Comparison of novel and existing methods for detection of linkage disequilibrium using parent-child trios in the GAW12 genetic isolate simulated data

J. E. Bailey-Wilson; A. J M Sorant; J. D. Malley; S. Presciuttini; R. A. Redner; T. A. Severini; J. A. Badner; S. Pajevic; R. Jufer; A. Baffoe-Bonnie; L. Kao; B. Q. Doan; J. L. Goldstein; T. N. Holmes; D. Behneman; D. M. Mandal; T. N. Turley; K. A. Weissbecker; J. O'Neill; E. W. Pugh

doi:10.1002/gepi.2001.21.s1.s378

Comparison of novel and existing methods for detection of linkage disequilibrium using parent-child trios in the GAW12 genetic isolate simulated data

J. E. Bailey-Wilson^*, A. J M Sorant, J. D. Malley, S. Presciuttini, R. A. Redner, T. A. Severini, J. A. Badner, S. Pajevic, R. Jufer, A. Baffoe-Bonnie, L. Kao, B. Q. Doan, J. L. Goldstein, T. N. Holmes, D. Behneman, D. M. Mandal, T. N. Turley, K. A. Weissbecker, J. O'Neill, E. W. Pugh

^*Corresponding author for this work

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Abstract

A novel method for joint detection of association caused by linkage disequilibrium (LD) and estimation of both recombination fraction and linkage disequilibrium parameters was compared to several existing implementations of the transmission/disequilibrium test (TDT) and modifications of the TDT in the simulated genetic isolate data from Genetic Analysis Workshop 12. The first completely genotyped trio of affected child and parents was selected from each family in each replicate so that the TDT tests are valid tests of linkage and association, rather than being only valid as tests for linkage. In general, power to detect LD using the genome-wide scan markers was inadequate in the individual replicate samples, but the power was better when analyzing several SNP markers in candidate gene 1.

Original language	English (US)
Pages (from-to)	S378-S383
Journal	Genetic Epidemiology
Volume	21
Issue number	SUPPL. 1
DOIs	https://doi.org/10.1002/gepi.2001.21.s1.s378
State	Published - 2001

Keywords

Association
ELAAT
Linkage disequilibrium
Power
TDT

ASJC Scopus subject areas

Genetics(clinical)
Epidemiology

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10.1002/gepi.2001.21.s1.s378

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Bailey-Wilson, J. E., Sorant, A. J. M., Malley, J. D., Presciuttini, S., Redner, R. A., Severini, T. A., Badner, J. A., Pajevic, S., Jufer, R., Baffoe-Bonnie, A., Kao, L., Doan, B. Q., Goldstein, J. L., Holmes, T. N., Behneman, D., Mandal, D. M., Turley, T. N., Weissbecker, K. A., O'Neill, J., & Pugh, E. W. (2001). Comparison of novel and existing methods for detection of linkage disequilibrium using parent-child trios in the GAW12 genetic isolate simulated data. Genetic Epidemiology, 21(SUPPL. 1), S378-S383. https://doi.org/10.1002/gepi.2001.21.s1.s378

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title = "Comparison of novel and existing methods for detection of linkage disequilibrium using parent-child trios in the GAW12 genetic isolate simulated data",

abstract = "A novel method for joint detection of association caused by linkage disequilibrium (LD) and estimation of both recombination fraction and linkage disequilibrium parameters was compared to several existing implementations of the transmission/disequilibrium test (TDT) and modifications of the TDT in the simulated genetic isolate data from Genetic Analysis Workshop 12. The first completely genotyped trio of affected child and parents was selected from each family in each replicate so that the TDT tests are valid tests of linkage and association, rather than being only valid as tests for linkage. In general, power to detect LD using the genome-wide scan markers was inadequate in the individual replicate samples, but the power was better when analyzing several SNP markers in candidate gene 1.",

