The first complete NGS workflow in one system

The GeneReader NGS System has been designed to perform the whole next-generation sequencing (NGS) workflow: from nucleic acid extraction to DNA library preparation, from sequencing to data analysis. The system consists of several modules: the QIAcube Classic for DNA purification and library preparation, the GeneRead QIAcube for clonal amplification step of library template preparation, the GeneReader instrument for DNA sequencing and the PowerStation for data analysis and traceability. The GeneReader platform performs fluorescence-based sequencing according to unique reversible terminated and fluorescent-labeled dNTPs in a sequencing-by-synthesis paradigm.

Efficient sequencing chemistry

The sequencing part in the GeneReader NGS System consists of several steps: the library DNA fragments are first clonally amplified on sequencing beads generating single strand DNA templates. These are then allowed to hybridize with a sequencing primer giving rise to primer-template carrying beads. Subsequently the beads are deposited onto a surface-coated flow cell and covalently linked to a glass slide generating a high-density array. The flow cell is then loaded into the GeneReader sequencer where the array of DNA fragments is subjected to reagents containing unique reversible terminated and fluorescent-labeled dNTPs. The sequencing chemistry uses four dye colors for labeling, one for each different DNA base, and the reversible terminators allow the addition of a single engineered nucleotide to each single DNA template. After each addition of dNTPs, the array is scanned and the fluorescence of the four dyes is recorded. At the end of each cycle the dyes and the reversible terminators are cleaved off, allowing the next cycle of dNTPs incorporation to follow. Once the sequencing has been finalized, the GeneReader software provides the sequence information in a FASTQ file format to be analyzed by the QCI Analyze software, in order to generate a variant analysis report.

Versatile process with multiple applications

The process can easily be adapted to the user’s needs. The batch sizes are scalable and the system also allows continuous loading as well as the use of multiple flow cells (1-3). When it comes to applications, the GeneReader NGS System can be used to provide fast and deep knowledge in cancer research using gene panels such as the GeneRead QIAact Actionable Insights Tumor Panel, which can detect 1,250 clinically relevant genetic mutations, as well as the GeneRead QIAact BRCA 1/2 DNA panel and the GeneRead QIAact Lung DNA and RNA panels, for somatic and fusion variant analysis. Moreover the release of the GeneReader QIAact DNA Custom Panels pipeline leverages the GeneReader NGS System flexibility in meeting any customer need.

Case Study GeneReader

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The Challenge

The capacity to sequence all 3.2 billion bases of the human genome has increased from 1.3 human genomes sequenced annually to 18,000 human genomes a year within a decade. Despite this improvement sequencing a genome is still an extremely complex procedure, which prevents its broad use in routine human diagnostics.

The Goal

Build a complete NGS workflow with seamlessly integrated automated components offering ease of use and efficiency from sample to result. Provide actionable insights with validated gene panels and fully integrated bioinformatics.

The Result

The GeneReader is the only integrated NGS workflow from sample to insight.

The Approach

The GeneReader workflow includes the following 6 processes: sequencing primer hybridization, flow cell preparation, reagents preparation, experiment set-up, flow cell loading and run start and post-run maintenance wash.