The ability to single out the Y chromosome and genotype male-specific markers is proving popular among forensic pathologists, because fully sequencing each DNA sample is prohibitively expensive. “With our Y genotyping kit, it is possible to screen many pieces of evidence at a relatively modest cost,” says James Lazar, vice-president of research and development at Marligen Biosciences in Ijamsville, Maryland.
Marligen's Signet Y-SNP Identification System detects 43 single-nucleotide polymorphisms (SNPs) from the Y chromosome simultaneously. If these fail to match those of a suspect, he can be eliminated from consideration. And in rape cases, the ability to single out male DNA is a boon. Population genetics is another application.
“All SNPs in our panel have been widely studied and there is a lot of literature on the frequency of those SNPs in different populations. So one can figure out the ethnic background in a broad sense by looking at those SNPs,” says Lazar.
When samples have been out in the woods for weeks, or only a piece of bone is found, nuclear DNA can be degraded, yet the more plentiful mitochondrial DNA remains intact. A full forensic analysis of mitochondrial DNA can cost thousands of dollars, but Marligen provides an inexpensive alternative: the Signet Mitochondrial DNA Screening System, which analyses 30 variations at a cost of less than $20 per sample.
Marligen's products all use the xMAP technology developed by Luminex in Austin, Texas. This combines microbead-based assays with detection by small lasers. The current platform uses 100 different colour-coded microspheres, to which capture probes are coupled. For many studies an array platform with 100 features is quite enough for large-scale high throughput. “It turns out you are usually only interested in screening a few dozen SNPs rather than tens of thousands,” says Jim Jacobson, vice-president of research and development at Luminex.
The small number of features was decisive for Marligen. “In many disease states it is emerging that 20–50 genes are important. That's where we expect science to take us — more than one gene but less than 100,” says Lazar.
The Luminex system allows multiplexing of up to 50 SNPs in a single well, saving up to tenfold on reagents and allowing the detection of 10,000 SNPs a day. “It's highly reproducible and very fast. To read a 96-well plate takes 30–40 minutes,” says Lazar.
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Crime busters. Nature 422, 917 (2003). https://doi.org/10.1038/422917b