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Results for “allele frequency”

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At least 19 recordsLinked to original sources
PubMedDate not supplied

Allele frequencies in a cat population in Budapest.

Allelic frequencies were determined for the domestic cat population of Budapest, Hungary. Most of the frequencies are in the range of those of western European populations, but there are two unusual features. The first is the apparent absence of blotched tabby and a relatively high frequency of Abyssinian tabby. The second is in the distribution of frequencies of white spotting phenotypes. There is an approximately normal distribution around the most common pattern, which is 50 percent white fur, contrasted to western populations in which frequency is maximal between approximately 10-30 percent white fur and declines with increasing white fur.

Alleles↗
PubMed2026

Sperm subpopulations differing in mitochondrial abundance show divergent nuclear allele frequencies.

Mammalian ejaculates contain heterogeneous sperm subpopulations that differ in subcellular architecture and developmental history, despite appearing morphologically uniform. The extent to which this cellular heterogeneity reflects underlying nuclear genomic structure within a sire remains largely unexplored. Mitochondrial architecture in sperm is established during spermatogenesis, with final assembly and organization occurring during spermiogenesis under nuclear genomic control, positioning variation in mitochondrial abundance and organization as a potential phenomic indicator of within-sire allelic segregation. Here, we tested whether sperm subpopulations defined by differing mitochondrial abundance exhibit systematic differences in nuclear allele representation. Boar sperm were resolved into low and high mitochondrial subpopulations using fluorescence-activated cell sorting based on MitoTracker™ Green fluorescence while excluding debris, doublets, and non-viable cells. Epifluorescence microscopy confirmed that high MitoTracker™ Green fluorescence sperm possessed longer mitochondrial sheaths, validating a structural distinction between subpopulations. Whole-genome sequencing of paired mitochondrial subpopulations from three boars was performed, and allelic ratio distortion was evaluated relative to heterozygous baseline populations. Analyses across heterozygous loci genome-wide identified candidate allele frequency shifts between mitochondrial-defined subpopulations, suggesting non-random segregation of alleles within ejaculates. Using a minimum sequencing depth of 30 reads in both sorted fractions, 182 candidate SNPs were identified with evidence of allele-frequency differences between mitochondrial fluorescence-defined subpopulations. These findings suggest that sperm mitochondrial abundance can potentially serve as an indirect, high-throughput marker of nuclear genomic heterogeneity within sires. This proof-of-concept framework establishes a foundation for future studies integrating sperm phenotyping, genome-wide allele-frequency analysis and functional validation to better characterize gamete-level heterogeneity.

Male↗
PubMed1978

Stepwise mutation model and distribution of allelic frequencies in a finite population.

A mathematical theory is developed that enables us to derive a formula for the equilibrium distribution of allelic frequencies in a finite population when selectively neutral alleles are produced in stepwise fashion (stepwise mutation model). It is shown that the stepwise mutation model has a remarkable property that distinguishes it from the conventional infinite allele model (Kimura-Crow model): as the population size increases indefinitely while the product of the effective population size and the mutation rate is kept at a fixed value, the mean number of different alleles contained in the population rapidly reaches a plateau which is not much larger than the effective number of alleles (reciprocal of homozygosity).

Alleles↗
PubMed1977

Variation in allele frequencies among caste groups of the Dhangars of Maharashtra, India: an analysis with Wright's Fst statistic.

Variations in allelle frequencies at 11 serological and biochemical loci among 21 endogamous Dhangar castes of Maharashtra, India, have been studied using Wright's FST statistic. Gene differentiation among these castes is only about 4 per cent at these polymorphic loci. The distributional form of FST is explicable by random genetic drift at this early stage of differentiation of these caste groups. The empirical relationship between the average allele frequencies and the ration of within to total gene diversity of the caste groups is also studied.

Alleles↗
PubMed2026

Faster inference of complex demographic models from large allele frequency spectra.

MOTIVATION: Demographic inference from the joint site frequency spectrum is limited by computation when many populations or many samples are analyzed. RESULTS: We present momi3, a JAX-based method for inferring complex demographic models from large allele frequency spectra. It supports continuous migration, GPU execution, automatic differentiation, standardized demographic model input, and genealogical pruning. These changes yield speedups up to 1000× over existing methods and enable analysis of archaic admixture models using hundreds of human genomes. AVAILABILITY AND IMPLEMENTATION: momi3 is implemented in Python/JAX as part of demestats. Source code is available at https://github.com/jthlab/demestats; documentation is available at https://demestats.readthedocs.org.

