### Abstract

We analyzed part of the Genetic Analysis Workshop (GAW) 12 simulated data using Monte Carlo Markov chain (MCMC) methods that are implemented in the computer program Loki. The MCMC method reports the "probability of linkage" (PL) across the chromosomal regions of interest. The point of maximum PL can then be taken as a "location estimate" for the location of the quantitative trait locus (QTL). However, Loki does not provide a formal statistical test of linkage. In this paper, we explore how the bin width used in the calculations affects the max PL and the location estimate. We analyzed age at onset (AO) and quantitative trait number 5, Q5, from 26 replicates of the general simulated data in one region where we knew a major gene, MG5, is located. For each trait, we found the max PL and the corresponding location estimate, using four different bin widths. We found that bin width, as expected, does affect the max PL and the location estimate, and we recommend that users of Loki explore how their results vary with different bin widths.

Original language | English (US) |
---|---|

Journal | Genetic Epidemiology |

Volume | 21 |

Issue number | SUPPL. 1 |

State | Published - 2001 |

### Fingerprint

### Keywords

- Loki
- MCMC
- Quantitative trait

### ASJC Scopus subject areas

- Genetics(clinical)
- Epidemiology

### Cite this

*Genetic Epidemiology*,

*21*(SUPPL. 1).

**Markov chain Monte Carlo linkage analysis : Effect of bin width on the probability of linkage.** / Slager, Susan L; Juo, S. H.; Durner, M.; Hodge, S. E.

Research output: Contribution to journal › Article

*Genetic Epidemiology*, vol. 21, no. SUPPL. 1.

}

TY - JOUR

T1 - Markov chain Monte Carlo linkage analysis

T2 - Effect of bin width on the probability of linkage

AU - Slager, Susan L

AU - Juo, S. H.

AU - Durner, M.

AU - Hodge, S. E.

PY - 2001

Y1 - 2001

N2 - We analyzed part of the Genetic Analysis Workshop (GAW) 12 simulated data using Monte Carlo Markov chain (MCMC) methods that are implemented in the computer program Loki. The MCMC method reports the "probability of linkage" (PL) across the chromosomal regions of interest. The point of maximum PL can then be taken as a "location estimate" for the location of the quantitative trait locus (QTL). However, Loki does not provide a formal statistical test of linkage. In this paper, we explore how the bin width used in the calculations affects the max PL and the location estimate. We analyzed age at onset (AO) and quantitative trait number 5, Q5, from 26 replicates of the general simulated data in one region where we knew a major gene, MG5, is located. For each trait, we found the max PL and the corresponding location estimate, using four different bin widths. We found that bin width, as expected, does affect the max PL and the location estimate, and we recommend that users of Loki explore how their results vary with different bin widths.

AB - We analyzed part of the Genetic Analysis Workshop (GAW) 12 simulated data using Monte Carlo Markov chain (MCMC) methods that are implemented in the computer program Loki. The MCMC method reports the "probability of linkage" (PL) across the chromosomal regions of interest. The point of maximum PL can then be taken as a "location estimate" for the location of the quantitative trait locus (QTL). However, Loki does not provide a formal statistical test of linkage. In this paper, we explore how the bin width used in the calculations affects the max PL and the location estimate. We analyzed age at onset (AO) and quantitative trait number 5, Q5, from 26 replicates of the general simulated data in one region where we knew a major gene, MG5, is located. For each trait, we found the max PL and the corresponding location estimate, using four different bin widths. We found that bin width, as expected, does affect the max PL and the location estimate, and we recommend that users of Loki explore how their results vary with different bin widths.

KW - Loki

KW - MCMC

KW - Quantitative trait

UR - http://www.scopus.com/inward/record.url?scp=0034793338&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0034793338&partnerID=8YFLogxK

M3 - Article

C2 - 11793764

AN - SCOPUS:0034793338

VL - 21

JO - Genetic Epidemiology

JF - Genetic Epidemiology

SN - 0741-0395

IS - SUPPL. 1

ER -