QIAseq xHYB Human Hybrid Capture Panels

• Panels for covering HGMD-curated whole genes and protein coding sequences (CDS)
• Single-day workflow with hybrid capture flexibility ranging from 30 minutes to overnight
• Reduced fold-80 base penalty that maximizes on-target coverage and lowers sequencing cost
• Eliminate data bottlenecks and reduce overall turnaround time with rapid data analysis and variant interpretation

The QIAseq xHYB portfolio consists of multiple large panels targeting genomic regions with known relevant genomic variants. The content has been built by leveraging variant information from the Human Gene Mutation Database (HGMD) and delivers high coverage of regions in over 10,000 genes. Optimized probe design provides efficient coverage of even the most challenging genomic regions, such as high GC-content regions.

QIAseq xHYB Human Portfolio is able to maximize read utilization and reduce sequencing costs by up to 50%, while providing high-quality SNV, indel and CNV calls from a curated design. The panel delivers 99% base-level coverage at ≥20x depth, enabling >98% combined sensitivity for SNVs and indels, while minimizing dropouts. The single-day, automation-compatible sample-to-sequencing workflow is >33% faster than other exome workflows, and delivers exceptional coverage uniformity with variable hybridization times, in as little as 30 minutes (even from FFPE and cfDNA samples).

The portfolio consists of curated content associated with exome-wide variants in the QIAseq xHYB Actionable Exome Panel and over 400 genes related to carrier status with the QIAseq xHYB Carrier Panel. In addition, a spike-in for the full mitochondrial genome is available with the QIAseq xHYB Mitochondrial Panel. The automation-friendly workflow can also be supplemented with the QIAseq xHYB Automation Kit, which provides all the consumables needed for enrichment. This kit functions to support a broad range of requirements across any automation platform.

Pre-capture libraries are prepared with UDI-enabled QIAseq FX library preparation reagents, which enzymatically generate up to 384 unique dual-indexed libraries with a 2.5 hour workflow. Expanded compatibility with other sample types is also enabled with QIAseq cfDNA Library Kits and QIAseq Ultralow Input Library Kits. Library kits are purchased separately, see below. Exome enrichment is carried out using QIAseq Human Exome Kits, which include exome probes, streptavidin beads, and enrichment and amplification reagents.

The QIAseq xHYB Portfolio delivers exceptional coverage uniformity regardless of the panel content’s GC composition of the targets, facilitating >99% base-level coverage of targets at ≥20x, and driving the comprehensive and sensitive detection of variants (>98% combined sensitivity for SNVs and indels) while minimizing drop-out.

The QIAseq Human Exome provides:

• Maximized read utilization resulting in up to 50% reduction in sequencing costs
• A single-day, automation-compatible sample to sequencing workflow that is at least 33% faster than other exome workflows
• Pre-optimized analysis and variant interpretation workflows that reduce the burden of interpreting the tens of thousands of variants that result from exome sequencing

CNV detection is readily enabled due to the exceptional coverage uniformity provided by the panel in combination with the pre-optimized QIAseq Human Exome workflow within QIAGEN CLC Genomics Workbench. This approach delivers additional information not readily achievable with other commercially available exome sequencing solutions.

Exome and other types of comprehensive genomic profiling (CGP) has been widely adopted in the last 10 years as an efficient way of screening the genome for disease-associated mutations. By focusing reads on curated coding regions, which harbor >80% of disease-causing mutations, the probability of identifying variants associated with disease is increased. At the same time, the amount of sequencing required is reduced by 99% compared to whole genomes, significantly minimizing the cost of sequencing.

The method is built upon the hybrid capture approach for target enrichment where probes, complementary in sequence to its targets, are designed and function as baits to “fish out" its target from a library of DNA molecules. Once the probes are hybridized to their targets, these probe-target hybrids are then bound to streptavidin-coated magnetic beads through interaction with the biotin label on the probes. A magnet is then used to keep these beads with the probe-target hybrids on the side of the tube while the rest of the DNA that is not of interest, is washed away, reducing off-target effects. After washing away unbound DNA, the targets are then amplified and prepared for sequencing.

