Logo of University of Cologne

Technologies

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.

 

PlattformCompanyMain applications
3730 ABI sanger sequencing; microsatallite analysis
LC480 Roche Real time PCR; Expression profiling; melting point analysis; genotyping
PSQ 96MA Qiagen Genotyping; micro haplotyping and sequencing; Methylation studies
PSQ HS96A Qiagen Genotyping; micro haplotyping and sequencing
7900HT ABI Real time PCR; Expression profiling; genotyping (TaqMan)
Autopure LS Qiagen automated DNA preparation from tissues
GeneTitan Affymetrix large-scale genotyping and expression profiling
iSCAN+Autoloader Illumina large-scale genotyping and expression profiling
Beadstation 500 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.

 

MethodSNP plex levelgenotypes per day**samples per day**plate formatAmount DNA per sampleApplicationsFlexibilityplusminusHands on timePrice 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 + +++++
TaqMan OpenArray single 30K   variable   validation +++ robust; proven; fast; lower costs medium DNA requirements; minimum order of 10 arrays ++ ++++
SNPsream low (48) 73K 1536 384 6ng validation ++++ very low DNA requirements conversion rate 80-95% ++++ ++++
Golden Gate low/medium (96-1536) 300K 192 96 250ng validation ++++ low DNA requirements; many preselected panels available conversion rate 85-95% ++ +++
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