Blood cancer profiling challenges with NGS
Hematology oncology research has greatly benefited from next generation sequencing (NGS) methods to identify relevant cancer-driving biomarkers. Heme malignancies have a complex biomarker spectrum, but NGS methods to detect relative fusions, splicing,
expression, copy number variants, single nucleotide variants, and complex alterations have been vital to labs.
However, traditional NGS methods may not provide all relevant information and can have difficult workflows and analysis. One specific challenge in blood cancer profiling is myeloid-relevant genes rich in GC-content, such as CEBPA, are difficult
to amplify and sequence with NGS. Additionally, internal tandem duplications (ITDs), such as FLT3-ITD relevant in AML, can be difficult to detect with NGS due to variable locations and lengths along with random sequence insertions which can
confound genome aligners. Due to this, most NGS methods have difficulty detecting ITDs of all sizes and insertion points, and sensitivity dramatically reduces above 100 bp ITDs. Finally, there are a multitude of relevant fusions in hematological neoplasms,
including many novel fusions. In fact, one study found that 41% of acute myeloid leukemias and 88% of myelodysplastic syndromes had novel fusions . However, since these are relatively rare, traditional opposing primer-based NGS methods may not be
designed with primers to detect all of them, thus missing potentially relevant biomarkers (Figure 1).