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PubMed2005

Heterogeneity: GAW Group 15.

This paper summarizes the contributions to Group 15 of Genetic Analysis Workshop (GAW) 14, which focused on methods for dealing with heterogeneity in linkage and association analysis. A variety of methods were employed, ranging from manipulation of the phenotype and/or identification of endophenotypes prior to analysis, to statistical methods allowing for heterogeneity in the analysis of simple dichotomous phenotypes as provided with the data. Overall, it was difficult to draw broad conclusions from these applications. Groups that focused on the simulated data had fairly consistent success in mapping the major genes (but not the two minor genes). However, this appeared to be the case regardless of whether heterogeneity was explicitly modeled, either at the phenotypic or statistical level, with relatively crude statistical methods applied to the simulated simple dichotomous trait Kofendrerd personality disorder also enjoying considerable success.

Alcoholism↗
PubMed2006

Implications of small effect sizes of individual genetic variants on the design and interpretation of genetic association studies of complex diseases.

Accumulated evidence from searching for candidate gene-disease associations of complex diseases can offer some insights as the field moves toward discovery-oriented approaches with massive genome-wide testing. Meta-analyses of 50 non-human lymphocyte antigen gene-disease associations with documented overall statistical significance (752 studies) show summary odds ratios with a median of 1.43 (interquartile range, 1.28-1.65). Many different biases may operate in this field, for both single studies and meta-analyses, and these biases could invalidate some of these seemingly "validated" associations. Studies with a sample size of >500 show a median odds ratio of only 1.15. The median sample size required to detect the observed summary effects in each population addressed in the 752 studies is estimated to be 3,535 (interquartile range, 1,936-9,119 for cases and controls combined). These estimates are steeply inflated in the presence of modest bias. Population heterogeneity, as well as gene-gene and gene-environment interactions, could steeply increase these estimates and may be difficult to address even by very large biobanks and observational cohorts. The one visible solution is for a large number of teams to join forces on the same research platforms. These collaborative studies ideally should be designed up front to also assess more complex gene-gene and gene-environment interactions.

Alleles↗
PubMed1977

The genetical analysis of covariance structure.

The analysis of covariance structures (Jöreskog, 1973) is adapted to the simultaneous maximum likelihood estimation of genetical and environmental factor loadings and specific variances. The goodness of fit is tested by chi square and standard errors of parameter estimates can be obtained. Any linear model used in univariate genetical analyses can be extended to the multivariate case. Most biological hypotheses about the relationships between variables can be specified by a variety of factor models. Individual parameters can be given fixed values or set to zero and hypotheses concerning the congruence of genetical and environmental correlations can be tested. The method is illustrated with published twin data on cognitive abilities.

Factor Analysis, Statistical↗
PubMed2001

Detection and characterization of quantitative trait loci for meat quality traits in pigs.

In an experimental cross between Meishan and Dutch Large White and Landrace lines, 785 F2 animals with carcass information and their parents were typed for molecular markers covering the entire porcine genome. Linkage was studied between these markers and eight meat quality traits. Quantitative trait locus analyses were performed using interval mapping by regression under two genetic models: 1) the line-cross approach, where the founder lines were assumed to be fixed for different QTL alleles and 2) a half-sib model where a unique allele substitution effect was fitted within each of the 38 half-sib families. The line-cross approach included tests for genomic imprinting and sex-specific QTL effects. In total, three genome-wide significant and 26 suggestive QTL were detected. The significant QTL on chromosomes 3, 4, and 13, affecting meat color, were only detected under the half-sib model. Failure of the line-cross approach to detect the meat color QTL suggests that the founder lines have similar allele frequencies for these QTL. This study provides information on new QTL affecting meat quality traits. It also shows the benefit of analyzing experimental data under different genetic and statistical models.

Alleles↗
PubMed1997

The role of smoothing techniques in the interpretation of results from genomic scans using sib-pair data.

We compare the results of genomic scans conducted with the Haseman-Elston sib-pair method using either (1) the average marker information from several adjacent loci or (2) each marker individually. Under smoothing, the squared sib-pair trait difference is regressed on the average number of alleles shared identical by descent averaged at several adjacent loci. This results in a significant decrease in the number of false-positives when compared to the individual marker approach. Linkage of Q4 to MG4 was found only with smoothing but not the individual marker approach. Overall, smoothing resulted in the loss of two true linkages.

