NGS FFPE QC Kit
Formalin-fixed paraffin-embedded tissue represents a valuable sample source for molecular cancer research. These samples provide a contextual snapshot of the tissue at a specific time point and stage of disease but are highly challenging to analyze, especially using next generation sequencing. DNA derived from FFPE is oftentimes highly fragmented, cross-linked with protein and has a high proportion of single-stranded DNA. making it challenging for adaptor ligation and amplification, steps that are critical for successful preparation of sequencing libraries.
The Agilent NGS FFPE QC kit is a qPCR-based assay that enables functional DNA quality assessment of input DNA prior to preparation of next generation sequencing libraries. This kit enables assessment of the integrity of DNA as well as accurate quantitation of amplifiable template going into library preparation. Furthermore, optimizations to the SureSelectxt workflows based on the sample quality score are enabled.
產品特點
Accurate qualification and quantitation of amplifiable DNA
The Agilent NGS FFPE QC kit is a qPCR-based assay that enables functional DNA quality assessment of inputDNA prior to preparation of next generation sequencing libraries. This kit enables assessment of the integrityof DNA as well as accurate quantitation of amplifiable template going into library preparation. Sample integrityis assessed using two primer pairs that generate differently sized amplicons, a 42bp and a 123bp. Thisdifference in the amplicon sizes allow for discrimination between samples that have sufficient intact amplifiableDNA and those that have a higher degree of fragmentation, effectively eliminating the need for agarose gelelectrophoresis. In addition, since the assay is qPCR-based, functionality of the FFPE DNA as template for PCRis also assessed allowing for increased probability of successful preparation of next generation sequencinglibraries (Figure 1).
Figure 1. Sample quality is determinedbased on the ∆∆Cq between the sample andthe reference. Briefly, amplification of twodifferentially sized amplicons are assessed.The ∆Cq of the sample is the differencebetween the Cq of amplicon B (123 bp) andthe Cq of amplicon A (42 bp). The qualityscore or ∆∆Cq is then calculated as thedifference between the ∆Cq of the sampleand the ∆Cq of the reference. Quantitation,on the other hand, is based on the Cq ofamplicon A alone.Optimized low input library prep workflow for improved complexity and target coverage
Figure 2. The Agilent NGS FFPE QC protocol provides recommendations to optimize preparation of enrichedlibraries for sequencing based on the quality score (∆∆Cq). Optimizations for lower quality FFPE samples includeincreasing amplification cycles for the pre-capture library to ensure sufficient template molecules are introducedinto the hybridization, and increasing sequencing depth to enable better target coverage.Complete cancer research solutions from sample to data
Figure 3. The Agilent NGS FFPE QC kit is part of the complete workflow solution that enables optimal data generation from even low quality FFPE samples. Complementary solutions for library prep, enrichment and data analysis are available providing support from sample pre-qualification all the way to variant calling.產品列表
| 貨號 | 產品 | 數量 | |
|---|---|---|---|
| G9700A | Agilent NGS FFPE QC Kit | 16 rxns | |
| G9700B | Agilent NGS FFPE QC Kit | 96 rxns |
NGS QC Kit
- Accurately qualify and quantify amplifiable DNA in challenging samples
- Optimized low input library prep workflow for improved complexity and target coverage
- Complete cancer research solutions from sample to data
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