University of São Paulo: Genetic testing and counseling can save lives and help understand who we are

DNA can tell a lot about us: inside each of our cells there is information about the body’s past, present and future. To discover this information, the key is the genome , the set of genetic information (i.e. the genes) of an organism. It is the genome’s role to command our cells to build, rebuild and manage our bodies throughout our lives. Genes are small functional stretches of this genome, essential for biological functioning.

The genetic material that makes up the genome can take two forms: condensed, becoming a chromosome , or open, with its huge DNA molecules unfurled (there are 2 meters of DNA inside each of our cells).

As the body’s manager, the genome contains a lot of valuable information about us and even about our ancestors. To obtain them, scientists have created different analysis techniques: there are macro tests, analyzing the chromosomes, and more focused tests, which look at groups of specific genes within the DNA strands.



From diagnosing diseases to identifying the father and ancestry, genetic tests can save lives and be a source of discoveries for individuals and an entire people.
If you’ve come across repeated cases of cancer, neuromuscular disease, birth defects or malformations in your family, genetic testing may help. They are recommended when there is a suspicion of a condition with a genetic cause, as in the examples above, or a rare disease (80% of them are genetic in origin). It is important to highlight that the tests must always be reconciled with the patient’s clinical data. These genetic tests can be used both to obtain the diagnosis of an existing disease and to prevent a child from being born with the gene that develops the disease.

But not only diseases live genetics: our cells also tell who our father is and where our family came from, which helps to rescue the history of a people. Below, you will learn about the main genetic analysis techniques and types of tests, and the work of Genome USP , the largest care center for people with genetic diseases in Latin America, which develops a series of important research in the area of ​​genetics and offers tests at low cost to the population.

TESTS BY CHROMOSOME ANALYSIS
Because it is larger and more visible, the chromosome was the first genetic structure we were able to observe.

KARYOTYPE
In the karyotype, the first type of genetic test developed in history, someone’s chromosomes are observed under a microscope, from the harvest of some cell. The purpose of the karyotype is to analyze whether there is a change in the number of chromosomes of the individual and even in the structure of any of the chromosomes, mainly in relation to size, also detecting the exchange of pieces between them. In this test it is possible to identify, for example, Down Syndrome, which is characterized by the presence of a surplus chromosome, called “21”.

GENOMIC ARRAYS
More recent, arrays are able to identify alterations with a greater level of detail, verifying smaller losses or gains of genetic material in the chromosomes and evaluating the amount of DNA present in the individual. They are indicated to diagnose diseases resulting from excess and lack of genetic material.
TESTS BY GENE ANALYSIS
The latest tests are able to analyze not only the chromosome, but also smaller stretches of the open DNA molecules, in much more detail, identifying the gene sequence letter by letter.

Sanger sequencing
As the complete set of genetic information is very large, three different types of analysis are used depending on what you want to find.

Frederick Sanger developed the first form of DNA sequencing in history, which reigned from the 1980s to the 2000s — from there, the techniques began to sequence DNA on a large scale, with millions or billions of fragments at once, while the Sanger sequencing can only sequence a fragment.

This technique does a focused analysis to read specific genes (or groups of genes). Although older, it can be recommended when there is a suspicion that a single gene, or a small number of genes, is responsible for a clinical condition. For example, if a child is suspected of having a neuromuscular disease, Sanger Sequencing would be ideal for testing it for genes already known to be associated with neuromuscular disease.

Exome sequencing
This is a newer test that uses the technique of Next Generation Sequencing (NGS), which sequences millions or billions of DNA fragments at once.

The test simultaneously analyzes all known human genes that encode the synthesis of products in cells — that is, whose functions in the cell are defined — and this set is called an Exome.

Unlike the case of Sanger Sequencing, Exome Sequencing is indicated for situations in which it is not possible to formulate a hypothesis of which gene, or which genes, are responsible for the occurrence of a given disease.

genome sequencing
When Sanger Sequencing and Exome Sequencing do not detect what is the change in genetic material that explains a person’s disease, it is possible that this change is outside the sequence of known genes.

In these cases, which are very specific, full genome sequencing may be recommended. However, Genome Sequencing is a low cost-benefit test, as science still knows very little about genes outside the Exome.

PAST, PRESENT AND FUTURE
Genetics allows us to diagnose diseases in newborns, find out who the father of a child is, and what peoples we are descended from.

PATERNITY TEST
DNA has many variations that create an individual’s unique imprint. These variations can be used to compare people. In the paternity test, the procedure analyzes whether the child has a part of the possible father’s marks. It is customary to use blood or saliva to do the test.

ANCESTRALITY TEST
A genetic ancestry test aims to try to define the geographic origin of someone’s ancestors.

And how is that possible? There are variations in parts of the genome of individuals that are found with high frequency among peoples of a certain geographic origin. These genetic markers can be read as characteristic of a population.

