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PubMed2026

What do you mean by PitNETs in WHO Classification 2022?

This review is aimed at clarifying the background and the meaning of new terminology "pituitary neuroendocrine tumours" (PitNETs) in WHO Classification 2022. The PitNETs share the unique structures of secretory granules (SG) with other neuroendocrine tumors, the good example of which is the pancreatic NETs which are now considered to be potentially aggressive, i.e., invasive and metastatic. The PitNETs share these features of pancreatic NETs and now are considered to be potentially aggressive tumors. The PitNETs are classified according to the functions (hormones) and transcription factors, PIT1, TPIT and SF1. The PitNETs are usually slow growing tumors with generally low (<3%) Ki-67 indices. PitNETs show some morphologic features which are more closely related to aggressive growths, such as Crooke cells. The questions how those particular PitNETs are aggressive have been approached by molecular techniques such as single cell RNA seq to clarify the genomic heterogeneity and the biology of individual tumor cells. It is expected that the PitNETs will be clarified and classified with more biologically and therapeutically oriented manner.

Neuroendocrine neoplasms (NEN)↗

PubMed2026

Azacitidine-Venetoclax or Induction Chemotherapy for Acute Myeloid Leukemia.

BACKGROUND: Induction chemotherapy has long been a key component of curative therapy for fit patients with acute myeloid leukemia (AML), despite its frequently severe side effects and substantial health care utilization. For patients who are ineligible for induction chemotherapy, hypomethylating therapy plus venetoclax is the standard treatment owing to its efficacy and side-effect profile. METHODS: In this multicenter, phase 2 trial, we randomly assigned, in a 1:1 ratio, previously untreated adults with AML who were eligible for induction chemotherapy to receive either azacitidine plus venetoclax or induction chemotherapy. Patients with core binding factor fusions, mutations in the gene encoding FMS-like tyrosine kinase 3 (FLT3), or mutations in the gene encoding nucleophosmin-1 (NPM1; unless the patient was ≥60 years of age) were excluded. The primary end point was event-free survival. RESULTS: A total of 172 patients underwent randomization, with 86 patients assigned to each group. The median age of the patients was 64 years. A total of 72% of the patients had adverse-risk disease according to the European LeukemiaNet 2022 classification. At a median follow-up of 21.9 months, the median event-free survival was 14.5 months (95% confidence interval [CI], 10.4 to 24.4) in the azacitidine-venetoclax group, as compared with 6.2 months (95% CI, 4.1 to 10.1) in the induction chemotherapy group, corresponding to a hazard ratio for event or death of 0.57 (95% CI, 0.39 to 0.84; P = 0.002 by the stratified log-rank test). Infection of grade 3 or higher occurred in 28% of the patients (95% CI, 19 to 39) receiving azacitidine-venetoclax and in 41% of those (95% CI, 30 to 52) receiving induction chemotherapy; hemorrhage of grade 3 or higher occurred in 2% (95% CI, 0.3 to 8) and 12% (95% CI, 6 to 20), respectively. CONCLUSIONS: In this phase 2, randomized trial, azacitidine-venetoclax therapy led to significantly longer event-free survival than induction chemotherapy among induction-eligible patients with AML. (Funded by AbbVie and others; PARADIGM ClinicalTrials.gov number, NCT04801797.).

Adult↗

PubMed2026

Clinical Relevance of Genomics Defined WHO5 Subtypes of Pediatric B-ALL in the Context of Measurable Residual Disease-Directed Risk-Based Therapy.

