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Transmission Disequilibrium Test
In genetics, 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 affected offsprings have parents. These can be represented by the transmitted a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Genetics
Genetics is the study of genes, genetic variation, and heredity in organisms.Hartl D, Jones E (2005) It is an important branch in biology because heredity is vital to organisms' evolution. Gregor Mendel, a Moravian Augustinians, Augustinian friar working in the 19th century in Brno, was the first to study genetics scientifically. Mendel studied "trait inheritance", patterns in the way traits are handed down from parents to offspring over time. He observed that organisms (pea plants) inherit traits by way of discrete "units of inheritance". This term, still used today, is a somewhat ambiguous definition of what is referred to as a gene. Phenotypic trait, Trait inheritance and Molecular genetics, molecular inheritance mechanisms of genes are still primary principles of genetics in the 21st century, but modern genetics has expanded to study the function and behavior of genes. Gene structure and function, variation, and distribution are studied within the context of the Cell (bi ... [...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 Foundati ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Genetic Linkage
Genetic linkage is the tendency of Nucleic acid sequence, DNA sequences that are close together on a chromosome to be inherited together during the meiosis phase of sexual reproduction. Two Genetic marker, genetic markers that are physically near to each other are unlikely to be separated onto different Chromatid, chromatids during chromosomal crossover, and are therefore said to be more ''linked'' than markers that are far apart. In other words, the nearer two Gene, genes are on a chromosome, the lower the chance of Genetic recombination, 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 M ... [...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 possible mapping efforts. 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 ar ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
McNemar's Test
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 and presume ... [...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 phenotype, phenotypic trait association (statistics), 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 treatment and control groups, diseased subjects and healthy controls). Genetic association studies 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 exome sequencing, 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 polymorphism ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Population Structure (genetics)
Population structure (also called genetic structure and population stratification) is the presence of a systematic difference in allele frequencies between subpopulations. In a randomly mating (or ''panmictic'') population, allele frequencies are expected to be roughly similar between groups. However, mating tends to be non-random to some degree, causing structure to arise. For example, a barrier like a river can separate two groups of the same species and make it difficult for potential mates to cross; if a mutation occurs, over many generations it can spread and become common in one subpopulation while being completely absent in the other. Genetic variants do not necessarily cause observable changes in organisms, but can be correlated by coincidence because of population structure—a variant that is common in a population that has a high rate of disease may erroneously be thought to cause the disease. For this reason, population structure is a common confounding variable in med ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Binomial Test
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 A binomial test is a statistical hypothesis test used to determine whether the proportion of successes in a sample differs from an expected proportion in a binomial distribution. It is useful for situations when there are two possible outcomes (e.g., success/failure, yes/no, heads/tails), i.e., where repeated experiments produce binary data. If one assumes an underlying probability \pi_0 between 0 and 1, the null hypothesis is : H_0\colon\pi=\pi_0 For a sample of size n, we would expect n\pi_0 successes. The formula of the binomial distribution gives the probability of those n samples instead producing k successes: : \Pr(X=k)=\binom\pi_0^k(1-\pi_0)^ Suppose that we want to test the alternative hypothesis : H_\colon\pi\pi_0 using the summation of the range from k to n instead. Calculating a p-val ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Chi-squared Test
A chi-squared test (also chi-square or test) is a Statistical hypothesis testing, 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 Validity (statistics), valid when the test statistic is chi-squared distribution, 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 Statistical significance, statistically significant difference between the expected frequency (statistics), 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 application ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Null Hypothesis
The null hypothesis (often denoted ''H''0) is the claim in scientific research that the effect being studied does not exist. The null hypothesis can also be described as the hypothesis in which no relationship exists between two sets of data or variables being analyzed. If the null hypothesis is true, any experimentally observed effect is due to chance alone, hence the term "null". In contrast with the null hypothesis, an alternative hypothesis (often denoted ''H''A or ''H''1) is 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 to make statistical inferences, which are formal methods of reaching conclusions and separating scientific claims from statistical noise. The statement being tested in a test of statistical significance is called the null hypothesis. The test of significance is designed to assess the strength of the e ... [...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 (genotype) that also expresses an associated trait (phenotype). In medical genetics, the penetrance of a disease-causing mutation is the proportion of individuals with the mutation that exhibit clinical Symptom, 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 go on to develop the disease, showing its phenotype, whereas 5% will not. Penetrance only refers to whether an individual with a specific genotype exhibits any phenotypic signs or symptoms, and is not to be confused with Expressivity (genetics), variable expressivity which is to what extent or degree the symptoms for said disease are shown (the expression of the phenotypic trait). Meaning that, even if the same disease-causing mutation affects separate individ ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
