SNP Genotyping

The GSR provides SNP genotyping and mutation detection services on several different platforms depending on the size and scope of your project. 

  • Whole Genome (GWAS) - Illumina BeadChips
  • Targeted, high throughput – Sequenom iPLEX and Illumina Goldengate
  • Targeted, few mutations or SNPs – TaqMan and SYBR green PCR assays

Whole Genome:

The Infinium HD products include the HumanOmni family of BeadChips. The Illumina BeadChips provide a broad spectrum of whole-genome DNA Analysis products to support a variety of experimental designs.  Researchers have the flexibility to use panels of 700,000 to nearly 5,000,000 markers per sample, depending on their study goals. All of these BeadChips provide powerful and integrated genome-wide SNP genotyping, LOH and CNV detection.

 

BeadChip

Array Format

Markers per Sample

HumanOmni5-Quad

4

~ 4.3 million

HumanOmni2.5S

8

~ 2.5 million

HumanOmni2.5-8

8

~ 2.5 million

HumanOmni1S

8

~ 1.25 million

HumanOmni1-Quad

4

~ 1.1 million

HumanOmniExpress

12

~ 700,000

HumanCytoSNP-12

12

~ 300,000

Sample Requirements:500ng DNA calculated using the picogreen assay (not a NanoDrop) and A260:280 of 1.7-2.0 is required for Infinium array services unless the user agrees to assay these samples at their own risk.  Investigators can retain the labs services to quantitate the DNA after which time only samples meeting stringent QC will be genotyped.

 

Targeted 10-300 SNP and mutations:

Agena – Targeted SNP genotyping using Agena iPLEX is best suited for genotyping 50s - 1000s of samples for 10s-300s of SNPs. All assays are performed in 384 well plates, so sample sizes (4 x 96 well, 8 x 96 well, etc.) that fill these plates are most efficiently assayed.  Currently, multiplexing permits determination of up to 30 SNPs in a single well of a 384 well plate.  Orders consisting of < 20 SNPs are more expensive per genotype than larger projects because smaller SNP sets usually lead to lower plexes which results in an increased cost per SNP-genotype. Thus, after the assay design stage, we provide a statement of work for the customer to allow him/her to decide which SNP assays should be run, providing information on the efficiency of the SNP pools designed, the number of samples and a per sample-genotype cost. Orders with low sample numbers with any number of SNP assays are possible using the Agena MassARRAY platform but they require special DNA plate layout to be cost effective. Contact us for details.

The costs are dependent on the number of samples assayed and the number of SNP assays designed.  Once a project begins, we will not accept additional SNPs into the existing assays.  Any new SNPs can be included in a separate project with their own associated costs.  Our targeted Agena genotyping service includes primer and assay design through to production of SNP genotypes.  Each project cost will be calculated on an individual basis, but the following is a breakdown by plate & SNP.

Sample requirements:We require 200ng DNA dried down in 96-W plates, calculated using the picogreen assay (not a NanoDrop) with four wells remaining empty for inclusion of facility QC positive and negative control samples.  A260:280 of 1.7-2.0 is required for Agena iPLEX genotyping unless the user agrees to assay these samples at their own risk.  Users are responsible for providing documented, high-quality DNA for genotyping assays.  Investigators can retain the labs services to quantitate the DNA after which time only samples meeting stringent QC will be genotyped.

Targeted 1-10 SNPs:

TaqMan assays - >4.5M predesigned TaqMan SNP assays are available from Applied Biosystems for SNP genotyping in humans and mice. The TaqMan assay provides allelic discrimination through the use of oligonucleotide probes specific for each allele and each labeled with a different fluorescent dye, and are detected on our ABI 7900HT SDS. TaqMan assays are best for samples sizes of ~750 or greater, which reduces the cost per genotype.

SNP Sequence - Simply submit a target SNP sequence(s) for any genome and we will design, manufacture and/or order a custom SNP genotyping assay for you. To design custom multiplexes for the MassARRAY, you can use SNPs from a variety of sources, including SNPs you already have and those from public databases. 

Project Design

Because of the unique characteristics of any genotyping project and the high quality we aim for, we are required to meet with each investigator who wishes to use our service. Deciding which platform to use is made jointly with the investigator after discussing project scope, size, aims, samples and budget.   After choosing a platform, primer and assay design are carried out and a second meeting will occur to discuss the results. Depending on those results, we will provide a statement of work and proceed with the project or consider alternative genotyping methods as necessary. The assay design software will reject sequences that are considered problematic, but the user will have the option to include these at their discretion. We strongly recommend that the user include 5-10 % sample redundancy and a number of SNP-specific positive control DNAs in their sample plates to ensure proper calls.  Genotype results are provided to the user in an electronic format with support from the facility.

SNP failures

All customers must be aware that not all SNPs submitted can be designed into successful assays. At the assay design stage, there is a drop-out rate of 10-15% of SNPs which fail assay design completely. This can be due to the sequence surrounding the SNP containing repeat regions, other SNPs in close proximity to the SNP of interest, database errors, AT rich regions and runs of nucleotides next to the SNP of interest.

If it is possible to design an assay, there is then a further chance of the assay not generating good quality genotype data. In the past, we have seen up to a 10% further loss of SNP assays at this stage. Only those SNP assays which we consider to produce reliable genotypes will be delivered to the customer, unless that data is specifically requested by the customer.  With Agena, each SNP assay is validated on the Coriell SNP 500 DNA set and CEPH trios to allow us to identify and remove poor quality assays before analyzing customer samples.  This cost is associated with the oligo set up fee.  

Our goal is to achieve > 97% success rate in genotype calls for a SNP, with a minimum cut-off of >95%. When lower success rates are achieved, it is the user’s choice as to whether to have the data.

This assay is intended solely for research purposes.  The results provided in this report are not certified by the New York State Department of Health for or intended for use in clinical diagnostic testing or treatment. In using these assay results, the user agrees that Roswell Park Comprehensive Cancer Center shall have no liability for claims by, or damages of any kind whatsoever to, a user of these assay results for a decision or action taken in reliance on the information provided in the results, including any direct, indirect, special, incidental or consequential damages relating to its use.  Roswell Park Comprehensive Cancer Center makes no warranties of any kind, express or implied, as to the merchantability or fitness for a particular use of the assay results.  These assay results are provided "as is" and without warranty that their use will not infringe any patent or other proprietary right of a third party.