Genome-Wide Human SNP Array 6.0 - FAQs

We recommend reviewing the Microarrays for Preemptive Pharmacogenomics page to determine a potential alternative.

If you have any questions you can email Tech Support at techsupport@thermofisher.com.

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There are 549,673 SNPs that are genotyped on CytoScanHD which match to a marker on the Genome-Wide Human SNP Array 6.0.
Note: CytoScan HD Array can be ordered as part of the following kits: CytoScan HD Array Kit and Reagent Kit Bundle (Cat. No. 901835) and CytoScan HD Training Kit (Cat. No. 901834)

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Blood and cell line sources of human genomic DNA have been successfully tested in the laboratories at Affymetrix. Success with other types of samples such as formalin-fixed paraffin-embedded tissue will depend on quality (degree of degradation, degree of inhibitors present, etc.), quantity of genomic DNA extracted, and purity of these types of samples.
For information on whole-genome amplification, refer to the following technical note which is available on our website: Linking Whole-genome Amplification to SNP Genotyping (https://assets.thermofisher.com/TFS-Assets/LSG/brochures/wga_snp_technote.pdf).
This technical note contains recommendations for whole-genome amplification of small amounts of genomic DNA for analysis using the Affymetrix Genome-Wide Human SNP Array 6.0. These recommendations were developed by the systematic assessment of assay performance using different starting genomic DNA amounts and cleanup options.

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There are 4,304 non-synonymous SNPs based on the RefSeq transcript descriptions on the Genome-Wide Human SNP Array 6.0.
There are 4,699 non-synonymous SNPs based on the Ensembl transcript descriptions on the Genome-Wide Human SNP Array 6.0

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According to the reference NA32 genome, there are 411 mitochondrial SNPs on the Genome-Wide Human SNP Array 6.0.

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No, we do not recommend using the GeneChip HWS kit for mapping arrays.

We recommend using the SNP 6 Core Reagent Kit (Cat. No. 901706) for the SNP array 6.0, which includes a hybridization, wash, and stain component. See this link: http://www.affymetrix.com/estore/browse/products.jsp?productId=prod460004&categoryId=35586&productName=Affymetrix%26%23174%3B-SNP-6-Core-Reagent-Kit#1_1

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The Genome-Wide Human SNP Array 6.0 has not been tested for whole genome amplification.

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The Genome-Wide Human SNP Array 6.0 annotation file lists all SNPs on the array, but not all SNPs are used in the default analysis configuration. In the 'Final List' column, a 'No' will be next to the SNPs that are masked out in the analysis. SNPs may be excluded because they are controls, or because empirical testing has shown that they do not work well.

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The scan time for Genome-Wide Human SNP Array 6.0 is 35 min.

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906,600 SNPs on the SNP 6.0 array can be accessed utilizing Genotyping Console 2.1. In addition, the SNP 6.0 array contains 945,826 non-polymorphic “potential” copy number variation probes.

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Genome-Wide Human SNP Array 6.0, Fluidic Scripts for FS450 is GenomeWideSNP6_450, Library Files named GenomeWideSNP_6

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There are a couple ways to determine how a specific gene of interest is covered by the SNP 6.0 array. The first would be to use the Affymetrix NetAffx website and query the gene of interest in the genotyping search field. This will return the list of SNPs and their annotations to the gene. Within one of these records is a link to the UCSC browser which is a nice visual display of the SNPs on your gene of interest.

Another way to determine how a specific gene of interest is covered by the SNP 6.0 array would be to go to the UCSC genome browser directly and search for the gene of interest. Please be sure that the SNP field is visible and not hidden under the option

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Scanning an individual SNP 6.0 array takes about 35 minutes.

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The recommended number of samples that should be clustered and analyzed using the Birdseed v1 algorithm is a minimum of 44. A minimum of 15 female samples should be included for robust gender determination results.

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DNA is digested with Nsp I and Sty I restriction enzymes and ligated to adaptors that recognize the cohesive four base pair (bp) overhangs. All fragments resulting from restriction enzyme digestion, regardless of size, are substrates for adaptor ligation. A generic primer that recognizes the adaptor sequence is used to amplify adaptor-ligated DNA fragments. PCR conditions have been optimized to preferentially amplify fragments in the 200 to 1,100 bp size range. PCR amplification products for each restriction enzyme digest are combined and purified using activated beads. The amplified DNA is then fragmented, labeled, and hybridized to a Genome-Wide Human SNP 6.0 Array.

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500 ng of total genomic DNA is required for the Genome-Wide Human SNP Array 6.0.

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-The lower the better
-In a whole genome study, the general P-value significance cutoff for genes associated with a disease is 10-4 or less

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-Contains over 906k SNPs
-Contains 946,000 non-polymorphic probes for CN variation
-CN/SNP combined intermarker genome coverage of 680 bp


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-The chp file is 66 MB
-The chp file is 30 MB

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-Genotyping Console 4.2
-Algorithm Birdseedv2

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-GeneChip Scanner 3000 7G System
-Fluidics Station 450 (Please note that the FS400 is not supported with SNP 6.0 arrays.)

