Mutational profiling in acute lymphoblastic leukemia by RNA sequencing and chromosomal genomic array testing

Area of Science:

• Oncology
• Genetics
• Molecular Biology

Background:

• Comprehensive molecular and cytogenetic profiling is crucial for B-acute lymphoblastic leukemia (B-ALL) patient care.
• Current standards necessitate efficient diagnostic tools for B-ALL management.

Purpose of the Study:

• To introduce a rapid, combined approach using FusionPlex RNA next-generation sequencing (NGS) and DNA chromosome genomic array testing (CGAT) for B-ALL.
• To evaluate the efficiency of this integrated method in managing B-ALL patients.

Main Methods:

• RNA NGS and CGAT were performed on 28 B-ALL samples.
• Four patients had fixed cell pellets compared to cryopreserved samples to assess fixed pellet utility for gene expression analysis.

Main Results:

• RNA NGS demonstrated 100% sensitivity and specificity in detecting fusions in fixed specimens, confirmed against karyotype, FISH, CGAT, and RT-qPCR.
• Fusions were 100% concordant between fixed and fresh cryopreserved samples in paired analyses.
• Four patients had mutations detected by RNA sequencing, with three linked to known drug resistance.

Conclusions:

• FusionPlex is a reliable platform for detecting fusions in both fresh and fixed B-ALL samples.
• Gene expression data is obtainable from fresh samples, and critical variants can be identified alongside fusions.