Which buffer is recommended for DNA storage?

TE buffer with a composition of 10 mM Tris, pH7.5; 1 mM EDTA.

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What quality of DNA is needed for genotyping?

Our platform works best with relatively intact, high-quality DNA. For the Infinium Assay, we recommend fragment sizes of at least 2kb.

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Which amounts of genomic DNA are needed for genotyping?

For Infinium assays we require a minimum of 0,6 µg (12 µl at 50 ng/µl)

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How do I need to determine the concentration of my DNA?

We recommend Picogreen assays, as this method is highly accurate for double stranded DNA (please contact us for support if needed). Alternatively, you might quantify your genomic DNA using a Nandrop system. In this case you need to make sure that your DNA is not too viscous and you need to apply 2 microliters for each measurement. Using the Nandrop you want to measure each DNA twice.

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Can you assay all SNP classes (A/T, C/G, A/C, A/G, T/C, T/G) in your genotyping setting?

Yes, all biallelic SNPs can be assayed by the Infinium and GoldenGate technology.

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Can you identify tag SNPs for me?

You may provide either a list of rs numbers, sequences, regions (by coordinate) of interest, or a gene list.

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Can I use whole-genome amplified (WGA) DNA for genotyping?

We do NOT recommend using WGA samples as input for the Infinium assays at all. It has been reported that up to a 4% decrease in call rate was observed (information from Illumina). The decrease in call rate will vary depending on the specific sample and WGA method used. Additionally, any allelic bias present in the original WGA sample may be compounded by another WGA reaction.
Please refer to the Illumina technical note on this subject, entitled "Using Whole-Genome Amplified (WGA) DNA Samples in the GoldenGate Genotyping Assay" before deciding about your genotyping experiment. You might also like to review Barker et al., (2004), who have evaluated different WGA methods for the amplification of genomic DNa during sample preparation.

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Can I use formalin-fixed paraffin-embedded (FFPE) samples for genotyping?

Yes, that’s possible for many Infinium assays. Nevertheless, decreased call rates from FFPE samples compared to genomic DNA samples may be observed and the decrease in call rate depends on the level of sample degradation.

What are the call rates for Infinium genotyping?

The call rates for Infinium BeadChips are routinely >99%.

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Can I add SNPs or customize the Infinium assay according to my demand?

Yes there are possibilities for adding additional SNPs to Human OmniExpress+ BeadChip. Please contact us for more details.

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At what point is it efficient to customize Infinium BeadChips?

You should have at least 100 samples or more to consider customization of Infinium BeadChips.

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What criteria should I use for LOH/CNV analysis?

You should consider density, physical spacing, and Minor Allele Frequency (MAF). Loci with high MAF (~ 0.5) may be more informative than rare polymorphisms for this type of analysis. The control set must match the test sample population (MAF). You must have control samples with minimal amounts of chromosomal aberrations.

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last update:
25/02/2019
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