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Transmission Disequilibrium Test
The transmission disequilibrium test (TDT) was proposed by Spielman, McGinnis and Ewens (1993) as a family-based association test for the presence of genetic linkage between a genetic marker and a trait. It is an application of McNemar's test. A specificity of the TDT is that it will detect genetic linkage only in the presence of genetic association. While genetic association can be caused by population structure, genetic linkage will not be affected, which makes the TDT robust to the presence of population structure. The case of trios: one affected child per family Description of the test We first describe the TDT in the case where families consist of trios (two parents and one affected child). Our description follows the notations used in Spielman, McGinnis & Ewens (1993). The TDT measures the over-transmission of an allele from heterozygous parents to affected offsprings. The ''n'' affected offsprings have 2''n'' parents. These can be represented by the transmitted and ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Warren Ewens
Warren John Ewens (born 23 January 1937 in Canberra) is an Australian-born mathematician who has been Professor of Biology at the University of Pennsylvania since 1997. (He also held that position 1972–1977.) He concentrates his research on the mathematical, statistical and theoretical aspects of population genetics. Ewens has worked in mathematical population genetics, computational biology, and evolutionary population genetics. He introduced Ewens's sampling formula. Ewens received a B.A. (1958) and M.A. (1960) in Mathematical Statistics from the University of Melbourne, where he was a resident student at Trinity College,"Salvete 1955", The Fleur-de-Lys', Nov. 1955, p. 14. and a Ph.D. from the Australian National University (1963) under P. A. P. Moran. He first joined the department of biology at the University of Pennsylvania in 1972, and in 2006 was named the Christopher H. Browne Distinguished Professor of Biology. Positions held include: *1967–1972 Foundation ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Genetic Linkage
Genetic linkage is the tendency of DNA sequences that are close together on a chromosome to be inherited together during the meiosis phase of sexual reproduction. Two genetic markers that are physically near to each other are unlikely to be separated onto different chromatids during chromosomal crossover, and are therefore said to be more ''linked'' than markers that are far apart. In other words, the nearer two genes are on a chromosome, the lower the chance of recombination between them, and the more likely they are to be inherited together. Markers on different chromosomes are perfectly ''unlinked'', although the penetrance of potentially deleterious alleles may be influenced by the presence of other alleles, and these other alleles may be located on other chromosomes than that on which a particular potentially deleterious allele is located. Genetic linkage is the most prominent exception to Gregor Mendel's Law of Independent Assortment. The first experiment to demonstrate li ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Genetic Marker
A genetic marker is a gene or DNA sequence with a known location on a chromosome that can be used to identify individuals or species. It can be described as a variation (which may arise due to mutation or alteration in the genomic loci) that can be observed. A genetic marker may be a short DNA sequence, such as a sequence surrounding a single base-pair change ( single nucleotide polymorphism, SNP), or a long one, like minisatellites. Background For many years, gene mapping was limited to identifying organisms by traditional phenotypes markers. This included genes that encoded easily observable characteristics such as blood types or seed shapes. The insufficient number of these types of characteristics in several organisms limited the mapping efforts that could be done. This prompted the development of gene markers which could identify genetic characteristics that are not readily observable in organisms (such as protein variation). Types Some commonly used types of genetic markers ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
McNemar's Test
In statistics, McNemar's test is a statistical test used on paired nominal data. It is applied to 2 × 2 contingency tables with a dichotomous trait, with matched pairs of subjects, to determine whether the row and column marginal frequencies are equal (that is, whether there is "marginal homogeneity"). It is named after Quinn McNemar, who introduced it in 1947. An application of the test in genetics is the transmission disequilibrium test for detecting linkage disequilibrium. The commonly used parameters to assess a diagnostic test in medical sciences are sensitivity and specificity. Sensitivity (or recall) is the ability of a test to correctly identify the people with disease. Specificity is the ability of the test to correctly identify those without the disease. Now presume two tests are performed on the same group of patients. And also presume that these tests have identical sensitivity and specificity. In this situation one is carried away by these findings ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Genetic Association
