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Khabre desk
Recent reporting, analysis and explainers from the genetics desk.
health
A single-nucleus atlas of colorectal tumours found a higher stromal-to-epithelial ratio in younger patients with microsatellite-stable cancer. The study also identified age-associated RNA signals and differences in computationally inferred cell communication.
health
A medRxiv preprint describes three machine-learning-derived autism profiles in two cohorts of autistic children. The profiles showed different associations with common and rare genetic variants, although the authors say larger-cohort validation is needed.
science
A bioRxiv preprint reports that nonsense-mediated decay suppresses many RNA isoforms created when transposable-element sequences become part of genes. The findings suggest this cellular quality-control system helps regulate a pool of potential evolutionary novelty.
health
A medRxiv preprint reports five genetic loci associated with age at Parkinson’s disease onset in a meta-analysis of 50,859 people with the disease. The findings include signals near SNCA, GBA1 and HIP1R, while the APOE association may reflect effects on longevity.
science
A bioRxiv preprint reports that lipopolysaccharide supports several distinct functions in the cell envelope of two Gram-negative bacteria. Experiments suggest that its mechanical role alone cannot explain why it is essential for growth.
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A medRxiv preprint analysed gene activity in 1.4 million immune cells from 345 people across 13 Indigenous South American populations. Genetic ancestry was associated with many expression differences, often after immune stimulation.
science
OpenAI says it worked with PerturbAI and Scripps Research to use thousands of GPT-Rosalind agents to analyse a whole-brain mouse CRISPR atlas in 32 minutes. The agents linked gene-disruption effects with scientific literature to produce leads for follow-up research.
science
A bioRxiv preprint reports that canary breeds selected for song differ from other breeds in neural development, song-related brain regions and auditory sensitivity. Genome-wide findings point to many genes contributing to song divergence, including an ADGRV1 variant associated with singing and hearing traits.
health
A bioRxiv preprint reports that an antisense oligonucleotide targeting expanded human ATN1 improved seizure-related outcomes in a humanized mouse model of DRPLA. The findings come from mice, not a human treatment study.
science
A bioRxiv preprint describes RaMN-Seq, a roughly two-hour method for purifying micronuclei and sequencing their DNA. The researchers report tests in induced chromosome-missegregation experiments and cancer cell lines and tumour samples.
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A medRxiv preprint reports rare biallelic BECN1 variants in two unrelated families and connects the gene to AMPA-receptor regulation. Mouse and zebrafish experiments support the proposed biological mechanism.
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A single-centre retrospective study found routine clinical data could help rank likely genetic conditions in children with congenital heart disease. The AI models were evaluated in a selected cohort, so the results are a research finding rather than evidence of clinical diagnostic performance.
health
A medRxiv preprint reports five DNA-methylation clusters in 138 Wilms tumours and a classifier that identified WT1-driven tumours with about 90% accuracy. The researchers say using these patterns to guide genetic reanalysis uncovered previously unrecognised WT1 variants, including one that led to surveillance enrolment.
science
An Anthropic-authored bioRxiv preprint reports that Claude Code agents surveyed 1.9 billion protein clusters and identified a family of phage reverse transcriptases associated with tandem DNA repeats. The researchers also report that the repeat arrays are highly expressed during Staphylococcus phage infection.
science
A bioRxiv preprint reports that tunicamycin, a compound produced by Streptomyces bacteria, induced unisexual reproduction in Cryptococcus fungi. The reported cycle included meiotic recombination and spore formation.
health
A study of 62,560 individuals across diverse ancestries found no evidence that rare variants in TMEM106B are associated with Parkinson's disease risk. The findings suggest the gene's rare variation does not play a major role in PD susceptibility, despite evidence that TMEM106B expression is altered in the brains of people with the disease.
health
A bioRxiv preprint reports a ClinVar-derived AlphaGenome Variant Impact quantile cutoff of 0.9938 for prioritising single-nucleotide variants. Nearly half of the uncertain variants assessed exceeded that threshold, but the result is a prioritisation signal, not a clinical reclassification.