Humans↗
PubMed2025

Carrying APOL1 G1 allele is associated with cardiovascular complications during COVID-19 in an admixed population.

BACKGROUND: The APOL1 G1 and G2 alleles were selected in the Sub-Saharan African population by conferring resistance to trypanosome infection. However, these alleles are associated with kidney diseases, and their role in cardiovascular complications remains uncertain. A second hit mediated by an inflammatory state is necessary for APOL1-mediated phenotypes. Thus, this cross-sectional study investigates the association of APOL1 alleles with COVID-19 outcomes such as cardiovascular complications and kidney injury in an admixed population. Whole-genome sequencing was performed for 485 patients with different outcomes from a Biobank in Southern Brazil. RESULTS: COVID-19 individuals presented median age of 51 years, 281 were hospitalized, and 10.9% had CKD previous to the infection. Global ancestry inference revealed 12.8% of African ancestry. The G1 allele frequency was 2.7% and G2 allele was 1.2%. Local ancestry inference evidenced African ancestry in the locus of APOL1 alleles. The G1 allele frequency was higher among patients with severe outcomes. The presence of this allele was associated with kidney injury (OR = 2.78; 95% CI = 1.04-7.42; p = 0.041) using a minimally adjusted model and cardiovascular complications with a minimally (OR = 4.61; 95% CI = 1.61-13.19; p = 0.004) and fully adjusted model (OR = 4.59; 95% CI = 1.41-14.96; p = 0.011). Four individuals carried two alleles (three G1/G1 and one G1/G2) and three of them progressed to severe COVID-19 developing kidney injury. CONCLUSION: APOL1 risk alleles are present in the Brazilian population due to genetic admixture and the G1 allele was associated with COVID-19 outcomes.

Humans↗
PubMed1977

[Genetic structure of 2 isolated populations of native inhabitants of Sibiria (Northern Altaics) according to the results of a study of blood groups and isoenzymes].

The article comprises the results of the investigation of the frequencies of alleles of 9 gene loci controlling the blood groups, isoenzymes in populations and subpopulations of Cumandinians and Chelkanians. The presence of alleles A2 r(cde) and K at low concentrations was discovered in both groups. The method of genetic distances was used for the investigation of the inter- and intragroup divergence. With respect to certain loci a considerable variation of allelic frequencies from village to village was established.

Adenylate Kinase↗
PubMed1978

The relation between transferrin locus and the breeding quality traits of our country cattle race: lowland black-white and lowland red-white.

The relation between transferrin locus and the breeding quality, especially such traits as--milk quantity, fattening and fertility rate expressed through nine traits, were analyzed. There are presented some results of phenotypes distribution and frequency of alleles of transferrin. Changing of allele frequencies in time in certain direction was observed. The calculated coefficients of regression of frequency on a year in race lrw were: bA = -0.0080; bD = 0.0137; BE = -0.0057 and in race lbw: bA = 0.0134; bD = -0.0034; bE = -0.0089.

Animal Husbandry↗
PubMedDate not supplied

Lactate dehydrogenase: a polymorphism of Anoplarchus purpurescens: geographic variation in central California.

Previous studies on the muscle lactate dehydrogenase polymorphism of the stichaeid fish Anoplarchus purpurescens in Puget Sound have demonstrated the existence of a clinal pattern of allele frequency. The LDH-A' allele was observed to increase toward the south, with several environmental factors showing correlation with this change in allele frequency. Populations from California were sampled in the present study to determine whether or not gene frequencies along an independent transect near the southern end of the species distribution are consistent with the interpretation that the geographic patterns reflect the influence of environmental factors. In California, the LDH-A' allele decreases in frequency to the south. This observation necessitates the reevaluation of possible environmental influences on the LDH polymorphism. Only one of several proposed hypotheses is completely consistent with the geographic patterns observed along both the Washington and California transects. However, the genetic differentiation along the California coast cannot be unequivically ascribed to the influence of environmental factors; current morphological data indicate the possibility of historical influences on the population genetic structure of California A. purpurescens.

