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The Cologne Center for Genomics has been acquired leading-edge technologies to help research groups of the Faculty of Medicine and the Faculty of Mathematics and Natural Sciences at the University of Cologne (UoC) 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 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)
GeneTitan Thermo Fisher Scientific 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 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 + +++++
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.


Genotyping Team