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Series GSE124974 Query DataSets for GSE124974
Status Public on May 07, 2019
Title Spatial co-fragmentation pattern of cell-free DNA recapitulates in vivo chromatin organization and identifies tissue-of-origin
Organism Homo sapiens
Experiment type Other
Summary Three-dimensional chromatin organization varies across different cell types and is essential for gene regulation. However, current technologies are unable to assess in vivo genome-wide chromatin organization non-invasively. Here, we showed that long-range correlations in the fragment length of cell-free DNA (cfDNA) estimated from whole-genome sequencing recapitulate three-dimensional chromatin organization. The inferred organization is highly concordant with that measured by Hi-C in white blood cells from healthy donors, and is not explained by technical bias or sequence composition. Furthermore, the inferred organization reflects the differing genome organizations in the various cell types contributing to cfDNA, allowing quantification of cfDNA tissue-of-origin that is concordant with previous methods, but at much lower required DNA input. Our results, demonstrated in cfDNA from healthy individuals and cancer patients, may enable noninvasive monitoring of in vivo genome organization and accurate quantification of cell death in different clinical conditions.
Overall design Compare two-dimensional fragmentation pattern in cell free DNA with Hi-C at white blood cell and then deconvolute the signals to reference cell types
Contributor(s) Liu Y
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Submission date Jan 11, 2019
Last update date May 10, 2019
Contact name Yaping Liu
Organization name Cincinnati Children's Hospital Medical Center
Department Department of Pediatrics
Lab EpiFluid Lab in Division of Human Genetics
Street address 3333 Burnet Ave
City Cincinnati
State/province OH
ZIP/Postal code 45229
Country USA
Platforms (2)
GPL20795 HiSeq X Ten (Homo sapiens)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (3)
GSM3560407 HiC_wbc_rep1
GSM3560408 HiC_wbc_rep2
GSM3560409 HiC_neutrophil
BioProject PRJNA514727
SRA SRP178527

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Supplementary file Size Download File type/resource
GSE124974_RAW.tar 31.1 Gb (http)(custom) TAR (of HIC)
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Raw data are available in SRA
Processed data provided as supplementary file

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