Target Enrichment

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

DNAseq NGS workflow
Focused amplification using PCR-based targeted exon enrichment
Answer specific biological questions quickly and easily with GeneRead DNAseq Gene Panels, which use fast, multiplex-PCR-based target enrichment to allow ultra-deep sequencing of specific genes of interest in a wide range of cancer types (see figure GeneRead DNAseq Gene Panel System). Integrated DNA quality and target enrichment controls, sophisticated, laboratory-verified primer design, and optimized target enrichment chemistry ensure high design coverage, specificity, and uniformity. More than 90% of exonic regions are covered by the panel primer design, enabling deep sequencing and the identification of low-frequency genetic variants that might otherwise go undetected (see table "Identification of low-frequency variants").

Identification of low-frequency variants
Sample	Gene	Codon change	Variant frequency (%)	AA change
Tumor sample 1	KRAS	c.35G>T	38	p.G12V
	BRAF	c.462A>C	15	p.K154N
	PDGFRA	c.1432T>C	54	p.S478P
	TP53	c.817C>T	24	p.R273C
Tumor sample 2	ERBB2	c.3590C>G	9	p.P1197R
Tumor sample 2	KRAS	c.35G>T	30	p.G12V
Tumor sample 3	EGFR	c.1496G>A	7	p.C499Y
	KRAS	c.35G>T	23	p.G12V
	PDGFRA	c.1432T>C	59	p.S478P
	TP53	c.817C>T	11	p.R273C

DNA resequencing is a useful tool to detect genetic variations, including somatic mutations, SNPs, and small insertions and deletions. However, sequencing the genome can be time-consuming. Targeted enrichment technology enables NGS platform users to sequence specific regions of interest instead of the entire genome, thereby achieving more sensitive mutation detection. GeneRead DNAseq Gene Panels 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. Laboratory-verified primer sets are available for most popular genes, as well as custom panels with any set of genes in the human genome.

GeneRead DNAseq Targeted Exon Enrichment Panels include the 20 genes most commonly mutated in specific human cancers (see table "GeneRead DNAseq Gene Panels"). The mutations in the tumor suppressor genes and oncogenes that make up the panel 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 using GeneRead DNAseq Mix-n-Match or Custom Panels.

GeneRead DNAseq Gene Panels
GeneRead DNAseq Targeted Exome Enrichment Panels
	Cancer panel (20 GOI)	High content cancer panel (124 GOI)
	Breast cancer	Comprehensive cancer panel
	Colon cancer
	Leukemia
	Liver cancer
	Lung cancer
	Ovarian cancer
	Prostate cancer
	Gastric cancer
GeneRead DNAseq Mix-n-Match Panels
	Create your own panel from 124 genes
GeneRead DNAseq Custom Panels
	Create your own panels from any gene(s) from 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 Gene Panels are designed to cover the entire exonic region (UTR + CDS) of any protein coding region of any gene in the human genome. The overlapping PCR products produced by the overlapping primer sets yield greater than 90% coverage of the exonic region of the genes with more than 85% of sequence specificity.

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).

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.