scholarly journals Selection and subsequent analysis of sib pair data for QTL detection

2001 ◽  
Vol 78 (2) ◽  
pp. 177-186 ◽  
Author(s):  
DIMITRIOS G. CHATZIPLIS ◽  
HENNING HAMANN ◽  
CHRIS S. HALEY
Keyword(s):  
Robust Regression ◽  
Expected Value ◽  
Regression Method ◽  
Qtl Detection ◽  
Selection Scheme ◽  
Phenotypic Differences ◽  
Effective Selection ◽  
The Difference ◽  
Trait Locus ◽  
Sib Pairs

Haseman and Elston (1972) developed a robust regression method for the detection of linkage between a marker and a quantitative trait locus (QTL) using sib pair data. The principle underlying this method is that the difference in phenotypes between pairs of sibs becomes larger as they share a decreasing number of alleles at a particular QTL identical by descent (IBD) from their parents. In this case, phenotypically very different sibs will also on average share a proportion of alleles IBD at any marker linked to the QTL that is lower than the expected value of 0·5. Thus, the deviation of the proportion of marker alleles IBD from the expected value in pairs of sibs selected to be phenotypically different (i.e. discordant) can provide a test for the presence of a QTL. A simple regression method for QTL detection in sib pairs selected for high phenotypic differences is presented here. The power of the analytical method was found to be greater than the power obtained using the standard analysis when samples of sib pairs with high phenotypic differences were used. However, the use of discordant sib pairs was found to be less powerful for QTL detection than alternative selective genotyping schemes based on the phenotypic values of the sibs except with intense selection, when its advantage was only marginal. The most effective selection scheme overall was the use of sib pairs from entire families selected on the basis of high within-family variance for the trait in question. There is little effect of selection on QTL position estimates, which are in good agreement with the simulated values. However, QTL variance estimates are biased to a greater or lesser degree, depending on the selection method.

scholarly journals How informative is Wright's estimator of the number of genes affecting a quantitative character?

Genetics ◽  
1990 ◽  
Vol 126 (1) ◽  
pp. 235-247 ◽  
Author(s):  
Z B Zeng ◽  
D Houle ◽  
C C Cockerham
Keyword(s):  
Genetic Variance ◽  
Estimation Procedure ◽  
Expected Value ◽  
Allele Frequencies ◽  
Quantitative Character ◽  
Base Population ◽  
Single Population ◽  
Number Of Genes ◽  
Selection Limit ◽  
The Difference

Abstract S. Wright suggested an estimator, m, of the number of loci, m, contributing to the difference in a quantitative character between two differentiated populations, which is calculated from the phenotypic means and variances in the two parental populations and their F1 and F2 hybrids. The same method can also be used to estimate m contributing to the genetic variance within a single population, by using divergent selection to create differentiated lines from the base population. In this paper we systematically examine the utility and problems of this technique under the influences of unequal allelic effects and initial allele frequencies, and linkage, which are known to lead m to underestimate m. In addition, we examine the effects of population size and selection intensity during the generations of selection. During selection, the estimator m rapidly approaches its expected value at the selection limit. With reasonable assumptions about unequal allelic effects and initial allele frequencies, the expected value of m without linkage is likely to be on the order of one-third of the number of genes. The estimates suffer most seriously from linkage. The practical maximum expectation of m is just about the number of chromosomes, considerably less than the "recombination index" which has been assumed to be the upper limit. The estimates are also associated with large sampling variances. An estimator of the variance of m derived by R. Lande substantially underestimates the actual variance. Modifications to the method can ameliorate some of the problems. These include using F3 or later generation variances or the genetic variance in the base population, and replicating the experiments and estimation procedure. However, even in the best of circumstances, information from m is very limited and can be misleading.

scholarly journals Quantitative trait loci mapping for cholesterol gallstones in AKR/J and C57L/J strains of mice

2000 ◽  
Vol 4 (1) ◽  
pp. 59-65 ◽  
Author(s):  
BEVERLY PAIGEN ◽  
NICHOLAS J. SCHORK ◽  
KAREN L. SVENSON ◽  
YIN-CHAI CHEAH ◽  
JIAN-LONG MU ◽  
...  
Keyword(s):  
Quantitative Trait ◽  
Congenic Strain ◽  
Cholesterol Gallstone ◽  
Gallstone Disease ◽  
Gallstone Formation ◽  
Quantitative Trait Loci Mapping ◽  
Cholesterol Gallstones ◽  
Lithogenic Diet ◽  
The Difference ◽  
Trait Locus

