Search

As an internationally accepted diagnostic system, the Paris classification has achieved a global breakthrough in the standardization of diagnoses in urine cytology. Based on experience over the past few years since its first publication, the new edition of the Paris classification refines the diagnostic criteria and discusses diagnostic pitfalls. While the detection of high-grade urothelial carcinoma remains the main focus, other aspects of urine cytology, including cytology of the upper urinary tract and the associated challenges, have also been addressed. Low-grade urothelial neoplasia is no longer listed as a separate category but is now included in the category "negative for high-grade urothelial carcinoma" (NGHUC). Essentially, the Paris classification provides an important basis for estimating the risk of malignancy and further clinical management., (© 2024. The Author(s).)

An increasing number of individuals with intellectual developmental disorder (IDD) and heterozygous variants in BCL11A are identified, yet our knowledge of manifestations and mutational spectrum is lacking. To address this, we performed detailed analysis of 42 individuals with BCL11A-related IDD (BCL11A-IDD, a.k.a. Dias-Logan syndrome) ascertained through an international collaborative network, and reviewed 35 additional previously reported patients. Analysis of 77 affected individuals identified 60 unique disease-causing variants (30 frameshift, 7 missense, 6 splice-site, 17 stop-gain) and 8 unique BCL11A microdeletions. We define the most prevalent features of BCL11A-IDD: IDD, postnatal-onset microcephaly, hypotonia, behavioral abnormalities, autism spectrum disorder, and persistence of fetal hemoglobin (HbF), and identify autonomic dysregulation as new feature. BCL11A-IDD is distinguished from 2p16 microdeletion syndrome, which has a higher incidence of congenital anomalies. Our results underscore BCL11A as an important transcription factor in human hindbrain development, identifying a previously underrecognized phenotype of a small brainstem with a reduced pons/medulla ratio. Genotype-phenotype correlation revealed an isoform-dependent trend in severity of truncating variants: those affecting all isoforms are associated with higher frequency of hypotonia, and those affecting the long (BCL11A-L) and extra-long (-XL) isoforms, sparing the short (-S), are associated with higher frequency of postnatal microcephaly. With the largest international cohort to date, this study highlights persistence of fetal hemoglobin as a consistent biomarker and hindbrain abnormalities as a common feature. It contributes significantly to our understanding of BCL11A-IDD through an extensive unbiased multi-center assessment, providing valuable insights for diagnosis, management and counselling, and into BCL11A's role in brain development., (© 2024. The Author(s).)

A patient with gastrointestinal stroma tumor (GIST) and KIT p.V559D and BRAF p.G469A alterations was referred to our institutional molecular tumor board (MTB) to discuss therapeutic implications. The patient had been diagnosed with B-cell chronic lymphocytic leukemia (CLL) years prior to the MTB presentation. GIST had been diagnosed 1 month earlier. After structured clinical annotation of the molecular alterations and interdisciplinary discussion, we considered BRAF/KIT co-mutation unlikely in a treatment-naïve GIST. Discordant variant allele frequencies furthermore suggested a second malignancy. NGS of a CLL sample revealed the identical class 2 BRAF alteration, thus supporting admixture of CLL cells in the paragastric mass, leading to the detection of 2 alterations. Following the MTB recommendation, the patient received imatinib and had a radiographic response. Structured annotation and interdisciplinary discussion in specialized tumor boards facilitate the clinical management of complex molecular findings. Coexisting malignancies and clonal hematopoiesis warrant consideration in case of complex and uncommon molecular findings., (© The Author(s) 2024. Published by Oxford University Press.)

GORAB is a key regulator of Golgi vesicle transport and protein glycanation. Loss of GORAB function in gerodermia osteodysplastica (GO) causes shortening of glycosaminoglycan chains, leading to extracellular matrix disorganization that results in wrinkled skin, osteoporosis and elevated TGF-β signaling. In this study, we investigated the role of TGF-β-signaling, oxidative stress, and resulting cellular senescence in the osteoporosis phenotype of GO. Treatment of Gorab Prx1 conditional knockouts with the TGF-β neutralizing antibody 1D11 rescued the trabecular bone loss, indicating that TGF-β overactivation causes osteoporosis in GO. Using an inducible knockout system, we demonstrated that TGF-β dysregulation was not a cell-intrinsic effect of GORAB inactivation, but a consequence of a disorganized extracellular matrix. Enhanced TGF-β signaling caused elevated Nox4 expression in Gorab Prx1 mutants and in GO patients' fibroblasts, resulting in overproduction of mitochondrial superoxide. The resulting oxidative stress was detected in GORAB null cells and also in wildtype bystander cells. The same effect was observed in zebrafish after TALEN-mediated gorab inactivation, indicating that the pathway is evolutionarily conserved. Treating Gorab Prx1 mutants with the antioxidant N-acetylcysteine ameliorated the osteoporosis phenotype. TGF-β induced oxidative stress coincided with accumulation of DNA damage and elevated expression of senescence markers. Inactivation of Cdkn2a in the Gorab Prx1 rescued the osteoporosis phenotype. Reduced colony formation and altered subpopulations of bone marrow stromal cells were normalized upon inactivation of Cdkn2a, thus further demonstrating the relevance of cellular senescence in the pathogenesis. Our results shed light on the causative role of a TGF-β-Nox4-senescence axis and therapeutic strategies for GO., (© 2024 The Author(s). Aging Cell published by Anatomical Society and John Wiley & Sons Ltd.)

