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Monday - Friday: 9am-5pm
or call for special arrangements.

We provide a sample drop off freezer if no one is available to take your samples. Instructions and a form are available in the Main lab.

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Affymetrix Genotyping Arrays - Technology


Methodology:
The GeneChip Mapping Assay couples a highly reproducible generic sample preparation process with an accurate allele-specific hybridization method for making genotype calls, while utilizing the GeneChip microarray technology. The sample preparation avoids the use of individual SNP-specific primers, an important factor given that many SNPs are being interrogated. The sample reduction and amplification is highly reproducible, capturing a majority of the same SNPs across many samples. Total genomic DNA is digested, the fragments are then ligated to adaptors, which are amplified using adaptor-specific PCR primers. The amplified products are cleaned, fragmented, denatured and end-labeled before being hybridized to an array.

SNP Selection Coverage and Controls:

SNPs tiled on the 10K, 100K, 500K & 5.0 arrays were selected using an un-biased, content optimized approach that results in even spacing across the genome. SNPs were further chosen based on accuracy and call rate. There is no bias with respect to genetic or functional criteria [i.e. SNPs appear in coding regions, genic regions & conĀ¬served areas of the genome]. Furthermore, because SNPs are selected at a specific density and not based on Tag SNP Panels, the performance of any single SNP is less important for finding genes. If one SNP drops-out there is often another to back it up, a design that makes Affy SNP arrays resistant to missing data. This redundancy or over-sampling also allows for internal validation of identified associations and provides consistent coveĀ¬rage across all populations. Finally, copy number analysis works much better using unbiased high-density SNP panels.

In the 500K Array Set, SNPs reside on both the NspI and StyI arrays that serve as controls allowing the operator to cross-check genotypes from the same sample and thus verify that both arrays remain together from DNA preparation to data analysis. Likewise, additional controls reside on the 500K mapping arrays, which allow similar cross-checking with previous arrays, allowing Users to increase power in ongoing studies.

In the 6.0 Array, 482,000 SNPs were selected using the unbiased approach described above. This array also houses an additional 424,000 SNPs comprised of Tag SNPs derived from the HapMap project, SNPs from the x & y chromosomes, mitochrondrial SNPs and SNPs on recombinational hotspots.

Critical Specifications of Affymetrix Mapping Arrays:
Parameter 10k 100k 500k 5.0 6.0
Number of SNPs 11,500 116,204 500,568 500,568 906,600
Number of Non-polymorphic Probes       420,000 946,600
Average Minor Allele Frequency   0.22 0.21 0.22
Average Heterozygosity 0.37 0.30 0.29 0.31 0.26
Median Inter-Marker Distance 105 kb 8.5 kb 2.5 kb   < 700 bp