When we want to study epigenetic effects of bush/wild fires, using an ongoing cohort, we need to focus on a limited list of CpGs. Although necessary, the funding agency does not allow exploratory research. We are considering to include CpGs that are differentially methylation after exposure to smoking (568 CpGs), to PM10 and PM2.5 exposure (~70CpGs), and to stress (?? CpGs).
However, we need a smaller list.
Any preliminary data is welcome.
Dr. Kari Nadeau and Dr. Mary Prunicki will have a poster at AAI 2020 titled "Wildfire smoke exposure is associated with decreased methylation of the PDL2 gene"
Thank you so much. I contacted Dr. Kari Nadeau and Dr. Mary Prunick.
Wilfried Karmaus
Hi,
Why do you need a smaller list? is it for budget purpose?
what technology do you plan to use for methylation analysis? EPIC 850K is the most cost-effective and will probably cover all smoker CpGs and many others.
What is the size of your cohort?
I see you've been in touch already about EPIC array. I'll be happy to discuss over the phone if you want to.
Best,
Geoffrey
Thank you Geoffrey:
In this Australian cohort, we do not have the sample size to test 850k.
We may need to focus on 5-10 CpG with sufficient statistical power. However, we can use a screening method for exploration.
We are already working with 450k and 850k data, which using cord blood, Guthrie cards, adult blood and saliva.
Wilfried
Hi Wilfried,
My point is just that most part of the time it's cheaper to do 850K ($250-$350 per sample) than designing a more targeted approach unless you have thousands of samples. So I think it's worth to look at that option if the CpGs you are looking at are covered in 850K. it's easier, faster and cheaper.
but we can also help design the targeted by BSAS or Pyro if you want.
Geoffrey
- Badges
- Science topic
- Similar topics
- Biological Science
- Molecular Cell Biology
- Culture Cells
- Cell Line