PURPOSE: WHO5 (2022) classification of B-lymphoblastic leukemia (B-ALL) incorporates several novel entities requiring high-throughput sequencing for their accurate characterization. The clinical relevance of this classification in the context of contemporary measurable residual disease (MRD)-directed therapy is unclear. METHODS: We analyzed 533 pediatric B-ALL uniformly treated with Indian Collaborative Childhood Leukaemia group (ICiCLe)-ALL-14 protocol as defined by WHO-2016 and reclassified them as per WHO5 using targeted sequencing, FISH, and cytogenetics. RESULTS: Subtype-defining genomic abnormalities were identified in 81.2% of the cohort as per the WHO5 classification. Among the new subtypes, PAX5alt and MEF2D-r were associated with a trend toward an inferior 3-year event-free survival (EFS) of 32.8% (P = .003) and 33.7% (P = .091), respectively. We developed a three-tier genomic risk stratification model incorporating 15 genomic subtypes and the IKZF1 deletion. Children with standard (SGR), intermediate (IGR), and high genomic risk (HGR) demonstrated 3-year EFS of 80.4%, 59.3%, and 45.8% (P < .0001), and 3-year overall survival of 89.6%, 75.3%, and 62.3% (P < .0001), respectively. Genomic risk further identified heterogeneous outcomes among ICiCLe risk groups (P < .0001). SGR was associated with superior EFS irrespective of MRD status (3-year EFS 80.5% in postinduction [PI] MRD-negative v 80.8% PI-MRD-positive patients, P = .530). On multivariable analysis, genomic risk (hazard ratio [HR], 1.7 [95% CI, 1.41 to 2.01]; P < .0001), initial ICiCLe risk (HR, 1.3 [95% CI, 1.06 to 1.49]; P = .009), and PI-MRD (HR, 2.2 [95% CI, 1.66 to 2.90]; P < .0001) independently predicted EFS. CONCLUSION: The study demonstrates the potential role of genomic risk stratification, in conjunction with MRD, in stratifying patients into clinically relevant risk categories.

Humans↗

PubMed2025

Recent Advances in nccRCC Classification and Therapeutic Approaches.

Non-clear cell renal cell carcinoma (nccRCC) constitutes a biologically diverse category of renal malignancies. The 2022 WHO classification framework has significantly evolved to incorporate molecularly defined entities alongside traditional histologic subtypes, reflecting the growing recognition of distinct pathogenic drivers. Current therapeutic paradigms for advanced disease remain suboptimal, with treatment strategies often extrapolated from clear cell renal cell carcinoma (ccRCC). In this review, we highlight transformative multi-omics approaches to address nccRCC's profound heterogeneity, which enables molecular stratification beyond conventional pathology, identifying novel subtypes characterized by unique immune microenvironment features, metabolic profiles, and genomic instability patterns. This molecular reclassification provides a foundational framework for precision oncology, facilitating patient selection for targeted therapies and immunomodulatory strategies. Advancements in multi-omics subtyping represent a pivotal shift toward biologically guided clinical management and underscore the imperative for biomarker-driven therapeutic development in nccRCC.

Humans↗

PubMed2026

AML, Myelodysplasia-Related: Beyond Classification-Toward Precision Decision-Making.

Acute myeloid leukemia, myelodysplasia-related (AML-MR), represents a genetically defined and clinically heterogeneous entity characterized by myelodysplasia-related gene (MRG) mutations, specific cytogenetic abnormalities, and frequently a previous history of myelodysplastic syndromes (MDS) or MDS/myeloproliferative neoplasm (MDS-MPN). The transition from the World Health Organization (WHO) 2016 classification to the 2022 WHO and International Consensus Classification (ICC) systems reflects a paradigm shift from morphology-based definitions toward genomics-driven disease entities. However, while diagnostic precision has improved, translation of these classifications into clinically actionable strategies remains incomplete. This review critically examines the biological and prognostic implications of MRG mutations, their interaction with key molecular subgroups such as NPM1- and FLT3-mutated AML, and their impact on therapeutic decision-making. We highlight unresolved issues, including the context-dependent prognostic value of MRG mutations, limitations of static risk stratification, and the need to integrate measurable residual disease (MRD), genomics, and patient fitness into therapeutic algorithms. At the clinical level, many studies have explored the sensitivity of AML-MR to various induction treatments in both younger and older AML patients, with significant improvements in survival. The main objective of these different induction therapy strategies is to achieve a complete remission with minimal toxicity, particularly in older patients, allowing patients to proceed to allogeneic hematopoietic stem cell transplantation, the only curative option so far.

AML MDS-related↗

PubMed2026

Early infantile developmental and epileptic encephalopathy: clinical spectrum, diagnosis, outcomes, and evolving treatment strategies.