Background: Neurodevelopmental disorder with dysmorphic facies and distal limb anomalies (NEDDFL) is associated to BPTF gene haploinsufficiency. Epilepsy was not included in the initial descriptions of NEDDFL, but emerging evidence indicates that epileptic seizures occur in some affected individuals. This study aims to investigate the electroclinical epilepsy features in individuals with NEDDFL., Methods: We enrolled individuals with BPTF-related seizures or interictal epileptiform discharges (IEDs) on electroencephalography (EEG). Demographic, clinical, genetic, raw EEG, and neuroimaging data as well as response to antiseizure medication were assessed., Results: We studied 11 individuals with a null variant in BPTF, including five previously unpublished ones. Median age at last observation was 9 years (range: 4 to 43 years). Eight individuals had epilepsy, one had a single unprovoked seizure, and two showed IEDs only. Key features included (1) early childhood epilepsy onset (median 4 years, range: 10 months to 7 years), (2) well-organized EEG background (all cases) and brief bursts of spikes and slow waves (50% of individuals), and (3) developmental delay preceding seizure onset. Spectrum of epilepsy severity varied from drug-resistant epilepsy (27%) to isolated IEDs without seizures (18%). Levetiracetam was widely used and reduced seizure frequency in 67% of the cases., Conclusions: Our study provides the first characterization of BPTF-related epilepsy. Early-childhood-onset epilepsy occurs in 19% of subjects, all presenting with a well-organized EEG background associated with generalized interictal epileptiform abnormalities in half of these cases. Drug resistance is rare., Competing Interests: Declaration of competing interest None., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Anastasis is a phenomenon observed in cancer cells, where cells that have initiated apoptosis are able to recover and survive. This molecular event is increasingly recognized as a potential contributor to cancer metastasis, facilitating the survival and migration of tumor cells. Nevertheless, the identification of a specific surface marker for detecting cancer cells in anastasis remained elusive. Here we report our observation that the cell surface expression of CD24 is preferentially enriched in a non-adherent FSC low SSC high melanoma subpopulation, which is generally considered a non-viable population in cultivated melanoma cell lines. More than 90% of non-adherent FSC low SSC high CD24 +ve metastatic melanoma cells exhibited bonafide features of apoptosis on the cell surface and in the nucleus, marking apoptotic or seemingly apoptotic subpopulations of the in vitro cultivated metastatic melanoma cell lines. Unexpectedly, however, the CD24 +ve subpopulation, despite being apoptotic, showed evidence of metabolic activity and exhibited proliferative capacities, including anchorage-independent growth, when inoculated in soft agarose growth medium. These findings indicate that apoptotic FSC low SSC high CD24 +ve melanoma subpopulations are capable of reversing the progression of apoptosis. We report CD24 as the first novel cell surface marker for anastasis in melanoma cells., (© 2024. The Author(s).)

Duchenne and Becker muscular dystrophies, caused by pathogenic variants in DMD , are the most common inherited neuromuscular conditions in childhood. These diseases follow an X-linked recessive inheritance pattern, and mainly males are affected. The most prevalent pathogenic variants in the DMD gene are copy number variants (CNVs), and most patients achieve their genetic diagnosis through Multiplex Ligation-dependent Probe Amplification (MLPA) or exome sequencing. Here, we investigated a female patient presenting with muscular dystrophy who remained genetically undiagnosed after MLPA and exome sequencing. RNA sequencing (RNAseq) from the patient's muscle biopsy identified an 85% reduction in DMD expression compared to 116 muscle samples included in the cohort. A de novo balanced translocation between chromosome 17 and the X chromosome (t(X;17)(p21.1;q23.2)) disrupting the DMD and BCAS3 genes was identified through trio whole genome sequencing (WGS). The combined analysis of RNAseq and WGS played a crucial role in the detection and characterisation of the disease-causing variant in this patient, who had been undiagnosed for over two decades. This case illustrates the diagnostic odyssey of female DMD patients with complex structural variants that are not detected by current panel or exome sequencing analysis.

Creating pedigree charts is a recurring task in biomedical research, but there are few online tools for drawing complex human pedigrees available and even fewer are free. With DrawPed we aim to close this gap. DrawPed automatically draws pedigree charts from standard PED format pedigree files. Users can also create pedigrees from scratch and interactively edit existing pedigrees. The application can display conditions not captured in a PED file such as deceased persons or suspected consanguinity of parents. Pedigree charts are displayed as SVGs, which are scalable and hence publication-ready. Pedigrees can be exported as PED files for storage, exchange, or use in other applications. DrawPed is open source and freely available at https://www.genecascade.org/DrawPed/., (© The Author(s) 2024. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Pathogenic variants in TRIO, encoding the guanine nucleotide exchange factor, are associated with two distinct neurodevelopmental delay phenotypes: gain-of-function missense mutations within the spectrin repeats are causative for a severe developmental delay with macrocephaly (MIM: 618825), whereas loss-of-function missense variants in the GEF1 domain and truncating variants throughout the gene lead to a milder developmental delay and microcephaly (MIM: 617061). In three affected family members with mild intellectual disability/NDD and microcephaly, we detected a novel heterozygous TRIO variant at the last coding base of exon 31 (NM_007118.4:c.4716G>A). RNA analysis from patient-derived lymphoblastoid cells confirmed aberrant splicing resulting in the skipping of exon 31 (r.4615_4716del), leading to an in-frame deletion in the first Pleckstrin homology subdomain of the GEF1 domain: p.(Thr1539_Lys1572del). To test for a distinct gestalt, facial characteristics of the family members and 41 previously published TRIO cases were systematically evaluated via GestaltMatcher. Computational analysis of the facial gestalt suggests a distinguishable facial TRIO-phenotype not outlined in the existing literature., (© 2024 The Authors. American Journal of Medical Genetics Part A published by Wiley Periodicals LLC.)

