Tips for carrier screening testing for latent genetic diseases

Tips for carrier screening testing for latent genetic diseases

Along with the important points of the American College of Obstetricians and Gynecologists (ACOG) Theory Committee published in March 2017

Carrier Screening is a term used to describe a genetic test.

Which is performed on asymptomatic individuals

 To determine whether it has a mutation or an abnormal allele that leads to a specific disease. .

This screening is done for a specific disease or several diseases at the same time.

In general, carrier screening to detect the status of carriers in asymptomatic patients for:

Screening for defeated genetic diseases (either autosomal recessive ‌ - or dependent on the X-linked recessive chromosome ‌ -) in asymptomatic couples who have no increased initial risk of having a The carrier condition for a particular disease is used according to their family history or that of their unmarried spouse.

In total, 1,300 diseases fall into these two groups of genetic diseases.

The incidence of these diseases in newborns in the whole society is between 2 to 3 percent, which in family marriages reaches 2 to 3 times the general population (ie the prevalence in consanguineous marriages is 6 to 3 percent). Reaches 8%).

Importance of carrier screening:

If both parents are carriers of a defective gene, they have a 25% chance of getting sick and a 50% chance of getting the carrier (similar to their parents). .

If a healthy mother carries a mutation in one of her X chromosomes, her baby's chances of getting sick are 50% and her daughter's chances of getting sick are 50%.

More than 80% of children with latent genetic disorders are born into families with no family history of the disorder. .

20% of neonatal deaths in the United States are due to latent genetic disorders.

Definitions of some genetic terms:

Alleles: Allergies are different forms of a gene, which occupy the same place on homologous chromosomes and affect a particular trait in different ways.
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Homozygote: When a person has the same pair of alleles, they are said to be homozygous.
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Heterozygous: فردی When a person has a different pair of alleles, it is said to be heterozygous (heterozygous).
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Compound heterozygotes: مرک The term compound heterozygotes is used to describe a genotype in which there are two different mutated alleles of a gene, not a natural allele and a mutated allele.

Variants: Alleles with a frequency of less than 1% are called variants.

Mutation: A genetic change in which the biological traits of some individuals change a species.

More precisely, mutations are changes in the DNA sequence.

Mutations can occur in any area of ​​DNA
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Genetic diseases: They are caused by different types of mutations (point mutations, elimination, replacement, doubling, displacement, and reversal) in genes.

These mutations may occur in structural sequences of genes or regulatory sequences
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Interns: These are parts of the genome; In the process of transcribing DNA codes, copies are made from them, but in the process of trimming, they are removed with the help of the trimmer enzyme.

Therefore, in the process, proteins are not made from them.

For this purpose, they are called introns, which are found in the DNA arrangement in the labia and between the gene codes گز (Exxon) as well as in the RNA sequence after transcribing the DNA codes. .

These strains are found in many organisms and even in some viruses.

Their size can be very large. The word intron means the area between the intragenic region genes.

However, it also means intervening sequences.

Exon or statement: Nucleic sequences are acidic; Which were always RNA; They can be used to make protein.

They are separated from the introns by the RNA فر stopping process and the connection of the exons to each other and the removal of the introns.

It has even been observed that sometimes exons on different and distant genes can be linked together.

According to the Hardy-Weinberg formula

(P + q) 2 = 1

  p2 + 2pq + q2 = 1

p = ‌ In autosomal recessive diseases, the rare defeat equals 1 = the frequency of healthy alleles

q = Faulty allele frequency

2pq = car carrier frequency or ‌ (carrier frequency)

q2 = disease incidence or disease incidence rate in the community جامعه (disease incidence)

For example, if the prevalence of the disease in a society is 1 in 10,000, then the frequency of carriers is 1:50.

And if the carrier frequency of a disease is 1: 100 (‌ 2pq‌), the prevalence of the disease is 1 in 40,000 (because q = 1: 200‌). .

• Note: For two reasons, the prevalence of latent genetic diseases in Iran is higher:

1 - The prevalence of consanguineous marriages,

2 - High intra-marital coefficient ‌ (is the probability of inheriting a pair of alleles by a person from his ancestor through parents),

- The total rate of consanguineous marriage in Iran is 38.6% (fifth in the region after Saudi Arabia (54%), Kuwait (54%), Jordan (50%) and Pakistan (40-40%).

        2. Intra-marital coefficient in Saudi Arabia 0.024
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- Intra-marital coefficient in Iran ‌ ‌ ‌. ‌ 1 0.0185
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      درون - Intra-marital coefficient in Canada ‌ 0.00004 to 0.0008

       درون - Intra-marital coefficient in the United States 0.001 to 0.005

Therefore, in general, latent genetic diseases alone may be a rare disease, but the cumulative prevalence of these diseases is relatively high.

