4.2 Article

Sensitive and reproducible cell-free methylome quantification with synthetic spike-in controls

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CELL REPORTS METHODS
卷 2, 期 9, 页码 -

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CELL PRESS
DOI: 10.1016/j.crmeth.2022.100294

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资金

  1. Canadian Institutes of Health Research [389866, MFE-171256]
  2. McLaughlin Centre [MC-2019-07]
  3. Molly Towell Perinatal Research Foundation
  4. Princess Margaret Cancer Foundation
  5. Van Andel Institute
  6. Michigan Economic Development Corporation
  7. Michelle Lunn Hope Foundation
  8. 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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