Next-generation Sequencing Research Articles

From Genomic Exploration to Personalized Treatment: Next-Generation Sequencing in Oncology

Next-generation sequencing (NGS) has revolutionized personalized oncology care by providing exceptional insights into the complex genomic landscape. NGS offers comprehensive cancer profiling, which enables clinicians and researchers to better understand the molecular basis of cancer and to tailor treatment strategies accordingly. Targeted therapies based on genomic alterations identified through NGS have shown promise in improving patient outcomes across various cancer types, circumventing resistance mechanisms and enhancing treatment efficacy. Moreover, NGS facilitates the identification of predictive biomarkers and prognostic indicators, aiding in patient stratification and personalized treatment approaches. By uncovering driver mutations and actionable alterations, NGS empowers clinicians to make informed decisions regarding treatment selection and patient management. However, the full potential of NGS in personalized oncology can only be realized through bioinformatics analyses. Bioinformatics plays a crucial role in processing raw sequencing data, identifying clinically relevant variants, and interpreting complex genomic landscapes. This comprehensive review investigates the diverse NGS techniques, including whole-genome sequencing (WGS), whole-exome sequencing (WES), and single-cell RNA sequencing (sc-RNA-Seq), elucidating their roles in understanding the complex genomic/transcriptomic landscape of cancer. Furthermore, the review explores the integration of NGS data with bioinformatics tools to facilitate personalized oncology approaches, from understanding tumor heterogeneity to identifying driver mutations and predicting therapeutic responses. Challenges and future directions in NGS-based cancer research are also discussed, underscoring the transformative impact of these technologies on cancer diagnosis, management, and treatment strategies.

Cost-effectiveness and other considerations for different research techniques applied in ancient DNA analysis.

Ancient DNA (aDNA) analysis has developed rapidly since it first emerged in the 1980s, becoming an almost indispensable tool in anthropological and archaeological sciences. Earlier aDNA study was based on the polymerase chain reaction (PCR) technique, with which, unfortunately, modern DNA contamination and other authenticity issues were often incurred. These technical hurdles were soon overcome by application of advancements in the forms of the next generation sequencing (NGS) technique and others. However, since NGS requires money, time, and, in the case of large projects, manpower as well, genetic analysis of some ancient samples considered to be insignificant is commonly delayed or, in the worst cases, neglected entirely. We acknowledge that as a diagnostic tool in aDNA analysis, PCR is less accurate than NGS and more easily affected by modern DNA contamination; but it also has advantages, such as simplicity, time-saving, and greater ease of interpretation, among others. The role of PCR in aDNA analysis, then, should be reconsidered.

The Evolving Molecular Landscape and Actionable Alterations in Urologic Cancers

The genetic landscape of urologic cancers has evolved with the identification of actionable mutations that impact diagnosis, prognosis, and therapeutic strategies. This narrative review consolidates existing literature on genetic mutations across key urologic cancers, including bladder, renal, prostate, upper tract urothelial, testicular, and penile. The review highlights mutations in DNA damage repair genes, such as BRCA1/2 and PTEN, as well as pathway alterations like FGFR and PD-L1 overexpression. These mutations influence tumor behavior and therapeutic outcomes, emphasizing the need for precision oncology approaches. Molecular profiling, through tools like next-generation sequencing, has revolutionized patient care by enabling targeted treatment strategies, especially in cancers with distinct molecular subtypes such as luminal or basal bladder cancer and clear cell renal carcinoma. Emerging therapies, including FGFR inhibitors and immune checkpoint blockade, offer new treatment avenues, although resistance mechanisms remain a challenge. We also emphasize the importance of biomarker identification for personalized management, especially in metastatic settings where treatment intensification is often required. Future research is needed to further elucidate our understanding of the genetics affecting urologic cancers, which will help develop novel, individualized therapies to enhance oncologic outcomes.

Paediatric Acute Lymphoblastic Leukaemia: A Narrative Review of Current Knowledge and Advancements.

