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PubMed2026

Carbapenemase-producing Acinetobacter baumannii from Spanish hospitals, 2016-2020: Interregional spread of ST2PAS isolates co-harbouring blaOXA-23, blaOXA-66 and armA genes.

INTRODUCTION AND AIMS: Carbapenem-resistant Acinetobacter baumannii (CRAB) poses a serious global threat, prioritized by the World Health Organization for new antibiotic development. The European Centre for Disease Prevention and Control proposed the integration of genomic sequencing into surveillance. This study characterizes phenotypic and genotypic features of nationwide-collected CRAB isolates from Spanish hospitals (2016-2020). MATERIALS AND METHODS: A total of 822 CRAB isolates sent to the Spanish reference laboratory were analysed, and 108 representative isolates were selected from 48 hospitals in 25 Spanish provinces. Antibiotic susceptibility was determined according to European Committee on Antimicrobial Susceptibility Testing guidelines, and WGS was performed by Illumina. Resistome, virulome, phylogeny (core-genome Multi-Locus Sequence-Typing; 2390 genes), insertion sequences and plasmids were analysed. RESULTS: Of the 108 representative isolates, 68.5% produced OXA-23, 10.2% OXA-24, 7.4% OXA-58, 1.9% NDM-1 and 2.7% others. 3.7% co-produced two acquired carbapenemases, and six that did not have them showed the ISAba1 upstream of the blaOXA-51 like. The predominant sequence types were ST2pas (82.4%) and ST218Oxf (61.1%). blaOXA-66 chromosomal carbapenemase allele was present in 75% of the 108 isolates, armA 16 s rRNA methyltransferase gene in 61.1%, and the kL-7/OCL-18 was present in 59.3% of the isolates. The most active antibiotic was colistin. Overall, 65.4% of invasive cases were caused by isolates harbouring all 38 virulence genes tested. In 64.8% of isolates a plasmid type was detected, mainly pS32-1-like (54.6%). CONCLUSIONS: In Spain, CRAB dissemination is driven by interregional spread of isolates belonging to the ST218Oxf/ST2Pas clones, characterized by the blaOXA-23/blaOXA-66 genotype, the presence of armA, the KL7/OCL18 capsular profile and the presence of pS32-1 plasmid.

K Locus↗
PubMed2025

Phenotypic and genotypic profiles of clinical isolates of various Nocardia species to carbapenems and fluoroquinolones.

OBJECTIVES: To establish patterns of the antimicrobial susceptibility of Nocardia species to carbapenems and fluoroquinolones and analysis of phenotypic-genotypic correlations. METHODS: Isolates were identified to the species using 16S rRNA, secA1, or rpoB gene sequencing analysis. The antimicrobial susceptibility testing was performed using the broth microdilution method, and WGS was employed to analyse the presence of resistance genes and/or mutations of Nocardia species against carbapenems and fluoroquinolones. RESULTS: Among 143 Nocardia isolates, N. farcinica (27.27%, 39/143) and N. cyriacigeorgica (25.17%, 36/143) were the most common species, followed by N. abscessus Complex (18.88%, 27/143). The MIC90s of the seven carbapenems were 8 mg/L for doripenem, 8 mg/L for meropenem, 16 mg/L for ertapenem, 16 mg/L for biapenem, 64 mg/L for imipenem, 64 mg/L for faropenem and 128 mg/L for tebipenem, respectively. The susceptibility rates to imipenem were 76.9% and 88.9% for N. farcinica and N. cyriacigeorgica, respectively, but only 14.3% and 0% for N. otitidiscavarium and N. brasiliensis, respectively. Further, 90% of N. brasiliensis and 50% of N. otitidiscaviarum isolates were susceptible and intermediate to meropenem. WGS identified blaFAR-1 gene in N. farcinica and blaAST-1 gene in N. cyriacigeorgica, respectively. The MIC90s of the four fluoroquinolones were 1 mg/L for sitafloxacin, 4 mg/L for nemonoxacin, 4 mg/L for moxifloxacin and 16 mg/L for ciprofloxacin, respectively. The susceptibility rate of Nocardia species to ciprofloxacin was low except for N. farcinica. The resistance to fluoroquinolones arise from mutations in the gyrA gene. CONCLUSIONS: Nocardia spp. exhibited varying patterns of susceptibility to carbapenems and fluoroquinolones respectively. Importantly, different Nocardia spp. exhibited different patterns of susceptibility to carbapenems and fluoroquinolones, respectively.

