AlleleN=342N=650N=97N=509N=236N=296N=361U.S. BlackJapan (Tokyo)U.S. AsianArgentina (Buenos Aires)U.S. HispanicSweden (Stockholm)U.S. Caucasian90.00292∗––––––100.00439∗––0.009820.00212∗0.007∗0.00831110.00146∗0.008–0.011790.01480.005∗0.0097120.0760.0520.03610.123770.1140.1180.114130.04090.1930.2160.132610.1230.1550.12313.20.00439∗0.003∗–––––140.07160.1960.2370.206290.1610.1940.13414.2–0.002∗–0.00196∗0.00212∗–0.00139∗150.1650.1660.1800.125740.1590.1370.17015.20.00146∗––––––160.1710.1590.1290.129670.1250.1130.14716.2––––––0.00139∗170.1520.0820.0670.109040.1250.1130.139180.1210.0440.03090.079570.07840.0830.0776190.09940.0260.04120.034380.04660.0410.0402200.06290.0270.02580.020630.02750.0120.018210.01020.0260.0103∗0.007860.00847∗0.0140.009721.20.00146∗––––––220.007310.0060.0155∗0.00393∗0.01060.008∗0.00693230.00439∗0.0050.00515∗0.00196∗–––240.00146∗0.003∗–0.000980.00212∗––25–0.002∗–––––28––0.00515∗––––Minimum allele frequency0.007310.003850.02580.004910.01060.008450.00693 Show
Data sets are grouped according to ethnic/racial classification which categories are often defined by self-declaration when samples are collected. Alleles with an asterisk are below the recommended minimum allele frequency of 5/2N (NRC 1996). Bold font highlights the most frequent allele in each group. Results are listed according to number of significant figures reported in the original publication. An examination of allele 14 in Table 10.2 is instructive. Values range from about 7% to almost 24%. Clearly genotype frequency calculations will differ depending on which population data are used. The potential difference that can exist between population groups is a primary reason that the National Research Council in its 1992 report recommended that “data on at least three major ‘races’ (e.g. Caucasians, Blacks, Hispanics, Asians, and Native Americans) should be analyzed” (NRC 1992, p. 15; see also Appendix 2). It is therefore common practice in forensic DNA laboratory reports to include statistical calculations from multiple population groups in order to provide a range for potential DNA profile frequency estimates. View chapterPurchase book Read full chapter URL: https://www.sciencedirect.com/science/article/pii/B9780124052130000105 Genotyping Techniques to Address Diversity in TumorsDavid Lindgren, ... Johan Vallon-Christersson, in Advances in Cancer Research, 2011 C The B Allele Frequency and Relative Copy NumberThe BAF, first presented using Illumina data (Peiffer et al., 2006), is calculated for each SNP individually by transformation of allele intensities and represents the proportion of DNA content for allele B as compared to the total DNA content of A and B alleles together. The proposed transformation involves linear interpolation of allele frequencies from reference data derived from normal samples. Since BAF simply describes the total number of B allele copies divided by the total number of allele copies for that specific locus, a theoretical BAF can be calculated for any given genotype using the following equation: (1)BAF=NB/(NA+NB) In Eq. (1), NB is the total number of B allele copies and NA is the total number of A allele copies. Apart from genotyping, SNP arrays provide means for quantification of relative copy numbers at each given loci and current SNP arrays typically contain large numbers of probes that are solely designed to assay copy number and target nonsequence polymorphic loci. These probes can be used for the analysis of CNVs but many are also added to provide increased power and resolution when analyzing acquired copy-number aberrations in tumors. Relative copy-number ratio values are calculated by comparing observed normalized intensities (sum of A and B) to the expected, similarly to how BAF is derived, and is typically presented as Log2 relative ratio (LRR). Data from Affymetrix can be converted into BAF and LRR by appropriate normalization and transformation (Sun et al., 2009; Wang et al., 2007). Examples of expected BAF and LRR values for a normal genome and how these values are affected by acquired genetic aberrations are further discussed below. View chapterPurchase book Read full chapter URL: https://www.sciencedirect.com/science/article/pii/B9780123876881000065 Population GeneticsBrian Charlesworth, in Encyclopedia of Biodiversity (Second Edition), 2013 GlossaryAllele frequency The frequency of a variant form of a genetic locus within a population. Genetic driftEvolutionary changes caused by random sampling of genotype frequencies in a finite population. GenotypeThe