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A bioRxiv preprint analysing 231 haplotype-resolved human pangenomes reports that variable transposable elements can gain, change or lose regulatory effects before they become fixed. Their effects depend on DNA methylation and transcript context.
health
A medRxiv preprint introduces GenSep, a framework that estimates how distinct disease subtypes could be using genetic information and compares that benchmark with polygenic risk scores. Across 18 subtype pairs, the authors report that current scores captured a small share of the estimated genetic separation.
health
In a first-in-human phase 1 trial, the oral WRN inhibitor RO7589831 produced disease control in 74.2% of 66 evaluable patients with MSI cancers, with confirmed partial responses in seven. The study selected two doses for further testing, while tumour biopsies did not provide a conclusive measure of target engagement.
science
A bioRxiv preprint reports that TabICL and TabPFN prediction performance declines as genetic ancestry dispersion increases in evaluation data. The authors also report that instruction-tuning TabICL on synthetic tasks designed to model ancestry-dependent effects improves performance stability across ancestry-distance groups.
science
Researchers report a single-nucleus atlas spanning 21 adult human tissues and four donors, combining gene-expression and chromatin-accessibility data. It maps candidate regulatory elements and gene links, and uses sequence-to-function models to predict effects of fine-mapped variants.
science
A bioRxiv preprint reports that mitochondrial DNA mutations arising during mice’s first two months were sufficient to drive age-related pathologies. The authors also found that tissue-specific selection and mitochondrial fusion influenced the mutations’ later fate.
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A bioRxiv preprint reports that rare and common STARD9 variants are associated with different lipid disorders and opposite changes in lysosome positioning. The authors connect those differences to cholesterol handling in cells and, in knockout mice, to intestinal cholesterol absorption.
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A bioRxiv preprint reports that UHRF1 reads ubiquitin marks it places on histone H3, promoting further marking and supporting DNA methylation maintenance in CpG-sparse regions.
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A bioRxiv preprint uses a polymer-physics model to explain how ecDNA copy number may shape regulatory contacts in cancer-cell condensates. In the model, contacts in oncogene-associated regions grow stronger and become less variable as copy number increases.
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A bioRxiv preprint reports that RELAX produced different likelihood estimates in repeated runs, with some changes reversing statistical conclusions. The authors link the instability to site-class models and show that a seed alone did not ensure repeatable results in their tests.
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A bioRxiv preprint reports nine high-confidence hybrids between invasive Bursaphelenchus xylophilus and native B. mucronatus in Japanese field samples. Genome-wide analyses identified both F1-like and advanced backcross-like individuals, including some missed by a single-locus test.
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A study used single-nucleus data from human prefrontal cortex to map genetically regulated gene-expression signals across 12 brain disorders. Its cell-type and ancestry-aware models identified associations that bulk-tissue analyses missed.
health
A bioRxiv preprint links NR2F1-related changes in retinoic-acid signalling in mouse retinas with foveal abnormalities seen on OCT in people with BBSOAS. The findings point to a retinal component of the syndrome’s visual pathology.
science
A bioRxiv preprint reports genome-pattern evidence for an ancient whole-genome duplication shared by bryozoans. Few duplicate genes remain, but retained copies are enriched for cilia-related genes.
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A bioRxiv preprint reports that changes involving DNMT1 can reduce CTCF binding at the KMT2A gene and promote copy gains and rearrangements. The findings come from experimental molecular research, not a clinical study.
science
Researchers developed an engineered budding-yeast system to test resistance-conferring mutations in genes from several pathogenic fungi. They also used random mutagenesis to identify new candidate mutations.
