Single-cell RNA sequencing (scRNA-seq) resolves the phenotypic heterogeneity of tumors but rarely observes the somatic mutations that drive it: a variant is legible only where its gene is expressed, the mutant allele is transcribed, and reads span the variant site, so an absent variant read is fundamentally ambiguous. Bulk tumor cohorts have the opposite profile-matched genotype and expression for hundreds of patients, but no cellular resolution. We present scOPE ( s ingle- c ell O ncological P rediction E xplorer), which learns cancer-specific, driver-associated expression axes from bulk tumors, freezes them, and projects single-cell transcriptomes onto the fixed axes without refitting to the target cohort. Our central finding is that this transfer is selective rather than general: of 158 audited driver-cancer models across seven malignancies, 102 met predefined claim-safety criteria and only 11 reached out-of-fold AUROC ≥ 0.90, led by acute myeloid leukemia (AML) NPM1 (0.971), glioblastoma IDH1 (0.963), and pancreatic adenocarcinoma KRAS (0.944). Determining which programs transfer therefore becomes the central task. We address it with a ground-truth-free confidence score-integrating bulk transferability, spatial coherence, score concentration, and copy-number (CNV) agreement-that within AML ranked the three independently supported programs above the remainder (AUROC 0.85 across 12 truth-evaluable drivers, of which three were supported), a triage signal rather than a validated genotype classifier. Against expressed-mutation labels, cell-state-residual scores were enriched in mutant-labeled cells for NPM1 , TP53 , and DNMT3A , and the NPM1 separation survived aggregation to patients. Critically, matched genotype-score maps show that even supported programs occupy restricted transcriptional subspaces rather than uniformly marking mutation-positive tumors, and the NPM1 program contracted during treatment across multiple patients. Transferred scores tracked inferred CNV burden yet also resolved discordant malignant populations invisible to aneuploidy alone. scOPE does not call alleles; it recovers continuous, mutation-associated transcriptional axes from existing scRNA-seq data, together with explicit diagnostics for when that reading should be withheld.

For decades, population geneticists have relied upon a formula derived by Malécot and by Kimura to estimate the fixation probability of mutant alleles ( ϕ ). Among other things, this formula leads to the conclusion that in sufficiently large populations ϕ asymptotically approaches 2 s ( N e /N ) (for small s ), where s is the relative selective advantage of the mutant allele, and N e and N respectively denote the effective and absolute (haploid) population sizes. In contrast, in sufficiently small populations, ϕ = 1 /N , with the two domains of behavior being separated at the point where s ⋍ 1 / (2 N e ). These results hold when s, N , and N e remain constant during the fixation process, but require modification when populations are changing in size. Here, we show that if there are ecological effects associated with competing alleles, such that the genetic composition of the population influences the total population size, the fixation probability of a beneficial allele can substantially deviate from the levels suggested above, even in the domain of effective neutrality (i.e., | s | ≲1 / (2 N e )). We obtain analytical results for a variety of frequency-dependent functions for the overall population size, and show that the overall effect is largely a function of the response at low mutant-allele frequency. We also derive expressions for times to fixation and for fixation probabilities of deleterious alleles, and show how our results relate to prior work for the situation in which population sizes change in frequency-independent manners.

Genome evolution in eukaryotes is predominantly driven by the dynamics of repetitive sequences, which vary widely in both copy number and sequence composition. Rates of repeat evolution differ between and within species and are likely modulated by both genetics and environment. To uncover factors shaping the rate of genome content evolution, we analyzed 1,142 resequenced Arabidopsis thaliana genomes using a novel K-mer based approach to characterize genome content variation and identify hypervariable regions underlying differences in repeat abundance. We next treated repeat abundance as a quantitative trait and performed genome-wide association analyses across more than 400 repeat families to identify the genetic basis of copy number variation. Integrating these results through a meta-GWAS approach revealed both cis-acting variants and more than 50 trans-acting loci that regulate repeat abundance genome-wide. Cis-acting variation was predominantly localized to pericentromeric and centromeric regions, whereas trans-acting loci were enriched for candidate genes involved in DNA replication, DNA repair, DNA methylation regulation. Finally, we found evidence that purifying selection acts against mutations that accelerate genome content divergence, favoring alleles that constrain repeat expansion. Together, these findings provide new insights into the genetic architecture and evolutionary forces shaping genome evolution in A. thaliana and establish a framework for investigating these processes in other plant species.

