Abstract 2756: Whole-exome sequencing reveals a novel germline variant in CEBPA-associated familial acute myeloid leukemia: 45-year follow-up of a large family

Abstract Among acute myeloid leukemia (AML) patients with a normal karyotype (CN-AML), NPM1 and CEBPA mutations define World Health Organization 2008 provisional entities accounting for approximately 60% of patients, but the remaining 40% are molecularly poorly characterized. Using whole-exome sequencing of one CN-AML patient lacking mutations in NPM1, CEBPA, FLT3-ITD, IDH1, and MLL-PTD, we newly identified a clonal somatic mutation in BCOR (BCL6 corepressor), a gene located on chromosome Xp11.4. Further analyses of 553 AML patients showed that BCOR mutations occurred in 3.8% of unselected CN-AML patients and represented a substantial fraction (17.1%) of CN-AML patients showing the same genotype as the AML index patient subjected to whole-exome sequencing. BCOR somatic mutations were: (1) disruptive events similar to the germline BCOR mutations causing the oculo-facio-cardio-dental genetic syndrome; (2) associated with decreased BCOR mRNA levels, absence of full-length BCOR, and absent or low expression of a truncated BCOR protein; (3) virtually mutually exclusive with NPM1 mutations; and (4) frequently associated with DNMT3A mutations, suggesting cooperativity among these genetic alterations. Finally, BCOR mutations tended to be associated with an inferior outcome in a cohort of 422 CN-AML patients (25.6% vs 56.7% overall survival at 2 years; P = .032). Our results for the first time implicate BCOR in CN-AML pathogenesis.

Download Full-text

Single Cell Whole Exome Sequencing in NPM1/Flt3 Positive Pediatric Acute Myeloid Leukemia

Blood ◽

10.1182/blood.v124.21.1043.1043 ◽

2014 ◽

Vol 124 (21) ◽

pp. 1043-1043

Author(s):

Christiane Walter ◽

Winfried Hofmann ◽

Katarina Reinhardt ◽

Dirk Reinhardt ◽

Nils von Neuhoff

Keyword(s):

Acute Myeloid Leukemia ◽

Single Cell ◽

Exome Sequencing ◽

Whole Exome Sequencing ◽

Myeloid Leukemia ◽

Single Cells ◽

Clonal Evolution ◽

Npm1 Mutation ◽

Whole Exome ◽

Acute Myeloid

Abstract Introduction: Acute myeloid leukemia (AML) is one of the most frequent forms of leukemia in children younger than 15 years. The detection of several mutations in a blast population of pediatric AML (pAML) is supposed to be caused by a clonal evolution from a leukemic stem cell (LSC) to leukemic blasts. LSC are believed to be more resistant to chemotherapy, to be able to survive during treatment and to be responsible for the emergence of a relapse due to the persistence in the bone marrow (BM) niche. Since LSC and potential leukemic subclones are only present in small subpopulations, it has been a major technical challenge to particular analyse only the specific population. To acquire a better understanding of the underlying mechanisms of mutagenesis, clonal evolution and leukemogenesis, the aim of this study was to establish methods that allow the analysis and detection of mutations in single cells of a subpopulation known to contain HSC as well as LSC (CD34+CD38-). We especially focused on a pAML subgroup with mutations in Nucleophosmin (NPM1) and/or fms related tyrosine kinase 3 (Flt3). Methods and Results: We established methods to perform single cell sorting, whole genome amplification (WGA) using multiple displacement amplification (MDA) technology (Qiagen) and subsequent whole exome sequencing. The sorting efficiency was checked as Hoechst stained cells were sorted onto glas slides with 48 defined spots and the presence of single cells was checked under an inverse fluorescent microscope. Subsequently, single CD34+CD38- patient derived cells were sorted into 0,5ml low binding tubes containing 4µl PBS followed by WGA and whole exome sequencing. The mutational status of the sorted single cells from three patients suffering from pAML was analysed and compared to mutations detected at initial diagnosis in DNA from a bulk of BM cells. WGA from single CD34+CD38-PI- cells resulted in an amount of 29 to 31.7µg DNA from each of five single cells. The quality of the amplified DNA was sufficient for whole exome sequencing. A 4bp insertion in exon 12 of NPM1 reflecting a common NPM1 mutation (MutA) initially detected from a bulk of cells was identified in amplified DNA from single cells using whole exome sequencing in 2/3 patients. Internal tandem duplications in Flt3 indicated by mismatches in the alignment could be detected in amplified DNA from single cells of two patients. The detected ITD resemble those initially detected in DNA from a bulk of BM cells. Discussion and Conclusion: Single cell sequencing provides a useful tool to amend the detection of genetic aberrations from a bulk of cells and to confirm the presence of specific mutations in single cells from small subpopulations. It therefore helps to get further insights into the clonal evolution in pAML. Disclosures No relevant conflicts of interest to declare.

