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BACKGROUND. Cystic kidney disease (CyKD) is a predominantly familial disease in which gene discovery has been led by family-based and candidate gene studies, an approach that is susceptible to ascertainment and other biases. METHODS. Using whole-genome sequencing data from 1,209 cases and 26,096 ancestry-matched controls participating in the 100,000 Genomes Project, we adopted hypothesis-free approaches to generate quantitative estimates of disease risk for each genetic contributor to CyKD, across genes, variant types and allelic frequencies. RESULTS. In 82.3% of cases, a qualifying potentially disease-causing rare variant in an established gene was found. There was an enrichment of rare coding, splicing, and structural variants in known CyKD genes, with statistically significant gene-based signals in COL4A3 and (monoallelic) PKHD1. Quantification of disease risk for each gene (with replication in the separate UK Biobank study) revealed substantially lower risk associated with genes more recently associated with autosomal dominant polycystic kidney disease, with odds ratios for some below what might usually be regarded as necessary for classical Mendelian inheritance. Meta-analysis of common variants did not reveal significant associations, but suggested this category of variation contributes 3%-9% to the heritability of CyKD across European ancestries. CONCLUSION. By providing unbiased quantification of risk effects per gene, this research suggests that not all rare variant genetic contributors to CyKD are equally likely to manifest as a Mendelian trait in families. This information may inform genetic testing and counseling in the clinic., Introduction Cystic kidney disease (CyKD) is a term for any disease that causes multiple fluid-filled cysts within the kidney (excluding cystic degeneration of chronically diseased/failed kidneys). The term polycystic kidney [...]

African swine fever (ASF), a nonzoonotic, World Organisation for Animal Health (WOAH) notifiable disease, is a devasting hemorrhagic infectious disease of domestic (Sus domesticus) and wild (Sus scrofa) swine populations [...]

Listeria monocytogenes is a gram-positive pathogen responsible for listeriosis, a severe foodborne infection that causes high hospitalization and mortality rates in at-risk populations, including older adults, immunocompromised persons, pregnant women, [...]

Human mpox (formerly monkeypox) is an emerging zoonotic disease caused by monkeypox virus (MPXV) (1,2). Since the 1970s, mpox outbreaks in humans have occurred sporadically, mainly in Africa (3). In [...]

Targeted metagenomic sequencing is an emerging strategy to survey disease- specific microbiome biomarkers for clinical diagnosis and prognosis. However, this approach often yields inconsistent or conflicting results owing to inadequate study power and sequencing bias. We introduce Taxa4Meta, a bioinformatics pipeline explicitly designed to compensate for technical and demographic bias. We designed and validated Taxa4Meta for accurate taxonomic profiling of 16S rRNA amplicon data acquired from different sequencing strategies. Taxa4Meta offers significant potential in identifying clinical dysbiotic features that can reliably predict human disease, validated comprehensively via reanalysis of individual patient 16S data sets. We leveraged the power of Taxa4Meta's pan-microbiome profiling to generate 16S-based classifiers that exhibited excellent utility for stratification of diarrheal patients with Clostridioides difficile infection, irritable bowel syndrome, or inflammatory bowel diseases, which represent common misdiagnoses and pose significant challenges for clinical management. We believe that Taxa4Meta represents a new 'best practices' approach to individual microbiome surveys that can be used to define gut dysbiosis at a population-scale level., Introduction Targeted metagenomic sequencing is commonly used for the identification of disease-causing bacteria, archaea, and fungi. In addition, 16S rRNA gene surveys are increasingly being adopted as diagnostic tools to [...]

Periploca forrestii, a medicinal plant of the family Apocynaceae, is known as an effective and widely used clinical prescription for the treatment of rheumatoid diseases. In this study, we de novo sequenced and assembled the completement chloroplast (cp) genome of P. forrestii based on combined Oxford Nanopore PromethION and Illumina data. The cp genome was 153 724 bp in length and had four subregions. Moreover, an 84433 bp large single-copy and a 17 731 bp small single-copy were separated by 25 780 bp inverted repeats (IRs). The cp genome included 132 genes with 18 duplicates in the IRs. A total of 45 repeat structures and 183 simple sequence repeats were detected. Codon usage showed a bias toward A/T-ending codons. A comparative study of Apocynaceae revealed that an IR expansion occurred on P. forrestii. The Ka/Ks values of eight species of Apocynaceae suggested that positive selection was exerted on the psaI and ycf2 genes, which might reflect specific adaptions to the P. forrestii particular growth environment. Phylogenetic analysis indicated that Periplocoideae was a sister to Asclepiadoideae, forming a monophyletic group in the family Apocynaceae. This study provided an important P. forrestii genomic resource for future evolutionary studies and the phylogenetic reconstruction of the family Apocynaceae. Key words: Periploca forrestii, chloroplast genome, genomic structure, comparative analysis, molecular evolution analysis, Introduction Periploca forrestii Schlechter belongs to the family Apocynaceae (Byng et al. 2016) and grows mainly in the karst areas in the southwest of China, where the population suffering from [...]