This review aims to provide an update on current knowledge regarding paediatric acute lymphoblastic leukaemia (ALL), focusing on recent advancements in diagnosis and treatment, as well as future directions in the field. ALL is the most frequently diagnosed paediatric malignancy, with advances leading to a 90% survival rate. The heterogeneity of childhood ALL requires a precise diagnostic algorithm incorporating morphological, immunophenotypic, and cytogenetic analyses. Research is exploring next-generation sequencing and artificial intelligence-aided techniques for future diagnostic approaches. Despite these advancements, global disparities in healthcare access hinder prompt diagnosis and management. The pathophysiology of ALL involves chromosomal and genetic alterations which disrupt cell-cycle regulation and result in uncontrolled lymphoblast proliferation. Environmental factors also contribute to leukaemogenesis. Risk-stratification based on genetic subtypes has significant implications for risk-based therapy. Chemotherapy is administered in three phases: induction, consolidation, and maintenance, with prophylactic intrathecal chemotherapy considered essential. For high-risk, refractory, or relapsed ALL, haematopoietic stem cell transplantation and novel therapies such as tyrosine kinase inhibitors, chimeric antigen receptor T-cell therapy, and blinatumomab immunotherapy, have improved outcomes. Ongoing clinical trials aim to further improve treatment efficacy, reduce toxicity, and increase survival. Although prevention strategies for ALL exist at three levels, the supporting evidence remains limited, highlighting a need for further research. Continued research and clinical trials are essential to addressing the gaps treatment efficacy and prevention strategies. Efforts to improve global healthcare access and integrate novel diagnostic and therapeutic approaches are crucial for advancing outcomes for paediatric patients with ALL.

Preliminary assessment of the diagnostic accuracy of cutaneous T-cell lymphoma through deep sequencing of T-cell receptor gamma gene

Abstract Background The diagnostic challenges in early mycosis fungoides (MF) and other cutaneous T-cell lymphomas (CTCL) persist despite advancements in molecular methods. Aim The study aims to provide a preliminary assessment of next-generation sequencing in analyzing T-cell receptor gamma (TRG) sequences for distinguishing CTCL from benign inflammatory disorders. Methods Skin samples from CTCL and benign inflammatory skin disorders proven clinicopathologically were assessed for TRG by NGS. Results Our study analyzed skin samples from a total of 36 subjects, comprising 22 cases of CTCL, including 14 MF and 8 other CTCLs, alongside 14 cases of benign inflammatory skin disorders. According to the LymphoTrack criteria, monoclonality was detected in 75.0 % of the overall 24 CTCL patients. Specifically, in MF cases, 10 out of 14 were identified as monoclonality, with all four non-monoclonal cases being in the patch stage. For the other CTCL, 6 out of 8 cases displayed monoclonality. Among the overall 22 CTCL patients, 11 had multiple biopsies, with 9 displaying the same dominant clone across different sites. Among the 14 benign cases, only the case with erythrodermic psoriasis exhibited monoclonality. Our decision tree analysis suggests that a high frequency of the most abundant clone, its ratio to the third most abundant clone, and TRG V-I segment usage are effective markers aiding in diagnosing CTCL. Conclusion Combination of the clone frequencies, and TRG V segment usage may enhance diagnosis for MF and other CTCLs, aiding in differentiating them from benign conditions. However, molecular diagnosis for patch-stage MF remains challenging.

The genomic landscape of papillary thyroid carcinoma on next-generation sequencing in patients undergoing total thyroidectomy.

Thyroidectomy is increasingly performed for suspected malignancy. This cohort study aimed to identify genetic markers associated with malignancy and determine the molecular landscape of papillary thyroid carcinoma (PTC) through next-generation sequencing (NGS) in patients undergoing total thyroidectomy. Among 116 surgical candidates, 103 patients (age=42.9±13.7years; Male: Female=14:89) with benign or malignant thyroid nodules were eligible. Live thyroid tissue samples harvested intraoperatively with adequate DNA and RNA yield were subjected to NGS on the Illumina NovaSeq 6000 platform for genomic and transcriptomic analysis, respectively. Histopathology comprised 20 malignant (19.4%) and 83 benign (80.6%) cases, including 16 PTC (15.5%) cases. On NGS, single nucleotidepolymorphisms (SNPs) in NTRK1 at NC_000001.11:156879016 on chromosome 1 and ALK at NC_000002.12:29717663 on chromosome 2 were frequent in malignant lesions (p<0.05). A SNP in ALK at NC_000002.12:29193706 was consistently a homozygous alternate alleleacross the cohort. DNA-sequencing of PTC lesions identified recurrentsomatic mutations in BRAF (100%), ALK (56.3%), RET (18.8%), PIK3CA (12.5%), NTRK1 (12.5%), NTRK2 (87.5%), NTRK3(12.5%), NRAS(6.3%), and PTCH1 (31.3%) genes. RNA sequencing revealednovelfusiongenes, including MKRN1-BRAF, RN7SL1-CDH1, IRF2BPL-MED12, MED12-IRF2BPL, CPM-MDM2, and AC005895.3-PDGFRB. Inreceiveroperative characteristics analysis, the AUCs ofALKmutationpredictingrecurrence and metastases were 0.818 and 0.783. This Indian study identified novel somatic mutations and fusion genes in PTC, revealing a distinct genomic landscape with implications in precision diagnostics and personalized therapies. NGS with intraoperative live sampling shows promise in prognostication and therapeutic optimization of advanced/metastatic PTC cases. CTRI/2020/09/027607dt 04/09/2020; REF/2020/08/036119.