Early infantile developmental and epileptic encephalopathy (EIDEE) is among the most severe epilepsy syndromes, with onset before three months of age and an estimated incidence of approximately 10 per 100,000 live births. The 2022 International League Against Epilepsy classification unified the historically distinct Ohtahara syndrome and early myoclonic encephalopathy under a single diagnostic framework defined by frequent drug-resistant tonic and/or myoclonic seizures, an abnormal neurological examination, and an abnormal interictal electroencephalogram-most characteristically a burst-suppression pattern. This narrative review synthesizes the clinical, electrophysiological, neuroimaging, genetic, and therapeutic literature within the EIDEE framework. The clinical phenotype is characterized by central hypotonia, postnatal microcephaly, cortical visual impairment, and age-dependent syndromic evolution toward infantile epileptic spasms syndrome or Lennox-Gastaut syndrome in the majority of patients. Electroencephalography remains essential for syndromic classification, while systematic metabolic screening and early trio whole-exome or whole-genome sequencing are central to the etiologic workup, achieving diagnostic yields of 60-65%. The most commonly identified genetic causes include STXBP1, KCNQ2, and SCN2A variants. Outcomes are poor overall and strongly etiology-dependent: vitamin-responsive disorders carry a substantially more favorable prognosis, whereas mortality reaches 25% in genetic cohorts. Genotype-guided pharmacotherapy is now applicable to a clinically meaningful subset of patients, with sodium channel blockers, potassium channel openers, and emerging antisense oligonucleotide therapies representing important therapeutic advances. Gene therapy trials are underway but have encountered early safety signals, underscoring the vulnerability of this population. Critical unmet needs include earlier molecular diagnosis, precision therapies targeting developmental outcomes beyond seizure control, and prospective international registries to characterize the long-term natural history of EIDEE.

Humans↗

PubMed2025

The British Society for Antimicrobial Chemotherapy Resistance Surveillance Project: methods and limitations.

OBJECTIVES: The BSAC Bacteraemia and Respiratory Resistance Surveillance Programmes provided long-term surveillance of antibiotic resistance in key pathogens of bloodstream and both community- and hospital-acquired respiratory infections in the UK and Ireland. This paper details the methodologies used. Data limitations are discussed. METHODS: Sentinel laboratories across the UK and Ireland contributed up to a fixed annual quota of isolates of defined bacterial groups. For each Programme, a Central Laboratory confirmed bacterial identifications, measured MICs by the BSAC agar dilution method, investigated mechanisms of resistance and determined serotypes of Streptococcus pneumoniae. Identification methods evolved over time, e.g. with adoption of MALDI-TOF. Classification of susceptibility and resistance follows the 2022 (not contemporaneous) EUCAST guidance. RESULTS: Seventy-nine laboratories contributed 30 716 community respiratory isolates from 1999/2000 to 2018/19; 65 laboratories contributed 13 508 hospital respiratory isolates from 2008/09 to 2018/19; 81 laboratories contributed 56 064 bacteraemia isolates from 2001 to 2019. Although large and teaching hospitals were over-represented, the resistance rates for bacteraemia organisms collected in England mirror more extensive (but less standardized or detailed) national data gathered from laboratories by the UK Health Security Agency and its predecessor organizations, which provided a bespoke data extract. CONCLUSIONS: These surveillance Programmes have provided comprehensive and reliable information on antibiotic susceptibility in the UK and Ireland over two decades. Detailed results, showing resistance trends and mechanisms of antibiotic resistance, are presented in five papers in this Supplement.

Antimicrobial Stewardship↗

PubMed2026

Defining and managing high-risk acute myeloid leukemia (AML) in 2026.

Acute myeloid leukemia (AML) remains a highly heterogeneous malignancy in which outcomes are particularly poor for patients classified as having high-risk disease. Traditionally, high-risk AML has been defined by adverse baseline genetic features, including complex cytogenetics, TP53 alterations, and mutations associated with secondary or therapy-related disease. However, this static, genetics-centered definition is increasingly insufficient in the modern therapeutic era. Emerging evidence supports a more dynamic and context-dependent model in which risk is shaped not only by molecular architecture but also by treatment intensity, patient fitness, measurable residual disease (MRD), and evolving resistance mechanisms. Advances in genomic profiling have refined risk stratification frameworks, including ELN 2022 for intensively treated patients and the ELN 2024 classification for those receiving less-intensive therapies. In parallel, MRD has emerged as a powerful biomarker that reclassifies patients during treatment, identifying those with persistent, therapy-resistant disease despite morphologic remission. Biologically, high-risk AML is driven by the interplay of clonal evolution, epigenetic plasticity, leukemic stem cell persistence, and protective microenvironmental and immune interactions, all of which contribute to relapse. Therapeutically, the landscape has expanded to include targeted agents, venetoclax-based combinations, and transplantation strategies, yet outcomes remain limited in key high-risk subsets, particularly TP53-mutated disease and post-venetoclax relapse. Accordingly, current strategies emphasize rational combination therapies, MRD-guided treatment adaptation, and approaches targeting both leukemic cells and their supportive niches. In 2026, high-risk AML is best understood as a dynamic, treatment-context-dependent state. Improving outcomes will require integration of precision diagnostics, biologically informed therapy, and adaptive strategies designed to anticipate and overcome resistance.

