A two-stage variable-stringency semiparametric method for mapping quantitative-trait loci with the use of genomewide-scan data on sib pairs.
- Authors
- Ghosh, S; Majumder, P P
- Year
- 2000
- Journal
- American journal of human genetics
- PMID
- 10712217
- DOI
- 10.1086/302815
- PMCID
- PMC1288141
Genomewide scans for mapping loci have proved to be extremely powerful and popular. We present a semiparametric method of mapping a quantitative-trait locus (QTL) or QTLs with the use of sib-pair data generated from a two-stage genomic scan. In a two-stage genomic scan, either the entire genome or a large portion of the genome is saturated with low-density markers at the first stage. At the second stage, the intervals that are identified as probable locations of the trait loci, by means of analysis of data from the first stage, are then saturated with higher-density markers. These data are then analyzed for fine mapping of the loci. Our statistical strategy for analysis of data from the first stage is a low-stringency method based on the rank correlation of squared trait-difference values of the sib pairs and the estimated identity-by-descent scores at the marker loci. We suggest the use of a low-stringency method at the first stage, to save on computational time and to avoid missing any marker interval that may contain the trait loci. For analysis of data from the second stage, we have developed a high-stringency nonparametric-regression approach, using the kernel-smoothing technique. Through extensive simulations, we show that this approach is more powerful than is a currently used method for mapping QTLs by use of sib pairs, particularly in the presence of dominance and epistatic effects at the trait loci.
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In this knowledge base
| Title | Year | PMID |
|---|---|---|
| A novel non-parametric regression reveals linkage on chromosome 4 for the number of externalizing symptoms in sib-pairs. | 2008 | 18454434 |
External
| Title | Authors | Journal | Year | Link |
|---|---|---|---|---|
| A novel non-parametric regression reveals linkage on chromosome 4 for the number of externalizing symptoms in sib-pairs. | Ghosh S et al. | — | 2008 | → |
| A nonparametric regression-based linkage scan of rheumatoid factor-IgM using sib-pair squared sums and differences. | Ghosh S et al. | — | 2007 | → |
| Linkage analyses of rheumatoid arthritis and related quantitative phenotypes: the GAW15 experience. | Ghosh S et al. | — | 2007 | → |
| Mapping quantitative trait loci in humans: achievements and limitations. | Majumder PP et al. | — | 2005 | → |
| Linkage mapping of beta 2 EEG waves via non-parametric regression. | Ghosh S et al. | — | 2003 | → |
| Linkage mapping of total cholesterol level in a young cohort via nonparametric regression. | Ghosh S et al. | — | 2003 | → |