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Tallis [1962] formulated and solved the problem of constructing a selection index whose use will produce changes in the means of genotypic values of various traits that are proportional to ultimately desired changes. Several meaningful variations of this problem are described, and their solutions are presented in a common framework.
The identification and characterization of susceptibility genes for common complex multifactorial human diseases remains a statistical and computational challenge. Parametric statistical methods such as logistic regression are limited in their ability to identify genes whose effects are dependent solely or partially on interactions with other genes and environmental exposures. We introduce cellular automata (CA) as a novel computational approach for identifying combinations of single-nucleotide polymorphisms (SNPs) associated with clinical endpoints. This alternative approach is nonparametric (i.e. no hypothesis about the value of a statistical parameter is made), is model-free (i.e. assumes no particular inheritance model), and is directly applicable to case-control and discordant sib-pair study designs. We demonstrate using simulated data that the approach has good power for identifying high-order nonlinear interactions (i.e. epistasis) among four SNPs in the absence of independent main effects.
OBJECTIVE: To figure out the polymorphism of three Y-STR loci in isolated populations and explore the consanguinity of the populations with the use of Y-STR. METHODS: Male samples were selected from two isolated populations(80 and 60 males) in Zhejiang province and one open population (36 males), genescan was performed with males' DNA by genescan technology with ABI PRISM 377 sequencer at Y chromosome loci DYS388, DYS390 and DYS395. RESULTS: DYS388, DYS390, DYS395 allele counts in Yushan island population, Taohua island population and open population were 8, 9, 7, 5, 6, 7 and 6, 6, 5 respectively. Gene diversity was between 0.70-0.80 in the three populations. There was no difference in distribution of allele frequency and shared genotypes between the isolated populations and the open population by statistical test. Genetic distance is long between Taohua island population and open population, short between Yushan island population and open population, and moderate between Yushan island population and Taohua island population. CONCLUSION: The main allele is 129 at DYS388; 215 at DYS390; and 119 at DYS395. The distribution of allele frequency and gene diversity at DYS388, DYS390, DYS395 loci, and the shared genotypes between populations as well as the genetic distance are unable to explain the blood relationship between the isolated and open populations, suggesting the additional studies in large sample size will be necessary to use Y-STR for exploring the blood relationship between populations.
OBJECTIVE: To investigate the correlation between the polymorphism of IL-4 and IL-10 gene promoters and the susceptibility of Chinese children to asthma and to study the impact of such polymorphism upon cytokine production. METHODS: The data of medical history, pulmonary function, hypersensitive test, and serum IgE were recorded among 168 unrelated Chinese children with asthma aged 5 approximately 15. Four polymorphism sites of IL-4 and IL-10 gen promoter regions were determined by PCR/RFLP. The peripheral blood monocyte (PBMC) was cultured and stimulated by lipopolysacchride (LPS). Then the contents of IL-4 and IL-10 gene promoter regions were determined by ELISA. 53 age-matched children without asthma were used as control. RESULTS: (1) The allele frequencies of-598 (C/T) site of IL-4 gene promoter was significantly different between Chinese children and children of Caucasian and Afro-American origin (P = 0.01). The allele frequency of -1082 (G/A) site, -819 (C/T) site, and -592 (A/C) site in IL-10 gene promoter was significantly different between Chinese children and their British counterparts (P = 0.01). (2) The serum total IgE level was significantly different among children with different allelic sites in IL-4 and IL-10 gene promoters. A allele in IL-10 - 1082 (G/A) site and T allele in IL-10 - 819 (C/T) site -1082 were associated with elevated total serum IgE (P < 0.01, OR = 3.16; P < 0.05, OR = 1.84). (3) The IL-10 level in the supernatant of PBMC culture of children with homozygous genotypes of -819 TT and ATA/ATA in IL-10 gene promoter after stimulation of LPS was the lowest in comparison with those in the supernatant of PBMC culture of children with other genotypes (all P < 0.05). (4) No correlation was found between -589 (C/T) site in IL-4 gene promoter and asthma. There was no significant difference between the increase of IL-4 level in the supernatant of PBMC culture of children with the two different homozygous genotypes of IL-4 gene promoter. CONCLUSIONS: (1) There is no significant correlation between the polymorphism sites in IL-4 and IL-10 gene promoters and the susceptibility to asthma among Chinese. (2) The polymorphism of IL-10 gene promoter may be an important candidate gene for severity of asthma. The allele -819T plays an important role in increase of the total serum IgE by reducing the upregulation of IL-10 gene expression.