Humans↗

PubMed2026

Stage-Independent Real-Time Subtype Classification and Comprehensive Biopsy Profiling of Urothelial Carcinomas by the Lund Taxonomy System.

Bladder cancer is a heterogeneous malignancy with diverse clinical outcomes, and conventional pathological assessment alone is insufficient to capture its underlying biology. Gene expression profiling can stratify tumors into molecular subtypes with prognostic and predictive potential, but the reliability of transcriptomic classification and its clinical utility remains to be established. The translational/observational UROSCANSEQ study (ISRCTN15459149) prospectively evaluates RNA-based Lund Taxonomy (LundTax) molecular subtype classification in a clinical setting. Among 784 consecutive biopsies collected between 2018 and 2022, RNA sequencing was successful for 90% of all biopsies, encompassing 662 bladder cancer patients with a stage distribution of 48% Ta, 27% T1, 24% ≥T2, and 1% CIS. We demonstrate that the LundTax subtype classification algorithm, applied to individual samples, accurately identifies cancer cell phenotypes with characteristic gene and protein expression patterns in a manner robust to RNA quality, data preprocessing strategies, and batch effects, supporting its clinical feasibility across both non-muscle-invasive and muscle-invasive disease. We further extend the LundTax framework by incorporating single-sample molecular risk scores reflecting tumor grade, proliferation, and progression risk, as well as tumor microenvironment signatures. Both risk scores and overall immune and stromal content in biopsies were significantly associated with an increased risk of clinical progression in noninvasive disease. In a separate analysis of the relative cellular composition of the tumor microenvironment, however, only the fraction of natural killer cells remained significant. Together, the expanded LundTax system provides a comprehensive molecular portrait of individual tumor biopsies. By explicitly separating cancer cell-intrinsic phenotypes, prognostic indexes, and microenvironmental signals, the framework minimizes biological confounding and establishes a strong foundation for future studies evaluating clinical outcomes and treatment responses.

Humans↗

PubMed2026

Responding to a protracted tuberculosis outbreak: lessons from multiple rounds of investigation in a Chinese boarding school.

PURPOSE: This study analysed a multi-semester pulmonary tuberculosis (PTB) cluster outbreak in a Chinese boarding school to provide evidence for future epidemic control. METHODS: Contacts were screened via symptoms, infection tests and chest radiography. Screening expanded progressively from close contacts to same-floor contacts, then all students and staff. Whole-genome sequencing (WGS) with single nucleotide polymorphism (SNP) and bioinformatics analysis was used for lineage classification, transmission clustering (≤12 SNPs defining a cluster) and drug resistance prediction. RESULTS: From 2020 to 2022, 20 students were diagnosed with PTB, half laboratory-confirmed. Most cases clustered in class 16 and were epidemiologically linked to the primary case (case 0), who had household PTB exposure. Case 0 and case 1 had diagnostic delays exceeding 3 and 6 months, respectively. WGS of five isolates (case 1, 3, 4, 9 and 10) collected over three semesters showed all belonged to lineage 2 and differed by ≤12 SNPs, confirming the same transmission chain. The infection rate in class 16 (46.34%) was significantly higher than other case classes (19.05%) and classes without cases (8.27%) (χ2 = 61.169, p < 0.001). No new cases were detected during a one-year follow-up of students involved in the outbreak after the final round of screening, nor among household contacts of all cases followed up to the present. CONCLUSIONS: Lack of entry health examinations facilitated the outbreak. Delayed diagnosis, incomplete contact screening and absence of preventive treatment led to cross-semester persistence. The infection rate disparity confirms class 16 as the outbreak epicentre. Improving community case management, extending contact follow-up and enhancing cluster outbreak measures are recommended to prevent future outbreaks.

