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This is a scoping review protocol, which will be conducted in accordance with the JBI methodology for scoping reviews (Peters et al., 2020) and in line with the Preferred Reporting Items for Systematic Reviews and Meta-Analysis Extension for Scoping Reviews (PRISMA-ScR) checklist (Tricco et al., 2018)

DNA methylation is an epigenetic marker that has been shown to vary significantly across different tissues. Taking advantage of the methylation differences between placenta-derived cell-free DNA and maternal blood, several groups employed different approaches for the discovery of fetal-specific biomarkers. The aim of this study was to analyse whole-genome fetal and maternal methylomes in order to identify and confirm the presence of differentially methylated regions (DMRs). We have initially utilized methylated DNA immunoprecipitation (MeDIP) and next-generation sequencing (NGS) to identify genome-wide DMRs between chorionic villus sampling (CVS) and female non-pregnant plasma (PL) and peripheral blood (WBF) samples. Next, using specific criteria, 331 fetal-specific DMRs were selected and confirmed in eight CVS, eight WBF and eight PL samples by combining MeDIP and in-solution targeted enrichment followed by NGS. Results showed higher enrichment in CVS samples as compared to both WBF and PL samples, confirming the distinct methylation levels between fetal and maternal DNA for the selected DMRs. We have successfully implemented a novel approach for the discovery and confirmation of a significant number of fetal-specific DMRs by combining for the first time MeDIP and in-solution targeted enrichment followed by NGS. The implementation of this double-enrichment approach is highly efficient and enables the detailed analysis of multiple DMRs by targeted NGS. Also, this is, to our knowledge, the first reported application of MeDIP on plasma samples, which leverages the implementation of our enrichment methodology in the detection of fetal abnormalities in maternal plasma. 98 e15 e15 ID: 27834155 Accession Number: 27834155. Language: English. Date Revised: 20170316. Date Created: 20161111. Date Completed: 20170316. Update Code: 20170317. Publication Type: Journal Article. Journal ID: 101550220. Publication Model: Electronic. Cited Medium: Internet. NLM ISO Abbr: Genet Res (Camb). Linking ISSN: 00166723. Subset: IM Date of Electronic Publication: 2016 Nov 11. Original Imprints: Publication: Cambridge New York : Cambridge University Press, c2008

Background: DNA methylation is the most studied form of epigenetic regulation, a process by which chromatin composition and transcription factor binding is altered to influence tissue specific gene expression and differentiation. Such tissue specific methylation patterns are investigated as biomarkers for cancer and cell-free fetal DNA using various methodologies. Results: We have utilized methylation DNA immunoprecipitation (MeDIP) and real-time quantitative PCR to investigate the inter-individual methylation variability of differentially methylated regions (DMRs) on chromosomes 18 and 21. We have characterized 15 newly selected and seven previously validated DMRs in 50, 1(st) trimester Chorionic villus samplings (CVS) and 50 female non-pregnant peripheral blood (WBF) samples. qPCR results from MeDIP and genomic DNA (Input) assays were used to calculate fold enrichment values for each DMR. For all regions tested, enrichment was higher in CVS than in WBF samples with mean enrichments ranging from 0.22 to 6.4 and 0.017 to 1 respectively. Despite inter-individual variability, mean enrichment values for CVS were significantly different than those for WBF in all DMRs tested (p ID: 25426166 Accession Number: 25426166. Language: English. Date Revised: 20141215. Date Created: 20141126. Date Completed: 20141126. Update Code: 20161213. Publication Type: Journal Article. Journal ID: 101317942. Publication Model: Electronic-eCollection eCollection. Cited Medium: Print. NLM ISO Abbr: Mol Cytogenet. PubMed Central ID: PMC4243368. Linking ISSN: 17558166. Subset: PubMed-not-MEDLINE Date of Electronic Publication: 20141101. Original Imprints: Publication: London : BioMed Central

Introduction: Non-invasive prenatal diagnosis (NIPD) of Down syndrome is rapidly evolving. Currently, two applications for NIPD of Down syndrome have been developed with potential and have displayed positive results the NIPD using next-generation sequencing technologies and the NIPD using the methylated DNA immunoprecipitation (MeDIP) real-time quantitative polymerase chain reaction (qPCR). Areas covered: The MeDIP real-time qPCR approach is based on the identification of differentially methylated regions (DMRs) and their use for discriminating normal from Down syndrome cases. DMRs were identified using high-resolution oligo-arrays. A subgroup of DMRs was selected for further investigation. Through the design of a discriminant equation which combines the results obtained from different DMRs, normal and abnormal cases are correctly classified indicating 100% sensitivity and specificity. Expert opinion: Previous studies have also identified DMRs between non-pregnant female blood and placental DNA. However, these methods have been associated with a number of limitations including the low sensitivity and/or specificity of the assays, the limited number of identified DMRs or methylation sensitive sites and SNPs located on DMRs. These limitations have been overawed by the development of the MeDIP real-time qPCR-based methodology. © 2012 Informa UK, Ltd. 12 SUPPL. 1 S155 S161 Cited By :10

Diagnostic and prognostic research 6, 14 (2022). doi:10.1186/s41512-022-00128-8, Published by BioMed Central, [London]