Nocardia↗
PubMed2025

Analysis of genetic differences underlying chilling stress tolerance using whole genome Re-Sequencing in walnut (Juglans regia L.).

Walnut (Juglans regia L.) is prized worldwide for both its nutritional value and economic importance, yet it remains vulnerable to cold stress, with significant differences in tolerance among varieties. This study combined physiological analyses with whole-genome resequencing (WGS) to evaluate the cold stress responses of two varieties, &#x2018;Qingxiang&#x2019; and &#x2018;Liaoning No.8&#x2019;. Under chilling stress (0&#xa0;&#xb0;C), we measured electrolyte leakage and antioxidant enzyme activity, applying both exogenous methyl jasmonate (MeJA) and the jasmonate inhibitor DIECA. Genomic variations were analyzed using WGS. Results showed that &#x2018;Liaoning No.8&#x2019; exhibited superior cold tolerance. Application of MeJA reduced electrolyte leakage by 37% and MDA accumulation by 52% on average, whereas DIECA exacerbated stress-related damage. WGS achieved 16.24&#x2013;16.26&#xd7; coverage and identified 2.73&#x2013;2.78&#xa0;million SNPs, 378&#x2013;382k InDels, 25&#x2013;26k SVs, and 7.2&#x2013;7.9k CNVs. Twenty genes containing sequence variants showed transcriptional responses under cold stress that were significantly correlated with mutation density (r&#x2009;=&#x2009;0.62, P&#x2009;<&#x2009;0.01). One gene, XM_018985465.2, which lacked SNPs in &#x2018;Liaoning No.8&#x2019;, was expressed 4.2 times more in this variety, suggesting cis-regulatory influence. These findings highlight the role of jasmonic acid signaling in enhancing cold tolerance in walnut and offer genomic insights into its underlying adaptive mechanisms.

Juglans↗
PubMed2026

Genomic and food-safety evaluation of Staphylococcus chromogenes in Chinese dairy milk.

Non-aureus staphylococci and mammaliicocci (NASM) cause mastitis and may contaminate milk and dairy products. Milk samples (n&#xa0;=&#xa0;1916) from cows with subclinical or clinical mastitis (SCM and CM, respectively) were collected from 28 large-scale (> 500 lactating cows) Chinese dairy farms. Overall, 999 NASM isolates representing 19 species were identified by MALDI-TOF MS and cpn60 sequencing, with Staphylococcuschromogenes, Mammaliicoccus sciuri and Staphylococcus haemolyticus being most prevalent. Antimicrobial resistance (AMR) was determined with disc diffusion; non-susceptible to penicillin was most common (SCM, 30% and CM, 29%) whereas cefoxitin non-susceptible NASM accounted for 8-10% of isolates; among these, 12.5% carried mecA but none carried mecC. Galleria mellonella was used to assess virulence of 78 strains of S. chromogenes, a dominant species; subsequently, 32 strains, representing higher- and lower-virulence in the Galleria model, were selected for whole-genome sequencing and comparative genomics. S. chromogenes isolates from CM had higher virulence (p&#xa0;<&#xa0;0.05) than those from SCM. The 32 genomes comprised 20 sequence types, indicating high genetic diversity. No robust genomic marker of Galleria virulence phenotype was identified in this selected WGS subset. Acquired resistance genes (n&#xa0;=&#xa0;5) were detected, including a first report of fusC in S. chromogenes; the fusC-positive isolate had an elevated fusidic acid MIC (8&#xa0;mg/L). Although S. chromogenes persisted in milk at 4&#xa0;&#xb0;C, pasteurization (64&#xa0;&#xb0;C for 30&#xa0;min) reduced viable counts to below detection. This study provided new insights into the prevalence, AMR, genomic diversity, and dairy-chain relevance of milk-derived NASM, particularly S. chromogenes. However, the genomic findings were based on an intentionally selected WGS subset and should be interpreted as hypothesis-generating rather than population-representative.

