Proper controls for SNP studies?
Kari Hemminki and
Asta Försti
Department Biosciences, Karolinska Institute, Novum, 141 57 Huddinge, Sweden
Email: kari.hemminki{at}cnt.ki.se
Recent letters in Carcinogenesis have discussed the selection of proper controls for an association study on a metabolic genotype in colorectal cancer (13): a most acute general theme because of the vast interest in testing candidate-genes in case-control studies of cancer (46). There has been a lot of frustration about the poor replicability of the findings (7,8), and some authors, such as those of the letter demand that cases and controls need to be tightly matched when the effects of single-nucleotide polymorphisms (SNP) are tested (2). This requirement is justified if the effects of environmental factors or geneenvironment interactions are tested (9), which was not the case in the referred study (1). The only real concerns for bias in SNP association studies are ethnic asymmetries and lethal genotypes. Matching for ethnicity is usually considered (10), and the genotype differences between, for example, European populations appear to be small (11,12). It would be highly unlikely that many SNPs with a minor change in protein would cause lethality, particularly in a heterozygous state. However, there is a way to test for the effect of lethality, because the genotype distribution would then deviate from the HardyWeinberg equilibrium (HWE). There is evidence for fetal lethality at least for one BRCA2 variant (13). Variant homozygotes, with an estimated fitness of 0.82, were in less than expected numbers based on HWE. Methylenetetrahydofolate reductase (MTHFR) polymorphisms have also been suggested to cause fetal mortality but the evidence has remained controversial (14,15). Extreme differences between ages of cases and controls may lead to differences in genotype distributions because of selective mortality due to diseases, again resulting in a deviation from HWE. It would seem that increasing the sample size would be more useful for SNP association studies than spending efforts on tight matching. The SNP communities working on various diseases would benefit greatly if population genotype frequencies were available from large numbers of healthy adults, for example on blood donors, to be used as controls or at least for reference purposes.
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Received April 19, 2002;
accepted April 23, 2002.