DEEP SEQUENCING OF 23 GENES DESIGNATED BY TCGA STUDY IN ACUTE MYELOID LEUKEMIA PATIENTS WITH NORMAL KARYOTYPE
(Abstract release date: 05/19/16)
EHA Library. Ibañez M. 06/09/16; 132445; E896
Dr. Mariam Ibañez
Contributions
Contributions
Abstract
Abstract: E896
Type: Eposter Presentation
Background
In the study carried out by The Cancer Genome Atlas Research Network (TCGA), 99% of patients with acute myeloid leukemia (AML) presented at list one mutation over 23 genes (NPM1, FLT3, ASXL1, BCOR, CEBPA, DNMT3A, EZH2, IDH1, IDH2, KDM6A, KIT, KRAS, NRAS, PTPN11, RAD21, RUNX1, STAG2, SMC1A, SMC3, TET2, TP53, U2AF1 and WT1). However, there are not studies focused on these 23 genes to evaluate their incidence and clinical role within independent cohorts of patients lacking chromosomal aberrations, which represents nearly 50% of patients (NKAML)
Aims
To establish the frequency and prognostic influence of mutations and their interactions in the 23 genes designated by TCGA study in the context of other prognostic clinical and molecular markers in a cohort of de novo NKAML patients
Methods
The study includes 112 adult patients with de novo AML (excluding acute promyelocytic leukemia) with normal karyotype. Available DNA sample at diagnosis was the only limiting criterion. DNA samples from Hospital Universitari i Politècnic La Fe were provided by Biobank La Fe. We carried out targeted gene sequencing (Ion Torrent Proton System–Life Technologies) using a 23 genes custom panel including all coding regions (NPM1, FLT3, ASXL1, BCOR, CEBPA, DNMT3A, EZH2, IDH1, IDH2, KDM6A, KIT, KRAS, NRAS, PTPN11, RAD21, RUNX1, STAG2, SMC1A, SMC3, TET2, TP53, U2AF1 and WT1). Selected variants were annotated using IonReporter® Software for clinical reporting. Non-pathogenic variants were filtered out by excluding synonymous, intronic and polymorphic variants (major allele frequency (MAF) ≥ 0,01 and/or included in dbSNP). FLT3-ITD mutations were assessed as previously reported. 1
Results
After filtering procedure we identified a total of 314 high-confidence variants, with an average of 3 mutations per sample, (range 0-7). Mutations in at least one of the genes were found in 103 out of 112 patients (95%). The most commonly mutated genes were DNMT3A (n= 43, 39%), NPM1 (n= 37, 33%), FLT3-ITD (n=33, 29%), IDH (n=31, 28%), TET2 (n=30, 27%), RUNX1 (n=19, 17%), ASXL1 (n=17, 15%), KDM6A (n=14, 13%), WT1 (n=11, 15%) and PTPN11 (n= 9, 12%). Of the 112 samples, 91% contained at least one mutation in one of eight categories defined according to biologic function with a putative role in AML pathogenesis: DNA-methylation–related (71%), encoding nucleophosmin (NPM1) (33%), activated signalling (37%), chromatin-modifying (27%), myeloid transcription-factor (25%), cohesin-complex (20%), tumor suppressor (16%), and spliceosome-complex (U2AF1)(4%). In addition, we identified a strong pattern of mutual exclusivity between ASXL1 mutations and three other genes, in an independently manner, U2AF1 (P = 0.011), TET2 (P = 0.032) and DNMT3A (P = 0.03). In addition, we found a significant co-occurrence between mutations in DNMT3A and NPM1, (P = 0.001) and TET2 and IDH2 or NRAS (P = 0.004; P = 0.039, respectively). In univariate analyses, NKAML patients carrying indels in TET2 or in ASXL1 showed a significantly worse outcome (5-year OS, wt34% vs. mut 7%, P = 0.025; 5-year OS, wt 30% vs. mut 12%, P = 0.001, respectively). Further results will be presented in the meeting
Conclusion
Over 23 genes described by TCGA, 91% de novo NKAML patients showed at least one mutation. The most frequently mutated functional category was DNA-methylation (71%), which might trigger the process of leukemogenesis in NKAML.This work was supported by: Fundación Española de Hematología (FEHH), PI12/01047, RD12/0036/0014, PIE13/00046, PI13/01640, PI13/02387, PT13/0010/0026, PI14/01649 and PROMETEOII/2014/025.1. Moreno I, et al. Haematologica 2003;88 1: 19–24.