Animals↗
PubMed2026

FuFiHLA: a tool for full-field HLA typing from long-read data.

MOTIVATION: Allele typing for Human Leukocyte Antigen (HLA) genes has many important clinical applications. Popular short-read typing can only accurately distinguish alleles at the coding sequence level, which potentially limit our understanding of the effect of variants in non-coding region. Long read data has been proved to be useful in typing HLA alleles in full resolution, but only a few tools are publicly available and with significant limitations in practical application. RESULTS: We developed FuFiHLA, a lightweight open-source software, to type HLA alleles. Currently it supports typing alleles of six HLA genes (HLA-A, HLA-B, HLA-C, HLA-DRB1, HLA-DQA1, and HLA-DQB1) from long reads. Evaluation using 233 PacBio HiFi WGS samples from HPRC shows that FuFiHLA achieves 99.6% accuracy in the full field allele typing and QV as 51.8 for consensus allele sequence construction. Additional testing on four Nanopore R10 reads demonstrates slightly reduced accuracy in the fourth field. AVAILABILITY: FuFiHLA is available at https://github.com/jingqing-hu/FuFiHLA under MIT License.

Humans↗
PubMed2026

Whole genome analysis of a multidrug-resistant blaNDM-5-carrying Escherichia coli Sequence Type (ST) 167 strain isolated from seafood in Mumbai, India.

BACKGROUND: E. coli ST167 is an emerging extraintestinal pathogenic Escherichia coli (ExPEC) clone. This study reports the whole genome sequence analysis of a multidrug-resistant, blaNDM-5 harboring E. coli ST167 (EC121) isolated from seafood. The antibiotic susceptibility pattern was determined using the standard disc diffusion method. Genomic DNA was extracted, purified, and sequenced using the Illumina platform. The whole genome sequence was analyzed to determine the genome characteristics, including sequence type, serotype, phylogroup, antibiotic resistance genes, virulence attributes, and phylogenetic analysis. RESULTS: Phenotypically, this isolate was resistant to 26 of the 33 antibiotics tested, which correlated well with in-silico prediction. Multilocus sequence typing (MLST) analysis revealed that this strain belonged to sequence type 167, serotype O101:H9, and phylogroup A and harbored different virulence genes, suggesting it was a potential human pathogen. Many acquired antibiotic resistance genes were detected, including blaNDM-5, blaCMY-42, blaOXA-1, blaTEM-116, catA1, sul2, and tet(B). Point mutations in gyrA and parC responsible for quinolone resistance were also detected. CONCLUSION: The combinations of virulence and antibiotic resistance genes in this strain highlight the significant risk associated with emerging E. coli clonal types contaminating the seafood supply chain. Fecal contamination of seafood can contribute to the community dissemination of multidrug-resistant E. coli, necessitating effective monitoring measures.

Seafood↗
PubMed2025

Investigating genetic, antigenic, and structural diversity in the Neisseria gonorrhoeae outer membrane protein, PorB: implications for vaccine design.

