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PubMed1978

Dissection of a continuous distribution: red cell galactokinase activity in blacks.

A significant difference between blacks and whites in the distribution of red cell galactokinase (GALK) has been found by Tedesco et al. [2]. From the shapes of the distributions, it was inferred that whites are essentially all homozygous for one allele (GALKA), but blacks are polymorphic. A second allele (GALKP), for lower GALK activity, is presented at high frequency in blacks but rare or absent in whites. This paper presents a method which, assuming the genetic model presented, estimates the genotype composition of the black sample. We make some reasonable biochemical assumptions and fit a mixture of three normal distributions to the black data to obtain an estimate of p, the frequency of GALKA in blacks. The fit of the model to the data is excellent and the best estimate of p is .217 +/- .025. Since admixture of white genes in blacks from the United States is known to be about 20%, the value of p implies that virtually all GALKA alleles were introduced by admixture, and that the ancestral black population was monomorphic for GALKP. If whites are indeed monomorphic for GALKA, they differ from unmixed blacks by a full gene substitution at the locus for GALK.

Alleles↗
PubMed1977

Segregation analysis of thalassemia in Ferrara.

Segregation analysis of 996 families in which the gene for beta-thalassemia was segregating showed no distortion of expected Mendelian ratios. No appreciable frequency of sporadic cases was detected. It was suggested that segregation distortion is not a mechanism which contributes to the maintenance of polymorphism in the beta-thalassemia system in the population of the Ferrara area.

Computers↗
PubMed1979

A comparison of two methods for making statistical inferences on Nei's measure of genetic distance.

The delta and jackknife methods can be used to estimate Nei's measure of genetic distance and calculate confidence intervals for this estimate. Computer stimulations were used to study the bias and variance of each estimator and the accuracy of the corresponding approximate 95% confidence intervals. The simulations were conducted using 3 sets of data and several sample sizes. The results showed: (1) the jackknife reduced bias; (2) in 8 out of 9 cases the variance and mean square error of the jackknife estimator were less; (3) a second order jackknife reduced the bias the most but suffered a corresponding increase in variance; (4) both the first order jackknife and delta methods yielded intervals whose confidence levels were approximately equal but less than 95%.

Alleles↗
PubMed2026

From family trials to genomic mate allocation: statistical and genomic strategies to accelerate sugarcane genetic improvement.

Sugarcane (Saccharum spp.) underpins global sugar and bioenergy supply and is increasingly valued as a renewable biomass feedstock. Sustained improvement in commercial traits and resilience is constrained by long breeding cycles, clonal propagation, multi-stage testing, and a highly polyploid, heterozygous, and frequently aneuploid genome with substantial non-additive genetic variation. Genomic selection has demonstrated value for predicting elite-clone performance, yet its operational use remains limited at earlier decision points, including family selection, parent evaluation, and cross design. This review examines the biological, statistical, and genomic factors that shape these decisions, with emphasis on the Australian breeding context based on progeny assessment trials (PATs), clonal assessment trials (CATs), and final assessment trials (FATs). We evaluate challenges arising from family plot means, the use of different full-sib samples as nominal family replicates, spatial heterogeneity, competition, genotype-by-environment interaction, and the partitioning of additive and non-additive effects. We also assess the integration of pedigree and genomic relationship, genotype representation, allele-dosage estimation, aneuploidy, genomic prediction models, and training-population design. We then consider genomic prediction of cross performance and constrained mate allocation as approaches for improving expected family performance, accounting for cross-specific non-additive effects and managing relatedness. We propose a decision-centred framework that links family and clonal data across breeding stages, tracks the propagation of information and uncertainty, and supports parent recycling and cross allocation. We conclude with a practical research agenda for stage-integrated mixed-model and single-step analyses that connect early family evaluation with genomic prediction and cross-level decision support in sugarcane breeding.

Saccharum↗
PubMed2026

Evaluation of the efficacy of optical genome mapping in prenatal diagnosis: a retrospective cohort study.