state of an individual with respect to a defined genetic locus or set of loci. HeritabilityThe proportion of the variance in a trait that is due to additive genetic effects. InbreedingMatings between close relatives. Mutation rateThe frequency with which new mutations arise per generation. Neutral mutationsMutations whose effects on fitness are either nonexistent or so small that their fate is controlled by genetic drift rather than by selection. PhenotypeThe state of an individual with respect to a trait of interest. PolymorphismThe existence at intermediate frequencies of two or more variants at a locus within a population. SelectionThe differential survival or reproductive success of individuals, associated with differences in phenotype or genotype. View chapterPurchase book Read full chapter URL: https://www.sciencedirect.com/science/article/pii/B9780123847195001167 Forensics and PaternityFrank H. Stephenson, in Calculations for Molecular Biology and Biotechnology (Third Edition), 2016 13.1.2 Calculating Allele FrequenciesAn allele frequency is the proportion of the total number of alleles in a population represented by a particular allele. For any polymorphism other than those present on the X or Y chromosome, each individual carries two alleles per locus, one inherited from the mother, the other from the father. Within a population, therefore, there are twice as many total alleles as there are people. When calculating the number of a particular allele, homozygous individuals each contribute two of that allele to the total number of that particular allele. Heterozygous individuals each contribute one of a particular allele to the total number of that allele. For example, if there are six individuals with the AA genotype, they contribute 12 A alleles. Thirty-four AB heterozygous individuals contribute a total of 34 A alleles and 34 B alleles to the total. The frequency of the A allele in a three-allele system is calculated as Aallelefrequency=[2(#ofAA′s)+(#ofAB′s)+(#ofAC′s)]2n where n is the number of people in the survey. The frequencies for the other alleles are calculated in a similar manner. The sum of all allele frequencies for a specific locus should equal 1.0. Problem 13.3 What are the frequencies for the A, B, and C alleles described in Problem 13.2? Solution 13.3 We will assign a frequency of p to the A allele, q to the B allele, and r to the C allele. We have the following genotype data. GenotypeNumber of individualsAA6AB34AC46BB12BC60CC42Total200 The allele frequencies are then calculated as follows: pA=[2(6)+34+46]2(200)=92400=0.230 qB=[2(12)+34+60]2(200)=118400=0.295 rC=[2(42)+46+60]2(200)=190400=0.475 Therefore, the allele frequency of A is 0.230, the allele frequency of B is 0.295, and the allele frequency of C is 0.475. Note that the allele frequencies add up to 1.000 (0.230 + 0.295 + 0.475 = 1.000). View chapterPurchase book Read full chapter URL: https://www.sciencedirect.com/science/article/pii/B9780128022115000138 Biological Distances and Population Genetics in BioarchaeologyJ.H. Relethford, in Biological Distance Analysis, 2016 R-Matrix Theory and Biological DistanceFor allele frequency data, one of the many genetic distance measures that have been developed is based on R-matrix theory. An R matrix provides information on genetic similarity within and between populations based on standardized allele/haplotype frequency differences. Much of the development of R-matrix theory can be found in Harpending and Jenkins (1973) and Workman et al. (1973). For an analysis of g populations, the R matrix consists of g rows and g columns. For any given allele, the element of the R matrix for populations i and j is (2.3)rij=(pi−p¯)(pj−p¯)p¯(1−p¯) where pi and pj are the allele frequencies in populations i and j, respectively, and p¯is the mean allele frequency over all populations in the analysis (not just i and j). The overall R matrix is obtained by averaging Eq. (2.3) over all alleles. The R matrix is a variance–covariance matrix of standardized allele frequencies. The mean allele frequency p¯is derived by weighting each population's allele frequency by its corresponding population size (not sample size). This weighting is used in order to obtain the expected mean allele frequency under random mating (no population subdivision), as this value is dependent on the total number of a given allele in the total population. The elements of the R matrix can be used to estimate other useful population-genetic measures. One of these is the