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. 2024 Sep;71(9):e31129.
doi: 10.1002/pbc.31129. Epub 2024 Jul 2.

The impact of comparative genomic hybridization/single-nucleotide polymorphism microarray in risk stratification of pediatric acute lymphoblastic leukemia

Antoine Gourmel  1 , Héloïse Perrault  1 , Marie-Laure Colaiacovo  1 , Louise Laramée  2 , Marieke Rozendaal  2 , Henrique Bittencourt  1   2 , Caroline Laverdière  1   2 , Josette Champagne  1   2 , Sonia Cellot  1   2 , Lewis B Silverman  3 , Emmanuelle Lemyre  4 , Catalina Maftei  4 , Géraldine Mathonnet  4 , Frédérique Tihy  4 , Marie-Claude Pelland-Marcotte  5 , France Léveillé  4 , Thai Hoa Tran  1   2
Affiliations

The impact of comparative genomic hybridization/single-nucleotide polymorphism microarray in risk stratification of pediatric acute lymphoblastic leukemia

Antoine Gourmel et al. Pediatr Blood Cancer. 2024 Sep.

Abstract

Background: The objective of this study is to assess the concordance and added value of combined comparative genomic hybridization plus single-nucleotide polymorphism microarray (CGH/SNP) analyses in pediatric acute lymphoblastic leukemia (ALL) risk stratification compared to conventional cytogenetic methods.

Procedure: This is a retrospective study that included patients aged 1-18 years diagnosed with de novo ALL at Sainte-Justine Hospital between 2016 and 2021. Results from conventional cytogenetic and molecular analyses were collected and compared to those of CGH/SNP.

Results: A total of 135 ALL patients were included. Sample failures or non-diagnostic analyses occurred in 17.8% cases with G-banding karyotypes versus 1.5% cases with CGH/SNP. The mean turnaround time for results was significantly faster for CGH/SNP than karyotype with 5.8 versus 10.7 days, respectively. The comparison of ploidy assessment by CGH/SNP and G-banding karyotype showed strong concordance (r = .82, p < .001, r2 = .68). Furthermore, G-banding karyotype did not detect additional clinically relevant aberrations that were missed by the combined analysis of CGH/SNP and fluorescence in situ hybridization. The most common gene alterations detected by CGH/SNP were deletions involving CDKN2A (35.8%), ETV6 (31.3%), CDKN2B (28.4%), PAX5 (20.1%), IKZF1 (12.7%), and copy-neutral loss of heterozygosity (CN-LOH) of 9p (9.0%). Among these, only ETV6 deletion was found to have a significant prognostic impact with superior event-free survival in both univariate and multivariate analyses (adjusted hazard ratio 0.08, 95% confidence interval: 0.01-0.50, p = .02).

Conclusion: CGH/SNP provided faster, reliable, and highly concordant results than those obtained by conventional cytogenetics. CGH/SNP identified recurrent gene deletions in pediatric ALL, of which ETV6 deletion conferred a favorable prognosis.

Keywords: ALL; cytogenetics; molecular biology; oncogenes; pediatric hematology/oncology.

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