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Population stratifications can cause false positive linkage results if founders are untyped

We wish to draw attention to the fact that population stratifications can produce a bias towards yielding false positive linkage results when founder genotypes are missing. It is now fairly well known that misspecification of allele frequencies can produce such a bias ‐ if a common allele is misspecified as rare then the fact that it is frequently observed among affected individuals will be incorrectly taken as evidence of increased sharing of alleles identical‐by‐descent (Ott, 1992). What may be less widely recognized is that similar effects can occur even if the correct population allele frequencies are used. Independently of us, Miller et al. (1995) and Gu et al. (1995) have recently shown that population stratifications can produce false positive linkage results for Lange's (1985) identity‐by‐state affected sib‐set analysis and for the affected‐pedigree‐member method (APM, Weeks & Lange, 1988). In fact, the problem applies to any method of linkage analysis when applied to datasets with untyped founders.