The oral verruciform xanthoma (OVX) is a rare, benign lesion that occurs predominantly in the masticatory region of the oral cavity. The OVX is small, slow growing, and mostly free of clinical symptoms. The exact pathogenesis is unknown, and a viral etiology such as from a human papillomavirus (HPV) infection has not been proven. Although primarily observed in healthy individuals, there have been cases in patients with autoimmune diseases and with chronic graft-versus-host disease (GvHD). The treatment of choice is complete excision of the lesion. This case report showcases a successful surgical removal of an oral verruciform xanthoma on the left buccal mucosa in a 56-year-old patient with GvHD 14 years after allo-genic stem cell transplantation due to a Non-Hodgkin lymphoma., (Copyright 2024 L. Velte, T. Menter, M. M. Bornstein. License: This work is licensed under a Creative Commons Attribution 4.0 International License.)

Purpose: Osteosarcoma may arise as a secondary cancer following leukemias or lymphomas. We intended to increase the knowledge about such rare events., Patients and Methods: We searched the Cooperative Osteosarcoma Study Group's database for individuals who developed their osteosarcoma following a previous hematological malignancy. The presentation and treatment of both malignancies was investigated, and additional neoplasms were noted. Outcomes after osteosarcoma were analyzed and potential prognostic factors were searched for., Results: A total of 33 eligible patients were identified (male: 23, female: 10; median age: 12.9 years at diagnosis of hematological cancer; 20 lymphomas, 13 leukemias). A cancer predisposition syndrome was evident in one patient only. The hematological cancers had been treated by radiotherapy in 28 (1 unknown) and chemotherapy in 26 cases, including bone-marrow transplantation in 9. The secondary bone sarcomas (high-grade central 27, periosteal 2, extra-osseous 2, undifferentiated pleomorphic sarcoma of bone 2) arose after a median lag-time of 9.4 years, when patients were a median of 19.1 years old. Tumors were considered radiation-related in 26 cases (1 unknown). Osteosarcoma-sites were in the extremities (19), trunk (12), or head and neck (2). Metastases at diagnosis affected eight patients. Information on osteosarcoma therapy was available for 31 cases. All of these received chemotherapy. Local therapy involved surgery in 27 patients, with a good response reported for 9/18 eligible patients. Local radiotherapy was given to three patients. The median follow-up was 3.9 (0.3-12.0) years after bone tumor diagnosis. During this period, 21 patients had developed events as defined, and 15 had died, resulting in 5-year event-free and overall survival rates of 40% (standard error: 9%) and 56% (10%), respectively. There were multiple instances of additional neoplasms. Several factors were found to be of prognostic value ( p < 0.05) for event-free (osteosarcoma site in the extremities) or overall (achievement of a surgical osteosarcoma-remission, receiving chemotherapy for the hematologic malignancy) survival., Conclusions: We were able to prove radiation therapy for hematological malignancies to be the predominant risk factor for later osteosarcomas. A resulting overrepresentation of axial and a tendency towards additional neoplasms affects prognosis. Still, selected patients may become long-term survivors with appropriate therapies, which is an argument against therapeutic negligence.

DNA methylation analysis based on supervised machine learning algorithms with static reference data, allowing diagnostic tumour typing with unprecedented precision, has quickly become a new standard of care. Whereas genome-wide diagnostic methylation profiling is mostly performed on microarrays, an increasing number of institutions additionally employ nanopore sequencing as a faster alternative. In addition, methylation-specific parallel sequencing can generate methylation and genomic copy number data. Given these diverse approaches to methylation profiling, to date, there is no single tool that allows (1) classification and interpretation of microarray, nanopore and parallel sequencing data, (2) direct control of nanopore sequencers, and (3) the integration of microarray-based methylation reference data. Furthermore, no software capable of entirely running in routine diagnostic laboratory environments lacking high-performance computing and network infrastructure exists. To overcome these shortcomings, we present EpiDiP/NanoDiP as an open-source DNA methylation and copy number profiling suite, which has been benchmarked against an established supervised machine learning approach using in-house routine diagnostics data obtained between 2019 and 2021. Running locally on portable, cost- and energy-saving system-on-chip as well as gpGPU-augmented edge computing devices, NanoDiP works in offline mode, ensuring data privacy. It does not require the rigid training data annotation of supervised approaches. Furthermore, NanoDiP is the core of our public, free-of-charge EpiDiP web service which enables comparative methylation data analysis against an extensive reference data collection. We envision this versatile platform as a useful resource not only for neuropathologists and surgical pathologists but also for the tumour epigenetics research community. In daily diagnostic routine, analysis of native, unfixed biopsies by NanoDiP delivers molecular tumour classification in an intraoperative time frame., (© 2024. The Author(s).)

