- Which buffer is recommended for DNA storage?
- What quality of DNA is needed for genotyping?
- Which amounts of genomic DNA are needed for genotyping?
- How do I need to determine the concentration of my DNA?
- Can you assay all SNP classes (A/T, C/G, A/C, A/G, T/C, T/G) in your genotyping setting?
- Can you identify tag SNPs for me?
- Can I use whole-genome amplified DNA for genotyping?
- Can I use formalin-fixed paraffin-embedded samples for genotyping?
- What are the call rates for Infinium genotyping?
- Can I ad SNPs/customize the Infinium assay according to my demand?
- At what point is it efficient to customize Infinium BeadChips?
- What criteria should I use for LOH/CNV analysis?
TE buffer with a composition of 10 mM Tris, pH7.5; 1 mM EDTA.
Our platform works best with relatively intact, high-quality DNA. For the Infinium Assay, we recommend fragment sizes of at least 2kb.
For Infinium assays we require a minimum of 0,6 Âµg (12 Âµl at 50 ng/Âµl)
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.
Yes, all biallelic SNPs can be assayed by the Infinium and GoldenGate technology.
You may provide either a list of rs numbers, sequences, regions (by coordinate) of interest, or a gene list.
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.
Yes, thatâ€™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.
The call rates for Infinium BeadChips are routinely >99%.
Yes there are possibilities for adding additional SNPs to Human OmniExpress+ BeadChip. Please contact us for more details.
You should have at least 100 samples or more to consider customization of Infinium BeadChips.
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.