Sensitive and reproducible cell-free methylome quantification with synthetic spike-in controls.
Cell Rep Methods
; 2(9): 100294, 2022 09 19.
Article
in En
| MEDLINE
| ID: mdl-36160046
ABSTRACT
Cell-free methylated DNA immunoprecipitation sequencing (cfMeDIP-seq) identifies genomic regions with DNA methylation, using a protocol adapted to work with low-input DNA samples and with cell-free DNA (cfDNA). We developed a set of synthetic spike-in DNA controls for cfMeDIP-seq to provide a simple and inexpensive reference for quantitative normalization. We designed 54 DNA fragments with combinations of methylation status (methylated and unmethylated), fragment length (80 bp, 160 bp, 320 bp), G + C content (35%, 50%, 65%), and fraction of CpG dinucleotides within the fragment (1/80 bp, 1/40 bp, 1/20 bp). Using 0.01 ng of spike-in controls enables training a generalized linear model that absolutely quantifies methylated cfDNA in MeDIP-seq experiments. It mitigates batch effects and corrects for biases in enrichment due to known biophysical properties of DNA fragments and other technical biases.
Key words
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Cell-Free Nucleic Acids
/
Epigenome
Type of study:
Diagnostic_studies
/
Screening_studies
Language:
En
Journal:
Cell Rep Methods
Year:
2022
Document type:
Article
Affiliation country:
Canada