Capillary electrophoresis and Genotyping
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.
|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