Infinium Assay Modifications for FFPE Samples Used with Genotyping Arrays

Formalin-fixed, paraffin-embedded (FFPE) samples yield highly degraded DNA and typically perform poorly in array-based applications.

To improve sample performance, Illumina recommends using the Infinium FFPE QC and DNA Restoration Kits when processing FFPE samples on Infinium Genotyping Arrays.

• The Infinium FFPE QC Kit uses a real-time PCR assay to assess the quality of extracted DNA from FFPE samples.

• Extracted FFPE samples that pass the QC assessment are eligible for restoration using the Infinium HD FFPE Restore Kit.

After completing the DNA QC and restoration steps, follow the Infinium Assay Modifications for Genotyping Arrays as outlined in the technical note Analyzing FFPE Samples with Infinium Microarrays.

For both manual and automated workflows, the amplification step must be performed as instructed in the manual protocol with the following modifications:

Infinium HD Super Protocol:

To prepare the MSA1 plate ("Make MSA1 Plate" step), add 8 μl of the repaired sample DNA to each corresponding wells in the MSA1 plate, instead of the standard 4 μl.

Infinium HTS and HD Ultra Protocols:

To prepare the MSA3 plate ("Make MSA3 Plate" step), add 8 μl of the repaired sample DNA to each corresponding wells in the MSA3 plate, instead of the standard 4 μl.

Infinium LCG Protocol:

To prepare the MSA6 plate ("Make MSA6 Plate" step), add 8 μl of the repaired sample DNA to each corresponding wells in the MSA6 plate, instead of the standard 4 μl.

Note: No other changes to reagent volumes are required. Use the standard protocol volumes of reagents for all subsequent steps and reactions.

Reference:

Infinium HD Methylation assay workflow for fresh/frozen versus FFPE samples Modifications to the Infinium Methylation workflow

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