NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE164600 Query DataSets for GSE164600
Status Public on Jan 12, 2021
Title CelFiE:  Comprehensive cell type decomposition of circulating cell-free DNA
Organism Homo sapiens
Experiment type Methylation profiling by high throughput sequencing
Summary Circulating cell-free DNA (cfDNA) in the bloodstream originates from dying cells and is a promising non-invasive biomarker for cell death. Here, we propose an algorithm, CelFiE, to accurately estimate relative abundances of cell types and tissues contributing to cfDNA from epigenetic cfDNA sequencing. In contrast to previous work, CelFiE accommodates low coverage data, does not rely on CpG site curation, and estimates contributions from multiple unknown cell types that are not available in external reference data. In simulations, CelFiE accurately estimates known and unknown cell type proportions from low coverage and noisy cfDNA mixtures, including from rare cell types composing less than 1% of the total mixture. In a positive control of cfDNA extracted from pregnant and non-pregnant women, CelFiE correctly estimates a large placenta component specifically in pregnant women (p = 4.5x10^-5). In cfDNA from ALS patients and age-matched controls, we observed increased cfDNA concentrations in ALS patients (p = 5.0x10^-3), and CelFiE identified a corresponding increased skeletal muscle component (p = 2.4x10^-3), consistent with muscle impairment characterizing ALS. Together these results show CelFiE may be a useful tool for biomarker discovery and monitoring of degenerative disease progression.
 
Overall design 12 ALS and 12 age-matched controls were recruited from the UCSF ALS Center. cfDNA was extracted from 5mL of blood.
 
Contributor(s) Caggiano C, Celona B, Garton F, Mefford J, Black BL, Henderson R, Lomen-Hoerth C, Dahl A, Zaitlen N
Citation(s) 33976150
Submission date Jan 11, 2021
Last update date May 20, 2021
Contact name Noah Zaitlen
E-mail(s) nzaitlen@g.ucla.edu
Organization name UCLA
Department Neurology
Street address 675 Charles E Young Dr S
City Los Angeles
State/province CA
ZIP/Postal code 90095
Country USA
 
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (24)
GSM5014683 ALS1
GSM5014684 ALS2
GSM5014685 ALS3
Relations
BioProject PRJNA691320
SRA SRP301293

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE164600_RAW.tar 4.4 Gb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap
External link. Please review our privacy policy.