Genetics

• Prenatal constitutional genetics
• Postnatal constitutional genetics
• Somatic genetics
• New technologies

Eurofins Biomnis, as a medical biological laboratory, is authorised to perform genetic examinations as part of prenatal screening, prenatal diagnosis and to study the genetic makeup of an individual. In addition, the individuals performing these examinations are either certified by the biomedicine agency or have demonstrated expertise in the field. Finally, the analyses are subject to accreditation according to ISO15189.

The Human Genetics department has laboratories specifically designed for DNA analysis. These methods are derived from PCR (Polymerase Chain Reaction). The diagnostic strategies use a range of different methods, depending on the type of gene investigated: PCR using hydrolysis probes, PCR-RFLP, PCR-SSO, methylation-specific PCR, LAMP-PCR, the study of microsatellite markers or sequencing.

Eurofins Biomnis also uses cutting-edge technologies, namely SNP (Single Nucleotide Polymorphism) array or DNA chips and NGS (Next Generation Sequencing) or high-throughput sequencing.

• The SNP array technology uses a complete analysis of the genome to identify any gain (duplication, triplication, etc.) or loss (deletion) imbalances in the genetic material. These imbalances are also referred to as CNV (Copy Number Variation) and can be the cause of genetic diseases.
• High-throughput sequencing is able to simultaneously sequence millions of DNA fragments from a single sample.
• A sample can also be prepared so that only gene coding regions are sequenced, as in exome sequencing, or only for limited number of genes, as in panels. This means that high-throughput sequencing can be used to identify minute variations in nucleotides.

The everyday activities of the genetics department and its development projects are performed by a dedicated multidisciplinary team, consisting of expert technicians, scientific managers, bioinformatics specialists and clinical biologists.

Prenatal constitutional genetics

When screening freely circulating foetal DNA for Down’s syndrome, previously referred to as NIPT (non-invasive prenatal testing), the data generated from the sequencing allows screening for Down’s syndrome as well as other foetal chromosomal abnormalities. This test is based on the presence of freely circulating foetal DNA in the blood of pregnant women. The conditions for prescribing and performing this test are governed by the Decree of 14 December 2018 on the conditions for the performance of prenatal screening and diagnosis in France.
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Diagnosis of foetal chromosomal abnormalities

Rapid screening for the main types of aneuploidy from foetal samples

When taking a foetal sample (chorionic villi, amniotic fluid, foetal blood, we primarily screen for Down’s syndrome, Edward’s syndrome or Patau syndrome and sex chromosome abnormalities using a rapid technique called QF PCR (quantitative fluorescent PCR), which can give an initial rapid result in 48 hours. This result will then be confirmed using a conventional cytogenetics analysis (karyotype) or chromosomal microarray analysis (CGH array or SNP array).

Chromosomal microarray analysis (CGH array or SNP array)

In the antenatal period, if a sample of chorionic villi, amniotic fluid or foetal blood is taken, a chromosomal microarray analysis (CMA) can be conducted. It is mainly recommended when there are ultrasound warning signs. This pangenomic chromosome analysis can identify minute chromosomal imbalances that are difficult or impossible to identify using a karyotype. Gain (duplication, triplication, etc.) or loss (deletion) imbalances in the genetic material are referred to as CNVs (Copy Number Variation).

Eurofins Biomnis has SNP array (Single Nucleotide Polymorphism) technology, which in addition to being able to identify CNVs, can identify regions of loss of heterozygosity (LOH). The SNP array technique can also be used to identify triploidy, and can thus be used in the genetic study of foetal death.

Diagnosis of foetal molecular abnormalities

In cases of a family history of severe genetic diseases or concerning foetal ultrasounds, most often at the request of a CPDPN (French Multidisciplinary Centre for Prenatal Diagnosis), we offer routine screening using molecular biology for certain genetic diseases.

As such, we offer the following prenatal screening tests: fragile X syndrome, mucoviscidosis, Prader–Willi syndrome, Angelman syndrome and screening for uniparental disomy (primarily chromosomes 14 and 15).

In addition, in certain specific cases, we offer screening for specific mutations linked to a familial genetic disease using targeted Sanger sequencing.

Postnatal constitutional genetics

Pangenomic analyses (screening for genetic abnormalities across the entire genome)

Exome

For rare diseases, new diagnostic methods such as whole exome sequencing improve the speed and effectiveness of diagnosis.

This technique has been offered by Eurofins Biomnis since 2016 and can simultaneously sequence the coding regions of genes that can contain 95% of currently known mutations. With strong experience in this field, Eurofins Biomnis offers this examination for aetiological investigation of mental disorders, neurodevelopmental disorders or syndrome-based disorders, for clinical pictures that do not suggest screening for an abnormality in a gene or panel of genes (or if the results were negative for these tests), or where an organ is affected (kidney, heart, etc.).

