) tests, analysis of cell-free DNA (cfDNA) or circulating tumor DNA (ctDNA) can find traces of cancer in the bloodstream.

• Assessing Familial Risk: Identifying inherited genetic mutations helps assess cancer risk for the patient's family members. For example, BRCA1 or BRCA2 mutations increase susceptibility to breast and ovarian cancer.

Samples Used for Genetic Analysis in Cancer

The types of samples used to analyze a cancer's genetic makeup directly affect the quality and significance of the data obtained. The main sample types are:

1. Tumor Samples

Biopsies from cancerous tissues or surgically removed tumor specimens are the materials most commonly used for genetic analysis.

• Biopsy: A small sample of tumor tissue is taken. This is particularly preferred for localized cancers.
• Resection: Surgically removed tumor tissue allows more extensive genetic analysis.

These samples are processed in the pathology laboratory to understand the genetic makeup of cancer cells and then prepared for sequencing.

2. Germline (Inherited) Samples

Samples from a patient's normal tissue or blood are used to identify germline (inherited) mutations . Detecting inherited mutations allows genetic risk to be assessed for the patient's family.

• For example, by detecting germline mutations such as a TP53 mutation, we can identify hereditary cancer predisposition syndromes such as Li-Fraumeni syndrome through this analysis.

3. Cell-Free DNA (cfDNA)

DNA fragments released into the bloodstream when cancer cells die offer a major opportunity to understand a cancer's genetic makeup. Because cfDNA analysis is noninvasive, it is useful when a biopsy cannot be performed. In metastatic cancer, it is also effective for understanding genetic diversity across different tumor regions.

What Is Genetic Sequencing and How Is It Performed?

Genetic sequencing analyzes the DNA sequence to identify genetic variations. This technology can detect mutations in cancer cells. The advanced technique most commonly used for this purpose today is NSG technology.

1. The Sequencing Process

• First, the sample to be analyzed (tumor, germline or cfDNA) is sent to the laboratory.
• The sample is processed to extract and purify DNA.
• The DNA sequence is determined using highly sensitive instruments.
• The results are analyzed using bioinformatics software.

2. Interpreting Sequencing Results

Sequencing results go beyond identifying genetic mutations. The data obtained:

• Determine whether mutations are somatic or inherited.
• Help assess targeted treatment options.
• Track changes that develop during treatment.

Tumor Heterogeneity: The Dynamic Nature of Cancer

A cancer's genetic makeup is not static. Different regions of even the same tumor may contain different genetic mutations. This is called "tumor heterogeneity."

Understanding Heterogeneity Through Examples

• Of two samples taken from different regions of a tumor, one may carry mutations in genes A and B while the other may not.
• In metastatic cancer, a sample from one lesion may also differ genetically from samples of other metastatic lesions.

Using multiple samples when mapping a tumor's genetics therefore allows more accurate results.

The image above simply summarizes the sample types used to understand cancer genetics and how they contribute to genetic analysis results. The following explanations will help clarify the image:

1. Tumor Samples (Orange)

   • Tumor Sample #1: The first biopsy sample taken from a tumor or a tissue specimen removed by surgical resection. This sample allows the genetic mutations of cancer cells to be analyzed. The mutations shown as orange stars in the image are somatic mutations detected in this tumor sample.
   • Tumor Sample #2: A second sample taken from another region of the same tumor or a metastatic lesion. The image emphasizes that this sample may contain different mutations, that the tumor is heterogeneous and that mutations can change over time.

2. Germline Samples (Purple)

   • Germline DNA (Normal Tissue or Blood): Germline samples obtained from healthy noncancerous tissues or blood are used to identify inherited mutations. The absence of orange stars in the germline sample in the image indicates that these mutations are not inherited but occurred during cancer development.

3. Cell-Free DNA (cfDNA) Sample (DNA in the Blood)

   • cfDNA Sample: DNA fragments released from tumor cells into the bloodstream. The image shows a mixture of mutations from the tumor samples in the cfDNA sample. This illustrates the potential of cfDNA to detect the cancer's overall genetic makeup and mutations from all tumor regions.

4. Tumor Heterogeneity

   • The diagram in the upper-right corner of the image highlights cancer's dynamic and heterogeneous nature. Genetic differences between tumor samples #1 and #2 (such as different mutations in genes A, B and C and a newly emerging mutation in gene F) represent changes in cancer over time. This explains why analyzing multiple tumor samples is important for treatment planning.

The Difference Between Inherited and Somatic Mutations

There are two main types of genetic mutations in cancer:

1. Inherited Mutations (Germline): Present in all cells of the body and can be passed on to family members.
2. Somatic Mutations: Occur only in cancer cells and are associated with environmental factors.

Effects on Treatment

• Inherited mutations require genetic counseling as well as targeted therapies.
• Somatic mutations play a critical role in understanding cancer development.

Cell-Free DNA: A Technology of the Future

Cell-free DNA analysis is a revolutionary method in cancer genetics. Its advantages include:

• It is noninvasive (performed using a blood test).
• It provides the overall genetic profile of the tumor in metastatic cancer.
• It can be used to monitor treatment response or detect early recurrence.

However, this technology still has limitations, and more research is needed for wider use in clinical practice.

The Future of Genetic Analyses in Cancer

Genetic analyses form the cornerstone of personalized medicine in cancer. The future will bring:

• More sensitive genetic tests,
• Widespread cell-free DNA analysis for early diagnosis,
• Algorithms capable of predicting treatment resistance in advance.

Conclusion

Genetic tests in cancer are among the most powerful tools in modern medicine. They not only personalize treatment options but also help us understand cancer's dynamic nature and develop more effective strategies. However, accurate interpretation of genetic analyses and assessment in a patient-specific context are essential. For patients and healthcare professionals alike, these results offer a promising light in the fight against cancer.