Session topic: E-poster
Keyword(s): Acute myeloid leukemia, Molecular markers
Type: Eposter Presentation
Background
In the study carried out by The Cancer Genome Atlas Research Network (TCGA), 99% of patients with acute myeloid leukemia (AML) presented at list one mutation over 23 genes (NPM1, FLT3, ASXL1, BCOR, CEBPA, DNMT3A, EZH2, IDH1, IDH2, KDM6A, KIT, KRAS, NRAS, PTPN11, RAD21, RUNX1, STAG2, SMC1A, SMC3, TET2, TP53, U2AF1 and WT1). However, there are not studies focused on these 23 genes to evaluate their incidence and clinical role within independent cohorts of patients lacking chromosomal aberrations, which represents nearly 50% of patients (NKAML)
Aims
To establish the frequency and prognostic influence of mutations and their interactions in the 23 genes designated by TCGA study in the context of other prognostic clinical and molecular markers in a cohort of de novo NKAML patients
Methods
The study includes 112 adult patients with de novo AML (excluding acute promyelocytic leukemia) with normal karyotype. Available DNA sample at diagnosis was the only limiting criterion. DNA samples from Hospital Universitari i Politècnic La Fe were provided by Biobank La Fe. We carried out targeted gene sequencing (Ion Torrent Proton System–Life Technologies) using a 23 genes custom panel including all coding regions (NPM1, FLT3, ASXL1, BCOR, CEBPA, DNMT3A, EZH2, IDH1, IDH2, KDM6A, KIT, KRAS, NRAS, PTPN11, RAD21, RUNX1, STAG2, SMC1A, SMC3, TET2, TP53, U2AF1 and WT1). Selected variants were annotated using IonReporter® Software for clinical reporting. Non-pathogenic variants were filtered out by excluding synonymous, intronic and polymorphic variants (major allele frequency (MAF) ≥ 0,01 and/or included in dbSNP). FLT3-ITD mutations were assessed as previously reported. 1
Results
After filtering procedure we identified a total of 314 high-confidence variants, with an average of 3 mutations per sample, (range 0-7). Mutations in at least one of the genes were found in 103 out of 112 patients (95%). The most commonly mutated genes were DNMT3A (n= 43, 39%), NPM1 (n= 37, 33%), FLT3-ITD (n=33, 29%), IDH (n=31, 28%), TET2 (n=30, 27%), RUNX1 (n=19, 17%), ASXL1 (n=17, 15%), KDM6A (n=14, 13%), WT1 (n=11, 15%) and PTPN11 (n= 9, 12%). Of the 112 samples, 91% contained at least one mutation in one of eight categories defined according to biologic function with a putative role in AML pathogenesis: DNA-methylation–related (71%), encoding nucleophosmin (NPM1) (33%), activated signalling (37%), chromatin-modifying (27%), myeloid transcription-factor (25%), cohesin-complex (20%), tumor suppressor (16%), and spliceosome-complex (U2AF1)(4%). In addition, we identified a strong pattern of mutual exclusivity between ASXL1 mutations and three other genes, in an independently manner, U2AF1 (P = 0.011), TET2 (P = 0.032) and DNMT3A (P = 0.03). In addition, we found a significant co-occurrence between mutations in DNMT3A and NPM1, (P = 0.001) and TET2 and IDH2 or NRAS (P = 0.004; P = 0.039, respectively). In univariate analyses, NKAML patients carrying indels in TET2 or in ASXL1 showed a significantly worse outcome (5-year OS, wt34% vs. mut 7%, P = 0.025; 5-year OS, wt 30% vs. mut 12%, P = 0.001, respectively). Further results will be presented in the meeting
Conclusion
Over 23 genes described by TCGA, 91% de novo NKAML patients showed at least one mutation. The most frequently mutated functional category was DNA-methylation (71%), which might trigger the process of leukemogenesis in NKAML.This work was supported by: Fundación Española de Hematología (FEHH), PI12/01047, RD12/0036/0014, PIE13/00046, PI13/01640, PI13/02387, PT13/0010/0026, PI14/01649 and PROMETEOII/2014/025.1. Moreno I, et al. Haematologica 2003;88 1: 19–24.