Culturally responsive strategies and practical considerations for live tissue studies in Māori participant cohorts

IntroductionIndigenous communities globally are inequitably affected by non-communicable diseases such as cancer and coronary artery disease. Increased focus on personalized medicine approaches for the treatment of these diseases offers opportunities to improve the health of Indigenous people. Conversely, poorly implemented approaches pose increased risk of further exacerbating current inequities in health outcomes for Indigenous peoples. The advancement of modern biology techniques, such as three-dimensional (3D) in vitro models and next generation sequencing (NGS) technologies, have enhanced our understanding of disease mechanisms and individualized treatment responses. However, current representation of Indigenous peoples in these datasets is lacking. It is crucial that there is appropriate and ethical representation of Indigenous peoples in generated datasets to ensure these technologies can be used to maximize the benefit of personalized medicine for Indigenous peoples.MethodsThis project discusses the use of 3D tumor organoids and single cell/nucleus RNA sequencing to study cancer treatment responses and explore immune cell roles in coronary artery disease. Using key pillars from currently available Indigenous bioethics frameworks, strategies were developed for the use of Māori participant samples for live tissue and sequencing studies. These were based on extensive collaborations with local Māori community, scientific leaders, clinical experts, and international collaborators from the Broad Institute of MIT and Harvard. Issues surrounding the use of live tissue, genomic data, sending samples overseas and Indigenous data sovereignty were discussed.ResultsThis paper illustrates a real-world example of how collaboration with community and the incorporation of Indigenous worldviews can be applied to molecular biology studies in a practical and culturally responsive manner, ensuring fair and equitable representation of Indigenous peoples in modern scientific data.

Antimicrobial susceptibility of enterobacterales causing bloodstream infection in United States medical centres: comparison of aztreonam-avibactam with beta-lactams active against carbapenem-resistant enterobacterales.

Bloodstream infection (BSI) is associated with poor outcomes especially when effective antimicrobial therapy and control of infection source are delayed. As the frequency of Enterobacterales producing metallo-β-lactamases (MBL) and/or OXA-48-like carbapenemases is increasing in some United States (US) medical centres, effective antimicrobials to treat the infections caused by these organisms are urgently needed. Aztreonam-avibactam is under clinical development for treatment of infections caused by Gram-negative bacteria, including MBL producers. To evaluate the antimicrobial susceptibility of Enterobacterales causing BSI in US medical centres and compare the activity of aztreonam-avibactam with ceftazidime-avibactam, meropenem-vaborbactam, imipenem-relebactam, cefiderocol, and other antimicrobials used to treat BSI. 4,802 Enterobacterales were consecutively collected (1/patient) from 72 US medical centres in 2020-2022 and susceptibility tested by broth microdilution. Aztreonam-avibactam was tested with avibactam at a fixed concentration of 4mg/L. A pharmacokinetic/pharmacodynamic susceptible breakpoint of ≤ 8mg/L was applied for aztreonam-avibactam for comparison. Carbapenem-resistant Enterobacterales (CRE) isolates were tested for β-lactamase-encoding genes using Next-generation sequencing. Aztreonam-avibactam was highly active against Enterobacterales; only 2 isolates showed aztreonam-avibactam MICs > 8mg/L: 1 meropenem-susceptible E. coli and 1 K. aerogenes (CRE). All carbapenemase producers and 98.0% of CRE were inhibited at an aztreonam-avibactam MIC of ≤ 8mg/L. CRE susceptibility rates were 81.6% for ceftazidime-avibactam, 65.3% for meropenem-vaborbactam, 61.2% for imipenem-relebactam, and 87.8% for cefiderocol. Aztreonam-avibactam retained activity (MIC, ≤ 8mg/L) against all (100.0%) meropenem-vaborbactam nonsusceptible (n = 17), 99.5% of imipenem-relebactam nonsusceptible (n = 206), and 90.0% of ceftazidime-avibactam nonsusceptible (n = 10) isolates. The most common carbapenemases were KPC-2/3 (57.1% of CREs), OXA-48-like (16.3%), and NDM (14.3%). A carbapenemase gene was not observed in 12.3% of CREs. Ceftazidime-avibactam and meropenem-vaborbactam were active against 100.0% of KPC producers, but ceftazidime-avibactam showed limited activity against MBL producers and meropenem-vaborbactam showed limited activity against OXA-48-like and MBL producers. The most active non-β-lactam comparators against CRE were gentamicin (49.0% susceptible) and amikacin (44.9% susceptible). Aztreonam-avibactam demonstrated potent activity against a large collection of Enterobacterales isolated from patients with BSI in US hospitals, including CRE, MBL producers, and isolates resistant to recently approved β-lactamase inhibitor combinations.