The paper presents a proposition for detection of linkage of genes responsible for metrical traits. Taking into account the expected means for early generations (F(1), F(2), F(3)) and a population of homozygous lines (in this case doubled haploid lines, DH derived from a cross between two homozygous parents) as well as estimators of genetic parameters m, [d], [i], [h] and [l], the expected values for these parameters in the presence of linkage have been formulated. It was found that when there is no linkage, the expression F(1) - 6F(2) + 8F(3) - 3DH(mean) is equal to zero. Thus, an experiment covering DH lines and F(1), F(2), F(3) hybrids makes it possible to obtain, beside information of interest, also information on presence or absence of linkage.
Allocation to sexual reproduction is an important life-history trait in clonal plants. Different selection pressures between competitive and competition-free environments are likely to result in the evolution of specialized genotypes and to maintain genetic variation in reproductive allocation. Moreover, selection may also result in the evolution of plastic allocation strategies. The necessary prerequisite for evolution, heritable genetic variation, can best be studied with selection experiments. Starting from a base population of 102 replicated genotypes of the clonal herb Ranunculus reptans, we imposed selection on the proportion of flowering rosettes in the absence of competition (base population: mean = 0.391, broad-sense heritability = 0.307). We also selected on the plasticity in this trait in response to competition with a naturally coexisting grass in a parallel experiment (base population: 14% lower mean in the presence of competition, broad-sense heritability = 0.072). After two generations of bidirectional selection, the proportion of flowering rosettes was 26% higher in the high line than in the low line (realized heritability +/- SE = 0.205 +/- 0.017). Moreover, genotypes of the high line had 11% fewer carpels per flower, a 22% lower proportion of rooted rosettes, and a 39% smaller average distance between rosettes within a clone. In the second experiment, we found no significant responses to selection for high and low plasticity in the proportion of flowering rosettes (realized heritability +/- SE = -0.002 +/- 0.013). Our study indicates a high heritability and potential for further evolution of the proportion of flowering rosettes in R. reptans, but not for its plasticity, which may have been fixed by past evolution at its current level. Moreover, our results demonstrate strong genetic correlations between allocation to sexual reproduction and other clonal life-history characteristics.
Simulation experiments were performed to assess the power of the lod method for detecting linkage between a quantitative trait and a qualitative marker. Using family data on the Amy2-Duffy linkage, it was found that linkage detection is feasible in certain limited circumstances. The same qualitative data yielded no evidence for a significant difference in male and female recombination fractions.
In patients with dementia, 29 diagnosed as probably suffering from Alzheimer's disease and 46 subjects with dementia of vascular origin, and in 41 non demented control subjects LDL oxidation in vitro was compared in carriers of various apolipoprotein E alleles. Restriction isotyping was performed by gene amplification and cleavage with Hhal, LDL oxidation was investigated by determination of conjugated dienes and vitamin E (alpha tocopherol) plasma level was measured by HPLC. In subjects with dementia oxidation of LDL was shown to be higher in carriers of epsilon4 allele as compared with non-carriers of this allele. It was especially observed in the propagation phase, which illustrates oxidation intensity after the exhaustion of the antioxidant reserve in LDL. Vitamin E level did not show differences between carriers of different alleles. It is concluded that the differences in oxidation susceptibility of LDL between demented subjects possessing particular apolipoprotein E forms can result partially from differing antioxidant properties of apolipoprotein E isoforms and, in a substantial degree, from the size and quality of LDL.
The new technique, polymerase chain reaction, used for in vitro DNA fragments amplification is described. The conditions of the reaction and methods of data analysis are discussed as well as the usefulness of this technique in research and medical practice.
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Twenty-eight microsatellite markers were used to analyze the conservation efficiency of two local chicken breeds (Dagu Chicken and Beijing Fatty Chicken) in different farms. Genotypes were detected in 125 samples. The genetic variations among and within the populations were calculated by the number of alleles, gene frequency, genetic heterozygosity (H), PIC, F-statistics, Nei's genetic distance and UPGMA. High polymorphism was found in the four populations, and H and PIC values of each population were more than 0. 5. All loci detected in the study showed polymorphism and the number of alleles ranged from 2 to 22 in total population. Most of these loci were at Hardy-Weinberg equilibrium except two loci (LE110194, MCW0032). The four conservation farms for the two breeds were shown to have retained substantial biodiversity, indicating that the conservation programs are efficient. However, differences between the farms of the same breeds were observed.