Genetic association is when one or more genotypes within a population co-occur with a phenotypic trait more often than would be expected by chance occurrence. Studies of genetic association aim to test whether single-locus alleles or genotype frequencies (or more generally, multilocus haplotype frequencies) differ between two groups of individuals (usually diseased subjects and healthy controls). Genetic association studies today are based on the principle that genotypes can be compared "directly", i.e. with the sequences of the actual genomes or exomes via whole genome sequencing or whole exome sequencing. Before 2010, DNA sequencing methods were used. Description Genetic association can be between phenotypes, such as visible characteristics such as flower color or height, between a phenotype and a genetic polymorphism, such as a single nucleotide polymorphism (SNP), or between two genetic polymorphisms. Association between genetic polymorphisms occurs when there is non-rando ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Binomial Test
In statistics, the binomial test is an exact test of the statistical significance of deviations from a theoretically expected distribution of observations into two categories using sample data. Usage The binomial test is useful to test hypotheses about the probability (\pi) of success: : H_0:\pi=\pi_0 where \pi_0 is a user-defined value between 0 and 1. If in a sample of size n there are k successes, while we expect n\pi_0, the formula of the binomial distribution gives the probability of finding this value: : \Pr(X=k)=\binomp^k(1-p)^ If the null hypothesis H_0 were correct, then the expected number of successes would be n\pi_0. We find our p-value for this test by considering the probability of seeing an outcome as, or more, extreme. For a one-tailed test, this is straightforward to compute. Suppose that we want to test if \pi\pi_0 using the summation of the range from k to n instead. Calculating a p-value for a two-tailed test is slightly more complicated, since a bin ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Chi-squared Test
A chi-squared test (also chi-square or test) is a statistical hypothesis test used in the analysis of contingency tables when the sample sizes are large. In simpler terms, this test is primarily used to examine whether two categorical variables (''two dimensions of the contingency table'') are independent in influencing the test statistic (''values within the table''). The test is valid when the test statistic is chi-squared distributed under the null hypothesis, specifically Pearson's chi-squared test and variants thereof. Pearson's chi-squared test is used to determine whether there is a statistically significant difference between the expected frequencies and the observed frequencies in one or more categories of a contingency table. For contingency tables with smaller sample sizes, a Fisher's exact test is used instead. In the standard applications of this test, the observations are classified into mutually exclusive classes. If the null hypothesis that there are no di ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Null Hypothesis
In scientific research, the null hypothesis (often denoted ''H''0) is the claim that no difference or relationship exists between two sets of data or variables being analyzed. The null hypothesis is that any experimentally observed difference is due to chance alone, and an underlying causative relationship does not exist, hence the term "null". In addition to the null hypothesis, an alternative hypothesis is also developed, which claims that a relationship does exist between two variables. Basic definitions The ''null hypothesis'' and the ''alternative hypothesis'' are types of conjectures used in statistical tests, which are formal methods of reaching conclusions or making decisions on the basis of data. The hypotheses are conjectures about a statistical model of the population, which are based on a sample of the population. The tests are core elements of statistical inference, heavily used in the interpretation of scientific experimental data, to separate scientific claims fr ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Penetrance
Penetrance in genetics is the proportion of individuals carrying a particular variant (or allele) of a gene (the genotype) that also express an associated trait (the phenotype). In medical genetics, the penetrance of a disease-causing mutation is the proportion of individuals with the mutation who exhibit clinical symptoms among all individuals with such mutation. For example, if a mutation in the gene responsible for a particular autosomal dominant disorder has 95% penetrance, then 95% of those with the mutation will develop the disease, while 5% will not. A condition, most commonly inherited in an autosomal dominant manner, is said to show complete penetrance if clinical symptoms are present in all individuals who have the disease-causing mutation. A condition which shows complete penetrance is neurofibromatosis type 1 – every person who has a mutation in the gene will show symptoms of the condition. The penetrance is 100%. Common examples used to show degrees of penetrance are ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
