Characterization of gene mutations and copy number changes in acute myeloid leukemia using a rapid target enrichment protocol.
Prognostic stratification is critical for making therapeutic decisions and maximizing survival of patients with acute myeloid leukemia. Advances in the genomics of acute myeloid leukemia have identified several recurrent gene mutations whose prognostic impact is being deciphered. We used HaloPlex target enrichment and Illumina-based next generation sequencing to study 24 recurrently mutated genes in 42 samples of acute myeloid leukemia with a normal karyotype. Read depth varied between and within genes for the same sample, but was predictable and highly consistent across samples. Consequently, we were able to detect copy number changes, such as an interstitial deletion of BCOR, three MLL partial tandem duplications, and a novel KRAS amplification. With regards to coding mutations, we identified likely oncogenic variants in 41 of 42 samples. NPM1 mutations were the most frequent, followed by FLT3, DNMT3A and TET2. NPM1 and FLT3 indels were reported with good efficiency. We also showed that DNMT3A mutations can persist post-chemotherapy and in 2 cases studied at diagnosis and relapse, we were able to delineate the dynamics of tumor evolution and give insights into order of acquisition of variants. HaloPlex is a quick and reliable target enrichment method that can aid diagnosis and prognostic stratification of acute myeloid leukemia patients.
Cancer Genome Project, Wellcome Trust Sanger Institute, Cambridge, UK Department of Haematology, University of Cambridge, UK Department of Haematology, Addenbrookes Hospital, Cambridge, UK.
Niccolò
N
Bolli
Department of Haematology, Addenbrookes Hospital, Cambridge, UK Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Cambridge, UK.
Nicla
N
Manes
Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Cambridge, UK.
Thomas
T
McKerrell
The Center for the Study of Haematological Malignancies, Nicosia, Cyprus.
Jianxiang
J
Chi
Sequencing Research and Development, Wellcome Trust Sanger Institute, Cambridge, UK.
Naomi
N
Park
Cancer Genome Project, Wellcome Trust Sanger Institute, Cambridge, UK.
Gunes
G
Gundem
Sequencing Research and Development, Wellcome Trust Sanger Institute, Cambridge, UK.
Michael A
MA
Quail
Cancer Genome Project, Wellcome Trust Sanger Institute, Cambridge, UK.
Vijitha
V
Sathiaseelan
Agilent Technologies, Agilent Technologies LDA UK Ltd., Cheadle, UK.
Bram
B
Herman
Department of Haematology, Addenbrookes Hospital, Cambridge, UK.
Charles
C
Crawley
Department of Haematology, Addenbrookes Hospital, Cambridge, UK.
Jenny I O
JI
Craig
Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Cambridge, UK EMBL-European Bioinformatics Institute, Cambridge, UK.
Natalie
N
Conte
Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Cambridge, UK.
Carolyn
C
Grove
Cancer Genome Project, Wellcome Trust Sanger Institute, Cambridge, UK.
Elli
E
Papaemmanuil
Cancer Genome Project, Wellcome Trust Sanger Institute, Cambridge, UK.
Peter J
PJ
Campbell
Instituto de Biomedicina y Biotecnología de Cantabria (CSIC-UC-Sodercan), Departamento de Biología Molecular, Universidad de Cantabria, Santander, Spain.
Ignacio
I
Varela
The Center for the Study of Haematological Malignancies, Nicosia, Cyprus Molecular Haematology and Immunogenetics Center, The Karaiskakio Foundation, Nicosia, Cyprus.
Paul
P
Costeas
Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Cambridge, UK nb8@sanger.ac.uk gsv20@sanger.ac.uk.
George S
GS
Vassiliou
D000465:Algorithms; D016022:Case-Control Studies; D056915:DNA Copy Number Variations / Q000235:genetics*; D005500:Follow-Up Studies; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D015470:Leukemia, Myeloid, Acute / Q000235:genetics* / Q000473:pathology; D009154:Mutation / Q000235:genetics*; D009363:Neoplasm Proteins / Q000235:genetics*; D009367:Neoplasm Staging; D000090243:Nucleophosmin; D011379:Prognosis
C000716967:NPM1 protein, human; D009363:Neoplasm Proteins; D000090243:Nucleophosmin