Small Variants Research Articles

Analysis of DMD gene variants in a single center

Objective: To investigate the DMD genetic variants of the Chinese population with Duchenne (DMD) and Becker muscular dystrophies (BMD). Methods: A cross-sectional study was conducted on 2 690 unrelated patients with DMD and BMD aged 0-18 who visited the Genetic and Prenatal Diagnosis Center of the First Affiliated Hospital of Zhengzhou University from January 2005 to February 2022. The clinical data, such as gender, age, clinical manifestations, and address, were collected. Multiplex ligation-dependent probe amplification, next generation sequencing panel, Sanger sequencing, and PCR amplification were used to detect the variants of the DMD gene in the patients, whose clinical information and gene detection results were descriptively analyzed. Results: The 2 690 patients included 2 648 males and 42 females, with an age of 6.0 (4.0, 9.0) years. The serum creatine kinase increased in all patients. Pathogenic DMD gene variants were detected in the 2 618 patients, including 1 875 cases (71.6%) large deletions, 231 cases (8.8%) duplications, and 512 cases (19.6%) small variants. Among the deletion variants, the deletion of 3 exons was the most common, accounting for 15.4% (288/1 875); and hotspot deletion involved exons 45 to 50, accounting for 6.3% (119/1 875). Exon 2 was the most common type duplication region, accounting for 13.0% (30/231). Small variants were distributed in all 79 exons of the DMD gene, with no hotspots. In addition, the 46 small variants were previously unreported. Conclusion: Exon deletion is the most common type of DMD gene variant, followed by small variants and exon duplication.

Abstract PR005: Tracing the clonal dynamic of metastatic castration-resistant prostate cancer over immunotherapy using circulating tumor DNA

Abstract Human cancer tissues are known to release their own DNA into body fluids such as plasma. These DNA molecules derived from tumors, collectively known as circulating tumor DNA (ctDNA), contain genetic information about disease progression at the time of sampling. Importantly, ctDNA has recently been utilized for capturing the whole-body disease profile and when sampled at various time points over the treatment, can inform the dynamic of clonal heterogeneity and its contribution to therapy failures. Metastatic castration-resistant prostate cancer (mCRPC) is a class of cancerous diseases with a high degree of clonal heterogeneity and high mortality which is largely due to the frequent emergence of therapy resistance. Therefore, reconstructing the clonal history for mCRPC diseases using ctDNA has great potential in identification of novel and targetable molecular mechanisms that drive mCRPC progression. To assess this possibility, we hypothesize that tumor clones that are responsible for therapy resistance carry distinct genomic profiles, which are captured in plasma ctDNA and could be computationally resolved through genomic sequencing and clonal reconstruction. To address this question, we obtained plasma cell-free DNA (cfDNA), a mixture of ctDNA and other tissue-derived DNA, from 38 individuals treated with combination PD-L1 and PARP inhibition involved in a recent clinical trial (NCT02484404). Whole-genome sequencing was performed using cfDNA and fragmented buffy coat DNA as germline control. cfDNA samples with a tumor fraction of lower than 10% were excluded. Various computational strategies were used to model the clonal structures of diseases and estimate the temporal order in which small and large structural variants emerged. Through this approach, we observed a negative association between cfDNA tumor fraction and therapy response. Multiple clonal evolutionary patterns leading to therapy failures were observed. For example, both gain and loss of activating androgen receptor mutations were detected in different cases following the treatment, which represents two distinct mechanisms of evading immunotherapy targeting. As a result, changes in the relevant transcriptional activities were also detected through ctDNA fragment-based computational inference. Additionally, clonal persistence was detected in multiple cases that exhibited stable diseases upon the treatment, which involves loss-of-function mutations in p53, ATM, and CDK12. To estimate the potential contribution to plasma ctDNA by metastatic diseases, multi-region whole genome and exome sequencing data of the tumors that are available for some cases prior to the treatment were also analyzed. Clones resolved from analyzing ctDNA were computationally mapped to the primary disease or metastatic tissue with a shared set of mutations in a subset of cases and may explain the patterns of treatment response. Our novel findings from this study will fill in a critical gap of knowledge about the complex genetic mechanisms driving mCRPC immunotherapy resistance. Citation Format: Chennan Li, Anna Baj, Clara C. Y. Seo, Nicholas T. Terrigino, John R. Bright, S. Thomas Hennigan, Isaiah M. King, Scott Wilkinson, Shana Y. Trostel, William D. Figg, William L. Dahut, Jung Min Lee, David Y. Takeda, Fatima Karzai, Adam G. Sowalsky. Tracing the clonal dynamic of metastatic castration-resistant prostate cancer over immunotherapy using circulating tumor DNA [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Translating Cancer Evolution and Data Science: The Next Frontier; 2023 Dec 3-6; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_2):Abstract nr PR005.

