scholarly journals New perspectives on multilocus ancestry informativeness

2018 ◽  
Author(s):  
Omri Tal ◽  
Tat Dat Tran
Keyword(s):  
Mutual Information ◽  
Genetic Markers ◽  
Genetic Variants ◽  
Population Genetic ◽  
Finite Population ◽  
Axiomatic Approach ◽  
Amount Of Information ◽  
Individual Ancestry

AbstractWe present an axiomatic approach for multilocus informativeness measures for determining the amount of information that a set of polymorphic genetic markers provides about individual ancestry. We then reveal several surprising properties of a decision-theoretic based measure that is consistent with the set of proposed criteria for multilocus informativeness. In particular, these properties highlight the interplay between information originating from population priors and the information extractable from the population genetic variants. This analysis then reveals a certain deficiency of mutual information based multilocus informativeness measures when such population priors are incorporated. Finally, we analyse and quantify the inevitable inherent decrease in informativeness due to learning from finite population samples.

Polymorphic population genetic markers for the Australian wood cockroach Panesthia australis

2006 ◽  
Vol 6 (3) ◽  
pp. 765-766 ◽  
Author(s):  
D. RUNCIMAN ◽  
M. J. BLACKET ◽  
C. SCHMUKI ◽  
P. SUNNUCKS
Keyword(s):  
Genetic Markers ◽  
Population Genetic

Mutual Information as an Index of Diagnostic Test Performance

2003 ◽  
Vol 42 (03) ◽  
pp. 260-264 ◽  
Author(s):  
W. A. Benish
Keyword(s):  
Mutual Information ◽  
Diagnostic Test ◽  
Test Performance ◽  
Random Variable ◽  
Disease State ◽  
Necessary Condition ◽  
Conditional Probabilities ◽  
Amount Of Information ◽  
Diagnostic Test Performance ◽  
Test Result

Summary Objectives: This paper demonstrates that diagnostic test performance can be quantified as the average amount of information the test result (R) provides about the disease state (D). Methods: A fundamental concept of information theory, mutual information, is directly applicable to this problem. This statistic quantifies the amount of information that one random variable contains about another random variable. Prior to performing a diagnostic test, R and D are random variables. Hence, their mutual information, I(D;R), is the amount of information that R provides about D. Results: I(D;R) is a function of both 1) the pretest probabilities of the disease state and 2) the set of conditional probabilities relating each possible test result to each possible disease state. The area under the receiver operating characteristic curve (AUC) is a popular measure of diagnostic test performance which, in contrast to I(D;R), is independent of the pretest probabilities; it is a function of only the set of conditional probabilities. The AUC is not a measure of diagnostic information. Conclusions: Because I(D;R) is dependent upon pretest probabilities, knowledge of the setting in which a diagnostic test is employed is a necessary condition for quantifying the amount of information it provides. Advantages of I(D;R) over the AUC are that it can be calculated without invoking an arbitrary curve fitting routine, it is applicable to situations in which multiple diagnoses are under consideration, and it quantifies test performance in meaningful units (bits of information).

scholarly journals An efficient method to find potentially universal population genetic markers, applied to metazoans

2010 ◽  
Vol 10 (1) ◽  
pp. 276 ◽  
Author(s):  
Anne Chenuil ◽  
Thierry B Hoareau ◽  
Emilie Egea ◽  
Gwilherm Penant ◽  
Caroline Rocher ◽  
...  
Keyword(s):  
Genetic Markers ◽  
Efficient Method ◽  
Population Genetic

scholarly journals Informational-Statistical Aspects of Genetic Diversity in Tsigai and Tsurcana Ecotypes from Romania

2017 ◽  
Vol 74 (2) ◽  
pp. 127
Author(s):  
Gheorghe HRINCĂ
Keyword(s):  
Genetic Diversity ◽  
Genetic Markers ◽  
Genetic Variants ◽  
Point Of View ◽  
Habitat Conditions ◽  
Sheep Breeds ◽  
Allelic Distribution ◽  
Biochemical Genetic ◽  
Genetic Structures ◽  
Genetic Diversity Level