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A medRxiv preprint identifies a MYOF missense variant associated with arrhythmogenic cardiomyopathy and describes a calcium-handling mechanism in patient-derived heart cells and mice. The findings point to the MYOF–CaV1.2 pathway as a potential therapeutic target, but remain preclinical.
science
A bioRxiv preprint profiles RISC-bound small interfering RNAs produced after insecticidal double-stranded RNA was injected into Tribolium castaneum larvae. The study links strand representation and terminal RNA modifications with sequence and structural features that could improve future pest-control design.
science
A bioRxiv preprint reports that trimethoprim reduced phage production and toxin production in laboratory experiments with a clinical Shiga toxin-producing E. coli isolate. The effect persisted alongside DNA-damaging antibiotics that normally increase phage activity.
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A bioRxiv preprint describes BRIDGE, a platform that transferred a 16-kilobase, five-gene violacein pathway into ten phylogenetically diverse yeast genera. Expression was strongest across six tested Saccharomyces species and varied in other yeasts.
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A bioRxiv preprint introduces ARCHER-LD, a multi-GPU tool for calculating linkage disequilibrium across very large sequencing datasets. The authors report speedups of about eightfold to 28-fold over PLINK in benchmark tests and complete a 10-quadrillion-element LD matrix in under six hours on 512 GPUs.
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A bioRxiv preprint reports that DNA recovered from museum hair samples attributed to Thomas Jefferson supports his direct paternity of children descended from Sally Hemings. The study compares inherited DNA shared with known and putative descendants and remains a preprint.
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A bioRxiv preprint identifies the nuclear enzyme MSK1 as a regulator of TRPV1 expression in a specific subset of pain-sensing neurons. In experimental models, blocking this inflammatory pathway reduced heat hypersensitivity while preserving acute heat sensation and body-temperature control.
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A bioRxiv preprint links a focal 2026 meningococcal outbreak in Kent, UK, to genetic changes that may have been acquired from carriage-associated Neisseria. The researchers propose that such highly invasive variants can emerge briefly and then disappear because they are poorly suited to sustained transmission.
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A bioRxiv preprint finds that the reproducibility of functional assays can cap measured performance for variant-effect predictors. Correcting for assay reliability shifts the apparent prediction gap from canonical splice sites toward intronic regions 11–50 base pairs from the splice boundary.
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A bioRxiv preprint presents Z-Hunt-DP, a dynamic-programming reformulation of a thermodynamic Z-DNA prediction method. The authors report that it preserved the original minimum-energy result while producing a 3.30 × 10^5 speedup at 20 dinucleotide positions.
health
A genome-wide association study of 140,559 adults from the Mexico City Prospective Study identified 78 independent signals for systolic blood pressure and hundreds more for other blood pressure traits, including variants rare in other populations.
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A Nature essay examines zoologist Paul Kammerer’s controversial experiments on inherited traits, the specimen-tampering accusation that damaged his reputation and why his scientific questions still resonate with modern biology.
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A bioRxiv preprint tracking seven Burkholderia multivorans strains from chronic infections in eight cystic fibrosis patients found that the emergence of a dominant bacterial lineage was associated with faster lung-function decline. The study also identified repeated evolutionary changes affecting bacterial functions linked to persistence in the airways.
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A bioRxiv preprint reports that neonatal AAV-SIL1 gene therapy prevented neurological and muscle disease in a mouse model of Marinesco-Sjögren syndrome. The treatment preserved cerebellar Purkinje cells and maintained its effects through 26 weeks.
health
A man with slowly progressing ALS caused by a rare CHCHD10 mutation showed improved motor-function scores and a biomarker associated with nerve damage returned to the normal reference range one year after receiving a mutation-targeted antisense oligonucleotide treatment.
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A bioRxiv preprint presents GAVURD, a trio whole-genome analysis system for finding potentially pathogenic variants outside protein-coding regions. In a proof-of-concept involving 10 unresolved rare-disease cases, it prioritised six potentially causal variants for further study.