Utility of long-read sequencing for All of Us

The All of Us (AoU) initiative aims to sequence the genomes of over one million Americans from diverse ethnic backgrounds to improve personalized medical care. In a recent technical pilot, we compare the performance of traditional short-read sequencing with long-read sequencing in a small cohort of samples from the HapMap project and two AoU control samples representing eight datasets. Our analysis reveals substantial differences in the ability of these technologies to accurately sequence complex medically relevant genes, particularly in terms of gene coverage and pathogenic variant identification. We also consider the advantages and challenges of using low coverage sequencing to increase sample numbers in large cohort analysis. Our results show that HiFi reads produce the most accurate results for both small and large variants. Further, we present a cloud-based pipeline to optimize SNV, indel and SV calling at scale for long-reads analysis. These results lead to widespread improvements across AoU.

HiPhase: jointly phasing small, structural, and tandem repeat variants from HiFi sequencing.

In diploid organisms, phasing is the problem of assigning the alleles at heterozygous variants to one of two haplotypes. Reads from PacBio HiFi sequencing provide long, accurate observations that can be used as the basis for both calling and phasing variants. HiFi reads also excel at calling larger classes of variation, such as structural or tandem repeat variants. However, current phasing tools typically only phase small variants, leaving larger variants unphased. We developed HiPhase, a tool that jointly phases SNVs, indels, structural, and tandem repeat variants. The main benefits of HiPhase are (i) dual mode allele assignment for detecting large variants, (ii) a novel application of the A*-algorithm to phasing, and (iii) logic allowing phase blocks to span breaks caused by alignment issues around reference gaps and homozygous deletions. In our assessment, HiPhase produced an average phase block NG50 of 480 kb with 929 switchflip errors and fully phased 93.8% of genes, improving over the current state of the art. Additionally, HiPhase jointly phases SNVs, indels, structural, and tandem repeat variants and includes innate multi-threading, statistics gathering, and concurrent phased alignment output generation. HiPhase is available as source code and a pre-compiled Linux binary with a user guide at https://github.com/PacificBiosciences/HiPhase.

Extended application of PGT-M strategies for small pathogenic CNVs.

The preimplantation genetic testing for aneuploidy (PGT-A) platform is not currently available for small copy-number variants (CNVs), especially those < 1 Mb. Through strategies used in PGT for monogenic disease (PGT-M), this study intended to perform PGT for families with small pathogenic CNVs. Couples who carried small pathogenic CNVs and underwent PGT at the Reproductive and Genetic Hospital of CITIC-Xiangya (Hunan, China) between November 2019 and April 2023 were included in this study. Haplotype analysis was performed through two platforms (targeted sequencing and whole-genome arrays) to identify the unaffected embryos, which were subjected to transplantation. Prenatal diagnosis using amniotic fluid was performed during 18-20 weeks of pregnancy. PGT was successfully performed for 20 small CNVs (15 microdeletions and 5 microduplications) in 20 families. These CNVs distributed on chromosomes 1, 2, 6, 7, 13, 15, 16, and X with sizes ranging from 57 to 2120 kb. Three haplotyping-based PGT-M strategies were applied. A total of 89 embryos were identified in 25 PGT cycles for the 20 families. The diagnostic yield was 98.9% (88/89). Nineteen transfers were performed for 17 women, resulting in a 78.9% (15/19) clinical pregnancy rate after each transplantation. Of the nine women who had healthy babies, eight accepted prenatal diagnosis and the results showed no related pathogenic CNVs. Our results show that the extended haplotyping-based PGT-M strategy application for small pathogenic CNVs compensated for the insufficient resolution of PGT-A. These three PGT-M strategies could be applied to couples with small pathogenic CNVs.