Alleles↗
PubMed2004

Theoretical basis for genetic linkage analysis in autotetraploid species.

Linkage analysis in autotetraploid species has been an historical challenge in quantitative genetics theory and is a stumbling block that urgently needs to be removed in the rapidly emerging genome research on this species, such as cultivated potato. This article presents theory of a full model of tetrasomic linkage and develops a statistical framework for the linkage analysis. The model considers both double reduction and recombination, the most essential features of tetrasomic inheritance with linked loci, whereas the statistical method takes appropriate account of the major complexities in analyzing both dominant and codominant molecular marker data during map reconstruction in tetraploid species. These complexities include the problems arising from multiple dosage of allelic inheritance, the null allele, allelic segregation distortion, mixed bivalent and quadrivalent pairing in meiosis, and incomplete information of marker phenotype data. The theoretical analysis established the relationship between the coefficients of double reduction at linked loci, which is essential in the present tetrasomic linkage analysis and in assessing the impact of double reduction on the evolution of tetraploid populations. The statistical method, based on the combination of theoretical analysis and a computer-based algorithm, provided analytical tools for predicting the maximum-likelihood estimates of the model parameters. A simulation study showed the feasibility of a practical implementation of the method, detailed the procedure of the analysis, validated the power and reliability in the parameter estimation, and compared the present method with those proposed in the current literature.

Computer Simulation↗
PubMedDate not supplied

[Profile of former students of the Medical School of the University of São Paulo].

The authors present results of an inquiry involving 3,309 physicians graduated at the University of S. Paulo School of Medicine in the 1958-1989 period. Concerning sex, there were 79% male and 21% female students (6% female in 1958-1963 period and 38% in 1958-1989). Medical residence (1-4 years) were done by 91% of all inquired physicians. Postgraduate education was performed by 26% of the graduates in master degree and by 29% in doctorate degree. In reference to professional work, 26% exert surgical specialties, 20% clinical specialties, 13% pediatric specialties, 9% gynecology and obstetrics, 9% psychiatry and 5% neurology. Eighty por cent of them perform their activity as non employed professionals, sometimes associated with some other form of work; of those, 40% earn more than 60% of their total income as non employed professionals. Three different curricular structures were analyzed in this inquiry. In the period 1958-1980 (traditional curriculum), the areas considered more attractive and important were: medical and surgical clinics, pediatrics, anatomy, physiology and pathological anatomy. The less motivating were: legal medicine, psychiatry, phthisiology. In the experimental curriculum (1974-1980) the more attractive areas were: biochemistry, pediatrics, surgical and pediatric internship, general pathology and medical clinics. The less motivating areas were: mathematics, statistics, medical deontology, preventive medicine, ophthalmology and psychiatry. In the unified curriculum (1980-1989), the preferred areas were: general pathology, medical and surgical propedeutics, infantile-maternal, clinical and surgical internship. The less motivating ones were: preventive medicine, otorhynolaringology, anesthesiology, genetics and statistics.

Adult↗
PubMed1973

The genetic origin of leucocytic mucopolysaccharides in cancer patients.

The presence or absence of lymphocytic mucopolysaccharides (MPS) is studied in 223 subjects: 100 normals (controls); 8 cancer patients cured for more than 6 years; 30 cancer patients at the start of their treatment; and 85 relatives of first degree consanguinity of these last patients. The data are studied by statistical and genetic analysis. The results confirm the findings reported earlier and show that the difference in the probability of a high frequency of leucocytic MPS between the relatives of cancer patients and the controls is highly significant. Furthermore, this probability in a relative of first degree of consanguinity of a cancer patient is more than three times greater than in an individual of the general population. Genetic segregation analysis shows that the high leucocytic MPS trait segregates in the families of cancer patients after a classic pattern of dominant autosomal inheritance. Applying Falconer's nomogram it is concluded that the whole of this phenotypic variation is of genetic origin. Its interrelationships with cancer are discussed and it is postulated that this disturbance of the lymphocytic MPS represents a subclinical variant, not known until now, of the clinical mucopolysaccaridoses.

Chromosome Aberrations↗
PubMed1999

Genetic diversity in mesoamerican populations of mahogany (Swietenia macrophylla), assessed using RAPDs.

