The right equipment
"One of the challenges is obtaining high-enough quality DNA to obtain a full profile with these samples," she says. DNA extracted from bone and teeth is typically low quantity, and it's often low quality in historical contexts. Acidic, very wet or dry soil is also destructive and not ideal for sample recovery.
Similarly, quantity and quality factors are relevant to the forensics of modern sites as well, Elkins says. “Sometimes when DNA is old or improperly stored or just low in quantity from crime scenes, you don't get a complete profile using the traditional methods. NGS is much more sensitive. We can get more data out of degraded samples than ever before."
"We use a lot of QIAGEN equipment," Elkins says, “such as the BioRobot® EZ1 instrument for DNA extraction of six samples at a time. For our level of throughput, the instrument is absolutely perfect. Students get experience with robots, but we don't waste a lot of supplies - we only use one cartridge for one sample at a time."
They use one of their two QIAGEN Rotor-Gene Qs to amplify and quantify the DNA. "It is such a robust and reliable instrument," she says. "We primarily use them for commercial qPCR kits and for in-house assays that we've designed ourselves."
Also important are the Rotor-Gene ScreenClust HRM Software, a principal component analysis tool used for molecular genotype analyses, and the PyroMark sequencer for SNP genotyping and body fluid analysis.
There's also the MiSeq FGx, an MPS instrument tailored for forensic genomics. "In about 27 to 30 hours, we can sequence and analyze up to 96 samples with that instrument." That is important because student research projects can involve a high number of samples that need to be run in multiple replicates. "It's great to be able to put all of the class samples in the instrument at one time and run them over a weekend," she says. "They can analyze everything when they're back in class on Monday."