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Background information

Technique

We offer molecular diagnostics of disease-associated variants conducted with targeted Next Generation Sequencing (NGS). For each disease available we considered the relevant genes. Targeted gene panels and single genes can be requested. This service for variant analysis is often an addition to our biochemical and functional testing, but can also be used for the initial diagnosis of a specific defect. Specific target genes for each disease are brought together in panels, with which we perform diagnostics for genetic variants in the context of blood clotting, the complement system, red blood cell membrane defects, red blood cell enzyme deficiencies, hemoglobinopathies, thrombocytopathies, hematological malignancies, bone marrow failure and immune deficiencies.
We make use of Ion Torrent Systems and AmpliSeq panels for those tests. Using this technique it is possible to identify single nucleotide variants, small insertions and small deletions. Copy number variations (CNV), variants in repeat sequences, large homopolymers and large insertions/deletions are difficult to identify or cannot be identified.
Our tests are based on targeted sequencing and therefore genetic abnormalities in genes or regions outside the specified target areas will not be detected. All characteristics concerning coverage are described under specifications for each panel. 


Reporting

Variants are classified according to a 5-tiers variant classification (see Wallis et al Practice Guidelines for the Evaluation of Pathogenicity and the Reporting of Sequence Variants in Clinical Molecular Genetics. January 2013). Class 1 and 2 variants will not be reported. Heterozygous class 3 variants in recessive genes will not always be reported. Only variants which can be the cause of the clinical phenotype of the patient will be reported. Variants with uncertain clinical significance in genes associated with diseases not related to the clinical phenotype of the patient will not be reported.
NGS data are interpreted with the current knowledge concerning variants in relation to disease or as explanation of a phenotype. For reporting variants the following guidelines will be followed: ‘Best Practice Guidelines for Reporting Molecular Genetics results’ written by R.J.L. Treacy and D.O. Robinson. The authorisation of the results is done by a recognized Clinical molecular geneticist.
All variants are annotated and reported as designated by the Human Genome Variation Society (HGVS) nomenclature, as described at their website

Regions within regiona of interest that fail to achieve 100% coverage and that are not mentioned under specifications, will be reported as well if relevant to the phenotype of the patient and/or other laboratorial test results.