Sensitive and reproducible cell-free methylome quantification with synthetic spike-in controls
Summary: 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...
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| Format: | Article |
| Language: | English |
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Elsevier
2022-09-01
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| Series: | Cell Reports: Methods |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S266723752200176X |
| _version_ | 1811183460897783808 |
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| author | Samantha L. Wilson Shu Yi Shen Lauren Harmon Justin M. Burgener Tim Triche, Jr. Scott V. Bratman Daniel D. De Carvalho Michael M. Hoffman |
| author_facet | Samantha L. Wilson Shu Yi Shen Lauren Harmon Justin M. Burgener Tim Triche, Jr. Scott V. Bratman Daniel D. De Carvalho Michael M. Hoffman |
| author_sort | Samantha L. Wilson |
| collection | DOAJ |
| description | Summary: 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. Motivation: For robust quantitative comparisons between samples, immunoprecipitation enrichment methods such as cfMeDIP-seq require normalization against common reference controls. Common reference controls can correct for technical variation in the processing of different samples. They can also correct for biases in enrichment due to known biophysical properties of DNA fragments such as fragment length, G + C content, and fraction of CpG dinucleotides. Furthermore, common reference controls can provide an experimental standard for quality control. We sought to provide synthetic spike-in DNA fragments that would fulfill these reference control purposes in cfMeDIP-seq experiments. |
| first_indexed | 2024-04-11T09:47:34Z |
| format | Article |
| id | doaj.art-8df9a2a8c6e84980b59dbd24e459a70f |
| institution | Directory Open Access Journal |
| issn | 2667-2375 |
| language | English |
| last_indexed | 2024-04-11T09:47:34Z |
| publishDate | 2022-09-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Cell Reports: Methods |
| spelling | doaj.art-8df9a2a8c6e84980b59dbd24e459a70f2022-12-22T04:30:55ZengElsevierCell Reports: Methods2667-23752022-09-0129100294Sensitive and reproducible cell-free methylome quantification with synthetic spike-in controlsSamantha L. Wilson0Shu Yi Shen1Lauren Harmon2Justin M. Burgener3Tim Triche, Jr.4Scott V. Bratman5Daniel D. De Carvalho6Michael M. Hoffman7Princess Margaret Cancer Centre, University Health Network, Toronto, ON, CanadaPrincess Margaret Cancer Centre, University Health Network, Toronto, ON, CanadaVan Andel Institute, Grand Rapids, MI, USAPrincess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, CanadaVan Andel Institute, Grand Rapids, MI, USAPrincess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, CanadaPrincess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, CanadaPrincess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada; Department of Computer Science, University of Toronto, Toronto, ON, Canada; Vector Institute for Artificial Intelligence, Toronto, ON, Canada; Corresponding authorSummary: 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. Motivation: For robust quantitative comparisons between samples, immunoprecipitation enrichment methods such as cfMeDIP-seq require normalization against common reference controls. Common reference controls can correct for technical variation in the processing of different samples. They can also correct for biases in enrichment due to known biophysical properties of DNA fragments such as fragment length, G + C content, and fraction of CpG dinucleotides. Furthermore, common reference controls can provide an experimental standard for quality control. We sought to provide synthetic spike-in DNA fragments that would fulfill these reference control purposes in cfMeDIP-seq experiments.http://www.sciencedirect.com/science/article/pii/S266723752200176Xcell-free methylated DNA immunoprecipitationcfMeDIPspike-in controlsDNA methylationcell-free DNAcfDNA |
| spellingShingle | Samantha L. Wilson Shu Yi Shen Lauren Harmon Justin M. Burgener Tim Triche, Jr. Scott V. Bratman Daniel D. De Carvalho Michael M. Hoffman Sensitive and reproducible cell-free methylome quantification with synthetic spike-in controls Cell Reports: Methods cell-free methylated DNA immunoprecipitation cfMeDIP spike-in controls DNA methylation cell-free DNA cfDNA |
| title | Sensitive and reproducible cell-free methylome quantification with synthetic spike-in controls |
| title_full | Sensitive and reproducible cell-free methylome quantification with synthetic spike-in controls |
| title_fullStr | Sensitive and reproducible cell-free methylome quantification with synthetic spike-in controls |
| title_full_unstemmed | Sensitive and reproducible cell-free methylome quantification with synthetic spike-in controls |
| title_short | Sensitive and reproducible cell-free methylome quantification with synthetic spike-in controls |
| title_sort | sensitive and reproducible cell free methylome quantification with synthetic spike in controls |
| topic | cell-free methylated DNA immunoprecipitation cfMeDIP spike-in controls DNA methylation cell-free DNA cfDNA |
| url | http://www.sciencedirect.com/science/article/pii/S266723752200176X |
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