FREQUENCY OF COPY NUMBER ABNORMALITIES IN COMMON GENES ASSOCIATED WITH BCP-ALL CYTOGENETIC SUBTYPES IN BRAZILIAN CHILDREN
(Abstract release date: 05/21/15)
EHA Library. C Barbosa T. 06/12/15; 102904; PB1588
Thayana C Barbosa
Contributions
Contributions
Abstract
Abstract: PB1588
Type: Publication Only
Background
Copy number alterations (CNAs) in genes committed to B-cell precursors have been associated with poor survival in subgroups of B-cell precursor acute lymphoblastic leukemia (BCP-ALL).
Aims
Therefore, the aim of this study was to determine the frequency of gene deletions and the significance of copy number alterations in IKZF1, CDKN2A/B, PAX5, EBF1, ETV6, BTG1, RB1, CSF2RA, IL3RA and CRLF2 within a cohort of Brazilian pediatric BCP-ALL patients.
Methods
Bone marrow and peripheral blood aspirates samples from 274 BCP-ALL patients were analyzed prior to any oncological treatment (period 2004-2011). The inclusion criteria were the quality of the frozen diagnostic material, having at least 30% blast cells, patients with ≤18 years old at the time of BCP-ALL diagnosis. The exclusion criteria were acute leukemia in children with Down syndrome, samples collected in heparin, and DNA of insufficient quality. DNA was analyzed by the SALSA multiplex ligation-dependent probe amplification (MLPA) kit (P335-A4). IKZF1 deletion results were confirmed using a P202 IKZF1 SALSA MLPA kit. The age at diagnosis and white blood cell (WBC) count were the criteria for assigning prognostic risk of ALL, according to the National Cancer Institute (NCI). The disease risk associated with CNA occurrence across overall and subgroups of patients was determined by calculating odds ratios (ORs) with a 95% confidence interval (CI). Overall survival (OS) was defined as the time from diagnosis to last event (death or alive). The OS analysis were obtained by the Kaplan-Meier method and log-rank test.
Results
Deletions/amplifications in at least one gene were identified in 83% of the total series. In children older than two years, there was a predominance of CNAs involving deletions in IKZF1, CDKN2A and CDKN2B, whereas IL3RA and CSF2RA had deletions that were found more frequently in infants (P<0.05). Multiple gene deletions occurred in the same patients. Sixty-three patients had both CDKN2A and CDKN2B deletions (P<0.01). Deletions of CDKN2A and CDKN2B also coincided significantly with deletions in PAX5 (P<0.01) and IKZF1 (P<0.05). IKZF1 deletions were also found concomitantly with BTG1 and EBF1 deletions (P<0.05 and P<0.01, respectively). ETV6 deletions overlapped with PAX5, BTG1, EBF1 (P<0.01) and CRLF2 deletions (P<0.05). Based on the cytogenetic subgroups, favorable cytogenetic subgroups (i.e. ETV6-RUNX1 and hyperdiploiy) showed more deletions than other subgroups, specifically ETV6 deletions (P<0.05). TCF3-PBX1 was frequently deleted in RB1, and an absence of deletions was observed in IKZF1 and genes localized to the PAR1 region. IKZF1 deletions (P=0.01, 30.2 months, 95% CI 8.5-52.0) and RB1 deletions (P<0.01, 16.8 months, 95% CI 0.0-46.1) confered poorer OS to standard risk patients.
Summary
The results corroborate previous genome-wide data and are an important validation of the impact of IKZF1 deletions in the prognosis of BCP-ALL. The obtained results emphasize the need for including screening of submicroscopic alterations as additional markers for risk stratification, especially in standard risk patients.
Keyword(s): Acute lymphoblastic leukemia, Ikaros
Session topic: Publication Only
Type: Publication Only
Background
Copy number alterations (CNAs) in genes committed to B-cell precursors have been associated with poor survival in subgroups of B-cell precursor acute lymphoblastic leukemia (BCP-ALL).
Aims
Therefore, the aim of this study was to determine the frequency of gene deletions and the significance of copy number alterations in IKZF1, CDKN2A/B, PAX5, EBF1, ETV6, BTG1, RB1, CSF2RA, IL3RA and CRLF2 within a cohort of Brazilian pediatric BCP-ALL patients.