Humans↗

PubMed2026

Survey of diagnostic laboratories highlights need for improved standards in somatic genomic testing and reporting.

There is a growing international need to support somatic genomic testing, standardised variant curation and improved patient access to molecular profiling for somatic conditions, including cancer. We conducted a survey of scope, curation, reporting and sharing practices of diagnostic laboratories performing somatic testing in Australia and New Zealand. Laboratories with accreditation (n = 41) were invited in 2023 to complete a semi-structured, 25-question interview. Responses were received for 27 laboratories (66% response rate) offering solid tumour, haematological malignancy and non-cancer services. Only 36% of laboratories offered tests capturing the full breadth of variants, from single-nucleotide variants to gene fusions. Knowledge sharing was rare, with only one laboratory submitting variant classifications to a public knowledge base. Most laboratories (96%) conducted somatic testing in oncology. Of cancer laboratories, 35% offered testing considered capable of comprehensive genomic profiling (CGP). Almost half of cancer laboratories had already adopted the 2022 ClinGen/CGC/VICC oncogenicity guidelines, and 84% were using AMP/ASCO/CAP 2017 clinical significance guidelines. Only 47% of mixed discipline cancer laboratories reported biomarkers such as tumour mutational burden, with wide variation in reporting of matched therapy options. Our study has generated a unique overview of somatic laboratory practices in the region, and areas for global standardisation in somatic molecular testing and reporting. We also provide a model for practice and guideline uptake assessment, for application by other country-wide networks. This is particularly relevant in anticipation of CGP mainstreaming, with the increasing complexity of sequencing interpretation for laboratories and clinicians.

Humans↗

PubMed2026

sWGS Identifies a Copy-Number-High Subset of TP53-mutated Multiple-Classifier Endometrial Carcinomas With Adverse Clinicopathological Features.

TP53-mutated "multiple-classifier" endometrial carcinomas represent a diagnostically challenging subgroup within current molecular classification algorithms. Although these tumors are assigned to POLE-mutated or mismatch repair-deficient categories according to current ESGO/FIGO-based algorithms, their biological heterogeneity remains incompletely characterized. Herein, we retrospectively analyzed TP53-mutated multiple-classifier endometrial carcinomas identified through routine molecular profiling at our institution between 2022 and 2025 using an integrated histopathological, immunohistochemical, targeted sequencing, and shallow whole-genome sequencing approach. Copy-number alteration-high (CNA-high) status was defined as ≥5 large-scale genomic alterations, corresponding to copy-number gains or losses ≥3 Mb within a single chromosomal arm excluding whole-arm alterations. Among 33 analyzable TP53-mutated multiple-classifier endometrial carcinomas, sWGS identified 12 CNA-high tumors (36.4%) and 21 CNA-low tumors (63.6%). CNA-high tumors were more frequently non-endometrioid, high-grade, and advanced-stage according to FIGO 2023. They showed higher TP53 variant allele frequencies (VAF) and higher TP53 VAF-to-tumor-cellularity ratios. After a median follow-up of 12.8 months, recurrences (6/33; 18.2%) and disease-related deaths (3/33; 9.1%) were observed in the CNA-high subgroup, whereas no recurrence or disease-related death was observed among CNA-low patients. These findings indicate that TP53-mutated multiple-classifier endometrial carcinomas comprise biologically distinct subsets that are not fully captured by current 4-tier TCGA-based molecular classification and ESGO-based risk stratification. In this cohort, sWGS identified a CNA-high group with adverse clinicopathological features and clinical events suggesting a potentially more aggressive clinical course. Integration of genome-wide copy-number profiling may therefore refine the biological interpretation of TP53 alterations in multiple-classifier endometrial carcinomas and warrants validation in larger multicenter cohorts.

TP53↗

PubMed2026

Pandemic-Related Disruptions and Hepatocellular Carcinoma Surveillance in Safety-Net Settings.

