Molecular Genetics

Scientists in Charge:

Dr Ilenia Simeoni (myeloid) (01223 3488660)

Calogero Casa (lymphoid) (01223 3488660)

About the molecular genetics service

The East GLH molecular genetics laboratory works in partnership with HODS to offer a wide range of molecular tests to identify acquired genetic changes of diagnostic, prognostic and therapeutic significance in both haematological and solid tumour malignancies. 

Please refer to the NHS England National Genomic Test Directories for a comprehensive list of haemato-oncology molecular assays, not all of which are provided by each GLH. Please see also the East GLH website: https://www.eastgenomics.nhs.uk/. The GLH results are integrated with other testing modalities provided by HODS. Enquires about sample requirements, turn-around-times and availability of results can be sent to cuh.eastglh-haemonc-molecular@nhs.net. 

Many haematological malignancies have characteristic genetic abnormalities that are either the key entity-defining criteria or important for diagnosis and management. Some abnormalities occur at the chromosomal level and lead to the production of a novel fusion gene or aberrant expression of an oncogene. These abnormalities can be detected by cytogenetic methods and confirmed by molecular methods. In addition, an increasing number of mutations are associated with malignancies. 

Available methods include: 

• Polymerase Chain Reaction (PCR) 

• Reverse Transcription PCR (RT-PCR) 

• Real Time PCR 

• High-Resolution Melt Analysis 

• Fragment Analysis 

• Next-Generation Sequencing (NGS) 

• RNA Fusion Panel 

Molecular genetic analysis is often the most sensitive technique for detecting minimal residual disease (MRD). Other assays use short tandem repeats (STR) to assess the proportion of cells carrying donor-derived haematopoietic cells after an allogeneic stem cell transplant (e.g. for chimerism analysis).

Next generation sequencing (NGS) 

Next generation sequencing (NGS) is an accurate, high-throughout, and cost-effective alternative to single-gene methods and can simultaneously identify mutations across multiple genes in one assay from one sample. The GLH laboratory currently offers several NGS-based assays, with panel testing expected to replace many single-gene tests. 

Targeted NGS panels do not always examine the entire gene, so absence of a variant does not completely rule out the presence of a mutation elsewhere in the gene. The formal lower limit of detection is 5%, although lower-level mutations will typically be reported if confidently detected. 

Variants of uncertain significance 

Some gene variants may be novel and will be reported as ‘variants of uncertain significance’. A variant of uncertain significance (VUS) may represent: 1) an uncommon germline variant that is of no consequence (VAF typically close to 50%); or 2) an acquired or germline variant which may or may not have a pathogenic effect but for which there is currently inadequate supportive evidence to classify as such. A VUS must not in isolation be considered evidence of a clonal disorder. These can be discussed with a HODS consultant if the clinical implications are unclear. Formal Genomic Tumour Advisory Boards meet weekly to discuss the significance of challenging variants. 

Germline variants

NGS panels on a diagnostic haematopathology sample sequence a tumour sample and are not directly intended to identify germline variants. However, reports will state if any potential germline variants have been detected (e.g. variant allele frequencies > 30%). Where potential pathogenic variants have been identified in genes pertinent to germline predispositions to haematological malignancies, cases will routinely be referred to the East GLH Genomics Tumour Advisory Board so that appropriate advice can be given about further counselling and testing.