FFPE Sample Analysis

Simple Analysis of FFPE Samples

Specifically designed to meet the challenges of utilizing formalin-fixed, paraffin-embedded (FFPE) samples for genetic analyses, the Illumina portfolio of FFPE solutions provides a comprehensive range of FFPE sequencing and microarray applications. These solutions leverage optimized workflows and technologies for FFPE samples, which generally contain partially degraded or limited genomic material. Researchers can now analyze previously inaccessible samples to derive high-quality genomic data and insight. Simple preparation methods, innovative next-generation sequencing and array platforms, and intuitive data analysis tools facilitate FFPE sample sequencing and array studies.

QC Method for FFPE Sequencing

A novel QC approach enables researchers to sequence degraded DNA from FFPE tumor samples successfully.

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Targeted DNA Sequencing

Targeted sequencing focuses on a select set of genes or gene regions that are chosen based on a priori knowledge. By sequencing targeted DNA regions, researchers can perform cost-effective, high-depth sequencing with a streamlined data analysis pipeline.

To facilitate targeted cancer FFPE sequencing studies, Illumina offers fixed panels for guaranteed performance, and custom amplicon solutions where researchers can choose their amplicons of interest.

TruSight Oncology 500: Assay targeting multiple variant types, including tumor mutational burden (TMB) and microsatellite instability (MSI), even from low-quality samples.

TruSight Tumor 15 enables molecular profiling studies of solid tumor specimens from FFPE tissue samples, delivering a high level of sensitivity for minor allele detection.

AmpliSeq for Illumina Cancer HotSpot Panel v2: Targeted research panel for investigating hotspot regions of 50 genes with known associations to cancer.

AmpliSeq for Illumina Comprehensive Cancer Panel: Targeted research panel for investigating the exonic regions of 409 genes with known associations to cancer.

FFPE Sample QC Recommendations

Extraction methods for FFPE tissue generally yield highly degraded DNA and RNA. Read our FFPE quality control recommendations to determine whether your FFPE samples are viable input material for Illumina library preparation kits.

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FFPE Sample QC Recommendations

RNA Sequencing

Accurately measure gene expression at the transcript level and discover gene fusions with our portfolio of RNA sequencing (RNA-Seq) library prep kits for FFPE sequencing studies.

Learn More About FFPE RNA-Seq
Sequencing FFPE Tumor Samples

Researchers sequence challenging FFPE cancer samples to identify driver genes and novel biomarkers.

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Featured RNA-Seq Solutions

The TruSight RNA Pan-Cancer Panel enables comprehensive detection of 1385 gene fusions and gene expression changes, providing researchers with a focused view of the functionally relevant changes occurring in cancer. The panel is compatible with FFPE tissue and accommodates as little as 20 ng of total RNA input from FFPE. The TruSight RNA Pan-Cancer Panel provides a sensitive, reproducible, and economical solution for studies of expression dynamics and functional mechanisms in cancer.

TruSight Oncology 500: Assay targeting multiple DNA and RNA variant types, including tumor mutational burden (TMB) and microsatellite instability (MSI), even from low-quality samples.

Illumina RNA Prep with Enrichment allows you to achieve rapid, targeted interrogation of an expansive number of target genes with exceptional capture efficiency and coverage uniformity.

Illumina Stranded Total RNA Prep with Ribo-Zero Plus offers rapid library preparation from a broad range of sample types for studying the coding and non-coding transcriptome with unparalleled study flexibility.

Targeted RNA Sequencing is an accurate and economical method for measuring dozens to thousands of RNA targets simultaneously, making it ideal for confirming findings from gene expression arrays and RNA-Seq studies.

Genotyping FFPE Samples

Illumina custom, semi-custom, and commercially available arrays can be used to genotype FFPE samples. This workflow utilizes the Infinium FFPE DNA Restoration Solution, which simplifies upfront sample processing by identifying samples of sufficient quality and repairing the damaged DNA in the samples for downstream genotyping.

Learn More About Genotyping

Methylation Arrays

Methylation arrays enable quantitative interrogation of selected methylation sites across the genome at single-nucleotide resolution. Illumina methylation arrays provide a unique combination of comprehensive, expert-selected coverage, FFPE sample compatibility, high sample throughput, and an affordable price.

Explore Methylation Arrays

Recent Developments in Cancer Research

The spatial multiomics revolution
The spatial multiomics revolution

NanoString Technologies and Illumina to discuss benefits of whole transcriptome spatial analyses at AGBT


Future Medicine Research InstituteのChief ResearcherであるSookyoung Kim氏がIllumina DNA Prep with Exome 2.0 Plus Enrichmentの評価結果について語ります。


AJ Patelは6カ月生存しました。8年後、彼はバイオマーカー検査がいかにすべてを変化させたか、私たちに話してくれました。

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