IMPORTANCE: Pandemic-related disruptions in cirrhosis care resulted in major gaps and delays in surveillance for hepatocellular carcinoma (HCC). Whether these initial declines improved and rebounded to prepandemic levels remains unclear. OBJECTIVE: To evaluate contemporary clinical practice data on HCC surveillance utilization from before the COVID-19 pandemic to 4 years after the onset of the pandemic among safety-net populations with cirrhosis. DESIGN, SETTING, AND PARTICIPANTS: This retrospective cohort study was conducted at 5 safety-net health systems in the US. Adults with cirrhosis were evaluated longitudinally across 3 time periods: March 1, 2018, to February 29, 2020 (pre-COVID-19 period), March 1, 2020, to February 28, 2022 (COVID-19 era), and March 1, 2022, to February 29, 2024 (post-COVID-19 period). MAIN OUTCOMES AND MEASURES: The primary outcome was undergoing HCC surveillance identified using Current Procedural Terminology codes for ultrasonography, computed tomography, and magnetic resonance imaging, and corresponding International Statistical Classification of Diseases, Tenth Revision, Clinical Modification diagnosis codes for indication. Comparisons of HCC surveillance across time periods used paired t tests, and comparisons of HCC surveillance between subgroups within the same time period used χ2 tests. RESULTS: Among 6940 patients with cirrhosis, 4001 (57.7%) were men (median [IQR] age, 58 [52-64] years), 206 (3.0%) were Asian, 1720 (24.8%) were Hispanic, 1672 (24.1%) were non-Hispanic Black or African American, and 3081 (44.4%) were non-Hispanic White. The proportion who underwent HCC surveillance within 6 months after diagnosis was 30.8% (1940 patients) in the pre-COVID-19 era, which declined to 21.1% (1468 patients) in the COVID-19 era, and remained at 22.3% (1405 patients) in the post-COVID-19 era. Consistent trends were observed among men and women and among all age and race groups, except for Asian individuals, for whom there was an observed increase in the post-COVID-19 era. Similar trends of low HCC surveillance post-COVID-19 were observed across insurance types but was particularly concerning among uninsured or indigent care covered patients, among whom only 116 of 997 (11.9%) underwent surveillance in the most recent period. CONCLUSIONS AND RELEVANCE: In this observational study of US safety-net populations with cirrhosis, rates of HCC surveillance following pandemic-related declines remained persistently low even up to 4 years after the onset of the COVID-19 pandemic, with fewer than 1 in 4 patients having undergone guideline-concordant HCC surveillance.

Humans↗

PubMed2026

A systematic approach to standardizing the visual appearance of endometriotic lesions for artificial intelligence recognition.

INTRODUCTION: Numerous studies have shown that the diagnostic performance and reproducibility of visual recognition of endometriosis during laparoscopy are poor. The use of artificial intelligence (AI) seems relevant for exhaustive lesion recognition. Standardization of the visual classification of lesions, in the form of an ontology, is an essential prerequisite to enable medical experts to annotate surgical data consistently and subsequently allow engineers to train and build an artificial intelligence tool for endometriosis recognition. MATERIAL AND METHODS: A systematic search was conducted in the MEDLINE (via PubMed), EMBASE, and the Cochrane Library databases up to May 2022, aiming to identify studies describing the laparoscopic visual appearance of superficial endometriosis, endometriomas, and deep infiltrating endometriosis. The accumulated data in the literature concerning the visual appearance of the different forms of endometriosis were used to create an ontology that could be used for artificial intelligence applications. RESULTS: Out of 932 articles screened, 35 studies were selected based on the inclusion criteria of human subjects with histologically confirmed endometriosis lesions visualized via laparoscopy. The selected studies were reviewed to develop a visual ontology of endometriosis lesions observed via laparoscopy. The lesions were categorized into 4 classes and further subdivided into 11 subclasses: superficial (black, red, white, or subtle), adhesions (dense or filmy), deep (obliteration, retraction, or deformation), and ovarian (endometrioma or chocolate fluid). The positive predictive value (PPV) varied across lesion types: black lesions (PPV 47%-97%), red lesions (PPV 33%-100%), white lesions (PPV 20%-81%), and ovarian endometriosis (PPV 42%-98%). Nonspecific lesions such as adhesions (PPV 16%-50%) and subtle superficial lesions (PPV 0%-67%) presented lower PPVs. Deep endometriosis lesions, often buried within organs, required indirect signs (obliteration, retraction, deformation) for identification. CONCLUSIONS: The visual ontology proposed in this systematic search could facilitate the detection and classification of endometriosis lesions using artificial intelligence. This study highlights the challenges of reaching a consensus on lesion recognition and classification in AI projects due to the diverse visual presentations of endometriosis.

