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Genotyping / CNV Analysis

Genotyping provides a measurement of the genetic variation between members of a species. Single nucleotide polymorphisms (SNP) are the most common type of genetic variation. A SNP is a single base pair mutation at a specific locus, usually consisting of two alleles (where the rare allele frequency is >1%; random definition). SNPs are often found to be the etiology of many human diseases and are becoming of particular interest in pharmacogenetics (Evans and McLeod 2003, Weinshilboum 2003). Because SNPs are evolutionary conserved, they have been proposed as a markers for use in quantitative trait loci (QTL) analysis and in association studies. Previously these studies were done using microsatellites. The use of SNPs is being extended in the HapMap project, which is attempting to provide the minimal set of SNPs needed to genotype the human genome.

At the microarray unit of GPCF we provide access to full service of state-of-the-art genotyping of customized SNP sets, focused SNP sets, and genome-wide screens covering up to 2.500.000 SNPs on BeadChips (Illumina). Beside standard genotyping, we support loss-of heterocygosity (LOH), and copy number variation (CNV) studies.
For the analysis of genetic variation and function, we make use of the Illumina Beadchip technology.

Genome-wide SNP Analysis

We provide service, using all available Illumina Infinium BeadChips that carry a fixed-content of SNPs for whole genome genotyping screens. This offers virtually unconstrained locus selection for high-value content coupled with high resolution. Until now we've analyzed more than 2000 samples. Find more details on genome-wide genotyping here.

Applications include

  • Whole-genome association studies
  • Fine-mapping studies
  • Whole genome LOH / copy number variation analysis (CNV)
  • cytogenetic analysis
  • Disease-associated copy number variation analysis

 

Customized SNP Analysis

Custom GoldenGate® Genotyping

We offer highly customized SNP assays, based on Illuminas GoldenGate® technology. The number of SNPs is flexible and can be multiplexed starting from 96 SNP loci, up to 3072 SNPs per sample at a time. SNPs can be freely selected and combined. The GoldenGate Assay is a proven technology that has been used in key genotyping projects worldwide such as the International HapMap Project. The combination of multiplexing and multisample processing decreases screening cost significantly, while ensuring high call rates.

We have analyzed so far more than 14.000 samples using GoldenGate Genotyping.

Please contact us for more details and project planning beforehand. The material costs depend highly on sample size and number of analyzed SNPs in a not linear manner. So don't hesitate to request cost estimates as soon as the need will arise.

Find basic information about the underlying technology here.

last update:
24/04/2013
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