Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Effect of Hormonal Contraceptives on Circulating Biomarkers of Inflammation, Chemotaxis, Angiogenesis, and Vascular Stress.

APMIS : acta pathologica, microbiologica, et immunologica Scandinavica·2026
Same author

Resistant Hypertension Variants Link to Hyperaldosteronism and Potassium Levels.

Hypertension (Dallas, Tex. : 1979)·2026
Same author

Early osseointegration of two in-house 3D-printed porous titanium implant designs: an <i>in vivo</i> sheep study.

Frontiers in surgery·2026
Same author

Changes in Genetic Contributions to ASD and ADHD by Year of Diagnosis.

JAMA psychiatry·2026
Same author

In-house 3D printed porous implants: does strontium-coating enhance osseointegration? An <i>in-vivo</i> study in large animals.

Frontiers in surgery·2026
Same author

Genome-wide meta-analysis identifies genetic drivers of bile acid metabolism in intrahepatic cholestasis of pregnancy.

Nature communications·2026

Related Experiment Video

Updated: Mar 9, 2026

Optimized Analysis of DNA Methylation and Gene Expression from Small, Anatomically-defined Areas of the Brain
13:11

Optimized Analysis of DNA Methylation and Gene Expression from Small, Anatomically-defined Areas of the Brain

Published on: July 12, 2012

19.4K

Evaluating the Feasibility of DNA Methylation Analyses Using Long-Term Archived Brain Formalin-Fixed

Stine T Bak1, Nicklas H Staunstrup1,2,3,4, Anna Starnawska1,3,4

  • 1Department of Biomedicine, Aarhus University, Bartholin building, DK-8000, Aarhus C, Denmark.

Molecular Neurobiology
|December 21, 2016
PubMed
Summary

Archival formalin-fixed paraffin-embedded (FFPE) brain tissue can be a valuable resource for genetic and DNA methylation studies of brain diseases. Despite low DNA quality, specific methods can yield reliable data from these precious samples.

Keywords:
Archival FFPE samplesBiobanksEpigeneticsPost mortem examinationTissue procurementTissue quality

More Related Videos

A Chromatin Assay for Human Brain Tissue
11:31

A Chromatin Assay for Human Brain Tissue

Published on: March 21, 2008

13.5K
Preparation of Formalin-fixed Paraffin-embedded Tissue Cores for both RNA and DNA Extraction
08:30

Preparation of Formalin-fixed Paraffin-embedded Tissue Cores for both RNA and DNA Extraction

Published on: August 21, 2016

52.2K

Related Experiment Videos

Last Updated: Mar 9, 2026

Optimized Analysis of DNA Methylation and Gene Expression from Small, Anatomically-defined Areas of the Brain
13:11

Optimized Analysis of DNA Methylation and Gene Expression from Small, Anatomically-defined Areas of the Brain

Published on: July 12, 2012

19.4K
A Chromatin Assay for Human Brain Tissue
11:31

A Chromatin Assay for Human Brain Tissue

Published on: March 21, 2008

13.5K
Preparation of Formalin-fixed Paraffin-embedded Tissue Cores for both RNA and DNA Extraction
08:30

Preparation of Formalin-fixed Paraffin-embedded Tissue Cores for both RNA and DNA Extraction

Published on: August 21, 2016

52.2K

Area of Science:

  • Neuroscience
  • Genetics
  • Epigenetics

Background:

  • Archival formalin-fixed paraffin-embedded (FFPE) tissues are crucial for retrospective studies.
  • The usability of FFPE brain tissue for genetic and DNA methylation analyses is not fully characterized.
  • The Brain Collection (AUBC) houses one of the largest FFPE brain tissue collections globally.

Purpose of the Study:

  • To assess the utility of archival FFPE brain tissue for genetic and DNA methylation analyses.
  • To determine the impact of storage time on DNA quality and usability.
  • To identify suitable molecular techniques for analyzing FFPE brain DNA.

Main Methods:

  • DNA extraction from 9479 FFPE brain samples.
  • Assessment of DNA quality and integrity.
  • Application of various molecular techniques including methylated DNA immunoprecipitation, clonal bisulfite sequencing, pyrosequencing, and PCR-based quality control.
  • Proof-of-principle experiments for sex prediction using methylation status and chromosomal genotype differences.

Main Results:

  • DNA quality in FFPE samples is inversely correlated with storage duration.
  • DNA quality was insufficient for standard Illumina methylation arrays.
  • Despite low DNA quality, methylation patterns were preserved using specific techniques.
  • Sex prediction based on methylation and chromosomal analysis showed consistency in a subset of samples.
  • Simple PCR-based quality control can identify suitable FFPE samples.

Conclusions:

  • Archival FFPE brain tissue, though challenging, can yield reliable genetic and DNA methylation data with appropriate methodologies.
  • Methodologies designed for small DNA fragments are essential for FFPE sample analysis.
  • Quality control is critical for selecting the best-performing FFPE samples for research.
  • Preserved genetic and epigenetic patterns in FFPE samples offer new avenues for studying brain-manifested diseases.