Custom SNP Genotyping
Single nucleotide polymorphisms (SNPs) represent the most frequent type of DNA variation. Utilising a variety of platforms, AGRF offers a custom SNP service which can be tailored to meet specific project requirements. The custom SNP Genotyping services is based on the following:
- Sequenom platform which has the capacity to analyse SNPs ranging from only one SNP to >500 SNPs to genotype for virtually any number of samples.
- The illumina Golden Gate Genotyping System which offers custom SNP panels from 96 - to 1536-plex and has the capacity to analyse SNPs ranging from 300 to 10 000 SNPs.
Custom SNP: Sample Submission Requirements
Sequenom Custom SNP Genotyping
AGRF's Sequenom custom SNP genotyping service is run on the Sequenom MassARRAY system and utilises a homogenous MassExtend (hME – single base extension) reaction termed iPLEX GOLD, for analysis of up to 36 SNP's in a single multiplex. SNP assays are designed by the AGRF based on provided SNP sequences (RS Numbers). Oligonucleotides are then obtained by the AGRF and used to process samples in multiplex format. Following the MassExtend reaction, oligonucleotides are printed onto specialised Spectro CHIPs and anaylsed by the Sequenom mass spectrometer. This platform has the ability to replex SNP panels so SNPs can be dropped or added at a later date.
Sequenom Homogenous MassExtend Bulletin (PDF)
Sequenom iPlex Application Note (PDF)
Sequenom Custom SNP Genotyping Service Process
Sequenom Custom SNP Allelotyping
AGRF offers a rapid and accurate custom SNP validation using a sample-pooling technique called allelotyping. The allelotyping technique rapidly screens and confirms the presence of a SNP and its allelic frequency in cohort populations. The accuracy of the Sequenom MassARRAY technology is able to determine SNP allele frequencies with high precision in pooled samples, thereby replacing hundreds of individual measurements with one consolidated analysis. The MassARRAY has the capacity to pre-evaluate SNPs, which means only SNPs that prove informative in the pool-to-pool comparison are included in individual genotyping projects, significantly reducing the total workload for individual genotyping. Allelotyping may also be used when looking for allele bias in cDNA.
AGRF allelotyping service requires a SNP sequence with a minimum 50 bases either side of the SNP site and extracted DNA pools (screening 300-500 individuals per patient pool is recommend for greatest statistical relevance). SNP assays are then designed by the AGRF and PCR oligonucleotides are obtained. PCR utilises the homogenous MassExtend (hME – single base extension) reaction termed iPLEX GOLD, with pooled samples then being processing on a mass spectrometer. The mass spectrometer provides a high level of sensitivity, capable of detecting allele frequencies as low as 3% on average.
Sequenom Homogenous MassExtend Bulletin (PDF)
Sequenom iPlex Application Note (PDF)
Sequenom Custom SNP Allelotyping Service Process