Disruptions in purine metabolism contribute to a range of human diseases, from rare genetic disorders such as Lesch-Nyhan syndrome and xanthinuria to common conditions including gout and cancer. To better understand the metabolic networks that regulate purine homeostasis, we developed a Caenorhabditis elegans model of xanthine dehydrogenase ( xdh-1 ) deficiency. Remarkably, xdh-1 mutant animals form rare xanthine stones, recapitulating a hallmark of human xanthinuria. To uncover genetic regulators of purine homeostasis, we performed a forward genetic screen for mutations that exacerbate xanthine stone formation in xdh-1 mutants. This approach identified multiple loss-of-function alleles in a previously uncharacterized gene, which we named gda-1 . We show that gda-1 encodes an intestinal guanine deaminase that mediates a key enzymatic step in purine catabolism. The C. elegans genome also encodes a paralog, gda-2 , which shares guanine deaminase activity but is expressed in distinct tissues. While gda-2 can compensate for gda-1 loss in guanine metabolism, the two genes exhibit non-redundant roles in regulating xanthine accumulation and stone formation. Interestingly, our evolutionary analyses suggest that gda-2 was acquired by nematodes via horizontal gene transfer from bacteria. These findings reveal a spatially regulated purine catabolism pathway in C. elegans and suggest that acquisition of bacterial genes has shaped a core nematode metabolic network.

NAT2 encodes arylamine N-acetyltransferase 2, a key enzyme in the phase II metabolism of arylamines and arylhydrazines. NAT2 is highly polymorphic, resulting in variable distributions of rapid and poor metabolizers across global populations. Here, we detail the process undertaken by the Clinical Pharmacogenetics Implementation Consortium (CPIC) NAT2 Pharmacogene Curation Expert Panel (PCEP) to assign clinical function to NAT2 star (*) alleles using CPIC's standard terminology. Given the observed impact of NAT2 genetic variability on drug response, CPIC convened the NAT2-PCEP to standardize clinical allele function assignments. The NAT2-PCEP is comprised of multidisciplinary and international members, including researchers, clinicians, and implementers with expertise in pharmacogenomics and NAT2 molecular biology. Extensive in vitro and clinical literature was curated from PubMed and other sources to assess NAT2 genotype-to-phenotype concordance as well as the biochemical function of NAT2 star alleles. The NAT2-PCEP assigned allele clinical function using CPIC's standard terminology (increased, decreased, uncertain, and unknown function) to 59 star alleles cataloged by the Pharmacogene Variation Consortium (PharmVar). Two alleles, NAT2*1 and NAT2*4, were assigned increased function (historically known as rapid), 40 alleles were assigned decreased function (historically known as slow), 10 alleles were assigned uncertain function, and seven alleles were assigned unknown function. Rigorous evidence review and in-depth PCEP discussion were crucial in determining these function assignments. The findings reported here underscore the importance of standardized allele functional terms and diplotype-to-phenotype assignments to further the clinical implementation of NAT2 pharmacogenetic test results.

Germline mutations play a pivotal role in evolution and are the primary cause of hereditary diseases in humans. Although interpopulation and interspecific variations in the mutation rate and spectrum are observed, their underlying genetic basis is still unclear. In this study, we explore the genetic regulation of germline mutation rates using one of the largest publicly available datasets derived from parent-offspring whole-genome sequencing. We first showed that germline mutation rates are strongly correlated between siblings, suggesting the influence of heritable factors. We then performed a genome-wide association study (GWAS), identifying 14 loci significantly associated with mutation rates, Notably, a lead single-nucleotide polymorphism (SNP) in the NHEJ1 gene, critical for DNA repair, was linked to a 27% increase in maternal mutation rates and a significant shift toward A-to-T mutations only in females. This mutator allele is particularly prevalent in East Asian populations, where a similar shift in the A-to-T mutation spectrum has been observed. Evolutionary analysis suggests that this allele likely emerged in the common ancestor of humans and the Pan genus. Furthermore, the genotype at the lead SNP position in Pan species is also the same as the human mutator allele, supporting the potential role for this allele to explain the accelerated A-to-T mutations observed in the human-Pan lineage. Together, these results indicate that genetic variants, particularly in DNA repair pathways, contribute to variation in mutation rates and spectra across individuals and populations, with a notable sex-specific effect.

Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is one of the most destructive foliar diseases of wheat. Wild emmer wheat (Triticum dicoccoides, WEW), a progenitor species of bread wheat, rich in disease resistance genes, serves as a vital genetic resource for resistance breeding in bread wheat. In this study, we identified a hexaploid wheat introgression line, 7D72, derived from WEW, that exhibits high resistance to powdery mildew. An F2 population from a cross between 7D72 and the susceptible Chinese cultivar Shiyou 20 (SY20) was used to map the underlying resistance. Bulked segregant analysis combined with DNA sequencing (BSA-Seq) and genetic linkage mapping localized a single recessive resistance locus to a 2.4-cM interval on chromosome 2BS, which overlaps with the recently cloned Pm26 locus. Sequence analysis of 7D72 confirmed that TdCNL1 and TdCNL5 are identical to the Pm26 alleles, confirming that 7D72 contains Pm26 introgressed from WEW. In addition to disease resistance, 7D72 shows improved agronomic performance, including increased grain length and thousand-kernel weight compared with its recurrent parent Han87-1. Collectively, this study represents the first successful introgression of Pm26 into common wheat without observable linkage drag, validating its function as a powdery mildew resistance source in 7D72 and providing a valuable pre-breeding germplasm that combines effective disease resistance with enhanced yield-related traits.

CYP2C19 plays an important role in the metabolism of many medications, including the antiplatelet agent clopidogrel, the antifungal agent voriconazole, selective serotonin reuptake inhibitors, select tricyclic antidepressants, and proton pump inhibitors. The Clinical Pharmacogenetics Implementation Consortium has published several guidelines emphasizing the importance of CYP2C19 genotype-guided therapy to optimize patient outcomes. Formerly, the no function CYP2C19*2 allele was defined by three variants, c.332-23A>G (splice defect), c.681G>A (splice defect), and c.991A>G (p.I331V). The discovery of two new haplotypes, one containing only a single variant, c.681G>A, and another with only c.681G>A and c.991A>G, challenged the assumption that c.681G>A always occurred together with c.332-23A>G. PharmVar designated these new haplotypes as CYP2C19*2.018 and *2.019, respectively, prompting the revision of the CYP2C19*2 core allele to be defined solely by the single variant, c.681G>A. Although the variants interrogated to identify CYP2C19*2 and *35 remain the same, subjects who are heterozygous for c.332-23A>G (present on most CYP2C19*2 and all *35 alleles) and c.681G>A (present on all CYP2C19*2 alleles) may, in rare cases, have a CYP2C19*2/*35 poor metabolizer diplotype (variants in trans) and not a CYP2C19*1/*2 intermediate metabolizer diplotype (variants in cis). CYP2C19*2 alleles with c.681G>A, but not c.332-23A>G, were found in subjects across diverse populations and are estimated to have a frequency around 0.03%. These findings, along with the revision of the CYP2C19*2 core allele definition, have implications for variant testing, test interpretation and reporting.

Dual antiplatelet therapy (DAPT) with aspirin and clopidogrel is commonly used for secondary prevention following acute ischemic stroke (AIS) and neurointerventional procedures. However, the efficacy of clopidogrel is reduced in carriers of CYP2C19 no-function alleles. While CYP2C19-guided DAPT is well-established for some cardiovascular indications, its use in neurovascular settings has remained limited until recently. This study characterized current implementation strategies for CYP2C19-guided DAPT for neurovascular indications across institutions in the Pharmacogenomics Global Research Network Implementation Working Group. A REDCap survey was distributed to 54 institutions targeting those currently utilizing or planning to implement CYP2C19 testing to guide clopidogrel use for neurovascular indications. The survey collected data on implementation status, workflows, testing logistics, clinical decision support (CDS), and guideline concordance. Fifteen institutions met inclusion criteria; 80% were in the United States and 87% were academic centers. CYP2C19 testing was used for neurovascular indications at 12 sites, most commonly for AIS, intracranial aneurysm repair, and intracranial stenting. Implementation was often built on infrastructure previously established for cardiovascular indications. Most sites used multigene panels, offered testing in both inpatient and outpatient settings, and returned results within 7 days. Eighty percent of sites provided CDS to support application of results. All sites recommended an alternative P2Y12 inhibitor (e.g., ticagrelor) for poor metabolizers, and most did for intermediate metabolizers. CYP2C19-guided antiplatelet therapy for neurovascular indications is expanding, with many implementations leveraging preexisting infrastructure from cardiovascular settings. Broader adoption and outcome-focused research are needed to optimize the clinical utility of genotype-guided DAPT in neurovascular care.

