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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 Affymetrix large-scale genotyping and expression profiling
iSCAN+Autoloader Illumina large-scale genotyping and expression profiling


Comparison of SNP genotyping platforms available at the CCG

On the CCG many genotyping methods can be performed. 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 SNPstream and GoldenGate. TaqMan OpenArray as a single plex method uses a low volume approach to step into the field that low plex methods normally fill out.

Finally, as a rule, some important or difficult SNPs remain that are genotyped with single plex procedures - such as TaqMan/OpenArray 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 HD (Human1M-Duo*) 1.2M     Duo-Chip 750ng GWAS, CNV + robust; proven; good coverage; high call rates 60K CNV ++ ++
GeneChip (Genome-Wide Human SNP Array 6.0*) 900K     Mono-chip 500ng GWAS, CNV + 950K CNV   ++ ++
Axiom* 550K 82M 150 16/24/96 200ng costumized GWAS +++ fast; cheap no CNV +  

* Current human high end array as en example; other products are available
** throughput on the CCG platforms