UNLABELLED: Vaccines targeting Neisseria gonorrhoeae are needed to reduce disease burden and help address the problem of antimicrobial resistance, with an understanding of relationships between gonococcal genetics and molecules influencing diversity, infection, and the immune response essential for developing effective vaccine formulations. Whole-genome sequence data can be used to investigate these relationships among thousands of gonococcal isolates, allowing the study of antigenic diversity on a population scale. Such analyses typically examine antigenic diversity occurring in complete protein sequences, generating mean diversity indices and phylogenetic analyses that can inform on vaccine potential; however, to detect and measure the immune responses elicited, epitope characterization within an antigen helps guide vaccine formulations, with epitopes commonly located in surface-exposed regions of a protein. Here, we analyzed the genetic diversity of the major gonococcal antigen, PorB, in WGS from 22,227 N. gonorrhoeae isolates. We characterized the diversity of all eight surface-exposed outer membrane loops, or variable regions (VRs), and generated a PorB VR subtyping scheme to facilitate the global and temporal detection of circulating PorB subtypes. These analyses identified the presence of dominant VR combinations that persisted over time, indicative of (i) epistatic interactions between VRs and (ii) positive selection. Strain-specific, anti-PorB IgG responses directed toward distinct VR subtypes were detected in sera obtained from participants vaccinated with 4CMenB. The deconstruction of PorB into each surface-exposed loop provides a powerful approach for evaluating vaccine candidates: the methods used here allow immunodominant regions to be detected, which is invaluable for further vaccine investigations. IMPORTANCE: In the context of rising global gonorrhea cases, the development of vaccines becomes a priority; however, N. gonorrhoeae antigenic diversity and its ability to evade the immune system complicate vaccine development. This study characterizes the genetic diversity of the outer membrane protein, PorB, a key component of the outer membrane and a major gonococcal antigen. Using genomics and machine-learning techniques, this research identified dominant PorB variants that drive the immune response, proposing potential vaccine candidates and improving our understanding of the evolutionary forces maintaining genome structure and biological fitness. Understanding these processes is crucial for designing vaccines that effectively target N. gonorrhoeae and combat the spread of multidrug-resistant gonococci.

Neisseria gonorrhoeae↗
PubMed2026

Analysis of APC promoter 1B deletions in Russian families with familial adenomatous polyposis.

OBJECTIVE: Familial adenomatous polyposis (FAP) is a severe autosomal dominant hereditary cancer syndrome. Patients develop hundreds of adenomatous polyps throughout the colon with the risk of colorectal cancer, if untreated, approaching 100%. FAP is caused by pathogenic germline variants in the APC gene. Deletions in the APC 1B promoter cause FAP in a small subgroup of patients. Previous studies suggested that the APC promoter deletions in unrelated FAP patients from the US and Italy are identical and may thus have spread from a single founder. The aim of this study was to investigate whether a similar founder effect can be detected in the Russian population. PATIENTS AND METHODS: We performed whole-genome sequencing on five unrelated patients (three males and two females) with extensive (over 100) colon polyps, family history of FAP, and germline APC 1B promoter deletions previously detected by the multiplex ligation-dependent probe amplification (MLPA) and detected precise deletion boundaries. RESULTS: The patients carried deletions in the APC 1B promoter ranging from ~3 to ~122 kbp. We found no association between the deletion size and either the age of the onset or severity of the disease. All deletions were unique and no identical deletion boundaries were observed. However, in four patients, the right deletion breakpoints fell into a 1 kbp region downstream of the 1B promoter. The right breakpoints of several deletions detected in FAP patients from other countries also fell into this narrow region. CONCLUSION: The APC 1B promoter deletions analyzed in this study had arisen independently and there is thus no evidence of a founder effect. Therefore, at least for the cohort of FAP patients with APC 1B promoter deletions studied here, WGS did not provide an added diagnostic benefit to MLPA aside from precisely determining the deletion breakpoints.

APC promoter 1B deletion↗
PubMed2025

Co-existence of the oxazolidinone resistance genes cfr and optrA on a novel multiresistance plasmid from a methicillin-resistant Macrococcoides bohemicum strain.

OBJECTIVES: To identify and characterize the oxazolidinone resistance genes cfr and optrA from a methicillin-resistant Macrococcoides bohemicum strain of chicken origin. METHODS: The presence of mobile oxazolidinone resistance genes was detected by PCR. Antimicrobial susceptibility testing was conducted by broth microdilution. Transfer experiments were carried out to evaluate horizontal transferability of the plasmid. WGS was performed using a combination of Illumina NovaSeq/Oxford Nanopore PromethION platforms. RESULTS: The M. bohemicum strain HLJ23 exhibited an MDR phenotype and was positive for both cfr and optrA genes. WGS revealed that the genes cfr and optrA co-exist on the novel MDR plasmid pHLJ23-71kb. Although conjugation experiments were unsuccessful, plasmid pHLJ23-71kb could be transferred to Staphylococcus aureus RN4220 by electrotransformation. Genetic context analysis showed that the cfr and optrA together with another four antimicrobial resistance genes are located in an MDR region on plasmid pHLJ23-71kb. Sequence analysis suggested that this MDR region possibly originated from Mammaliicoccus or Staphylococcus spp. CONCLUSIONS: To the best of our knowledge, this study represents the first report of the oxazolidinone resistance genes cfr and optrA in the genus Macrococcoides. Furthermore, attention should be paid to the exchange of resistance determinants between members of the genera Staphylococcus, Mammaliicoccus and Macrococcoides.

