Transcriptomics,Genomics

Dataset Information

43

Epigenomics Studies in Acute Myeloid Leukemia disease progression [RNAseq]


ABSTRACT: We report the DNA methylation and transcriptional molecular features of paired diagnosis and relapsed Acute Myeloid Leukemia samples Overall design: To determine if epigenetic features at gene promoters can affect gene trancription during disease progression in AML, we profiled nineteen paired diagnosis and relapse AML patient samples using RNAseq and performed correlation analysis between transcriptional variance and epigenetic heterogeneity at respective gene promoters (normalized transcript counts are included in Dx_Rel_AML_RNAseq_rpkm.txt) To determine if epigenetic features at gene promoters can affect gene trancription in AML, we profiled 96 cells from a relapsed AML case using single cell RNA-sequencing and correlated transript variance with epigenetic heterogeneity at respective gene promoters (normalized transcript counts are included in AML_130_Rel_scRNAseq_rpkm.txt) Raw data has been deposited to dbGaP (controlled access) due to patient privacy concerns: http://www.ncbi.nlm.nih.gov/gap/?term=phs001027.v1.p1

INSTRUMENT(S): Illumina HiSeq 2000 (Homo sapiens)

SUBMITTER: Francine E. Garrett-Bakelman  

PROVIDER: GSE83533 | GEO | 2016-06-21

SECONDARY ACCESSION(S): PRJNA326266

REPOSITORIES: GEO

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Publications

Distinct evolution and dynamics of epigenetic and genetic heterogeneity in acute myeloid leukemia.

Li Sheng S   Garrett-Bakelman Francine E FE   Chung Stephen S SS   Sanders Mathijs A MA   Hricik Todd T   Rapaport Franck F   Patel Jay J   Dillon Richard R   Vijay Priyanka P   Brown Anna L AL   Perl Alexander E AE   Cannon Joy J   Bullinger Lars L   Luger Selina S   Becker Michael M   Lewis Ian D ID   To Luen Bik LB   Delwel Ruud R   Löwenberg Bob B   Döhner Hartmut H   Döhner Konstanze K   Guzman Monica L ML   Hassane Duane C DC   Roboz Gail J GJ   Grimwade David D   Valk Peter J M PJ   D'Andrea Richard J RJ   Carroll Martin M   Park Christopher Y CY   Neuberg Donna D   Levine Ross R   Melnick Ari M AM   Mason Christopher E CE  

Nature medicine 20160620 7


Genetic heterogeneity contributes to clinical outcome and progression of most tumors, but little is known about allelic diversity for epigenetic compartments, and almost no data exist for acute myeloid leukemia (AML). We examined epigenetic heterogeneity as assessed by cytosine methylation within defined genomic loci with four CpGs (epialleles), somatic mutations, and transcriptomes of AML patient samples at serial time points. We observed that epigenetic allele burden is linked to inferior outc  ...[more]

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