The main objective of this paper is to measure the relationships between the ecotypes belonging to the Tigai and Tsurcana breeds of Romania and to quantify the genetic diversity within them from the informational statistics point of view, depending on the relief forms of the biotope in which they live, using the genetic variants of some selective genetic markers. The researches were carried out on ecotypes of the most ubiquitous sheep breeds in Romania, Tsigai and Tsurcana whose biotopes are circumscribed by more relief forms: plain, hilly, sub-mountainous and mountainous. The sheep were electrophoretically typified at the determinant loci of haemoglobin and transferrin. Using the allelic frequencies of the haemoglobin and transferrin systems that have been processed by concepts of informational statistics, the differentiation / similarity degree among ecotypes within the two breeds was quantified by the genetic distance (D) and the informational correlation coefficient (Rx,y), as well as the diversity level (d) of the genetic structures of these ecotypes on the basis of informational energy (e). Also, the heterozygosity degree (Ht) at the Hb and Tf loci was calculated in relation to the genetic diversity level. The paper analyzes the causes of genetic similarities and differentiations among the ecotypes of these two breeds at the level of the two biochemical-genetic loci: allelic distribution of haemoglobin and transferrin, altitude of relief forms, habitat conditions etc. The benefits of such studies are also presented for the improvement, breeding and conservation of the ecotypes of these two sheep breeds from Romania.

scholarly journals Population Genetic Analysis of the Protease Locus of Human Immunodeficiency Virus Type 1 Quasispecies Undergoing Drug Selection, Using a Denaturing Gradient-Heteroduplex Tracking Assay

2001 ◽  
Vol 75 (14) ◽  
pp. 6729-6736 ◽  
Author(s):  
Laurence Doukhan ◽  
Eric Delwart
Keyword(s):  
Genetic Diversity ◽  
Genetic Variants ◽  
Population Genetic ◽  
Protease Gene ◽  
Plasma Viremia ◽  
Viral Quasispecies ◽  
Immunodeficiency Virus ◽  
Pcr Products ◽  
Hiv 1

ABSTRACT Monitoring the evolution of human immunodeficiency virus type 1 (HIV-1) drug resistance requires measuring the frequency of closely related genetic variants making up the complex viral quasispecies found in vivo. In order to resolve both major and minor (≥2%) protease gene variants differing by one or more nucleotide substitutions, we analyzed PCR products derived from plasma viral quasispecies by using a combination of denaturing gradient gel electrophoresis and DNA heteroduplex tracking assays. Correct population sampling of the high level of genetic diversity present within viral quasispecies could be documented by parallel analysis of duplicate, independently generated PCR products. The composition of genetically complex protease gene quasispecies remained constant over short periods of time in the absence of treatment and while plasma viremia fell >100-fold following the initiation of protease inhibitor ritonavir monotherapy. Within a month of initiating therapy, a strong reduction in the genetic diversity of plasma viral populations at the selected protease locus was associated with rising plasma viremia and the emergence of drug resistance. The high levels of protease genetic diversity seen before treatment reemerged only months later. In one patient, reduction in genetic diversity at the protease gene was observed concomitantly with an increase in diversity at the envelope gene (E. L. Delwart, P. Heng, A. Neumann, and M. Markowitz, J. Virol. 72:2416-2421, 1998), indicating that opposite population genetic changes can take place in different HIV-1 loci. The rapid emergence of drug-resistant HIV-1 was therefore associated with a strong, although only transient, reduction in genetic diversity at the selected locus. The denaturing gradient-heteroduplex tracking assay is a simple method for the separation and quantitation of very closely related, low-frequency, genetic variants within complex viral populations.

scholarly journals Identification of species-specific nuclear insertions of mitochondrial DNA (numts) in gorillas and their potential as population genetic markers

2014 ◽  
Vol 81 ◽  
pp. 61-70 ◽  
Author(s):  
Iván Darío Soto-Calderón ◽  
Nicholas Jonathan Clark ◽  
Julia Vera Halo Wildschutte ◽  
Kelly DiMattio ◽  
Michael Ignatius Jensen-Seaman ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Genetic Markers ◽  
Population Genetic ◽  
Identification Of Species ◽  
Species Specific

scholarly journals Genetic markers of canine hip dysplasia

2018 ◽  
Vol 74 (2) ◽  
pp. 6069-2018
Author(s):  
PAULINA KRZEMIŃSKA ◽  
MACIEJ GOGULSKI ◽  
ROMAN ALEKSIEWICZ ◽  
MAREK ŚWITOŃSKI
Keyword(s):  
Genetic Markers ◽  
Genetic Variants ◽  
Hip Dysplasia ◽  
Skeletal Development ◽  
Molecular Testing ◽  
Gene Pools ◽  
German Shepherd ◽  
Skeletal Malformation ◽  
Early Risk ◽  
Canine Hip Dysplasia

