SNP Genotyping and CNV Analysis
We offer a suite of SNP genotyping platforms and services to meet your SNP genotyping needs, from whole genome genotyping to individual SNPs. Contact Connie Zhao (Connie.Zhao@rockefeller.edu) if you have questions about choosing platforms.
Affymetrix Whole Genome Mapping Arrays
- Affymetrix Genome-wide Human SNP Arrays (10K, 100K, 500K, SNP 5.0, and SNP 6.0)
- Affymetrix Cytogenetics 2.7 M arrays (contains 2.7 million markers for chromosomal copy number analysis)
- Affymetrix Mouse Diversity Genotyping Arrays
- Affymetrix DMET array for drug metabolism analysis
Our Affymetrix whole genome SNP genotyping service can be used in two ways:
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Full service: Users only need to provide us genomic DNA samples. We will check sample quality on agarose gel, amplify and label the samples, set up hybridization, process and scan the arrays, and transfer data to users.
Sample submission: Minimum 10 µl of genomic DNA at 50 ng/µl in low-EDTA TE buffer (10 mM Tris, 0.1 mM EDTA, pH 8.0).
Samples must not be significantly degraded. Samples should be free of PCR inhibitors. We recommend that users perform regular PCR to ensure that the genomics DNA samples amplify well.
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Array hybridization and processing only: Users provide us biotin-labeled, fragmented DNA samples. We will set up hybridization, process and scan the arrays, and transfer data to users.
Sample submission:
The amount of sample needed depends on the specific type of Affymetrix SNP array. Please contact us at genomics@rockefeller.edu.
Agilent Microarrays
- Human Genome CGH Microarrays
- Mouse Genome CGH Microarrays
- Rat Genome CGH Microarrays
- Custom Genome CGH Microarrays
- ChIP-on-chip Microarrays
- MicroRNA Microarrays
We currently only provide full service for Agilent CGH arrays. Users need to provide us minimum 1ug genomic DNA samples. We will label the samples, set up hybridization, process and scan the arrays, and transfer data to users.
For all other Agilent microarrays, users need to provide us labeled samples and we will set up hybridization, process and scan the arrays, and transfer data to users.
Illumina Human Whole Genome Mapping Arrays
- Human Whole Genome Mapping Arrays
- Mouse SNP panel (1449 loci)
- Custom SNP panels (48-1536 loci)
Services:
Because there are several special instruments needed to label the samples for Illumina arrays, users may not be able to do the labeling in their own labs. We provide full service for these products.
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Full service: Users only need to provide us genomic DNA samples. We will check sample quality on agarose gel, amplify and label the samples, set up hybridization, process and scan the arrays, and transfer data to users.
Sample submission:
Minimum 10 µl of genomic DNA at 100 ng/µl in TE buffer.Samples must not be significantly degraded. Samples should be free of PCR inhibitors. We recommend that users perform regular PCR to ensure that the genomics DNA samples amplify well.
- Array hybridization and processing only:
Not available
Taqman Assay for Genotyping Individual SNPs
If you have only a few SNPs to genotype, you can use Taqman assays on our Applied Biosystems 7900 System. You can chose from over 160,000 pre-validated assays (assay-by-demand), or you can have Applied Biosystems design custom SNP assays for you (assay-by-design).
For more information and for searching a SNP assay, go to www.appliedbiosystems.com