Lyme disease is a multisystem disorder caused by infection with bacteria of the Borrelia burgdorferi sensu lato species complex. Three members of this complex, B. burgdorferi sensu stricto, B. garinii, [...]

The Bacillus cereus group of bacteria is a complex of closely related species with varying pathogenic potential (1). Notable members, as defined in the US Food and Drug Administration's Bacteriological [...]

The World Health Organization declared the 2022 mpox (formerly monkeypox) outbreak a public health emergency of international concern on July 23, 2022, after cases were identified in nearly 80 countries [...]

Context.-Minimal residual disease (MRD) is a major prognostic factor in multiple myeloma, although validated technologies are limited. Objective.-To standardize the performance of the LymphoTrack next-generation sequencing (NGS) assays (Invivoscribe), targeting clonal immunoglobulin rearrangements, in order to reproduce the detection of tumor clonotypes and MRD quantitation in myeloma. Design.-The quantification ability of the assay was evaluated through serial dilution experiments. Paired samples from 101 patients were tested by LymphoTrack, using Sanger sequencing and EuroFlow's next-generation flow (NGF) assay as validated references for diagnostic and follow-up evaluation, respectively. MRD studies using LymphoTrack were performed in parallel at 2 laboratories to evaluate reproducibility. Results.-Sensitivity was set as 1.3 tumor cells per total number of input cells. Clonality was confirmed in 99% and 100% of cases with Sanger and NGS, respectively, showing great concordance (97.9%), although several samples had minor discordances in the nucleotide sequence of rearrangements. Parallel NGS was performed in 82 follow-up cases, achieving a median sensitivity of 0.001%, while for NGF, median sensitivity was 0.0002%. Reproducibility of LymphoTrack-based MRD studies (85.4%) and correlation with NGF ([R.sup.2] > 0.800) were high. Bland-Altman tests showed highly significant levels of agreement between flow and sequencing. Conclusions.-Taken together, we have shown that LymphoTrack is a suitable strategy for clonality detection and MRD evaluation, with results comparable to gold standard procedures., Multiple myeloma (MM) is a plasma-cell dyscrasia characterized by the accumulation of plasma cells in the bone marrow that produces an excess of clonal immunoglobulins (M-protein or monoclonal component). (1) [...]

* Context.--Associations between granulomatous lobular mastitis (GLM) and Corynebacterium kroppenstedtii have been reported since 2002, but large-scale studies to assess the actual prevalence of this bacterium in GLM have not been performed. Objective.--To assess the prevalence of C kroppenstedtii in GLM using real-time polymerase chain reaction and Sanger sequencing. Design.--We analyzed formalin-fixed, paraffin-embedded tissues from 67 cases of GLM by sequential DNA amplification and sequencing to assess the rate of C kroppenstedtii detection in GLM. A retrospective analysis including patient demographics, history of pregnancy and lactation, clinical signs and symptoms, radiographic findings, histologic pattern, Gram stain results, and microbial cultures was performed on 67 cases of GLM. In addition, 10 cases of nongranulomatous breast abscess were included as controls. Results.--C kroppenstedtii 16S rRNA SYBR real-time polymerase chain reaction was positive on formalin-fixed, paraffin-embedded tissues from 46 of 67 (68.7%) GLM cases, while all control cases were negative. Among the positive cases, the majority showed features of cystic neutrophilic granulomatous mastitis. Conclusions.--C kroppenstedtii was highly prevalent in GLM cases and was not found to be associated with nongranulomatous breast abscess in our study (P < .001)., Granulomatous lobular mastitis (GLM) is an uncommon benign, inflammatory disease of the breast first described in 1972 by Kessler and Wolloch (1) that characteristically affects women of childbearing age with [...]