average diagonal element of the R matrix (i = j), weighted by population size, which gives an estimate of Wright's FST as (2.4)FST=∑wirii where wi is the relative population size of population i (=Ni/NT, where NT is the total population size summed over all groups). FST is a measure of genetic differentiation among groups relative to the total amount of genetic variation expected under no subdivision. FST can be difficult to interpret and compare across studies because it is affected by population size, rates of local and long-range gene flow, and time depth, among other influences. The R matrix can also be used to derive the genetic distance between pairs of populations. The squared genetic distance between populations i and j is (Harpending and Jenkins, 1973; Morton, 1975) (2.5)Dij2=rii+rjj−2rij. Further extensions to R-matrix theory include adjustments for sampling bias, as described by Workman et al. (1973). View chapterPurchase book Read full chapter URL: https://www.sciencedirect.com/science/article/pii/B9780128019665000020 Race, Human Variation, and Health, the Interaction ofA.H. Goodman, in International Encyclopedia of Public Health, 2008 The Structure of Human VariationIf the idea of race – dividing humans into some three or more racial groups – approximated in a useful way the geographic structure of human variation, then one might support the notion that race is an imperfect but acceptable stand-in for human genetic variation. So framed, the association of place and genetic variation does not explain everything, but it is a sort of ‘quick and dirty’ approximation (Satel, 2002). This position may have been defensible prior to the application of modern genetics to human evolutionary studies. However, it is not defensible now for the following reasons. Human variation is continuousAllele frequencies tend to vary gradually across human populations. Definitions of race as a discontinuous category, reflecting clear ‘breaks’ in gene frequency, are thus conceptually flawed: It is impossible to identify where one race begins and another ends. Skin color, for example, varies widely by latitude and degree of exposure to ultraviolet. Since Africa covers such a wide span of latitude, it is reasonable that African groups exhibit a wide range of skin colors that overlap tremendously with individuals from other continents. Human traits vary independently from each otherTraits tend to vary independently of other traits. Race categories will therefore vary by the traits used to classify. A classification based on sickle cell trait might include equatorial Africans, Greeks, and Turks, while another classification based on lactase enzyme deficiency might include eastern and southern Africans with southern Europeans, Japanese, and Native Americans. There is no possibility for consistency. As skin color is only correlated with a few other phenotypic traits such as hair and eye color, it is true to say that ‘race is only skin deep.’ Within-race-group genetic variation is much greater than variation among ‘races’Starting with Lewontin (1972), studies have statistically apportioned variation in different genetic systems to different levels: among ‘races’ and within ‘races’ and smaller populations such as the Hopi, the Ainu, and the Irish. Lewontin collected data on blood group polymorphisms in different groups and races. He found that blood group variation between races statistically explains only about 6% of the total variation. These results show that if one is to adopt a racial paradigm, one must acknowledge that race will statistically explain only a small proportion of genetic variation. Moreover, this small variation is better explained by geographic distance (Templeton, 1998). Yu et al. (2002) more recently compared a large sequence of DNA, 25 000 letters or base pairs long, of ten individuals from each of the three main ‘races’ typically used in medical studies: Asian, European, and African. They counted out the number of differences between any two individuals and found that the average number of differences between any two individuals from Africa was greater than the average number of differences between an African and a European or an African and an Asian. These results support the understanding that there is greater genetic variation in Africa because of the increased evolutionary time humans have spent in Africa. Most startling perhaps is that Europeans and Asians, rather than being genetically separable, appear more accurately to be subsets of Africans. We