Humans↗

PubMed2024

A corpus of GA4GH phenopackets: Case-level phenotyping for genomic diagnostics and discovery.

The Global Alliance for Genomics and Health (GA4GH) Phenopacket Schema was released in 2022 and approved by ISO as a standard for sharing clinical and genomic information about an individual, including phenotypic descriptions, numerical measurements, genetic information, diagnoses, and treatments. A phenopacket can be used as an input file for software that supports phenotype-driven genomic diagnostics and for algorithms that facilitate patient classification and stratification for identifying new diseases and treatments. There has been a great need for a collection of phenopackets to test software pipelines and algorithms. Here, we present Phenopacket Store. Phenopacket Store v.0.1.19 includes 6,668 phenopackets representing 475 Mendelian and chromosomal diseases associated with 423 genes and 3,834 unique pathogenic alleles curated from 959 different publications. This represents the first large-scale collection of case-level, standardized phenotypic information derived from case reports in the literature with detailed descriptions of the clinical data and will be useful for many purposes, including the development and testing of software for prioritizing genes and diseases in diagnostic genomics, machine learning analysis of clinical phenotype data, patient stratification, and genotype-phenotype correlations. This corpus also provides best-practice examples for curating literature-derived data using the GA4GH Phenopacket Schema.

Humans↗

PubMed2025

Whole genome sequencing and phylogenetic classification accelerate the implementation of respiratory syncytial virus genomic surveillance in Canada: a pilot study.

UNLABELLED: Whole genome sequencing (WGS) has emerged as a powerful tool to facilitate the study of existing and emerging infectious diseases. WGS-based genomic surveillance provides information on the genetic diversity and tracks the evolution of important viral pathogens, including respiratory syncytial virus (RSV). Multiplex tiling polymerase chain reaction (PCR) assays have been used to facilitate sequencing of a variety of pathogens in support of genomics-based surveillance initiatives. We developed, optimized, and implemented multiplex tiling PCR assays for RSVA and RSVB capable of generating near-complete genomes in the majority of contemporaneous specimens tested. A pilot data set comprising 52 RSVA and 37 RSVB genomes derived from Canadian clinical specimens during the 2022-2023 respiratory virus season was used to perform phylogenetic analyses using both near-complete genome and glycoprotein (G) sequences. Overall, the RSV phylogenetic tree built with whole genomes showed identical lineage clusters as compared to the G gene but was more discriminatory. Moreover, the availability of complete genomes enables the identification of a broader range of mutations. For instance, mutations identified in the fusion protein among Canadian isolates tested here, including S377N, K272M, S276N, S211N, S206I, and S209Q, could affect the efficacy of current vaccines or antiviral-based therapeutics. In conclusion, our work reinforces other recent studies demonstrating the utility of multiplex tiling PCR assays to facilitate high-throughput WGS of RSV, which is capable of supporting enhanced genomic surveillance initiatives, as well as the more comprehensive genomic analyses required to inform public health strategies for the development and usage of vaccines and antiviral drugs. IMPORTANCE: We present assays to efficiently sequence genomes of RSVA and RSVB. This enables researchers and public health agencies to acquire high-quality genomic data using rapid and cost-effective approaches. Genomic data-based comparative analysis can be used to conduct surveillance and monitor circulating isolates for efficacy of vaccines and antiviral therapeutics.

Humans↗

PubMed2024

Genome-Wide Association Study of Accessory Atrioventricular Pathways.