From the genotype of an individual, which has many of these markers, it is possible to create a kind of map where it is defined, with a high probability of success, from which geographic region of the planet each DNA segment of that person came.
In addition to curiosity, ancestry tests can be important for science and public health policies: it is possible to observe the different portions of the genome with different ancestries and estimate which genetic diseases are most likely to be developed within that group, according to with the genetic frequency of the source populations.

Genome USP does not offer ancestry tests as a service to the population, but uses them in its research.
foot test
FOOT TEST
All children in Brazil must do so, it is mandatory by law. Despite not directly analyzing DNA, the heel prick test is considered a genetic test, since when analyzing an error in the baby’s ability to digest a certain substance, it is possible to discover an error in the DNA.

This test was initially created to detect phenylketonuria, a disease that makes the child unable to degrade an amino acid that comes from proteins, phenylalanine. As a result, the substance accumulates in the nervous system and leads to intellectual disability.
The heel prick test can include different diseases. The basic version tests for phenylketonuria, hypothyroidism, and cystic fibrosis. Other conditions may be included depending on the cost and frequency of illness in a particular region of the country.

The private network offers an expanded test, which detects 48 conditions. But the vast majority of them have a very low frequency in the Brazilian population, which does not make their testing viable in the Unified Health System (SUS).

USP GENOME SERVICES
Genome USP maintains counseling and genetic testing services for the population. The works are not for profit and are offered at more affordable prices than the market. Patients collaborate for research while scientific advances contribute to people’s health
genetic counseling
GENETIC COUNSELING
In genetic counseling, the patient will be able to obtain detailed information about a certain condition that he has and may be of genetic origin.

For this, a personal and family history is first collected with the evaluation of clinical and genetic tests that the patient has already had at other times. If necessary, new tests are indicated.

Then, data from past and current exams is analyzed so providers can diagnose, confirm, or rule out a known genetic condition.

The laboratory also offers prenatal guidance for couples or pregnant women at risk of occurrence or recurrence of genetic diseases in their offspring.

In addition to genetic counseling, Genome USP also provides genetic consulting services , aimed at health professionals and researchers, which may include: interpretation of genomic tests, such as complete exome sequencing, panels and even array-CGH (microarrays genomics) and analysis of exome and genome data.

Who is genetic counseling recommended for?
People who were born with a disease
People who suspect they have a genetic disorder or who have relatives diagnosed with a genetic disorder
Children with delayed physical, neurological or motor development
Couples who are having difficulty getting pregnant or who have had more than two miscarriages
People with visual or hearing impairment that could be genetic
The USP Genome meets
Neuromuscular and neurodegenerative diseases
craniofacial diseases
Autism, developmental disorders and intellectual disability
hereditary cancer
How much does it cost?
Test values ​​are variable. The cheapest — which cover specific diseases — are in the range of R$ 550. The most complete exams can cost up to R$ 11 thousand, but the values ​​are below what is charged in private laboratories.
Once the genetic condition is identified, Genome USP informs the patient of the implications for physical or mental health. In addition, the researchers explain to the patient the mechanism of inheritance of the genetic condition and present the calculation of the risk of occurrence or recurrence in the individual’s siblings or children. Asymptomatic family members — who do not have symptoms but carry the change in their genes — and the risk of developing the disease or passing it on to their descendants are also identified.

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GENETIC TESTING LABORATORY
COVID-19
Genome USP offers rapid molecular testing for the detection of SARS-CoV-2 virus from saliva samples. The test is low cost
LABORATORY, CALL AND RESEARCH CENTER
Born in the 2000s, the USP Genome is linked to the USP Biosciences Institute (IB). The largest care center for people with genetic diseases in Latin America carries out research in Human and Medical Genetics, maintains a Genetic Counseling service and genetic tests for the population, in addition to developing activities related to education and technology transfer.

It all started in the 1960s, with the creation of the Department of Human Genetics at USP by Oswaldo Frota-Pessoa, one of the pioneers of Medical Genetics in Brazil, who began to care for families with genetic diseases and in socioeconomic vulnerability.

In the following years, researchers began to develop biochemical and cytogenetic tests associated with their research projects in different genetic diseases.

It was in the 1980s, with the introduction of Molecular Biology techniques applied to Human Genetics, that a great revolution in the knowledge of the area occurred. The group pioneered research on the location and identification of new genes and pathogenic variants responsible for diseases.

In 2000, the Center for Research on the Human Genome and Stem Cells (CEGH-CEL) was founded , which is one of FAPESP’s seventeen Research, Innovation and Dissemination Centers. With the creation of the Center and the large number of genetic tests that had already been developed over the years, a centralized laboratory was created exclusively for diagnosis as a service: the Laboratory of Genetic Tests of CEGH-Cel (LabTEG).

As LaBTEG is located at CEGH-CEL, a leading and internationally recognized research center, patients benefit from the latest scientific advances. Currently, with its own infrastructure and modern methodologies, such as Next Generation Sequencing, Genome USP offers tests for approximately 570 genes/diseases.

Genome USP has a team made up of professors, researchers, doctors, health professionals and specialized technicians, with the participation of undergraduate and graduate students, totaling around 120 participants.

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