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The optimal measure of allelic association

The optimal measure of allelic association
The optimal measure of allelic association
Allelic association between pairs of loci is derived in terms of the association probability ρ as a function of recombination ρ, effective population size N, linear systematic pressure v, and time t, predicting both ρrt, the decrease of association from founders and ρct, the increase by genetic drift, with ρt = ρrt + ρct. These results conform to the Malecot equation, with time replaced by distance on the genetic map, or on the physical map if recombination in the region is uniform. Earlier evidence suggested that is less sensitive to variations in marker allele frequencies than alternative metrics for which there is no probability theory. This robustness is confirmed for six alternatives in eight samples. In none of these 48 tests was the residual variance as small as for ρ. Overall, efficiency was less than 80% for all alternatives, and less than 30% for two of them. Efficiency of alternatives did not increase when information was estimated simultaneously. The swept radius within which substantial values of ρ are conserved lies between 385 and 893 kb, but deviation of parameters between measures is enormously significant. The large effort now being devoted to allelic association has little value unless the ρ metric with the strongest theoretical basis and least sensitivity to marker allele frequencies is used for mapping of marker association and localization of disease loci.
0027-8424
5217-5221
Morton, N.E.
c668e2be-074a-4a0a-a2ca-e8f51830ebb7
Zhang, W.
1c80d4f2-4ba8-41f6-85a6-a76a4d65dc9b
Taillon-Miller, P.
6f72eea0-063f-4cfd-98aa-969cea2a3566
Ennis, S.
7b57f188-9d91-4beb-b217-09856146f1e9
Kwok, P.Y.
f13657cb-a00b-4ea3-877c-78f42f83ab59
Collins, A.
7daa83eb-0b21-43b2-af1a-e38fb36e2a64
Morton, N.E.
c668e2be-074a-4a0a-a2ca-e8f51830ebb7
Zhang, W.
1c80d4f2-4ba8-41f6-85a6-a76a4d65dc9b
Taillon-Miller, P.
6f72eea0-063f-4cfd-98aa-969cea2a3566
Ennis, S.
7b57f188-9d91-4beb-b217-09856146f1e9
Kwok, P.Y.
f13657cb-a00b-4ea3-877c-78f42f83ab59
Collins, A.
7daa83eb-0b21-43b2-af1a-e38fb36e2a64

Morton, N.E., Zhang, W., Taillon-Miller, P., Ennis, S., Kwok, P.Y. and Collins, A. (2001) The optimal measure of allelic association. Proceedings of the National Academy of Sciences of the United States of America, 98 (9), 5217-5221. (doi:10.1073/pnas.091062198).

Record type: Article

Abstract

Allelic association between pairs of loci is derived in terms of the association probability ρ as a function of recombination ρ, effective population size N, linear systematic pressure v, and time t, predicting both ρrt, the decrease of association from founders and ρct, the increase by genetic drift, with ρt = ρrt + ρct. These results conform to the Malecot equation, with time replaced by distance on the genetic map, or on the physical map if recombination in the region is uniform. Earlier evidence suggested that is less sensitive to variations in marker allele frequencies than alternative metrics for which there is no probability theory. This robustness is confirmed for six alternatives in eight samples. In none of these 48 tests was the residual variance as small as for ρ. Overall, efficiency was less than 80% for all alternatives, and less than 30% for two of them. Efficiency of alternatives did not increase when information was estimated simultaneously. The swept radius within which substantial values of ρ are conserved lies between 385 and 893 kb, but deviation of parameters between measures is enormously significant. The large effort now being devoted to allelic association has little value unless the ρ metric with the strongest theoretical basis and least sensitivity to marker allele frequencies is used for mapping of marker association and localization of disease loci.

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More information

Published date: 2001
Additional Information: Published online before print April 17, 2001
Organisations: Human Genetics

Identifiers

Local EPrints ID: 24874
URI: http://eprints.soton.ac.uk/id/eprint/24874
ISSN: 0027-8424
PURE UUID: 677f0b9f-38ab-40ce-8cd0-36e2b24163ae
ORCID for S. Ennis: ORCID iD orcid.org/0000-0003-2648-0869
ORCID for A. Collins: ORCID iD orcid.org/0000-0001-7108-0771

Catalogue record

Date deposited: 06 Apr 2006
Last modified: 16 Mar 2024 03:07

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Contributors

Author: N.E. Morton
Author: W. Zhang
Author: P. Taillon-Miller
Author: S. Ennis ORCID iD
Author: P.Y. Kwok
Author: A. Collins ORCID iD

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