Attenuation of neurovirulence of chikungunya virus by a single amino acid mutation in viral E2 envelope protein

BackgroundChikungunya virus (CHIKV) has reemerged as a major public health concern, causing chikungunya fever with increasing cases and neurological complications.MethodsIn the present study, we investigated a low-passage human isolate of the East/ Central/South African (ECSA) lineage of CHIKV strain LK(EH)CH6708, which exhibited a mix of small and large viral plaques. The small and large plaque variants were isolated and designated as CHIKV-SP and CHIKV-BP, respectively. CHIKV-SP and CHIKV-BP were characterized in vitro and in vivo to compare their virus production and virulence. Additionally, whole viral genome analysis and reverse genetics were employed to identify genomic virulence factors.ResultsCHIKV-SP demonstrated lower virus production in mammalian cells and attenuated virulence in a murine model. On the other hand, CHIKV-BP induced higher pro-inflammatory cytokine levels, compromised the integrity of the blood–brain barrier, and led to astrocyte infection in mouse brains. Furthermore, the CHIKV-SP variant had limited transmission potential in Aedesalbopictus mosquitoes, likely due to restricted dissemination. Whole viral genome analysis revealed multiple genetic mutations in the CHIKV-SP variant, including a Glycine (G) to Arginine (R) mutation at position 55 in the viral E2 glycoprotein. Reverse genetics experiments confirmed that the E2-G55R mutation alone was sufficient to reduce virus production in vitro and virulence in mice.ConclusionsThese findings highlight the attenuating effects of the E2-G55R mutation on CHIKV pathogenicity and neurovirulence and emphasize the importance of monitoring this mutation in natural infections.

Formation mechanism of skarn iron deposit: Evidence from Fe-rich enclave in porphyritic monzonite

Skarn deposits constitute a significant reservoir of high-grade iron (Fe) ores in China, yet the metallogenic processes remain debated. This study focuses on the iron-rich enclaves embedded within porphyritic monzonite, aiming to unravel the metallogenic mechanisms underlying skarn Fe deposits. The host porphyritic monzonite intrudes into porphyritic diorite. Within the iron-rich enclaves three types of magnetite (Mt) are discerned. Mt-I, ranging from 50 to 100 μm in size, predominantly occupies the core of the enclave, enshrouding diopside at its center. Mt-II, with a size range of 20–40 μm, is primarily distributed in the middle of the enclave. The smallest variant, Mt-III, measuring approximately 1 μm, typically manifests at the peripheries of Mt-I and Mt-II. Comparative analysis reveals that Mt-II exhibits higher total rare earth elements (REE), Sr, Ca, alongside lower TiO2 content in contrast to Mt-I. Notably, Mt-II displays a characteristic W-type tetrad effect of REE, indicative of crystallization in a fluid-saturated environment. In contrast, Mt-III, characterized by microcrystalline magnetite, is inferred to have formed under conditions of rapid cooling.Our interpretation posits a two-stage genesis for these enclaves. The initial stage involves the formation of iron-rich magma within a magma chamber situated at depths of 8–10 km, during which Mt-I crystallizes. Subsequently, the second stage unfolds as mantle-derived fluids infiltrate the magma chamber, leading to the formation of Mt-II. The fluid overpressure within the magma chamber triggers a swift ascent of iron-bearing melt-fluid, localized at depths ranging from 1.5 to 2.6 km, resulting in the crystallization of Mt-III. Our results provide valuable insights into the metallogenic processes governing skarn Fe deposits, and the complex geological evolution of these deposits.

