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

Yuan Gao; Yidong Chen; Jie Qiao; Jin Huang; Lu Wen

doi:10.1016/j.xpro.2023.102247

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

STAR Protoc. 2023 Apr 21;4(2):102247. doi: 10.1016/j.xpro.2023.102247. Online ahead of print.

Authors

Yuan Gao¹, Yidong Chen², Jie Qiao³, Jin Huang⁴, Lu Wen⁵

Affiliations

¹ Biomedical Pioneering Innovation Center, Department of Obstetrics and Gynecology, Third Hospital, School of Life Sciences, Peking University, Beijing 100871, China; Beijing Advanced Innovation Center for Genomics, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China. Electronic address: gaoyuan18@pku.edu.cn.
² Biomedical Pioneering Innovation Center, Department of Obstetrics and Gynecology, Third Hospital, School of Life Sciences, Peking University, Beijing 100871, China; Beijing Advanced Innovation Center for Genomics, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing 100871, China; Key Laboratory of Assisted Reproduction, Key Laboratory of Cell Proliferation and Differentiation, Ministry of Education, Beijing 100871, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100871, China. Electronic address: chenyidongahu@163.com.
³ Biomedical Pioneering Innovation Center, Department of Obstetrics and Gynecology, Third Hospital, School of Life Sciences, Peking University, Beijing 100871, China; Beijing Advanced Innovation Center for Genomics, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China; Key Laboratory of Assisted Reproduction, Key Laboratory of Cell Proliferation and Differentiation, Ministry of Education, Beijing 100871, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100871, China.
⁴ Biomedical Pioneering Innovation Center, Department of Obstetrics and Gynecology, Third Hospital, School of Life Sciences, Peking University, Beijing 100871, China; Beijing Advanced Innovation Center for Genomics, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing 100871, China; Key Laboratory of Assisted Reproduction, Key Laboratory of Cell Proliferation and Differentiation, Ministry of Education, Beijing 100871, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100871, China. Electronic address: huangjin-2004@163.com.
⁵ Biomedical Pioneering Innovation Center, Department of Obstetrics and Gynecology, Third Hospital, School of Life Sciences, Peking University, Beijing 100871, China; Beijing Advanced Innovation Center for Genomics, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing 100871, China; Key Laboratory of Assisted Reproduction, Key Laboratory of Cell Proliferation and Differentiation, Ministry of Education, Beijing 100871, China. Electronic address: wenlu@pku.edu.cn.

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.

Keywords: Bioinformatics; Cell Biology; Sequence Analysis; Sequencing.