If you are planning to outsource the genotyping, kindly contact Kbiosciences now LCGgenomics). We are outsourcing SNPs genotyping with them and they are available through phone calls to discuss and assess the feasibility of your experimentation. website: http://www.lgcgenomics.com/genotyping/index/.

We use multiplex nested PCR following by hybridization on hydrogel biochips. Sensitivity - 6-10 genomes.

Have you looked at Sequenom's iPLEX technology? It has been shown to work with a lot of diiferent types of low quality DNA samples. It is based on multiplex PCR also.

I see no problem in using low amount of DNA (can be amplified) and genotyping technologies used few nanograms per assay, I also don't see a problem with degraded DNA, several technologies only need fragments of around 50 base-pair to place probes and primers. My concern is with contamination. If contamination is with other species may not be a problem at all, the polymorphic position may not be even conserved, if is from close specie or several individuals from the same that could make the difference. I have been using Taqman, LGC Genomics assays, and also MassArray and custom Illumina genotyping. and their use depend on number of SNPs to genotype (you say you want to analyse hundreds!!) and price. For hundreds may be good to check iPLEX-MassARRAy technology (can work with amplified DNA and with low amounts, price is ok), Illumina may work, they have an application for few hundred SNPs, amount required a little bit high, better to use original genomic DNA. LGC genomics works fantastic, but one by one! So good luck.

It would be good to first carry out a whole genome amplification (WGA). This can be done efficiently using a commencial kit available from GE (GenomePhi DNA amp Kit cat# 25-660-32). The amplified DNA is then used as a template in individual genotyping reactions. For genotyping, I would recommend either TaqMan approach or Illumina platforms.

try to make barcoded sequencing libraries for illumina. Either whole genome or RAD/GBS.

We have used Taqman Open Array (256 SNPs max) in degraded samples and the presence of contaminating DNA, such as saliva samples. The result is good, although it is necessary that this well purified DNA. The price depends on the number of samples to analyze, but economical for more than 1000 samples.

I would do as Helena suggests, use a WGA then try and PCR from this. If that doesn't yield results I would use a nested approach, which works for me even when there is no visible product from the first round of PCR. But, like Gloria, I would be concerned about contamination, which will only be exacerbated using a nested approach.

One can also use the InfiniumHD FFPE Restore Kit (Cat.Num. WG-321-1002) and then genotype with any Infinium BeadChip of Illumina Inc.

Taqman assays using Open Array or TLDA cards (depends on the SNPs number). We've already used for low amount of target DNA and degraded DNA. As the assays are based on primers and probes they are very specific.