Mobile element insertions (MEIs) are a known cause of genetic disease but have been underexplored due to technical limitations of genetic testing methods. Various bioinformatic tools have been developed to identify MEIs in Next Generation Sequencing data. However, most tools have been developed specifically for genome sequencing (GS) data rather than exome sequencing (ES) data, which remains more widely used for routine diagnostic testing. In this study, we benchmarked six MEI detection tools (ERVcaller, MELT, Mobster, SCRAMble, TEMP2 and xTea) on ES data and on GS data from publicly available genomic samples (HG002, NA12878). For all the tools we evaluated sensitivity and precision of different filtering strategies. Results show that there were substantial differences in tool performance between ES and GS data. MELT performed best with ES data and its combination with SCRAMble increased substantially the detection rate of MEIs. By applying both tools to 10,890 ES samples from Solve-RD and 52,624 samples from Radboudumc we were able to diagnose 10 patients who had remained undiagnosed by conventional ES analysis until now. Our study shows that MELT and SCRAMble can be used reliably to identify clinically relevant MEIs in ES data. This may lead to an additional diagnosis for 1 in 3000 to 4000 patients in routine clinical ES., (© 2023. The Author(s).)

Clinical exome and genome sequencing have revolutionized the understanding of human disease genetics. Yet many genes remain functionally uncharacterized, complicating the establishment of causal disease links for genetic variants. While several scoring methods have been devised to prioritize these candidate genes, these methods fall short of capturing the expression heterogeneity across cell subpopulations within tissues. Here, we introduce single-cell tissue-specific gene prioritization using machine learning (STIGMA), an approach that leverages single-cell RNA-seq (scRNA-seq) data to prioritize candidate genes associated with rare congenital diseases. STIGMA prioritizes genes by learning the temporal dynamics of gene expression across cell types during healthy organogenesis. To assess the efficacy of our framework, we applied STIGMA to mouse limb and human fetal heart scRNA-seq datasets. In a cohort of individuals with congenital limb malformation, STIGMA prioritized 469 variants in 345 genes, with UBA2 as a notable example. For congenital heart defects, we detected 34 genes harboring nonsynonymous de novo variants (nsDNVs) in two or more individuals from a set of 7,958 individuals, including the ortholog of Prdm1, which is associated with hypoplastic left ventricle and hypoplastic aortic arch. Overall, our findings demonstrate that STIGMA effectively prioritizes tissue-specific candidate genes by utilizing single-cell transcriptome data. The ability to capture the heterogeneity of gene expression across cell populations makes STIGMA a powerful tool for the discovery of disease-associated genes and facilitates the identification of causal variants underlying human genetic disorders., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.)

Acknowledgeing that the group of follicular lymphomas is to be regarded as very heterogeneous, a group of follicular lymphomas has been delineated in recent years that was characterised by an often diffuse growth (without formation of evident follicular structures) as well as expression of CD23 in the lymphoma cells and the absence of the classic BCL2 translocation. Further characteristics are a preferred inguinal localisation of the lymphomas and a localised stage with a good prognosis. Genetically, this lymphoma group is characterised by a high rate of either STAT6 or SOCS1 mutations.The ICC classification took this development into account by introducing the provisional entity CD23 positive, BCL2 rearrangement-negative germinal centre lymphoma. Further studies must now show how exactly this entity can be defined (combination of morphology, immunohistochemical phenotype, focus on genetic alterations) in order to pave the way towards a uniform classification and a better clinical characterisation of these cases - especially with regard to possible new therapeutic treatment options., (© 2023. The Author(s).)

Purpose: HOXD13 is an important regulator of limb development. Pathogenic variants in HOXD13 cause synpolydactyly type 1 (SPD1). How different types and positions of HOXD13 variants contribute to genotype-phenotype correlations, penetrance, and expressivity of SPD1 remains elusive. Here, we present a novel cohort and a literature review to elucidate HOXD13 phenotype-genotype correlations., Methods: Patients with limb anomalies suggestive of SPD1 were selected for analysis of HOXD13 by Sanger sequencing, repeat length analysis, and next-generation sequencing. Literature was reviewed for HOXD13 heterozygotes. Variants were annotated for phenotypic data. Severity was calculated, and cluster and decision-tree analyses were performed., Results: We identified 98 affected members of 38 families featuring 11 different (likely) causative variants and 4 variants of uncertain significance. The most frequent (25/38) were alanine repeat expansions. Phenotypes ranged from unaffected heterozygotes to severe osseous synpolydactyly, with intra- and inter-familial heterogeneity and asymmetry. A literature review provided 160 evaluable affected members of 49 families with SPD1. Computer-aided analysis only corroborated a positive correlation between alanine repeat length and phenotype severity., Conclusion: Our findings support that HOXD13-protein condensation in addition to haploinsufficiency is the molecular pathomechanism of SPD1. Our data may, also, facilitate the interpretation of synpolydactyly radiographs by future automated tools., Competing Interests: Conflict of Interest The authors declare no conflicts of interest., (Copyright © 2023 American College of Medical Genetics and Genomics. Published by Elsevier Inc. All rights reserved.)