keywords = "Association, ELAAT, Linkage disequilibrium, Power, TDT",

author = "Bailey-Wilson, {J. E.} and Sorant, {A. J M} and Malley, {J. D.} and S. Presciuttini and Redner, {R. A.} and Severini, {T. A.} and Badner, {J. A.} and S. Pajevic and R. Jufer and A. Baffoe-Bonnie and L. Kao and Doan, {B. Q.} and Goldstein, {J. L.} and Holmes, {T. N.} and D. Behneman and Mandal, {D. M.} and Turley, {T. N.} and Weissbecker, {K. A.} and J. O'Neill and Pugh, {E. W.}",

year = "2001",

doi = "10.1002/gepi.2001.21.s1.s378",

language = "English (US)",

volume = "21",

pages = "S378--S383",

journal = "Genetic Epidemiology",

issn = "0741-0395",

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number = "SUPPL. 1",

}

Bailey-Wilson, JE, Sorant, AJM, Malley, JD, Presciuttini, S, Redner, RA, Severini, TA, Badner, JA, Pajevic, S, Jufer, R, Baffoe-Bonnie, A, Kao, L, Doan, BQ, Goldstein, JL, Holmes, TN, Behneman, D, Mandal, DM, Turley, TN, Weissbecker, KA, O'Neill, J & Pugh, EW 2001, 'Comparison of novel and existing methods for detection of linkage disequilibrium using parent-child trios in the GAW12 genetic isolate simulated data', Genetic Epidemiology, vol. 21, no. SUPPL. 1, pp. S378-S383. https://doi.org/10.1002/gepi.2001.21.s1.s378

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T1 - Comparison of novel and existing methods for detection of linkage disequilibrium using parent-child trios in the GAW12 genetic isolate simulated data

AU - Bailey-Wilson, J. E.

AU - Sorant, A. J M

AU - Malley, J. D.

AU - Presciuttini, S.

AU - Redner, R. A.

AU - Severini, T. A.

AU - Badner, J. A.

AU - Pajevic, S.

AU - Jufer, R.

AU - Baffoe-Bonnie, A.

AU - Kao, L.

AU - Doan, B. Q.

AU - Goldstein, J. L.

AU - Holmes, T. N.

AU - Behneman, D.

AU - Mandal, D. M.

AU - Turley, T. N.

AU - Weissbecker, K. A.

AU - O'Neill, J.

AU - Pugh, E. W.

PY - 2001

Y1 - 2001

N2 - A novel method for joint detection of association caused by linkage disequilibrium (LD) and estimation of both recombination fraction and linkage disequilibrium parameters was compared to several existing implementations of the transmission/disequilibrium test (TDT) and modifications of the TDT in the simulated genetic isolate data from Genetic Analysis Workshop 12. The first completely genotyped trio of affected child and parents was selected from each family in each replicate so that the TDT tests are valid tests of linkage and association, rather than being only valid as tests for linkage. In general, power to detect LD using the genome-wide scan markers was inadequate in the individual replicate samples, but the power was better when analyzing several SNP markers in candidate gene 1.

AB - A novel method for joint detection of association caused by linkage disequilibrium (LD) and estimation of both recombination fraction and linkage disequilibrium parameters was compared to several existing implementations of the transmission/disequilibrium test (TDT) and modifications of the TDT in the simulated genetic isolate data from Genetic Analysis Workshop 12. The first completely genotyped trio of affected child and parents was selected from each family in each replicate so that the TDT tests are valid tests of linkage and association, rather than being only valid as tests for linkage. In general, power to detect LD using the genome-wide scan markers was inadequate in the individual replicate samples, but the power was better when analyzing several SNP markers in candidate gene 1.

KW - Association

KW - ELAAT

KW - Linkage disequilibrium

KW - Power

KW - TDT

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ER -

Comparison of novel and existing methods for detection of linkage disequilibrium using parent-child trios in the GAW12 genetic isolate simulated data

Abstract

Keywords

ASJC Scopus subject areas

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