Referral for molecular genetic analysis is to:
- confirm or support a clinical diagnosis in an affected individual (differential diagnosis)
- determine carrier status and/or the risk of developing symptoms in a relative of an affected individual (carrier or predictive testing)
- perform further analysis on a variant of uncertain significance (VUS) in additional family members (segregation analysis)
Variant screening for inherited cardiac and respiratory conditions
Next-generation sequencing (NGS) including the analysis of copy number variants (CNVs)
Next-generation sequencing assays sequence genes associated with a range of inherited cardiac and respiratory conditions. Our 'Tests Available' page has more details of the indications for which testing is available, as well as information about the gene content of our NGS panels.
All our panels use targeted capture and sequencing is undertaken on Illumina MiSeq or NextSeq550 automated sequencers. Sequencing data is generated on many genes, with comprehensive bioinformatic analysis including copy number variant analysis, clinical interpretation and variant confirmation, only reported on genes of clinical relevance to the indication requested.
After sequencing, data passes through our state-of-the-art specialist bioinformatics pipeline, developed and maintained by highly-trained bioinformaticians in our group. Sequencing reads are mapped to [build GRCh38 of] the human genome. Target regions are defined as coding regions ± 15bp to include important splice regions. All bases in exons of core genes are guaranteed to have a minimum of 20x coverage.
We provide a comprehensive specialist interpretation of variants found in the genes relevant to the indication. Variant annotation and assessment are carried out with public and in-house databases, to accurately assess the likelihood of pathogenicity. On completion of the analysis, a report incorporating clinical interpretation of the variants identified is provided.
Sensitivity / specificity / limitations
Analytical sensitivity has been estimated to be more than 99.9% for bases covered to a minimum read depth of 20x. Analytical sensitivity for insertions and deletions may be lower in intronic poly-mononucleotide repeat regions. Specificity and precision are verified to be 100%.
Targeted variant analysis and familial testing
If a pathogenic or likely pathogenic variant is detected in a family, affected and unaffected relatives of the proband may wish to be tested for the variant. For this, we use Sanger sequencing, MLPA or ddPCR, depending on the type of variant. We may also do family studies to assist with variant interpretation, for example to determine if a variant was inherited, has arisen de novo, or if the variant co-segregates with disease in a family. Predictive or testing in asymptomatic individuals (for unaffected relatives) should only be requested via a Clinical Geneticist or another referring clinician in association with a Clinical Geneticist.
All requests for familial testing must include a copy of the proband’s report, or their full details if tested in our laboratory. It is the responsibility of the referring clinician to provide this.
Cystic fibrosis (CF)
Testing for 36 common CFTR variants is carried out using the Devyser CFTR Core kit (link). If two CF-causing variants are not detected, sequencing of the entire CFTR gene and CNV analysis is available as part of the inherited respiratory condition (Respigene) NGS panel.
Sample identity testing
Sample contamination (including Maternal Cell Contamination) detection and familial relationship confirmation can be undertaken using the PowerPlex15 kit, upon request.
We follow ACGS Genetic Laboratory Reporting Time Targets:
- Prenatal testing – 3 calendar days
- Predictive testing – 14 calendar days
- Familial variant testing (non-predictive), CF common mutation screening – 42 calendar days
- Next-generation sequencing panels – 42-84 calendar days, depending on the number of genes analysed.
If unexpected delays occur during the issuing of results, we will keep service users informed of revised turnaround times.
Clinical genetics and genomics laboratory
Ground floor (level 2), Sydney wing, Royal Brompton Hospital, Sydney Street, London, SW3 6NP
NHS test request order and consent form (PDF, 384KB)
NHS test request order and consent form (editable) (Word, 241KB)