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At least 19 recordsLinked to original sources
PubMed2026

Not Forgotten: Patient Experiences with Genetic Variant Reclassifications.

PURPOSE: Genetic variant reclassification is increasingly common in clinical genomics, yet limited data describe how patients experience re-contact and variant reclassification in routine clinical care. METHODS: We conducted semi-structured qualitative interviews with 20 adult patients who received a variant reclassification following routine clinical genetic testing. Interviews explored emotional responses, communication experiences, and perceived value of genetic testing. Data were analyzed using Template Analysis, a form of thematic analysis. RESULTS: Three overarching themes were identified. Participants identified a need for improved communication of reclassified results, particularly with respect to timing, modality, and contextualization (Theme 1). Experiences with reclassification also shaped perceptions of the value of genetic testing, with most participants viewing testing as worthwhile despite its evolving nature (Theme 2). Finally, many participants interpreted reclassification as evidence of personalized and ongoing care, reinforcing trust in genetic testing and biomedical research (Theme 3). Participants generally preferred to be informed of reclassified results regardless of reclassification type, although the direction of reclassification influenced emotional responses and preferred modes of communication. Downgrades from variants of uncertain significance to benign or likely benign were widely viewed as meaningful by participants. CONCLUSION: Variant reclassification was experienced as a signal of personalized, ongoing care. Timely, contextualized, patient-centered re-contact practices may reduce uncertainty, strengthen trust, and help patients not feel forgotten.

Journal Article↗
PubMed2025

Impact of laboratory-driven proactive reanalysis: Reclassification to positive in 5% of initially negative or uncertain exome sequencing cases.

PURPOSE: Reanalysis of exome sequencing (ES) data increases diagnostic utility; however, there is no consensus on when and under what circumstances reanalysis should occur. Requesting and performing ES reanalysis burdens both clinical and laboratory workflows. Maximizing the potential for reclassification is essential. Here, we describe the impact of a laboratory-driven proactive reanalysis process that triggers reanalysis when new evidence is identified. METHODS: We reviewed reanalysis outcomes of an ES cohort. Reanalysis events were categorized based on initiating factors (laboratory-driven proactive, family studies, and clinician-initiated). Laboratory-driven proactive reclassifications are prompted by systematic review of new scientific data. Outcomes were evaluated by initiating factors, reclassification types, evidence used, and time since original report. RESULTS: Overall, 23% of cases underwent at least 1 reanalysis, with 35% of reanalyses resulting in reclassification. There was a 4% increase in diagnostic yield, including 5% of initially unsolved ES receiving diagnostic reports. Diagnostic reclassifications rates were significantly higher for laboratory-driven proactive reanalyses (54%; P < .0001) than family studies (18%) and clinician-initiated reanalyses (4%). New gene-disease relationships were the most efficacious evidence source. Laboratory-driven proactive reclassifications occurred steadily over time. CONCLUSION: Laboratory-driven proactive reanalysis effectively provides more diagnostic reclassifications compared with clinician-initiated reanalysis. Laboratories should curate and integrate emerging evidence into ES reanalysis.

Humans↗
PubMed2025

Imprecision medicine: Systematic gaps in reporting variants of uncertain significance (VUS) and their reclassifications.

PURPOSE: Variants of uncertain significance (VUS) are frequently encountered during clinical genetic testing. To explore the clinical burden of VUS, we developed the Brotman Baty Institute Clinical Variant Database, which is an electronic health record (EHR)-linked database of clinical germline genetic variant information from patients with rare genetic disorders seen at 2 tertiary academic medical centers. METHODS: We retrospectively reviewed EHRs and genetic testing reports from 5158 patients seen across diverse adult genetics practices at these institutions from 2015 to 2024. We also compared these EHR-based variant classifications with those in ClinVar. RESULTS: The number of reported VUS relative to pathogenic or likely pathogenic variants can vary by over 14-fold depending on the primary indication for genetic testing and 3-fold depending on self-reported race. Furthermore, at least 1.6% of variant classifications used in the EHR for clinical care are outdated based on ClinVar variant classifications, including 26 instances in which the testing lab updated ClinVar, but the reclassification was never communicated to the patient. CONCLUSION: Our findings reveal that the clinical burden of VUS in adult medical genetics is unequally distributed across patients. We also highlight a deficiency in existing systems for communicating variant reclassifications to ClinVar, patients, and providers.

Humans↗
PubMed1977

Reclassification in a small decentralized medical library.

