Methods for Outbreaks Using Genomic Data
Leonhard Held, Niel Hens, Philip O’Neill, Jacco Wallinga in Handbook of Infectious Disease Data Analysis, 2019
In the genetic model it is assumed that each host harbors a single genetic sequence, which is sampled and transmitted to secondary cases. Mutations take place during the transmission event so that the next host in the transmission chain may carry a slightly different sequence. Each nucleotide changes with probability at each transmission event. Thus, the genetic likelihood is a product of terms for each edge in the transmission tree: in which is the genetic distance between hosts and , and is the total shared sequence length of hosts and .
Of what are epidemics the symptom?
Ann H. Kelly, Frédéric Keck, Christos Lynteris in The Anthropology of Epidemics, 2019
Microbial phylogenies map space and time. Space is plotted out in terms of genetic distance, assumed to correspond to real-world geographic and biological distance. Distantly related micro-organisms are unlikely to be found in the same hosts from whom they acquired the infection; they are found in individuals separated by a longer chain of transmission than close relatives, whose more recent common ancestor was not too far back in time and not too far back in terms of transmission. In other words, as a micro-organism moves from host to host, it mutates. Mutations that give the bearer an advantage when they move to hosts whose immune systems are more efficient at killing certain microbial offspring or variants give a survival advantage, establishing a genetic beachhead that gradually spreads throughout the viral population). Genetic sequences archive space and time. Or, alternatively, they are the materialisation of speed: space over time. Faster transmission means more mutations, more change. Speed is sedimented in viral genomes; snapshots of mutation that are stills of ceaseless viral change. Molecular epidemiology, through phylogenetic analyses, charts viral speed and progress. What is amenable to ethnographic investigation are the collective representations – kinship, culture, identity – and the material correlates of speed. These are the infrastructures of connection: transport links, commerce, and the Internet that collectively shape social connectedness.
An Approach to Inherited Pulmonary Disease
Stephen D. Litwin in Genetic Determinants of Pulmonary Disease, 2020
In the absence of an exchange of chromosomal material in the interval between two loci the genes at each locus on one chromosome are transmitted to an offspring together. Genes at linked loci on the same single chromosome are said to be in coupling; genes at linked loci on different chromosomes are said to be in repulsion. Genes in repulsion can demonstrate linkage if the progeny show the phenotypes of both genes in the same individual with a frequency less than expected. The extent of deviation from independent assortment is a measurement of the genetic distance between the two loci, with large deviations indicating close linkage. The results of linkage experiments in mice and other organisms in which matings can be arranged indicate that distances between loci are additive and form a linear genetic map.
Genetic polymorphism and forensic application of 23 autosomal STR loci in the Han population of Panjin City, Liaoning Province, Northeastern China
Published in Annals of Human Biology, 2022
Hongbo Wang, Cairui Xin, Xinyao Meng, Shihan Xing, Baotong Guo, Yuhan Chen, Bao-jie Wang, Jun Yao
The allele frequencies of samples, exact tests of Hardy-Weinberg equilibrium (HWE), and pair linkage disequilibrium (LD) tests were calculated with the PowerMarker v3.25 (Liu and Muse 2005). The values for matching probability (MP), power of discrimination (PD), polymorphism information content (PIC), power of exclusion (PE), typical paternity index (TPI), gene diversity (GD), and heterozygosity (He) were calculated using the PowerStats software v1.2 (Promega, Madison, WI, USA) (Tereba 1999), which was modified from Silva, et al. in order to support and manage the large number of samples (Cabezas Silva et al. 2016). Reynold's genetic distance, based on allele frequencies across the 15 autosomal loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818, and FGA) shared by the included compared populations, and exact test p values were generated using PowerMarker v3.25. Nei’s standard genetic distance between populations was calculated using the allele frequencies by Phylip 3.69 package (Felsenstein 2009) and visualised by MEGA v7.0.26 software (Kumar et al. 2016). Finally, MDS analyses on the basis of Reynold’s genetic distance matrix were performed using SPSS 26.0 software (IBM Corp., Armonk, NY).
Genetic polymorphisms, forensic efficiency and phylogenetic analysis of 17 autosomal STR loci in the Han population of Wuxi, Eastern China
Published in Annals of Human Biology, 2019
Yan Lu, Hong-jie Sun, Ji-chuan Zhou, Xu Wu
The allele frequencies of the samples, Hardy-Weinberg equilibrium (HWE) and pair linkage disequilibrium were calculated using PowerMarker v3.25 (Liu and Muse 2005). The values for matching probability, power of discrimination (PD), polymorphism information content (PIC), power of exclusion (PE), typical paternity index, gene diversity and heterozygosity were calculated using the PowerStats v1.2 software (Tereba 1999) modified by Cabezas Silva et al. (2016) to support and manage a large number of samples. Nei’s standard genetic distance between populations was calculated on the basis of the allele frequencies by using the Phylip 3.69 package (Felsenstein 2005). A multidimensional scaling (MDS) plot was constructed using SPSS 13.0 statistical software (SPSS Inc., Chicago, IL) on the basis of Nei’s standard genetic distance values.
Genetic diversity of 15 autosomal STRs in a sample of Berbers from Aurès region in the Northeast of Algeria and genetic relationships with other neighbouring samples
Published in Annals of Human Biology, 2020
Amine Abdeli, Traki Benhassine
To study the genetic affinity between our Aurès samples (Oum El Bouaghi, Khenchela, and Batna) and 25 other published populations, the Nei’s standard genetic distances based on allele frequency distribution of the 10 autosomal STR loci were calculated and represented in Supplementary Table 3. The largest genetic distance observed between our samples (Oum El Bouaghi, Khenchela, and Batna) and other samples available in the literature was for the Iran sample (0.185325, 0.198784 and 0.195747, respectively) followed by the Matmata sample (Tunisia3) (0.171592, 0.186124, and 0.178735, respectively), whereas the shortest genetic distance found was between the samples of Doukkala (Morroco3) (0.026097) and Batna. The genetic distance between Oum El Bouaghi and the sample of Berbers from Bejaia was also weak (0.031223).
Related Knowledge Centers
- Allele
- Allele Frequency
- Biodiversity
- Genetic Drift
- Mutation
- Genetics
- Species
- Common Descent
- Gene
- Locus