Plasmids↗
PubMed2026

Mechanisms of cefiderocol resistance in carbapenem-resistant Acinetobacter baumannii: a Swiss 2023-2025 collection.

OBJECTIVES: The numbers of infections caused by carbapenem-resistant Acinetobacter baumannii (CRAB) are increasing globally and present a significant burden on healthcare systems. This study describes the CRAB isolates received at the Swiss National Reference Centre for Emerging Antibiotic Resistance (NARA) over a 3-year period, from January 2022 to December 2025, and aimed to characterize the prevalence and mechanisms of FDC resistance. METHODS: Two-hundred and thirty-four non-duplicate CRAB isolates were submitted to NARA over the study period from hospitals and laboratories across Switzerland. Susceptibility testing was performed by disk diffusion and broth microdilution, according to EUCAST methodology. Whole-genome sequencing was performed on 11 isolates. ADC alleles were cloned into vector pVRL1 and transformed into Escherichia coli Top10. RESULTS: All isolates exhibited resistance to the carbapenems, and most were resistant to cephalosporins. Most isolates harboured an acquired class D carbapenemase, most frequently OXA-23 (181/234; 77.4%). One quarter of isolates were resistant to cefiderocol (FDC), exhibiting MICs ranging from 4->32 mg/L. Whole genome sequencing analyses, performed on 11 FDC-resistant isolates, identified that FDC resistance was due a combination of mechanisms including NDM and PER-production, mutations within the iron transporters, piuA and pirA, and the overexpression of ADC variants. CONCLUSIONS: This study showed that OXA-23 was the dominant mechanism of carbapenem-resistance in CRAB in Switzerland. Almost one quarter of CRAB isolates were resistant to "last resort" antimicrobial, FDC. The mechanisms of FDC resistance identified in this study emphasise that resistance to this antimicrobial is often complex and multifactorial, requiring high-resolution methods, including WGS, to identify.

Acinetobacter baumannii↗
PubMed1990

Coordination of sucking, swallowing and breathing in the newborn: its relationship to infant feeding and normal development.

Non-invasive, sensitive equipment was designed to record nasal air flow, the timing and volume of milk flow, intraoral pressure and swallowing in normal full-term newborn babies artificially fed under strictly controlled conditions. Synchronous recordings of these events are presented in chart form. Interpretation of the charts, with the aid of applied anatomy, suggests an hypothesis of the probable sequence of events during an ideal feeding cycle under the test conditions. This emphasises the importance of complete coordination between breathing, sucking and swallowing. The feeding respiratory pattern and its relationship to the other events was different from the non-nutritive respiratory pattern. The complexity of the coordinated patterns, the small bolus size which influenced the respiratory pattern, together with the coordination of all these events when milk was present in the mouth, emphasise the importance of the sensory mechanisms. The discussion considers (1) the relationship between these results, those reported by other workers under other feeding conditions and the author's (WGS) clinical experience, (2) factors which appear to be essential to permit conventional bottle feeding and (3) the importance of the coordination between the muscles of articulation, by which babies obtain their nourishment in relation to normal development and maturation.

Child Development↗
PubMed2004

Analysis of segmental duplications and genome assembly in the mouse.

