-- Click here for a PDF of Submission Guidelines --

Please use this MS Excel Submission Form to submit samples to the CAG biorepository. In order for us to proceed with sample-precessing, it is important that all fields be completed. If you have any questions, please contact This email address is being protected from spambots. You need JavaScript enabled to view it..

DNA quality

  • NOTE: We cannot take saliva DNA unless collected with Oragene or iSWAB kits
  • All DNA should be at a minimum concentration of 50 ng/μl in TE (10mM Tris, 1mM EDTA), low conc. EDTA TE (10mM Tris, 0.1-.05mM EDTA) or Tris.
  • Minimum volume of 25 g/μl, for a total DNA quantity between 0.75-1.0. Please note that concentrations between 50-100ng are best suited for our genotyping assays.
  • The 260/280 ratio from a UV spec. reading should be 1.65-2.1. Samples with 260/280 ratios below 1.65 will result in lower call rates. If 260/280 ratio is low, the DNA should be re-extracted.
  • The CAG will run DNAs on an agarose gel to test for DNA quality and quantity. If the samples do not meet our specifications, the CAG reserves the right to refrain from genotyping them.
  • Whole-Genome Amplified DNA must be a fresh amplification using Repli-G (Qiagen). Others kits have been shown (through collaborators) to amplify the water control. The concentration must be measured with picogreen. Older amplifications have been shown to give less than 96 percent call rates and will yield unusable results.
  • We cannot use DNA extracted from fixed tissue for the Infinium assay, but can for the GoldenGate assay. The GoldenGate Assay can tolerate relatively short stretches of target DNA (200 bp) and can be quite tolerant of degraded FFPE samples. Internal experience with FFPE samples used with the GoldenGate Assay indicates that high-quality genotyping data can still be obtained by using FFPE samples with the GoldenGate Assay. Decreased call rates from FFPE samples compared to genomic DNA samples may be observed and the decrease in call rate depends on the level of sample degradation.
  • If you need to concentrate your DNA, please use a speedvac and refrain from precipitating using NaOAC or other salts + ethanol

Plating samples

Tubes vs. Trays

  • If you are sending between 1-8 samples, please send your samples in 1.5mL centrifuge tubes.
  • If you are sending any number greater than 8 samples, please send your samples in 96 well plate.

Don'ts

  • Do not leave any wells empty or fill with water/TE.
  • Do not duplicate samples. REPEAT: DO NOT plate duplicates!
  • Do not use an ELISA plate or any flat-bottom plate.

Dos

  • Plate DNA into a 96 well 0.2ml, V bottom, skirted plate (Fisher AB-0800, USA Scientific 1402-9800, or World Wide Medical Products 41081006)
  • Fill out a DNA manifest:
    • Plate Label: Plate ID, make sure that manifest name matches what is written on the actual plate
    • Well: Fill in the well locations.
    • Sample Label: Unique sample ID without any patient identifiers (no initials, D.O.B., SS)
    • Sex: to best of your ability fill out the gender
    • Volume: As stated above, the volume should be at least 15ul
    • Concentration: at least 50 ng/μl in TE (10mM Tris, 1mM EDTA)
    • Tissue Source: What is the source of DNA: blood, tissue, cells?
    • Age: Age of person at sample collection
    • Primary phenotype: Chief diagnosis. Please indicate primary phenotype, i.e. what disorder does this person have? Please note of the sample is a control
    • Family ID: if applicable, if you do not have mother, fill with "0"
    • Paternal ID: Sample ID of case study's father, if you do not have father, fill with "0"
    • Maternal ID: Sample ID Case study's mother, if you do not have mother, fill with "0"
    • Secondary phenotype: any diagnosis other than primary phenotype
    • Co-variants 1 and Co-variants 2: other available phenotype
    • IS control: please leave this column filled with zeros
  • Seal the plate with an adhesive foil seal (Beckman Coulter, BK538619). This particular seal remains intact from room temperature through -80 degrees. Make sure the seal is secure by pressing down on each individual well with your finger.
  • To submit samples or if you have any questions, please e-mail This email address is being protected from spambots. You need JavaScript enabled to view it..

Shipping samples

The following shipping guidelines were set up so that your DNA arrives safely. Please follow as closely as possible.

  • Ship DNA overnight on dry ice Monday – Thursday (no one will be here to receive the package on weekends), in compliance with local, state, and federal regulatory commissions.
  • Freeze the sealed plate in the -20 degree before placing on dry ice. If you were to place the plate directly on dry ice, the plate will crack.
  • Wrap plates in paper towels or bench pads. Do not cram plates into a small box, but use a larger box, and leave enough room for ample dry ice and padding. Ensure that the adhesive seals do not come in contact with other plates or sides of the box.
  • Seal the 96 well plate with an appropriate adhesive seal that will withstand the shipping, and place in a water tight bag. We suggest sealing each individual well by rubbing your fingers across the seal. If shipping more than one plate, stack them so there is padding between the plates. This padding prevents one plate from puncturing the seal of another. Further, provide enough padding to keep the plates from shifting inside the package during the shipping process.

Our shipping address

Laboratory Manager
The Center for Applied Genomics
Children's Hospital of Philadelphia
3615 Civic Center Blvd.
Abramson Research Center, 1215A
Philadelphia, PA 19104

Common errors

The following are a list of common errors to AVOID when shipping samples to our lab:

  • Frozen plates with holes in the foil seals from another plate sitting on top of it
  • Frozen plates where the seal has lifted off of the plate completely and samples evaporated
  • Frozen plates where the wells were completely cracked, broken off, or chipped into pieces
  • Room temperature plates where the seals have completely lifted off and the DNAs seeped into other wells, contaminating other samples
  • Room temperature plates with wells completely dried out
  • ELISA/TC plates used with an adhesive seal + lid on top…most wells were evaporated.
  • Manifest plate labels not matching what was written on the actual plate
  • Manifests indicating an empty well when there is no DNA
  • Manifests indicating DNA and nothing is in the well (Even after elution, we found no DNA)
  • Manifests with incorrect sample well locations and incorrect IDs