Information:
Error:
ID
45925
Description
Principal Investigator: Francine Garrett-Bakelman, MD, PhD, University of Virginia, Charlottesville, VA, USA; Weill Cornell Medical College, New York, NY, USA MeSH: Acute Myeloid Leukemia https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001027 Acute Myeloid Leukemia (AML) remains a clinical challenge since most patients diagnosed with AML will die from the disease. Some patients harbor treatment-refractory disease and many others relapse with disease that in many cases is resistant to treatments. Our study was designed to understand the molecular basis of disease progression in AML through assessing genomics signatures in patient specimens collected through an international collaboration which assembled samples from 138 AML patients which experienced disease relapse and normal hematopoietic cells (n=15). It is hoped that this resource will help researchers understand mechanisms of disease relapse in AML and contribute to the general pool of data available for analyses for this disease and general research use.
Link
Keywords
Versions (1)
- 2/27/24 2/27/24 - Simon Heim
Copyright Holder
Francine Garrett-Bakelman, MD, PhD, University of Virginia, Charlottesville, VA, USA; Weill Cornell Medical College, New York, NY, USA
Uploaded on
February 27, 2024
DOI
To request one please log in.
License
Creative Commons BY 4.0
Model comments :
You can comment on the data model here. Via the speech bubbles at the itemgroups and items you can add comments to those specificially.
Itemgroup comments for :
Item comments for :
In order to download data models you must be logged in. Please log in or register for free.
dbGaP phs001027 Epigenomics Studies in Acute Myeloid Leukemia (AML)
This subject phenotype data table contains age at time of sample collection, disease stage, time to relapse, cytogenetics results, clinically-annotated mutant genes, FAB classification, WBC counts, and affection status. Cases are patients diagnosed with non-M3 Acute Myeloid Leukemia (AML). Controls are age-matched individuals and without any known hematological conditions.
- StudyEvent: SEV1
- Eligibility Criteria
- This subject consent data table includes subject IDs, consent group information, subject aliases, and subject's sex.
- This subject sample mapping data table includes a mapping of study subject IDs to sample IDs. Samples are the final preps submitted for genotyping, sequencing, and/or expression data. For example, if one patient (subject ID) gave one sample, and that sample was processed differently to generate 2 sequencing runs, there would be two rows, both using the same subject ID, but having 2 unique sample IDs.
- This subject phenotype data table contains age at time of sample collection, disease stage, time to relapse, cytogenetics results, clinically-annotated mutant genes, FAB classification, WBC counts, and affection status. Cases are patients diagnosed with non-M3 Acute Myeloid Leukemia (AML). Controls are age-matched individuals and without any known hematological conditions.
- This sample attributes data table includes body site where sample was collected, analyte type, tumor status, histological type, metastatic status, primary tumor location, tumor stage and grade, tumor treatment, and sequencing center.
- This subject GEO data table contains a mapping of subject IDs to NCBI GEO (GSM#) accessions.
Similar models
This subject phenotype data table contains age at time of sample collection, disease stage, time to relapse, cytogenetics results, clinically-annotated mutant genes, FAB classification, WBC counts, and affection status. Cases are patients diagnosed with non-M3 Acute Myeloid Leukemia (AML). Controls are age-matched individuals and without any known hematological conditions.
- StudyEvent: SEV1
- Eligibility Criteria
- This subject consent data table includes subject IDs, consent group information, subject aliases, and subject's sex.
- This subject sample mapping data table includes a mapping of study subject IDs to sample IDs. Samples are the final preps submitted for genotyping, sequencing, and/or expression data. For example, if one patient (subject ID) gave one sample, and that sample was processed differently to generate 2 sequencing runs, there would be two rows, both using the same subject ID, but having 2 unique sample IDs.
- This subject phenotype data table contains age at time of sample collection, disease stage, time to relapse, cytogenetics results, clinically-annotated mutant genes, FAB classification, WBC counts, and affection status. Cases are patients diagnosed with non-M3 Acute Myeloid Leukemia (AML). Controls are age-matched individuals and without any known hematological conditions.
- This sample attributes data table includes body site where sample was collected, analyte type, tumor status, histological type, metastatic status, primary tumor location, tumor stage and grade, tumor treatment, and sequencing center.
- This subject GEO data table contains a mapping of subject IDs to NCBI GEO (GSM#) accessions.