Development of a whole-cell SELEX process to select species-specific aptamers against Aspergillus niger.

Spores produced by the filamentous fungus Aspergillus niger are abundant in a variety of environments. The proliferation of this fungus in indoor environments has been associated to health risks and its conidia can cause allergic reaction and severe invasive disease in animals and humans. Therefore, the detection and monitoring of Aspergillus conidia is of utmost importance to prevent serious fungal infections and contaminations. Among others, aptamers could serve as biosensors for the specific detection of fungal spores. In this study, DNA aptamers specific to conidia of A. niger were developed by optimizing a whole-cell SELEX approach. Three whole-cells SELEX experiments were performed in parallel with similar conditions. Quantification of recovered ssDNA and melting curve analyses were applied to monitor the ongoing SELEX process. Next-generation sequencing was performed on selected recovered ssDNA pools, allowing the identification of DNA aptamers which bind with high affinity to the target cells. The developed aptamers were shown to be species-specific, being able to bind to A. niger but not to A. tubingensis or to A. nidulans. The binding affinity of two aptamers (AN01-R9-006 and AN02-R9-185) was measured to be 58.97nM and 138.71nM, respectively, which is in the range of previously developed aptamers. This study demonstrates that species-specific aptamers can be successfully developed via whole-cell SELEX to distinguish different Aspergillus species and opens up new opportunities in the field of diagnostics of fungal infections.

Targeted NGS Revealed Pathogenic Mutation in a 13-Year-Old Patient with Homozygous Familial Hypercholesterolemia: A Case Report

Familial hypercholesterolemia is an autosomal hereditary disease defined by an increased level of low-density lipoprotein cholesterol (LDL-C), which predisposes significant risks for premature cardiovascular disorders. We present a family trio study: proband, a 13-year-old Kazakh girl with homozygous familial hypercholesterolemia (HoFH) and her parents. HoFH is much more rare and severe than a heterozygous form of the disorder. HoFH patients generally present with LDL-C levels exceeding 13 mmol/L, resulting in early and life-threatening cardiovascular events within the first decades of life. In cases of neglected treatment, young patients have a risk of death from coronary diseases before the age of 30. The aim of this research was to identify genetic mutations in the affected patient and her parents. Genetic testing was necessary due to highly elevated LDL-C levels and the presence of multiple xanthomas. Targeted next-generation sequencing (NGS) was performed in this study using the Illumina TruSight cardio panel, which targets 174 genes related to cardiac disorders. The girl was diagnosed with HoFH based on the results of genetic testing. A biallelic mutation was observed in exon 3 of the low-density lipoprotein receptor (LDLR): c. 295 G&gt;A (p.Glu99Lys). Sanger sequencing confirmed that the mutant gene was inherited from both parents. After confirming the genetic diagnosis of HoFH, the patient was treated with LDL apheresis and statins. This case report is the first study of HoFH in a pediatric patient from the Central Asian region. Globally, it emphasizes the need for increased clinical awareness among healthcare providers, as early detection and intervention are important for improving outcomes, particularly in pediatric patients with this rare genetic disorder.

Peroxisome proliferator-activated receptor agonists as an adjuvant for cancer therapy: A review

Cancer is now one of the leading diseases responsible for the highest mortality rates worldwide. Cancer treatment is extremely intricate and is often associated with less targeted effects and more side effects. In the last few years, two significant revolutions in cancer treatment have altered treatment paradigms: immuno-oncology and the pursuit of actionable changes in oncogene-driven cancers. Significant obstacles continue to exist in both areas of cancer treatment. Next-generation sequencing technologies for molecular prescreening in clinical research are advancing, but their widespread clinical use is hindered by challenges related to the clinical interpretation of large genomic data. Moreover, cancer mono-chemotherapy is associated with issues such as inadequate efficacy, drug resistance, and systemic toxicity. It is not possible to administer cytotoxic drugs limitlessly. Combination therapy was developed in response to this circumstance, with the expectation of achieving high therapeutic efficacy at lower dosages of medication. Peroxisome proliferator-activated receptors (PPARs) are a group of essential lipid sensors and metabolic pathway regulators. In addition, they possess the ability to modulate immunity, inflammation, and endothelial nitric oxide synthase activation. Alongside their well-established functions, new insights into the roles of PPAR agonists in cancer research are emerging. After reviewing current research, it is evident that PPAR modulators have significant potential for managing cancer. This review aims to consolidate the functions of PPAR ligands alongside other cancer therapies. We provide a comprehensive perspective on the applicability of PPAR ligands in cancer treatment as an adjuvant.