ZnO-templated hollow amorphous carbon: oxygen adsorption and doping synergy for enhanced ORR catalysis.

In pursuit of highly active zinc-air battery (ZAB) catalysts, nitrogen doping has proven key to enhancing carbon-based non-metallic catalysts' performance in the oxygen reduction reaction (ORR). This study employed a novel method to synthesize variously sized ZnO materials coated with ZIF-8. Notably, smaller particle sizes correlated with reduced activation energy. ZnO-12, the smallest variant, fully carbonized at 800 °C, resulting in zinc ion evaporation and the formation of an amorphous carbon nano-hollow structure, ZIF8/ZnO-12. This material showcased remarkable ORR properties, with an onset potential of 0.9 V (vs. RHE) and a Tafel slope of 71.4 mV dec-1, surpassing the benchmark Pt/C catalyst and exhibiting excellent stability. Moreover, in ZAB tests, ZIF8/ZnO-12 achieved a specific capacity of 816 mA h g-1, outperforming Pt/C. DFT calculations indicate that under alkaline conditions, nitrogen-doped carbon materials containing adsorbed oxygen and doped oxygen exhibit lower catalytic activation energy for the ORR, which is beneficial for accelerating the ORR. This research provides valuable insights into designing more efficient carbon-based non-metallic catalysts for ZABs.

Normalizing Swiss German Dialects with the Power of Large Language Models

Swiss German dialects pose significant challenges for natural language processing (NLP) applications, due to their lack of standard orthography, linguistic diversity, and scarcity of annotated data. We introduce a novel method for normalizing Swiss German text to Standard German by employing the mT5 model, a cutting-edge large language model (LLM) that can perform various text-to-text transformations across multiple languages. Our approach not only aims to enhance the processing of Swiss German dialects but also seeks to broaden the understanding of the adaptability of pre-trained LLMs in the realm of dialect normalization. By fine-tuning the mT5 model across its small, base, and large variants with the SwissDial dataset under various hyperparameter settings, we evaluated the performance of these models using the character n-gram F-score (ChrF) and the COMET metrics. The results demonstrated that the mT5 model, particularly its smallest variant, can achieve high-quality normalization of Swiss German dialects with minimal performance differences between the model sizes. This indicates that the SwissDial dataset is sufficiently extensive for effective fine-tuning, suggesting that even less resource-intensive models are viable for this task. Our findings advocate for the potential of LLMs, like mT5, as powerful instruments for dialect normalization and other NLP challenges, offering a promising alternative to traditional methods.

Insights for precision oncology from the integration of genomic and clinical data of 13,880 tumors from the 100,000 Genomes Cancer Programme

The Cancer Programme of the 100,000 Genomes Project was an initiative to provide whole-genome sequencing (WGS) for patients with cancer, evaluating opportunities for precision cancer care within the UK National Healthcare System (NHS). Genomics England, alongside NHS England, analyzed WGS data from 13,880 solid tumors spanning 33 cancer types, integrating genomic data with real-world treatment and outcome data, within a secure Research Environment. Incidence of somatic mutations in genes recommended for standard-of-care testing varied across cancer types. For instance, in glioblastoma multiforme, small variants were present in 94% of cases and copy number aberrations in at least one gene in 58% of cases, while sarcoma demonstrated the highest occurrence of actionable structural variants (13%). Homologous recombination deficiency was identified in 40% of high-grade serous ovarian cancer cases with 30% linked to pathogenic germline variants, highlighting the value of combined somatic and germline analysis. The linkage of WGS and longitudinal life course clinical data allowed the assessment of treatment outcomes for patients stratified according to pangenomic markers. Our findings demonstrate the utility of linking genomic and real-world clinical data to enable survival analysis to identify cancer genes that affect prognosis and advance our understanding of how cancer genomics impacts patient outcomes.