Animals↗
PubMed2001

The power to detect linkage disequilibrium with quantitative traits in selected samples.

Results from power studies for linkage detection have led to many ongoing and planned collections of phenotypically extreme nuclear families. Given the great expense of collecting these families and the imminent availability of a dense diallelic marker map, the families are likely to be used in allelic-association as well as linkage studies. However, optimal selection strategies for linkage may not be equally powerful for association. We examine the power to detect linkage disequilibrium for quantitative traits after phenotypic selection. The results encompass six selection strategies that are in widespread use, including single selection (two designs), affected sib pairs, concordant and discordant pairs, and the extreme-concordant and -discordant design. Selection of sibships on the basis of one extreme proband with high or low trait scores provides as much power as discordant sib pairs but requires the screening and phenotyping of substantially fewer initial families from which to select. Analysis of the role of allele frequencies within each selection design indicates that common trait alleles generally offer the most power, but similarities between the marker- and trait-allele frequencies are much more important than the trait-locus frequency alone. Some of the most widespread selection designs, such as single selection, yield power gains only when both the marker and quantitative trait loci (QTL) are relatively rare in the population. In contrast, discordant pairs and the extreme-proband design provide power for the broadest range of QTL-marker-allele frequency differences. Overall, proband selection from either tail provides the best balance of power, robustness, and simplicity of ascertainment for family-based association analysis.

Alleles↗
PubMed2026

Equity in genome sequencing for rare disease diagnosis: a cross-sectional analysis of data from the UK 100,000 Genomes Project.

BACKGROUND: Genome sequencing has improved rare disease diagnosis and is now part of routine clinical care in the National Health Service in England. Automated prioritisation pipelines narrow millions of variants per patient to a small subset for clinical review, a process that relies on allele frequency resources that do not fully represent human genetic diversity. We assessed ancestry-related differences in variant prioritisation and diagnostic outcomes in patients from the UK 100,000 Genomes Project. METHODS: We analysed 29,405 rare disease probands with genome sequencing and linked clinical outcomes data. We used multivariable regression to assess ancestry-related differences in the number of variants prioritised for clinical review, the proportion of prioritised variants that were recorded as diagnostic, and diagnostic yield. We also evaluated the use of ancestry-stratified allele frequency filters derived from an independent, diverse UK cohort (n = 33,724). FINDINGS: Compared with the European ancestry group, the East African group had nearly three times more variants prioritised for clinical review (IRR 2.77, 95% CI 2.33-3.29). Other non-European groups also had significantly higher counts. Diagnostic yield was similar across ancestry groups after adjustment (LRT p = 0.1650). Prioritised variants were less likely to be recorded as diagnostic in East African (OR 0.32, 95% CI 0.22-0.46), West African (0.47, 0.39-0.57), South Asian (0.65, 0.58-0.73), and Middle Eastern (0.68, 0.54-0.86) groups. Applying ancestry-stratified allele-frequency filters removed 3.1% of prioritised variants overall-24.3% in the East African group-without loss of diagnostic sensitivity, including 29.5% of recorded VUS in this group. INTERPRETATION: Differences in the likelihood of prioritised variants being recorded as diagnostic partly reflect limitations of current allele frequency resources, which use broad population groupings that mask within-group diversity. Increased representation of diverse ancestries in reference databases and better estimation of ancestry-appropriate allele frequencies will help reduce inefficiencies and improve equity in variant prioritisation for rare disease diagnosis. FUNDING: The UK Department of Health and Social Care and the EU's Horizon 2020 Research and Innovation Programme.

Humans↗
PubMed2026

needLR: long-read structural variant annotation with population-scale frequency estimation.

SUMMARY: We present needLR, a structural variant (SV) annotation tool that can be used for filtering and prioritization of candidate pathogenic SVs from long-read sequencing data using population allele frequencies, annotations for genomic context, and gene-phenotype associations. When using population data from 500 presumably healthy individuals to evaluate nine test cases with known pathogenic SVs, needLR assigned allele frequencies to over 97.5% of all detected SVs and reduced the average number of novel genic SVs to 121 per case while retaining all known pathogenic variants. AVAILABILITY AND IMPLEMENTATION: needLR is implemented in bash with dependencies including Truvari v4.2.2, BEDTools v2.31.1, and BCFtools v1.19. Source code, documentation, and pre-computed population allele frequency data are freely available at https://github.com/jgust1/needLR under an MIT license and archived on Zenodo at https://zenodo.org/records/19463479.