Exploring the appropriate situation of performing CSF mNGS in patients with proposed intracranial infections.

Identifying the responsible pathogen is crucial for precision medicine in intracranial infections, and Cerebrospinal Fluid (CSF) Metagenomic Next-Generation Sequencing (mNGS) is a reliable method for this detection. However, the indiscriminate utilization of this approach may impose a financial burden on both patients and society. The study aims to investigate the optimal conditions for applying CSF mNGS in patients with suspected intracranial infections, offering valuable references for precision medicine of intracranial infections. A total of 175 hospitalized patients presenting with suspected intracranial infections were selected for retrospective analysis. Base on the detection of responsible pathogens using CSF mNGS, the patients were categorized into two groups, responsible pathogens in Group A were detected but not in Group B. The types of responsible pathogens in group A and the final diagnosis of patients in group B were analyzed. Demographic data, clinical presentation, CSF analysis, imaging results, and electroencephalography (EEG) findings were analyzed for both groups. Finally, a scoring system was established to promptly assess the appropriateness of CSF mNGS for patients with suspected intracranial infections. Each independent predictor was assigned a score of 1, and the patients were subsequently scored. We advocate sending patients' CSF for mNGS when the cumulative score is ≥ 2. In Group A, the predominant responsible pathogen was the varicella-zoster virus (VZV), while Group B exhibited the highest proportion of final diagnoses related to epilepsy. The logistic regression model indicates that headache [OR = 2.982, 95% CI (1.204-7.383), p = 0.018], increased cerebrospinal fluid white cell count [OR = 4.022, 95% CI (1.331-12.156), p = 0.014], and decreased cerebrospinal fluid glucose levels [OR = 9.006, 95% CI (2.778-29.194), P < 0.001] are independent predictive factors for intracranial infection pathogens detected by CSF mNGS. Under this scoring system, the sensitivity for detecting the responsible pathogen was 57.5%, and the specificity was 87.4%. The likelihood of detecting the responsible pathogen through CSF mNGS in patients with suspected intracranial infections can be evaluated using the scoring system. Furthermore, it is crucial to consider the possibility of another condition, such as epilepsy, when the responsible pathogen is not detected using cerebrospinal fluid mNGS.

Direct testing of natural twister ribozymes from over a thousand organisms reveals a broad tolerance for structural imperfections.

Twister ribozymes are an extensively studied class of nucleolytic RNAs. Thousands of natural twisters have been proposed using sequence homology and structural descriptors. Yet, most of these candidates have not been validated experimentally. To address this gap, we developed Cleavage High-Throughput Assay (CHiTA), a high-throughput pipeline utilizing massively parallel oligonucleotide synthesis and next-generation sequencing to test putative ribozymes en masse in a scarless fashion. As proof of principle, we applied CHiTA to a small set of known active and mutant ribozymes. We then used CHiTA to test two large sets of naturally occurring twister ribozymes: over 1600 previously reported putative twisters and ∼1000 new candidate twisters. The new candidates were identified computationally in ∼1000 organisms, representing a massive increase in the number of ribozyme-harboring organisms. Approximately 94% of the twisters we tested were active and cleaved site-specifically. Analysis of their structural features revealed that many substitutions and helical imperfections can be tolerated. We repeated our computational search with structural descriptors updated from this analysis, whereupon we identified and confirmed the first intrinsically active twister ribozyme in mammals. CHiTA broadly expands the number of active twister ribozymes found in nature and provides a powerful method for functional analyses of other RNAs.

TP53 Mutation Status in Myelodysplastic Neoplasm and Acute Myeloid Leukemia: Impact of Reclassification Based on the 5th WHO and International Consensus Classification Criteria: A Korean Multicenter Study.

