Characteristics and prognostic significance of genetic mutations in acute myeloid leukemia based on a targeted next‐generation sequencing technique

Abstract Circulating cell-free DNA (ccfDNA) allows for noninvasive peripheral blood sampling of cancer-associated mutations and has established clinical utility in several solid tumors. We performed targeted next-generation sequencing of ccfDNA and bone marrow at the time of diagnosis and after achieving remission in 22 patients with acute myeloid leukemia (AML). Among 28 genes sequenced by both platforms, a total of 39 unique somatic mutations were detected. Five mutations (13%) were detected only in ccfDNA, and 15 (38%) were detected only in bone marrow. Among the 19 mutations detected in both sources, the concordance of variant allelic frequency (VAF) assessment by both methods was high (R2 = 0.849). Mutations detected in only 1 source generally had lower VAF than those detected in both sources, suggesting that either method may miss small subclonal populations. In 3 patients, sequencing of ccfDNA detected new or persistent leukemia-associated mutations during remission that appeared to herald overt relapse. Overall, this study demonstrates that sequencing of ccfDNA in patients with AML can identify clinically relevant mutations not detected in the bone marrow and may play a role in the assessment of measurable residual disease. However, mutations were missed by both ccfDNA and bone marrow analyses, particularly when the VAF was <10%, suggesting that ccfDNA and bone marrow may be complementary in the assessment and monitoring of patients with AML.

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A targeted next-generation sequencing in the molecular risk stratification of adult acute myeloid leukemia: implications for clinical practice

Cancer Medicine ◽

10.1002/cam4.969 ◽

2017 ◽

Vol 6 (2) ◽

pp. 349-360 ◽

Cited By ~ 21

Author(s):

Po-Han Lin ◽

Huei-Ying Li ◽

Sheng-Chih Fan ◽

Tzu-Hang Yuan ◽

Ming Chen ◽

...

Keyword(s):

Acute Myeloid Leukemia ◽

Clinical Practice ◽

Next Generation Sequencing ◽

Risk Stratification ◽

Myeloid Leukemia ◽

Next Generation ◽

Targeted Next Generation Sequencing ◽

Generation Sequencing ◽

Acute Myeloid

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Evaluation of a 42-Gene Next-Generation Sequencing Panel for Detection of Acute Myeloid Leukemia Mutations for Clinical Use

American Journal of Clinical Pathology ◽

10.1093/ajcp/aqz121.024 ◽

2019 ◽

Vol 152 (Supplement_1) ◽

pp. S114-S114

Author(s):

Sun Hee Rosenthal ◽

Anna Gerasimova ◽

Charles Ma ◽

Daniel Sugganth ◽

Frederick Racke ◽

...

Keyword(s):

Acute Myeloid Leukemia ◽

Next Generation Sequencing ◽

Clinical Diagnosis ◽

Myeloid Leukemia ◽

Prognostic Significance ◽

Genetic Alterations ◽

Analytical Sensitivity ◽

Next Generation ◽

Generation Sequencing ◽

Acute Myeloid

Abstract Objectives Identification of genetic alterations by molecular and cytogenetic testing has an important role in the classification, risk stratification, and management of acute myeloid leukemia (AML). We evaluated a next-generation sequencing (NGS) panel that assesses IDH2, FLT3, NPM1, and TP3 and 38 other genes associated with diagnostic, prognostic, and/or therapeutic utility in AML, with a turnaround time of 8 to 14 days, using a DNA input of 50 ng. Methods In total, 110 patients, 65 males and 45 females, at a median age of 58 years (range: 2-68 years) with clinical diagnosis of AML were included in this study. Targeted regions were captured by hybridization with complementary biotinylated DNA baits, and NGS was performed on an Illumina NextSeq500 instrument. Sequence reads were analyzed using a bioinformatics pipeline that was developed in house. Analytical sensitivity of the assay is ~5% mutated alleles with 100% specificity. Results A total of 296 pathogenic mutations in 38 genes were detected in 95 of 110 samples (86%). On average, three mutations (range 1-10) were detected per positive sample. Variant frequency ranged from 3.0% to 96.1%. Most frequently mutated genes were TET2 (18.2%), FLT3 (18.2%), TP53 (17.3%), RUNX1 (15.5%), NPM1 (14.5%), ASXL1 (12.7%), NRAS (11.8%), and CEBPA (10.9%). In total, 166 of 296 (56%) mutations from 13 genes had prognostic significance, 42 of 296 (14%) mutations from three genes (CEBPA, NPM1, RUNX1) had diagnostic significance, and 40 of 296 (14%) mutations from three genes (IDH1, IDH2, FLT3) had therapeutic significance. Conclusion This focused 42-gene targeted panel identifies mutations of clinical significance in over 85% of patients with a clinical diagnosis of AML.

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