Methods
Bone marrow and peripheral blood aspirates samples from 274 BCP-ALL patients were analyzed prior to any oncological treatment (period 2004-2011). The inclusion criteria were the quality of the frozen diagnostic material, having at least 30% blast cells, patients with ≤18 years old at the time of BCP-ALL diagnosis. The exclusion criteria were acute leukemia in children with Down syndrome, samples collected in heparin, and DNA of insufficient quality. DNA was analyzed by the SALSA multiplex ligation-dependent probe amplification (MLPA) kit (P335-A4). IKZF1 deletion results were confirmed using a P202 IKZF1 SALSA MLPA kit. The age at diagnosis and white blood cell (WBC) count were the criteria for assigning prognostic risk of ALL, according to the National Cancer Institute (NCI). The disease risk associated with CNA occurrence across overall and subgroups of patients was determined by calculating odds ratios (ORs) with a 95% confidence interval (CI). Overall survival (OS) was defined as the time from diagnosis to last event (death or alive). The OS analysis were obtained by the Kaplan-Meier method and log-rank test.
Results
Deletions/amplifications in at least one gene were identified in 83% of the total series. In children older than two years, there was a predominance of CNAs involving deletions in IKZF1, CDKN2A and CDKN2B, whereas IL3RA and CSF2RA had deletions that were found more frequently in infants (P<0.05). Multiple gene deletions occurred in the same patients. Sixty-three patients had both CDKN2A and CDKN2B deletions (P<0.01). Deletions of CDKN2A and CDKN2B also coincided significantly with deletions in PAX5 (P<0.01) and IKZF1 (P<0.05). IKZF1 deletions were also found concomitantly with BTG1 and EBF1 deletions (P<0.05 and P<0.01, respectively). ETV6 deletions overlapped with PAX5, BTG1, EBF1 (P<0.01) and CRLF2 deletions (P<0.05). Based on the cytogenetic subgroups, favorable cytogenetic subgroups (i.e. ETV6-RUNX1 and hyperdiploiy) showed more deletions than other subgroups, specifically ETV6 deletions (P<0.05). TCF3-PBX1 was frequently deleted in RB1, and an absence of deletions was observed in IKZF1 and genes localized to the PAR1 region. IKZF1 deletions (P=0.01, 30.2 months, 95% CI 8.5-52.0) and RB1 deletions (P<0.01, 16.8 months, 95% CI 0.0-46.1) confered poorer OS to standard risk patients.
Summary
The results corroborate previous genome-wide data and are an important validation of the impact of IKZF1 deletions in the prognosis of BCP-ALL. The obtained results emphasize the need for including screening of submicroscopic alterations as additional markers for risk stratification, especially in standard risk patients.
Keyword(s): Acute lymphoblastic leukemia, Ikaros
Session topic: Publication Only
Abstract: PB1588
Type: Publication Only
Background
Copy number alterations (CNAs) in genes committed to B-cell precursors have been associated with poor survival in subgroups of B-cell precursor acute lymphoblastic leukemia (BCP-ALL).
Aims
Therefore, the aim of this study was to determine the frequency of gene deletions and the significance of copy number alterations in IKZF1, CDKN2A/B, PAX5, EBF1, ETV6, BTG1, RB1, CSF2RA, IL3RA and CRLF2 within a cohort of Brazilian pediatric BCP-ALL patients.
Methods
Bone marrow and peripheral blood aspirates samples from 274 BCP-ALL patients were analyzed prior to any oncological treatment (period 2004-2011). The inclusion criteria were the quality of the frozen diagnostic material, having at least 30% blast cells, patients with ≤18 years old at the time of BCP-ALL diagnosis. The exclusion criteria were acute leukemia in children with Down syndrome, samples collected in heparin, and DNA of insufficient quality. DNA was analyzed by the SALSA multiplex ligation-dependent probe amplification (MLPA) kit (P335-A4). IKZF1 deletion results were confirmed using a P202 IKZF1 SALSA MLPA kit. The age at diagnosis and white blood cell (WBC) count were the criteria for assigning prognostic risk of ALL, according to the National Cancer Institute (NCI). The disease risk associated with CNA occurrence across overall and subgroups of patients was determined by calculating odds ratios (ORs) with a 95% confidence interval (CI). Overall survival (OS) was defined as the time from diagnosis to last event (death or alive). The OS analysis were obtained by the Kaplan-Meier method and log-rank test.
