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Study Description

Pediatric de novo acute myeloid leukemia (AML) is a heterogeneous disease that can be divided into clinically distinct subtypes based on the presence of specific chromosomal abnormalities or gene alterations. One of the best characterized subtypes of AML involves leukemias with alterations of the core-binding factor (CBF)-complex, which comprises the FAB subtypes M2 and M4Eo and associates with a favorable outcome. Patients with the AML M2 subtype harbor a translocation between chromosomes 8 and 21 [t(8;21)] that yields the chimeric fusion gene RUNX1(AML1)-RUNX1T1(ETO), while patients with AML M4Eo express the chimeric fusion gene CBFβ-SMMHC(MYH11) as a result of an inversion/translocation event of chromosome 16 [inv(16)/t(16;16)]. In an effort to define the total complement of genetic changes in CBF-leukemia, we performed paired-end whole genome sequencing (WGS) on diagnostic leukemia blasts and matched germ line samples from 17 pediatric CBF-leukemia patients using the Illumina platform. Somatic alterations, including single nucleotide variations (SNVs) and structural variations (SVs), including insertions, deletions, inversions, and inter- and intra-chromosomal rearrangements, were detected using complementary analysis pipelines (Bambino, CREST and CONSERTING). Recurrent screening of identified mutations will be performed in a cohort of approximately 94 cases of CBF-leukemias.

  • Study Types: Case Set, Tumor vs. Matched-Normal, Whole Genome Sequencing
  • Number of study subjects that have individual level data available through Authorized Access: 17

Authorized Access
Publicly Available Data (Public ftp)

Connect to the public download site. The site contains release notes and manifests. If available, the site also contains data dictionaries, variable summaries, documents, and truncated analyses.

Study Inclusion/Exclusion Criteria

Cases of core-binding factor leukemia and their matched normal DNA. The cases were selected based on if they had appropriate consent for genetic studies and suitable material for sequencing (high purity tumor populations and available normal DNA obtained at disease remission).

Molecular Data
TypeSourcePlatformNumber of Oligos/SNPsSNP Batch IdComment
Whole Genome Sequencing Illumina HiSeq 2000 N/A N/A
Whole Genome Sequencing Illumina Genome Analyzer II N/A N/A
Study History

Whole genome sequence data from 17 cases of core-binding factor leukemia and matched normal DNA samples. We also performed recurrence screening of selected genes in a cohort of approximately 94 cases of core-binding factor leukemia samples.

Selected publications
Diseases/Traits Related to Study (MESH terms)
Links to Other NCBI Resources
Authorized Data Access Requests
Study Attribution
  • Principal Investigator
    • James R. Downing, MD. Dept. of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
  • Institute
    • St. Jude Children's Research Hospital, Memphis, TN, USA