YOLOv5 vs. YOLOv8: Performance Benchmarking in Wildfire and Smoke Detection Scenarios

This paper provides a thorough analysis and comparison of the YOLOv5 and YOLOv8 models for wildfire and smoke detection, using the Foggia dataset for evaluation. The study examines the small (s), medium (m), and large (l) variants of each architecture and employs various metrics, including recall, precision, F1-Score, and mAP@50, to assess performance. Additional considerations such as training and inference times, along with the number of epochs required for optimal recall, are also evaluated to gauge the models’ real-world efficiency and effectiveness. Quantitatively, YOLOv5 models generally outperform YOLOv8, with the YOLOv5s variant achieving the highest scores across all metrics. However, visual assessments reveal that YOLOv8 models exhibit similar, and in some cases superior, capabilities, particularly in detecting dark and dense smoke. Training times favor YOLOv5 models, contributing to their efficiency, and their shorter inference times offer advantages for real-time applications. While the “best model” variants confirm YOLOv5’s numerical dominance, YOLOv8’s “best models” also display competitive performance. Future research will explore model evaluation on diverse datasets and hyperparameter optimization to further enhance performance, adaptability, and applicability in various real-world object detection scenarios.

Eligibility and Endpoints for Clinical Trials in Trimodality Therapy for Bladder Cancer.

Trimodality therapy (TMT) is a viable option for muscle-invasive localized bladder cancer, providing an alternative to radical cystectomy in properly selected patients. The approval of novel therapeutics in different stages of bladder cancer treatment has sparked interest in exploring concurrent systemic therapies with radiation in clinical trials to enhance long-term outcomes. Achieving uniformity in trial eligibility criteria and endpoint definitions is imperative in describing clinical significance, comparing trials, and changing standard of care guidelines. To delineate eligibility criteria and appropriate endpoints for TMT clinical trials in an attempt to achieve uniformity in trial eligibility criteria and endpoint definitions which will then help move the field of bladder preservation forward and improve the current standard of care. An expert panel, comprising individuals with extensive experience in bladder cancer clinical trials, clinical practice focused on bladder cancer treatment, and patient advocacy, was assembled. The panel systematically reviewed phase II/III clinical trials previously published and assessing the role of radiation in definitive therapy with the specific goal of preserving native bladder function during bladder cancer treatment. Recommendations were summarized based on review of these trials and past experiences of the investigators. To ensure a holistic perspective, the summary was further subjected to rigorous reevaluation by a patient advocate, who added valuable insights from a patient's standpoint. The resulting consensus statements were summarized in this publication to contribute to the evolving landscape of bladder cancer research and treatment. The eligibility criteria for TMT should be pragmatic to encompass patients with an Eastern Cooperative Oncology Group (ECOG) performance status of 0-2, bladder cancer stage T2-T4a N0±N1M0, unilateral tumor-associated hydronephrosis, attempted maximal transurethral resection of bladder tumor (TURBT), both pure urothelial carcinoma and/or mixed histologic subtypes (excluding rare and aggressive small cell variants) and patients who are non- cystectomy candidates. Bladder intact event-free survival (BIEFS) is proposed as a suitable endpoint for registration trials designed to compare two different treatment interventions, defined as the time from randomization to muscle-invasive or locoregional recurrence, systemic recurrence, radical cystectomy from any cause, or death from any cause. Overall survival is deemed an appropriate secondary endpoint or a co-primary end point as recent improvements in systemic therapy can produce significant improvement in long-term outcomes. Primary and secondary endpoints should be supported with patient-reported quality of life assessments, when available. The standardization of clinical trial design, eligibility criteria, and endpoints is essential for expediting progress in the field. Inclusivity, patient-centricity, and clinically meaningful endpoints will facilitate the analysis, comparison, and meta-analysis of different trials, fostering advancements in bladder cancer treatment.

Polymeric bis(triphenylphosphine)iminium chloride as a recyclable catalyst.

