The accuracy of lactase persistence phenotyping using breath hydrogen and blood glucose tests is limited by asymmetric false positive and false negative rates, which must be accounted for in genetic association studies to avoid misclassification bias.

Some people who can digest milk still show low hydrogen in their breath or small blood sugar spikes because their gut bacteria produce hydrogen slowly or their intestines absorb sugar quickly, making them look like they can't digest milk. Others who can't digest milk show high hydrogen or big sugar spikes because their gut bacteria ferment milk sugar loudly or their intestines absorb sugar poorly, making them look like they can digest milk. These mistakes happen because the tests measure side effects of digestion, not the gene itself, and those side effects vary too much between people.