Context.--Measurable (minimal) residual disease (MRD) is an independent prognostic factor for survival outcomes in patients with lymphoid and plasma cell malignancies and has been incorporated into consensus criteria regarding treatment response, strategy, and clinical trial endpoints. clonoSEQ (a next-generation sequencing [NGS]-MRD assay) uses multiplex polymerase chain reaction and NGS to identify clonotypic rearrangements at the immunoglobulin (Ig) H, IgK, IgL, T-cell receptor (TCR)-[beta], and TCR-[gamma] loci, as well as translocated B-cell lymphoma 1/IgH and 2/IgH sequences for MRD assessment. Additionally, it can be used to confirm diagnoses of cutaneous T-cell lymphoma (CTCL). Objective.--To review the technical aspects of our experience using the clonoSEQ Assay in routine clinical practice. Design.--In this single-center experience, 390 patients with lymphoid and plasma cell malignancies were assessed with the NGS-MRD Assay at a central laboratory. Results.--Median time from arrival of the shipment to initiation of the assay (defined as captured in Adaptive's secure tracking system) was 2.1 hours. Overall, 317 patients had 1 or more samples submitted for sequence identification. Of these, 290 (91.5%) had trackable sequences identified. The median calibration rate of samples by malignancy (where n [greater than or equal to] 10 samples, excluding CTCL samples) was 88.1%, across a variety of fresh and archived sample sources (177 of 201 samples). TCR-[beta] and/ or TCR-[gamma] clonotypes were identified in 40 of 95 samples (42.1%) from 66 patients with suspected CTCL. Conclusions.--This NGS-MRD Assay is a valuable and sensitive tool for monitoring MRD in patients with plasma cell and lymphoid malignancies and assisting in the diagnosis of CTCL., In the past decade, the clinical utility of assessing measurable (minimal) residual disease (MRD) in patients with plasma cell and lymphoid malignancies has been recognized increasingly. (1) MRD has been [...]

Monkeypox virus (MPXV) is a zoonotic pathogen that causes mpox (formerly monkeypox), a febrile rash disease, in humans. It has caused multiple outbreaks in the past (1) but recently acquired [...]

Genomic surveillance to detect SARS-CoV-2 variants has become a critical component of monitoring the virus over time. Both patient- and community-level surveillance through the sequencing of clinical specimens and wastewater [...]

Epidemics of infectious viral diseases seriously threaten human health and safety as well as social stability and development. In recent years, outbreaks of diseases such as influenza A(H7N9) (2), Ebola [...]

To limit spread of novel SARS-CoV-2 variants such as Omicron B.1.1.529, early detection is crucial. Wastewater surveillance has been suggested as an early warning system for SARS-CoV-2 spread in low-prevalence [...]

Context.--Dedifferentiated chondrosarcoma is a rare adult bone tumor with a dismal prognosis and is composed of a conventional chondrosarcoma juxtaposed to high-grade nonchondrogenic sarcoma. Dedifferentiated chondrosarcomas may represent tumor progression from a differentiated to a primitive histotype. Objective.--To determine the genetic and molecular events that drive progression from a conventional chondrosarcoma to high grade nonchondrogenic sarcoma. Design.--We analyzed the genomic landscape of paired conventional and dedifferentiated components of 11 dedifferentiated chondrosarcoma using targeted next-generation DNA sequencing with immunohistochemical validation. Clinical, radiographic, and pathologic features of tumors were reviewed. Capture-based DNA sequencing targeting the coding regions of 479 cancer genes and select introns was performed. Results.--The tumors arose in the femur (n = 4; 36%), scapula (n = 3; 27%), pelvis (n = 3; 27%), and humerus (n = 1; 9%) of 7 men (64%) and 4 women (36%; median age, 61 years). DNA was adequate for sequencing from all 11 dedifferentiated components (100%) and 9 paired conventional chondrosarcoma components (82%). All tumors (100%) harbored either IDH1 p.R132 or IDH2 p.R172S hotspot mutations. Seven tumors (64%) displayed COL2A1 alterations. TERT promoter mutations were present in 5 of 9 pairs (56%) and 2 (22%) additional unpaired dedifferentiated components. IDH1/2, COL2A1, and TERT mutations were identical in both components of the paired samples. Pathogenic missense or truncating mutations in TP53 and large-scale copy number alterations were more common in dedifferentiated components than in those of matched conventional components. Conclusions.--The results support IDH1/2, COL2A1, and TERT promoter mutations being common in dedifferentiated chondrosarcoma and as likely early events in progression, whereas inactivating mutation of TP53 and high-level copy number alterations may be later events in the dedifferentiated phenotype. doi: 10.5858/arpa.2020-0379-OA, Dedifferentiated chondrosarcoma (DDCS) is a rare, highly aggressive mesenchymal tumor of the skeleton with reproducible pathologic, radiographic, and clinical features. (1) A biphasic tumor that consists of conventional chondrosarcoma component [...]