TP53 mutations are associated with poor prognosis in myelodysplastic neoplasm (MDS) and AML. The updated 5th WHO classification and International Consensus Classification (ICC) categorize TP53-mutated MDS and AML as unique entities. We conducted a multicenter study in Korea to investigate the characteristics of TP53-mutated MDS and AML, focusing on diagnostic aspects based on updated classifications. This study included patients aged ≥ 18 yrs who were diagnosed as having MDS (N=1,244) or AML (N=2,115) at six institutions. The results of bone marrow examination, cytogenetic studies, and targeted next-generation sequencing, including TP53, were collected and analyzed. TP53 mutations were detected in 9.3% and 9.2% of patients with MDS and AML, respectively. Missense mutation was the most common, with hotspot codons R248/R273/G245/Y220/R175/C238 accounting for 25.4% of TP53 mutations. Ten percent of patients had multiple TP53 mutations, and 78.4% had a complex karyotype. The median variant allele frequency (VAF) of TP53 mutations was 41.5%, with a notable difference according to the presence of a complex karyotype. According to the 5th WHO classification and ICC, the multi-hit TP53 mutation criteria were met in 58.6% and 75% of MDS patients, respectively, and the primary determinants were a TP53 VAF >50% for the 5th WHO classification and the presence of a complex karyotype for the ICC. Collectively, we elucidated the molecular genetic characteristics of patients with TP53-mutated MDS and AML, highlighting key factors in applying TP53 mutation-related criteria in updated classifications, which will aid in establishing diagnostic strategies.

Duration of onset, body temperature and C-reactive protein can be used to predict the results of pus culture in children with acute osteomyelitis of long bones.

With the application of PCR testing and Metagenomic Next-Generation Sequencing(mNGS), the detection rate of causative organisms in paediatric bone and joint infections has been greatly improved. The aim of our study is to identify some indicators that could be used to distinguish the culture results to optimize the use of PCR and mNGS. In this study, a total of 117 cases of acute osteomyelitis of long bones in children who underwent pus culture were included. Patients were grouped as culture-negative (n:21) and culture-positive (n:96) groups according to the results of pus culture. Age, sex, duration of onset, maximum body temperature at onset, inflammatory indicators and D-dimer after admission were systematically collected for all patients and were compared for both groups. ROC curve (ROC) was used to evaluate the diagnostic efficiency of culture-negative. Logistic regression analysis was conducted to determine independent risk factors for culture-negative. There was no significant difference in age, sex and erythrocyte sedimentation rate between culture-negative group and culture-positive group (P > 0.05). The duration of onset was longer, and the temperature, white blood cells, neutrophils count, C-reactive protein and D-dimer were less elevated in culture-negative acute osteomyelitis (P < 0.05). Duration of onset, maximum body temperature at onset, white blood cell count, neutrophil count, C-reactive protein, and D-dimer have certain diagnostic efficacy in judging the efficacy of negative culture. Logistic regression analysis indicated that the duration of onset more than 6.5 days, the maximum body temperature at onset lower than 38.35℃ and C-reactive protein lower than 78.40mg/L were independent risk factors for negative culture (P < 0.05). Our study revealed that duration of onset more than 6.5 days, maximum body temperature at onset lower than 38.35℃ and C-reactive protein lower than 78.40mg/L were independent risk factors for predicting negative culture. In children with this type of acute osteomyelitis, we recommend that the pus be tested by PCR or mNGS as a priority.

Evaluating methods for identifying and quantifying Streptococcus pneumoniae co-colonization using next-generation sequencing data.

