• We are sorry, but NCBI web applications do not support your browser and may not function properly. More information
Logo of geneticsGeneticsCurrent IssueInformation for AuthorsEditorial BoardSubscribeSubmit a Manuscript
Genetics. May 1995; 140(1): 377–388.
PMCID: PMC1206563

The Detection of Linkage Disequilibrium in Molecular Sequence Data

Abstract

Studies of genetic variation in natural populations at the sequence level usually show that most polymorphic sites are very asymmetrical in allele frequencies, with the rarer allele at a site near fixation. When the rarer allele at a site is present only a few times in the sample, say below five representatives, it becomes very difficult to detect linkage disequilibrium between sites from tests of association. This is a consequence of the numerical properties of even the most powerful test of association, Fisher's exact test. Sites with fewer than five representatives in the sample should be excluded from association tests, but this generally leaves few site pairs eligible for testing. A test for overall linkage disequilibrium, based on the sign of the observed linkage disequilibria, is derived which can use all the data. It is shown that more power can be achieved by increasing the length of sequence determined than by increasing the number of genomes sampled for the same total work.

Full Text

The Full Text of this article is available as a PDF (951K).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Brown AH. Sample sizes required to detect linkage disequilibrium between two or three loci. Theor Popul Biol. 1975 Oct;8(2):184–201. [PubMed]
  • Lewontin RC. The Interaction of Selection and Linkage. I. General Considerations; Heterotic Models. Genetics. 1964 Jan;49(1):49–67. [PMC free article] [PubMed]
  • Overall JE, Rhoades HM, Starbuck RR. Small-sample tests for homogeneity of response probabilities in 2 X 2 contingency tables. Psychol Bull. 1987 Sep;102(2):307–314. [PubMed]
  • Riley MA, Hallas ME, Lewontin RC. Distinguishing the forces controlling genetic variation at the Xdh locus in Drosophila pseudoobscura. Genetics. 1989 Oct;123(2):359–369. [PMC free article] [PubMed]

Articles from Genetics are provided here courtesy of Genetics Society of America

Formats:

Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...

Links

  • PubMed
    PubMed
    PubMed citations for these articles

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...