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A tournament of linkage tests in complex inheritance

A tournament of linkage tests in complex inheritance
A tournament of linkage tests in complex inheritance
The performance of some weakly parametric linkage tests in common use was compared on 200 replicates of oligogenic inheritance from Genetic Analysis Workshop 10. Each random sample for the quantitative trait was dichotomized at different thresholds and also selected through 2 affected sibs, generating 8 combinations of sample and variable. The variance component program SOLAR performed best with a continuous trait, even in selected samples, when the population mean was used. The sib-pair program SIBPAL2 was best in most other cases when the phenotype product, population mean, and empirical estimates of pair correlations were used. The BETA program that introduced phenotype products was slightly more powerful than maximum likelihood scores under the null hypothesis and approached but did not exceed SIBPAL2 under its optimal conditions. Type I errors generally exceeded expectations from a chi2 test, but were conservative with respect to bounds on lods. All methods can be improved by use of the population mean, empirical correlations, logistic representation for affection status, and correct lods for samples that favour the null hypothesis. It remains uncertain whether all information can be extracted by weakly parametric methods and whether correction for ascertainment bias demands a strongly parametric model. Performance on a standard set of simulated data is indispensable for recognising optimal methods.
variance components, sib pairs, haseman-elston test, phenotype products, quantitative trait, binary trait
0001-5652
140-148
Zhang, W.
1c80d4f2-4ba8-41f6-85a6-a76a4d65dc9b
Tapper, W.
9d5ddc92-a8dd-4c78-ac67-c5867b62724c
Collins, A.
7daa83eb-0b21-43b2-af1a-e38fb36e2a64
Jacobs, K.B.
c433c325-aaae-465c-a226-7b5e69bddddd
Elston, R.C.
1c030579-c75c-469f-8fd6-b39906371750
Morton, N.E.
c668e2be-074a-4a0a-a2ca-e8f51830ebb7
Zhang, W.
1c80d4f2-4ba8-41f6-85a6-a76a4d65dc9b
Tapper, W.
9d5ddc92-a8dd-4c78-ac67-c5867b62724c
Collins, A.
7daa83eb-0b21-43b2-af1a-e38fb36e2a64
Jacobs, K.B.
c433c325-aaae-465c-a226-7b5e69bddddd
Elston, R.C.
1c030579-c75c-469f-8fd6-b39906371750
Morton, N.E.
c668e2be-074a-4a0a-a2ca-e8f51830ebb7

Zhang, W., Tapper, W., Collins, A., Jacobs, K.B., Elston, R.C. and Morton, N.E. (2001) A tournament of linkage tests in complex inheritance. Human Heredity, 52 (3), 140-148. (doi:10.1159/000053369).

Record type: Article

Abstract

The performance of some weakly parametric linkage tests in common use was compared on 200 replicates of oligogenic inheritance from Genetic Analysis Workshop 10. Each random sample for the quantitative trait was dichotomized at different thresholds and also selected through 2 affected sibs, generating 8 combinations of sample and variable. The variance component program SOLAR performed best with a continuous trait, even in selected samples, when the population mean was used. The sib-pair program SIBPAL2 was best in most other cases when the phenotype product, population mean, and empirical estimates of pair correlations were used. The BETA program that introduced phenotype products was slightly more powerful than maximum likelihood scores under the null hypothesis and approached but did not exceed SIBPAL2 under its optimal conditions. Type I errors generally exceeded expectations from a chi2 test, but were conservative with respect to bounds on lods. All methods can be improved by use of the population mean, empirical correlations, logistic representation for affection status, and correct lods for samples that favour the null hypothesis. It remains uncertain whether all information can be extracted by weakly parametric methods and whether correction for ascertainment bias demands a strongly parametric model. Performance on a standard set of simulated data is indispensable for recognising optimal methods.

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More information

Published date: September 2001
Keywords: variance components, sib pairs, haseman-elston test, phenotype products, quantitative trait, binary trait

Identifiers

Local EPrints ID: 25063
URI: http://eprints.soton.ac.uk/id/eprint/25063
ISSN: 0001-5652
PURE UUID: 5e7eff42-089e-41e5-9251-504a5672fdf6
ORCID for W. Tapper: ORCID iD orcid.org/0000-0002-5896-1889
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: W. Zhang
Author: W. Tapper ORCID iD
Author: A. Collins ORCID iD
Author: K.B. Jacobs
Author: R.C. Elston
Author: N.E. Morton

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