Capillary electrophoresis and Genotyping
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The Cologne Center for Genomics has been acquired leading-edge technologies to help research groups of the University of Cologne finding answers in biology and medicine. The following table gives you a short overview about available platforms and their major application areas in regard to capillary electrophoresis and genotyping.
| Plattform | Company | Main applications |
|---|---|---|
| 3730 | ABI | sanger sequencing; microsatallite analysis |
| PSQ HS96A | Qiagen | Genotyping; micro haplotyping and sequencing |
| 7900HT | ABI | Real time PCR; Expression profiling; genotyping (TaqMan) |
| Qiasymphony SP | Qiagen | automated DNA preparation from blood samples |
| GeneTitan | Thermo Fisher Scientific | large-scale genotyping and expression profiling |
| iSCAN+Autoloader | Illumina | large-scale genotyping and expression profiling |
Comparison of SNP genotyping platforms available at the CCG
Many genotyping methods can be performed by the CCG. These can be grouped according to their plex level.
A typical GWA study of thousands of samples could for example start with high plex arrays from Illumina and Affymetrix. Such studies typically provide a number (typically many hundreds) of positive signals that need to be verified in other collectives. Therefore other methods with a low/medium plex level must be used - eg Pyrosequencing or TaqMan. Finally, as a rule, some important or difficult SNPs remain that are genotyped with single plex procedures - such as TaqMan or pyrosequencing.This strategy maximizes the amount of genetic information that can be achieved with the available study resources.
| Method | SNP plex level | genotypes per day** | samples per day** | plate format | Amount DNA per sample | Applications | Flexibility | plus | minus | Hands on time | Price per genotype |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Pyrosequencing | single | 768 | 768 | 96 | 6ng | validation | +++++ | real sequencing; haplotyping | expensive/high DNA requirements | ++++ | +++++ |
| TaqMan 7900HT | single | 9K | 9K | 384 | 6ng | validation | ++++ | robust; proven | expensive/high DNA requirements; high set up costs | + | +++++ |
| iSelect HD | medium/high (3K-200K) | 12/24 | high end validation; costumized GWAS | minimum order size sufficient for 1152 samples | ++ | ||||||
| Infinium Omni5-4 -quad* | 4.3M | 16/48/96 | 400ng | GWAS, CNV | + | robust; proven; good coverage; high call rates | ++ | ++ | |||
| GeneChip (Genome-Wide Human SNP Array 6.0*) | 900K | Mono-chip | 500ng | GWAS, CNV | + | 950K CNV | ++ | ++ | |||
| Axiom Precision Medicine Research Array (PMRA)* | 900K | 96 | 200ng | GWAS, costumized GWAS, linkage analysis, CNV | +++ | fast; cheap; disease associated variants included (100K) | + | + |
* Current human high end array as an example; other products are available.
Contact
email: ccg-service@uni-koeln.de