Contributions
Abstract: PB1618
Type: Publication Only
Background
Childhood acute lymphoblastic leukemia (ALL) is the most common of pediatric malignancies, but intensive chemotherapy now allows to obtain complete remission in over 90% of the cases. Nevertheless, 1 out of 5 children will relapse.
Aims
In order to identify new markers prognostic of relapse, we analyzed SNP arrays of paired diagnosis and relapse samples from 8 B-ALL children.
Methods
The cohort included 3 males and 5 females, aged between 6 months and 21 years old (median age 4 years old). Bone marrow samples were analyzed by multiparameter flow cytometry, standard karyotype and FISH. SNP array (Affymetrix®) performed on cryopreserved cells at diagnosis and relapse investigated copy number alterations (CNA) and loss of heterozygosity (LOH). TP53 mutation was studied on paired samples by Sanger sequencing.
Results
No modification was observed in the EGIL classification between diagnosis and relapse. Diagnostic cytogenetics prognosis was good for 3 children, poor for 3 (iAmpAML1, KNMT2A and complexe caryotype) intermediate for 2 (normal karyotype). Three patients showed additional karyotypic anomalies at relapse. SNP array showed a mean of 10 CNA and 3 LOH at diagnosis with 4 CNA and 0,6 LOH modulations at relapse. Seven of the 8 patients presented modulation in CNA and LOH during evolution with a median of 4. Some anomalies observed by cytogenetics were refined by SNP analysis, notably all chromosomal gains and losses were recovered and precisely located. Moreover, a t(4;8) translocation was found to be more complex with 7 and 8 CNA on chromosomes 4 and 8. Patients with the most CNA and LOH also had a complex karyotype. Anomalies were observed in hot spot regions in 9p (encompassing CDKN2A/2B, PAX5 and JAK2) for 5 patients and 12p (including ETV6) for 3. Stable CNA were observed in the JAK/STAT pathway in 2 patients (JAK2) and LOH in the RAS/MAPk pathway (NRAS) in 1. Using the genetic classification of Moorman et al based on SNP array for 8 genes at diagnosis (IKZF1, CDKN2A/2B, PAR 1, BTG1, EBF1, PAX5, ETV6 and RB1), SNP reclassified our patients in 3 of good prognosis and 5 of poor prognosis, with a median of 2 CNA for the 8 genes of interest. The 2 patients with cytogenetic intermediate prognosis would thus probably have been considered for a more intense therapeutic regimen, i.e. allogeneic stem-cell transplantation. Moreover, SNP showed that 2 patients acquired an IKZF1 deletion, also of poor prognosis, while none of the children had TP53 mutation at diagnosis nor relapse.
Conclusion
SNP array allowed to identify additional anomalies (compared to karyotype) in all children tested and changed the prognostic value of diagnostic anomalies. Moreover, the identification of anomalies in the JAK/STAT pathway could indicate a treatment by tyrosine kinase inhibitors, which would possibly have positively modified outcome. Taken together, this new technology combined with classical analyses at diagnosis might modify therapeutic options in childhood ALL, especially in the subgroup with a normal karyotype.
Session topic: 1. Acute lymphoblastic leukemia - Biology
Keyword(s): SNP, Relapsed acute lymphoblastic leukemia, Cytogenetic abnormalities, ALL
Abstract: PB1618
Type: Publication Only
Background
Childhood acute lymphoblastic leukemia (ALL) is the most common of pediatric malignancies, but intensive chemotherapy now allows to obtain complete remission in over 90% of the cases. Nevertheless, 1 out of 5 children will relapse.
Aims
In order to identify new markers prognostic of relapse, we analyzed SNP arrays of paired diagnosis and relapse samples from 8 B-ALL children.
Methods
The cohort included 3 males and 5 females, aged between 6 months and 21 years old (median age 4 years old). Bone marrow samples were analyzed by multiparameter flow cytometry, standard karyotype and FISH. SNP array (Affymetrix®) performed on cryopreserved cells at diagnosis and relapse investigated copy number alterations (CNA) and loss of heterozygosity (LOH). TP53 mutation was studied on paired samples by Sanger sequencing.
Results
No modification was observed in the EGIL classification between diagnosis and relapse. Diagnostic cytogenetics prognosis was good for 3 children, poor for 3 (iAmpAML1, KNMT2A and complexe caryotype) intermediate for 2 (normal karyotype). Three patients showed additional karyotypic anomalies at relapse. SNP array showed a mean of 10 CNA and 3 LOH at diagnosis with 4 CNA and 0,6 LOH modulations at relapse. Seven of the 8 patients presented modulation in CNA and LOH during evolution with a median of 4. Some anomalies observed by cytogenetics were refined by SNP analysis, notably all chromosomal gains and losses were recovered and precisely located. Moreover, a t(4;8) translocation was found to be more complex with 7 and 8 CNA on chromosomes 4 and 8. Patients with the most CNA and LOH also had a complex karyotype. Anomalies were observed in hot spot regions in 9p (encompassing CDKN2A/2B, PAX5 and JAK2) for 5 patients and 12p (including ETV6) for 3. Stable CNA were observed in the JAK/STAT pathway in 2 patients (JAK2) and LOH in the RAS/MAPk pathway (NRAS) in 1. Using the genetic classification of Moorman et al based on SNP array for 8 genes at diagnosis (IKZF1, CDKN2A/2B, PAR 1, BTG1, EBF1, PAX5, ETV6 and RB1), SNP reclassified our patients in 3 of good prognosis and 5 of poor prognosis, with a median of 2 CNA for the 8 genes of interest. The 2 patients with cytogenetic intermediate prognosis would thus probably have been considered for a more intense therapeutic regimen, i.e. allogeneic stem-cell transplantation. Moreover, SNP showed that 2 patients acquired an IKZF1 deletion, also of poor prognosis, while none of the children had TP53 mutation at diagnosis nor relapse.
Conclusion
SNP array allowed to identify additional anomalies (compared to karyotype) in all children tested and changed the prognostic value of diagnostic anomalies. Moreover, the identification of anomalies in the JAK/STAT pathway could indicate a treatment by tyrosine kinase inhibitors, which would possibly have positively modified outcome. Taken together, this new technology combined with classical analyses at diagnosis might modify therapeutic options in childhood ALL, especially in the subgroup with a normal karyotype.
Session topic: 1. Acute lymphoblastic leukemia - Biology
Keyword(s): SNP, Relapsed acute lymphoblastic leukemia, Cytogenetic abnormalities, ALL