CHRONIC LYMPHOCYTIC LEUKAEMIA (CLL)

Detection of loss of TP53 (17p13), 13q14 and the ATM gene region on 11q23 and trisomy 12 using MLPA.

Chromosomal translocations are rare events in CLL. Copy number changes of certain chromosomal regions are however frequent. Some of these have been found to be highly prognostic markers of this disease. CLL testing is performed by MLPA (Multiplex Ligation-dependent Probe Amplification) using a commercial kit manufactured by MRC-Holland. This MLPA test can be used to determine the loss of TP53 (17p13), the RB1 / DLEU / MIRN15A-16 region on 13q14, the ATM gene region on 11q23 and also trisomy 12. This test is designed to detect copy number variation in patients at diagnosis where leukaemic cells represent >30% of cells (Coll-Mulet et al. 2008 BJH 142(5):793-801). Copy number variation is unlikely to be detectable using MLPA in patients with lower levels of leukaemia cells. This assay is designed to identify deletions involving one or more exons but it is not suitable for the detection of single nucleotide variants or small deletions.

 

Detection of TP53 gene variants using Sanger sequencing analysis.

TP53 gene variants are associated with resistance to chemoimmunotherapy and a poor clinical outcome (ERIC recommendations for TP53 mutation analysis in CLL – update on methodological approaches and results interpretation – Leukemia Feb 2018 – online publication https://doi.org/10.1038/s41375-017-0007-7. Sanger sequencing analysis of exons 2 to 11 of the TP53 gene (NM_ 000546.4) is used to detect TP53 gene variants. This assay can only detect a variant present at a level of greater than 10% in a background of genomic DNA. Please note that germline TP53 gene variants may also be detected using this assay, which has implications for patient’s family members. The patient should therefore be questioned regarding their family history of cancer prior to this testing, please refer to guidelines provided by the Exeter Clinical Genetics Department Family history questioning prior to testing for TP53 variants –  Jan 2018.docx. Patients fulfilling the Li-Fraumeni Syndrome Chompret criteria must be referred to Clinical Genetics prior to testing for TP53 gene variants. It is not possible to determine from a blood sample alone if any TP53 gene variants detected are germline or somatic, a further sample would be required for this analysis (CD3+ cells, skin biopsy). Referral to Clinical Genetics is highly recommended prior to testing for germline variants.

Laboratory contact: Dr Caroline Wickham 01392 408252 caroline.wickham@nhs.net

Clinical contact: Dr Paul Kerr 01392 402917 paul.kerr1@nhs.net