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

Shiva Rezaei; Julia Uffenorde; Oliver Gimm; Mohammad Ali Hosseinpour Feizi; Stefan Miemczyk; Luiz Lehmann Coutinho; Per Jensen; Carlos Guerrero-Bosagna; Fábio Pértille

doi:10.1016/j.xpro.2022.101202

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

STAR Protoc. 2022 Mar 3;3(1):101202. doi: 10.1016/j.xpro.2022.101202. eCollection 2022 Mar 18.

Authors

Shiva Rezaei^{1

2}, Julia Uffenorde³, Oliver Gimm³, Mohammad Ali Hosseinpour Feizi¹, Stefan Miemczyk², Luiz Lehmann Coutinho⁴, Per Jensen², Carlos Guerrero-Bosagna^{2

4}, Fábio Pértille^{3

2

4

5}

Affiliations

¹ Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz 5166616471, Iran.
² Avian Behavioral Genomics and Physiology Group, Department of Physics, Chemistry and Biology (IFM), Linköping University, 581 83 Linköping, Sweden.
³ Department of Surgery and Department of Biomedical and Clinical Sciences (BKV), Linköping University, 581 83 Linköping, Sweden.
⁴ Environmental Toxicology Program, Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden.
⁵ Animal Biotechnology Laboratory, Animal Science Department, University of São Paulo (USP)/ Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo 13418-900, Brazil.

Abstract

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.

Keywords: Cancer; Clinical Protocol; Genomics; High Throughput Screening; Molecular Biology; Sequencing.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

DNA Methylation* / genetics
DNA* / genetics
Epigenesis, Genetic
Genotype
Humans
Immunoprecipitation

Substances

DNA