| Literature DB >> 22443496 |
Song Wu1, Guifang Fu, Yunmei Chen, Zhong Wang, Rongling Wu.
Abstract
BACKGROUND: Genetic mapping has been used as a tool to study the genetic architecture of complex traits by localizing their underlying quantitative trait loci (QTLs). Statistical methods for genetic mapping rely on a key assumption, that is, traits obey a parametric distribution. However, in practice real data may not perfectly follow the specified distribution.Entities:
Mesh:
Year: 2012 PMID: 22443496 PMCID: PMC3353242 DOI: 10.1186/1471-2156-13-20
Source DB: PubMed Journal: BMC Genet ISSN: 1471-2156 Impact factor: 2.797
Figure 1Mice data density plot. The empirical density for the growth rate of body mass from ages 5 weeks to 10 weeks in an F2 mapping population of 500 mice.
Figure 2Comparison between the two implementations of the L. (a) Using the true density of the error term. (b) Using the true density of the observed data. The arrows to the x-axe indicate the peak of the ED profile. The true position of the QTL is at 86 cM from the left end of the simulated chromosome.
Simulation scenario 1.
| Parameter | True Value | L2E | ML | L2E | ML | L2E | ML |
|---|---|---|---|---|---|---|---|
| 35 | 35(0.0685) | 35(0.0514) | 35.1(0.1061) | 35(0.0833) | 35.2(0.1653) | 35.2(0.1396) | |
| 30 | 30(0.0332) | 30(0.0286) | 30.1(0.0706) | 30.1(0.0522) | 30(0.1087) | 30(0.0909) | |
| 25 | 25(0.0724) | 25.1(0.057) | 25.1(0.0881) | 25.1(0.0768) | 24.9(0.1489) | 24.8(0.1118) | |
| sigma | 4.3 | 4.3(0.0228) | 4.3(0.0165) | ||||
| sigma | 7.1 | 7.0(0.0344) | 7.1(0.0282) | ||||
| sigma | 10.6 | 10.4(0.0548) | 10.6(0.0375) | ||||
| Position | 86 | 85.7(0.1386) | 85.8(0.101) | 85.9(0.2335) | 86.4(0.1433) | 86.0(0.5101) | 85.8(0.2537) |
The L2 and ML estimates of QTL parameters from an F2population of 400 individuals for the phenotypic data simulated from normal distributions. Numbers in the parentheses are the mean square errors (MSE) of the estimates
Simulation scenario 2.
| df = 2 | df = 3 | df = 4 | |||||
|---|---|---|---|---|---|---|---|
| Parameter | True Value | L2E | ML | L2E | ML | L2E | ML |
| 35 | 35.0(0.0168) | 39.3(4.0988) | 35.0(0.0139) | 35.1(0.0185) | 35.0(0.0117) | 35.1(0.0133) | |
| 30 | 30.0(0.0105) | 30.0(0.0349) | 30.0(0.0104) | 30.0(0.0102) | 30.0(0.0102) | 30.0(0.0093) | |
| 25 | 25.0(0.0163) | 19.0(4.4676) | 25.0(0.0158) | 24.9(0.0192) | 25.0(0.0131) | 25.0(0.0133) | |
| sigma | - | 1.2(0.0083) | 2.6(0.0971) | 1.1(0.0077) | 1.5(0.0337) | 1.1(0.0056) | 1.3(0.0099) |
| Position | 86 | 86.4(0.0649) | 85.6(0.0971) | 86.1(0.053) | 86.2(0.0591) | 86.1(0.0609) | 86.4(0.0498) |
The L2 and ML estimates of QTL parameters from an F2population of 400 individuals with heritability of 0.4 for the phenotypic data simulated from t distributions. Numbers in the parentheses are the mean square errors (MSE) of the estimates
Simulation scenario 3.