BACKGROUND: Optical genome mapping (OGM) is an emerging cytogenetic method for concurrently detecting structural variants (SVs) and copy number variants (CNVs). However, its clinical application in prenatal diagnosis remains underexplored. METHODS: This study retrospectively evaluated the clinical validity of OGM in prenatal diagnosis by comparing with two routine genetic testing methods: karyotyping and chromosomal microarray analysis (CMA). Both positive and negative cases detected by routine genetic methods were enrolled to evaluate the technical concordance of OGM and its capability to improve diagnostic rate in negative cases. The exclusion criteria were balanced centromeric translocations, mosaic cases with cellular fractions&#x2009;<&#x2009;20%, and loss of heterozygosity (LOH)&#x2009;<&#x2009;25&#xa0;Mb. All samples subjected to OGM testing were anonymized and analyzed blindly. The results from OGM were compared with those from routine genetic testing, and statistical analyses were performed to assess technical concordance and diagnostic rate. RESULTS: Of 217 samples (166 positive samples and 51 negative samples for routine genetic testing), all were successfully tested with OGM, including 2 umbilical cord blood samples, 4 chorionic villi samples, and 211 cultured amniotic fluid samples. Of the 207 reportable chromosomal aberrations from 166 positive samples, the blinded concordance between OGM and CMA, karyotyping, and combination of karyotyping plus CMA was 97.81%, 96.36%, and 97.10%, respectively. OGM missed six aberrations initially, including one LOH, two marker chromosomes, and three microdeletions. However, after reanalysis, its concordance improved to 100% with CMA and 99.03% with karyotyping plus CMA. OGM also diagnosed one additional case of a 3-kb deletion in 51 negative samples, improving the diagnostic rate by 1.96%. Moreover, OGM reclassified the pathogenicity of two microdeletions from pathogenic to uncertain significance in 2 positive cases. Furthermore, OGM clarified the diagnosis suspected by routine genetic testing and improved diagnostic accuracy in some cases. CONCLUSION: As far as we know, this is the largest retrospective study on OGM in prenatal diagnosis, and it includes a broad range of sample types. The results showed that OGM exhibits high concordance among the tested methods and increases the diagnostic rate. Thus, OGM has the potential to become a first-line technique for prenatal diagnosis in the future.

Humans↗
PubMed1978

Frequency distribution and discrimination probability of twelve protein genetic variants in human blood as functions of race, sex, and age.

Fresh blood samples were obtained from 6004 whites, 1025 blacks, 1596 Chicano/Amerindians, and 3053 Asians of California and Hawaii. The samples were typed for ABO and Rh groups and were analyzed electrophoretically for ten genetically determined protein variant systems. The effects of race, age, and sex on phenotypic frequencies within each of the twelve genetic systems were investigated. Large frequency differences were found between races but not between different age and sex subgroups within races. It was also demonstrated that the twelve genetic systems behaved statistically independently. Discrimination probabilities were computed for each of the four ethnic groups. These serve as a measure of the effectiveness of the twelve genetic systems examined in individualizing blood samples. The method is discussed for computing the probability that a randomly chosen individual of a given ethnic group possesses the same blood phenotypes as found in a predetermined sample of blood. The results presented here should prove useful in the investigation of civil and criminal cases involving blood samples.

ABO Blood-Group System↗
PubMed2025

RAD-Seq-derived SNPs reveal no local population structure in the commercially important deep-sea queen snapper (Etelis oculatus) in Puerto Rico.

UNLABELLED: The queen snapper (Etelis oculatus Valenciennes in Cuvier & Valenciennes, 1828) is a deep-sea snapper whose commercial importance continues to increase in the US Caribbean. However, little is known about the biology and ecology of this species. In this study, the presence of a fine-scale population structure and genetic diversity of queen snapper from Puerto Rico was assessed through 16,188 SNPs derived from the Restriction site Associated DNA Sequencing (RAD-Seq) technique. Summary statistics estimated low genetic diversity (HO&#x2009;=&#x2009;0.333-0.264) and did not reveal population differentiation within our samples (F ST&#x2009;=&#x2009;-&#xa0;0.001-0.025). Principal component analysis and a model-based clustering method did not detect a fine-scale subpopulation structure among sampling sites, however, there was genetic variability within regions and sites. Our results have revealed comparable genetic and dispersal patterns to those observed in other shallow-water snapper species in Puerto Rico waters. It is crucial to further enhance our understanding of the ecological and biological aspect of the queen snapper to effectively manage and conserve this species as fishing pressure has been extended to deep water species in the US Caribbean. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-025-00289-7.

Caribbean Fisheries↗
PubMed1978

Is there a pattern of gene differentiation in the Indian populations.

Indian populations divided into a number of endogamous groups consisting of different castes, languages, religions, and tribes provide unique opportunities for examining the extent and nature of genetic differentiation at a microevolutionary stage. The genetic relationships between some of these Indian population groups have been examined using electrophoretic data from several biochemical loci in a gene diversity analysis. Does this type of analysis provide any insight into what causes such gene differentiation? What patterns of genetic variation emerge from these empirical findings? Answers are sought by relating the observed heterozygosity, genetic distance, and allied statistics to a mutation-drift hypothesis. The statistics used are: (1) interlocus mean and variance of heterozygosity, (2) mean and variance of genetic distance, and (3) correlation of heterozygosity and gene identity. The observed relationships between these sets of statistics agree well with the ones predicted by the hypothesis that different alleles at protein loci are selectively equivalent and gene frequency change occurs predominantly due to genetic drift.

