CCDC - Childhood Cancer Data Catalog

Whole genome sequencing of core-binding factor leukemia

dbGaP

Data Resource: dbGaP

Point of Contact:

James R. Downing, MD,

james.downing@stjude.org

Project

About This Dataset

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 CBFB-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.

Core Data Elements

Number of Cases

17

Case Sex

Not Reported (17)

Case Age At Diagnosis

Pediatric and Young Adult (<40 years) (17)

Case Race

Not Reported (17)

Case Ethnicity

Not Reported (17)

Case Disease Diagnosis

Core Binding Factor Leukemia (17)

Number of Samples

34

Sample Assay Method

Whole Genome Sequencing (34)

Sample Anatomic Site

Bone Marrow (31); Peripheral Blood (3)

Sample Is Normal

Yes (17); No (17)

Additional Data Elements

DBGAP STUDY IDENTIFIER

Charts

Not Reported (17)