The received sample (blood, saliva or frozen tissue or paraffin) is processed to extract DNA. DNA is measured to assess its quality and to ensure that processing is effective and cost-effective. If for some reason this sample is not of the required quality, it is not processed and a second sample is requested.
Protocols are used to prepare libraries (Agilent Technologies, Inc., USA). We use panels that are updated as new genes are discovered. Due to its quality, the panel allows to evaluate not only point variants but also indels and structural variants such as copy-number-variations (CNVs).
Once the results of the panel are obtained, they are evaluated to detect genetic variants that are considered potentially pathogenic. For this task, we have developed our own computer program and a comparison of the variants with international databases, as well as with our own database. Variants are finally evaluated with in-silico tools to assess pathogenicity, in a process that ends up selecting those that are potentially causing the disease.
Genetic variants that are considered potentially associated with the disease are confirmed by a second technique, which may be Sanger sequencing, MLPA, or HRM RT-PCR, depending on the type of genetic variant identified.
Once the potentially pathogenic variants have been detected, in collaboration with the requesting physicians, an assessment of the clinical context is made, interweaving the clinical and genetic data, to assess whether the variants explain the disease.
Once the potentially pathogenic variants have been detected, all the published information on the variant, which we have available in our own database, is incorporated to have information on how the variant behaves in other families.
A report with the genetic assessment is written. If you are interested, support is provided for clinical decision making and recommendations. This report is discussed with the responsible physician / advisor to ensure that all information has been understood and to resolve any questions.