TARGET investigators are analyzing tumors from pediatric patients, many who have relapsed, to identify biomarkers that correlate with poor clinical outcome and/or new therapeutic approaches to treat childhood AML. The tissues used in this study were collected from patients enrolled in Children's Oncology Group (COG) biology studies and clinical trials.
The AML project team members (like other TARGET researchers) are generating data in two phases: Discovery and Validation. Visit the TARGET Research page to learn more.
Discovery Dataset
The TARGET AML project has produced comprehensive genomic profiles of nearly 200 relapse-enriched, clinically annotated patient cases in the discovery dataset. This cohort includes ~100 patients with adequate relapse specimens to study as trios (see three sample types below). Each fully-characterized TARGET AML case includes data from nucleic acid samples extracted from peripheral blood or bone marrow tissues as follows:
- Primary tumor sample collected at diagnosis
- Case-matched tissue sample collected at remission (<5% blasts detected following standard induction therapy)
- Relapsed tumor sample (case-matched) when available; ~50% cases have 3rd sample (those cases are considered a “trio”)
Additional cases with partial molecular characterization and/or sequencing data are available to the research community.
Case Selection Criteria
Tissues and clinical data used for the TARGET AML project were obtained from patients enrolled on biology studies and clinical trials managed through the Children’s Oncology Group (COG). Patient samples with full characterization were chosen based on the following criteria:
- Patients achieved a remission following a standard two rounds of induction therapy (fewer than 5% blasts)
- Bone marrow and peripheral blood blast counts of >50% in tumor specimens
- Adequate amount of high-quality nucleic acids for comprehensive genomic profiling
- 3 or fewer clinically-relevant cytogenetic findings (majority of cases)
Molecular Characterization
The TARGET AML project team relied on a variety of platforms to obtain a fully characterized dataset of ~200 relapse-enriched cases. The COG AML Statistics and Data Center provided clinical annotations and outcome data for all cases. Visit the TARGET Project Experimental Methods page for detailed information and protocols.
| General Methodology |
Platform |
|---|
| Clinical Annotation |
COG Protocols (CCG-2961, AAML03P1, AAML0531) |
| Gene Expression |
Affymetrix Gene ST Array |
| Chromosome Copy Number Analyses & Loss of Heterozygosity |
Affymetrix SNP 6.0 Array |
| Epigenetics (DNA Methylation) |
Illumina Infinium 27K or 450K |
| Whole Genome Sequencing |
Complete Genomics Incorporated |
| Whole Exome Sequencing |
Illumina Hi-Seq 2000 |
| mRNA-seq |
Illumina Hi-Seq 2000 |
| miRNA-seq |
Illumina Hi-Seq 2000 |
Verification of Discovery Variants
The TARGET AML project team utilized a variety of sequencing approaches to confirm candidate variants identified in the discovery sample cohort as somatic. For example, mRNA-seq results are being used to determine variants which were expressed and originally identified through whole genome or exome sequencing. These verified variants will be made available as open-access data. The TARGET AML project team has additionally employed the same targeted capture sequencing approach described in the validation strategy below to verify variants seen in a variety of tumor, remission and/or relapse samples from a majority of fully-characterized patient cases in the TARGET AML discovery cohort.
Validation Strategy
Some sequence mutations identified in the relapse-enriched discovery cohort, along with some previously published variants in adult AML, were further analyzed in an additional 600-plus cases. The TARGET AML project team employed targeted capture sequencing to look at the presence and frequency of alterations in 400 gene variants. This validation effort was performed in an unbiased cohort that was randomly selected from patients enrolled on a single COG protocol, which allowed for determination of the frequency of these changes across a broader spectrum of AML subtypes.
FHCRC AML Dataset
Children with AML whose disease is refractory to standard induction chemotherapy therapy or who experience relapse after initial response have dismal outcomes. Pediatric AML miRNA samples were sequenced to identify dysregulated genes and assess the utility of miRNA signature for improved outcome prediction. RNA-seq and other high-throughput next-generation sequencing platforms have emerged as powerful approaches for discovering pathogenic pathways and potential targets for clinical intervention in patients with AML. Within the Fred Hutchinson Cancer Research Center (FHCRC) AML dataset, there are 18 cases which got RNA-seq that overlap with the AML Discovery cohort and 26 cases that overlap with the AML Validation cohort. These data from the Children’s Oncology Group are stored together at the Data Coordinating Center and Genomic Data Commons for ease of use.
All data from the discovery and validation efforts are made available as specified in the Using TARGET Data and TARGET Publication Guidelines pages. The TARGET Data Matrix provides an overview of the data generated and described above.