The benefits of this approach are that all of the genes are studied simultaneously and the interpretation of the results can rapidly incorporate the latest medical discoveries.

Chromosomal microarray analysis (CGH array)

In postnatal genetics, chromosomal microarray analysis (SNP array) is recommended as a first-line investigation of neurodevelopmental disorders, facial dysmorphism or malformations. This pangenomic chromosome analysis can identify minute chromosomal imbalances that are difficult or impossible to identify using a karyotype or CNV (Copy Number Variation).

Eurofins Biomnis has SNP array (Single Nucleotide Polymorphism) technology, which in addition to being able to identify CNVs can identify regions of loss of heterozygosity (LOH).

Targets analyses (study of a gene or gene position)

In certain cases, clinical parameters allow the prescribing physician to suggest a targeted genetic study, of a specific gene or a specified gene position.

Genetics related to haematology and immunochemistry

Several areas of haematology are explored using techniques of molecular genetics.

In haemostasis, these techniques are used to study the constitutional factors that predispose an individual to venous thrombosis: factor V Leiden mutation, G20210A Factor II gene mutation and MTHFR mutations (c.677C>T and c.1298A>C).
The most common iron overload syndrome, Type 1 haemochromatosis, is diagnosed based on identification of a major C282Y mutation, and the minor H63D and S65C mutations, of the HFE gene.

Human leukocyte antigen (HLA) typing is performed to identify risk factors for several diseases. The most common associations investigated for HLA class I alleles are HLA B27/ankylosing spondylitis, HLA A29/birdshot retinopathy, HLA B51/Behcet’s disease, HLA B57:01/abacavir hypersensitivity. For class II HLA alleles, the most common associations are HLA DQ2 and DQ8/coeliac disease.

The SERPINA1 gene expressing alpha-1-antrypsin is investigated to identify the S and Z mutations because the ZZ and SZ genotypes are responsible for the low protein concentrations associated with emphysema or liver disease.

Pharmacogenetics

Pharmacogenetics consists of oncology and psychiatry, as part of personalised medicine.

Fluoropyrimidines (5-FU and capecitabine) are anti-cancer drugs and are included in close to 60% of chemotherapy protocols for a range of tumours (digestive tract, pancreas, breast, etc.), however these drugs have significant toxic effects, starting from the first course of treatment. This toxicity is linked to a deficit of the degradative enzyme for fluoropyrimidine: DPD. Testing for risk of fluoropyrimidines uses a multiparametric approach, combining genotyping and DPD phenotyping. In addition, when a risk of toxicity is identified, an adjustment is proposed for the dose of fluoropyrimidine to be used.
Moreover, screening for polymorphism of gene UGT1A1 helps with the diagnosis of Gilbert’s syndrome and can be used to estimate the risk of irinotecan toxicity, another anti-cancer drug, which is metabolised by the enzyme UGT1A1.

First-line treatment of depression is based, another other approaches, on antidepressants. For many antidepressants, diffusion in brain tissue is what determines their effectiveness, which is dependent on a protein, P-glycoprotein (P-gp), which is encoded by the gene ABCB1. Genotyping of ABCB1 allows the identification of the different forms of P-gp which reduce or promote passage of several antidepressants through the blood-brain barrier, which allows the treatment strategy to be adapted.

Oncogenetics

In France, close to 5% of cancer diagnoses are linked to the presence of constitutional genetic mutations. Individuals carrying these mutations are at a greater risk of developing cancer. Identifying this greater risk means that a screening programme, preventive measures and proactive, adapted treatments can be proposed.

The two genetic predispositions most frequently screened for are breast and ovarian cancer, and Lynch syndrome.

Infertility

In cases of infertility, the following screening may be performed in addition to the prescription of a karyotype:

• For men, mutations of the mucoviscidosis gene (CFTR) and microdeletions of the Y chromosome.
• For women, premutation of the FMR1 gene in cases of premature ovarian failure (early menopause).

Exome sequencing is also suggested with these indications.

Lactose intolerance

Primary lactose intolerance is linked to the absence or decreased production of lactase with age, responsible for degrading lactose, encoded by the LCT gene. Investigation of lactose intolerance includes screening for the presence of a 13910 C>T mutation on the LCT gene promoter, which allows lactase production sufficient for digestion of lactose to be maintained.

Neurological disorders

Fragile X syndrome can be screened for in cases of intellectual impairment in children or certain neurological diseases in adults. We also conduct screening for Prader–Willi syndrome and Angelman syndrome.

Other

In cases of suggestive clinical signs, we can also carry out screening for familial Mediterranean fever.