The screening panels used include:

- ethnic - specific.
Such as panels for Ashkenazi Jewish Jews, Eastern and Central European Jews, French Canadians, and Louisiana Americans (who are of French descent).

Tay-sachs, also known as Gangliosis GM2 and Hexamine A deficiency.

 And sometimes in Iran, it is mistakenly written and read as "Thai Sax".

 It is a storage disorder associated with mental retardation, blindness, seizures and death before the age of five.

It is a molecular ganglioside that is formed by combining two components of glycosafengolipid with one or more silicic acids such as n-acetyl norepinephrine acid.

Due to the high prevalence of sickle cell anemia in African Americans, panels containing genes involved in the disease are used.

- pan-ethnic:
It can be performed for all patients, regardless of ethnicity or race, and includes several limited diseases with a relatively high prevalence.

Diseases such as Cystic Fibrosis, Fragile X Syndrome and SMA are found in almost all breeds with the same prevalence and fall into this category.

- Expanded:
This panel can be performed for all patients regardless of ethnicity or race and can be screened by different laboratories, including 5 to 10 patients, up to several hundred diseases simultaneously.

Almost all ECS panels are based on the NGS method, and simultaneously this test can screen hundreds of defective genetic disorders in one thigh.

Just make sure that this method is not able to diagnose SMA (Spinal muscular atrophy) ‌ (in general, the NGS method is not able to diagnose genetic disorders caused by large deletions).

And SMA is a gene deletion on chromosome 5 that is responsible for producing the protein SMN ‌ - ‌ survival of motor neuron.

That plays an important role in keeping motor neurons alive) and that another method (such as MLPA) should be used to screen for SMA at the same time.
Carrier screening should be made available to women as an acceptable strategy for pregnant women and as a prenatal care.

It should be recommended to all pregnant women or on the eve of pregnancy (especially for cystic fibrosis and spinal muscular atrophy with CBC for thalassemia screening and other hemoglobinopathies) and should be given as needed.

 And the patient can do this test voluntarily or not.

 This task has been assigned by this guideline to obstetricians, health care providers and genetic counselors.

In today's multi-racial societies, especially in some countries, it is becoming increasingly difficult to determine an individual's ancestry.

Note that these tests cannot detect all screened patients, and there is always a residual risk in each test.

Because no test is able to screen all mutations or alleles that cause the disease, it is also possible to increase de novo (or new) mutations.

Fragile X screening for permutation carrier screening in women with a family history of fragile X یا disorders or mental disability suggesting fragile X syndrome, or in women with a history of ovarian insufficiency ) Should be recommended. .

- Additional screening should be based on family history or specific ethnicities.

- Married couples should be given genetic counseling and explained that they are at high risk for developing autosomal recessive disorders, as well as the limitations and benefits of testing should be explained to patients.

- This screening does not replace neonatal screening, but effectively covers the shortcomings of this screening.

- If a woman is a carrier of a particular disease, her husband must also be screened and genetically engineered for that particular gene.

- If both couples are carriers and are diagnosed before pregnancy, the patient should be given various suggestions such as donated gamete, PGD Pre (Preimplantation genetic diagnosis) or diagnosis during pregnancy.

People who have a family history of a genetic disorder are more likely to benefit from carrier screening than the type of mutation involved.

 By diagnosing the type of mutation, we can make faster diagnoses for them during pregnancy.

Diseases reported in this panel must have a number of criteria, including:

- Its transport frequency is 1: 100 or more.

For example, the frequency of transmission in some diseases in the white population is as follows:
CF: 1 in 25
SMA: 1 in 35
PKU: 1 in 50
MCAD Def: 1 in 50
Galactosemia: 1 in 87
Gaucher disease: 1 in 100

- The disease has a definite and defined phenotype.

- Have detrimental effects on quality of life.

- Cause physical or cognitive impairment.

- Need medical or surgical interventions.

- Begin the disease from the beginning of life.

- Screening conditions should be such that the disease is diagnosed during prenatal period and the opportunity:

- Interventions during this period to improve the outcome of pregnancy

- Changing the management of childbirth in order to optimize the outcome of the baby

- Teach parents about the special care needed after birth.

- Screened diseases should not include diseases that are the beginning of the disease in adulthood.

In the past, ACOG has supported ethnic-specific panels and recommended that they be done before and during pregnancy.

However, by consulting with the patient and explaining the limitations, benefits and alternatives of the tests.

But at Gideline March 2017, ACOG should explain to all couples of the same age cons (consanguinity) genetic counseling and their increased risk for recurrent disorders that can affect their child, and for Encourage carrier screening.

Finally, it should be made clear that screening is an optional condition, and after counseling, the patient can do it or not at all.