Session topic: E-poster
Keyword(s): Acute myeloid leukemia, Molecular markers
Abstract: E896
Type: Eposter Presentation
Background
In the study carried out by The Cancer Genome Atlas Research Network (TCGA), 99% of patients with acute myeloid leukemia (AML) presented at list one mutation over 23 genes (NPM1, FLT3, ASXL1, BCOR, CEBPA, DNMT3A, EZH2, IDH1, IDH2, KDM6A, KIT, KRAS, NRAS, PTPN11, RAD21, RUNX1, STAG2, SMC1A, SMC3, TET2, TP53, U2AF1 and WT1). However, there are not studies focused on these 23 genes to evaluate their incidence and clinical role within independent cohorts of patients lacking chromosomal aberrations, which represents nearly 50% of patients (NKAML)
Aims
To establish the frequency and prognostic influence of mutations and their interactions in the 23 genes designated by TCGA study in the context of other prognostic clinical and molecular markers in a cohort of de novo NKAML patients
Methods
The study includes 112 adult patients with de novo AML (excluding acute promyelocytic leukemia) with normal karyotype. Available DNA sample at diagnosis was the only limiting criterion. DNA samples from Hospital Universitari i Politècnic La Fe were provided by Biobank La Fe. We carried out targeted gene sequencing (Ion Torrent Proton System–Life Technologies) using a 23 genes custom panel including all coding regions (NPM1, FLT3, ASXL1, BCOR, CEBPA, DNMT3A, EZH2, IDH1, IDH2, KDM6A, KIT, KRAS, NRAS, PTPN11, RAD21, RUNX1, STAG2, SMC1A, SMC3, TET2, TP53, U2AF1 and WT1). Selected variants were annotated using IonReporter® Software for clinical reporting. Non-pathogenic variants were filtered out by excluding synonymous, intronic and polymorphic variants (major allele frequency (MAF) ≥ 0,01 and/or included in dbSNP). FLT3-ITD mutations were assessed as previously reported. 1
Results
After filtering procedure we identified a total of 314 high-confidence variants, with an average of 3 mutations per sample, (range 0-7). Mutations in at least one of the genes were found in 103 out of 112 patients (95%). The most commonly mutated genes were DNMT3A (n= 43, 39%), NPM1 (n= 37, 33%), FLT3-ITD (n=33, 29%), IDH (n=31, 28%), TET2 (n=30, 27%), RUNX1 (n=19, 17%), ASXL1 (n=17, 15%), KDM6A (n=14, 13%), WT1 (n=11, 15%) and PTPN11 (n= 9, 12%). Of the 112 samples, 91% contained at least one mutation in one of eight categories defined according to biologic function with a putative role in AML pathogenesis: DNA-methylation–related (71%), encoding nucleophosmin (NPM1) (33%), activated signalling (37%), chromatin-modifying (27%), myeloid transcription-factor (25%), cohesin-complex (20%), tumor suppressor (16%), and spliceosome-complex (U2AF1)(4%). In addition, we identified a strong pattern of mutual exclusivity between ASXL1 mutations and three other genes, in an independently manner, U2AF1 (P = 0.011), TET2 (P = 0.032) and DNMT3A (P = 0.03). In addition, we found a significant co-occurrence between mutations in DNMT3A and NPM1, (P = 0.001) and TET2 and IDH2 or NRAS (P = 0.004; P = 0.039, respectively). In univariate analyses, NKAML patients carrying indels in TET2 or in ASXL1 showed a significantly worse outcome (5-year OS, wt34% vs. mut 7%, P = 0.025; 5-year OS, wt 30% vs. mut 12%, P = 0.001, respectively). Further results will be presented in the meeting
Conclusion
Over 23 genes described by TCGA, 91% de novo NKAML patients showed at least one mutation. The most frequently mutated functional category was DNA-methylation (71%), which might trigger the process of leukemogenesis in NKAML.This work was supported by: Fundación Española de Hematología (FEHH), PI12/01047, RD12/0036/0014, PIE13/00046, PI13/01640, PI13/02387, PT13/0010/0026, PI14/01649 and PROMETEOII/2014/025.1. Moreno I, et al. Haematologica 2003;88 1: 19–24.