Metal-free catalysts have garnered considerable interest as an environmental and economical alternative to precious metal catalysts. Bis(triphenylphosphine)iminium chloride (PPNCl) has emerged as a prominent choice due to its air and thermal stability and broad reactivity, especially in applications where a bulky cation is needed. The high phosphorus content and synthetic effort required for catalyst synthesis increase environmental impact; the recyclability of PPNCl in catalytic processes remains largely unexplored. The potential development of a polymer-supported PPNCl catalysts therefore desirable to enable this recyclability. In this work, we synthesise polymeric PPNCl (poly(PPNCl)) for the first time. Poly(PPNCl) demonstrates a comparative catalytic reactivity to its small molecule variant when employed as a catalyst in halogen-exchange reactions and CO2/epoxide coupling. For the latter the effect of catalyst loading, CO2 pressure, reaction time and addition of co-catalyst on conversion and selectivity was investigated. Poly(PPNCl) was easily recovered from the crude product by simple precipitation and its catalytic reactivity was well-maintained over three reaction cycles, providing environmental and economic advantages for sustainable reaction development.

Real-World Concordance between Germline and Tumour BRCA1/2 Status in Epithelial Ovarian Cancer.

Patients diagnosed with epithelial ovarian cancer may undergo reflex tumour BRCA1/2 testing followed by germline BRCA1/2 testing in patients with a positive tumour test result. This testing model relies on tumour BRCA1/2 tests being able to detect all types of pathogenic variant. We analysed germline and tumour BRCA1/2 test results from patients treated for epithelial ovarian cancer at our specialist oncological referral centre. Tumour BRCA1/2 testing was performed using the next-generation sequencing (NGS)-based myChoice® companion diagnostic (CDx; Myriad Genetics, Inc.). Germline BRCA1/2 testing was performed in the North West Genomic Laboratory Hub using NGS and multiplex ligation-dependent probe amplification. Between 11 April 2021 and 11 October 2023, 382 patients were successfully tested for tumour BRCA1 and BRCA2 variants. Of these, 367 (96.1%) patients were tested for germline BRCA1/2 variants. In those patients who underwent tumour and germline testing, 15.3% (56/367) had a BRCA1/2 pathogenic variant (36 germline and 20 somatic). All germline BRCA1/2 pathogenic small sequencing variants were detected in tumour DNA. By contrast, 3 out of 8 germline BRCA1/2 pathogenic large rearrangements were not reported in tumour DNA. The overall concordance of germline BRCA1/2 pathogenic variants detected in germline and tumour DNA was clinically acceptable at 91.7% (33/36). The myChoice® CDx was able to detect most germline BRCA1/2 pathogenic variants in tumour DNA, although a proportion of pathogenic large rearrangements were not reported. If Myriad's myChoice® CDx is used for tumour BRCA1/2 testing, our data supports a testing strategy of germline and tumour BRCA1/2 testing in all patients diagnosed with epithelial ovarian cancer aged < 79 years old, with germline BRCA1/2 testing only necessary for patients aged ≥ 80 years old with a tumour BRCA1/2 pathogenic variant.

A Novel Tissue-Free Method to Estimate Tumor-Derived Cell-Free DNA Quantity Using Tumor Methylation Patterns.

Estimating the abundance of cell-free DNA (cfDNA) fragments shed from a tumor (i.e., circulating tumor DNA (ctDNA)) can approximate tumor burden, which has numerous clinical applications. We derived a novel, broadly applicable statistical method to quantify cancer-indicative methylation patterns within cfDNA to estimate ctDNA abundance, even at low levels. Our algorithm identified differentially methylated regions (DMRs) between a reference database of cancer tissue biopsy samples and cfDNA from individuals without cancer. Then, without utilizing matched tissue biopsy, counts of fragments matching the cancer-indicative hyper/hypo-methylated patterns within DMRs were used to determine a tumor methylated fraction (TMeF; a methylation-based quantification of the circulating tumor allele fraction and estimate of ctDNA abundance) for plasma samples. TMeF and small variant allele fraction (SVAF) estimates of the same cancer plasma samples were correlated (Spearman's correlation coefficient: 0.73), and synthetic dilutions to expected TMeF of 10-3 and 10-4 had estimated TMeF within two-fold for 95% and 77% of samples, respectively. TMeF increased with cancer stage and tumor size and inversely correlated with survival probability. Therefore, tumor-derived fragments in the cfDNA of patients with cancer can be leveraged to estimate ctDNA abundance without the need for a tumor biopsy, which may provide non-invasive clinical approximations of tumor burden.

