Genetic aberrations in chronic myeloid neoplasms

  • Sophie Laird

Student thesis: Unknown

Abstract

Chronic myeloid neoplasms (CMNs) are a heterogeneous group of clonal blood disorders with diverse clinical outcomes. Genetic analysis plays a key role in the diagnosis of CMN, as well as identifying specific targets for therapy, indicators of prognosis and markers that can be used to gauge response to therapy. Until recently, such analysis mainly involved cytogenetics along with a limited number of targeted tests to detect specific somatic abnormalities. The development of genomic technologies, however, has greatly expanded our understanding of the pathogenesis of CMN, and presented new challenges to diagnostic laboratories which need to implement these complex tests in a way that fulfils the requirements of accreditation as well as producing quality controlled, reproducible and clinically useful results. Interpretation of genomic data is complicated by a number of factors, including uncertainty as to whether variants are drivers or passengers, somatic or germline and drivers of disease or age-related changes. Within this context I aimed to develop and apply myeloid panel next generation sequencing testing within the Wessex Regional Genetics Laboratory (WRGL), and utilise the panel along with other techniques to help understand the significance of JAK2 V617F at low variant allele frequency (VAF) and to characterise a recurrent cytogenetic abnormality, the der(6)t(1;6). Initially I describe the development of a standardised two-step process for the interpretation of variants detected by gene panels. A classification of pathogenicity is assigned using weighted evidence and then the clinical significance is assessed which informs whether the finding should be reported and how it is interpreted. This protocol has been successfully implemented into the WRGL and used to interpret >1,700 variants to date, with each classification recorded and auditable in accordance with strict quality management requirements for diagnostic laboratories. I undertook an audit to understand how the myeloid panel was being used clinically at an early stage of implementation which demonstrated clear clinical utility of the test, in particular when trying to formalise or exclude a diagnosis or when looking for prognostically significant markers in an already confirmed diagnosis. For cases of suspected myelodysplastic syndrome (MDS), the absence of mutations was a particularly useful piece of evidence for exclusion of neoplastic condition and enabled many patients to avoid an invasive bone marrow procedure. In the second part of the study the clinical significance of low level JAK2 V617F in suspected myeloproliferative neoplasm (MPN) referrals was investigated. Using digital droplet PCR I found no evidence that low level (
Date of Award1 Aug 2021
Original languageEnglish
Awarding Institution
  • The University of Manchester
SupervisorJohn Burthem (Supervisor)

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