Canine hip dysplasia is a complex skeletal malformation caused by genetic and environmental factors. The prevalence of hip dysplasia in different canine breeds ranges widely, from 1% (for Whippet and Borzoi) to over 70% (for Bulldog and Pug). These differences indicate the presence of genetic variants predisposing to or preventing this disorder in gene pools of particular breeds. The importance of genetic factors is also confirmed by a high coefficient of heritability (h2) of canine hip dysplasia, which for most breeds oscillates around 0.5 – 0.6. Application of modern genomic methods, that is, mainly genome scanning (based previously on microsatellite markers and currently on SNP microarrays) has led in recent years to the identification of potential genetic markers associated with this disorder. Such studies were carried out mostly in two breeds: Labrador retriever and German shepherd. Some of the markers were found in the vicinity of genes involved in skeletal development. Following these achievements, the use of some markers has been suggested for early risk diagnosis of hip dysplasia. This shows that molecular testing is becoming important for not only monogenic, but also polygenic canine diseases and disorders. Identification of genetic markers associated with predisposition to hip dysplasia offers an opportunity for an early risk evaluation of this disorder (prior to its first signs). Moreover, it facilitates effective breeding selection aimed at eradicating undesirable genetic variants from the gene pool of a given breed..

scholarly journals Efficient Informative Sensing using Multiple Robots

2009 ◽  
Vol 34 ◽  
pp. 707-755 ◽  
Author(s):  
A. Singh ◽  
A. Krause ◽  
C. Guestrin ◽  
W. J. Kaiser
Keyword(s):  
Mutual Information ◽  
Resource Constraints ◽  
Temporal Dynamics ◽  
Optimal Solution ◽  
Water Quality Monitoring ◽  
General Technique ◽  
Amount Of Information ◽  
Sensing Applications ◽  
Spatial Coverage ◽  
Multi Robot

The need for efficient monitoring of spatio-temporal dynamics in large environmental applications, such as the water quality monitoring in rivers and lakes, motivates the use of robotic sensors in order to achieve sufficient spatial coverage. Typically, these robots have bounded resources, such as limited battery or limited amounts of time to obtain measurements. Thus, careful coordination of their paths is required in order to maximize the amount of information collected, while respecting the resource constraints. In this paper, we present an efficient approach for near-optimally solving the NP-hard optimization problem of planning such informative paths. In particular, we first develop eSIP (efficient Single-robot Informative Path planning), an approximation algorithm for optimizing the path of a single robot. Hereby, we use a Gaussian Process to model the underlying phenomenon, and use the mutual information between the visited locations and remainder of the space to quantify the amount of information collected. We prove that the mutual information collected using paths obtained by using eSIP is close to the information obtained by an optimal solution. We then provide a general technique, sequential allocation, which can be used to extend any single robot planning algorithm, such as eSIP, for the multi-robot problem. This procedure approximately generalizes any guarantees for the single-robot problem to the multi-robot case. We extensively evaluate the effectiveness of our approach on several experiments performed in-field for two important environmental sensing applications, lake and river monitoring, and simulation experiments performed using several real world sensor network data sets.

scholarly journals Cumulative Small Effect Genetic Markers and the Risk of Colorectal Cancer in Poland, Estonia, Lithuania, and Latvia

2015 ◽  
Vol 2015 ◽  
pp. 1-10 ◽  
Author(s):  
Pablo Serrano-Fernandez ◽  
Dagmara Dymerska ◽  
Grzegorz Kurzawski ◽  
Róża Derkacz ◽  
Tatiana Sobieszczańska ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Clinical Practice ◽  
High Risk ◽  
Genetic Markers ◽  
Genetic Variants ◽  
Cumulative Effect ◽  
Low Risk ◽  
Cumulative Effects ◽  
Risk Markers ◽  
Individual Effects

The continued identification of new low-penetrance genetic variants for colorectal cancer (CRC) raises the question of their potential cumulative effect among compound carriers. We focused on 6 SNPs (rs380284, rs4464148, rs4779584, rs4939827, rs6983267, and rs10795668), already described as risk markers, and tested their possible independent and combined contribution to CRC predisposition.Material and Methods.DNA was collected and genotyped from 2330 unselected consecutive CRC cases and controls from Estonia (166 cases and controls), Latvia (81 cases and controls), Lithuania (123 cases and controls), and Poland (795 cases and controls).Results.Beyond individual effects, the analysis revealed statistically significant linear cumulative effects for these 6 markers for all samples except of the Latvian one (correctedPvalue = 0.018 for the Estonian, correctedPvalue = 0.0034 for the Lithuanian, and correctedPvalue = 0.0076 for the Polish sample).Conclusions.The significant linear cumulative effects demonstrated here support the idea of using sets of low-risk markers for delimiting new groups with high-risk of CRC in clinical practice that are not carriers of the usual CRC high-risk markers.

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