BIOTECHNOLOGY
WH THE BENEFITS OF M
anja Meggendorfer, PhD is the head of Molecular Genetics at Munich Leukemia Laboratory (MLL), where she oversees various R&D activities to implement assays based on next generation sequencing (NGS) to advance personalised genomics research. Meggendorfer recently gave a presentation on the utility of whole exome sequencing (WES) in characterising the genetic profi le of biobanked haematological malignancy samples.
ADVANCING PERSONALISED GENOMICS Researchers use various methods to study and characterise haematological malignancies – focusing on either phenotypic appearance (e.g. cell type composition, antigen expression) or genetic profi les (e.g. copy number variations [CNV], single nucleotide variants [SNV], gene expression). However, each sample has a unique genetic profi le and precision medicine research aims to better understand how these profi les can potentially infl uence disease progression. To identify new markers for minimal
residual disease detection (MRD), a sample’s molecular profi le can be assessed by gene panel sequencing, ranging from a handful of genes to the whole exome (WES), or whole genome sequencing (WGS). Some diseases are defi ned by the expression of specifi c gene signatures that are detectable by whole transcriptome sequencing (WTS). WGS provides sequence information about the entire genome of the sample and is the most comprehensive of these approaches. Targeted sequencing achieves a higher sequencing depth[1]
retrospectively profi le biobanked samples from 19 individuals who had previously been diagnosed with myeloproliferative neoplasia (MPN) and subsequently progressed to blast phase (BP)[2]
Overview of workfl ow used by Meggendorfer et al
. A portion of individuals with MPN will see the disease progress to BP or acute myeloid leukaemia (AML), in which >20% of the blood or bone marrow gives rise to myeloblast (a type of white blood cell)[3,4]
when a mutation occurs in a blood stem cell[3]
.
Further research on the genetic background of MPN is needed to better understand the risk of MPN transition to BP. Meggendorfer incorporated the
; meaning it provides researchers with
more comprehensive data of individual genes or regions of interest. Meggendorfer et al used WES to
xGen Exome Hybridization Panel into the research, which used a fully automated hybridisation capture and enrichment workfl ow to sequence the exome of biobanked samples at two diff erent timepoints – when the sample was identifi ed to have MPN and when the concordant sample was identifi ed to have BP (MPN- BP). T e obtained data provided the basis to compare the genetic profi les of the paired samples, MPN versus MPN-BP, revealing an accumulation of splicing and chromatin modifying gene mutations, clonal evolution and gain of RAS pathway mutations during progression.
. MPNs are
blood cancers that begin in the bone marrow 42
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WES FOR IDENTIFYING GENETIC BIOMARKERS FOR PROGRESSION TO MPN-BP T e samples were sequenced with a median coverage of 257X across the exome. T e
. It was also noted that the number of samples with mutations in RAS pathway related genes was higher in the MPN-BP timepoint. Moreover, SRSF2 and TET2 were found to be potentially linked to the likelihood of progression from MPN to MPN-BP and were more frequently mutated in MPN-BP samples relative to a control group of biobanked samples that did not progress to MPN-BP[2]
median number of variants for MPN and MPN-BP samples was 80, however only 4.8% (MPN) and 5.2% (MPN-BP) of these genes were recurrently mutated (n > 2). Further, 50% of variants were determined to be specifi c to the samples, which suggests that these variants were not linked to the progress from MPN to MPN-BP. Focusing on the recurrent mutations in MPN timepoint samples, the most frequently mutated genes beside JAK2 and MPL were SRSF2, followed by TET2, ASXL1, RUNX1, DNMT3A, ZRSR2, SETBP1 and IDH2. Interestingly, their research found that 37% of samples lost their MPN defi ning JAK2 or MPL mutation during progression to MPN-BP and RUNX1 and TP53 were gained most often[1]
.
In addition to the detection of gene mutations, the WES can also be used to
OLE EXOME SEQUENCING
Courtney Thomas reports on work on retrospective genetic profi ling of biobanked samples from haematological malignancies using whole exome sequencing
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