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An Approach to Inherited Pulmonary Disease
Published in Stephen D. Litwin, 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.
Use of Mitochondrial Donation
Published in Botros Rizk, Yakoub Khalaf, Controversies in Assisted Reproduction, 2020
Mouse models have been an important tool in establishing the safety and efficacy of MD. PNT has been performed in mice since the mid-1980s, when it was first established that viable offspring were obtained following the transfer of fertilized egg pronuclei into enucleated parthenogenetic eggs (12). One set of experiments directly assessed whether PNT could be used to rescue respiration defects caused by a mtDNA deletion in offspring of the “mitomouse”: the data indicated successful rescue (13). Most experimentation suggests that PNT is efficient and reproducible when conducted with normally fertilized zygotes. However, some reports indicate that abnormalities in offspring can occur if the genetic distance between the mtDNA donor and nuclear DNA recipient strains is too great, such as between distinct subspecies of mice (14). This topic is revisited during a discussion of the possibility of “mitonuclear” incompatibility in the next section.
Methods for Outbreaks Using Genomic Data
Published in Leonhard Held, Niel Hens, Philip O’Neill, Jacco Wallinga, Handbook of Infectious Disease Data Analysis, 2019
Don Klinkenberg, Caroline Colijn, Xavier Didelot
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 .
Paternal lineage of the Berbers from Aurès in Algeria: estimate of their genetic variation
Published in Annals of Human Biology, 2019
Amine Abdeli, Traki Benhassine
Genetic relationships were assessed by pairwise genetic distances (Rst) (Reynolds et al. 1983; Slatkin 1995) using Arlequin ver 3.5.2.2 (Excoffier and Lischer 2010). Two comparative analyses were carried out, the first calculated between our sample and six other Algerian samples (Arab and Berber groups) available in the literature (Robino et al. 2008; Vermeulen et al. 2009; Bekada et al. 2015), and the second between our sample and 28 other populations from neighbouring regions or countries from North Africa (El-Sibai et al. 2009; Aboukhalid et al. 2010; Laouina et al. 2011; Ottoni et al. 2011; Elmrghni et al. 2012; Fadhlaoui‐Zid et al. 2012; Triki-Fendri et al. 2013), Sub-Saharan Africa (Purps et al. 2014; Larmuseau et al. 2015; Iacovacci et al. 2017), Middle East (El-Sibai et al. 2009; Purps et al. 2014; Taqi et al. 2015; Jones et al. 2017; Tokdemir and Tunçez 2017) and Europe (Purps et al. 2014; Ramos-Luis et al. 2014; Turrina et al. 2015; Martinez-Cadenas et al. 2016). The analyses were based on the same 14 Y-STR loci cited above for 532 males, including the 218 analysed in this study, from different regions of Algeria and for 8558 males from 26 countries. Data on origins, sample sizes and references from the populations used for the comparative analyses are summarised in Supplementary Table 1. The pairwise population comparisons were tested at a significance level of 0.05 with 10,000 permutations and p-values were revised with the sequential Bonferroni correction for multiple tests of significance (Rice 1989).
Genetic characterisation of 19 autosomal STR loci in a population sample from the Southeastern Anatolia Region of Turkey
Published in Annals of Human Biology, 2018
Nazli Bozman, Cemal Gurkan, Huseyin Sevay, Damla Kanliada Demirdov, Filiz Ozbas-Gerceker
Next, Nei’s DA distances between the new Southeastern Anatolia Region dataset and each of those from 26 nearby and distant populations were calculated. Table 4 provides the genetic distance matrix for the 27 population datasets that have seven common loci. Table 5 provides the genetic distance matrix for the 23 population datasets that have 13 common loci and, finally, Table 6 provides the genetic distance matrix for the nine population datasets that have 18 common loci. As expected, a largely linear correlation was observed between the estimated genetic distances and the actual geographic distances that exist in between the populations analysed. The shortest and longest genetic distances observed with respect to the Turkey V [SEA] dataset were those with (a) the Turkey IV [SEA] (0.006) and CEPH-HGDP [AFR] (0.070) datasets, respectively, at the 7-loci resolution, (b) the Turkey IV [SEA]/Turkey IV [MED]/Turkey IV [MAR exc. IST] (0.006) and CEPH-HGDP [AFR] (0.069) datasets, respectively, at the 13-loci resolution and (c) the Turkey II/Lebanon (0.008) and CEPH-HGDP [AFR] (0.066) datasets, respectively, at the 18-loci resolution.
Forensic parameters and admixture in seven geographical regions of the Guerrero state (South, Mexico) based on STRs of the Globalfiler® kit
Published in Annals of Human Biology, 2018
José Alonso Aguilar-Velázquez, Gorge Locia-Aguilar, Briselda López-Saucedo, Sandra Deheza-Bautista, Alma Faviola Favela-Mendoza, Héctor Rangel-Villalobos
Fortunately, we were able to confirm that the LOCPRIOR model in the Structure software offers better admixture estimates despite the small sample sizes and reduced number of markers (Pritchard et al. 2000; Falush et al. 2003). In addition, we consider that our Mexican Native American sample is probably a good ancestral reference because it includes 100 samples of six indigenous groups from four different geographic regions of the country: (1) North (Tarahumaras); (2) West-Centre (Nahuas and Purépechas); (3) South (Mazateco); and (4) Southeast (Mayas) (Aguilar-Velázquez et al. 2018). Pooling data from related ancestral population samples has been successfully used for anthropological analyses as a way to approximate a ‘mean’ ancestral gene pool (Wang et al. 2008). Conversely, Caucasian Americans and African Americans (US) probably constitute poor ancestral references, given that European ancestors of the Mexican Mestizos mainly came from the Iberian Peninsula (Grunberg 2004), whereas African ancestors are probably different from those that arrived in North America in large numbers (Aguirre-Beltrán 1972). On the other hand, although our population sample sizes are limited for individual regions, it has been demonstrated that sample sizes greater than 25 individuals do not have an appreciable effect on the genetic distance variance (Shriver et al. 1995). On the whole, although the reported ancestral estimations of the Guerrero state should be considered as preliminary, below we discuss their advantages given their close similarity with previous admixture estimates based on AIMs for the same geographic regions of Guerrero (Cahua-Pablo et al. 2017).