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SNP Genotyping Services on Affymetrix Platform (10K, 100K, 500K)

Complete Service

A complete SNP genotyping request includes sample processing from genomic DNA to fragmentation, hybridization to Affymetrix GeneChips, scanning, image acquisition, signal quantification and data upload.

Pricing for SNP Genotyping Arrays

Target Preparation: $150/sample
SNP Array Processing: $100/chip
Imaging: $25/chip

How to Submit Samples for a Complete SNP Genotyping Service

  1. Aliquots of genomic DNA submitted for a complete service must have a concentration of 0.05 µg/µl. An exact volume of 5 µl (a total of 250 ng) must be submitted.
  2. A separate request must be submitted for each method of 50K digestion (Xba I or Hind III).
  3. All samples must be frozen and transported on dry ice to the MCF at designated times only (Tuesdays and Thursdays 1:30 p.m. to 4 p.m.).
  4. All samples submitted to the MCF through LIMS are given a Core ID that is used to track the samples through the whole process. User must record the Core IDs generated by the LIMS at the time of sample submission GeneChips should be clearly labeled with Core IDs only. GeneChips submitted without Core IDs will not be accepted.
  5. At the time of sample submission, user must inform the MCF technician if leftover DNA samples should be discarded or returned. Leftover samples must be picked up within two weeks after completion.
  6. Once the DNA preparation is successfully completed the user will need to deliver GeneChips to MCF at designated times only (Tuesdays and Thursdays 1:30 p.m. to 4 p.m.).

Hybridization and Scanning

This service should be selected if target preparation is performed at a location other than the MCF. Samples must be submitted after fragmentation. This service includes preparation of hybridization cocktail, hybridization to Affymetrix GeneChips, scanning, image acquisition, signal quantification and data upload.

How to Submit Samples for a Hyb/Scan Genotyping Service

Samples provided for this service must be fragmented DNA. Please see Affymetrix guidelines for methods of fragmentation.

  1. The amount of DNA that must be fragmented for 10K samples is 20 µg in a maximum volume of 45 µl.
  2. The amount of DNA fragmented for 50K (Hind III or Xba I) samples must be 40 µg in a maximum volume of 45 µl.
  3. All samples must be frozen and transported on dry ice to the MCF at designated times only (Tuesdays and Thursdays 1:30 p.m. to 4 p.m.).
  4. All samples submitted to the MCF through LIMS are given a Core ID that is used to track the samples through the whole process. User must record the Core IDs generated by the LIMS at the time of sample submission GeneChips should be clearly labeled with Core IDs only. GeneChips submitted without Core IDs will not be accepted.
  5. GeneChips for 10K or 50K must be submitted at the sample time as samples for this service.
  6. At the time of sample submission, user must inform the MCF technician if leftover DNA samples should be discarded or returned. Leftover samples must be picked up within two weeks after completion.

Scan Only

This service should be selected if hybridization is performed at a location other than the MCF. This service includes, scanning hybridized GeneChips provided by the user, image acquisition, signal quantification and data upload.

How to Submit Samples for Scan Only Genotyping Service

  1. Genomics Core Facility requires two-day notice prior to submission of this request. Please contact MCF at 713-834-6199 to set a date.
  2. This service is completed the day the GeneChips are received. GeneChips should be delivered to MCF by 12 p.m. the day of the service.
  3. All samples submitted to the facility through LIMS are given a Core ID that is used to track the samples through the whole process. User must record the Core IDs generated by the LIMS at the time of sample submission GeneChips should be clearly labeled with Core IDs only. GeneChips submitted without Core IDs will not be accepted.

Please note: Data analysis is not a part of the SNP Genotyping services. A data analysis service must be requested for this purpose through the LIMS system.

The data generated by the facility is uploaded to the Biostatistics server via a tool called GeneDirector® (BioDiscovery, Inc.). Facility personnel create a GeneDirector account for each user (principal investigator) and upload data into relevant folders. For GeneDirector-related questions, please contact Clark Moore at clamoore@mdanderson.org.

The Bioinformatics group is responsible for all data analysis requests. For data analysis related questions, please contact Dr. Kevin Coombes at kcoombes@mdanderson.org.


© 2012 The University of Texas MD Anderson Cancer Center