Genotyping service:

High throughput Illumina genotyping

Vantage offers high throughput Illumina genotyping and customers can select the type of bead chip they would like to use. For additional information about the chip types, please refer to:

https://www.illumina.com/products/by-type/microarray-kits.html

We routinely utilize the infinium LCG chemistry along with the Multi-Ethnic Global Array (MEGA) with added custom content, which amounts to 1.8 million SNPs. Samples are processed in 96 well plates and each plate includes 4 controls which are a duplicate sample from either the same or a preceding plate as well as 3 Coriell HapMaps samples, usually a trio (https://www.coriell.org/0/Sections/Collections/NHGRI/hapmap.aspx?PgId=266). These controls enable us to perform the necessary lab QC prior to data release and include reproducibility and heritability checks.

The deliverables include:

  1. Folder containing raw data (idats)
  2. GTC files
  3. Sample sheet
  4. SNP manifest files in. bpm format
  5. Cluster file for the VUMC MEGA Ex’s custom chip
  6. PLINK files on forward strand, build 37
  7. README explaining the location of above files
  8. Project summary giving specific details related to your project
  9. Either Genome Studio Project or Beeline Project depending on size/number of samples

Please note, sample dropout rates for Illumina genotyping are typically 5-15%.

 

Sample requirement for Illumina genotyping:

  • 500ng gDNA at a minimum of 50ng/ul
  • If samples are delivered in plates, wells D2, D6, D10 and G2 should remain empty
  • Samples manifest must include gender and ethnicity.

To initiate a genotyping project, please submit a request via iLAB under “Genotyping Services (Genotyping)” and ill out the required information.

 

Taqman:

Vantage offers Taqman genotyping for single SNPs or short indels as well as copy number variant detection for certain genes. We run pre-designed assays or design custom assays depending on the target sequence for most SNPs. Customers should submit their list of target SNPs as rsID’s through iLab. Data will be reported as an excel file containing the reported genotyping results for each SNP as well as the context sequence and uploaded to the iLab project when complete.

Vantage offers various options for DNA extraction from blood and saliva samples that can then be processed for genotyping. Please inquire further about these options. The investigator can also have previously extracted DNA from outside of VANTAGE brought or shipped to the core for genotyping. As a rule of thumb, your DNA should have a concentration of 20ng/ul by Nanodrop or pico green quantitation and have a minimum volume of 25ul, however, DNA amounts and plating requirements will vary based on your genotyping needs.

Please contact Karen Beeri at karen.beeri@vumc.org for consultation.