Assessing the Reproducibility and Integrity of DNA Methylation

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The reliability of testing epigenetic DNA methylation using Illumina beadchips is of paramount importance due to the specific intricacies of this technology.

Illumina beadchips are widely used platforms for high throughput epigenetic analysis, employing thousands of probes to measure DNA methylation levels at specific genomic loci.

In this week’s Everything Epigenetics podcast, Dr. Karen Sugden and I talk about how the reliability of these probes directly impacts the accuracy and validity of the results obtained.

Additionally, keep in mind that in the context of Illumina beadchips, reliability refers to the consistent and accurate performance of each individual probe across multiple samples and experimental replicates. Each probe is designed to target a specific CpG site, and the methylation signal it generates must be dependable and reproducible.

We discuss how reliable probes ensure the accuracy of DNA methylation measurements and how the reliability of probes becomes crucial for reproducibility when conducting large scale studies using Illumina beadchips, such as epigenome-wide association studies (EWAS).

Dr. Sugden and I also discuss how the reliability of probes on Illumina beadchips has implications for cross-study comparisons. For example, if the probes exhibit inconsistent behavior across different experiments or cohorts, it becomes challenging to compare results and draw meaningful insights from combined analyses.

Furthermore, we chat about the efficient utilization of resources being linked to probe reliability. Unreliable probes might necessitate repeating experiments or allocating additional resources to validate results, potentially delaying research progress and increasing costs.

In the context of epigenetic research, where subtle changes in DNA methylation can hold profound biological significance, the accuracy and consistency of data generated by Illumina beadchips are pivotal.

Lastly, we explore Dr. Sugden’s current research. This includes how epigenetic clocks associate with cognitive impairment and dementia and marijuana use.

In this podcast you’ll learn about:

– Dr. Karen Sugden’s career
– Reliability and why it matters
– How unreliability arises in epigenetic research
– The process of measuring DNA methylation on Illumina beadchips (or microarrays)
– Technical errors that could arise when looking at DNA methylation
– Karen’s paper titled “Patterns of Reliability: Assessing the Reproducibility and Integrity of DNA Methylation Measurement”
– How to untangle data from different beadchips (27K vs. 450K vs. EPIC 850K)
– What constitutes a reliable probe vs. an unreliable probe
– How to handle unreliable probes
– Who is at fault for unreliable probes
– If reliability is the same for every beadchip
– How unreliability impacts epigenetic research
– How we can deal with unreliability
– The value of repeated data
– Creating a “gold standard” work flow for processing epigenetic data
– How epigenetic clocks associate with cognitive impairment and dementia
– The connection between epigenetic clocks and marijuana
– Dr. Sugden’s current research investigations

Where to find Dr. Karen Sugden:
Profile at Duke –
Association of Pace of Aging Measured by Blood-Based DNA Methylation With Age-Related Cognitive Impairment and Dementia –
Lifetime Marijuana Use and Epigenetic Age Acceleration: A 17-year Prospective Examination-

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