We amplify DNA from samples with limited amounts of DNA by whole genome amplification using an optimized high-throughput protocol based on the Phi29 polymerase. We will accept small amounts of genomic DNA, blood or buccal samples. As little as 10 ng for either 10 μg or 40 μg yield and 100 ng for 150 μg of DNA. Quality checks are performed by genotyping 10 highly informative microsatellite markers accross multiple chromosomes, including the X chromosome. This method has been validated for both microsatellite and SNP genotyping.

deCODE has created an automated sample processing and tracking software platform to support high-throughput data generation and monitoring. Samples are tracked using barcode labels and non-personally identifiable tracking numbers.

Prior to initiating a full-scale production effort, all samples for the project will be tested. For microsatellite genotyping we test 8 markers to identify problem samples. CEPH family DNA is used as control. For genotyping with Illumina Sentrix® arrays we test 7 client samples and one reference sample to identify potential problems. We do not request pedigree information, although data on family relationships of individuals in a sample set will allow more accurate quality control.

For microsatellite genotyping projects amplified fragments are analyzed by capillary electrophoresis utilizing ABI 3730 DNA analyzers. deCODE has optimized the protocol for rapid, accurate, and cost-effective analysis. deCODE uses it's proprietary deCODE Allele Caller (DAC) software for automated allele calling. The analysis consistently gives greater than 99% accuracy of genotyping calls. PCR reactions are set up in multiplex reactions with fluorescently-labeled primer pairs selected to amplify highly informative di-, tri-, and tetra-microsatellite loci. We have performed extensive optimization of each primer pair to improve performance and reliability. deCODE's facility is equipped with 4 high-throughput liquid handling robots with a total capacity to handle samples from over 1,000 individuals per day in preparation for genome-wide scans.

We use an in-house optimized platform based on technology developed by Nanogen, Inc. The platform uses the highly discriminating endonuclease IV and allelic discrimination is accomplished using detection probes specific to each expected genotype. We are able to analyze SNPs which have proven difficult to genotype by other platforms. SNPs are analyzed by end point scatter plot analysis using the ABI® 7900HT Sequence Detection System. deCODE uses it's proprietary deCODE Allele Caller (DAC) software for automated allele calling and Hardy-Weinberg checks and LD tests to ensure high-quality results.

We genotype samples using Illumina's Sentrix® BeadChips, powered by the Infinium® II assay. The Sentrix® arrays enable whole-genome genotyping of hundreds of thousands of tagSNP markers derived from the International HapMap project. TagSNPs are loci that can serve as proxies for many other SNPs and greatly improve the power of association studies. DNA samples are isothermally amplified and fragmented by a controlled enzymatic process. Samples are applied to BeadChips where DNA samples anneal to locus specific 50-mers during the hybridization step. Products are subsequently fluorescently stained and the intensities of the beads' fluorescenses is detected by an Illumina BeadArray Reader. We use Illumina's software for automated genotype calling.

For microsatellites genotyping results will be reported as allele sizes of the polymorphic markers of called alleles as well as values normalized to a CEPH individual. For SNPs genotyping results are reported as alleles of each marker. The data report is delivered as a ASCII text file, compatible with existing genetic linkage and association software packages. The data is delivered via a secure server, which can be accessed with a personal username and password, in strictest confidence.