Primary lymphoedema is a hereditary genetic disorder of the lymphatic system. These genetic disorders can result in malformation or dysfunction of the lymphatic system, which leads to an accumulation of fluid in the tissue and, thus to the formation of oedema. The most common form is peripheral lymphoedema of the lower limbs, but systemic manifestations such as intestinal lymphangiectasia, ascites, chylothorax or hydrops fetalis may also occur. The clinical presentation and the degree of lymphoedema varies depending on the causative gene and the specific gene alteration. Primary lymphoedema is divided into five categories: (1) disorders with somatic mosaicism and segmental growth abnormality, (2a) syndromal disorders, (2b) disorders with systemic involvement, (2c) congenital lymphoedema and (2d) disorders that occur after the first year of life (late onset lymphoedema). Targeted genetic diagnosis is based on the patient's clinical presentation and classification into one of the five categories. In general, the diagnosis usually starts with basic diagnostics, which include cytogenetic and molecular genetic testing. Subsequently, a molecular genetic diagnosis is made by performing single-gene analyses, gene panel examinations, exome sequencing or whole genome sequencing. This allows the identification of genetic variants or mutations that are considered to be causative for the presenting symptoms. Combined with human genetic counselling, the genetic diagnosis allows for conclusions about inheritance, the risk of recurrence and potential concomitant symptoms. In many cases, only this approach allows the definite form of primary lymphoedema to be described., (© 2023. The Author(s), under exclusive licence to Springer Medizin Verlag GmbH, ein Teil von Springer Nature.)

FINCA syndrome [MIM: 618278] is an autosomal recessive multisystem disorder characterized by fibrosis, neurodegeneration and cerebral angiomatosis. To date, 13 patients from nine families with biallelic NHLRC2 variants have been published. In all of them, the recurrent missense variant p.(Asp148Tyr) was detected on at least one allele. Common manifestations included lung or muscle fibrosis, respiratory distress, developmental delay, neuromuscular symptoms and seizures often followed by early death due to rapid disease progression.Here, we present 15 individuals from 12 families with an overlapping phenotype associated with nine novel NHLRC2 variants identified by exome analysis. All patients described here presented with moderate to severe global developmental delay and variable disease progression. Seizures, truncal hypotonia and movement disorders were frequently observed. Notably, we also present the first eight cases in which the recurrent p.(Asp148Tyr) variant was not detected in either homozygous or compound heterozygous state.We cloned and expressed all novel and most previously published non-truncating variants in HEK293-cells. From the results of these functional studies, we propose a potential genotype-phenotype correlation, with a greater reduction in protein expression being associated with a more severe phenotype.Taken together, our findings broaden the known phenotypic and molecular spectrum and emphasize that NHLRC2-related disease should be considered in patients presenting with intellectual disability, movement disorders, neuroregression and epilepsy with or without pulmonary involvement., (© 2023. The Author(s).)

The rapid and dynamic implementation of Next-Generation Sequencing (NGS)-based assays has revolutionized genetic testing, and in the near future, nearly all molecular alterations of the human genome will be diagnosable via massive parallel sequencing. While this progress will further corroborate the central role of human genetics in the multidisciplinary management of patients with genetic disorders, it must be accompanied by quality assurance measures in order to allow the safe and optimal use of knowledge ascertained from genome diagnostics. To achieve this, several valuable tools and guidelines have been developed to support the quality of genome diagnostics. In this paper, authors with experience in diverse aspects of genomic analysis summarize the current status of quality assurance in genome diagnostics, with the aim of facilitating further standardization and quality improvement in one of the core competencies of the field., Competing Interests: Competing interests: The authors have no conflicts of interest to declare., (© 2023 bei den Autorinnen und Autoren, publiziert von De Gruyter.)

Oral mucoceles are cystic changes in the minor salivary glands caused by traumatic damage to the salivary gland ducts or their obstruction with subsequent salivary congestion. In extravasation mucocele, saliva leaks from the ruptured duct into the surrounding tissue and causes a local inflammatory reaction. Thus, histopathologically, granulation tissue is seen around the salivary fluid, but no epithelial lining.

The 5th edition of the WHO classification (WHO-HAEM5) and the International Consensus Classification (ICC) show a broad consensus in the categorization of aggressive, large B‑cell lymphomas with expected minor impact only on the daily diagnostic routine. The changes compared to the 2017 revised WHO-HAEM4R are moderate and include updated names of entities, sharpened diagnostic criteria, and upgrades from provisional to definite entities. The definition of the most common aggressive B‑cell lymphoma, diffuse large B‑cell lymphoma (DLBCL), not otherwise specified (NOS), remains unchanged, and both classifications strongly encourage subtyping into germinal center B‑like (GCB) or the activated B‑like (ABC or non-GCB) DLBCL. DLBCL, NOS, should be separated from other large B‑cell lymphomas including large B‑cell lymphoma with IRF4 rearrangement (upgraded to a definite entity in both classifications) and large-cell/high-grade B‑cell lymphomas with 11q aberration. Aggressive B‑cell lymphomas with MYC and BCL2 rearrangements form a molecularly distinct group and are listed as definite entities in both classifications. This is in contrast to the more heterogeneous group of aggressive B‑cell lymphomas with MYC and BCL6 rearrangements that are recognized as a provisional entity in the ICC, while they fall into the DLBCL, NOS, or the HGBL, NOS, groups in the WHO-HAEM5., (© 2023. The Author(s).)

