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HomeBiomnis LiveShedding light onNew NextSeq2000 (Illumina) sequencer: cutting-edge innovation in the Eurofins Biomnis genetics department

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New NextSeq2000 (Illumina) sequencer: cutting-edge innovation in the Eurofins Biomnis genetics department

Pictogramme horloge Francis Rousseau Pictogramme horloge PhD – NGS Scientific Expert - Eurofins Biomnis Pictogramme horloge November 2020

Medical genetics has made tremendous strides in recent years. The development of massive parallel sequencing (more commonly referred to as next-generation sequencing – NGS) has been a major contributor to these advances. Sequencing now forms an integral part of everyday clinical practice: sequencing of all coding regions of a gene, a panel of genes, all coding regions of a genome, or even a whole genome.

For more than five years now, Eurofins Biomnis has been committed to making NGS a part of its routine practice by investing in Illumina systems.

These techniques can be used in a range of medical fields such as constitutional genetics, prenatal genetics and cancer genetics.

In constitutional genetics, full sequencing of the coding regions of the CFTR gene may be used, for example, to screen for genetic variants causing cystic fibrosis, or its milder forms such as congenital atresia of the vas deferens (causing infertility in men).

For the treatment of myeloproliferative neoplasms (MPN), molecular analysis, via a gene panel for example, can be used to confirm diagnoses as well as help establish a prognosis and in certain cases guide the patient treatment plan. With these goals in mind, our laboratory is now offering a new range of molecular tests and gene panels that use NGS, alongside cytology and conventional (haematological karyotype) and molecular (FISH) cytogenetics.

For non-invasive prenatal screening of foetal genetic abnormalities, foetal DNA extracted from a simple maternal blood sample can undergo NGS sequencing, identifying any foetal karyotype abnormalities, such as aneuploidies (like the most common trisomies of chromosomes  21, 18 or 13) or major structural abnormalities, avoiding invasive procedures such as amniocentesis in cases where serum markers return positive. The cost of this analysis has been reimbursed by the CPAM (French Health Insurance Fund) since January 2019, and is now routinely prescribed with Eurofins Biomnis being a major provider , performingover 50,000 tests in 2019.

Finally, for rare constitutional diseases and oncogenetics, exome sequencing has been offered by the genetics department of Eurofins Biomnis for over five years. This technique sequences the coding regions of the genes associated with over 95% of mutations currently identified as medically relevant.

The Eurofins Biomnis genetics department, based in Lyon, has developed in-depth expertise in NGS in the last few years. The team, consisting of more than 10 technicians, four scientific experts, four bioinformatics specialists and six clinical pathologists, work every day on the preparation, development, analysis and interpretation of these NGS techniques.

In order to carry out these various analyses, our genetics department operates a number of Illumina systems for the sequencing aspects. The laboratory’s equipment line-up consists of one MiSeq and six NextSeq500 systems. However, in view of the growing demand for NIPT screening (5,000 analyses monthly since 2019) and the increasing demand for exome sequencing (approx. 600 exomes sequenced in 2019, and already over 1,200 sequenced as of the end of October 2020), the acquisition of a new Next Generation Sequencer is essential to ensure that we can continue to deliver results rapidly.

 

Eurofins Biomnis is once again turning to Illumina to acquire a new NextSeq2000 system. This sequencer features innovative functionalities, and simplified, integrated bioinformatics for rapid secondary analysis. This device will be dedicated solely to exome analysis and will therefore allow us to significantly increase our monthly capacity to over 500 samples from the beginning of 2021.

 

With its wealth of expertise and cutting-edge equipment, the genetics department is constantly innovating in the field of molecular diagnosis to improve patient care.


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