Genomics

Dataset Information

22

Epigenomics Studies in Acute Myeloid Leukemia disease progression [enhanced RRBS-seq]


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 heterogeneity features are linked to clinical outcome and/or genetic features, change and/or affect gene transcription during disease progression in AML, we profiled 138 paired diagnosis and relapse patient samples using Enhanced Reduced Representation Bisulfite Sequening (PMC4354670) and 14 age-matched normal bone marrow controls. Analysis was performed to define genomic loci (epialleles) which undergo epigenetic shift (PMC4242486) and these were assessed for correlation with the parameters noted. 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 There are two categories processed data files: 1. tumor versus controls (AML*_epialleles.txt.tar.gz) coming from either a diagnosis (Dx) or Relapse (Rel) subject sample - each tumor sample is compared to 14 controls, hence the gzipped folders each contain 14 files, and linked to the corresponding sample (AML_*_Dx or AML_*_Rel sample); 2. relapse vs. diagnosis tumor (AML_*_Rel_AML_*_Dx_epiallele.txt.gz) for which there is only a single gzipped file, which is linked to the corresponding relapsed tumor sample record (i.e. AML_*_Rel). Please nothe that the AML_*_Rel_epialleles.txt.tar.gz (linked to each relapsed tumor sample) contains both AML_*_Rel_epialleles.txt.tar.gz and AML_*_Rel_AML_*_Dx_epiallele.txt.gz.

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

SUBMITTER: Francine E. Garrett-Bakelman  

PROVIDER: GSE83532 | GEO | 2016-06-21

SECONDARY ACCESSION(S): PRJNA326267

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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