# Guidelines for Sample Preparation for Infinium Genotyping Assay DNA input

### **Infinium Assay Sample Input Guidelines**Sample input guidelines:

![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-d02f8e8570974b783033413a836df1e9d604514c%2Fimage1.jpg?alt=media)

Any standard DNA extraction method or kit that provides **high quality** genomic DNA is suitable for Infinium Arrays.

#### **DNA quantity**

* Determine DNA concentration using a double stranded DNA specific fluorometric method (eg, Qubit, Quant-it, PicoGreen) for accurate measurement of double-stranded DNA.
* DNA quantification results from UV spectrophotometric methods do not accurately reflect the concentration of double-stranded DNA and are not recommended.
* Using the quantification values from the Bioanalyzer or Tapestation is not advised.

#### **DNA quality**

* The minimum recommended fragment size is 2 kb.
* Illumina does not provide DNA integrity (DIN) guidelines or cut-offs for DNA input into the Infinium assay. DIN values from a Tapestation or BioAnalyzer can be used to assess DNA quality, but are not required.
* The presence of RNA in samples does not interfere with the Infinium assay.
* UV spectrophotometry can be used to assess DNA purity and quality. Consider standard purity specifications:
  1. Protein/RNA free: 260/280 ratio >1.85
  2. Solvent free: 260/230 ratio >2.0
  3. Phenol free: no peak at 270 nm

EDTA is generally introduced through sample treatment or extraction method, and the presence of EDTA can affect the 260/280 and 260/230 ratio values. EDTA can affect enzyme activity during the initial amplification step of the Infinium assay, so it is recommended to reduce EDTA concentration or use Tris-HCl or nuclease free water as the elution buffer. For additional information, see Knowledge Base article [DNA/RNA isolation considerations for Illumina Library Preparation Kits](https://knowledge.illumina.com/library-preparation/general/library-preparation-general-reference_material-list/000001249). The information in this article can apply to DNA input preparation for Infinium arrays.

### **Recommendations for processing low quality DNA in the Infinium Assay**

FFPE samples generally yield highly degraded DNA and typically perform poorly in array-based applications such as whole-genome genotyping. Consider using the [Infinium FFPE QC and DNA Restoration Kits](https://www.illumina.com/products/by-type/molecular-biology-reagents/infinium-ffpe-qc-dna-restoration.html), which were designed for processing FFPE samples but can also be used on DNA degraded for other reasons.\
The Infinium FFPE QC Kit:

* Uses a real-time PCR assay to evaluate the quality of prospective DNA samples.
* Determines whether the DNA samples are suitable for the restoration step.
* Is only compatible with human samples.

The Infinium HD FFPE DNA Restore Kit:

* Restores degraded DNA to an amplifiable state that can be used as input for the Infinium assay.
* Is compatible with samples from any species.

For further information, refer to the following resources: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)

Knowledge Base articles:

* [Infinium Assay Modifications for FFPE samples for Genotyping Arrays](https://knowledge.illumina.com/microarray/general/microarray-general-faq-list/000006007)
* [DNA Input Guidelines for Infinium MethylationEPIC Arrays](https://knowledge.illumina.com/microarray/general/microarray-general-reference_material-list/000002679)
* [Infinium EX Methylation DNA input guidelines and compatible bisulfite conversion kits](https://knowledge.illumina.com/microarray/general/microarray-general-reference_material-list/000008604)

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