Neurofibromatosis type 1: Clinical characteristics and mutation spectrum in a North Indian cohort

BackgroundNeurofibromatosis type 1 (NF1) is a unique, highly penetrant neuro-cutaneous disorder with a wide range of manifestations. Though the clinical diagnosis of NF1 is straight forward, there can be other disorders which mimic NF1, especially its cutaneous features. Here we describe the clinical and mutation spectrum of a series of individuals whose primary diagnosis was NF1 or NF1 related disorders. MethodsWe have screened 29 unrelated individuals who fulfilled the clinical criteria of NF1. Whole exome sequencing (WES) was done in all individuals except one with suspected microdeletion syndrome with NF1 in whom Cytogenetic microarray (CMA) was done. ResultsOut of 29 suspected patients, 25 had germline pathogenic/likely pathogenic variants involving NF1 gene. Five novel and 20 known variants in coding and non-coding regions were identified, among them 7 variants were deletions (28%), 7 nonsense (28%), 3 splice-site (12%), 4 missense (16%), 2 duplications (8%) and 2 (8%) were contiguous deletions. In those where NF1 variants were not detected, 3 had neurofibromatosis type 2 (NF2) and 1 rare autosomal recessive form of Elher Danlos syndrome. ConclusionWe hereby present the wide range of manifestations in different age groups and the mutation spectrum ranging from small scale variants to contiguous gene deletion syndromes involving NF1 gene. We highlight the usefulness of molecular testing and its importance in tumor surveillance and genetic counseling in this disorder.

NR1D1-rearranged soft tissue tumour: A clinicopathological and molecular analysis of four additional cases.

Nuclear receptor subfamily 1 group D member 1 (NR1D1)-rearranged soft tissue tumour is a newly described entity with an epithelioid morphology and a potential for aggressive behaviour. Largely due to under-recognition, this tumour type has not yet been widely acknowledged. Herein, we report four additional cases to further expand its clinicopathological and molecular spectrum. Four mesenchymal tumours with NR1D1 rearrangement were identified from our consultation files. There were one male and three females with ages ranging from 19 to 47 years (median = 28.5 years). Tumour occurred in the tongue, neck, hip and index finger, respectively. Histologically, two tumours were composed predominantly of epithelioid cells; one tumour had admixed epithelioid-spindle cells and one tumour consisted of monomorphic small round to ovoid cells. By immunohistochemistry, none of the tumours expressed lineage-specific markers. Targeted RNA-sequencing identified NR1D1 fusions in all four tumours, the partner genes being MAML2, MAML3, KMT2A and NCOA2, respectively. The novel MAML3 and NCOA2 rearrangements were confirmed by fluorescence in-situ hybridisation analysis. On follow-up (2-23 months), one patient experienced local recurrence due to incomplete resection and one patient developed lung metastasis. The other two patients were alive without disease. This study adds more support for NR1D1-rearranged soft tissue tumour as an emerging entity. The occurrence of two additional tumours in the head and neck region, description of a small round cell variant and identification of novel MAML3, KMT2A and NCOA2 partners further expand its clinicopathological and molecular spectrum. More studies on larger series are necessary to validate the fully malignant potential of NR1D1-rearranged soft tissue tumour.

Strategy for Pediatric Patients with Relapsed or Refractory Anaplastic Lymphoma Kinase-Positive Anaplastic Large Cell Lymphoma: A Review.

