Abstract
Genome-wide scans for quantitative trait loci (QTL) have traditionally been summarized with plots of logarithm of odds (LOD) scores. A valuable modification is to supplement such plots with an additional vertical axis displaying quantiles of adjusted P values and labeling local maxima of the LOD scores with location-specific adjusted P values. This provides a visible gradation of genome-wide significance for the LOD score curve, instead of the stark dichotomy that a single threshold yields. Adjusted P values give genome-wide significance of individual LOD scores and are obtained through a straightforward modification of the familiar algorithm for generating permutation-based thresholds.
Full Text
The Full Text of this article is available as a PDF (104.7 KB).
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Broman Karl W. Mapping quantitative trait loci in the case of a spike in the phenotype distribution. Genetics. 2003 Mar;163(3):1169–1175. doi: 10.1093/genetics/163.3.1169. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Churchill G. A., Doerge R. W. Empirical threshold values for quantitative trait mapping. Genetics. 1994 Nov;138(3):963–971. doi: 10.1093/genetics/138.3.963. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Doerge R. W., Churchill G. A. Permutation tests for multiple loci affecting a quantitative character. Genetics. 1996 Jan;142(1):285–294. doi: 10.1093/genetics/142.1.285. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Dracheva S. V., Remmers E. F., Chen S., Chang L., Gulko P. S., Kawahito Y., Longman R. E., Wang J., Du Y., Shepard J. An integrated genetic linkage map with 1,137 markers constructed from five F2 crosses of autoimmune disease-prone and -resistant inbred rat strains. Genomics. 2000 Jan 15;63(2):202–226. doi: 10.1006/geno.1999.6074. [DOI] [PubMed] [Google Scholar]
- Haley C. S., Knott S. A. A simple regression method for mapping quantitative trait loci in line crosses using flanking markers. Heredity (Edinb) 1992 Oct;69(4):315–324. doi: 10.1038/hdy.1992.131. [DOI] [PubMed] [Google Scholar]
- Haley C. S., Knott S. A., Elsen J. M. Mapping quantitative trait loci in crosses between outbred lines using least squares. Genetics. 1994 Mar;136(3):1195–1207. doi: 10.1093/genetics/136.3.1195. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Jiang C., Zeng Z. B. Multiple trait analysis of genetic mapping for quantitative trait loci. Genetics. 1995 Jul;140(3):1111–1127. doi: 10.1093/genetics/140.3.1111. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kao C. H., Zeng Z. B., Teasdale R. D. Multiple interval mapping for quantitative trait loci. Genetics. 1999 Jul;152(3):1203–1216. doi: 10.1093/genetics/152.3.1203. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Knott S. A., Haley C. S. Multitrait least squares for quantitative trait loci detection. Genetics. 2000 Oct;156(2):899–911. doi: 10.1093/genetics/156.2.899. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Lander E. S., Botstein D. Mapping mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics. 1989 Jan;121(1):185–199. doi: 10.1093/genetics/121.1.185. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Lander E., Kruglyak L. Genetic dissection of complex traits: guidelines for interpreting and reporting linkage results. Nat Genet. 1995 Nov;11(3):241–247. doi: 10.1038/ng1195-241. [DOI] [PubMed] [Google Scholar]
- Nettleton D., Doerge R. W. Accounting for variability in the use of permutation testing to detect quantitative trait loci. Biometrics. 2000 Mar;56(1):52–58. doi: 10.1111/j.0006-341x.2000.00052.x. [DOI] [PubMed] [Google Scholar]
- Zeng Z. B. Precision mapping of quantitative trait loci. Genetics. 1994 Apr;136(4):1457–1468. doi: 10.1093/genetics/136.4.1457. [DOI] [PMC free article] [PubMed] [Google Scholar]