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

Cecilia Yeung1,2,3, Xiaoyu Qu3, Olga Sala-Torra1

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Cancer Medicine
|July 21, 2021
PubMed
Summary

FusionPlex RNA sequencing and DNA array testing offer a rapid, accurate method for detecting gene fusions in B-acute lymphoblastic leukemia (B-ALL). This combined approach enhances patient management by identifying critical mutations and drug resistance implications.

Keywords:
RT-qPCRleukemiamolecular pathologynext-generation sequencing

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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.