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查看更多产品信息 Genome-Wide Human SNP Array 6.0 - FAQs (901150)
22 个常见问题解答
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.
Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.
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)
Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.
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.
Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.
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
Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.
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
Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.
The Genome-Wide Human SNP Array 6.0 has not been tested for whole genome amplification.
Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.
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.
Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.
The scan time for Genome-Wide Human SNP Array 6.0 is 35 min.
Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.
1. Each SNP is represented by a pair of 2 Perfect Match (PM) probe sequences, one for Allele A and one for Allele B, which are placed in adjacent positions on the array.
2. Each pair of SNP probes is replicated at least 3 times on the array. The replicates are distributed across the array such that each replicate is located in a different quadrant.
3. Copy-number probes are Perfect Match (PM) non-polymorphic sequences located in the stripes between quadrants.
Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.
The SNP 6.0 HapMap CEL files have been archived by NCBI. The files are available for download through the NCBI ftp server. To get the full set of CEL files, all the files with the extension .tgz should be downloaded. Any .tgz files will need to be extracted (or unzipped) twice. There is freeware called 7-Zip File Manager that can be used to extract the files. For additional information, please contact support.
Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.
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.
Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.
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.
Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.
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.
Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.
MAPD is the recommended method of assessing noise in the SNP Array 6.0, Cytoscan HD and Cytoscan DX copy number data. The log2 distance between neighbors is calculated for all pairs and then the median is taken. This represents the typical distance between marker pairs with respect to log2 ratios. The higher the MAPD, the greater the noise between the array of interest and the reference set.
Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.