Short Communication, Jbrhd Vol: 6 Issue: 6
Successful Next-Generation Sequencing (NGS) for Exome Analysis from Formalin-Fixed and Paraffin-Embedded Tumor Tissue (FFPE) Samples
M Luisa Villahermosa
GENOMICA SAU (Pharmamar Group), Spain
Abstract
Formalin-fixed, paraffin-embedded tumor tissue (FFPE) is likely to be the preferred choice for tissue preservation in clinical practice for the Next Generation Sequencing (NGS) analysis. The efficiency of Exome sequencing from FFPE tissue depends of the amount and quality of DNA extracted. To generate accurate NGS data, we have implemented a specific protocol in order to obtain accurate sequencing of the exomes. We analyzed 21 tissue samples obtained at diagnosis from patients with solid tumors using Ion ampliseqTM Exome RDY (Thermofisher) with the objective of detecting germinal variants. Genomic DNA (gDNA) concentration was quantified using Qubit® fluorometry, and its quality was determined using the RNase P Taqman. Correct NGS libraries were obtained considering the degradation status: we increase the quantity of gDNA for performing the library according with the data obtained with the RNase P analysis in each sample.
Formalin-fixed, paraffin-embedded tumor tissue (FFPE) is likely to be the preferred choice for tissue preservation in clinical practice for the Next Generation Sequencing (NGS) analysis. The efficiency of Exome sequencing from FFPE tissue depends of the amount and quality of DNA extracted. To generate accurate NGS data, we have implemented a specific protocol in order to obtain accurate sequencing of the exomes. We analyzed 21 tissue samples obtained at diagnosis from patients with solid tumors using Ion ampliseqTM Exome RDY (Thermofisher) with the objective of detecting germinal variants. Genomic DNA (gDNA) concentration was quantified using Qubit® fluorometry, and its quality was determined using the RNase P Taqman. Correct NGS libraries were obtained considering the degradation status: we increase the quantity of gDNA for performing the library according with the data obtained with the RNase P analysis in each sample.
