Infinium Assay Modifications for FFPE samples for Genotyping Arrays

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

Illumina recommends the Infinium FFPE QC and DNA Restoration Kits when running FFPE samples on Infinium genotyping arrays.

• The Illumina FFPE QC Kit uses a real-time PCR assay to evaluate the quality of prospective DNA samples.

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

After DNA QC and Restore, follow the Infinium Assay Modifications for Genotyping arrays as described 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), 8 μl of the repaired sample DNA, instead of the standard 4 μl, are added to the corresponding wells in the MSA1 plate.

• Infinium HTS and HD Ultra Protocols: To prepare the MSA3 plate ("Make MSA3 Plate" step), 8 μl of the repaired sample DNA, instead of the standard 4 μl, are added to the corresponding wells in the MSA3 plate.

• Infinium LCG Protocol: To prepare the MSA6 plate ("Make MSA6 Plate" step), 8 μl of the repaired sample DNA, instead of the standard 4 μl, are added to the corresponding wells in the MSA6 plate.

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

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