Abstract
Background: B-acute lymphoblastic leukemia (B-ALL) is a hematological neoplasm of the stem lymphoid cell of the B lineage, characterized by the presence of genetic alterations closely related to the course of the disease. The number of alterations identified in these patients grows as studies of the disease progress, but in clinical practice, the conventional techniques frequently used are only capable of detecting the most common alterations. However, techniques, such as next-generation sequencing (NGS), are being implemented to detect a wide spectrum of new alterations that also include point mutations. Methods: In this study, we designed and validated a comprehensive custom NGS panel to detect the main genetic alterations present in the disease in a single step. For this purpose, 75 B-ALL diagnosis samples from patients previously characterized by standard-of-care diagnostic techniques were sequenced. Results: The use of the custom NGS panel allowed the correct detection of the main genetic alterations present in B-ALL patients, including the presence of an aneuploid clone in 14 of the samples and some of the recurrent fusion genes in 35 of the samples. The panel was also able to successfully detect a number of secondary alterations, such as single nucleotide variants (SNVs) and copy number variations (CNVs) in 66 and 46 of the samples analyzed, respectively, allowing for further refinement of the stratification of patients. The custom NGS panel could also detect alterations with a high level of sensitivity and reproducibility when the findings obtained by NGS were compared with those obtained from other conventional techniques. Conclusions: The use of this custom NGS panel allows us to quickly and efficiently detect the main genetic alterations present in B-ALL patients in a single assay (SNVs and insertions/deletions (INDELs), recurrent fusion genes, CNVs, aneuploidies, and single nucleotide polymorphisms (SNPs) associated with pharmacogenetics). The application of this panel would thus allow us to speed up and simplify the molecular diagnosis of patients, helping patient stratification and management.
Highlights
B-acute lymphoblastic leukemia (B-ALL) is a malignancy of hematopoietic stem cells, which originates in the B-line lymphoid and is characterized by the presence of a series of genetic alterations, mainly translocations, which determine the course of the disease
We proposed the use of a specific DNA-based panel to help overcome the limitations of the techniques conventionally used in clinical practice during the process of patient diagnosis
The incorporation of selective sequencing approaches in clinical practice could allow the single-step detection of the main genetic alterations present in B-ALL with greater sensitivity, in a fast, simple, and economic way. The applicability of this could be guaranteed since it is designed for use in bench-top sequencers. These alterations include: (a) aneuploidies, high hyperdiploid (>51 chromosomes), low hypodiploid (31-39 chromosomes), and near-haploid (24–30 chromosomes); (b) recurrent fusion genes (ETV6/RUNX1, BCR/ABL1 and MLLr); (c) intrachromosomal amplification of chromosome 21 and CRLF2 rearrangements; (d) copy number variations (CNVs), in particular, alterations in IKZF1, PAX5, CDKN2A, ETV6, BTG1, and RB1 genes; (e) candidate actionable genes, which can only be detected by next-generation sequencing (NGS); (f) polymorphisms or germinal mutations associated with treatment response
Summary
B-acute lymphoblastic leukemia (B-ALL) is a malignancy of hematopoietic stem cells, which originates in the B-line lymphoid and is characterized by the presence of a series of genetic alterations, mainly translocations, which determine the course of the disease. The applicability of this could be guaranteed since it is designed for use in bench-top sequencers These alterations include: (a) aneuploidies, high hyperdiploid (>51 chromosomes), low hypodiploid (31-39 chromosomes), and near-haploid (24–30 chromosomes); (b) recurrent fusion genes (ETV6/RUNX1, BCR/ABL1 and MLLr); (c) intrachromosomal amplification of chromosome 21 (iAMP21) and CRLF2 rearrangements; (d) CNVs, in particular, alterations in IKZF1, PAX5, CDKN2A, ETV6, BTG1, and RB1 genes; (e) candidate actionable genes, which can only be detected by NGS; (f) polymorphisms or germinal mutations associated with treatment response. The use of the custom NGS panel would allow the correct stratification, as well as a refined prognosis of patients by a genuinely comprehensive assessment of the molecular spectrum of alterations (CNVs, nucleotide mutations, SNPs associated with pharmacogenetic and fusion genes), as well as cooperating genetic aberrations (e.g., IKZF1, CDKN2A, PAX5, BTG1, and CRLF2 rearrangements)
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