Detection of multiple pneumococcal serotype carriage can enhance monitoring of pneumococcal vaccine impact, particularly among high-burden childhood populations. We assessed methods for identifying co-carriage of pneumococcal serotypes from whole-genome sequences. Twenty-four nasopharyngeal samples were collected during community carriage surveillance from healthy children in Blantyre, Malawi, which were then serotyped by microarray. Pneumococcal DNA from culture plate sweeps were sequenced using Illumina MiSeq, and genomic serotyping was carried out using SeroCall and PneumoKITy. Their sensitivity was calculated in reference to the microarray data. Local maxima in the single-nucleotide polymorphism (SNP) density distributions were assessed for their correspondence to the relative abundance of serotypes. Across the 24 individuals, the microarray detected 77 non-unique serotypes, of which 42 occurred at high relative abundance (>10%) (per individual, median, 3; range, 1-6 serotypes). The average sequencing depth was 57X (range: 21X-88X). The sensitivity of SeroCall for identifying high-abundance serotypes was 98% (95% CI, 0.87-1.00), 20% (0.08-0.36) for low abundance (<10%), and 62% (0.50-0.72) overall. PneumoKITy's sensitivity was 86% (0.72-0.95), 20% (0.06-0.32), and 56% (0.42-0.65), respectively. Local maxima in the SNP frequency distribution were highly correlated with the relative abundance of high-abundance serotypes. Six samples were resequenced, and the pooled runs had an average fourfold increase in sequencing depth. This allowed genomic serotyping of two of the previously undetectable seven low-abundance serotypes. Genomic serotyping is highly sensitive for the detection of high-abundance serotypes in samples with co-carriage. Serotype-associated reads may be identified through SNP frequency, and increased read depth can increase sensitivity for low-abundance serotype detection.IMPORTANCEPneumococcal carriage is a prerequisite for invasive pneumococcal disease, which is a leading cause of childhood pneumonia. Multiple carriage of unique pneumococcal serotypes at a single time point is prevalent among high-burden childhood populations. This study assessed the sensitivity of different genomic serotyping methods for identifying pneumococcal serotypes during co-carriage. These methods were evaluated against the current gold standard for co-carriage detection. The results showed that genomic serotyping methods have high sensitivity for detecting high-abundance serotypes in samples with co-carriage, and increasing sequencing depth can increase sensitivity for low-abundance serotypes. These results are important for monitoring vaccine impact, which aims to reduce the prevalence of specific pneumococcal serotypes. By accurately detecting and identifying multiple pneumococcal serotypes in carrier populations, we can better evaluate the effectiveness of vaccination programs.

Malignant Salivary Gland Neoplasm of the Tongue Base with EWSR1::BEND2 Fusion: An Unusual Case with Literature Review.

Salivary gland malignancies may have overlapping architectural patterns, tumor morphology, and immunohistochemical phenotypes, presenting challenges in precise classification. Molecular phenotyping has become quite useful for providing an additional diagnostic modality, and potential drug targets. Here we reported a young female patient with salivary gland tumor of the tongue base harboring genetic alterations by next generation sequencing (NGS). The morphological, immunohistochemical and molecular features of this case were described, and related literature was reviewed. The tumor showed an epithelial myoepithelial architecture arranged in cords and tubules interwoven with a chondromyxoid stroma, along with perineural invasion and adjacent striated muscle infiltration. Myoepithelial cells were positive for CK5/6, partially positive for P63 and CK7, and sporadically positive for S100. Immunoprofiling revealed a low density of infiltrating lymphocytes and macrophages and the absence of programmed death ligand 1 (PD-L1). Notably, RNA-based NGS showed EWSR1::BEND2 gene fusion in this tumor, and EWSR1 break-apart was confirmed by fluorescence in situ hybridization. This led to a final diagnosis of a minor salivary gland malignancy with EWSR1::BEND2 fusion. Only two other cases of salivary gland tumors with EWSR1::BEND2 fusion had been previously reported, which were also detected via RNA-based NGS. This study emphasized that EWSR1::BEND2 fusion may drive the carcinogenesis in salivary glands neoplasia. In clinic RNA-based NGS could be essential for precise genotyping of EWSR1 fusion in this rare disease.

Comparison of Four Different DNA Isolation Methods from MGIT Culture for Long-Read Whole Genome Sequencing of Mycobacterium tuberculosis

Background: Tuberculosis (TB) remains a global health challenge, particularly due to drug resistance and limitations in rapid diagnosis. Next-generation sequencing (NGS), especially long-read whole genome sequencing (WGS), shows promise for rapidly detecting TB and drug resistance, but it requires high-quality DNA, which is difficult to extract from Mycobacterium tuberculosis due to its complex cell wall. Objectives: This study evaluated four DNA isolation methods for extracting pure DNA from M. tuberculosis, aiming to standardize protocols for long-read WGS. Methods: Mycobacterium tuberculosis H37RV colonies were grown in BACTEC MGIT liquid medium. Two pellets were prepared as the initial material for the DNA extraction protocol: Pellets from 1 mL McFarland 2 suspensions and all growing colonies from two MGIT liquid cultures. Four DNA extraction methods were used: The cetyltrimethylammonium bromide (CTAB) method, GeneJET Genomic DNA Purification Kit, Quick-DNA Fecal/Soil Microbe Kit, and Genematrix Tissue/Bacterial DNA Purification Kit, with some modifications. DNA quality was assessed based on concentration, purity, and integrity. Results: Among the tested methods, the Quick-DNA Fecal/Soil Kit yielded approximately 85 ng/mL of DNA and a purity of 1.9 at 260/280 nm from the colonial pellet of two MGIT tubes. However, lower intact DNA [DNA integrity number (DIN) ~ 6.8] was obtained with this kit. The CTAB method provided the highest intact DNA (DIN ~ 9.5), although the purity of the DNA was not sufficient. Conclusions: Based on three repetitions of McF-2 and colonial pellet extractions, the Quick-DNA Fecal/Soil Kit yielded the highest DNA quantity and purity but showed lower integrity compared to other methods, indicating the need for adjustments. A pellet from two MGIT cultures (~ 100 µL) is suitable for long-read WGS with this kit. However, a larger sample size is required to generalize these findings. For effective long-read sequencing of M. tuberculosis, DNA extraction protocols must be optimized to balance yield, fragment size, and purity for accurate sequencing and drug resistance analysis.