The "Nosology of genetic skeletal disorders" has undergone its 11th revision and now contains 771 entries associated with 552 genes reflecting advances in molecular delineation of new disorders thanks to advances in DNA sequencing technology. The most significant change as compared to previous versions is the adoption of the dyadic naming system, systematically associating a phenotypic entity with the gene it arises from. We consider this a significant step forward as dyadic naming is more informative and less prone to errors than the traditional use of list numberings and eponyms. Despite the adoption of dyadic naming, efforts have been made to maintain strong ties to the MIM catalog and its historical data. As with the previous versions, the list of disorders and genes in the Nosology may be useful in considering the differential diagnosis in the clinic, directing bioinformatic analysis of next-generation sequencing results, and providing a basis for novel advances in biology and medicine., (© 2023 The Authors. American Journal of Medical Genetics Part A published by Wiley Periodicals LLC. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.)

Melkersson-Rosenthal syndrome (MRS) is a rare disease and is characterised by the classic triad of cheilitis granulomatosa, lingua plicata and peripheral facia- lis paresis. These symptoms rarely manifest themselves all at the same time, often only one of these clinical signs appears. In the literature, the umbrella term orofacial granulomatosis (OFG) is also used, which covers the occurrence of granulomas in the maxillofacial region without associated systemic diseases.

Angina bullosa haemorrhagica (ABH; also: bullosa haemorrhagica oralis or "benign hemorrhagic bullous stomatitis") was first defined by Badham in 1967 as recurrent formation of blood blisters on the oropharyngeal mucosa as a result of mechanically traumatic irri- tation. A possible connection with previous damage to the mucosa due to general medical findings such as hypertension, diabetes mellitus or chronic inhalation of corticosteroids has not yet been confirmed.

The ICD-10-GM coding system used in the German healthcare system only captures a minority of rare disease diagnoses. Therefore, information on the incidence and prevalence of rare diseases as well as necessary (financial) resources for the expert care required for evidence-based decisions by health insurers, care providers, and politicians are lacking. Furthermore, the missing information complicates and sometimes even precludes the generation of scientific knowledge on rare diseases. Therefore, starting in 2023, all in-patient cases in Germany with a rare disease diagnosis must be coded by an ORPHAcode using the Alpha-ID-SE file.The file Alpha-ID-SE links the ICD-10-GM codes to the internationally established ORPHAcodes for rare diseases. Commercially available software tools progressively support the coding of rare diseases. In several centers for rare diseases linked to university hospitals, IT tools and procedures were established to realize a complete coding of rare diseases. These include financial incentives for the institutions providing rare disease codes, systematic queries asking for rare disease codes during the coding process, and a semi-automated coding process for all patients with a rare disease previously seen at the institution. A combination of the different approaches probably results in the most complete coding.To get the complete picture of rare disease epidemiology and care requirements, a specific and unique coding of out-patient cases is also desirable. Furthermore, a structured reporting of phenotype is required, especially for complex rare diseases and for yet undiagnosed cases., (© 2022. The Author(s).)

In the European Union (EU), rare diseases (RDs) are diseases that affect no more than 5 in 10,000 people. Due to their rarity, clinical expertise and quality-assured care structures are scarce, and research is more difficult compared to other diseases. However, these problems can be overcome by means of national and transnational RD care networks. Data and expertise are pooled in these networks.In the EU, the European Reference Networks (ERNs) for Rare and Complex Diseases cooperate across borders. Important services provided by ERNs using health data include diagnostic coding of RDs, conducting virtual cross-border case conferences, and establishing European registries that are used to measure and improve the quality of care. In ERNs, local data generation and documentation combine with network-wide data infrastructures. This paper describes the data-based services in and for RD healthcare networks: (1) diagnostic coding, (2) cross-border case conferences, and (3) ERN registries for RD patient care. The final section discusses the integration of the networks into national healthcare systems.In order to achieve the best possible benefit for SE patients, ERN activities and structures need to be better integrated into national healthcare systems. In Germany, the Medical Informatics Initiative and the German Reference Networks play a central role in this regard., (© 2022. The Author(s).)

The use of standardized data formats (data standards) in healthcare supports four main goals: (1) exchange of data, (2) integration of computer systems and tools, (3) data storage and archiving, and (4) support of federated databases. Standards are especially important for rare-disease research and clinical care.In this review, we introduce healthcare standards and present a selection of standards that are commonly used in the field of rare diseases. The Human Phenotype Ontology (HPO) is the most commonly used standard for annotating phenotypic abnormalities and supporting phenotype-driven analysis of diagnostic exome and genome sequencing. Numerous standards for diseases are available that support a range of needs. Online Mendelian Inheritance in Man (OMIM) and the Orphanet Rare Disease Ontology (ORDO) are the most important standards developed specifically for rare diseases. The Mondo Disease Ontology (Mondo) is a new disease ontology that aims to integrate data from a comprehensive range of current nosologies. New standards and schemas such as the Medical Action Ontology (MAxO) and the Global Alliance for Genomics and Health (GA4GH) phenopacket are being introduced to extend the scope of standards that support rare disease research.In order to provide optimal care for patients with SE in different healthcare settings, it will be necessary to better integrate standards for rare disease with electronic healthcare resources such as the Fast Healthcare Interoperability Resources (FHIR) standard for healthcare data exchange., (© 2022. The Author(s).)