Swietenia macrophylla King, a timber species native to tropical America, is threatened by selective logging and deforestation. To quantify genetic diversity within the species and monitor the impact of selective logging, populations were sampled across Mesoamerica, from Mexico to Panama, and analysed for RAPD DNA variation. Ten decamer primers generated 102 polymorphic RAPD bands and pairwise distances were calculated between populations according to Nei, then used to construct a radial neighbour-joining dendrogram and examine intra- and interpopulation variance coefficients, by analysis of molecular variation (AMOVA). Populations from Mexico clustered closely together in the dendrogram and were distinct from the rest of the populations. Those from Belize also clustered closely together. Populations from Panama, Guatemala, Costa Rica, Nicaragua and Honduras, however, did not cluster closely by country but were more widely scattered throughout the dendrogram. This result was also reflected by an autocorrelation analysis of genetic and geographical distance. Genetic diversity estimates indicated that 80% of detected variation was maintained within populations and regression analysis demonstrated that logging significantly decreased population diversity (P = 0.034). This study represents one of the most wide-ranging surveys of molecular variation within a tropical tree species to date. It offers practical information for the future conservation of mahogany and highlights some factors that may have influenced the partitioning of genetic diversity in this species across Mesoamerica.

Central America↗
PubMed1987

Genetic variance of weight and length in infant twins.

A population-based cohort of 166 twin pairs (67 monozygotic and 99 dizygotic) born at the Jackson Memorial Hospital/University of Miami Medical Center, from July 1, 1976 to December 31, 1980 was identified. Body weight and length were measured at 14 days and at one, three, six, nine, and 12 months of age. Statistically significant genetic variance was found for both body weight and length at each data point. Heritability for body weight increased from 0.28 at 14 days to 0.64 at one year. Corresponding values for body length were 0.16 and 0.48.

Body Height↗
PubMed1995

DNA forensic science 1995.

After digression by a National Research Council committee, forensic use of DNA identification is returning to methods that do not violate population genetics and statistics. Polemic has been replaced by normal science as advances are made in molecular techniques and presentation of evidence. Rigorous quality control over the chain of custody and likelihood calculations still need to be implemented, and evidence extended on the structure of forensic populations and the operating characteristics of alternative tests.

Confidence Intervals↗
PubMed1984

Genetic variance and heritability of cardiovascular risk factors in Chinese adolescent twins.

In order to estimate genetic variance and heritability of systolic blood pressure (SBP), diastolic blood pressure (DBP), serum cholesterol and triglyceride levels, a total of 235 (79 male and 82 female MZ, 41 male and 33 female DZ) twin pairs, recruited from 12 junior high schools in Taipei city, were studied. Statistically significant genetic variance observed for SBP, DBP, serum cholesterol and triglycerides persisted after adjustment for age and anthropometric characteristics. However, further adjustment for dietary preference, beverage consumption, and other host and environmental factors gave different results: genetic variance of adjusted SBP and DBP was still significant, while significance was found only in males for cholesterol and in neither males nor females for triglycerides. Heritability estimates of unadjusted SBP, DBP, cholesterol and triglycerides were 0.27, 0.45, 0.21 and 0.41, respectively, for males, and 0.15, 0.42, 0.41 and 0.82, respectively, for females. After adjustment for age, anthropometric characteristics, host and environmental factors, the heritability estimates of SBP, DBP and cholesterol were 0.64, 0.72 and 0.50, respectively, for males, and 0.40, 0.60 and 0.37, respectively, for females.

Adolescent↗
PubMed1978

Genetic components in susceptibility to nasopharyngeal carcinoma.

A series of blood samples from more than 200 histologically confirmed Chinese patients with NPC in Singapore were typed for 25 genetically controlled red-cell enzyme and five serum protein systems. A comparable number of patients suspected of having NPC but histologically negative and a series of healthy unrelated Chinese were typed for the same systems. The gene frequencies of NPC patients and controls differed by 4% or more in four of the 11 systems that showed variation; a further system, G6PD deficiency, also showed a significant difference between the two series but was excluded because of possible unreliability of the results from patients. Smaller differences existed in several other systems, including chromosome 6 markers closely linked to HLA. An analysis of differences within dialect groups showed a consistent effect for PGD, but for red-cell acid phosphatase there was a reversal of the difference between patients and controls among the Cantonese. These results need a larger series to confirm their validity. A breakdown of patients into those 30 years of age or older and those under 30 slightly enhanced the differences in gene frequencies. A multivariate analysis, using genetic distance statistics, showed a significant difference between NPC patients and controls, which is evident also when they are compared in the separate dialect groups. The histologically negative patients occupied an intermediate position. The study indicates that etiological factors resulting in clinically and histologically confirmed NPC operate on a genetically distinct subpopulation of Chinese in Singapore.