Deciphering normal and cancer stem cell niches by spatial transcriptomics: opportunities and challenges.

Cancer stem cells (CSCs) often exhibit stem-like attributes that depend on an intricate stemness-promoting cellular ecosystem within their niche. The interplay between CSCs and their niche has been implicated in tumor heterogeneity and therapeutic resistance. Normal stem cells (NSCs) and CSCs share stemness features and common microenvironmental components, displaying significant phenotypic and functional plasticity. Investigating these properties across diverse organs during normal development and tumorigenesis is of paramount research interest and translational potential. Advancements in next-generation sequencing (NGS), single-cell transcriptomics, and spatial transcriptomics have ushered in a new era in cancer research, providing high-resolution and comprehensive molecular maps of diseased tissues. Various spatial technologies, with their unique ability to measure the location and molecular profile of a cell within tissue, have enabled studies on intratumoral architecture and cellular cross-talk within the specific niches. Moreover, delineation of spatial patterns for niche-specific properties such as hypoxia, glucose deprivation, and other microenvironmental remodeling are revealed through multilevel spatial sequencing. This tremendous progress in technology has also been paired with the advent of computational tools to mitigate technology-specific bottlenecks. Here we discuss how different spatial technologies are used to identify NSCs and CSCs, as well as their associated niches. Additionally, by exploring related public data sets, we review the current challenges in characterizing such niches, which are often hindered by technological limitations, and the computational solutions used to address them.

Germline Variants in DNA Interstrand-Cross Link Repair Genes May Contribute to Increased Susceptibility for Serrated Polyposis Syndrome

Serrated polyposis syndrome (SPS) is characterized by the development of multiple colorectal serrated polyps and increased predisposition to colorectal cancer (CRC). However, the molecular basis of SPS, especially in cases presenting family history of SPS and/or polyps and/or CRC in first-degree relatives (SPS-FHP/CRC), is still poorly understood. In a previous study, we proposed the existence of two molecular entities amongst SPS-FHP/CRC families, proximal/whole-colon and distal SPS-FHP/CRC, according to the preferential location of lesions and somatic events involved in tumor initiation. In the present study, we aimed to investigate these distinct subgroups of SPS patients in a larger cohort at the germline level and to identify the genetic defects underlying an inherited susceptibility for these two entities. Next-generation sequencing was performed using multigene analysis with a custom-designed panel in a Miseq platform in 60 SPS patients (with and without/unknown FHP/CRC). We found germline pathogenic variants in 6/60 patients (ATM, FANCM, MITF, RAD50, RAD51C, and RNF43). We also found variants of unknown significance (VUS), with prediction of probable damaging effect in 23/60 patients (ATM, BLM, BRCA1, FAN1, ERCC2, ERCC3, FANCA, FANCD2, FANCL, MSH2, MSH6, NTHL1, PALB2, PDGFRA, PMS2, PTCH1, RAD51C, RAD51D, RECQL4, TSC2, WRN, and XRCC5 genes). Most variants were detected in gene coding for proteins of the Fanconi Anemia (FA) pathway involved in the DNA Interstrand-Cross Link repair (ICLR). Notably, variants in ICLR genes were significantly more frequent in the proximal/whole-colon than in the distal subgroup [15/44 (34%) vs 1/16 (6%), p = 0.025], as opposed to the non-ICLR genes that were slightly more frequent in the distal group [8/44 (18%) vs. 5/16 (31%), p &gt; 0.05]. Germline defects in the DNA-ICLR genes may contribute to increased serrated colorectal polyps/carcinoma risk in SPS patients, particularly in proximal/whole-colon SPS. The inclusion of DNA-ICLR genes in the genetic diagnosis of SPS patients, mainly in those with proximal/whole-colon lesions, should be considered and validated by other studies. In addition, patients with germline defects in the DNA-ICLR genes may be more sensitive to treatment with platinum-based therapeutics, which can have implications in the clinical management of these patients.