GBS-MeDIP: A protocol for parallel identification of genetic and epigenetic variation in the same reduced fraction of genomes across individuals

The GBS-MeDIP protocol combines two previously described techniques, Genotype-by-Sequencing (GBS) and Methylated-DNA-Immunoprecipitation (MeDIP). Our method allows for parallel and cost-efficient interrogation of genetic and methylomic variants in the DNA of many reduced genomes, taking advantage of...

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Bibliographic Details
Published in:STAR protocols 2022-03, Vol.3 (1), p.101202-101202, Article 101202
Main Authors: Rezaei, Shiva, Uffenorde, Julia, Gimm, Oliver, Hosseinpour Feizi, Mohammad Ali, Miemczyk, Stefan, Coutinho, Luiz Lehmann, Jensen, Per, Guerrero-Bosagna, Carlos, Pértille, Fábio
Format: Article
Language:English
Subjects:
Cancer
Clinical Protocol
DNA - genetics
DNA Methylation - genetics
Epigenesis, Genetic
Genomics
Genotype
High Throughput Screening
Humans
Immunoprecipitation
Molecular Biology
Protocol
Sequencing
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Summary:The GBS-MeDIP protocol combines two previously described techniques, Genotype-by-Sequencing (GBS) and Methylated-DNA-Immunoprecipitation (MeDIP). Our method allows for parallel and cost-efficient interrogation of genetic and methylomic variants in the DNA of many reduced genomes, taking advantage of the barcoding of DNA samples performed in the GBS and the subsequent creation of DNA pools, then used as an input for the MeDIP. The GBS-MeDIP is particularly suitable to identify genetic and methylomic biomarkers when resources for whole genome interrogation are lacking. [Display omitted] •Our protocol combines two well-known techniques, GBS and MeDIP.•The GBS-MeDIP allows for parallel interrogation of genetic/methylomic variants.•Allows for cost-efficient analysis of reduced genomes from multiple individuals.•Ideal for the identification of genetic and/or methylomic markers at reduced cost. The GBS-MeDIP protocol combines two previously described techniques, Genotype-by-Sequencing (GBS) and Methylated-DNA-Immunoprecipitation (MeDIP). Our method allows for parallel and cost-efficient interrogation of genetic and methylomic variants in the DNA of many reduced genomes, taking advantage of the barcoding of DNA samples performed in the GBS and the subsequent creation of DNA pools, then used as an input for the MeDIP. The GBS-MeDIP is particularly suitable to identify genetic and methylomic biomarkers when resources for whole genome interrogation are lacking.
ISSN:2666-1667
2666-1667
DOI:10.1016/j.xpro.2022.101202