Next generation sequencing – targeted gene panels

Next Generation Sequencing – targeted gene panels

We use custom designed Agilent SureSelect Target Enrichment which allows detection of base substitutions (SNVs), small insertions and deletions (indels) and partial/whole gene deletions and duplications (CNVs) (PMID 23771172). Test sensitivity is >99% (CI 95%) for SNVs/ indels and >95% (CI 95%) for CNVs.

Targeted gene panel tests (see tables for full list of gene panels) are available for monogenic diabetes, hyperinsulinism, spondylocostal dysotosis, eye movement disorders, holoprosencephaly, pontocerebellar hypoplasia, porencephaly,  gastrointestinal atresia and a comprehensive range of endocrine disorders.  Please click links to see further information or go to the full list of panels with gene details. We also provide bespoke gene panel tests (click here to view our exome sequencing services).

Test limitations

These panels will identify the same types of mutations detected by Sanger sequencing and can detect large deletions or duplications previously identified by a separate dosage assay [1]. The test sensitivity is estimated at >97.5% (95% CI). Balanced translocations, inversions and intronic mutations located outside splice sites will not be detected. Sequence analysis includes the coding exons and flanking intronic regions (50 bp upstream to 10 bp downstream of each exon). There are some parts of the human genome that are not amenable to next generation sequencing; these include repetitive sequences and extremely GC-rich regions. Regions with <20 reads per base will be analysed using Sanger sequencing if indicated by the patient’s phenotype. Confirmation of mutations identified by tNGS is undertaken by Sanger sequencing, MLPA or droplet digital PCR (ddPCR).

Variant reporting policy

Sequencing a greater number of genes will identify more novel/rare variants whose clinical significance is uncertain. These include variants not seen before or identified in a small number of patients where the causal link to the disease is unproven. The clinical report will only include likely pathogenic mutations or variants where further investigation is recommended (for example by testing affected relatives to see if they have the same possible mutation).  New clinical or genetic information may change the interpretation of pathogenicity. In accordance with best practice guidelines, known polymorphisms are not reported.