SEARCH · Search PubMed

Results for “Admixture graph”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

7 recordsLinked to original sources

PubMed2019

Identifying loci under positive selection in complex population histories.

Detailed modeling of a species' history is of prime importance for understanding how natural selection operates over time. Most methods designed to detect positive selection along sequenced genomes, however, use simplified representations of past histories as null models of genetic drift. Here, we present the first method that can detect signatures of strong local adaptation across the genome using arbitrarily complex admixture graphs, which are typically used to describe the history of past divergence and admixture events among any number of populations. The method-called graph-aware retrieval of selective sweeps (GRoSS)-has good power to detect loci in the genome with strong evidence for past selective sweeps and can also identify which branch of the graph was most affected by the sweep. As evidence of its utility, we apply the method to bovine, codfish, and human population genomic data containing panels of multiple populations related in complex ways. We find new candidate genes for important adaptive functions, including immunity and metabolism in understudied human populations, as well as muscle mass, milk production, and tameness in specific bovine breeds. We are also able to pinpoint the emergence of large regions of differentiation owing to inversions in the history of Atlantic codfish.

Animals↗

PubMed2025

Beyond Level-1: Identifiability of a Class of Galled Tree-Child Networks.

Inference of phylogenetic networks is of increasing interest in the genomic era. However, the extent to which phylogenetic networks are identifiable from various types of data remains poorly understood, despite its crucial role in justifying methods. This work obtains strong identifiability results for large sub-classes of galled tree-child semidirected networks. Some of the conditions our proofs require, such as the identifiability of a network's tree of blobs or the circular order of 4 taxa around a cycle in a level-1 network, are already known to hold for many data types. We show that all these conditions hold for quartet concordance factor data under various gene tree models, yielding the strongest results from 2 or more samples per taxon. Although the network classes we consider have topological restrictions, they include non-planar networks of any level and are substantially more general than level-1 networks - the only class previously known to enjoy identifiability from many data types. Our work establishes a route for proving future identifiability results for tree-child galled networks from data types other than quartet concordance factors, by checking that explicit conditions are met.

Mathematical Concepts↗

PubMed2025

A genealogy-based approach for revealing ancestry-specific structures in admixed populations.

Elucidating ancestry-specific structures in admixed populations is crucial for comprehending population history and mitigating confounding effects in genome-wide association studies. Existing methods to reveal the ancestry-specific structures generally rely on frequency-based estimates of genetic relationship matrix (GRM) among admixed individuals after masking segments from ancestry components not being targeted for investigation. However, these approaches disregard linkage information between markers, potentially limiting their resolution in revealing structure within an ancestry component. We introduce ancestry-specific expected GRM (as-eGRM), a novel framework for estimating the relatedness within ancestry components between admixed individuals. The key design of as-eGRM consists of defining ancestry-specific pairwise relatedness between individuals based on genealogical trees encoded in the ancestral recombination graph (ARG) and local ancestry calls and then computing the expectation of the ancestry-specific relatedness across the genome. Comprehensive evaluations using both simulated stepping-stone models of population structure and empirical datasets based on three-way admixed Latino cohorts showed that analysis based on as-eGRM robustly outperforms existing methods in revealing the structure in admixed populations with diverse demographic histories, which in turn improves the robustness against confounding due to population structure in association testing.

Humans↗

PubMed1978

Serial determinations of oxygen profiles in infants with respiratory distress.

Serial oxygen profiles were determined for 20 newborn infants by measuring arterial tensions at low (20--40%), intermediate (60--80%), and high (95--100%) levels of inspired oxygen. These points were plotted on a graph which estimated the percentage of venous admixture at any particular level of inspired oxygen. The infants' oxygen profiles were then determined. As much as 25% of venous admixture could be attributed to the presence of diffusion and distribution abnormalities in infants with hyaline membrane disease. A substantial number of infants showed increased shunting at high levels of oxygen, even in the presence of continuous distending airway pressure. It is hypothesised that a rising shunt is due to complete absorption of gas in poorly ventilated alveoli at high concentrations of inspired oxygen, resulting in the presence of atelectasis and redistribution of blood to poorly ventilated areas.

