# 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](https://www.illumina.com/products/by-type/molecular-biology-reagents/infinium-ffpe-qc-dna-restoration.html) when running FFPE samples on Infinium genotyping arrays.

* The Illumina (Infinium) 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](https://www.illumina.com/content/dam/illumina-marketing/documents/products/technotes/technote-infinium-ffpe-sample-analysis.pdf).

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.

\
\
\ <br>

|                                                                                                                                                                                                                                                                                                                                                                   |
| :---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: |
| *For any feedback or questions regarding this article (Illumina Knowledge Article #6007), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000006007%20-%20Microarray%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |


---

# Agent Instructions: Querying This Documentation

If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question.

Perform an HTTP GET request on the current page URL with the `ask` query parameter:

```
GET https://knowledge.illumina.com/microarray/general/microarray-general-faq-list/000006007.md?ask=<question>
```

The question should be specific, self-contained, and written in natural language.
The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.