Instructions for:
GWAS                    Custom Illumina                Shipping

For GWAS projects with more than 94 samples, the pricing includes:
  • Our SNP barcode test panel (96 snps used to barcode the sample and verify the GWAS dataset released matches the sample submitted, as well as used to verify gender, family relationships, sample performance – can also be used to verify 3 main ethnic groups if desired).
  • Identification of problems and replacement of problem samples before running the sample on the GWAS arrays.
  • Two HapMap controls per 96 well plate and 1 blind duplicate every other plate.
  • Repetition of any sample which has less than a 96.5% call rate for an Illumina array. We attempt the GWAS assay only twice.

All DNAs 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.

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.

Back to top

For custom Illumina genotyping products, the pricing includes:
  • each plate can hold up to 92 samples (90 unique samples, 2 duplicates).
  • Four wells on each plate are reserved for internal controls. No discounts will be given for partially filled plates.
  • Products priced on a per sample basis must meet minimum sample requirements.
  • We are occasionally able to combine small projects to meet minimum sample requirements, but this is dependent on the availability of another project of the same type.
  • Pretesting is not included with these products, but is available at an additional charge.

Concentration:

  • Genomic DNA: 75 – 150 ng/µl
  • Whole genome amplified (WGA) products: 200 -300 ng/µl, depending on source of original DNA. We advise you to discuss issues concerning WGA samples with our staff prior to beginning your study. Please be sure of your concentrations. We will not adjust concentrations for you.

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.

Back to top

Shipment for Illumina genotyping:

DNAs 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:
GRCF/CIDR
Attn: DNA Techs
333 Cassell Dr.
Suite 2000
Baltimore, MD 21224

Shipment for Cell Line Authentication (customers outside of Johns Hopkins)

Laura Kasch
Fragment Analysis Facility
Johns Hopkins University
2760 Lighthouse Point East, Suite 201
Baltimore, MD 21224
Phone (443) 287-7948

Back to top