Genomic DNA for SNP Genotyping
- Genomic DNA concentrations should be the same for all samples. Samples should be free of phenol residue as seen by an absorbance at 270 nm on NanoDrop. The 260/280 and 260/230 OD ratio of DNA should be at least 1.7 to 2.
- Genomic DNA must be run on an agarose gel (e.g. 150 ng/sample on a 1% gel). Samples should not have fragments that run below 2 kb. If a gel cannot be run, a note of permission to process without gel image should be included with the sample submission. Whole genome amplified (WGA) samples will have reduced genotype call rates. WGA samples are processed at the user's own risk.
- Genomic DNA should be diluted in TE buffer (10 mM Tris, 1mM EDTA, pH 8.0).
- Illumina projects: Genomic DNA should be submitted in 96-well plates. All samples should be at the same concentration (70 ng/ul). If submitting in a 96-well plate, PLEASE load samples in columns (vertically) as opposed to across the plate (rows/horizontally). This removes complexity involved in assembling the amplification plate. Please provide an electronic file with sample identities and plate coordinates.
- Illumina projects: Due to pre‐packaged reagent limitations samples should be submitted in multiples of 16 (e.g. 16, 32, 48, etc.).
- Sequenom projects: Genomic DNA can be submitted in either 1.5 ml microfuge tubes or 96-well plates. If submitting in a 96-well plate, PLEASE load samples in rows (horizontally) and leave 2 wells blank. This removes complexity involved in assembling the amplification plate. Please provide an electronic file with sample identities and plate coordinates.
- Sequenom SNP submission: “rs” numbers should in a single column in excel or text (.txt) format.
- For very large projects, users are encouraged to run some test samples in the first plate that are indicative of various DNA extraction techniques used for sample collection. For example, if some samples contained in the project originate from whole blood and some from buccal swabs, running test samples from both sets would ensure that there were no differences in assay performance between extraction techniques.
- It is the responsibility of the user to collect any unused sample from us within 60 days of receiving the data. Samples will be discarded without notice after this timeframe.
|platform||assay||min. amount||min. conc. by spec|
|illumina||infinium HD, LCG||> 1 ug||= 70 ng/ul|
|illumina||infinium methylation beadchip||> 1 ug||= 70 ng/ul|
|illumina||golden gate||> 1 ug||= 70 ng/ul|
|nimblegen||genotyping||> 2.5 ug||> 1 ug/ul|
|nimblegen||genotyping hyb only||> 13 ug||> 1 ug/ul|
|sequenom||genotyping||> 200 ng||> 10 ng/ul|