Target Enrichment

Sample Technology
Get answers to specific biological questions with focused target enrichment
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Today’s NGS applications increasingly depend on the ability to rapidly and accurately obtain specific sequencing data from complex samples. QIAGEN’s target enrichment solutions allow you to quickly answer specific biological questions and use valuable resources more effectively with focused target enrichment that enables sequencing of the specific nucleic acids most relevant to your research.

Innovative NGS target enrichment solutions deliver:
  • Disease-focused gene panels for ultra-deep sequencing 
  • Efficient and specific removal of >99.5% ribosomal RNA
  • Time savings with automated solutions on the QIAcube
DNAseq NGS workflow
Focused amplification using PCR-based targeted exon enrichment

RNAseq NGS workflow
Highly efficient and selective rRNA depletion
Automated rRNA depletion on the QIAcube
GeneRead DNAseq NGS workflow
Targeted enrichment using multiplex PCR
Answer specific biological and clinical research questions quickly and easily with GeneRead DNAseq Panels V2, which use fast, multiplex-PCR-based targeted enrichment to allow deep sequencing of specific genes or genomic regions of interest in a wide range of asmples (see GeneRead DNAseq Targeted Panel System). Integrated DNA quality and targeted enrichment controls, sophisticated, wet-bench verified primer design, and optimized targeted enrichment chemistry ensure high design coverage, specificity, and uniformity. More than 90% of targeted regions are covered by the panel primer design, enabling deep sequencing and the identification of low-frequency genetic variants that might otherwise go undetected.

DNA sequencing is a useful tool to detect genetic variations, including somatic mutations, SNPs, and small insertions and deletions (indels). However, sequencing the genome can be time-consuming and costly. Targeted enrichment technology enables NGS platform users to sequence specific regions of interest instead of the entire genome, thereby achieving more sensitive mutation detection and reduced costs. GeneRead DNAseq Panels V2 are designed to analyze a panel of genes related to a disease state and can be used with any major NGS platform. Targeted enrichment is particularly well suited for medium-throughput sequencers, including Life Technologies’ Ion Torrent PGM Sequencer and Illumina’s MiSeq Personal Sequencer. Wet-bench verified primer sets are available for most popular genes, as well as custom panels with any set of genes or genomic regions in the human genome.

GeneRead DNAseq Targeted Panels V2 include the most commonly mutated genes in specific human disease states (see table "GeneRead DNAseq Panels V2"). The mutations in the tumor suppressor genes and oncogenes that make up the cancer-specific and comprehensive panels are often relevant for tumor classification and warrant extensive investigation to enhance our understanding of carcinogenesis. You can also analyze a specific set of genes or genomic regions using GeneRead DNAseq Mix-n-Match or Custom Panels V2.

GeneRead DNAseq Panels V2
 GeneRead DNAseq Targeted Panels V2  
  Tissue-specific panels (<100 genes) Comprehensive panels (>100 genes) Clinically relevant panels 
   Breast Cancer  Comprehensive Cancer  Tumor Actionable Mutations
   Colorectal Cancer  Carrier Testing  Clinically Relevant Tumor
   Myeloid Neoplasms  Cancer Predisposition  
   Liver Cancer    
   Lung Cancer    
   Ovarian Cancer    
   Prostate Cancer    
   Gastric Cancer    
   Cardiomyopathy    
 GeneRead DNAseq Mix-n-Match Panel V2  
   Build your own panel from QIAGEN's pool of 570 wet-bench verified genes    
 GeneRead DNAseq Custom Panel V2  
   Build your own panel to target any gene or genomic region in the human genome  

Overlapping primer sets across the exonic portions of a gene maximize target coverage and minimize non-specific amplification (see figure PCR-enabled targeted enrichment). GeneRead DNAseq Targeted Panels V2 are designed to cover the coding sequences of any protein coding region of any gene in the human genome. The overlapping PCR products (amplicons) produced by the overlapping primer sets yield greater than 90% coverage of the targeted genes and more than 90% of sequence specificity.

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RNAseq NGS workflow
Highly efficient and selective rRNA depletion
Ribosomal RNA (rRNA) makes up 85–90% of total RNA, taking up valuable sequencing capacity and resulting in a high signal-to-noise ratio that can make detection of the RNA species of interest difficult. The GeneRead rRNA Depletion Kit effectively removes ribosomal RNA, while ensuring complete recovery of mRNA and noncoding RNA from various species, including human, mouse, and rat (see figure GeneRead combines DNA/RNA sequence specificity and antibody binding). By improving the ratio of useful data, decreasing bias, and preserving non-coding RNA species, the kit provides high-quality RNA that is especially suited for NGS applications.
Efficient removal of all rRNA species
The GeneRead rRNA Depletion Kit efficiently removes all types of rRNA, including the 4 main ribosomal RNAs, as well as mitochondrial rRNA. QIAxcel Advanced data showing rat spleen RNA demonstrates complete removal of the 18S and 28S ribosomal RNA peaks compared to total RNA (see figure Highly efficient rRNA removal). In this experiment, more than 99.9% of all types of ribosomal RNA were removed with the kit.
Highly specific rRNA depletion with no artificial depletion of protein-coding genes
The biotype distribution of sequenced RNA following rRNA depletion demonstrates that the GeneRead rRNA Depletion Kit effectively eliminates rRNA, while preserving more miRNA and other noncoding RNA than rRNA depletion kits from other suppliers (see figure More effective and specific rRNA depletion). The biotype distribution of RNA prepared using kits from Suppliers E and I revealed significantly less effective rRNA elimination, while the kit from Supplier E enriched for scRNA (e.g., 7SL and Alu RNA).