IMPORTANCE: Understanding of the genetics of accessory atrioventricular pathways (APs) and affiliated arrhythmias is limited. OBJECTIVE: To investigate the genetics of APs and affiliated arrhythmias. DESIGN, SETTING, AND PARTICIPANTS: This was a genome-wide association study (GWAS) of APs, defined by International Classification of Diseases (ICD) codes and/or confirmed by electrophysiology (EP) study. Genome-wide significant AP variants were tested for association with AP-affiliated arrhythmias: paroxysmal supraventricular tachycardia (PSVT), atrial fibrillation (AF), ventricular tachycardia, and cardiac arrest. AP variants were also tested in data on other heart diseases and measures of cardiac physiology. Individuals with APs and control individuals from Iceland (deCODE Genetics), Denmark (Copenhagen Hospital Biobank, Danish Blood Donor Study, and SupraGen/the Danish General Suburban Population Study [GESUS]), the US (Intermountain Healthcare), and the United Kingdom (UK Biobank) were included. Time of phenotype data collection ranged from January 1983 to December 2022. Data were analyzed from August 2022 to January 2024. EXPOSURES: Sequence variants. MAIN OUTCOMES AND MEASURES: Genome-wide significant association of sequence variants with APs. RESULTS: The GWAS included 2310 individuals with APs (median [IQR] age, 43 [28-57] years; 1252 [54.2%] male and 1058 [45.8%] female) and 1 206 977 control individuals (median [IQR] year of birth, 1955 [1945-1970]; 632 888 [52.4%] female and 574 089 [47.6%] male). Of the individuals with APs, 909 had been confirmed in EP study. Three common missense variants were associated with APs, in the genes CCDC141 (p.Arg935Trp: adjusted odds ratio [aOR], 1.37; 95% CI, 1.24-1.52, and p.Ala141Val: aOR, 1.55; 95% CI 1.34-1.80) and SCN10A (p.Ala1073Val: OR, 1.22; 95% CI, 1.15-1.30). The 3 variants associated with PSVT and the SCN10A variant associated with AF, supporting an effect on AP-affiliated arrhythmias. All 3 AP risk alleles were associated with higher heart rate and shorter PR interval, and have reported associations with chronotropic response. CONCLUSIONS AND RELEVANCE: Associations were found between sequence variants and APs that were also associated with risk of PSVT, and thus likely atrioventricular reentrant tachycardia, but had allele-specific associations with AF and conduction disorders. Genetic variation in the modulation of heart rate, chronotropic response, and atrial or atrioventricular node conduction velocity may play a role in the risk of AP-affiliated arrhythmias. Further research into CCDC141 could provide insights for antiarrhythmic therapeutic targeting in the presence of an AP.

Humans↗

PubMed2026

The Impact of Molecular Characteristics on the Efficacy of Frontline Immune Checkpoint Inhibitor Therapy in Patients with Metastatic Melanoma.

Background: Metastatic melanoma in East Asian populations is enriched for acral and mucosal subtypes and harbors a distinct molecular landscape compared with Western cutaneous melanoma. However, data on the efficacy of first-line immune checkpoint inhibitor (ICI) therapy and on the impact of molecular characteristics on treatment effect in this population remain limited. We aimed to characterize the genomic landscape of an East Asian metastatic melanoma cohort and to evaluate the predictive values of molecular markers for first-line ICI therapy. Methods: This study included 135 patients with metastatic melanoma who received first-line ICI at Samsung Medical Center between January 2022 and December 2025. Of these, 108 with paired next-generation sequencing (NGS) data were included in the molecular analysis. Survival outcomes were estimated by the Kaplan-Meier method, and the prognostic value of molecular subtype was assessed using univariable and multivariable Cox proportional hazards models. Results: Mucosal melanoma was the most common primary site (58, 43.0%), followed by acral melanoma (31, 23.0%) and cutaneous melanoma (25, 18.5%); 4 (3.0%) had uveal melanoma and 17 (12.6%) had melanoma of other or unknown primary origin. The overall objective response rate to first-line ICI was 37.8% (51 of 135), and median progression-free survival (PFS) was 6.2 months (95% confidence interval [CI] 4.0-9.6). Using the hierarchical classification, 108 patients were classified into five molecular subtypes: BRAF-altered (n = 17, 15.7%), RAS-altered (n = 17, 15.7%), KIT-altered (n = 15, 13.9%), and NF1-altered (n = 7, 6.5%), and quadruple-wild-type (n = 52, 48.1%). TMB-high status (10.2%) showed no significant association with outcomes. Molecular subtype was significantly associated with PFS (log-rank p = 0.009). After multivariable adjustment, BRAF fusion (hazard ratio [HR] 5.05, 95% CI 1.70-14.98, p = 0.003) and KIT-altered status (HR 2.91, 95% CI 1.46-5.77, p = 0.002) emerged as independent adverse prognostic factors, whereas BRAF V600 single-nucleotide variants did not differ significantly from quadruple-wild-type. Conclusions: In this East Asian metastatic melanoma cohort, BRAF fusion and KIT alterations were independent adverse prognostic factors for first-line ICI. These findings suggest that BRAF fusion and KIT-altered tumors may represent distinct subgroups that warrant further investigation.

immune checkpoint inhibitor↗