Gene Frequency↗
PubMed1978

Bilateral asymmetry of human skeletal non-metric traits.

The use of non-metric skeletal traits to compute population distance statistics assumes strong genetic control of trait expression. An investigation of bilateral asymmetry frequencies of human cranial and postcranial non-metric traits shows that asymmetry is common. This suggests that environmental stress, as well as the genotype, is important in controlling trait frequencies.

Adult↗
PubMed2026

Developmental and cellular vulnerabilities underlie genetic architecture of schizophrenia.

Schizophrenia (SZ) is a highly heritable neuropsychiatric condition with complex polygenic architecture. Elucidating the cellular and developmental substrates vulnerable to the genetic risk is essential for understanding the underlying neurobiological mechanisms. Here, we integrated genome-wide association study (GWAS) and whole-exome sequencing (WES) data with a developmental multi-omics atlas of the human cortex (including 5 cortical regions), comprising about 3 million single-nucleus RNA sequencing (snRNA-Seq) and single-nucleus assay for transposase-accessible chromatin using sequencing (snATAC-Seq) profiles across 8 neurodevelopmental processes, to map cell-type-specific enrichment of SZ genetic risk. Our enrichment analyses revealed that both common and rare genetic liabilities converged on broad excitatory and inhibitory neuronal classes. Across different statistical frameworks, we identified genetic enrichment within intratelencephalic (IT) projection neurons and layer 6b excitatory neurons (Ex-L6b) networks across multiple cortical regions. Stage-resolved developmental mapping in the frontal cortex showed that genetic liabilities, particularly the rare variants, are predominantly concentrated within early developmental processes, namely neurogenesis and neuronal migration. Differential expression analysis in postmortem frontal cortex snRNA-Seq datasets cross-validated the cellular substrates of the genetic liabilities. Collectively, our findings establish a high-resolution cellular and temporal framework of SZ susceptibility, implicating mature associative IT microcircuits, deep-layer thalamocortical-regulating networks, and early developmental specification windows as primary points of genetic convergence in SZ.

Journal Article↗
PubMed2005

Gene finding in the chicken genome.

BACKGROUND: Despite the continuous production of genome sequence for a number of organisms, reliable, comprehensive, and cost effective gene prediction remains problematic. This is particularly true for genomes for which there is not a large collection of known gene sequences, such as the recently published chicken genome. We used the chicken sequence to test comparative and homology-based gene-finding methods followed by experimental validation as an effective genome annotation method. RESULTS: We performed experimental evaluation by RT-PCR of three different computational gene finders, Ensembl, SGP2 and TWINSCAN, applied to the chicken genome. A Venn diagram was computed and each component of it was evaluated. The results showed that de novo comparative methods can identify up to about 700 chicken genes with no previous evidence of expression, and can correctly extend about 40% of homology-based predictions at the 5' end. CONCLUSIONS: De novo comparative gene prediction followed by experimental verification is effective at enhancing the annotation of the newly sequenced genomes provided by standard homology-based methods.

Animals↗
PubMed2026

Multi-Ancestry Genome-Wide Association with Fine-Mapping Identifies Novel Loci for Pigment Dispersion Syndrome and Pigmentary Glaucoma.

PURPOSE: Pigment dispersion syndrome and pigmentary glaucoma are important causes of ocular hypertension and glaucomatous optic neuropathy, yet their genetic determinants remain incompletely defined, particularly across diverse ancestries. This study aimed to use a large multi-ancestry cohort from the All of Us Research Program to investigate the genetic basis of pigment dispersion syndrome and pigmentary glaucoma. DESIGN: Case-control study. PARTICIPANTS: In total, 572 cases and 37&#x2009;808 controls with array genotyping and 537 cases and 35&#x2009;493 controls with whole-genome sequencing. METHODS: Using electronic health record phenotyping in the All of Us Research Program, we performed multi-ancestry genome-wide association analyses using both array-based data and whole-genome sequencing-based data, comparing patients with pigment dispersion syndrome or pigmentary glaucoma to those without either condition. We also performed Firth penalized regression and Fisher analyses, and we performed principal component analyses to assess effect sizes across genetic ancestries. We applied statistical fine-mapping, examined for cross-trait overlap, and assessed expression quantitative trait locus associations for lead variants. MAIN OUTCOME MEASURES: P values and odds ratios of lead loci from genome-wide association analyses; size of credible sets determined from fine-mapping; allele frequency of lead variants in cases, controls, and the general population; expression quantitative trait loci effect size and P values linking lead variants to gene expression. RESULTS: We identified 4 loci reaching genome-wide significance across analyses, including signals near EPHA7 (which mediates cell-cell signaling), within TYR (involved in melanin synthesis and replicated from prior studies), within LINC01138, and near OTX2. Statistical fine-mapping refined 3 of these loci to single-variant 95% credible sets and narrowed the TYR locus to small credible sets, prioritizing possible causal variants. Effect estimates were broadly consistent across genetic ancestry clusters. Lead variants showed regulatory evidence in expression quantitative trait locus, including reduced EPHA7 expression. CONCLUSIONS: These findings implicate both melanogenesis and cell-cell adhesion and signaling pathways in pigment dispersion syndrome and pigmentary glaucoma. FINANCIAL DISCLOSURE(S): Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.

