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Clinical applications of NGS

The main purpose of the classic medical genetics is to identify genetic alterations disease-causing and, further, those disease-protective and health-linked. In this context, NGS revolutionized molecular genetics studies and gave space for a new era of genetic studies.

Numerous studies have been conducted looking for genes and biomarkers that can determine health preservation or disease occurrence and the best therapeutic strategy for each individual.

In the following topics, we will describe some examples where NGS can be applied in clinical practice.

Precision Medicine

Personalized or precision medicine is a new concept of practicing medicine that aims to treat a patient’s health uniquely, based on the individual characteristics of each patient (genetics, environment, behavior) to optimize and customize prevention, detection, and treatment strategies. 

Classically, all individuals with a particular condition received the same treatment, which could be beneficial and effective for some, ineffective for others, and could cause adverse reactions in others.

Genomics researches have greatly contributed to the advancement of precision medicine mainly by predicting the way mutations generate diseases with different clinical behaviors concerning their aggressiveness and treatment response and thus providing specific diagnostic strategies and target therapies of different diseases.

Targeted therapies are already a reality in breast cancer, colon cancer, lung cancer, melanoma, leukemia, and lymphomas, for example.

Some applications of precision medicine

  • Diagnosis and treatment of diseases contribute through the identification of tissue-specific biomarkers, drug development and diagnostic tests such as liquid biopsy.
  • Identification of patient subgroups in cases of multifactorial diseases.
  • Recruitment of sick subjects most relevant to the study in clinical trials.
  • Supports research and development of custom molecules.

How does this happen in practice?

A known example is the sequencing of the BRCA1 and BRCA2 genes in familial cases of hereditary breast and ovarian cancer. Detection of pathogenic changes in one of these genes indicates susceptibility to disease and thus guides the physician’s conduct in preventive treatment.

The same is true for non-polypoid colon cancer or Lynch syndrome, where gene sequencing of the MLH1, MSH2, and MSH6 genes is recommended for surveillance and preventive treatment.

Another example is for melanoma patients who have a mutation of the amino acid Valine for Glutamic Acid exchange at position 600 of the BRAF gene, in these specific cases, treatment with veramufenib is most appropriate.

Pharmacogenomics

Pharmacogenomics studies the differences in metabolism between different individuals. An example is cytochrome P450 (CYP450), a large family of genes that encode liver enzymes responsible for the metabolism of drugs and toxins in the body.

Genetic variants of these enzymes are found among different ethnic populations, with a wide variation in the genetic profile. Depending on the variation in gene sequence of this family, the individual may be classified as a drug metabolizer:

  • Ultra fast
  • Extensive
  • Intermediary
  • Poor

The time of drug-metabolism influences the effect of the drug on the organism and consequently on side effects and treatment failure.

The sequencing of CYP450 family genes, such as CYP2D6, for example, may guide the treatment of depression. The CYP2D6 metabolizes many psychiatric drugs and the CYP2D6 metabolizer profile for each patient has an important impact on side effects and susceptibility to chemical dependence on these drugs, thus influencing hospitalization time and costs.

Microbiology

The use of NGS in microbiology allowed the replacement of detection and conventional characterization of microorganisms by analyzing morphology, staining properties and/or their metabolic criteria for molecular detection through the genome of microorganisms.

The microbiome is the genetic material of all microorganisms (bacteria, viruses, fungi, and archaea) in a given environment, such as the human body. Microorganisms interact dynamically with their hosts and among themselves.

These interactions determine the composition of the microbiome and influence not only the characteristics of the ecosystems in which they reside but may also have widespread effects affecting host physiology and/or site conditions.

By sequencing, the microbiome can identify all microorganisms in an environment as well as can detect the sensitivity of these microorganisms to a given drug or also track sources of outbreaks of infections.

Several studies are analyzing the composition and influence of microbiome changes in different areas such as:

Health:

  • Mother and child microbiome;
  • The microbiome of elderly individuals;
  • The microbiome of thin individuals.

Diseases:

  • Microbiome and pathophysiology of cancer;
  • Cancer prevention
  • Microbiome as a biomarker
  • Microbiome and obesity
  • Intestinal microbiome as a biomarker of chronic inflammatory diseases
  • Oral Microbiome and Cardiovascular Diseases
  • Nervous System and Intestinal Microbiome
  • Aging and gut microbiome
  • Microbiome and allergy
  • Microbiome and Inflammatory Bowel Diseases
  • Microbiome and autoimmune diseases

In addition to studies in the area of veterinary, environment and agriculture. 

Today, there are already laboratories that offer the microbiome sequencing service.

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