Can we apply NGS (next generation sequencing) on DNA extracted from formalin fixed paraffin embedded tissues (FFPE)?
Yes, it is possible to apply next-generation sequencing (NGS) on DNA extracted from formalin-fixed paraffin-embedded tissues (FFPE). FFPE tissues are commonly used for long-term storage in pathology laboratories, as they preserve histological architecture and cellular morphology. However, the formalin fixation process can cause DNA fragmentation and chemical modifications, making it challenging to obtain high-quality DNA for sequencing.
To overcome these challenges, there are specific DNA extraction protocols developed for FFPE tissues that aim to improve DNA quality and yield. These protocols involve deparaffinization, protein digestion, and DNA purification steps. Different commercial DNA extraction kits are available, specifically designed for FFPE samples.
After DNA extraction, several NGS technologies, such as whole-genome sequencing, targeted gene panel sequencing, exome sequencing, and RNA sequencing can be applied to study the genomic and transcriptomic profiles from FFPE samples. However, it is important to note that FFPE-derived DNA is often degraded and contains chemical modifications, which can affect sequencing quality and introduce sequencing artifacts. Hence, appropriate quality control measures and data analysis algorithms need to be employed to accurately interpret the sequencing results derived from FFPE samples.
In summary, NGS can be applied to DNA extracted from FFPE tissues with the use of specialized DNA extraction protocols. However, the quality and quantity of DNA obtained may be compromised, necessitating careful consideration during data analysis and interpretation.
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