Once the pre-capture libraries are generated, the libraries are hybridized to the exome probes. After hybridization, probe-target hybrids are then bound to streptavidin-coated magnetic beads and washed for stringency. Exome-enriched libraries are then amplified and prepared for sequencing on Illumina systems. Resulting FASTQ are uploaded into the QIAseq Human Exome workflow within the QIAGEN CLC Genomics Workbench for filtering, read mapping and variant calling. VCF output is then uploaded into QIAGEN Clinical Insight for QIAseq, which enables a variant filtering cascade that facilitates prioritization of variants for evidence-based interpretation.

The QIAseq xHYB Portfolio provides a scalable single-day, automation-compatible workflow that is adaptable to your unique needs or requirements of your application. Compatible with high-quality DNA, as well as cfDNA and DNA from FFPE samples, exceptional coverage uniformity and high-performance variant calling are achieved with variable hybridization times.

The QIAseq xHYB Portfolio leverages the QIAseq FX library preparation for generating highly complex, unbiased libraries, even from samples of lower quality, such as DNA derived from FFPE, in only 2.5 hours. Additionally, QIAseq xHYB products are compatible with QIAseq cfDNA library preparation. Libraries can be generated from enzymatically fragmented genomic DNA, physically sheared genomic DNA, as well as from circulating cell-free (ccf) DNA. Depending on the DNA input type, we recommend using the following library preparation kits: QIAseq FX DNA Library Kits, QIAseq Ultralow Input Library Kits and QIAseq cfDNA Library Kits (see the QIAseq Human Exome Handbook for more information).

The QIAseq xHYB Portfolio uses a hybridization capture-based target enrichment approach to specifically enrich curated sequences of the human genome associated with known variants from indexed whole genome libraries. The flexible workflow allows simultaneous hybridization capture from up to 8 samples with as little as 200 ng input per library.

Widespread adoption of exome sequencing has fueled many different, more cost-effective approaches to disease-based research. QIAseq Human Exome Kits can be used in a variety of applications that utilize exome sequencing, such as:

• Disease gene identification for rare and inherited disorders
• Population genetics and carrier screening
• Study of human disease pathways and mechanisms
• Study of pathogenic infection mechanisms

Disease gene identification and mutation analysis for rare and inherited disorders

Whole exome sequencing for rare disorders can be undertaken either as single exomes (proband [affected]-only) or as trio sequencing. Though the proband-only approach is more cost-effective, this typically results in a much higher number of variants compared to trio sequencing where both the biological parents are also sequenced in order to rule out private mutations and Mendelian inconsistencies, thereby narrowing down the set of variants for further investigation.

For mutation analysis in inherited disorders, exome sequencing is also becoming a widely used approach. By adopting an exome as a large panel from which disease-based gene sets can be screened, laboratories end up saving on reagent costs. In addition, labs can implement more standardized workflows, especially for automation, which decreases the introduction of type II errors. Furthermore, with the rapidly growing body of knowledge around human disease, the need to constantly update panels is mitigated by having an exome as a base panel since the exome already accounts for all the coding regions in the human genome.

Population genetics and carrier screening

The study of the pathogenesis of rare and complex diseases is complicated by the contribution of rare alleles that may exist in specific populations and variants that have a wide spectrum of allele frequencies that vary by ethnicity. Exome sequencing has been a tool widely used to profile various populations for such variants in order to better understand their frequencies within these specific groups. This enables better quantification of carrier risks, especially for debilitating diseases, enabling couples to plan better and make informed decisions, and for understanding susceptibility to the more common disorders that affect overall quality of life and/or impact lifetime healthcare costs.

Study of human disease pathways and mechanisms

The utility of exomes extends beyond just identifying the disease-causing variant. In the effort to understand the mechanisms that feed into and regulate the pathways that are directly implicated in disease progression, typically with the intent to target them for treatment, exomes have also become a useful tool in conjunction with transcriptome sequencing. By sequencing the exome, other variants that may be acting as modifiers can be identified, thereby highlighting candidate regulatory pathways.

Study of pathogenic infection mechanisms

Bacterial or viral infection mechanisms, as well as what makes people susceptible to infection, are important to understand in order to design preventive and therapeutic measures to counteract the spread of disease. Exome sequencing provides an approach for helping identify mutations within proteins, either expressed at the cell-surface or involved in other transport mechanisms, that may provide a path for the pathogen to enter and thrive within the human host environment. These types of studies are structured very similarly to population studies wherein results are correlated with metadata on the disease within the population in order to establish significant results.