Student DNA Genotyping by Mass Spectrometry: An Affordable Look into DNA Ancestry and Profiling

We present tests of a distributed system to genotype mitochondrial (mt) polymorphisms and predictors of taste, olfaction, and lactose tolerance using mass spectrometry – at a cost of about $8 per sample. Our genotype panel investigates 24 single nucleotide polymorphisms (SNPs) in the mt genome that identify major lineages from Africa, Europe, Asia, and the Americas. Three SNPs in the TAS2R38 bitter taste receptor predict the ability to phenylthiocarbamide (PTC), one SNP in the olfactory receptor OR11H7P predicts sensitivity to isovaleric acid (smelly socks), and four SNPs in the regulatory region of the lactase gene predict lactose tolerance in European and African populations.

Students safely isolate DNA using a saline mouthwash and quick Chelex extraction. Samples are then sent to a central laboratory for amplification of the 32 polymorphic loci. Primer extension generates allele-specific products with different masses, which are separated using time of flight mass spectrometry. Results are automatically uploaded to an online database, where students analyze their genotypes with simple bioinformatics tools and a phylogenic tree builder. Phenotype predictions are followed up with taste and smell tests.

The lineage analysis follows on our popular mtDNA sequencing kit and online tools that have been used to analyze more than 100,000 student sequences. The phenotype predictions illustrate the current use of mass spectrometry in forensic DNA profiling, which predicts the hair and eye color of a suspect from DNA collected at a crime scene. The PTC experiment extends our TAS2R38 SNP kit that uses agarose gel electrophoresis to analyze genotypes.