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DNA methylation protocol for analyzing cell-free DNA in the spent culture medium of human preimplantation embryos.

ABSTRACT: Cell-free DNA (cfDNA) in spent embryo culture media (SECM) provides prospects for noninvasive preimplantation genetic testing. Here, we present a post-bisulfite-adapter-tagging (PBAT)-based whole-genome DNA methylation sequencing protocol (SECM-PBAT) for human SECM cfDNA analysis. We describe steps for SECM lysis, bisulfite conversion and purification, preamplification by random priming, tagging adapter II, and library establishment. We then detail library quality control, sequencing, and bioinformatics analysis. This approach simultaneously detects chromosome aneuploidy and deduces the proportional contributions of cellular components. For complete details on the use and execution of this protocol, please refer to Chen et al. (2021).¹.

SUBMITTER: Gao Y

PROVIDER: S-EPMC10160802 | biostudies-literature | 2023 Apr

REPOSITORIES: biostudies-literature

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DNA methylation protocol for analyzing cell-free DNA in the spent culture medium of human preimplantation embryos.

Gao Yuan Y Chen Yidong Y Qiao Jie J Huang Jin J Wen Lu L

STAR protocols 20230421 2

Cell-free DNA (cfDNA) in spent embryo culture media (SECM) provides prospects for noninvasive preimplantation genetic testing. Here, we present a post-bisulfite-adapter-tagging (PBAT)-based whole-genome DNA methylation sequencing protocol (SECM-PBAT) for human SECM cfDNA analysis. We describe steps for SECM lysis, bisulfite conversion and purification, preamplification by random priming, tagging adapter II, and library establishment. We then detail library quality control, sequencing, and bioinf ...[more]

PMID: 37086412

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DNA methylome reveals cellular origin of cell-free DNA in spent medium of human preimplantation embryos.

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Cell-free DNA in spent culture medium effectively reflects the chromosomal status of embryos following culturing beyond implantation compared to trophectoderm biopsy.

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Abundance of cell-free mitochondrial DNA in spent culture medium associated with morphokinetics and blastocyst collapse of expanded blastocysts.

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Noninvasive preimplantation genetic testing for aneuploidy using blastocyst spent culture medium may serve as a backup of trophectoderm biopsy in conventional preimplantation genetic testing.

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