More information - Single Gene Diagnostics

Single Gene Diagnostics

For > 1100 genes (> 630 disorders) pre- and postnatal DNA analysis is offered. These analyses include sequencing of the full coding region and a full clinical interpretation of the detected genomic variants. In some cases Sanger sequencing is combined with MLPA analysis or other targeted techniques.

Two methods are used for the single gene diagnostics, which are described briefly below.

Sanger sequencing method

Sanger DNA-sequencing is widely accepted as the gold standard in diagnostic DNA sequencing. Originally, the method was based on the selective implementation of chain terminating dideoxy-nucleotides during DNA replication using radioactively labeled primers. Innovative dye-terminator sequencing methods allowed DNA-sequencing in a single reaction. It also allowed automation of DNA-sequencing.

Our Core Genome Analysis Laboratory (CGAL) uses robotics in a sophisticated high-throughput Sanger-sequencing pipeline. This high degree of automation is possible because we use generic amplification and purification conditions (currently we test for over 600 different genes). The use of barcodes from the moment (blood)samples arrive in our laboratory allows sample tracking during the entire automated workflow, i.e. DNA-isloation, PCR, amplicon sequencing, and DNA-sequence analysis. Automated DNA sequencers (ABI 3730 XL) produce DNA sequencing data of over ~300.000 amplicons generated annually. All this sequencing data is analyzed using a semi automated software module for the analysis of Sanger sequencing data (SequencePilot©(JSI medical systems)).

Targeted sequencing method

Our lab has recently implemented the Ion Torrent. This targeted sequencing method offers a faster diagnosis and therefor will be implemented for as many genes as possible. Currently 60% of the genes can be sequenced with this method.

MLPA

MLPA (Multiplex Ligation Probe Assay) is a technique to detect deletions and duplications in specific genes. This technique has proven its worth in the last fifteen years as a very useful addition to Sanger sequencing. MLPA analysis is offerd in addition to Sanger sequencing for those genes where deletions and/or duplications have been detected to be part of the mutational spectrum. We use commercially available kits or, if necessary, in-house developed synthetic kits. MLPA is included in the regular test when the percentage of deletions/duplications is substantial, but is not included when the percentage is relatively low. In the latter case, MLPA can be ordered separately. Check out our ordering site https://order.radboudumc.nl/en/services/deletion-duplication-diagnostics-mlpa for more details on specific genes.

Custom Gene Diagnostics

For all genes not listed on our website and clearly established to be causative of a certain genetic disease, a custom gene diagnostics is possible. Such tests are charged based upon the size of the gene, which is similar to the pricing of our established tests. An additional € 20 per amplicon is charged to cover primer costs. For an average gene of 20 exons/amplicons the costs are approximately €750 for the diagnostic gene sequencing plus € 400 for primers (total € 1150). These primer costs can be reduced or waived if multiple patients are sent for analysis.

Turn-around-time from request to custom diagnostic sequencing report is approximately 12 weeks. According to Dutch law, genetic laboratories are exempt from VAT charges, therefore no VAT will be charged.

Please contact us at info@genomediagnosticsnijmegen.nl for a specific quote.