Anaplastic lymphoma kinase (ALK)-positive anaplastic large cell lymphoma (ALCL) is an aggressive T-cell lymphoma characterized by large T-cells with strong CD30 and ALK expression. Although conventional chemotherapy is effective in most patients, approximately 30% experience a relapse or refractory disease and have a poor prognosis. Several risk factors associated with poor prognosis have been identified in pediatric ALK-positive ALCL. These include morphological patterns with the small cell variant or lymphohistiocytic variant, leukemic presentation, the presence of minimal disseminated disease, or involvement of the central nervous system. Relapsed or refractory ALK-positive ALCL is often resistant to conventional chemotherapy; therefore, salvage therapy is required. In recent years, targeted therapies such as ALK inhibitors and brentuximab vedotin (BV) have been developed. ALK inhibitors block the continuous activation of ALK kinase, a driver mutation that leads to cell proliferation in ALK-positive ALCL. Additionally, BV is an antibody-drug conjugate that targets CD30-positive cells. Both ALK inhibitors and BV have displayed dramatic effects in chemoresistant ALK-positive ALCL. Weekly vinblastine treatment and hematopoietic stem cell transplantation have also been reported to be effective therapies. This article reviews pediatric ALK-positive ALCL, focusing on risk factors and treatment strategies for pediatric patients with relapsed or refractory ALK-positive ALCL.

Structural Variants and Speciation: Multiple Processes at Play.

Research on the genomic architecture of speciation has increasingly revealed the importance of structural variants (SVs) that affect the presence, abundance, position, and/or direction of a nucleotide sequence. SVs include large chromosomal rearrangements such as fusion/fissions and inversions and translocations, as well as smaller variants such as duplications, insertions, and deletions (CNVs). Although we have ample evidence that SVs play a key role in speciation, the underlying mechanisms differ depending on the type and length of the SV, as well as the ecological, demographic, and historical context. We review predictions and empirical evidence for classic processes such as underdominance due to meiotic aberrations and the coupling effect of recombination suppression before exploring how recent sequencing methodologies illuminate the prevalence and diversity of SVs. We discuss specific properties of SVs and their impact throughout the genome, highlighting that multiple processes are at play, and possibly interacting, in the relationship between SVs and speciation.

Prenatal diagnosis of 1408 foetuses at risk of DMD/BMD by MLPA and Sanger sequencing combined with STR linkage analysis

ObjectiveThis study is a retrospective analysis of the prenatal genetic diagnosis results of 1408 foetuses at high risk of DMD/BMD to provide information for clinical genetic counselling.BackgroundDuchenne muscular dystrophy (DMD) is a severe neuromuscular disorder characterized by skeletal and cardiac muscle weakness. With the deepening of disease research, some treatments have been applied in clinics. Therefore, early and accurate prenatal diagnosis can inform pregnancy choices for high-risk families.MethodsA total of 1316 unrelated DMD/BMD families with confirmed genetic diagnoses were recruited from the Genetic and Prenatal Diagnosis Center of the First Affiliated Hospital of Zhengzhou University. Prenatal diagnosis of 1408 high-risk foetuses was performed by MLPA and Sanger sequencing combined with STR linkage analysis for all families.ResultsAmong the 1316 families, large deletions, duplications, and small variants of the DMD gene accounted for 70.4% (927/1316), 8.2% (108/1316), and 21.4% (281/1316), respectively. Among 1316 mothers, 863 (65.6%) were carriers, and 453 (34.4%) were not carriers. The rate of de novo variants was 34.4% (453/1316) in our study. In addition, gonadal mosaicism was observed in 11 pregnant females. Prenatal diagnosis was provided for 1408 high-risk foetuses; 282 foetuses were identified as male patients, 219 foetuses were female carriers, and the remainder had normal genetics. The results of prenatal diagnosis were consistent with the results of follow-up.ConclusionsAccurate and rapid prenatal diagnosis can be achieved using MLPA, Sanger sequencing, and STR linkage analysis. Furthermore, germline mosaicism in DMD should not be ignored; considering this, a prenatal diagnosis for all pregnant women with a family history of DMD/BMD regardless of whether they carried disease-causing variants is proposed. Genetic counselling and targeted prenatal diagnosis will continue to be a cornerstone of DMD/BMD family management in the future.