This study describes procedures and indentifies problems in the reclassification of a small medical school library collection that is decentralized into five locations in three different communities. A total of 9,915 monographic titles (14,911 volumes) were reclassified in a nine-month period. The reclassification staff consisted of one professional, two nonprofessionals, and one partime student assistant.

Book Classification↗
PubMed2026

Pseudaquabacterium prasiolae sp. nov., Isolated from the Freshwater Green Alga Prasiola japonica, and Rubrivivax soli sp. nov., Isolated from Soil, with Reclassification of Aquabacterium humicola as Pseudaquabacterium humicola comb. nov.

Two Gram-stain-negative, catalase- and oxidase-positive, strictly aerobic, non-flagellated rod-shaped bacteria, designated OR-4T and RP6-9T, were isolated from the freshwater green alga Prasiola japonica and soil in Republic of Korea, respectively. Strain OR-4T exhibited gliding motility, whereas strain RP6-9T lacked gliding motility. Strain OR-4T grew at 10-30&#xa0;&#xb0;C, pH 6.0-9.0, and 0-1.5% (w/v) NaCl, while strain RP6-9T grew at 20-35&#xa0;&#xb0;C, pH 6.0-9.0, and 0-1.0% (w/v) NaCl. Both strains contained ubiquinone-8 as the sole respiratory quinone and phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol as major polar lipids; strain OR-4T additionally possessed an unidentified phospholipid and an unidentified polar lipid. The predominant fatty acids of OR-4T were C12:0, C16:0, summed feature 3 (C16:1&#x3c9;6c and/or C16:1&#x3c9;7c), and summed feature 8 (C18:1&#x3c9;7c and/or C18:1&#x3c9;6c), whereas RP6-9T contained C12:0, C16:0, and summed feature 3 as major components. The genomic DNA G&#x2009;+&#x2009;C content of both strains was 71.0&#xa0;mol%. Whole-genome-based phylogenomic analyses placed OR-4T and RP6-9T within the genera Pseudaquabacterium and Rubrivivax, respectively, forming distinct lineages. Comparative analyses of average nucleotide identity, digital DNA-DNA hybridization, and average amino acid identity further supported their assignment to these genera while confirming their separation from previously described species. Based on combined phenotypic, chemotaxonomic, and genomic evidence, strains OR-4T and RP6-9T represent novel species, for which the names Pseudaquabacterium prasiolae sp. nov. (type strain OR-4T =KACC 22752T =NBRC 116024T) and Rubrivivax soli sp. nov. (type strain RP6-9T =KACC 24055T =DSM 119932T) are proposed. Phylogenomic analyses also support the reclassification of Aquabacterium humicola as Pseudaquabacterium humicola comb. nov. (type strain RJY3T =KCTC 92105T =NBRC 115831T).

Phylogeny↗
PubMed2026

Whole genome-based reclassification of the genus Metabacillus: Proposal for five novel genera, Chryseobacillus gen. nov., Cohnibacillus gen. nov., Salimetabacillus gen. nov., Pantoeobacillus gen. nov., and Lutimetabacillus gen. nov. and the description of one novel bacterial species, Chryseobacillus diguaensis sp. nov. isolated from soil in the Digua reservoir.

Comprehensive phylogenomic and comparative genomic analyses were conducted to clarify the taxonomic boundaries of the genus Metabacillus. Phylogenetic trees reconstructed from a set of single-copy orthologous proteins (SCOPs) revealed that the genus, as currently defined, is polyphyletic. The type species of the genus Metabacillus and its closest relatives formed a consistent clade, herein designated as Metabacillus sensu stricto. The remaining species were grouped into three well-supported clades: Kandeliae, Indicus, and Mangrovi, and two single-taxon lineages: M. arenae and M. lacus. The phylogenomic delineation found in these divergent taxa was corroborated by either inconsistent distribution patterns or the absence of previously defined conserved signature indels (CSIs) specific to Metabacillus. Genomic metrics, including Average Nucleotide Identity (ANI), Average Amino acid Identity (AAI), and digital DNA-DNA hybridization (dDDH) further supported the taxonomic delineation proposed here. The observed genomic divergence was mirrored by phenotypic differences, including variations in GC content ranges. Based on this polyphasic evidence, we propose the reclassification of the genus Metabacillus taxa into five novel genera: Chryseobacillus gen. nov. (encompassing the Kandeliae clade), Cohnibacillus gen. nov. (M. lacus), Salimetabacillus gen. nov. (M. arenae), Pantoeobacillus gen. nov. (Indicus clade), and Lutimetabacillus gen. nov. (Mangrovi clade). The core lineage is retained as Metabacillus sensu stricto, for which an emended description of the genus Metabacillus is also provided. A novel bacterial strain, designated as MAU-250T, was isolated from a soil sample collected on the shore of an artificial reservoir in the Andean foothills of the Maule Region in central Chile. Public metagenome screening supported a low-abundance taxon with broad ecological adaptability, preferentially associated with soil habitats. A polyphasic analysis based on phenotypic traits and genomic distances (78.0% ANIb and 19.8% dDDH against its closest relative) also supported its designation as a novel species, for which the name Chryseobacillus diguaensis sp. nov. is proposed. The type strain is MAU-250T (=RGM 3146T&#xa0;=&#xa0;IMI 507634T).