Carrier screening as a prepregnancy is the most ideal form of screening because:

If there is a mutation in the couple, it is possible to prevent the birth of the baby with the disease.

This prevention is done in one of the following four ways:

1- PND (prenatal diagnosis): In this method, if the couple identifies common mutations and if they have an abortion license for that specific disease, at a certain time during pregnancy, for sampling of placental or fluid villi. Amniotic fluid;

Then, that part of the gene will be examined in the embryonic cells, and if the fetus has the disease, an abortion permit will be issued by forensic medicine.

2- PGD (Preimplantation genetic diagnosis): This method is used in cases where the disease is not allowed to have a legal abortion or the abortion poses a high risk to the mother from the doctor's point of view.

In this procedure, the fetus is formed outside the uterus, and after examining a cell from the fetus and performing genetic tests, the fetus is transferred to the mother's uterus if it is not infected.

      3- They can use sperm, egg or embryo donation method

     4 - Finally, they can think of adoption.

Note that as carrier screening increases, care must be taken to ensure that a patient is not re-screened for a specific genetic disease that has already been screened and to avoid incurring unnecessary costs. .

Over time, genetic tests are offered with higher diagnostic power, but care must be taken that the patient should not be screened more than once for a specific genetic condition.

Why is pre-marriage pre-pregnancy testing preferable?

1- Concern about unwanted pregnancy and lack of sufficient opportunities for the required examinations

2- Having the opportunity for couples who, by obtaining information about the test results and being fully aware of the advantages and disadvantages of prevention methods (such as PGD and PND), can make an informed decision about the conditions ahead and if not Abandon marriage
Past studies:

1- In a study of 23453 patients from different races, it was found that 24% of patients are carriers of at least one defective gene based on mutation (417 mutations are related to 108 different diseases) and 5.2% of patients are carriers of more than They are a disorder.

2. In 2012, Dr. Benn et al., In a survey of 222 ACOG gynecologists, reported that only 15% of these physicians recommended ECS panels to their patients, and 52% of these patients. They have done the test. .

3. One of the largest studies of Dr. Haque IS et al. In 349,790 patients (who performed the test between 2012 and 2015) concluded that the prevalence of genetic disorders in the United States 1: 550 and 1: 516 in the Middle East.

4- In Dr. Strinivasan's study, it was found that 35% of carriers are at least 1 variant of pathogen or quasi-pathogen.

Preliminary results of our study in Iran:

In couples, it indicates that:

1. About 13.8% of couples have a pathogenic or quasi-pathogenic variant.

2. About 3.2% of couples have two pathogenic or quasi-pathogenic variants.

3. About 1.0% of couples have a combined heterozygous variant.

And in each person it indicates that:

1. About 36.2% of patients have a pathogenic or quasi-pathogenic variant.

2. About 11.8% of patients have two pathogenic or quasi-pathogenic variants.

3. About 4.3% of patients have a combined heterozygous variant.

Information analysis:
After the raw data of the patient is obtained, first the total number of variants of the two individuals is determined separately and jointly, and then using filters such as:

1- Heterozygous filter: The purpose of obtaining heterozygous variants is pathogenic or quasi-pathogenic, because homozygous variants, if they were pathogenic, would definitely show themselves in the parents.

2- Location: Only the areas where the most pathogenic mutations are observed are examined.

3- Minor allele frequency (MAF) ‌: The frequency of sub-alleles (which are in the second place after the main alleles or major) is used.
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The type of variant is then examined using databases such as ClinVar, which is affiliated with the US Department of Health and VarSome. (Switzerland).

These variants are then verified based on information that includes:

1- Quall: which shows the accuracy and quality of reading and numbers below 20 are rejected and numbers above 60 are approved.

2- CADD: It is a tool for assessing the dangerousness of any nucleotide change and in general the numbers below 14 are unacceptable and the larger the number, the more valid this change is.

3- Coverage and Allele Coverage: Shows the symmetry of the readings.

4 - Repeat: shows the number of repetitions of the variant in the study population and the higher this repetition, the better the variability of the variant.

It then compares the variants with other databases such as InterVar (which changes depending on which part of the protein the mutation is based on. In general, whatever the mutation is at the site of the protein or active site). Variation becomes even more important) and PolyPhen is reviewed and a final report is made.

Final recommendation

The American Society of Obstetricians and Gynecologists (ACOG) and the American Medical Genetics Association (ACMG) have recommended that this test be applied to all women of childbearing age.

Performing this test can provide important information to patients who:

- They are now pregnant or planning to become pregnant.

- They have a high risk of having a specific disease due to their special ethnicity.

- Have a family history of a genetic disorder,

- Have a plan to donate an egg, sperm or fetus,

- They like to know more about the risk of reproduction for the birth of a child with a genetic disorder.