TARGET’s Study of Acute Lymphoblastic Leukemia
About ALL
Acute lymphoblastic leukemia (ALL) is a cancer of white blood cells, the cells in the body that normally fight infection. It is the most common cancer in children. Over the last several decades, advances in the treatment and supportive care of pediatric ALL have dramatically increased its 5-year survival rate to about 90%.
Despite these improvements, a considerable number of children with ALL continue to relapse following standard treatment. Accurately diagnosing those patients who are high risk for relapse and treating them with targeted therapies may greatly enhance their outcomes.
The Therapeutically Applicable Research to Generate Effective Treatments (TARGET) ALL project occurred in 3 phases:
- Phase 1: pilot project characterizing 190 cases
- Phase 2: further characterization of 178 cases
- Phase 3: characterization of ALAL cases
Phase 1: Pilot ALL Project
The TARGET ALL pilot project produced comprehensive genomic profiles of 190 high-risk, clinically annotated, B-cell ALL patient cases from Children’s Oncology Group (COG) for molecular alterations. Each fully characterized TARGET ALL case includes data from
- primary tumor sample collected at diagnosis
- case-matched tissue sample extracted at the time of remission
- additional cases with partial molecular characterization and/or sequencing data are available to the research community
Tissues and clinical data used for the TARGET ALL pilot project were obtained from patients enrolled on biology studies and clinical trials managed through the COG, POG 9906 (clinical trial for patients with newly diagnosed ALL between March 2000 and April 2003 that were defined as high risk for relapse). Patient samples for full characterization were chosen based on the following criteria:
- the disease onset at >9 years of age
- did not have white blood cell count >50,000/µL
- did not express BCR/ABL fusion gene
- were not known to be hypodiploid (DNA index >0.95)
- achieved remission (fewer than 5% blasts) following the standard two rounds of induction therapy
In addition to the fully characterized cases outlined above, ALL patient cases with partial datasets are also available.
Phase 2: ALL Expansion
In the ALL expansion phase, TARGET investigators sought to study precursor B-cell ALL. They analyzed tumors from pediatric patients, most who experienced an early bone marrow relapse (within 4 years of initial diagnosis), in order to identify new therapeutic approaches and biomarkers that correlate with poor clinical outcome. The tissues used in this study were collected from patients enrolled in COG biology studies and clinical trials.
The expansion phase produced comprehensive genomic profiles of nearly 200 relapse-enriched, clinically annotated patient cases in the discovery dataset. The cohort includes more than 100 patients with adequate relapse specimens to study as trios (see three sample types below). Each 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 (FACS purified, <5% blasts detected following standard induction therapy)
- relapsed tumor sample (case-matched) when available; >50% cases have third sample (those cases are considered a “trio”)
- additional cases with partial molecular characterization and/or sequencing data are available to the research community
Tissues and clinical data used for the expansion phase were obtained from patients enrolled on biology studies and clinical trials managed through COG. Patient samples with full characterization were chosen based on the following criteria:
- experienced early bone marrow relapse (<4 years from time of diagnosis)
- adequate amount of high-quality nucleic acids for comprehensive genomic profiling
To validate sequence mutations identified in the relapse-enriched discovery cohort, along with some previously published variants in adult ALL, an additional 750 cases were further analyzed. The TARGET ALL project team used whole exome sequencing to look at the frequency of these mutations across a broader spectrum of ALL subtypes in an unbiased cohort of 500 precursor B-cell ALL and 250 T-cell lineage ALL cases. Patients were enrolled on a single COG protocol and selected for inclusion in the validation effort if DNA were available.
Phase 3: Acute Leukemia of Ambiguous Lineage (ALAL)
Leukemia can arise from distinct lineages of blood cells, either lymphoid or myeloid. On occasion, patients present with an acute leukemia for which a specific lineage cannot be clearly determined. These cases are classified as acute leukemias of ambiguous lineage (ALAL) and account for less than 4% of all acute leukemias across age groups.
TARGET investigators at St. Jude Children’s Research Hospital led an effort to better understand ALAL. The TARGET initiative contributed to this key study by characterizing ~50 ALAL cases. Each TARGET ALAL case includes whole genome sequencing, mRNA-sequencing, and miRNA-sequencing 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)
This high-risk subtype of leukemia has both myeloid and lymphoid features. In certain cases, fluorescence-activated cell sorting of tumor and normal tissue samples was employed to separate cell populations based on immunity markers expressed. TARGET analyses were published as part of a collaborative study by TARGET, COG, and St. Jude Children’s Research Hospital.
Altogether, the team analyzed 115 children (ages 0–18) diagnosed with ALAL across 13 cooperative groups and institutions. The tumor and remission samples were subjected to whole genome and/or exome sequencing, single-nucleotide polymorphism microarray genotyping, and RNA and microRNA sequencing.