We operate on a first-come first-served basis. Most clients get results within a couple weeks. We regret that we currently can't release results until the genotyping invoice is paid. The time each step takes is as follows:

• The iPlex (multiplex) design for your SNP list is usually completed in a day or two after receipt of your list.
• Primer orders usually take a week to be delivered.
• The actual genotyping often can be done the same day, if we have your samples and no other clients are ahead of you.
• Genotyping results are formatted and ready to send within the next day. Once we have received payment, the results are sent to the client within a day of payment.
• For repeat clients where the same multiplex is used repeatedly, a week to 10 days is saved because we don't have to design and wait for primers.

Sequenom recommends an A260/A280 ratio of 1.7 to 2.0, and 5 to 10 ng/ul of DNA for each sample in a multiplex. They found that the reactions work with up to 50ng DNA, above that performance degrades. We use 10 ng per multiplex.

We've had success with human samples with less DNA (down to 1 ng/ul), but the failure rate increases. We can only guarantee results for complex genomic DNA at 5 ng/ul. For simpler genomes (e.g., yeast) much less DNA is required (as long as the molar level for the genome is comparable to that used for more complex genomes).

Usually 80-100 bp.

Designs can fail at the PCR primer design or the extension primer design stage. We use up to 200 bases flanking each SNP for PCR design. The sequence (human and mouse only) has been masked for nearby SNPs, so no primer will include another known SNP. Reasons for failure in the PCR primer design:

• A SNP is rejected if PCR primers can't be identified that will produce a product mapping to one genomic location. (Currently we can do this check only for human genome.)
• SNPs embedded in high GC or AT regions will have trouble.

If both strand extension primers fail, the SNP design fails. Reasons for extension primer failure:

• Extension primer would include another close SNP (within 16 bases).
• Extension primer with high dimer potential.
• Extension primer with high false priming potential.

The design software checks for primer compatibility between assays, and cases where there is a high likelihood of false priming potential or dimerization are separated into different multiplexes. Also the extension product masses in one multiplex must be sufficiently separated to allow the genotypes to be discerned. The software can add, up to a point, non-genomic 5' bases to an extension primer to change extension product size, allowing more flexibility in any given multiplex. Our experience however is that for any given set of sequences, a few will fall into one or more low-level multiplexes.

We will accept replacements for one more round of designing at no extra cost. After that, each round of design will cost the client $100.

This can be done but is discouraged, as it increases the possibility of error. Each round of extra designs will cost the client $150.

If the DNA is capable of PCR, it should work. Because the PCR products used for our genotyping are very small (usually less than 100 bp), somewhat degraded DNA also works.

We've have variable success using WGA DNA. The best results are with samples that began with high quality genomic DNA. It appears that heterozygous results may be trusted, but some fraction of the homozygous genotypes will be spurious. This is probably due to selective amplification of one allele in the WGA process.

No, we have found that quality degrades after about 8 months. For best results when using the same multiplex on additional samples, we recommend replacing the primers after that amount of time.

We keep them at -20C degrees. The primers belong to the client, so clients may collect their primer plates and use them for their own purposes if desired. We will keep primer plates for one year.

We have limited storage space. We ask that you pick up your extra sample DNAs the week after you receive genotyping results. If left longer than one month, we will dispose the sample DNA (unless you've made special arrangements), but will try to contact you about it first.