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For the GenomeWideSNP 6.0, the intermarker spacing is shown below for the specific probe types:
-Probe type: CN; Average Inter-Marker Spacing (bp): 3160; Median Inter-Marker Spacing (bp): 2180
-Probe type: SNP; Average Inter-Marker Spacing (bp): 3230; Median Inter-Marker Spacing (bp): 1270
-Probe type: SNP plus CN; Average Inter-Marker Spacing (bp): 1600; Median Inter-Marker Spacing (bp): 680

The Average Minor Allele Frequency (MAF) is as follows: 19.6% in HapMap Caucasians, 18.2% in HapMap Asians, and 20.6% in HapMap Africans

The Average Hetrozygosity is as follows: 26.7% in HapMap Caucasians, 24.6% in HapMap Asians, 28.5% in HapMap Africans

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-Contains 906,600 SNPs
-Contains 946,000 Non-Polymorphic Probes
-All screened in 500 distinct samples (270 HapMap plus diversity panels)
-Unbiased selection of 494,000 SNPs from 5.0 and 500k tiled on the 6.0
-6k SNPs not tiled due to lack of cluster classification or multiple hits to the genome.
-482,000 SNPs; historical SNPs from 500k and 5.0 out of the 494,000 SNPs can be analyzed with the default library file and the SNP 6.0 genotyping algorithm (Birdseed)
-Selection of additional 424,000 SNPs
-Tag SNPs
-SNPs from chromosomes X
-Y Chromosome SNPs (257 in default, 900 in full)
-Y Chromosome CN Probes (8,583)
-Mitochondrial SNPs (119 in default, 465 in full)
-100K New SNPs added to the HapMap database
-SNPs in recombination hotspots

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49 format, 5 µm Feature Size

All the SNPs are tiled with PM only 3-4 replicated probe pairs per SNP.

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Yes. The combination of the SNP Array 6.0 and Genotyping Console 2.1 provides a great set of tools for researchers who would like to study copy number changes in cancer as well as copy number variation in association studies.

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Customers can run 48 samples per week (5 days) with three fluidics stations, 1 scanner, 1.5 technicians. Using the 96-sample protocol, customers can run 96 samples in 6 days, using the same instrumentation or 96 samples in 5 days using six fluidics stations and 2 scanners. If a group staggers the protocol during the week or has more instrumentation it is possible to get higher throughput, but this is the standard.

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SNP 5.0 scans require ~22 minutes per array.

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500,568 SNPs on the SNP 5.0 array can be accessed utilizing Genotyping Console 2.1. In addition, the SNP 5.0 array contains 420,000 non-polymorphic copy number probes.

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The SNP 6.0 Array uses the SNP 6.0 Core Kit. This Core Kit could probably be used for the SNP 5.0, but it was not validated.

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CNP analysis is supported in GTC 4.2 for the SNP Array 6.0.

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Yes, you can generate your own reference model files for copy number analysis. A user-generated reference set may better account for laboratory bias and may therefore improve resolution. Reference sets should contain at least 44 samples. To obtain good data on the X and Y chromosomes, you should use a minimum of 15 files from female samples and 15 files from male samples to generate the reference model file.

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GTC 4.2 can be used to perform the following copy number analyses for the SNP Array 6.0:

-Copy number (CN)
-Loss of heterozygosity (LOH)
-Copy number segment reporting
-Custom region copy number segment reporting

There are two options for copy number analysis workflows on the SNP Array 6.0:

-CN/LOH Reference Model File Creation and Analysis (Batch Sample Mode)
-CN/LOH Analysis with a Previously Created Reference Model File (Single Sample Mode)


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The Contrast QC threshold is 0.4 or greater. The overall quality of the data set is assessed by measuring the average Contrast QC for all passing samples. The average Contrast QC for all passing samples should be 1.7 or greater.

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Contrast QC measures how well experiments resolve SNP signals into three genotype clusters. It uses a subset of probes and measures the differences in contrast distributions for homozygote and heterozygote genotypes. In high-quality data sets, the homozygote distributions are well-resolved from the heterozygote distribution and the Contrast QC metric is higher than the 0.4 threshold. In poor quality data sets, the homozygote distributions are not well resolved from the heterozygote distribution and the Contrast QC metric is below the 0.4 threshold. Details on the Contrast QC metric are provided in Appendix of the GTC User Manual.

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Genotyping analysis:

-GeneChip Human Mapping 100K Set
-GeneChip Human Mapping 500K Array Set
-Affymetrix Genome-Wide Human SNP Array 5.0
-Affymetrix Genome-Wide Human SNP Array 6.0

Copy number/copy nmber segments/LOH analysis:
-GeneChip Human Mapping 100K Set
-GeneChip Human Mapping 500K Array Set
-Affymetrix Genome-Wide Human SNP Array 6.0

Copy number variation analysis:
-Affymetrix Genome-Wide Human SNP Array 6.0

The GeneChip Human Mapping 10K Array platform is not supported by GTC 3.0.1. The SNP Array 5.0 platform can be used with Partek for copy number analysis.

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