Lichen planus (synonym: lichen ruber; in the oral cavity: oral lichen planus = OLP) is a common, chronic inflammatory disease that affects the skin and mucous membranes (especially the oral and genital mucosa). With a prevalence of 1 to 2%, lichen planus is one of the most common mucodermatoses and is more common in women than in men.

Objective: In this study, we aim to assess the current situation of postgraduate medical education in obstetrics and gynaecology in Germany, Austria and Switzerland. In addition, we aim to determine transferable advantages amongst the countries. Study design: We performed a survey through a digital questionnaire with a total of 40 questions. The survey was advertised via communication channels of the German, Austrian and Swiss gynaecological societies; the participants were enrolled anonymously. Results: A total of 422 trainees took part in the survey. Differences within the three countries where found regarding the workload and the training of sub-specialties. Generally, the participants described to spend the majority of their daily working hours on documentation. Concerning assessment of current training regulations, more than half of trainees stated that they were actually faced with notable difficulties to fulfil the required obligatory numbers of self-performed interventions being documented. When asked for their intrinsic feeling of safety, around two-third of trainees felt "confident to very confident" during standard interventions. These numbers were up to 12% higher in the group of trainees who experienced simulation training during their education. Conclusion: With the help of this survey, weak points can be identified such as workload and implementation of current training regulations. Projects and ideas as EBCOG PACT, EPAs, the reduction of bureaucracy through digitization and deepening skills through simulation make a valuable contribution to compensate for these deficits and to adapt to future requirements., Competing Interests: The authors declare that they have no competing interests., (Copyright © 2022 Winder et al.)

A case of a patient suffering from COVID-19 with suspected associated myositis is reported, in which the initially limited information about the history and disease course led to difficulties in establishing a reasonable diagnosis. Through inquiry, further data could be collected, so that the diagnosis of an infection-associated thrombotic microangiopathy in the context of a Morganella morganii myositis could be made. This patient study shows that even in times of the omnipresent pandemic and despite the context of a positive COVID-19 test result, differential diagnoses and the integrative clinicopathologic approach in interpreting muscle biopsy findings should not be neglected., (© 2022. The Author(s), under exclusive licence to Springer Medizin Verlag GmbH, ein Teil von Springer Nature.)

Objectives: Current prospective studies investigating the frequency of hereditary criteria in a Caucasian population for adenocarcinoma of the esophagogastric junction (AEG) and stomach (GC) are missing. Genetic testing criteria (screening criteria) for hereditary diffuse gastric cancer (HDGC) were updated in 2020, but do not address patients with intestinal histology (familial intestinal gastric cancer FIGC). Thus, we prospectively screened patients residing in Berlin newly diagnosed with AEG or GC for hereditary criteria to gain insights into the frequency of HDGC., Methods: Prospective documentation of familial/clinical parameters in patients residing in Berlin with AEG or GC over three years was conducted. Besides HDGC criteria from 2015 and revised 2020, we also documented patients fulfilling these criteria but with intestinal type gastric cancer (FIGC). Statistical analysis was performed using X2-test., Results: One hundred fifty-three patients were finally included (92 GC; male: 50 (n.s.); 61 AEG; male: 47; p = 0.007). Hereditary criteria for HDGC were detected in 9/92 (9.8%) (2015 criteria) and in 14/92 (15.2%) (2020 criteria) of GC patients (AEG: 2015 criteria 3/61 (4.9%) versus 4/61 according to 2020 criteria (6.5%)). Patients fulfilling hereditary criteria but with intestinal histology (FIGC) increased from 8.7% (2015) to 14.1%, respectively (2020) (AEG: 3.2% (2015) versus 6.6% (2020)). Hereditary criteria including intestinal histology were found in 29.3% (GC) and 13.1% (AEG) ( p = 0.03) according to the 2020 criteria., Conclusions: HDGC criteria were found in 15.2% of GC patients according to the 2020 criteria. Percentage increased to 29.3% including patients with intestinal histology among the GC group, and was 13.1% in cases with AEG. These data indicate that family history seems to be of utmost importance in GC to further detect potential hereditary genetic risks. This equally applies for patients with intestinal subtype GC.

