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Contents

Setting Up a Genotyping Project at the Core

Before you bring samples to the Core for genotyping, you must meet with Core personnel to set up your project.

Call or e-mail for an appointment:

Uma Dandekar, GenoSeq Core Assistant Director
Email: uma@ucla.edu
Phone: 310-267-2461
Fax: 310-794-5446

Some of the things the Core will want to know about your proposed project are:

1. Number of samples
2. DNA:
  • Purity
  • Degradation - Do you have an agarose gel image?
  • Source. Is this DNA from whole genome amplification, blood, or other tissue?
  • Has the sample been used before? How did it perform?
3. Marker information:
Do you want to use one commercially available sets, or do you have custom markers?
For custom markers we want to know:
  • Sequence
  • Labels (are they compatible with our ABI dye set)?
  • Size
  • Repeat length (for microsatellites)
  • Minor allele frequency (for SNPs)
  • Have these markers been tested, and on what platform?
  • PCR conditions (standard protocol for all markers or different protocols for different markers)?
  • Do you have previous data with these markers?
  • Do you have your own controls?
  • Are there existing panels and if yes, what are the size ranges?
4. Schedule/deadlines

Submitting Samples

You must meet with Core personnel before submitting samples.

Format

The DNA should be in 96 well plate format. Microsatellite projects must have no more than 94 samples per 96 well plate (we need two wells for internal controls). SNPlex projects must have no more than 88 samples per 96 well plate (we need wells for positive and negative controls)

Concentration

The concentration should be 10 ng/μl for microstellites. It is of critical importance to the success of your study that you have a constant volume and concentration for all samples.

Quantity

We need 24 ng per reaction, a total of 10 μg of DNA for an LMSv2.5-MD10 - 10 cM scan; and 20 μg for an LMSv2.5-HD5 - 5 cM scan.

Accompanying files

All files must be submitted in electronic format. No hard copies or pedigree diagrams will be accepted. We will need a plate map giving sample names for the DNA plates. Please do not give the same name to more than one sample, even if they are on different plates. The Core tracks all your data, and does QC on your entire project, so re-using sample names will generate errors.

  • Important: You must generate an anonymous ID for each patient and family. The Genotyping Core will not accept any information that can identify your study subjects. This includes names, addresses, telephone numbers, or social security numbers. For studies where family structure information is collected, the Genotyping Core also requests a pedigree file at the time the samples are delivered. Please read these instructions before sending us a pedigree file.
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