Hello Jéssika Chagas Lesbon,

For FFPE samples, RIN values are typically lower ranging from 1.2 to 2.5. A higher RIN value (ideally 7 or higher) is generally recommended for optimal RNAsequencing. The FFPE samples often have lower RINs due to degradation during the fixation process. 

Though RIN is a good general indicator, there are alternatives. You should focus on DV200 or DV100 (Debris/Fragment Volume of 200 nucleotides/100 nucleotides), which is a quality metric used to assess the integrity of RNA samples, particularly in the context of next-generation sequencing. It represents the percentage of RNA fragments that are greater than 200 nucleotides or 100 nucleotides in length. 

DV200 or DV100 helps determine the extent of RNA degradation or fragmentation, as lower DV200 or DV100 values indicate a higher proportion of shorter, degraded fragments. DV200 or DV100 is particularly useful for assessing RNA quality from FFPE samples, where RNA degradation can be more common. 

For instance, DV100 values below 40% are likely to result in poor sequencing data. Your aim should be for DV100 > 50%, or even DV200 > 50%, if the RNA is not severely degraded. 

As an alternative quality metrics, you could try Reverse Transcription and PCR-based quality control. RT-qPCR, using primers and probes on well-characterized amplicons, can assess the amplifiable RNA content, indicating the proportion of RNA that can be successfully amplified.

Thus, by focusing on fragment size distribution and alternative quality metrics, it is possible to effectively assess RNA quality in FFPE samples, even with low RIN scores, as in your case

Dear Malcolm Nobre ,

Thank you very much for your kind and prompt response to my question. I truly appreciate you taking the time to share your expertise and clarify my doubts.

Your explanation was extremely helpful and has greatly contributed to my understanding of the subject.

With sincere gratitude,