With the GeneRead rRNA Depletion Kit, the distribution of multiple RNA types, such as miRNA and other noncoding RNAs, is also preserved compared to poly A+ purification, which enriches for protein-coding RNAs. Kits from other suppliers may skew the representation of protein-coding (poly A+) RNAs in a sample, particularly by nonspecific removal of non-ribosomal RNA. In contrast, the GeneRead rRNA Depletion Kit demonstrates greater concordance with poly purification and preserves the natural representation of other RNA species and protein-coding genes (see figures The GeneRead rRNA Depletion Kit ensures greater conservation of the mRNA profile and Better representation of protein coding genes).

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Automate your rRNA depletion with the QIAcube
The majority of the GeneRead rRNA Depletion Kit procedure, from hybridization and capture through to RNA cleanup, is automatable on the QIAcube. The innovative QIAcube uses advanced technology to process QIAGEN spin columns, enabling seamless integration of automated, low-throughput sample prep into your laboratory workflow. No change of purification chemistry is required, assuring fast startup and immediate results.

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S_3994_GeneReadDNASeq8103
For targeted enrichment prior to NGS using GeneRead DNAseq Panels V2
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S_3991_GeneReadDNAseq_8083
For targeted enrichment of a customized set of genes or genomic regions specific for your NGS needs
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QIAseq DNA QuantiMIZE Array Kit
For quantification and qualification of amplifiable DNA prior to NGS
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Accelerate your NGS performance through Sample to Insight solutions
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Multiplex PCR scheme for target enrichment.
PCR-enabled target enrichment.
The principle of the GeneRead DNAseq V2 System is to employ overlapping primer sets across the exonic portions of a gene or genes to maximize target coverage and minimize nonspecific amplification.
Actionable Insights Tumor Panel Workflow
GeneRead DNAseq Panel System V2 Workflow.
Genomic DNA (the QIAamp DNA Mini Kit, QIAamp DNA FFPE Tissue Kit, or GeneRead DNA FFPE Kit are recommended for extraction) can be quantified and qualified using the GeneRead DNA QuantiMIZE System. The GeneRead DNAseq Targeted Panels V2 are then used for targeted enrichment. Following target enrichment, construct your NGS library, quantify and quality-control using the GeneRead Library Quantification System, perform NGS, and analyze the data using the QIAGEN NGS Data Analysis Web Portal.
GeneRead combines  two steps of specificity: DNA/RNA sequence specificity and antibody binding
GeneRead combines DNA/RNA sequence specificity and antibody binding.
When the oligonucleotide probes are perfectly matched, both direct capture (e.g., using biotin-streptavidin beads) and antibody-mediated capture (GeneRead rRNA Depletion Kit) will successfully capture the rRNA targets. When probes cross-hybridize to RNA species other than rRNA, the mismatched probe/RNA will not be recognized by the GeneRead rRNA Depletion system, thereby avoiding non-specific depletion. In contrast, with direct capture, this second level of specificity does not exist and other RNA species may be co-depleted along with the rRNA.
The GeneRead rRNA Depletion Kit ensures greater conservation of the mRNA profile
Greater conservation of the mRNA profile.
The number of reads mapped to protein coding genes after sequencing of each depletion method was compared to those resulting from a poly A enrichment method to determine the specificity of the depletion method. (The purple dots indicate reads from mRNA species without poly A tails [e.g., histones] that are lost in poly A-based enrichment). The high linear correlation (R2) values of these results demonstrate that, compared to the rRNA depletion kits of Suppliers I and E, the GeneRead rRNA Depletion Kit (QIAGEN) is the best at preserving the profile of mRNA present in the original sample.
Highly efficient rRNA removal
Highly efficient rRNA removal.
[A] The lack of any rRNA peak in QIAxcel trace data demonstrates complete removal of rRNA in the rRNA-depleted sample, in contrast to the total RNA sample. [B] qRT-PCR assays indicate that more than 99.9% of all rRNA species, including mitochondrial rRNA, were removed with the kit in this experiment.
More effective and specific rRNA depletion
More effective and specific rRNA depletion.
Total RNA from Jurkat cells was treated according to the manufacturer’s instructions for each depletion or enrichment procedure. All depleted/enriched samples were made into libraries using the same method and sequenced in multiplex by Illumina sequencing on a MiSeq system. Sequencing reads were mapped by Bowtie 2 against the Ensembl RNA database and the percentage of mapped reads from each library for the Ensembl biotypes were plotted
Automate your sample enrichment with the QIAcube.
The innovative QIAcube uses advanced technology to process QIAGEN spin columns, enabling seamless integration of automated sample preparation into your NGS workflow.
Specific rRNA depletion for better representation of protein coding genes
Better representation of protein coding genes.
The abundance of specific proteincoding genes present in a sample following depletion of rRNA using kits from Supplier E, Supplier I, or the GeneRead rRNA Depletion Kit, was compared to a poly A purification method. Both the number of depleted genes and the magnitude of the depletion is significantly lower using the GeneRead rRNA Depletion Kit than with kits from Supplier E or Supplier I, which resulted in non-specific depletion of more than 70 times as many genes by a factor of 10 or more than the GeneRead Kit.