GeneTitan™ MC Fast Scan Instrument, international (220V) - FAQs

Specifications for the GeneTitan MC instrument can be found in the "Automated array processing with the GeneTitan family of instruments" data sheet (http://media.affymetrix.com/support/technical/datasheets/genetitan_family_instrument_datasheet.pdf).

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A number of service providers have experience running the Axiom Assay and the genotyping call algorithm that is used with the Axiom Genome-Wide BOS 1 Array Plate.

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The average sample file size is 28 MB.

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Dish QC (DQC) is the recommended QC metric for Axiom Genome-Wide Arrays in Genotyping Console Software. The default threshold is greater than or equal to 0.82 for each sample. It operates by measuring signal at a collection of sites in the genome that are known not to vary from one individual to the next. Because the metric monitors non-polymorphic locations, at each position it is known which of the two channels in the assay should contain signal and which should be just background. DQC is a measure of the extent to which the distribution of signal values is separated from background values, with 0 indicating no separation and 1 indicating perfect separation.

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Axiom Analysis Suite is used to analyze data from the Axiom Genome-Wide BOS 1 Array Plate.

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A variety of samples, including those originating from blood, semen, nasal swabs, hair bulbs, and ear punch tissue, were tested using the Axiom Genome-Wide BOS 1 Array.

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The assay requires 200 ng of high-quality, double-stranded genomic DNA that is not highly degraded. Genomic DNA must be of high purity and free of DNA polymerase inhibitors such as high salt, hemes, and chelating agents. For details about general assay requirements for genomic DNA, please refer to Chapter 2 of the Axiom 2.0 Genotyping Assay User Guide (https://tools.thermofisher.com/content/sfs/manuals/axiom_genotyping_solution_analysis_guide.pdf).

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The Axiom Genome-Wide BOS 1 Array Plate is designed for use with the Axiom 2.0 Reagent Kit. Assay kits are available for 96 (one plate), 192 (two plates), and 768 (eight plates) reactions.

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The performance of the array was measured across 20 breeds, and the average sample call rate is 99.62 percent.

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The reproducibility for the validated SNPs on the screening arrays is 99.94 percent.

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The Mendelian consistency rate of the validated SNPs on the Axiom Genome-Wide BOS 1 Array Plate is 99.96 percent among different experiments.

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There are no copy number probes on the array. However, measuring copy number variation (CNV) in the bovine genome can be performed using a custom whole-genome sampling assay design (a cartridge-based SNP Array 6.0 genotyping assay).

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LD calculations were carried out for each breed separately.

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Genetic coverage was calculated based on SNP pairwise LD (r2) results obtained from genotype data of reasonably unrelated samples within each breed of interest. The default r2 threshold for genetic coverage was 0.8. Unless otherwise specified, all SNPs with r2 results for a given breed are included in the target coverage set. This set includes all SNPs that are converted in the screen and have polymorphic genotype data for the breed of interest. For breeds for which bovine HapMap genotype data were available for enough of the samples used in the screen, HapMap SNPs with polymorphic genotypes were also included in the target coverage set.

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SNPs were selected to represent polymorphisms from a comprehensive set of commercially important breeds of dairy and beef cattle from both Bos indicus and Bos taurus. Our primary goal was to obtain high levels of genetic coverage. SNP pairwise linkage disequilibrium (LD) values (r2) were calculated to identify SNPs in strong LD. Then we selected the fewest number of SNPs to cover the known genetic variation for each breed we prioritized (first five breeds in Table 1). After SNPs were selected for optimal genetic coverage, the distances between the selected SNPs were calculated, and inter-SNP gaps filled (starting with the largest) by selecting polymorphic SNPs from the five major breeds: Holstein, Angus, Nelore, Jersey, and Fleckvieh.

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We obtained information for more than 46 million SNPs from sequencing efforts coordinated by the Affymetrix Bovine Consortium (basic and applied researchers in the bovine community). From these, we selected SNPs to use based on physical coverage of the bovine genome and the number of breeds in which the SNPs were observed.

We then screened many millions of SNPs against approximately 400 samples from the Affymetrix Bovine Consortium and bovine HapMap samples (Texas A&M University). The result is a database of ~3 million validated SNPs, which means each has been demonstrated as a real, truly polymorphic SNP and has been proven to work in the assay. This implies that customers should be able to select SNPs from our database and create their own custom array, and that the SNPs chosen should perform at a very high level in the assay.

Finally, we selected a subset of more than 648,000 SNPs primarily based on genetic coverage for a selection of breeds and secondarily based on physical coverage of the bovine genome.

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Approximately 648,000 SNPs are tiled on the array.

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