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A bioRxiv preprint presents a 658,059-cell reference atlas of human hippocampus development and uses it to study brain organoids carrying the familial Alzheimer’s disease-associated PSEN1 E280A variant. The organoids showed altered cell composition, gene expression and inferred neuronal maturation.
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A Purdue University team reports a loop-mediated isothermal amplification assay for detecting Balamuthia mandrillaris. In laboratory testing, the assay detected multiple isolates with higher sensitivity than conventional PCR and produced a visible colour-based result.
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A bioRxiv preprint reports that the protein PBF/PTTG1IP helps coordinate cell adhesion, front–rear polarity and directional movement. The findings come from mouse fibroblasts and human thyroid cancer cells, making them preclinical mechanistic evidence.
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A bioRxiv preprint reports severe growth depression in Chinese bahaba after two generations of closed captive breeding from 18 wild founders. Whole-genome analysis linked the decline to increased genomic inbreeding and identified candidate pathways relevant to conservation breeding.
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A bioRxiv preprint describes zAcademy, an open-source programmable arena for conditioning adult zebrafish. In experiments, avoidance responses differed between wild-type and shank3 knockout fish and were driven mainly by females.
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A bioRxiv preprint reports that parvalbumin interneurons and dentate-gyrus changes shape seizure susceptibility in Angelman syndrome model mice. The findings point to altered inhibitory control and homeostatic plasticity as possible drivers of epileptogenesis.
health
A genome-wide association study involving more than one million people examined how genetic variation contributes to personality traits and may influence physical health, mental health and behaviour. The findings highlight genetic effects without separating them from the role of environment.
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A bioRxiv preprint in a DYT-TOR1A mouse model links striatal cholinergic interneuron pathology to abnormal movements while showing that antimuscarinic drugs can act without those neurons being present. The findings separate a developmental role for the neurons from the circuit mechanism through which the drugs suppress movements.
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A bioRxiv preprint maps bacterial host factors involved in infection by single-stranded RNA and DNA bacteriophages. The study identifies conserved requirements for F-pilus-dependent infection and links an E. coli capsule architecture to selective phage access.
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A bioRxiv preprint identifies phosphatidylinositol (PI) as the preferred direct substrate of the enzyme PLCXD2. In a PLCXD2-deficient retinal model, the loss was associated with altered lipid products, synaptic abnormalities, retinal-layer thinning and weaker electrical responses from photoreceptors.
health
A medRxiv preprint reports 41 genetic risk regions associated with juvenile idiopathic arthritis, including 14 not previously reported in the analysis. The study also describes a polygenic risk score and possible mechanisms involving HLA-A*02:01, ERAP2 and DNA topology.
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A chromosome-level reference genome and resequencing data from 80 Saimaa ringed seals show extremely limited Y-chromosomal diversity compared with other ringed seals. The bioRxiv preprint estimates that the population retains about 1% of the broader Y-chromosomal diversity and 5% of mitochondrial diversity.
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A medRxiv preprint reports striatal atrophy and increased caudate iron accumulation in asymptomatic female carriers of the genetic variant associated with X-linked dystonia-parkinsonism. The findings came from multimodal MRI in 42 carriers compared with 61 healthy controls.
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A bioRxiv preprint integrates genome-wide maps of DNA breaks, replication and transcription in U2-OS and HeLa cancer cell lines. It reports that prolonged low-dose DNA polymerase inhibition redirects breaks toward late-replicating regions and identifies MUS81 as a regulator of recurrent break clusters.
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A bioRxiv preprint functionally profiled 80 human PRDM9 alleles and found that most produce similar genome-wide DNA-binding patterns despite extensive sequence diversity. Rare and infertility-associated variants showed unusually broad or minimal DNA binding, pointing to a possible role in disrupted meiotic recombination.
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Genetic ablation of the Unc13a cryptic exon preserved memory in a mouse model of TDP-43 dysfunction, supporting UNC13A as a therapeutic target for related dementias.