In the late nineteenth century Franz Boas was responsible for assembling anthropometric data from North Amerindians. Approximately 15,000 subjects were measured, but the data have never been systematically analyzed. Here we describe our efforts to develop a computerized database from Boas's data and present the first systematic analysis of these data. In addition to a general analysis of North Amerindian anthropometric variation, we also present a more detailed analysis of anthropometric variation among tribes located in the American Northwest. In the general analysis we find that anthropometric variation is strongly patterned along geographic lines. We examine geographic and language patterning by grouping tribes by culture area and language phylum. Both have high explanatory power, culture area being the higher. The Northwest analysis shows that both language and geographic location are important in explaining anthropometric variation.
INTRODUCTION: The paper presents data on population distribution of individual phenotypes and gene frequencies of alpha-amylase in random serum samples from the population of the South-Western regions of Bulgaria. MATERIAL AND METHODS: We studied 1939 individuals of both sexes aged between 18 and 45 years from the South-Western regions of Bulgaria. They were clinically healthy and without kinship ties. The blood was obtained by venous puncture. The amylase phenotypes were established by horizontal electrophoresis of blood serum on agar gel (1%) after the J. Kompf's method with some modification made in our laboratory. RESULTS: In the Bulgarian population of the South-Western regions of Bulgaria the most frequent alpha-amylase phenotype is Amy1A Amy2A--1603 (82.67) followed by AmylA Amy2A2B--162 (8.35%); Amy1 A1 B Amy2 A--92 (4.74%); AmylA1B Amy2A2B--58 (2.99%); AmylA Amy2B--17 (0.88%); Amy1c Amy2A--5 (0.26%); and Amy1c Amy2A2B--2 (0.11%). The revealed genetic frequencies are as follows: 1a = 0.9577, 1b = 0.0398, 1 degrees = 0.0025 and 2a = 0.9340 and 2b = 0.0660. CONCLUSIONS: The difference between the observed theoretically expected types of amylase is not significant so the population studied is in genetic balance regarding the enzyme system. This population does not differ significantly from other populations in gene frequency. A tendency of West-Eastern geographical distribution is evident. Allele frequencies of 1a and 2a tend to increase in that direction. Isoenzyme frequencies in the studied Bulgarian population do not differ significantly from those of the European populations.
OBJECTIVE: To investigate whether the polymorphisms of matrix metalloproteinase-2 (MMP-2) and -9 (MMP-9) promoters contribute to the development and progression of colorectal cancer in Chinese population. METHODS: the PCR-based denaturing high-performance liquid chromatography or PCR-restriction fragment length polymorphism technique respectively was applied to analyze the MMP-2 -1306C/T and MMP-9 -1562C/T polymorphisms in normal group (126 individuals) and colorectal cancer group (126 cases). Genotype frequencies were compared between patients and matched controls, and the association of genotypes with clinical-pathological parameters was studied. RESULTS: The frequency of the CC genotype in the MMP-2 gene polymorphism was significantly increased in colorectal cancer patients when compared with controls (P<0.05), and individuals with the CC genotype had an increased risk of developing colorectal cancer compared to those with CT+TT genotypes (OR: 1.959; 95%CI: 1.055-3.637). Significant correlation was found between the depth of tumor invasion and MMP-2 -1306C/T polymorphism in colorectal cancer patients. However, the genotype frequencies of MMP-9 -1562C/T in colorectal cancer patients were similar to those in control subjects. CONCLUSION: Our results indicate that MMP-2 -1306 C/T polymorphism may be associated with genetic susceptibility to colorectal cancer and the invasive capability of colorectal cancer in Chinese patients. And it is easier for the CC genotype cancer to invade through bowel wall.
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Examination of the equilibria of the standard two-locus two-allele selection model leads to the construction of a polynomial with coefficients derived from selective values in the genotypic fitness matrix. This polynomial can be partially factored algebraically and numerical techniques are available to extract the roots of the remainder. Each root provides a possible value of the disequilibrium coefficient and the gametic frequencies at equilibrium, and these can be readily checked for stability.