Instructions for:
GWAS                              Shipping

For GWAS projects with more than 94 samples, the pricing includes:
  • [Pretesting with the ability to replace/drop poor performing samples–if this price option is selected]
  • 2 controls per plate
  • Study duplicates (one per every other plate) at no additional cost
  • Individual sample reruns in the lab for poor performance (repeated 1X)
  • Full data release, which includes hapmap concordance, reproducibility of genotype calculations broken down by MAF bin for each sample pair, GenomeStudio project, SNP and samples tables, full SNP technical filter applied, samples reclustered on own data, final reports, PLINK file and README docs explaining the data in each directory

All DNA samples should be provided at a concentration between 50 ng/µl and 100 ng/µl, (genomic DNA) or 100ng/µl and 200ng/µl (whole-genome amplified DNA), 25 µl total volume. Concentrations at the higher end of the spectrum and high molecular weight DNA is recommended for downstream copy number analysis.

Poor quality DNAs or DNAs that have been amplified may not perform as well as unamplified genomic DNA. In particular there may be allele loss in the heterozygotes and a reduced call rate for whole genome amplified samples. Additionally, samples contaminated with heme may not work. Clients should be aware of these limitations prior to committing to a study.  Degraded DNA may be “rescued” using the Illumina restore kit.  This kit costs an additional $100/sample.

A note regarding the use of amplified DNA for Genome Wide products: The final concentration of WGA samples is not indicative of sample quality. Depending on the input DNA quality and quantity, the final WGA’ed product may not be a good genetic representative of the starting material, especially if the starting concentration was low or if contaminating DNA was present. As a result, we discourage use of WGA samples at this time. If you do submit WGA samples, you should anticipate a higher missing data rate and perhaps a slightly higher error rate than for genomic DNA samples.

Shipment Instructions for Illumina genotyping:

DNA samples must be sent in bar-coded plates provided by the GRCF, 92 samples per plate. Plates will be provided only after:
  1. arrangements for payment have been made,
  2. a pedigree file has been approved (required for both family based studies and case-control studies) and
  3. a copy of your IRB approval letter has been received
  4. a duplicates file has been approved

A DNA manifest template will be sent to you. Please read the instructions provided with the manifest carefully and follow them precisely. The manifest is our only record tying sample ID to plate and well location so please take care to ensure the accuracy of this document.
Please return the completed manifest file to project manager prior to shipping plates to the GRCF. Plates must be shipped on dry ice for arrival on Tuesday through Friday.

Shipping address for Illumina genotyping (external customers):
Johns Hopkins Genomics – CIDR
1812 Ashland Avenue
Room 245
Baltimore, MD 21205
410-614-0702

Email the tracking number to Roxann Ashworth.

Shipping address for plating services or individual Taqman assay genotyping (external customers):

Laura Kasch
GRCF, Fragment Analysis Facility
Johns Hopkins University
725 N. Wolfe Street, PCTB G20
Baltimore, MD 21224
Phone (443) 287-7948

Email the courier tracking number and GeneSifter order number to FAF@jhmi.edu.

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