Journal
CELL REPORTS METHODS
Volume 2, Issue 9, Pages -Publisher
CELL PRESS
DOI: 10.1016/j.crmeth.2022.100294
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Funding
- Canadian Institutes of Health Research [389866, MFE-171256]
- McLaughlin Centre [MC-2019-07]
- Molly Towell Perinatal Research Foundation
- Princess Margaret Cancer Foundation
- Van Andel Institute
- Michigan Economic Development Corporation
- Michelle Lunn Hope Foundation
- William F. Folz Fund for Cancer Research
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This study developed a method called cell-free methylated DNA immunoprecipitation sequencing (cfMeDIP-seq) and designed a set of synthetic spike-in DNA controls for quantitative normalization.
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.
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