What is the amount of DNA you need for a genotyping experiment and what are the quality requirements of the sample?
ServiceXS requires a minimum input of 2 µg DNA, 40 µl of volume and a normalized concentration of 50 ng/µl for the Illumina GoldenGate assay as well as the Infinium Assay. We ask you to determine the concentration of your DNA samples (recommended is the PicoGreen assay). Dilute the DNA concentration to 50 ng/µl in 10mM Tris/1nM EDTA pH=8 (TE). Perform a quality check on a 1% agarose gel. For the Infinium assay, fragments must be at least 2kb. The GoldenGate assay can tolerate fragments >200bp.
Contact ServiceXS upfront when the above mentioned sample requirements cannot be met. ServiceXS does not accept whole-genome amplified samples.
Is ServiceXS able to call SNP classes (A/T, C/G, A/C, A/G, T/C, T/G)?
Yes, we are able to distinguish all SNPs, from the more common ones to rare mutations.
What call rates can ServiceXS guarantee for custom GoldenGate genotyping?
For GoldenGate projects, ServiceXS does not guarantee a sample success rate or call rate as for custom OPA design, the locus conversion rate is highly dependent on the quality of genotyping assays that are chosen by the customer. However, ServiceXS closely monitors all relevant quality control parameters associated with GoldenGate performance. Generally a sample success rate of 90% for custom GoldenGate genotyping assay can be expected.
Does ServiceXS also perform RNA or DNA isolation?
No. ServiceXS does not do RNA or DNA isolations, but we can advise you on isolation kits to use. We recommend the Macherey-Nagel RNA isolation kit. For customers in BeNeLux, ServiceXS recommends products supplied by BIOKÉ.
What standard panels are available for GoldenGate genotyping?
Illumina has the following fixed panels: LinkageIVb, Mouse LD Linkage, MHC Panel Set, Cancer Panel, DNA Test Panel. For the most up-to-date list, contact ServiceXS or visit the Illumina website.
Can LOH (Loss of heterozygosity) and CN (Copy Number) analysis be performed with the GoldenGate genotyping assay?
LOH and CNV have only been validated using the Infinium assay. Illumina does not support interpretation of LOH/CNV data on the GoldenGate genotyping assay. Only with custom oligo assay pools (OPAs) with high density/resolution can an indication of LOH/CNV be generated.
If I want to detect chromosomal aberrations such as LOH or CNV, what should I take into account when designing my Beadchip?
When designing the BeadChip, keep in mind that you need sufficient high density of SNPs to detect changes of interest. Contact ServiceXS if you need help with designing the assay. Another difference compared to the GoldenGate assay, is that with Infinium, the effect of underlying polymorphisms is not critical to overall performance.