Discover rare cancer mutations in heterogeneous tumor cells using previously inaccessible samples
Overview
The RainDance DeepSeq FFPE Solution is the first ultra-deep targeted sequencing system for fresh-frozen and Formalin-Fixed, Paraffin-Embedded (FFPE) samples. For the first time, researchers can interrogate 500 targets across extensive collections of well-annotated clinical FFPE samples to discover rare cancer and other disease-specific mutations that represent as little as one percent of a heterogeneous sample.
Advantages
- Discover more rare mutations: Gain unprecedented single-base resolution of genomic mutations at a frequency as low as 1% of a heterogeneous sample.
- Utilize extensive collections of well-annotated clinical samples: Generate accurate and unbiased representations of the genome from FFPE and fresh-frozen samples.
- Interrogate any region of the genome: Analyze 500 target loci, including noncoding regions, repetitive sequences, and areas of high homology.
- Generate targets compatible with degraded FFPE samples: Construct short 200 base-pair amplicons using RainDance’s DeepSeq Primer Design Pipeline.
- Eliminate downstream library processing:Integrate next-generation sequencing adaptors and barcodes with RainDance’s 2-Step Tailed Primer Assay.
- Achieve results faster than ever before: Target regions of interest with more than 2 million PCR products per sample in less than 1 hour.
Workflow
The DeepSeq FFPE Solution features a simplified workflow that significantly reduces hands-on time and overall experimental cost.
RainDance’s DeepSeq FFPE Primer Library
The automated RainDance primer library design pipeline generates unique primers for typically greater than 99%coverage of targeted regions. Researchers are able to design a library that can analyze up to 500 targets. The pipeline generates 200 base amplicons compatible with FFPE samples and short-read sequencing technologies. This includes coding and noncoding regions, repetitive sequences, splice sites, regulatory regions and other locations that are difficult to reach with hybridization-based methods.
RainDance’s 2-Step Tailed Primer Assay
The 2-Step Tailed Primer Assay enables researchers to integrate NGS adaptors and barcodes directly into sequencing ready targets. The two steps enrich for the targets of interest and improve specificity of the mapped sequencing reads to the intended targets. Samples are processed with a RainDance DeepSeq FFPE Primer Library with primers containing target specific sequences (A, A’) and NGS partial adaptor tails (B, B’). After amplification in droplets and breaking of the emulsion, a second round of universal PCR is run utilizing primers that hybridize to the NGS adaptor sequences. This round of amplification incorporates the remainder of the NGS adaptor sequences and the barcodes (C, C’), which further improve sequencing capacity and efficiency with the ability to index up to 12 samples per sequencer lane.