Core FacilitiesHigh-Throughput Polymorphism
High-Throughput Polymorphism Detection Core
The mission of the High-Throughput Polymorphism Detection Core is to provide services to investigators conducting molecular analyses of somatic DNA collected as part of a wide range of investigations. This Core provides high-throughput assays of specific gene mutations and polymorphisms (SNPs) in the many situations where previously defined specific nucleotide alterations are of interest.
SNP Analysis using ABI Prism Taqman Allelic Discrimination Assay Single SNP allelic discrimination is carried out using the ABI 7900, which allows single-plex SNP interrogation over a large volume of samples.
Taqman Submission Guidelines
SNP analysis using Mass Spectrometry SNP genotyping by MALDI-TOF mass spectrometry is performed using the Sequenom mass spectrometry system. Multiplexing permits determination of up to 12 SNPs in a single well of a 384 well plate.
Sequenom Submission Guidelines
To use the Sequenom SNP Genotyping service, we require that you register at our secure site to submit DNA samples and SNP flanking sequence. Once you have registered and have had your application approved you can then go on to submit SNP flank sequence for assay design and DNA sample sheet information.
Links
- NCI Cohort Consortium - Taqman Genotyping Call Key
- CHIP Bioinformics
- BLAST Human Sequences
- To BLAST short sequences, de-select megablast and specify the these "Advanced options"
-e 10000 -W 8. This increases the number of expected hits to 10000 and decreases the word size to 8. Basically it increases the sensitivity of the search program.
- Applied Biosystems Assays - Applied Biosystems provides a wide selection of almost 2 million “off the shelf” Taqman SNP assays. Included are approximately 160,000 validated assays, 30,000 coding assays and 1.8 million pre-designed asssays that provide high density, genome-wide marker coverage.
- A collection of Taqman Drug Metabolism Assays- This is a collection of over 2000 genotyping assays target polymorphisms in 220 genes within the drug metabolism pathways that code for phase I, phase II, and transporter enzymes. Each assay has gone through an extensive amount of bioinformatics that include mapping to correctly identify the SNP and eliminate interference from pseudo genes.
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