Introduction: HIV rebounds after cessation of antiretroviral therapy, representing a barrier to cure. To better understand the virus reservoir, analysis pipelines have been developed that categorize proviral sequences as intact or defective, and further determine the precise nature of the sequence defects that may be present. We investigated the effects that different analysis pipelines had on the characterization of HIV-1 proviral sequences. Methods: We used single genome amplification to generate near full-length (NFL) HIV-1 proviral DNA sequences, defined as amplicons greater than 8000 base pairs in length, isolated from peripheral blood mononuclear cells (PBMC) of treated suppressed participants with HIV-1. Amplicons underwent direct next-generation single genome sequencing and were analysed using four HIV-1 proviral characterization pipelines. Sequences were characterized as intact or defective; defective sequences were assessed for the number and types of defects present. To confirm and extend our findings, 691 proviruses from the Proviral Sequence Database (PSD) were analysed and the ProSeq-IT tool of the PSD was used to characterize both the participant and PSD proviruses. Results and discussion: Virus sequences derived from thirteen ART-treated virologically suppressed participants with HIV were studied. A total of 693 HIV-1 proviral sequences were generated, 282 of which were NFL. An average of 53 sequences per participant was analysed. We found that proviruses often harbour multiple sequence defect types (mean 2.7, 95% confidence interval [CI] 2.5, 3.0); the elimination order used by each pipeline affected the percentage of proviruses allotted into each defect category. These differences varied between participants, depending on the number of defect categories present in a given provirus sequence. Pipeline-specific differences in characterizing the HIV-1 5' untranslated region (5' UTR) led to an overestimation of the number of intact NFL proviral sequences, a finding corroborated in the independent PSD analysis. A comparison of the four published pipelines to ProSeq-IT found that ProSeq IT was more likely to characterize proviruses as intact. Conclusions: The choice of pipeline used for HIV-1 provirus landscape analysis may bias the classification of defective sequences. To improve the comparison of provirus characterizations across research groups, the development of a consensus elimination pipeline should be prioritized. Keywords: proviral landscape; reservoir; HIV-1; near full-length genome; provirus characterization; analysis pipeline, 1 | INTRODUCTION During HIV-1 infection, viral DNA integrates into the genomes of [CD4.sup.+] T cells and can persist during antiretroviral therapy [1-3]. Previous work has investigated what proportion of [...]

* Context.--Bone and soft tissue tumors are heterogeneous, diagnostically challenging, and often defined by gene fusions. Objective.--To present our experience using a custom 34-gene targeted sequencing fusion panel. Design.--Total nucleic acid extracted from formalin-fixed, paraffin-embedded (FFPE) tumor specimens was subjected to open-ended, nested anchored multiplex polymerase chain reaction and enrichment of 34 gene targets, thus enabling detection of known and novel fusion partners. Results.--During a 12-month period, 147 patients were tested as part of routine clinical care. Tumor percentage ranged from 10% to 100% and turnaround time ranged from 3 to 15 (median, 7.9) days. The most common diagnostic groups were small round blue cell tumors, tumors of uncertain differentiation, fibroblastic/myofibroblastic tumors, and adipocytic tumors. In-frame fusion transcripts were identified in 64 of 142 cases sequenced (45%): in 62 cases, the detection of a disease-defining fusion confirmed the morphologic impression; in 2 cases, a germline TFG-GPR128 polymorphic fusion variant was detected. Several genes in the panel partnered with multiple fusion partners specific for different diagnoses, for example, EWSR1, NR4A3, FUS, NCOA2, and TFE3. Interesting examples are presented to highlight how fusion detection or lack thereof was instrumental in establishing accurate diagnoses. Novel fusion partners were detected for 2 cases of solid aneurysmal bone cysts (PTBP1-USP6, SLC38A2-USP6). Conclusions.--Multiplex detection of fusions in total nucleic acid purified from FFPE specimens facilitates diagnosis of bone and soft tissue tumors. This technology is particularly useful for morphologically challenging entities and in the absence of prior knowledge of fusion partners, and has the potential to discover novel fusion partners. (Arch Pathol Lab Med. 2021;145:851-863; doi: 10.5858/arpa.2020-0336-OA), Gene fusions occur frequently in bone and soft tissue (BST) neoplasms and, less frequently, in other kinds of solid tumors. (1-3) The observation of these fusions in patient specimens can [...]