Software↗
PubMed2026

An alignment-free strategy for circulating tumor DNA detection and tumor fraction estimation from whole-genome sequencing data.

Circulating tumor DNA (ctDNA) is emerging as a promising biomarker for postoperative monitoring of cancer patients. Precise estimation of circulating tumor fraction is crucial for evaluating treatment effects and timely detection of disease recurrence. All current ctDNA detection methods that utilize whole-genome sequencing (WGS) data rely on the reference genome alignment of sequencing reads and often apply separate tools for detecting different variant types. However, various bioinformatic analysis confounders and the application of external variant calling tools could be avoided by analyzing k-mers from unaligned sequencing reads. While k-mer-based methods have successfully been applied for somatic variant validation and detection, the potential of k-mer-based ctDNA detection is unexplored. We have developed a tumor-informed alignment-free ctDNA detection tool called ctDNAmer that detects tumor-specific somatic variation directly from unaligned sequencing data by identifying k-mers unique to the tumor DNA. ctDNAmer detects variant information across the genome by comparing the primary tumor and germline WGS data and accounts for sample-specific germline variability and technical noise in the same framework. We tested the utility of ctDNAmer for tumor fraction estimation on postoperative plasma cfDNA WGS data (mean sequencing depth ~ 28x) from 90 stage III colorectal cancer patients with three years of follow-up. The tumor fraction (TF) estimates agreed with the available clinical information and ctDNA was detected in 77% (17/22) of recurring patients with a median lead time of 8 months compared to radiological imaging. We further validated ctDNAmer's tumor fraction estimates based on a comparison with the mean cfDNA allele frequencies of somatic clonal SNVs identified from aligned primary tumor sequencing data. The TF estimates showed a strong Pearson correlation of 0.897 with the mean allele frequencies and improved ctDNA detection results across samples with an AUC of 0.79 compared to 0.75 if the mean allele frequency of clonal mutations is used.

Circulating Tumor DNA↗
PubMed1976

Survivorship and gene frequencies of Drosophila melanogaster populations in abnormal oxygen atmospheres.

Vestigial wing and wild type populations of Drosophila melanogaster were exposed to 5%, 20%, and 60% oxygen at normal atmospheric pressure. Adult mortality rates, larval production, and allele frequency changes in four gene-enzymes were examined in the populations. All flies in 60% oxygen survived as well as controls until day 20 and then died out within the next 10 to 12 d. In 5% oxygen, vestigial wing flies had mortality rates greater than the 20% controls initially, but the rate eventually approached that of the controls. Wild type flies in 5% oxygen survived as well as controls. Larval production and rate of eclosure in 60% oxygen were similar to controls, but reduced in 5% oxygen. Allele frequency shifts to 6-phosphogluconate dehydrogenase and phosphoglucomutase were observed in 5% oxygen, and a shift of alpha-glycerophosphate dehydrogenase allele frequencies occurred in 60% oxygen. There was no evidence of in vivo inactivation of ADH, 6-PGD, alpha-GPD or PGM in 60% oxygen.

Animals↗
PubMed1979

[Genetic distance of the malarial mosquitoes, Anopheles beklemishevi and Anopheles messeae (Diptera, Culiccidae), and their intraspecific polymorphism].

Allele frequencies at enzyme loci have been studied in Finnish populations of two species of the Anopheles maculipennis complex: A. beklemishevi and A. messeae. A. beklemishevi is spread over central and northern Finland, whereas A. messeae is found in southwestern and central Finland. The allele frequencies of these two species exhibit both similarities and differences. The results indicate that the two species do not interbreed in the nature. The allele frequencies at two loci--Hydroxybutyrate dehydrogenase (Hbdh) and Superoxide dismutase-2 (Su-2)--are almost totally different and adult individuals of the two species can be reliably diagnosed by these allelic differences. The genetic distance, D, between A. beklemishevi and A. messeae is 0.35. This value is compared with corresponding distances between other dipterans studied.

Alleles↗