Quantitative trait locus (QTL) mapping was used to locate genes that determine the difference in cholesterol gallstone disease between the gallstone-susceptible strain C57L/J and the gallstone-resistant strain AKR/J. Gallstone weight was determined in 231 male (AKR × C57L) F1× AKR backcross mice fed a lithogenic diet containing 1% cholesterol, 0.5% cholic acid, and 15% butterfat for 8 wk. Mice having no stones and mice having the largest stones were genotyped at ∼20-cM intervals to find the loci determining cholesterol gallstone formation. The major locus, Lith1, mapped near D2Mit56 and was confirmed by constructing a congenic strain, AK.L- Lith1s. Another locus, Lith2, mapped near D19Mit58 and was also confirmed by constructing a congenic strain AK.L- Lith2s. Other suggestive, but not statistically significant, loci mapped to chromosomes 6, 7, 8, 10, and X. The identification of these Lith genes will elucidate the pathophysiology of cholesterol gallstone formation.

Perception of Risk as Related to Choice in a Two-Dimensional Risk Situation

1978 ◽  
Vol 43 (3_suppl) ◽  
pp. 1059-1062 ◽  
Author(s):  
John W. Dickson
Keyword(s):  
Risky Choice ◽  
Expected Value ◽  
Two Dimensions ◽  
Choice Situation ◽  
Two Dimensional ◽  
Objective Risk ◽  
Subjective Risk ◽  
Risk Situation ◽  
The Difference ◽  
Two Alternatives

A risky choice was created by manipulating two dimensions of risk for 21 managers attending a conference. The first dimension varied risk by altering the difference in expected value between two alternatives of widely differing variance. The second dimension varied the expectancy of achieving a particular outcome. Whereas choice was significantly related to both dimensions of risk, it was not significantly related to estimates of the subjective risk inherent in the choice situation. It appears that subjective risk does not mediate between objective risk and choice.

scholarly journals PEMODELAN REGRESI RIDGE ROBUST-MM DALAM PENANGANAN MULTIKOLINIERITAS DAN PENCILAN (Studi Kasus : Faktor-Faktor yang Mempengaruhi AKB di Jawa Tengah Tahun 2017)

2019 ◽  
Vol 8 (1) ◽  
pp. 24-34
Author(s):  
Eka Destiyani ◽  
Rita Rahmawati ◽  
Suparti Suparti
Keyword(s):  
Least Squares ◽  
Robust Regression ◽  
Ordinary Least Squares ◽  
Regression Method ◽  
Predictor Variables ◽  
Healthy Life ◽  
Significance Level ◽  
Central Java ◽  
Regression Parameters

The Ordinary Least Squares (OLS) is one of the most commonly used method to estimate linear regression parameters. If multicollinearity is exist within predictor variables especially coupled with the outliers, then regression analysis with OLS is no longer used. One method that can be used to solve a multicollinearity and outliers problems is Ridge Robust-MM Regression. Ridge Robust-MM  Regression is a modification of the Ridge Regression method based on the MM-estimator of Robust Regression. The case study in this research is AKB in Central Java 2017 influenced by population dencity, the precentage of households behaving in a clean and healthy life, the number of low-weighted baby born, the number of babies who are given exclusive breastfeeding, the number of babies that receiving a neonatal visit once, and the number of babies who get health services. The result of estimation using OLS show that there is violation of multicollinearity and also the presence of outliers. Applied ridge robust-MM regression to case study proves ridge robust regression can improve parameter estimation. Based on t test at 5% significance level most of predictor variables have significant effect to variable AKB. The influence value of predictor variables to AKB is 47.68% and MSE value is 0.01538.Keywords:  Ordinary  Least  Squares  (OLS),  Multicollinearity,  Outliers,  RidgeRegression, Robust Regression, AKB.

scholarly journals Analisis Kepuasan Pengguna Website Asuransi Untuk Peningkatan Pelayanan Asuransi Studi Kasus www.Cakrawalaproteksi.Com