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A bioRxiv preprint reports that the palm pest Rhynchophorus ferrugineus established on mainland America through Uruguay, spread across nearly 80,000 square kilometres and reached Argentina. The weevil is now attacking several native South American palms.
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A bioRxiv preprint describes RNA-fragment end joining (REJ), a modular system that joins separate RNA units into functional coding mRNAs. The reported platform supports gene complementation, intersectional cell labeling and expression of large proteins.
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A bioRxiv preprint presents PHACTn, a training-free method that uses mammalian evolutionary history to infer how tolerable single-nucleotide variants may be across the human genome. The authors report strong performance on benchmark sets of non-coding variants using four interpretable parameters and no GPU.
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Whole-genome sequencing of 7,851 parent–offspring families linked distinct assisted reproductive technology procedures and parental age with de novo mutations associated with gestational duration and other birth outcomes.
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A Nature study analysed a large-scale proteogenomic dataset from 29 healthy human tissues and identified 13,910 protein variants, including non-genetic amino-acid substitutions. The findings suggest that errors and variation during protein production may expand the set of protein forms with potential biological functions.
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A bioRxiv preprint reports that blood DNA methylation patterns vary across development, chronic disease and aging in humans and other mammals. The researchers also describe epigenetic clocks designed to predict expected mortality across species and tissues.
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A bioRxiv preprint reports that binding of the substrate eIF2α relieves an autoinhibitory loop in the mammalian GCN2 kinase. The finding revises the proposed roles of ribosomes and deacylated tRNAs in the integrated stress response.
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A bioRxiv preprint identifies how the Pmk1, Mst12 and Bip1 network coordinates the infection process of the rice blast fungus. The network controls appressorium function, effector deployment and invasive growth.
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A bioRxiv preprint finds that some adult zebrafish fail to recover movement after complete spinal-cord transection despite forming a tissue bridge. Multi-omic analyses and genetic screening identified hoxb5a as a regulator associated with bridge formation, axon regrowth and functional recovery.
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A medRxiv preprint combining genetic and single-cell analyses identifies bone-marrow macrophages as a possible link between aging and osteoporosis. It nominates TGFB1 and HNRNPUL1 as regulators in this relationship, based on observational, genetic and transcriptomic evidence.
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A bioRxiv preprint comparing matched full-UDG and non-UDG libraries from two medieval Mongolian individuals found trade-offs between site retention, residual disagreement and kinship inference. Corrected mixed-library data supported a first-degree, likely mother–son relationship, while uncorrected data shifted one estimate towards second degree.
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A bioRxiv preprint from Queen Mary University of London presents a genome-wide framework that uses native Oxford Nanopore reads to measure molecule-level DNA methylation variation and co-methylation. In human lymphoblastoid cell data, the analysis found patterns hidden by site-level averages.
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A bioRxiv preprint describes Isocall, a deterministic method for jointly identifying known and novel transcripts across large PacBio long-read RNA-sequencing datasets. The authors report a joint call across 206 samples in 25 minutes after alignment and profiling.
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A bioRxiv preprint introduces RADIS, a chemical-probing strategy that maps RNA secondary structure across long, intron-rich genomic loci. The study applies it to splice sites, branchpoints and Alu elements, including deep intronic regions that are difficult to analyse experimentally.
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A bioRxiv preprint reports using six-base sequencing to analyse DNA modifications in cell-free DNA released by neural cells into cerebrospinal fluid. The authors say the approach could support liquid-biopsy research into neurodegenerative disease.
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Google DeepMind says AlphaGenome Atlas pre-calculates predicted molecular effects for approximately 9 billion possible single-nucleotide changes, giving researchers a searchable tool for prioritising variants.
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Google DeepMind says AlphaGenome Atlas precomputes molecular-effect predictions for approximately 9 billion single-nucleotide variants and provides scores and interpretation tools for non-commercial academic research.