Evaluating the genomic landscape of B cell malignancies

Abstract

Splenic marginal zone lymphoma (SMZL) and chronic lymphocytic leukaemia (CLL) are B cell malignancies, predominately affecting the elderly. The disease course of both SMZL and CLL is highly variable, with some patients dying rapidly within a month whilst other remain stable and live a normal lifespan. Biomarkers are used to help to distinguish those patients who may progress. Genomic abnormalities such as copy number alterations and mutation of genes may have prognostic value in CLL and SMZL. Several technologies were used to assess the genomic landscape in B cell malignancies; low resolution technology such as multiplex ligation-dependant probe amplification (MLPA) and Sanger sequencing as well as higher resolution methods such as SNP 6.0 arrays and next generation sequencing technologies; whole exome sequencing, TruSeq and Nextera XT. MLPA was used to assess both the copy number alterations (CNA) and mutational abnormalities in the well-defined CLL4 clinical trial cohort. Though the technology is restrictive in terms of probe location and sensitivity, there was statistical concordance with Sanger sequencing and fluorescence in situ hybridisation (FISH). Novel CNA, independently associated with survival were uncovered; 1) a very indolent disease course in patients carrying a biallelic 13q deletion with IGHV mutated genes and 2) a very poor prognosis in patients with a 9p deletion. Exome sequencing of CLL (n=6) and SMZL (n=7) patients uncovered novel variants via a bioinformatical pipeline; this pipeline was validated using more traditional sequencing methods. The candidate genes; U2AF1, BIRC3, POT1 and MYD88 are implicated in CLL and were screened in a larger cohorts of patients. Analysis of the 11q loci in relation to ATM and BIRC3 gene mutations, identified alterations of ATM that impact most significantly on survival. Nextera technology was optimised to screen ibrutinib treated CLL patients for BTK and PLCG2 mutations. DNAH9 and SPEN were also sequenced in a small cohort of patients. A breakpoint deletion was identified in the DNAH9 gene, suggesting this gene may be relevant in CLL. Further studies are needed to examine
these newly defined high and low risk groups, and other genetic abnormalities in another well-defined CLL cohort, to ascertain their pathogenic and biological significance.

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Identifiers

ORCID for Jonathan Strefford: orcid.org/0000-0002-0972-2881

ORCID for Mark Cragg: orcid.org/0000-0003-2077-089X

ORCID for Matthew Rose-Zerilli: orcid.org/0000-0002-1064-5350

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