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QIAseq Targeted Methyl Panels

A liquid biopsy-compatible solution for targeting methylation status of DNA, from as low as 1 ng input DNA from cells and tissues, or 10 ng from FFPE samples and liquid biopsies
  • Complete system to go from bisulfite-converted DNA to a sequencing-ready library using a single-day workflow
  • Error correction with Unique Molecular Indices (UMIs) to enhance NGS panel sensitivity
  • A single-primer extension (SPE) approach that increases sensitivity and overcomes targeting challenges compared to other NGS technologies
  • Integrated Sample to Insight analysis solutions with cloud-based QIAGEN GeneGlobe or locally-installed QIAGEN CLC Genomics Workbench software

QIAseq Targeted Methyl Panels offer a single-day solution capable of targeting thousands of CpG sites in the genome. As with targeted DNA panels, QIAseq solutions are based on single-primer extension (SPE) technology that provides a sensitive and specific solution for detecting regions all across the genome.

For customized products, please see our QIAseq Targeted Methyl Custom Panels.

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Cat No./ID: 335501
QIAseq Targeted Methyl Panel (8)
22,415.00 kr
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Kit containing reagents (except bisulfite conversion and indices) for targeted methylation sequencing; fixed panel for a total of 3 reactions, each using 8 samples (3 x 8 samples)

Cat No./ID: 335511
QIAseq Targeted Methyl Panel (96)
197,820.00 kr
Go to GeneGlobe

Kit containing reagents (except bisulfite conversion and indices) for targeted methylation sequencing; fixed panel for a total of 96 samples

Cat No./ID: 335580
QIAseq Methyl DNA 8-Index I
6,120.00 kr
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Box containing indices, enough to process a total of 24 samples, for indexing up to a total of 8 samples for QIAseq Targeted Methyl Panel sequencing runs on Illumina platforms
Cat No./ID: 335591
QIAseq Targeted Methyl 96 Index Set A
13,115.00 kr
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Box containing Set A indices, enough to process a total of 96 samples, for indexing up to a total of 96 samples for QIAseq Targeted Methyl Panel sequencing on Illumina platforms; one of four sets required for multiplexing 384 samples

Cat No./ID: 335592
QIAseq Targeted Methyl 96 Index Set B
13,115.00 kr
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Box containing Set B indices, enough to process a total of 96 samples, for indexing up to a total of 96 samples for QIAseq Targeted Methyl Panel sequencing on Illumina platforms; one of four sets required for multiplexing 384 samples

Cat No./ID: 335593
QIAseq Targeted Methyl 96 Index Set C
13,115.00 kr
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Box containing Set C indices, enough to process a total of 96 samples, for indexing up to a total of 96 samples for QIAseq Targeted Methyl Panel sequencing on Illumina platforms; one of four sets required for multiplexing 384 samples

Cat No./ID: 335594
QIAseq Targeted Methyl 96 Index Set D
13,115.00 kr
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Box containing Set D indices, enough to process a total of 96 samples, for indexing up to a total of 96 samples for QIAseq Targeted Methyl Panel sequencing on Illumina platforms; one of four sets required for multiplexing 384 samples

QIAseq Targeted Methyl Panels are intended for molecular biology applications. These products are not intended for the diagnosis, prevention, or treatment of a disease.

Product Details

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QIAseq Targeted Methyl Panel: methylation degree reproducibility
To test methylation degree accuracy and reproducibility, 40 ng control DNA with 0%, 50% and 100% methylation were processed using the QIAseq Targeted Methyl Panel, which consisted of 749 primers. Samples were sequenced on MiSeq and methylation degree of CpG covered by >30 UMI was evaluated, resulting in accurate and highly reproducible methylation calling.
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QIAseq Targeted Methyl Panel: methylation status of FFPE DNA: methylation degree

To test methylation status of FFPE DNA, the QIAseq Targeted Methyl Panel was used with 40 ng input FFPE DNA. The panel consisting of 93 primers covered 566 CpG sites. The evaluated methylation degree of 7 CpG sites of the MGMT gene highly correlates to the methylation degree that was previously validated with Pyrosequencing.

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QIAseq Targeted Methyl Panel – high correlation with established methods
To test correlation with established methods, the QIAseq Targeted Methyl Panel was used with 40 ng input gDNA from hepatocytes. The panel consisted of 102 primers, covering 71 CpGs. Compared to the Supplier I array, methylation degree resulted in high correlation.
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QIAseq Targeted Methyl Panel: mapping efficiency

Input >1 ng

– gDNA

– FFPE

– ccfDNA

Results show high mapping on primer and high unique mapping.

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QIAseq Targeted Methyl Panel sequencing workflow
QIAseq Targeted Methyl Panel sequencing workflow steps and details.
Performance
Principle

Epigenetics describes the study of heritable changes in gene function that occur without a change in the nuclear DNA sequence. In addition to RNA-associated silencing and histone modification, a major epigenetic mechanism in higher-order eukaryotes is DNA methylation. Epigenetic changes play a crucial role in the regulation of important cellular processes, such as gene expression and cellular differentiation, and were also identified as key factors in various diseases.

DNA methylation occurs on cytosine residues, especially in CpG islands, which are GC-rich regions. They are usually clustered around the regulatory region of genes and can affect their transcriptional regulation. Methylation of CpG islands is known to inactivate gene expression and plays an important role in normal and disease development. Cytosine methylation may also occur in non-CpG content, as described for embryonic stem cells.

QIAseq Targeted Methyl Panels enable Sample to Insight, targeted next-generation sequencing (NGS) to interrogate DNA methylation degree. This highly optimized solution facilitates sensitive DNA methylation detection using integrated Unique Molecular Indices (UMIs) from cells, tissues and biofluids. The required amount of template for a single QIAseq Targeted Methyl sequencing reaction ranges from 1–100 ng for fresh gDNA, 10–200 ng for FFPE DNA or 10–100 ng for ccfDNA.

Procedure

QIAseq Targeted Methyl Panels employ a streamlined workflow (figure QIAseq Targeted Methyl Panel sequencing workflow) for generating focused libraries from multiple input types, including difficult samples such as FFPE and liquid biopsy (ccfDNA). First, bisulfite conversion of isolated DNA is performed (recommended product: EpiTect Fast Bisulfite Kit), followed by DNA end repair. Afterwards, during target enrichment, a Unique Molecular Index (UMI) is added to the DNA library. UMIs are unique barcode sequences that enable bioinformatics analysis to exclude duplicates and error-correct the sample’s methylation status. QIAseq Targeted Methyl Panels utilize single primer extension (SPE), a PCR method that uses a single target-specific primer, with a universal primer. This approach increases the efficiency of design – making it more sensitive for challenging samples, while maximizing the coverage of the regions of interest.

Applications
  • Detection of methylation status from FFPE samples
  • Detection of methylation status from liquid biopsy
  • Detection of cell- and tissue-specific methylation markers

Product Resources

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