nRichDX’s Post

Name: nRichDX on LinkedIn: #sampleprepmatters #liquidbiopsy #cfrna #rnafusions #cancerresearch…
Uploaded: 2024-06-19T19:37:01.139Z
Channel: nRichDX

nRichDX

1,680 followers

3mo

nRichDX with Anchor Molecular presented a poster, "Exploring Liquid Biopsy for the Detection of Bladder Cancer: Unraveling RNA Fusions" on extraction of RNA fusions from urine samples at the recent American Association for Cancer Research's Special Conference on Bladder Cancer, 17-20 May 2024. Here is a short Q&A with one of the poster's authors, Nafiseh J. Jafari, Ph.D. discussing this pilot study and how Revolution Sample Prep was used. More info: https://lnkd.in/duAYyvwn #SamplePrepMatters #liquidbiopsy #cfRNA #RNAfusions #cancerresearch #oncologyresearch #urinesamples #RevolutionSamplePrep

Transcript

So the objective of this initial pilot study was a proof of principle to determine if RNA fusions could be extracted from urine samples using Revolution sample prep kit to have an increased sensitivity in a downstream assay We used an RNA fusion as standard from Anchor Molecular as our collaborator. So 20 mL urine samples were collected from healthy male donors and RNA fusion controls standards ETV6-NTRK3 and PRCC-TFE3 from anchor molecular were chosen as a spike material and we used a Revolution Sample Prep Max 20 kit for circulating cell free total nucleic acid to isolate these RNA fusions. In terms of the QC we used high sensitivity RNA ScreenTape from Agilent to look at the quality and integrity of RNA post extraction and to be able to measure the actual extraction efficiency. We used qPCR mutation detection assay specific for this mutation. So even though we use A 20 mL sample volume, we are able to elute in 50 uL. I noticed that the concentrations of the standard provided by Anchor Molecular, the PRC CTF E3 was one ng/mL and the other was at 10 ng/mL What was the significance of the difference in concentrations? We intentionally chose to test two different concentrations to be able to see how low we can detect these RNA fusions using the. extraction method. As a pilot study, we were able to only test for individual samples, but the tape station profile where showing prominent 18S and 28S RNA ribosomal peaks as well as high RIN number, which is indicative of RNA integrity number. This is very critical because RNA post extraction, especially after post. DNA treatment, tends to lose quality and yield, but we were able to extract with the high RIN number even post- extraction and post DNA treatment. Yes, so we used as I said mutation detection, qPCR assay to be able to truly measure the recovery of RNA fusions and we were able to see very highly significant Ct number compared to what we have tested on market and above 50% for RNA extraction efficiency post DNAase treatment. It is highly significant for RNA extraction and recovery and this can open up exciting possibilities for early diagnosis of bladder cancer. nRichDX is very interested in urine liquid biopsy and overall maximizing pre-analytical steps to improve downstream assay performance and sensitivity. First, we would love to see researchers and clinicians doing this study looking at this mutation and other relevant mutations for bladder cancer using a larger population and actually On patient samples. Also we are interested in collaborating with people that are interested in using large urine sample volumes to be able to improve asset sensitivity for earlier detection of bladder cancer because we think we've got a great method and we can handle large urine sample volumes in a single extraction without Yield-lowering additional steps and manual workflow to lower the RNA integrity and quality. We are able to have a streamlined workflow to be able to extract with the high quality and high yield of RNA fusion. So if you're doing that type of work, I'm interested to discuss your project and we might be able to help you.

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