Challenging Conventional Diagnostic Methods by Comprehensive Molecular Diagnostics: A Nationwide Prospective...

Area of Science:

• Hematology
• Oncology
• Molecular Diagnostics

Background:

• Acute lymphoblastic leukemia (ALL) treatment stratification relies on diverse genetic aberrations.
• Accurate and timely detection of these aberrations is essential for effective patient management.
• Current diagnostic workflows may require multiple tests, impacting turnaround time.

Purpose of the Study:

• To optimize the diagnostic workflow for ALL by evaluating various molecular tests.
• To identify a limited set of tests that can detect all relevant genetic aberrations within a clinically relevant timeframe.
• To compare the technical success, concordance, and turnaround time of different diagnostic methods.

Main Methods:

• A prospective study involving 467 pediatric and young adult ALL patients (0-20 years).
• Comparison of RNA sequencing (RNAseq), fluorescence in situ hybridization (FISH), reverse transcriptase polymerase chain reaction (RT-PCR), karyotyping, single-nucleotide polymorphism (SNP) array, and multiplex ligation-dependent probe amplification (MLPA).
• Evaluation of technical success, result concordance, and turnaround time for each method.

Main Results:

• RNAseq and FISH achieved high concordance (99%) for detecting key gene fusions.
• SNP array demonstrated superior performance over karyotyping for detecting aneuploidies and deletions.
• The combined RNAseq and SNP array approach detected all stratifying genetic aberrations with a turnaround time under 15 days.
• RNAseq identified novel gene fusions in a significant proportion of B-cell precursor-ALL and T-ALL cases.

Conclusions:

• Combining RNAseq and SNP array offers a superior diagnostic strategy for detecting genetic aberrations in ALL compared to current methods.
• This combined approach meets critical treatment decision time points with a turnaround time of less than 15 days.
• The integrated method also facilitates the discovery of new genetic lesions, aiding future research in ALL prognosis and pathobiology.