2020 ◽  
Vol 1 (1) ◽  
Author(s):  
Syafitri Mona Sari ◽  
Firdaus Firdaus ◽  
A. Haidar Mirza
Keyword(s):  
Social Media ◽  
Customer Satisfaction ◽  
Insurance Industry ◽  
Expected Value ◽  
Insurance Company ◽  
Simple Analysis ◽  
Internet Users ◽  
The Difference

Currently, technology has developed quite rapidly and covers all aspects, including in the insurance industry. Almost every insurance company has a website or social media that can be accessed by all internet users as a means of promotion and transactions. PT. Asuransi Cakrawala Proteksi is an insurance company that also carries out promotions through websites and social media. This research will discuss the customer satisfaction of PT. Asuransi Cakrawala Protection with the role of social media. Customer satisfaction is determined by looking at the difference between the actual value received and the expected value using the website and social media Facebook. From calculating the level of customer satisfaction with ServQual dimensions and simple analysis, a strategy will be produced to maintain or increase customer satisfaction.

scholarly journals Budidaya Terung Ungu di Pekarangan di Desa Ciawijapura Kecamatan Susukan Lebak Kabupaten Cirebon

2021 ◽  
Vol 2 (1) ◽  
pp. 39
Author(s):  
Umi Trisnaningsih ◽  
Siti Wahyuni ◽  
Wachdijono Wachdijono
Keyword(s):  
Community Service ◽  
Culture System ◽  
Expected Value ◽  
Family Welfare ◽  
Service Program ◽  
Dry Land ◽  
Before And After ◽  
The Difference

<p><em>Yard land can be used as a family food barn. One of the efforts to overcome the limitations of land is by cultivating in a limited place (bag culture system) such as polybags, pots or used buckets. In Ciawijapura Village, Susukan Lebak </em><em>Sub-district, Cirebon Regency, purple eggplant is commonly cultivated in dry land, as well as in yards. This Community Service Program (</em><em>Pengabdian Kepada Masyarakat/PKM) is aimed at increasing the knowledge of</em><em> Family Welfare Building Motivation Team (</em><em>Tim Penggerak Pembinaan Kesejahteraan Keluarga/TP-PKK</em><em>) cadres and members of Farmer Women Group </em><em>(</em><em>Kelompok Wanita Tani</em><em>/KWT</em><em>) Al Istiqomah about cultivating purple eggplant in a bag culture system. The methods used are training and mentoring. The evaluation results showed that there was a significant increase in knowledge between before and after the training, that is, from 73% to 89% of the total expected value. The participants were able to understand the difference between cultivating purple eggplant on land and in a bag culture system.</em></p>

Integrating spatial variations in the vineyard to enhance quantitative trait locus (QTL) detection

2019 ◽  
pp. 215-220
Author(s):  
X. de Badts ◽  
V. Dumas ◽  
N. Jaegli ◽  
L. Ley ◽  
D. Merdinoglu ◽  
...  
Keyword(s):  
Quantitative Trait Locus ◽  
Quantitative Trait ◽  
Spatial Variations ◽  
Qtl Detection ◽  
Trait Locus

scholarly journals Difference in persistent tuberculosis bacteria between in vitro and sputum from patients: implications for translational predictions

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Alan Faraj ◽  
Oskar Clewe ◽  
Robin J. Svensson ◽  
Galina V. Mukamolova ◽  
Michael R. Barer ◽  
...  
Keyword(s):  
Drug Response ◽  
Most Probable Number ◽  
Sputum Smear ◽  
Probable Number ◽  
Phenotypic Resistance ◽  
Phenotypic Differences ◽  
Model Based ◽  
Persistent Bacteria ◽  
The Difference

Abstract This study aimed to investigate the number of persistent bacteria in sputum from tuberculosis patients compared to in vitro and to suggest a model-based approach for accounting for the potential difference. Sputum smear positive patients (n = 25) provided sputum samples prior to onset of chemotherapy. The number of cells detected by conventional agar colony forming unit (CFU) and most probable number (MPN) with Rpf supplementation were quantified. Persistent bacteria was assumed to be the difference between MPNrpf and CFU. The difference in persistent bacteria between in vitro and human sputum prior to chemotherapy was quantified using different model-based approaches. The persistent bacteria in sputum was 17% of the in vitro levels, suggesting a difference in phenotypic resistance, whereas no difference was found for multiplying bacterial subpopulations. Clinical trial simulations showed that the predicted time to 2 log fall in MPNrpf in a Phase 2a setting using in vitro pre-clinical efficacy information, would be almost 3 days longer if drug response was predicted ignoring the difference in phenotypic resistance. The discovered phenotypic differences between in vitro and humans prior to chemotherapy could have implications on translational efforts but can be accounted for using a model-based approach for translating in vitro to human drug response.