truly are, it seems, all Africans. View chapterPurchase book Read full chapter URL: https://www.sciencedirect.com/science/article/pii/B9780123739605005086 Genetic DistanceM. Nei, in Encyclopedia of Genetics, 2001 F*ST DistanceThe allele frequencies of different populations may differentiate by genetic drift alone without any selection. When a population splits into many populations of effective size N in a generation, the extent of differentiation of allele frequencies in subsequent generations can be measured by Wright's FST Nei and Kumar, 2000. When there are only two populations but allele frequency data are available from many different loci, it is possible to develop a statistic whose expectation is equal to FST. One such statistic is given by (6)FST*=[(JˆX+JˆY)/2−JˆXY]/(1−JˆXY) where JˆX, JˆY, and JˆXYare unbiased estimators of the means (JX, JY, and JXY) of ∑xi2, ∑yi2, and ∑xiyiover all loci, respectively. For a single locus, unbiased estimates of ∑xi2, ∑yi2, and ∑xiyiare given by (7)jˆX=(2mX∑xˆi2−1)/(2mX−1) (8)jˆY=(2mY∑yˆi2−1)/(2mY−1) (9)jˆXY=∑xˆiyˆi where mX and mY are the numbers of diploid individuals sampled from populations X and Y, respectively, and xˆiand yˆiare the sample frequencies of allele Ai in populations X and Y. Therefore, JˆX, JˆY, and JˆXYare the means of jˆX, jˆY, and jˆXYover all loci, respectively. The expectation of FST*is given by (10)E(FST*)=1−e−t/(2N) where t is the number of generations after population splitting. Therefore, we have (11)DL=−ln(1−FST*) which is expected to be proportional to t when the number of loci used is large [E(DL) = t/(2N)]. This indicates that when evolutionary time is short and new mutations are negligible, one can estimate t by 2NDL if N is known. In practice, however, new mutations always occur, and this will disturb the linear relationship between DL and t when a relatively long evolutionary time is considered. N is also usually unknown. How do you calculate the frequency of a gene?Frequency of gene = Frequency of homozygote for that gene + 1/2 frequency of heterozygotes. Each individual will have two homologous chromosomes each carrying a particular allele, frequency of 'M' can be calculated by doubling the number of homologous 'M' blood type and adding to it the frequencies of heterozygous 'MN' blood type.
How do geneticists calculate the degree of genetic linkage?Geneticists calculate the corresponding percentage to assign the degree of genetic linkage, which has units of "centimorgans," or cM. In this case, the value is 0.20 times 100, or 20%. The lower the recombination frequency, the more closely the genes are physically linked.
How to calculate the relative expression of each gene?Here is what I have tried. I tried dividing the ct value of each gene by the the ct value of the reference gene (relative expression = ct (gene of interest) / ct (reference gene)).
What is a genetic map used to determine?A genetic map determines the relative positions of genes on chromosomes based on ______ frequency. Genes, detected by looking for phenotypic differences between individuals, are some of the most common markers used to construct ______ maps. ...
How is gene frequency calculated?In the equation, p2 represents the frequency of the homozygous genotype AA, q2 represents the frequency of the homozygous genotype aa, and 2pq represents the frequency of the heterozygous genotype Aa. In addition, the sum of the allele frequencies for all the alleles at the locus must be 1, so p + q = 1.
What is the relative frequency of a gene?Genetic variation is usually expressed as a relative frequency, which means a proportion of the total population under study. In other words, a relative frequency value represents the percentage of a given phenotype, genotype, or allele within a population.
How is genotype frequency calculated?The frequency of genotype AA is determined by squaring the allele frequency A. The frequency of genotype Aa is determined by multiplying 2 times the frequency of A times the frequency of a. The frequency of aa is determined by squaring a. Try changing p and q to other values, ensuring only that p and q always equal 1.
What determines frequency of recombination?We can see if two genes are linked, and how tightly, by using data from genetic crosses to calculate the recombination frequency. By finding recombination frequencies for many gene pairs, we can make linkage maps that show the order and relative distances of the genes on the chromosome.
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