Phylogeny↗
PubMed2026

Phylogenomics of Desulfuromonadia supports reclassification of Geobacter psychrophilus as Irobacter psychrophilus comb. nov. and proposal of Geosyntrophus gen. nov.

Genome-resolved phylogenomics reveals widespread misclassification of metal-reducing bacteria historically assigned to Geobacter based on 16S rRNA gene phylogeny, and highlights species that persist only as 16S rRNA entries without genomes for robust taxonomic resolution. Here, we resolve two such lineages by integrating whole-genome phylogeny with average amino acid identity (AAI) and percentage of conserved proteins (POCP) across 418 dereplicated genomes of Desulfuromonadia. We report a draft genome of the psychrophilic iron-reducing bacterium Geobacter psychrophilus (100% completeness). Phylogenomic analyses place both Geobacter psychrophilus and the GTDB placeholder genus g__JACRCG01 within the family 'Pseudopelobacteraceae', outside Geobacteraceae sensu stricto. Within this framework, G. psychrophilus forms a distinct, well-supported lineage separated from neighbouring genera by discontinuities in AAI and POCP, supporting its reclassification as Irobacter psychrophilus comb. nov. Additionally, we show that Geosyntrophus acetoxidans, a non-axenic syntrophic bacterium, forms a coherent genus with 51 other environmental genomes (placeholder genus g__JACRCG01), for which we propose the replacement name Geosyntrophus gen. nov. Comparative genome analysis revealed conserved family-level metabolic traits together with genus-specific differences in respiratory metabolism, while ANI-based clustering identified substantial species-level diversity within both proposed genera. Metagenome and 16S rRNA-gene survey data further show that Geosyntrophus and Irobacter occur in broadly similar aquatic and subsurface habitats spanning from the Arctic to the Antarctic. Together, these results resolve the taxonomy of two previously ambiguous Desulfuromonadales lineages and shed light on their environmental distribution.

AAI↗
PubMed2026

Phenotypic manifestations and variant reclassification of germline PTEN variants: a nationwide Danish study.

BACKGROUND: Classification of heterozygous germline PTEN variants in patients with, or suspected of having, PTEN hamartoma tumour syndrome (PHTS) remains challenging. Accurate classification is essential as these patients require lifelong cancer surveillance. METHODS: We identified all patients with a PTEN variant previously classified as a variant of uncertain significance (VUS), likely pathogenic (LP) or pathogenic (P), collected clinical data and reclassified all variants using the latest PTEN gene-specific American College of Medical Genetics (ACMG) guidelines. Moreover, genotype-phenotype correlations were assessed. RESULTS: 167 patients from 112 families were enrolled. Eighty-seven unique PTEN variants were identified, including 20 novel variants. After applying the PTEN gene-specific ACMG guidelines, 32 variants (36.8%) were reclassified, resulting in 60 PTEN variants classified as LP/P (69.0%), 18 variants classified as VUS (20.7%), while 9 variants were classified as LB/B (10.3%). Genotype-phenotype correlation was performed among 104 patients with LP/P variants: 51 cancer cases were recorded in 41 patients and a distinct PHTS phenotype was observed in 25% of patients, with macrocephaly being present in 99% of patients with a known head circumference. Twenty-three patients had neurodevelopmental delay and/or autism, and we observed an increased prevalence of missense variants in these patients. CONCLUSION: We identified 87 different PTEN variants, and application of PTEN gene-specific ACMG guidelines led to reclassification of 32 variants (36.8%), underscoring the importance of regular variant reassessment using the most recent gene-specific guidelines, ensuring optimal patient management and surveillance.