Download Full-text

Abstract A27: European Network NGS-PTL preliminary data: Whole exome sequencing identifies mutations of ALDH2, RETSAT, HSPG2, CHPF and other metabolic genes as a novel functional category in acute myeloid leukemia

10.1158/1557-3125.metca15-a27 ◽

2016 ◽

Author(s):

Giorgia Simonetti ◽

Antonella Padella ◽

Ilaria Iacobucci ◽

Italo Do Valle ◽

Gabriele Fontanarosa ◽

...

Keyword(s):

Acute Myeloid Leukemia ◽

Exome Sequencing ◽

Whole Exome Sequencing ◽

Preliminary Data ◽

Myeloid Leukemia ◽

Functional Category ◽

European Network ◽

Metabolic Genes ◽

Whole Exome ◽

Acute Myeloid

Download Full-text

Genomic complexity and dynamics of clonal evolution in childhood acute myeloid leukemia studied with whole-exome sequencing

Oncotarget ◽

10.18632/oncotarget.10778 ◽

2016 ◽

Vol 7 (35) ◽

pp. 56746-56757 ◽

Cited By ~ 13

Author(s):

Riccardo Masetti ◽

Ilaria Castelli ◽

Annalisa Astolfi ◽

Salvatore Nicola Bertuccio ◽

Valentina Indio ◽

...

Keyword(s):

Acute Myeloid Leukemia ◽

Exome Sequencing ◽

Whole Exome Sequencing ◽

Myeloid Leukemia ◽

Clonal Evolution ◽

Genomic Complexity ◽

Whole Exome ◽

Childhood Acute Myeloid Leukemia ◽

Acute Myeloid

Download Full-text

Whole exome sequencing identifies novel mutations of epigenetic regulators in chemorefractory pediatric acute myeloid leukemia

Leukemia Research ◽

10.1016/j.leukres.2017.12.001 ◽

2018 ◽

Vol 65 ◽

pp. 20-24 ◽

Cited By ~ 9

Author(s):

Di Zhan ◽

Yingchi Zhang ◽

Peifang Xiao ◽

Xinchang Zheng ◽

Min Ruan ◽

...

Keyword(s):

Acute Myeloid Leukemia ◽

Exome Sequencing ◽

Whole Exome Sequencing ◽

Myeloid Leukemia ◽

Novel Mutations ◽

Pediatric Acute Myeloid Leukemia ◽

Whole Exome ◽

Epigenetic Regulators ◽

Acute Myeloid

Download Full-text

Tracing the development of acute myeloid leukemia in CBL syndrome

Blood ◽

10.1182/blood-2013-10-533844 ◽

2014 ◽

Vol 123 (12) ◽

pp. 1883-1886 ◽

Cited By ~ 13

Author(s):

Heiko Becker ◽

Kenichi Yoshida ◽

Nadja Blagitko-Dorfs ◽

Rainer Claus ◽

Milena Pantic ◽

...

Keyword(s):

Acute Myeloid Leukemia ◽

Exome Sequencing ◽

Whole Exome Sequencing ◽

Myeloid Leukemia ◽

Juvenile Myelomonocytic Leukemia ◽

Whole Exome ◽

Key Points ◽

Myelomonocytic Leukemia ◽

Acute Myeloid

Key Points The CBL syndrome may predispose to myeloid neoplasias other than juvenile myelomonocytic leukemia. Whole-exome sequencing identifies mutations that possibly cooperate with mutant CBL in AML development.

Download Full-text