Limited comparative studies suggest that the human genome is particularly enriched for recent segmental duplications. The extent of segmental duplications in other mammalian genomes is unknown and confounded by methodological differences in genome assembly. Here, we present a detailed analysis of recent duplication content within the mouse genome using a whole-genome assembly comparison method and a novel assembly independent method, designed to take advantage of the reduced allelic variation of the C57BL/6J strain. We conservatively estimate that approximately 57% of all highly identical segmental duplications (>or=90%) were misassembled or collapsed within the working draft WGS assembly. The WGS approach often leaves duplications fragmented and unassigned to a chromosome when compared with the clone-ordered-based approach. Our preliminary analysis suggests that 1.7%-2.0% of the mouse genome is part of recent large segmental duplications (about half of what is observed for the human genome). We have constructed a mouse segmental duplication database to aid in the characterization of these regions and their integration into the final mouse genome assembly. This work suggests significant biological differences in the architecture of recent segmental duplications between human and mouse. In addition, our unique method provides the means for improving whole-genome shotgun sequence assembly of mouse and future mammalian genomes.

Animals↗
PubMed2026

Genomic characterization of avian metapneumovirus subtypes A and B in United States poultry by targeted amplicon sequencing.

Avian metapneumovirus (aMPV) subtypes A and B emerged in United States poultry in late 2023 and early 2024, prompting genome-scale surveillance from clinical samples. Here, we developed and optimized targeted amplicon sequencing (TAS) assays for both subtypes and applied them to 104 subtype-positive clinical samples collected from chicken and turkey farms across nine US states between early 2024 and early 2026. TAS recovered 91 genomes suitable for comparative analysis, including 44 aMPV-A and 47 aMPV-B sequences, with successful recovery extending to Ct values of 34.6 for aMPV-A and 31.2 for aMPV-B. Recovered genomes showed near-complete breadth and high mapping efficiency. Phylogenetic analyses of both G-gene and whole-genome datasets showed that US aMPV-A field strains formed a distinct monophyletic lineage within group IV and resolved into three closely related clusters. Cluster 2, first recognized in North Carolina and later detected in Ohio, spread across 30 turkey and chicken farms. Cluster 2 genomes were defined by a concentrated G-protein hotspot within residues 209-275, and most North Carolina Cluster 2 genomes carried 10-11 nonsynonymous substitutions in this region, including multiple proline substitutions suggestive of local structural change. Missouri Cluster 3 remained cohesive but distinct from both Cluster 1 and Cluster 2 in the G-gene and whole-genome trees. In contrast, US aMPV-B field strains remained highly homogeneous across hosts and states, with more than 99% nucleotide identity by both G-gene and WGS analyses. We also identified 12 vaccine-derived genomes on both vaccinated and nonvaccinated farms. These included six genomes related to aMPV-A vaccine and six related to aMPV-B vaccines (VCO3/50 and 1062), all of which retained vaccine-defining markers together with additional substitutions consistent with continued circulation after vaccine use in the field. Selection analyses showed that the G gene had the highest gene-wise dN/dS ratio in both subtypes. Additional elevated signal was observed in SH and M2, and candidate positively or episodically selected codons were concentrated in the subtype A Cluster 2 G-gene hotspot. These findings show that TAS supports direct-from-sample aMPV genomic surveillance and provides genomic context for field clusters, vaccine-derived lineages, and continued adaptive change in aMPV in US poultry.

Animals↗
PubMed2026

CBIcall: a configuration-driven framework for variant calling in large sequencing cohorts.

MOTIVATION: Variant calling for next-generation sequencing (NGS) data relies on a diverse ecosystem of tools and workflows. Large-scale collaborative studies increasingly adopt federated analysis, where each institution processes sensitive data locally using standardized pipelines. Deploying identical pipelines across multiple centers remains challenging because heterogeneous software environments and computing policies can cause workflow divergence and inconsistent results. RESULTS: We developed CBIcall, a workflow backend-flexible, configuration-driven framework that runs standardized variant-calling pipelines from raw FASTQ files to analysis-ready VCFs. Users define each analysis in a single YAML parameters file, which CBIcall resolves against a controlled workflow registry and resource catalog. The execution driver validates parameters and checks compatibility among pipelines, analysis modes, workflow backends, genome builds, tool versions, and resource bundles. CBIcall supports reproducibility auditing by comparing executions using recorded provenance and output fingerprints. CBIcall dispatches validated workflows natively through Bash, Cromwell, Nextflow and Snakemake backends and provides production-ready pipelines for germline WES, WGS (single-sample or cohort joint genotyping following GATK Best Practices), and mitochondrial DNA analysis. We evaluated analytical performance using public benchmark datasets and validated reproducibility across four computing environments. We further deployed CBIcall in the EU HEREDITARY project, where it processed 1102 samples with both WES and mtDNA pipelines on an institutional HPC system, supporting its suitability for reproducible cohort-scale genomic analyses. AVAILABILITY AND IMPLEMENTATION: CBIcall is open source (GPLv3) and distributed with ready-to-run pipelines; full dependency and installation documentation is available at https://github.com/CNAG-Biomedical-Informatics/cbicall.