Genetic Predisposition to Disease↗
PubMed2025

Distinct rates of VUS reclassification are observed when subclassifying VUS by evidence level.

PURPOSE: Genetic testing commonly yields a plethora of variants of uncertain significance (VUS) that can lead to ongoing uncertainty for patients and their caregivers. Although all VUS hold uncertainty, some VUS have more evidence in support of pathogenicity, whereas others have more evidence of a benign role. Sharing these nuances can help guide the investment in follow-up clinical and research investigations and may, at times, influence medical decision making despite appreciated uncertainty. METHODS: Four clinical laboratories have been subclassifying VUS to help prioritize investigation and guide reporting decisions. Each laboratory developed a distinct approach for how these subclasses are used in their laboratories and, in some cases, displayed on reports. We examined the composition of each laboratory's VUS subclasses and the likelihood variants from each subclass were reclassified toward pathogenic or benign. RESULTS: We found that variants in the lowest subclass of VUS were never reclassified as likely pathogenic or pathogenic, whereas those in the highest subclass were much more likely to be reclassified as pathogenic or likely pathogenic. CONCLUSION: Given that forthcoming professional guidance in variant classification will advise the use of VUS subclasses, the experience of our laboratories in using VUS subclasses can inform future practices.

Humans↗
PubMed1992

Alpha-mediated vasoconstriction: transmembrane signalling and receptor reclassification.

Apparent differences in the usage of different calcium pools for the processes of excitation-contraction provides support for further sub-classification of the alpha-adrenoceptors in blood vessels. Presently we have addressed this question by assessing the routes of calcium utilization and the involvement of G-proteins in mediating vasoconstriction in situ.

Adrenergic alpha-Agonists↗
PubMed2026

Corrigendum to "Whole genome-based reclassification of the genus Metabacillus: Proposal for five novel genera, Chryseobacillus gen. nov., Cohnibacillus gen. nov., Salimetabacillus gen. nov., Pantoeobacillus gen. nov., and Lutimetabacillus gen. nov. and the description of one novel bacterial species, Chryseobacillus diguaensis sp. nov. isolated from soil in the Digua reservoir" [Systemat. Appl. Microbiol. 49 (2026) 126734].

Explore the source record for details and available documents.

Published Erratum↗
PubMed1979

A retrospective histological study of 669 cases of primary cutaneous malignant melanoma in clinical stage I. The consequences of a reclassification of the original group of lentigo maligna melanomas.

A selected series of primary malignant melanoma of the skin, clinical stage I, was originally classified according to Clark's system. The consistency of this classification was tested by two Brisbane pathologists who indicated that we had misinterpreted some cases of superficial spreading malignant melanoma as lentigo maligna melanoma. We have therefore reclassified the original group of 86 lentigo maligna melanomas. This resulted in a total series of 37 (5.5%) lentigo maligna melanomas, 301 (45%) superficial spreading malignant melanomas, 194 (29%) nodular malignant melanomas (unchanged) and 137 (20.5%) unclassifiable malignant melanomas. The diagnosis of lentigo maligna melanoma was not made unless the epidermis was atrophic and dermal solar elastosis was present. The new group of lentigo maligna melanomas is dominated by cases on the head among patients over 50 years of age (especially women). This is in better agreement with other studies than our previous findings. The relationship with tumour cell type, pigmentation, mitotic count, atypia, transsectional profile, level of invasion, ulceration, vascular invasion, lymphocyte infiltration and prognosis shown by the new groups of lentigo maligna melanoma and superficial spreading malignant melanoma indicates that the cases by which the diagnosis has been changed are relatively benign. Our previous conclusions are still valid. The lentigo maligna melanoma is still the most benign type and nodular malignant melanoma still the most malignant type of melanoma. The superficial spreading malignant melanoma still represents an intermediate tumour type, although it has deviated in the benign direction.

Adult↗
PubMed1992

Histological reclassification of 101 intraoral salivary gland tumours (new WHO classification).

The epithelial salivary gland tumours have for many years been categorised according to the 1972 World Health Organisation (WHO) classification. In 1990 a proposed revision of this classification was elaborated. In this study 101 intraoral salivary gland tumours were reclassified accordingly. In 29 of the cases the original histological diagnosis was changed, which in most cases, occurred in the benign or malignant tumour groups. In seven cases the diagnosis was changed from benign to malignant or vice versa. The results of this study show that the histological classification of intraoral salivary gland tumours remains difficult, even when applying the new WHO classification.

Adolescent↗