Taste Thresholds in Twins and Siblings

1967 ◽  
Vol 16 (3) ◽  
pp. 229-243 ◽  
Author(s):  
A. R. Kaplan ◽  
R. Fischer ◽  
A. Karras ◽  
F. Griffin ◽  
W. Powell ◽  
...  
Keyword(s):  
Hydrochloric Acid ◽  
Monozygotic Twin ◽  
Quinine Sulfate ◽  
Dizygotic Twin ◽  
Same Sex ◽  
Significant Difference ◽  
The Difference ◽  
Taste Thresholds ◽  
Threshold Range ◽  
Sib Pairs

SummaryMonozygotic twin (MZ), dizygotic twin (DZ), and sibling (SIB) pairs were taste-tested for hydrochloric acid, 1-quinine sulfate, and 6-n-propylthiouracil (PROP). The numbers of pairs involved were 75 MZ, 70 DZ, and 78 SIB, for the latter two compounds; 26, 45, and 45, respectively, for the acid.There was a significant difference in intrapair variance, between the MZ and the same-sex DZ pairs, in thresholds for bitter-tasting 6-n-propylthiouracil (p < .001). The difference in intrapair threshold variance was not significant for bitter-tasting quinine (p > .05) or for sour-tasting hydrochloric acid (p > .10).The male MZ pairs had a significantly lower intrapair threshold variance than the male DZ or male SIB pairs for hydrochloric acid (p < .01), but the female pairs manifested no such difference. The intrapair variance in hydrochloric acid threshold was significantly less for the nine male MZ pairs than for the 17 female MZ pairs (p < .02).Repeated taste tests on the same subjects reproduced results similar within a single threshold range in a high proportion for each compound: for hydrochloric acid, 72.9% (N = 44); for quinine, 76.9% (N = 221); and for PROP, 76% (N = 225).Correlations between thresholds for the different substances were positive and significant (N = 308): between PROP and quinine, r = + 0.44 ± .05 (p < .01); between quinine and hydrochloric acid, r = + 0.35 ± .05 (p < .01); between PROP and hydrochloric acid, r = + 0.17 ± .06 (p < .05).

scholarly journals Synchronization of senescence and desynchronization of flowering in Arabidopsis thaliana

AoB Plants ◽  
2020 ◽  
Vol 12 (3) ◽  
Author(s):  
Matin Miryeganeh
Keyword(s):  
Arabidopsis Thaliana ◽  
Recombinant Inbred Lines ◽  
Life Stage ◽  
Reproductive Traits ◽  
Reproductive Timing ◽  
Qtl Detection ◽  
Timing Of Reproduction ◽  
Temperature Regimes ◽  
Trait Locus ◽  
Germination Timing

Abstract In a recent publication, we proposed that adjusting lifespan in order to synchronize senescence is important for timing of reproduction, and we quantified the synchrony of reproductive timing relative to germination timing. Here, in a second sequential seeding experiment (SSE), the germination timing of Arabidopsis thaliana accessions was manipulated and plants were then grown under two different temperature regimes. Life stage traits of plants in each temperature regime were analysed and it was evaluated whether the cohorts were grouped according to age and/or environmental conditions. While flowering-related traits showed desynchrony among cohorts, striking synchrony in the timing of senescence among cohorts for each group was found. A quantitative trait locus (QTL) analysis using a genotyped population of ‘Cvi/Ler’ recombinant inbred lines (RILs) was then conducted. Novel and known loci were assigned to flowering and senescence timing. However, senescence synchrony resulted in low variation in senescence time and weak QTL detection for flowering termination. Overlapping flowering and senescence genes with loci affecting either of those traits were found and suggest a potential interdependency of reproductive traits.

Sign in / Sign up

Export Citation Format

Share Document