Brucellosis, caused by bacteria of the Brucella genus, is a neglected zoonotic disease that affects marginalized populations worldwide (1). Human transmission occurs mainly through consumption of unpasteurized, contaminated dairy products [...]

Context.--The increasing use of large panel next-generation sequencing technologies in clinical settings has facilitated the identification of pan-cancer biomarkers, which can be diagnostic, prognostic, predictive, or most importantly, actionable. Objective.--To discuss recently approved and emerging pan-cancer and multihistology biomarkers as well as testing methodologies. Data Sources.--The US Food and Drug Administration approval documents, National Comprehensive Cancer Network guidelines, literature, and authors' own publications. Conclusions.--Since 2017, the US Food and Drug Administration has approved genotype-directed therapies for pan-cancer biomarkers, including microsatellite instability, neurotrophic receptor kinases fusions, and high-tumor mutation burden. Both the importance and rarity of these biomarkers have increased the prevalence of genomic profiling across solid malignancies. As an integral part of the management team of patients with advanced cancer, pathologists need to be aware of these emerging biomarkers, the therapies for which they determine eligibility, and the strengths and pitfalls of the available clinical assays. (Arch Pathol Lab Med. 2021;145:692-698; doi: 10.5858/arpa.2020-0513-RA, Massively parallel or next-generation sequencing (NGS) of large panels of genes in all tumor types has amplified our knowledge about the prevalence of certain oncogenic alterations and played a large [...]

Since its discovery, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused >100 million confirmed cases of coronavirus disease (COVID-19). The global effects of SARS-CoV-2 and the need to learn [...]

Abstract: A new species of mesophotic marine red algae, Ethelia hawaiiensis sp. nov., is illustrated and described. Ethelia hawaiiensis is distinguished from other members of the genus by its large [...]

On 1 August 2018, the Democratic Republic of the Congo (DRC) declared its tenth Ebola virus disease (EVD) outbreak. To aid the epidemiologic response, the Institut National de Recherche Biomédicale (INRB) implemented an end-to-end genomic surveillance system, including sequencing, bioinformatic analysis and dissemination of genomic epidemiologic results to frontline public health workers. We report 744 new genomes sampled between 27 July 2018 and 27 April 2020 generated by this surveillance effort. Together with previously available sequence data (n = 48 genomes), these data represent almost 24% of all laboratory-confirmed Ebola virus (EBOV) infections in DRC in the period analyzed. We inferred spatiotemporal transmission dynamics from the genomic data as new sequences were generated, and disseminated the results to support epidemiologic response efforts. Here we provide an overview of how this genomic surveillance system functioned, present a full phylodynamic analysis of 792 Ebola genomes from the Nord Kivu outbreak and discuss how the genomic surveillance data informed response efforts and public health decision making. Phylogeographic analysis of 792 Ebola virus genomes from the 2018 oubreak in the Democratic Republic of the Congo integrated into an end-to-end surveillance program demonstrates the feasibility of using genomic sequencing data to inform the public health epidemic response in near-real time., Author(s): Eddy Kinganda-Lusamaki [sup.1] [sup.2] , Allison Black [sup.3] [sup.4] , Daniel B. Mukadi [sup.2] , James Hadfield [sup.4] , Placide Mbala-Kingebeni [sup.1] [sup.2] , Catherine B. Pratt [sup.5] , [...]

Tuberculosis (TB), caused by Mycobacterium tuberculosis, is a major global public health issue. Southeast Asia contributes notably (44%) to global TB cases. Thailand is in the top 30 countries for [...]

A new analysis traces the story of the draft genome's impact on genomics since 2001, linking its effects on publications, drug approvals and understanding of disease. A new analysis traces the story of the draft genome's impact on genomics since 2001, linking its effects on publications, drug approvals and understanding of disease., Author(s): Alexander J. Gates, Deisy Morselli Gysi, Manolis Kellis, Albert-László Barabási Author Affiliations: A wealth of discovery built on the Human Genome Project -- by the numbers Data visualisation illustration [...]