Results
Deletions/amplifications in at least one gene were identified in 83% of the total series. In children older than two years, there was a predominance of CNAs involving deletions in IKZF1, CDKN2A and CDKN2B, whereas IL3RA and CSF2RA had deletions that were found more frequently in infants (P<0.05). Multiple gene deletions occurred in the same patients. Sixty-three patients had both CDKN2A and CDKN2B deletions (P<0.01). Deletions of CDKN2A and CDKN2B also coincided significantly with deletions in PAX5 (P<0.01) and IKZF1 (P<0.05). IKZF1 deletions were also found concomitantly with BTG1 and EBF1 deletions (P<0.05 and P<0.01, respectively). ETV6 deletions overlapped with PAX5, BTG1, EBF1 (P<0.01) and CRLF2 deletions (P<0.05). Based on the cytogenetic subgroups, favorable cytogenetic subgroups (i.e. ETV6-RUNX1 and hyperdiploiy) showed more deletions than other subgroups, specifically ETV6 deletions (P<0.05). TCF3-PBX1 was frequently deleted in RB1, and an absence of deletions was observed in IKZF1 and genes localized to the PAR1 region. IKZF1 deletions (P=0.01, 30.2 months, 95% CI 8.5-52.0) and RB1 deletions (P<0.01, 16.8 months, 95% CI 0.0-46.1) confered poorer OS to standard risk patients.
Summary
The results corroborate previous genome-wide data and are an important validation of the impact of IKZF1 deletions in the prognosis of BCP-ALL. The obtained results emphasize the need for including screening of submicroscopic alterations as additional markers for risk stratification, especially in standard risk patients.
Keyword(s): Acute lymphoblastic leukemia, Ikaros
Session topic: Publication Only
Type: Publication Only
Background
Copy number alterations (CNAs) in genes committed to B-cell precursors have been associated with poor survival in subgroups of B-cell precursor acute lymphoblastic leukemia (BCP-ALL).
Aims
Therefore, the aim of this study was to determine the frequency of gene deletions and the significance of copy number alterations in IKZF1, CDKN2A/B, PAX5, EBF1, ETV6, BTG1, RB1, CSF2RA, IL3RA and CRLF2 within a cohort of Brazilian pediatric BCP-ALL patients.
Methods
Bone marrow and peripheral blood aspirates samples from 274 BCP-ALL patients were analyzed prior to any oncological treatment (period 2004-2011). The inclusion criteria were the quality of the frozen diagnostic material, having at least 30% blast cells, patients with ≤18 years old at the time of BCP-ALL diagnosis. The exclusion criteria were acute leukemia in children with Down syndrome, samples collected in heparin, and DNA of insufficient quality. DNA was analyzed by the SALSA multiplex ligation-dependent probe amplification (MLPA) kit (P335-A4). IKZF1 deletion results were confirmed using a P202 IKZF1 SALSA MLPA kit. The age at diagnosis and white blood cell (WBC) count were the criteria for assigning prognostic risk of ALL, according to the National Cancer Institute (NCI). The disease risk associated with CNA occurrence across overall and subgroups of patients was determined by calculating odds ratios (ORs) with a 95% confidence interval (CI). Overall survival (OS) was defined as the time from diagnosis to last event (death or alive). The OS analysis were obtained by the Kaplan-Meier method and log-rank test.
Results
Deletions/amplifications in at least one gene were identified in 83% of the total series. In children older than two years, there was a predominance of CNAs involving deletions in IKZF1, CDKN2A and CDKN2B, whereas IL3RA and CSF2RA had deletions that were found more frequently in infants (P<0.05). Multiple gene deletions occurred in the same patients. Sixty-three patients had both CDKN2A and CDKN2B deletions (P<0.01). Deletions of CDKN2A and CDKN2B also coincided significantly with deletions in PAX5 (P<0.01) and IKZF1 (P<0.05). IKZF1 deletions were also found concomitantly with BTG1 and EBF1 deletions (P<0.05 and P<0.01, respectively). ETV6 deletions overlapped with PAX5, BTG1, EBF1 (P<0.01) and CRLF2 deletions (P<0.05). Based on the cytogenetic subgroups, favorable cytogenetic subgroups (i.e. ETV6-RUNX1 and hyperdiploiy) showed more deletions than other subgroups, specifically ETV6 deletions (P<0.05). TCF3-PBX1 was frequently deleted in RB1, and an absence of deletions was observed in IKZF1 and genes localized to the PAR1 region. IKZF1 deletions (P=0.01, 30.2 months, 95% CI 8.5-52.0) and RB1 deletions (P<0.01, 16.8 months, 95% CI 0.0-46.1) confered poorer OS to standard risk patients.
Summary
The results corroborate previous genome-wide data and are an important validation of the impact of IKZF1 deletions in the prognosis of BCP-ALL. The obtained results emphasize the need for including screening of submicroscopic alterations as additional markers for risk stratification, especially in standard risk patients.
Keyword(s): Acute lymphoblastic leukemia, Ikaros
Session topic: Publication Only
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