Genome-wide association study↗
PubMed1979

The estimation of mutation rates when premeiotic events are involved.

When mutation or recombination events occur premeiotically, the distribution of exceptional individuals among the offspring will be "clustered" as opposed to binomial. Even though the exact nature of the clustering is usually unknown, unbiased methods for measuring mutation rate and determining the precision of these measurements are given to replace a biased method now frequently used. When clustering is pronounced, the unweighted average mutation rate is found to be a more efficient estimator than the usual average weighted by family size. Methods of statistical inference and optimal experimental design in the absence of specific knowledge of the mechanism of clustering are also discussed.

Animals↗
PubMed2025

Genome-wide association studies in chronic venous disease: A systematic review.

BACKGROUND: Chronic venous disease (CVD) arises from venous hypertension secondary to impaired venous return, causing significant morbidity and diminished quality of life. Genetic factors are likely important in the pathogenesis and susceptibility of a patient to develop CVD. This systematic review summarizes genome-wide association studies (GWASs) that investigate the link between genetic variants and CVD. METHODS: A systematic review was conducted in accordance with the PRISMA guidelines, with the search dates ranging from January 1, 1994, to July 17, 2025. Abstract and full-text screening were completed by two independent reviewers, with any conflicts referred to a third senior reviewer. GWASs in adults investigating links between genetic variants and CVD were included. Exclusion criteria included patients with venous thromboembolism, arterial or diabetic disease, or animal models. RESULTS: Thirteen studies were included after screening 517 studies from a search of PubMed, EMBASE, and Ovid. Database sources included UK Biobank, FinnGen, PopGen, and country- or hospital-specific databases with a majority Caucasian and European patient cohort. A total of 602,760 patients were identified with varicose veins and 3,664,604 control cases that were studied with GWASs and other statistical methods including a two-sample Mendelian randomization approach, functional mapping, and genetic correlations. A variety of statistically significant genetic polymorphisms were identified that can be attributed to the heritability of varicose veins affecting inflammation and immunity (eg, PPP3R1, EBF1, and GATA2), hypertension (eg, CASZ1), and vascular architecture (eg, CASZ1, PIEZO1, and STIM2). Protective variants (eg, GJD3, MMP10, and 4EBP1) were also identified in Finnish populations. However, replication studies showed that these genetic polymorphisms are not generalizable to specific populations. CONCLUSIONS: This systematic review highlights genes contributing to the development of CVD that have been identified in the literature. An improved understanding of genetic contributions to the pathogenesis of CVD may inform future diagnostics, prognostics, and personalized treatment. Further larger scale studies representative of global populations, including meta-analyses of genome-wide association datasets, are required owing to individual GWASs being statistically insufficient to draw generalizable conclusions.

Humans↗
PubMed1977

The detection of sympatric sibling species using genetic correlation analysis. I. Two loci, two gamodemes.

Four models are presented describing zygotic frequencies at two loci for one or two sympatric but genetically differentiated populations of "gamodemes." Linkage disequilibrium within gamodemes is allowed in two of the models. Maximum likelihood criteria are used to fit the models to the observed numbers of zygotes in a sample. A fitting-testing sequence for choosing a best model is described and the power of the test is analyzed. The statistical characteristics of the genetic parameter estimates were examined by simulation studies. In general, estimates were reliable when allele frequency differences between gamodemes were greater than 0.30 at both loci. This method may be used to study the population structure of samples with fewer heterozygotes than expected for Hardy-Weinberg populations, including the detection and genetic description of sibling species having overlapping ranges.--An example is given for Drosophila longicornis and D. propachuca, two sibling species within the mulleri complex of the repleta group which have been studied in detail using more conventional techniques. The reanalysis using the approach derived in this paper confirmed the reproductive isolation of these two species, and hinted at the possibility of further subdivision within D. propachuca.

Alleles↗