Journal Article↗
PubMed2024

The Genetic Determinants and Genomic Consequences of Non-Leukemogenic Somatic Point Mutations.

Clonal hematopoiesis (CH) is defined by the expansion of a lineage of genetically identical cells in blood. Genetic lesions that confer a fitness advantage, such as point mutations or mosaic chromosomal alterations (mCAs) in genes associated with hematologic malignancy, are frequent mediators of CH. However, recent analyses of both single cell-derived colonies of hematopoietic cells and population sequencing cohorts have revealed CH frequently occurs in the absence of known driver genetic lesions. To characterize CH without known driver genetic lesions, we used 51,399 deeply sequenced whole genomes from the NHLBI TOPMed sequencing initiative to perform simultaneous germline and somatic mutation analyses among individuals without leukemogenic point mutations (LPM), which we term CH-LPMneg. We quantified CH by estimating the total mutation burden. Because estimating somatic mutation burden without a paired-tissue sample is challenging, we developed a novel statistical method, the Genomic and Epigenomic informed Mutation (GEM) rate, that uses external genomic and epigenomic data sources to distinguish artifactual signals from true somatic mutations. We performed a genome-wide association study of GEM to discover the germline determinants of CH-LPMneg. After fine-mapping and variant-to-gene analyses, we identified seven genes associated with CH-LPMneg (TCL1A, TERT, SMC4, NRIP1, PRDM16, MSRA, SCARB1), and one locus associated with a sex-associated mutation pathway (SRGAP2C). We performed a secondary analysis excluding individuals with mCAs, finding that the genetic architecture was largely unaffected by their inclusion. Functional analyses of SMC4 and NRIP1 implicated altered HSC self-renewal and proliferation as the primary mediator of mutation burden in blood. We then performed comprehensive multi-tissue transcriptomic analyses, finding that the expression levels of 404 genes are associated with GEM. Finally, we performed phenotypic association meta-analyses across four cohorts, finding that GEM is associated with increased white blood cell count and increased risk for incident peripheral artery disease, but is not significantly associated with incident stroke or coronary disease events. Overall, we develop GEM for quantifying mutation burden from WGS without a paired-tissue sample and use GEM to discover the genetic, genomic, and phenotypic correlates of CH-LPMneg.

Journal Article↗
PubMed2025

Construction of a Core Germplasm and Identification of Candidate SNPs Associated with Growth Performance of Epinephelus tukula by Whole-Genome Resequencing.

Epinephelus tukula is an economically important aquaculture animal, and a major parent in grouper crossbreeding. To better preserve and exploit E. tukula germplasm resources, a core collection (containing 34 individuals derived from 10 genetic groups) was first constructed based on phenotypic growth traits and whole-genome resequencing (WGS) data. The phenotypic traits of the individuals within the core collection were not significantly different from those in the original collection, suggesting effective representativeness of the core collection. Additionally, we performed genome-wide association study (GWAS) of E. tukula to identify candidate single nucleotide polymorphisms (SNPs) and genes associated with growth traits, to facilitate the improvements in the growth performance of this species. Twenty-six significant SNPs were identified, scattered among multiple chromosomes. Five SNPs were confirmed to be correlated with growth in another new group of 101 individuals. Based on the annotation results, these five SNPs were located in CCDC102A, NTRK2, CTSL, OTOF, and nestin, and were involved in cell development, differentiation and proliferation, glycolytic metabolism, neurological development, and myoblast differentiation. Our findings not only provide an effective basis for the conservation and utilization of E. tukula germplasm resources, but also promote the development of marker-assisted selection of E. tukula.

Polymorphism, Single Nucleotide↗