| 35 | 35.3(0.0709) | 35.9(0.0606) | - | 35.7(0.1028) | 35.9(0.0905) | - | 36(0.1646) | 36(0.1404) | - | |
| 30 | 30.1(0.0335) | 31.4(0.0389) | - | 30.7(0.074) | 31.5(0.0573) | - | 31(0.1108) | 31.4(0.0916) | - | |
| 25 | 25(0.0696) | 26.7(0.0774) | - | 25.4(0.0911) | 26.8(0.0881) | - | 25.8(0.1628) | 26.6(0.1244) | - | |
| sigma | 4.3 | 4.7(0.0238) | 6.2(0.022) | - | - | |||||
| sigma | 7.1 | 7.6(0.0386) | 8.3(0.0312) | |||||||
| sigma | 10.6 | 11.1(0.0567) | 11.5(0.0376) | |||||||
| Position | 86 | 85.5(0.1466) | 85.2(0.1712) | 86.7(0.1387) | 86(0.2272) | 85.1(0.2528) | 85.9(0.2562) | 85.7(0.4935) | 86.6(0.362) | 85.4(0.3452) |
The L2 and ML estimates of QTL parameters from an F2 population of 400 individuals for the phenotypic data simulated from normal distributions containing 10% noise points with mean g = 45. Numbers in the parentheses are the mean square errors (MSE) of the estimates
Simulation scenario 4.
| 35 | 35(0.0664) | 36.8(0.0789) | - | 35.1(0.1061) | 35(0.0833) | - | 36.1(0.1731) | 36.8(0.1494) | - | |
| 30 | 30(0.0325) | 32.3(0.0514) | - | 30.1(0.0706) | 30.1(0.0522) | - | 30.8(0.1156) | 32.5(0.1054) | - | |
| 25 | 25(0.0699) | 27.7(0.0872) | - | 25.1(0.0881) | 25.1(0.0768) | - | 25.4(0.1531) | 27.4(0.1412) | - | |
| sigma | 4.3 | 4.6(0.0231) | 8.4(0.0253) | - | ||||||
| sigma | 7.1 | 7.0(0.0344) | 7.1(0.0282) | - | ||||||
| sigma | 10.6 | 11.5(0.0588) | 12.8(0.0421) | - | ||||||
| Position | 86 | 85.6(0.1419) | 84.8(0.2242) | 86.7(0.1426) | 85.9(0.2335) | 86.4(0.1433) | 86.6(0.1737) | 85.5(0.5162) | 85(0.6221) | 85.8(0.4071) |
The L2 and ML estimates of QTL parameters from an F2 population of 400 individuals for the phenotypic data simulated from normal distributions containing 10% noise points with mean g = 55. Numbers in the parentheses are the mean square errors (MSE) of the estimates
Figure 3L. Genomic scanning profiles for mapping QTLs controlling the growth rate of body mass from weeks 5 to 10 by L2E (a) and ML approaches (b). The y-axes are the ED and LR test statistics, respectively. The dash dot line and the dash line are the chromosome-wide and genome-wide 0.05 cutoffs at the significant level of 0.05 based on the 1000 permutations, respectively. The x-axis ticks indicates the marker positions, the arrows to the × axes shows the genomic positions of the significant QTL at chromosome level, and the asterisk at chromosome 8 in the L2E profile marks a genome-wide significant QTL.
L2E mapping results of the mice data.
| Chromosome | Map | Flanking Markers | QTL associated effects | |||
|---|---|---|---|---|---|---|
| positiona | Marker 1 | Marker 2 | Additiveb | Dominanceb | %varc | |
| 8 | 2 | D8Mit293 | D8Mit25 | 0.012 | -0.044 | 8.68 |
Significant QTL for body mass ratio between week 10 and week 5 in an F2 mouse population detected from the genome-wide interval mapping scan by the L2E and ML methods at the 0.05 significance level
aMap position = population-estimated position in cM from the leftmost proximal marker.
bAdditive and dominance effects of the QTL
c%Var = percentage variance explained by the QTL.