Autoimmune responses are often attributed to failed tolerance to self-proteins, yet protein expression alone cannot explain why certain antigens dominate disease, why autoreactivity emerges under stress, or why specific HLA alleles shape risk. This review presents a framework in which autoimmunity arises from posttranslational remodeling of antigen identity. Rather than limiting PTMs to side chain chemistry, we consider how covalent modifications, altered processing, aberrant translation, peptide recombination, and supramolecular assembly expand the repertoire of molecular forms available for immune recognition. Classical PTMs such as citrullination, deamidation, oxidation, glycosylation, phosphorylation, sulfation, and ubiquitin-like remnants can modify proteolysis, HLA binding, and antibody recognition. Noncanonical pathways, including signal peptide processing, ERAP-dependent trimming, defective ribosomal products, cryptic ORFs, proteasome-catalyzed splicing, and hybrid insulin peptides, further demonstrate that the presented antigenome extends beyond annotated proteins. We also propose that aggregation functions as a supramolecular antigenic modification by altering uptake, persistence, protease accessibility, and local reaction chemistry. Examples from rheumatoid arthritis, celiac disease, type 1 diabetes, multiple sclerosis, systemic lupus erythematosus, inflammatory bowel disease, and autoimmune thyroid disease illustrate how these mechanisms converge. Finally, we discuss mass spectrometry and immunopeptidomics strategies for identifying, validating, and functionally interpreting remodeled antigens in autoimmune disease.

Improving grain yield and its components through a comprehensive understanding of genetic parameters continues to be a major challenge in wheat breeding, owing to the inherent complexity of simultaneously enhancing multiple agronomic traits. In the present study, the inheritance pattern of grain yield and its related traits in seven bread wheat (Triticum aestivum L.) genotypes, along with their F1 progeny, was investigated using Hayman's numerical and graphical diallel analyses within the framework of a randomized complete block design with three replications. Morley-Jones analysis revealed significant differences (p < 0.05 or 0.01) for grain yield and most traits. Inheritance was predominantly governed by both additive and dominant gene effects, such that non-additive action, particularly overdominance, played a fundamental role in grain yield per plant (GYP) and most traits. The parental genotypes exhibited a higher frequency of dominant alleles compared to recessive alleles, and favorable alleles outnumbered unfavorable ones. The results of regression analysis showed the absence of non-allelic interactions for the traits plant height (PH), spike length (SL), spike weight (SW), number of grains per spike (NGS), spike grain weight (SGW), and number of spikelets per spike (NSP); while the presence of epistatic interactions was detected for number of tillers (NT), number of spikes (NS), and GYP. Based on low Wr + Vr, it is inferred that dominant alleles primarily control SD, SGW, SW, and SL. Also, the results of graphical analysis showed that the partial dominance pattern prevailed for PH, SL, NT, NS, and GYP. In contrast, overdominance was observed for SGW, SD, NGS, and SW, whereas the trait number of NSP exhibited a complete dominance pattern. Genotypes P6 and P7 carried more recessive alleles, whereas P2 and P3 had higher dominant allele frequencies, suggesting potential hybridization to develop superior lines. GGE biplot analysis identified P2 (Sakha 93) as the top performer for SD, NS, NT, and NSP, while P2, P3, and P5 combined high stability and grain yield, positioning them near the ideal genotype.

Vietnamese indigenous chickens and their wild progenitors represent a critical but under-characterized reservoir of avian genetic diversity. This study used a multi-locus approach, incorporating 28 neutral microsatellite markers and candidate functional genes (HSP70, HSP90, and ADSL). We successfully delineated the genetic structure and adaptive potential of 12 native Vietnamese indigenous chicken populations and red junglefowl (Gallus gallus). Microsatellite analysis revealed high genetic diversity (411 alleles) and significant regional structuring into three primary groups, suggesting extensive historical gene flow and shared ancestral heritage with Thai indigenous breeds. High-throughput sequencing of functional loci identified five novel HSP70, 10 novel HSP90, and five novel ADSL alleles, underscoring the unique genetic heritage of Vietnamese avian resources. Selective signature analyses confirmed that, while purifying selection maintains core protein stability, specific codons, notably in HSP70 (18, 33, 41, and 42) and HSP90 (7), exhibit putative signals of positive selection. These loci emerge as compelling candidates for functional studies underlying thermal adaptation. Moreover, the meat quality gene ADSL exhibited diversifying selection at codon 58, highlighting a candidate molecular marker for the potential enhancement of savoriness and inosine monophosphate content. These findings, which reconcile neutral population structure with candidate signals of localized adaptive divergence, address a critical regional knowledge gap and provide a scientific foundation for future marker-assisted selection programs. By integrating these results into the Siam Chicken Bioresource Project, this study promotes transboundary conservation and the sustainable development of climate-resilient poultry systems in a warming world.