Humans↗

PubMed1985

Microcomputer-assisted monitoring system for measuring and processing cardiorespiratory variables: preliminary results of clinical trials.

A microcomputer-assisted monitoring system was developed for the continuous measuring and processing of cardiorespiratory variables, including: systemic and pulmonary arterial pressures, CVP, minute ventilation, inspired and expired O2 and CO2 concentrations, temperature, and heart rate. The primary data were converted to digital form, processed, displayed on a CRT monitor, and also stored for later evaluation. This system automatically calculated and displayed on-line and in real-time both primary measurements and derived cardiorespiratory variables, including: oxygen consumption, CO2 production, left and right ventricular stroke work, pulmonary venous admixture, and systemic and pulmonary vascular resistances. Printouts of the variables and trend graphs could be obtained for any desired time period. During its development, we tested this monitoring system in 30 critically ill patients, finding that the real-time calculation of cardiorespiratory variables was a great advantage during monitoring and treatment.

Adult↗

PubMed2025

Integrative Genotyping and Analysis of Canine Structural Variation Using Long-read and Short-read Data.

Structural variation makes an important contribution to canine evolution and phenotypic differences. Although recent advances in long-read sequencing have enabled the generation of multiple canine genome assemblies, most prior analyses of structural variation have relied on short-read sequencing. To offer a more complete assessment of structural variation in canines, we performed an integrative analysis of structural variants present in 12 canine samples with available long-read and short-read sequencing data along with genome assemblies. Use of long-reads permits the discovery of heterozygous variation that is absent in existing haploid assembly representations while offering a marked increase in the ability to identify insertion variants relative to short-read approaches. Examination of the size spectrum of structural variants shows that dimorphic LINE-1 and SINE variants account for over 45% of all deletions and identified 1,410 LINE-1s with intact open reading frames that show presence-absence dimorphism. Using a graph-based approach, we genotype newly discovered structural variants in an existing collection of 1,879 resequenced dogs and wolves, generating a variant catalog containing a 56.5% increase in the number of deletions and 705% increase in the number of insertions previously found in the analyzed samples. Examination of allele frequencies across admixture components present across breed clades identified 283 structural variants evolving with a signature of selection.

Animals↗

PubMed1978

Descriptive and analytical epidemiology of nasopharyngeal cancer.

Information concerning the descriptive and analytical epidemiology of NPC that has been reported mainly since the first international symposium on the subject in Singapore in 1964 are reviewed. NPC is rare in most countries in the world, with an age-adjusted incidence rate of less than 1 per 100,000, and the incidence rate is twice as high in males as in females. Chinese of southern origin have a uniquely high risk, the incidence rates per 100,000 being 10--20 in males and 5--10 in females. The greater the admixture of southern Chinese blood in a given ethnic group, the more likely it is that the NPC incidence rate in that group will be raised. The incidence in both sexes begins to rise after the ages of 20--24 and reaches a plateau at between 45 and 54. When the logarithm of mortality and morbidity is plotted against the logarithm of the age, the power of the age that provides the best fit to a straight line on a log-log graph is approximately two to four. These figures are lower than for other cancers. Seroepidemiological case-control studies indicate that both different birthplace and abnormal response to EBV antigen significantly enhance the risk for NPC; when these two factors are combined, the relative risk appears to rise further. The effect of other environmental chemicals, such as from cigarette smoking, shown to be significant in several retrospective studies, could explain in part epidemiological phenomena such as sex difference in incidence. The definitive reason for the uniquely high risk in southern Chinese should be further investigated by taking into account the interactions of host factors (birthplace, HLA, etc.) and environmental factors (EBV, chemical carcinogens including nitrosamines, excessive intake of salted fish, nutritional deficiencies, etc.).

Adolescent↗