Session topic: E-poster
Keyword(s): Acute myeloid leukemia, Molecular markers
Type: Eposter Presentation
Background
In the study carried out by The Cancer Genome Atlas Research Network (TCGA), 99% of patients with acute myeloid leukemia (AML) presented at list one mutation over 23 genes (NPM1, FLT3, ASXL1, BCOR, CEBPA, DNMT3A, EZH2, IDH1, IDH2, KDM6A, KIT, KRAS, NRAS, PTPN11, RAD21, RUNX1, STAG2, SMC1A, SMC3, TET2, TP53, U2AF1 and WT1). However, there are not studies focused on these 23 genes to evaluate their incidence and clinical role within independent cohorts of patients lacking chromosomal aberrations, which represents nearly 50% of patients (NKAML)
Aims
To establish the frequency and prognostic influence of mutations and their interactions in the 23 genes designated by TCGA study in the context of other prognostic clinical and molecular markers in a cohort of de novo NKAML patients
Methods
The study includes 112 adult patients with de novo AML (excluding acute promyelocytic leukemia) with normal karyotype. Available DNA sample at diagnosis was the only limiting criterion. DNA samples from Hospital Universitari i Politècnic La Fe were provided by Biobank La Fe. We carried out targeted gene sequencing (Ion Torrent Proton System–Life Technologies) using a 23 genes custom panel including all coding regions (NPM1, FLT3, ASXL1, BCOR, CEBPA, DNMT3A, EZH2, IDH1, IDH2, KDM6A, KIT, KRAS, NRAS, PTPN11, RAD21, RUNX1, STAG2, SMC1A, SMC3, TET2, TP53, U2AF1 and WT1). Selected variants were annotated using IonReporter® Software for clinical reporting. Non-pathogenic variants were filtered out by excluding synonymous, intronic and polymorphic variants (major allele frequency (MAF) ≥ 0,01 and/or included in dbSNP). FLT3-ITD mutations were assessed as previously reported. 1
Results
After filtering procedure we identified a total of 314 high-confidence variants, with an average of 3 mutations per sample, (range 0-7). Mutations in at least one of the genes were found in 103 out of 112 patients (95%). The most commonly mutated genes were DNMT3A (n= 43, 39%), NPM1 (n= 37, 33%), FLT3-ITD (n=33, 29%), IDH (n=31, 28%), TET2 (n=30, 27%), RUNX1 (n=19, 17%), ASXL1 (n=17, 15%), KDM6A (n=14, 13%), WT1 (n=11, 15%) and PTPN11 (n= 9, 12%). Of the 112 samples, 91% contained at least one mutation in one of eight categories defined according to biologic function with a putative role in AML pathogenesis: DNA-methylation–related (71%), encoding nucleophosmin (NPM1) (33%), activated signalling (37%), chromatin-modifying (27%), myeloid transcription-factor (25%), cohesin-complex (20%), tumor suppressor (16%), and spliceosome-complex (U2AF1)(4%). In addition, we identified a strong pattern of mutual exclusivity between ASXL1 mutations and three other genes, in an independently manner, U2AF1 (P = 0.011), TET2 (P = 0.032) and DNMT3A (P = 0.03). In addition, we found a significant co-occurrence between mutations in DNMT3A and NPM1, (P = 0.001) and TET2 and IDH2 or NRAS (P = 0.004; P = 0.039, respectively). In univariate analyses, NKAML patients carrying indels in TET2 or in ASXL1 showed a significantly worse outcome (5-year OS, wt34% vs. mut 7%, P = 0.025; 5-year OS, wt 30% vs. mut 12%, P = 0.001, respectively). Further results will be presented in the meeting
Conclusion
Over 23 genes described by TCGA, 91% de novo NKAML patients showed at least one mutation. The most frequently mutated functional category was DNA-methylation (71%), which might trigger the process of leukemogenesis in NKAML.This work was supported by: Fundación Española de Hematología (FEHH), PI12/01047, RD12/0036/0014, PIE13/00046, PI13/01640, PI13/02387, PT13/0010/0026, PI14/01649 and PROMETEOII/2014/025.1. Moreno I, et al. Haematologica 2003;88 1: 19–24.
Session topic: E-poster
Keyword(s): Acute myeloid leukemia, Molecular markers
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