title: Evaluating the Feasibility of DNA Methylation Analyses Using Long-Term Archived Brain Formalin-Fixed Paraffin-Embedded Samples.
abstract: We here characterize the usability of archival formalin-fixed paraffin-embedded (FFPE) brain tissue as a resource for genetic and DNA methylation analyses with potential relevance for brain-manifested diseases. We analyzed FFPE samples from The Brain Collection, Aarhus University Hospital Risskov, Denmark (AUBC), constituting 9479 formalin-fixated brains making it one of the largest collections worldwide. DNA extracted from brain FFPE tissue blocks was interrogated for quality and usability in genetic and DNA methylation analyses by different molecular techniques. Overall, we found that DNA quality was inversely correlated with storage time and DNA quality was insufficient for Illumina methylation arrays; data from methylated DNA immunoprecipitation, clonal bisulfite sequencing, and pyrosequencing of BDNF and ST6GALNAC1 suggested that the original methylation pattern is indeed preserved. Proof-of-principle experiments predicting sex based on the methylation status of the X-inactivated SLC9A7 gene, or genotype differences of the Y and X chromosomes, showed consistency between predicted and actual sex for a subset of FFPE samples. In conclusion, even though DNA from FFPE samples is of low quality and technically challenging, it is likely that a subset of samples can provide reliable data given that the methodology used is designed for small DNA fragments. We propose that simple PCR-based quality control experiments at the genetic and DNA methylation level, carried out at the beginning of any given project, can be used to enrich for the best-performing FFPE samples. The apparent preservation of genetic and DNA methylation patterns in archival FFPE samples may bring along new perspectives for the identification of genetic and epigenetic changes associated with brain-manifested diseases.
authors.affiliation: Department of Biomedicine, Aarhus University, Bartholin building, DK-8000, Aarhus C, Denmark.
authors.forename: Stine T
authors.initials: ST
authors.lastname: Bak
authors.affiliation: Department of Biomedicine, Aarhus University, Bartholin building, DK-8000, Aarhus C, Denmark.|Translational Neuropsychiatric Unit, Department of Clinical Medicine, Aarhus University Hospital, Risskov, Denmark.|The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark.|Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark.
authors.forename: Nicklas H
authors.initials: NH
authors.lastname: Staunstrup
authors.affiliation: Department of Biomedicine, Aarhus University, Bartholin building, DK-8000, Aarhus C, Denmark.|The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark.|Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark.
authors.forename: Anna
authors.initials: A
authors.lastname: Starnawska
authors.affiliation: Department of Biomedicine, Aarhus University, Bartholin building, DK-8000, Aarhus C, Denmark.
authors.forename: Tina F
authors.initials: TF
authors.lastname: Daugaard
authors.affiliation: Stereology and Electron Microscopy Laboratory, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.|Centre for Stochastic Geometry and Advanced Bioimaging (CSGB), Aarhus University, Aarhus, Denmark.
authors.forename: Jens R
authors.initials: JR
authors.lastname: Nyengaard
authors.affiliation: Department of Biomedicine, Aarhus University, Bartholin building, DK-8000, Aarhus C, Denmark.|The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark.
authors.forename: Mette
authors.initials: M
authors.lastname: Nyegaard
authors.affiliation: Department of Biomedicine, Aarhus University, Bartholin building, DK-8000, Aarhus C, Denmark.|The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark.|Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark.|Research Department P, Department of General Psychiatry, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.
authors.forename: Anders
authors.initials: A
authors.lastname: Børglum
authors.affiliation: The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark.|Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark.|Research Department P, Department of General Psychiatry, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.
authors.forename: Ole
authors.initials: O
authors.lastname: Mors
authors.affiliation: Translational Neuropsychiatric Unit, Department of Clinical Medicine, Aarhus University Hospital, Risskov, Denmark.|Centre for Stochastic Geometry and Advanced Bioimaging (CSGB), Aarhus University, Aarhus, Denmark.|Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh, Pittsburgh, USA.
authors.forename: Karl-Anton
authors.initials: KA
authors.lastname: Dorph-Petersen
authors.affiliation: Department of Biomedicine, Aarhus University, Bartholin building, DK-8000, Aarhus C, Denmark. aln@biomed.au.dk.|The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark. aln@biomed.au.dk.
authors.forename: Anders L
authors.identifier: 0000-0003-4372-9961
authors.initials: AL
authors.lastname: Nielsen
mesh_terms: D000368:Aged; D000369:Aged, 80 and over; D001921:Brain / Q000378:metabolism*; D018899:CpG Islands / Q000235:genetics; D004247:DNA / Q000378:metabolism; D019175:DNA Methylation / Q000235:genetics*; D044127:Epigenesis, Genetic; D005260:Female; D005557:Formaldehyde / Q000737:chemistry*; D056426:Genetic Loci; D006801:Humans; D008297:Male; D008875:Middle Aged; D016612:Paraffin Embedding; D010641:Phenotype; D013997:Time Factors; D014015:Tissue Banks; D016707:Tissue Fixation
chemical_list: D005557:Formaldehyde; D004247:DNA
keywords: Archival FFPE samples; Biobanks; Epigenetics; Post mortem examination; Tissue procurement; Tissue quality