Acid Phosphatase↗
PubMedDate not supplied

Genetic study of the craniofacial growth in male rats by factor scores.

The craniofacial growth of F1 male offspring produced by a complete diallel cross of five strains of rats was observed with the use of cephalometry. Factor analysis was applied to several dimensions of dorsoventral and lateral cephalograms to assess the integration of the craniofacial complex with growth. The first three factors were chosen in each cephalogram, resulting in an explanation of 50.7% and 59.3% of the variation in the dorsoventral and lateral cephalograms, respectively, on an average throughout the period of the experiment, and disclosing that Factor I was associated most closely with the change in the craniofacial growth of rats. A further genetic analysis of the factor scores of each offspring lead to the conclusion that the growth changes of craniofacial width and length were more strongly influenced by the genetic effects; while those of upper jaw, nasal cavity, and pharyngeal part were more strongly influenced by the environmental effects.

Animals↗
PubMed2005

A new method for estimating the size of small populations from genetic mark-recapture data.

The use of non-invasive genetic sampling to estimate population size in elusive or rare species is increasing. The data generated from this sampling differ from traditional mark-recapture data in that individuals may be captured multiple times within a session or there may only be a single sampling event. To accommodate this type of data, we develop a method, named capwire, based on a simple urn model containing individuals of two capture probabilities. The method is evaluated using simulations of an urn and of a more biologically realistic system where individuals occupy space, and display heterogeneous movement and DNA deposition patterns. We also analyse a small number of real data sets. The results indicate that when the data contain capture heterogeneity the method provides estimates with small bias and good coverage, along with high accuracy and precision. Performance is not as consistent when capture rates are homogeneous and when dealing with populations substantially larger than 100. For the few real data sets where N is approximately known, capwire's estimates are very good. We compare capwire's performance to commonly used rarefaction methods and to two heterogeneity estimators in program capture: Mh-Chao and Mh-jackknife. No method works best in all situations. While less precise, the Chao estimator is very robust. We also examine how large samples should be to achieve a given level of accuracy using capwire. We conclude that capwire provides an improved way to estimate N for some DNA-based data sets.

Computer Simulation↗
PubMed2004

Population genetic structure of Anopheles gambiae mosquitoes on Lake Victoria islands, west Kenya.

BACKGROUND: Understanding the genetic structure of island Anopheles gambiae populations is important for the current tactics in mosquito control and for the proposed strategy using genetically-modified mosquitoes (GMM). Genetically-isolated mosquito populations on islands are a potential site for testing GMM. The objective of this study was to determine the genetic structure of A. gambiae populations on the islands in Lake Victoria, western Kenya. METHODS: The genetic diversity and the population genetic structures of 13 A. gambiae populations from five islands on Lake Victoria and six villages from the surrounding mainland area in the Suba District were examined using six microsatellite markers. The distance range of sampling sites varied between 2.5 and 35.1 km. RESULTS: A similar level of genetic diversity between island mosquito populations and adjacent mainland populations was found. The average number of alleles per locus was 7.3 for the island populations and 6.8 for the mainland populations. The average observed heterozygosity was 0.32 and 0.28 for the island and mainland populations, respectively. A low but statistically significant genetic structure was detected among the island populations (FST = 0.019) and between the island and mainland populations (FST = 0.003). A total of 12 private alleles were found, and nine of them were from the island populations. CONCLUSION: A level of genetic differentiation between the island and mainland populations was found. Large extent of gene flow between the island and mainland mosquito populations may result from wind- or human-assisted dispersal. Should the islands on Lake Victoria be used as a trial site for the release program of GMM, mosquito dispersal between the islands and between the island and the mainland should be vigorously monitored.

Alleles↗
PubMed1989

On the information content of the genetic code.

In living organisms 20 amino acids along with the terminator value(s) are encoded by 64 codons giving a degeneracy of the codons as described by the genetic code. A basic theoretical problem of genetic codes is to explain the particular distribution of degeneracies of partitions involved in the codes. In this work the degeneracy problem is considered in the framework of information theory. It is shown by direct numerical evaluation of a certain degeneracy information function associated with the genetic code that the degeneracy of the codes is observed to be related to the optimization of this function.

Amino Acids↗