With the shift from SNP arrays to high-throughput sequencing, most researchers studying diseases in consanguineous families do not rely on linkage analysis any longer, but simply search for deleterious variants which are homozygous in all patients. AutozygosityMapper allows the fast and convenient identification of disease mutations in patients from consanguineous pedigrees by focussing on homozygous segments shared by all patients. Users can upload multi-sample VCF files, including WGS data, without any pre-processing. Genome-wide runs of homozygosity and the underlying genotypes are presented in graphical interfaces. AutozygosityMapper extends the functions of its predecessor, HomozygosityMapper, to the search for autozygous regions, in which all patients share the same homozygous genotype. We provide export of VCF files containing only the variants found in homozygous regions, this usually reduces the number of variants by two orders of magnitude. These regions can also directly be analysed with our disease mutation identification tool MutationDistiller. The application comes with simple and intuitive graphical interfaces for data upload, analysis, and results. We kept the structure of HomozygosityMapper so that previous users will find it easy to switch. With AutozygosityMapper, we provide a fast web-based way to identify disease mutations in consanguineous families. AutozygosityMapper is freely available at https://www.genecascade.org/AutozygosityMapper/., (© The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Precision medicine needs precise phenotypes. The Human Phenotype Ontology (HPO) uses clinical signs instead of diagnoses and has become the standard annotation for patients' phenotypes when describing single gene disorders. Use of the HPO beyond human genetics is however still limited. With SAMS (Symptom Annotation Made Simple), we want to bring sign-based phenotyping to routine clinical care, to hospital patients as well as to outpatients. Our web-based application provides access to three widely used annotation systems: HPO, OMIM, Orphanet. Whilst data can be stored in our database, phenotypes can also be imported and exported as Global Alliance for Genomics and Health (GA4GH) Phenopackets without using the database. The web interface can easily be integrated into local databases, e.g. clinical information systems. SAMS offers users to share their data with others, empowering patients to record their own signs and symptoms (or those of their children) and thus provide their doctors with additional information. We think that our approach will lead to better characterised patients which is not only helpful for finding disease mutations but also to better understand the pathophysiology of diseases and to recruit patients for studies and clinical trials. SAMS is freely available at https://www.genecascade.org/SAMS/., (© The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Reactive cytopenias are a frequent cause for bone marrow investigations, including bone marrow trephine biopsies, especially if clinical examination and laboratory analyses (e.g., detection of substrate deficiencies) cannot provide a sufficient explanation. The evaluation of such biopsies is primarily concerned with the exclusion of diseases that displace the normal hematopoiesis (infiltrates of acute leukemias or lymphomas and metastases), the exclusion of a myelodysplastic syndrome that classically results in ineffective hematopoiesis, or the detection of specific diseases, particularly infectious or histiocytic diseases (e.g., hemophagocytic lymphohistiocytosis).In this review, we describe characteristic morphologic changes of reactive cytopenias, focus on specific infectious and noninfectious clinical pictures, and distinguish them from malignant changes, especially myelodysplastic syndrome and underlying leukemia of large granular T lymphocytes. Drug-induced changes in hematopoiesis are described in another article in this issue., (© 2022. The Author(s).)

High-throughput technologies led to the generation of a wealth of data on regulatory DNA elements in the human genome. However, results from disease-driven studies are primarily shared in textual form as scientific articles. Information extraction (IE) algorithms allow this information to be (semi-)automatically accessed. Their development, however, is dependent on the availability of annotated corpora. Therefore, we introduce RegEl (Regulatory Elements), the first freely available corpus annotated with regulatory DNA elements comprising 305 PubMed abstracts for a total of 2690 sentences. We focus on enhancers, promoters and transcription factor binding sites. Three annotators worked in two stages, achieving an overall 0.73 F1 inter-annotator agreement and 0.46 for regulatory elements. Depending on the entity type, IE baselines reach F1-scores of 0.48-0.91 for entity detection and 0.71-0.88 for entity normalization. Next, we apply our entity detection models to the entire PubMed collection and extract co-occurrences of genes or diseases with regulatory elements. This generates large collections of regulatory elements associated with 137 870 unique genes and 7420 diseases, which we make openly available. Database URL: https://zenodo.org/record/6418451#.YqcLHvexVqg., (© The Author(s) 2022. Published by Oxford University Press.)

Predictive immunochemistry is a time-, tumor sample- and cost-efficient method for testing the increasing number of predictive biomarkers in advanced non-small cell lung cancer (NSCLC). Immunohistochemistry (IHC) on formalin-fixed, paraffin-embedded (FFPE) tumor tissue has an established role in detecting PD-L1 expression and in ALK, ROS1, and more recently NTRK testing. Cytology specimens as a source for predictive biomarker testing in NSCLC is very important as up to 40% of all NSCLC are diagnosed by cytology alone.Despite the established role of cytology in lung cancer diagnosis, no commercial IHC assays have been validated for cytology specimens.FFPE cell blocks (CB) are the most straightforward cytology preparation for predictive immunocytochemistry (ICC) as the results are valid using protocols standardized for FFPE histology. But CB are not always available.With non-CB cytology specimens being less standardized than FFPE histology and with considerable preanalytical variability, rigorous cytology-specific ICC protocol optimization, validation, and quality control are required. With this prerequisite, predictive ICC, most commonly performed on Papanicolaou-stained cytology specimens, is robust and reliable on non-CB preparations. This valuable material should not be underutilized for predictive biomarker testing, as this would put patients at risk of unnecessary repeat sampling. This review highlights preanalytical, analytical, and postanalytical aspects that may influence ICC results and summarizes the published data on predictive ICC for PD-L1, ALK, and ROS1 in NSCLC., (© 2022. The Author(s).)