Name
Type
Description | Question | Decode (Coded Value)
Data type
Alias
SUBJECT_ID
Item
De-identified Subject ID
string
C4684638 (UMLS CUI [1,1])
C2348585 (UMLS CUI [1,2])
C2348585 (UMLS CUI [1,2])
Age
Item
Age at time of sample collection
text
C0001779 (UMLS CUI [1,1])
C0011008 (UMLS CUI [1,2])
C0200345 (UMLS CUI [1,3])
C0011008 (UMLS CUI [1,2])
C0200345 (UMLS CUI [1,3])
Disease_stage
Item
Disease state at the time of sample collection or germline specimen collection
string
C3887610 (UMLS CUI [1,1])
C1442880 (UMLS CUI [1,2])
C0200345 (UMLS CUI [1,3])
C3845275 (UMLS CUI [1,4])
C1442880 (UMLS CUI [1,2])
C0200345 (UMLS CUI [1,3])
C3845275 (UMLS CUI [1,4])
Item
Case versus control samples. Cases are patients diagnosed with non-M3 Acute Myeloid Leukemia (AML), who received induction chemotherapy treatment with combination chemotherapy including, but not limited to an anthracycline and cytosine arabinoside, and patients from whom specimens with high blast cell percentages were available from diagnosis and relapse time points. Controls are age-matched individuals and without any known hematological conditions with CD34+ cell enrichment greater than 90%.
text
C0872128 (UMLS CUI [1,1])
C0370003 (UMLS CUI [1,2])
C5206782 (UMLS CUI [1,3])
C4272796 (UMLS CUI [1,4])
C1521750 (UMLS CUI [1,5])
C0332257 (UMLS CUI [1,6])
C5761267 (UMLS CUI [1,7])
C0010711 (UMLS CUI [1,8])
C0587348 (UMLS CUI [1,9])
C0011900 (UMLS CUI [1,10])
C1442880 (UMLS CUI [1,11])
C0035020 (UMLS CUI [1,12])
C0009932 (UMLS CUI [2,1])
C0150103 (UMLS CUI [2,2])
C0001779 (UMLS CUI [2,3])
C1335471 (UMLS CUI [2,4])
C0882849 (UMLS CUI [2,5])
C4724475 (UMLS CUI [2,6])
C1549488 (UMLS CUI [2,7])
C0370003 (UMLS CUI [1,2])
C5206782 (UMLS CUI [1,3])
C4272796 (UMLS CUI [1,4])
C1521750 (UMLS CUI [1,5])
C0332257 (UMLS CUI [1,6])
C5761267 (UMLS CUI [1,7])
C0010711 (UMLS CUI [1,8])
C0587348 (UMLS CUI [1,9])
C0011900 (UMLS CUI [1,10])
C1442880 (UMLS CUI [1,11])
C0035020 (UMLS CUI [1,12])
C0009932 (UMLS CUI [2,1])
C0150103 (UMLS CUI [2,2])
C0001779 (UMLS CUI [2,3])
C1335471 (UMLS CUI [2,4])
C0882849 (UMLS CUI [2,5])
C4724475 (UMLS CUI [2,6])
C1549488 (UMLS CUI [2,7])
Code List
Case versus control samples. Cases are patients diagnosed with non-M3 Acute Myeloid Leukemia (AML), who received induction chemotherapy treatment with combination chemotherapy including, but not limited to an anthracycline and cytosine arabinoside, and patients from whom specimens with high blast cell percentages were available from diagnosis and relapse time points. Controls are age-matched individuals and without any known hematological conditions with CD34+ cell enrichment greater than 90%.
CL Item
Control (1)
C3274648 (UMLS CUI [1,1])
CL Item
Case (2)
C3274647 (UMLS CUI [1,1])
Cytogenetics
Item
Cytogenetics results
string
C0010802 (UMLS CUI [1,1])
C1254595 (UMLS CUI [1,2])
C1254595 (UMLS CUI [1,2])
mutGenes
Item
Clinically-annotated mutant genes: NPM1 nucleophosmin, FLT3-ITD Fms-like tyrosine kinase 3 internal tandem duplication, FLT3-TKD Fms-like tyrosine kinase 3 tyrosine kinase domain, CEBPA CCAAT enhancer binding protein alpha
string
C3852951 (UMLS CUI [1,1])
C0678941 (UMLS CUI [1,2])
C4732353 (UMLS CUI [1,3])
C5414408 (UMLS CUI [1,4])
C0287186 (UMLS CUI [1,5])
C3708858 (UMLS CUI [1,6])
C0678941 (UMLS CUI [1,2])
C4732353 (UMLS CUI [1,3])
C5414408 (UMLS CUI [1,4])
C0287186 (UMLS CUI [1,5])
C3708858 (UMLS CUI [1,6])
FAB
Item
French American British disease classification: MLD = multi-lineage dysplasia, RAEB-t = refractory anemia with excess blasts in transformation
string
C2984084 (UMLS CUI [1,1])
C5418871 (UMLS CUI [1,2])
C0280028 (UMLS CUI [1,3])
C5418871 (UMLS CUI [1,2])
C0280028 (UMLS CUI [1,3])
WBC
Item
Peripheral blood white blood cell count
text
C0023508 (UMLS CUI [1,1])
C0229664 (UMLS CUI [1,2])
C0229664 (UMLS CUI [1,2])
CL Item
Not applicable (N/A)
C1272460 (UMLS CUI [1,1])