Abstract Linkage analysis maps genetic loci for a heritable trait by identifying genomic regions with excess relatedness among individuals with similar trait values. Analysis may be conducted on related individuals from families, or on samples of unrelated individuals from a population. For allelically heterogeneous traits, population‐based linkage analysis can be more powerful than genotypic‐association analysis. Here, we focus on linkage analysis in a population sample, but use sequences rather than individuals as our unit of observation. Earlier investigations of sequence‐based linkage mapping relied on known sequence relatedness, whereas we infer relatedness from the sequence data. We propose two ways to associate similarity in relatedness of sequences with similarity in their trait values and compare the resulting linkage methods to two genotypic‐association methods. We also introduce a procedure to label case sequences as potential carriers or noncarriers of causal variants after an association has been found. This post hoc labeling of case sequences is based on inferred relatedness to other case sequences. Our simulation results indicate that methods based on sequence relatedness improve localization and perform as well as genotypic‐association methods for detecting rare causal variants. Sequence‐based linkage analysis therefore has potential to fine‐map allelically heterogeneous disease traits.
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