Data Entry Maintenance

Metadata Commons Identifier

HMC000091

Project Title

Epigenetic Profiling of Human Acute Myeloid Leukemia Primary Samples

Project Description

Bone marrow mononuclear cells extracted from hip bone (>75% blasts) of nine Acute Myeloid Leukemia (AML) patients (age 40-65 years, 56% male) were sorted for viability using propidium iodide and then used for full epigenomic profiling: <ul> <li>RNA-seq</li> <li>Whole Genome DNA methylation using Post Bisulfite Adapter Ligation (PBAL)</li> <li>native ChIP-seq for the following histone marks: H3K4me3, H3K4me1, H3K9me3, H3K27ac, H2K27me3, H3K36me3, and input control</li> </ul> Some of these patients have mutations in Isocitrate Dehydrogenase (IDH) genes. Accession numbers at the Epigenome Reference Registry (EPIRR) (<a href="https://www.ebi.ac.uk/epirr">https://www.ebi.ac.uk/epirr</a>): <ul> <li>Sample 1 EPIRR ID: https://www.ebi.ac.uk/epirr/epigenomes/IHECRE00003824</li> <li>Sample 2 EPIRR ID: https://www.ebi.ac.uk/epirr/epigenomes/IHECRE00003829</li> <li>Sample 3 EPIRR ID: https://www.ebi.ac.uk/epirr/epigenomes/IHECRE00003830</li> <li>Sample 4 EPIRR ID: https://www.ebi.ac.uk/epirr/epigenomes/IHECRE00003833</li> <li>Sample 5 EPIRR ID: https://www.ebi.ac.uk/epirr/epigenomes/IHECRE00003835</li> <li>Sample 6 EPIRR ID: https://www.ebi.ac.uk/epirr/epigenomes/IHECRE00003843</li> <li>Sample 7 EPIRR ID: https://www.ebi.ac.uk/epirr/epigenomes/IHECRE00003844</li> <li>Sample 8 EPIRR ID: https://www.ebi.ac.uk/epirr/epigenomes/IHECRE00003846</li> <li>Sample 9 EPIRR ID: https://www.ebi.ac.uk/epirr/epigenomes/IHECRE00003847</li> </ul> These reference epigenomes were generated as part of the International Human Epigenomics Consortium (<a href="https://ihec-epigenomes.org/">IHEC</a>) Sequencing data have been deposited to European Genome-phenome Archive (EGA) and are available upon request at https://ega-archive.org/datasets/EGAD00001004950

Project Funder(s)

Genome Canada, Canadian Institutes of Health Research (CIHR), Terry Fox Research Institute

Project Institution(s)

University of British Columbia, BC Cancer Research Institute

Project Investigator(s)

Martin Hirst, Aly Karsan

Data Access Request URL*

https://ega-archive.org/datasets/EGAD00001004950

Keywords

AML, epigenomics, cancer, leukemia, bone marrow

Publication Link

Study Completed

Cohort Name

Epigenetic Profiling of Human Acute Myeloid Leukemia Primary Samples

Cohort Size

Disease/Condition Studied

acute myeloid leukemia

Enrollment Time Window

2015-2016

Biobanking Consent Available

Medical History Available

Ethnicity Availability

Time Course

Patient Phenotypes

Patient Outcomes

Clinical Data Types Available

Donor sex, age, life stage

Time Course Data Points

Enrollment City

Groups

Project

Cohort

Enrollment City

Groups

Samples and Omics