[PDF][PDF] Allele-sharing models: LOD scores and accurate linkage tests

A Kong, NJ Cox - The American Journal of Human Genetics, 1997 - cell.com
The American Journal of Human Genetics, 1997cell.com
Starting with a test statistic for linkage analysis based on allele sharing, we propose an
associated one-parameter model. Under general missing-data patterns, this model allows
exact calculation of likelihood ratios and LOD scores and has been implemented by a
simple modification of existing software. Most important, accurate linkage tests can be
performed. Using an example, we show that some previously suggested approaches to
handling less than perfectly informative data can be unacceptably conservative. Situations in …
Summary
Starting with a test statistic for linkage analysis based on allele sharing, we propose an associated one-parameter model. Under general missing-data patterns, this model allows exact calculation of likelihood ratios and LOD scores and has been implemented by a simple modification of existing software. Most important, accurate linkage tests can be performed. Using an example, we show that some previously suggested approaches to handling less than perfectly informative data can be unacceptably conservative. Situations in which this model may not perform well are discussed, and an alternative model that requires additional computations is suggested.
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