QIAseq Multimodal DNA/RNA Library Kit

• Simultaneous WGS and WTS library preparation from a single sample (compatible with various types)
• Integrated UMIs for both DNA and RNA libraries for enhanced sensitivity
• Compatible with downstream hybrid capture based target enrichment
• Integrated QIAseq FastSelect –rRNA HMR removal for optimized performance
• Single day workflow from samples to sequencing libraries

The QIAseq Multimodal DNA/RNA Library Kit allows the construction of whole genome sequencing (WGS) and whole transcriptome sequencing (WTS) libraries from either total nucleic acids or separately isolated DNA and RNA. Each molecule is tagged with a unique molecular index (UMI), enhancing the accuracy of sequencing data. Ideal for sensitive detection of DNA and RNA biomarkers such as single nucleotide variants (SNVs), insertion-deletion (InDels), copy number variations (CNVs), fusions, exon skipping events and gene expression levels, this kit is well-suited for studies involving cells, tissues (fresh, frozen and FFPE) and biofluids across various fields such as cancer and genetic research. This kit enables multiomic studies using different modalities for comprehensive understanding of molecular biology of genetic variations, leading to deeper and wider insights.

Enables the preparation of DNA and RNA libraries from total nucleic acid with a single-day workflow and high flexibility

The QIAseq Multimodal DNA/RNA Library Kit is designed for versatility, enabling the construction of both DNA and RNA libraries from a single sample (mix of DNA and RNA) within 6 hours. The generated DNA and RNA libraries can be sequenced directly or subjected to target enrichment by hybrid capture, such as exome and comprehensive genomic profiling (CGP) panels, making it suitable for a broad range of applications (see "QIAseq Multimodal DNA/RNA Library Kit workflow").

This kit can also be used for DNA-only and RNA-only workflows with a wide range of inputs of various sample types. The optional use of UMIs on the DNA library makes it suitable for WGS and whole exome sequencing (WES), as well as other target enrichment that require a higher sensitivity (see "The QIAseq Multimodal DNA/RNA Library Kit offers flexibility for many downstream applications").

DNA libraries generated with the QIAseq Multimodal DNA/RNA Library Kit show high library complexity and uniform coverage

Similar to the QIAseq FX DNA Library Kit, the QIAseq Multimodal DNA/RNA Library Kit generates DNA libraries with minimal GC bias by using sequence-independent enzymes for fragmentation. The presence of RNA in the initial sample did not decrease the overall performance. 

RNA libraries generated with the QIAseq Multimodal DNA/RNA Library kit showed high performance for whole transcriptomic analyses 

The use of QIAseq FastSelect –rRNA HMR Kit is highly efficient with only traces of ribosomal RNA (rRNA) remaining, making the RNA libraries suitable for WTS and better specificity of target enrichment using the hybrid capture technology (see "Performance of WTS library generated using QIAseq Multimodal DNA/RNA Library Kit"). The RNA libraries generated with the QIAseq Multimodal DNA/RNA Library Kit are suitable for complete transcriptomics, including gene expression analysis, as well as fusion detection.

Broad compatibility with various hybrid capture panels, maintaining reliable performance

DNA and RNA libraries can be subjected to target enrichment using hybrid capture technology and are compatible with the QIAseq xHYB Human Panels, as well as panels from other providers (see "WES performance of libraries generated with QIAseq Multimodal DNA/RNA Library Kit"). They can be used to detect large genomic rearrangements, SNVs, InDels and CNVs. 

Allows for the detection of fusions after target enrichment using hybrid capture technology

The RNA libraries generated can be used to detect expressed fusion genes and exon-skipping events (see "Target enrichment of the WTS libraries with the QIAseq xHYB Human Hybrid Capture Panel"). 

QIAseq blocking oligos show higher specificity compared with other blocking oligos

The QIAseq blocking oligos can be used during the hybrid capture workflow on libraries including TruSeq-adpater sequences (One-4-All Blocking Oligos) or on libraries including Nextera-adapter sequences (QIAseq N Blocking Oligos). The specificity obtained is higher than that obtained with blocking oligos from other providers (see "QIAseq blocking oligos show higher specificity compared with other blocking oligos"). 

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Multiomic studies have been increasingly adopted by the scientific community due to the greater insights generated by combining information from different modalities. Existing methods for interrogating DNA and RNA simultaneously have limitations, including the large amount of input samples required for separate DNA and RNA workflows, labor-intensive library preparation procedures, long turnaround time, etc.

The QIAseq Multimodal DNA/RNA Library Kit is designed with exceptional versatility. It can be used for generating DNA-only or RNA-only libraries, enabling labs to consolidate their workflow by reducing WGS and WTS library preps to a single kit, with compatibility with a wide range of input samples, such as tissue (fresh, frozen and FFPE), blood, and cfDNA. Furthermore, for DNA libraries, the use of UMI is optional (non-UMI and UMI adapters are both included in the kit; this option is included in the workflow). The UMI adapter option will allow higher sensitivity, which is required for specific applications. 

For RNA library construction, the kit uses UMIs for error correction, incorporates QIAseq FastSelect –rRNA HMR Kit to deplete rRNA and enable low-input compatibility, and includes a step to eliminate any remaining DNA before starting the reverse transcription process. This method ensures high-quality, reliable results, supporting more effective multiomic studies.

Overview of QIAseq Multimodal DNA/RNA Library Kit workflow

Nucleic acid fragmentation

In the QIAseq Multimodal DNA/RNA Library Kit, RNA molecules undergo heat fragmentation while DNA molecules are processed through enzymatic fragmentation, end-repaired, and A-tailed within a single multienzyme reaction. This step also integrates ribosomal rRNA removal using the QIAseq FastSelect –rRNA HMR Kit.

RNA polyadenylation

For RNA samples, synthetic polyadenylation is performed to create a binding site essential for the subsequent reverse transcription step.

DNA ligation

Specific to DNA, adaptors are ligated to the DNA fragments. Two adapter options are provided. 

• The non-UMI adapter does not contain a UMI 
• The UMI adapter includes a 14-base fully random UMI sequence and is additionally phased for optimal base diversity during sequencing.

For hybrid capture, the use of One-4-All Blocking Oligos (available separately or included in the QIAseq xHYB Human Reagent Kit) is recommended to block TruSeq adapter sequences effectively. These libraries are compatible with QIAseq Human Exome, QIAseq xHyb Human catalog and custom panels or third-party probes.

Reverse transcription and template switching

Specific to RNA, reverse transcription and template switching are performed. UMIs (random 10-base sequences) are incorporated in this step. If using hybrid capture for RNA libraries, which use Nextera adapter sequences, it is advisable to use QIAseq N Blocking Oligos (sold separately and not included in QIAseq xHYB Human Reagent Kit) to effectively block the adapters.

Library amplification/indexing

Separate universal PCR reactions are performed on DNA and RNA libraries to incorporate unique dual indices (UDI) for each library, ensuring accurate sample identification and minimizing the risk of cross-contamination.

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QIAseq Multimodal DNA/RNA Library Kit can be used for multiomic sequencing studies from a single sample, including WGS/WTS and hybrid capture based target enrichment, such as WES or CGP.  Variants from DNA and RNA include the following: 

• DNA: SNVs, InDels, CNVs
• RNA:  differential gene expression, fusions, exon skipping events.

Data Analysis

Data from QIAseq Multimodal DNA/RNA Library Kit can be analyzed using the QIAGEN CLC Genomics Workbench, which allows optimization of analysis parameters. All detected variants can be further interpreted using QIAGEN Clinical Insight – Interpret (QCI-I) for QIAseq.