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Analysis of Advanta Solid Tumor and RNA Fusions NGS Library Prep Assays (Fluidigm): Somatic Variant, CNV, and Fusion Detection

The Advanta™ Solid Tumor NGS Library Prep Assay with the automated Juno™ (Fluidigm®) system produces targeted amplicon-based barcoded libraries for subsequent analysis on Illumina® NGS platforms, optimizing interrogation of high-value, low-variant-frequency SNPs, indels and CNVs within oncology-relevant genes. The Advanta™ RNA Fusions NGS Library Prep Assay with the automated Juno™ system produces targeted amplicon-based libraries for subsequent analysis on Illumina® NGS platforms and optimized interrogation of high-value gene fusion pairs.


NextGENe® software includes features for the detection of the somatic variants, copy number variants, and gene fusion events that can be sequenced through these panels.


NextGENe’s Overlap Merger tool can be used to merge paired end reads into a single read prior to alignment to increase read lengths and improve accuracy.


Variant detection thresholds can be set to allow detection of low frequency somatic variants.

 

Figure 1: Variant Detection Thresholds: Minimum thresholds for frequency, reads containing the variant, and total coverage can be set individually for SNPs, indels, and homopolymer indels.

The CNV Tool compares samples to a control or batch of controls to detect copy number variations.


Figure 2: CNV Tool Graphics: Duplication calls are highlighted with green while deletion calls are highlighted in red.

 

NextGENe’s structural variant detection settings can be used for the detection of structural variants including fusion genes.

 


Figure 3: Structural Variation Report: Report output of a sample prepared with the Advanta RNA Fusions NGS Library Prep Assay, displaying an identified fusion event. The dual viewer allows side-by-side comparison of both sides of the fusion breakpoint.

 

NextGENe software offers templates that can be used to quickly set up the analysis of sequencing data generated from samples processed with the Advanta Solid Tumor and RNA Fusions NGS Library Prep Assays utilizing recommended settings.

 

Fluidigm products are for Research Use Only. Not for Use In Diagnostic Procedures.

 

For More Information Review or Download Application notes:
NextGENe Illumina SNP_Indel_Detection
Structural Variant Analysis
NextGENe software Variant Comparison Tool
NextGENe SNP & Indel Viewer
Whole Genome Alignment with NextGENe software
Paired end read merging with NextGENe software
Using NextGENe software's Pipeline Automation Tool
Somatic Mutation Analysis from Whole Exome Sequencing Data with NextGENe® Software
Highly Sensitive Somatic Mutation Detection from Biopsy Samples with Deep Sequencing using NextGENe® Software
NextGENe CNV Detection- Dispersion and HMM

 

Pricing & Trial Version:
Request 30-day trial/Price Quote

 

Reference Material:
Download/View NextGENe® Brochure
NextGENe User Manual
Annotated Reference Genomes

 

Track Manager Manual
Use the Reference & Track Manager tool to import and manage preloaded references and data from any public or proprietary variant database.
Download the manual

 

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