Deciphering genetic and nongenetic factors underlying tumour dormancy: insights from multiomics analysis of two syngeneic MRD models of melanoma and leukemia.

BACKGROUND: Tumour dormancy, a resistance mechanism employed by cancer cells, is a significant challenge in cancer treatment, contributing to minimal residual disease (MRD) and potential relapse. Despite its clinical importance, the mechanisms underlying tumour dormancy and MRD remain unclear. In this study, we employed two syngeneic murine models of myeloid leukemia and melanoma to investigate the genetic, epigenetic, transcriptomic and protein signatures associated with tumour dormancy. We used a multiomics approach to elucidate the molecular mechanisms driving MRD and identify potential therapeutic targets. RESULTS: We conducted an in-depth omics analysis encompassing whole-exome sequencing (WES), copy number variation (CNV) analysis, chromatin immunoprecipitation followed by sequencing (ChIP-seq), transcriptome and proteome investigations. WES analysis revealed a modest overlap of gene mutations between melanoma and leukemia dormancy models, with a significant number of mutated genes found exclusively in dormant cells. These exclusive genetic signatures suggest selective pressure during MRD, potentially conferring resistance to the microenvironment or therapies. CNV, histone marks and transcriptomic gene expression signatures combined with Gene Ontology (GO) enrichment analysis highlighted the potential functional roles of the mutated genes, providing insights into the pathways associated with MRD. In addition, we compared "murine MRD genes" profiles to the corresponding human disease through public datasets and highlighted common features according to disease progression. Proteomic analysis combined with multi-omics genetic investigations, revealed a dysregulated proteins signature in dormant cells with minimal genetic mechanism involvement. Pathway enrichment analysis revealed the metabolic, differentiation and cytoskeletal remodeling processes involved in MRD. Finally, we identified 11 common proteins differentially expressed in dormant cells from both pathologies. CONCLUSIONS: Our study underscores the complexity of tumour dormancy, implicating both genetic and nongenetic factors. By comparing genomic, transcriptomic, proteomic, and epigenomic datasets, our study provides a comprehensive understanding of the molecular landscape of minimal residual disease. These results provide a robust foundation for forthcoming investigations and offer potential avenues for the advancement of targeted MRD therapies in leukemia and melanoma patients, emphasizing the importance of considering both genetic and nongenetic factors in treatment strategies.

Transverse flow under oscillating stimulation in helical square ducts with cochlea-like geometrical curvature and torsion.

The cochlea, situated within the inner ear, is a spiral-shaped, liquid-filled organ responsible for hearing. The physiological significance of its shape remains uncertain. Previous research has scarcely addressed the occurrence of transverse flow within the cochlea, particularly in relation to its unique shape. This study aims to investigate the impact of the geometric features of the cochlea on fluid dynamics by characterizing transverse flow induced by harmonically oscillating axial flow in square ducts with curvature and torsion resembling human cochlear anatomy. We examined four geometries to investigate curvature and torsion effects on axial and transverse flow components. Twelve frequencies from 0.125 Hz to 256 Hz were studied, covering infrasound and low-frequency hearing, with mean inlet velocity amplitudes representing levels expected for normal conversation or louder situations. Our simulations show that torsion contributes significantly to transverse flow in unsteady conditions, and that its contribution increases with increasing oscillation frequency. Curvature alone has a small effect on transverse flow strength, which decreases rapidly with increasing frequency. Strikingly, the combined effect of curvature and torsion on transverse flow is greater than expected from a simple superposition of the two effects, especially when the relative contribution of curvature alone becomes negligible. These findings may be relevant to understanding physiological processes in the cochlea, including metabolite transport and wall shear stress. Further studies are needed to investigate possible implications for cochlear mechanics.

A multidisciplinary analysis of over 53,000 fascioliasis patients along the 1995-2019 countrywide spread in Vietnam defines a new epidemiological baseline for One Health approaches.

Fascioliasis, only foodborne trematodiasis of worldwide distribution, is caused by Fasciola hepatica and F. gigantica, liver flukes transmitted by freshwater snails. Southern and southeastern Asia is an emerging hot spot of F. gigantica, despite its hitherto less involvement in human infection. In Vietnam, increasing cases have been reported since 1995, whereas only sixteen throughout 1800-1994. A database was created to include epidemiological data of fascioliasis patients from the 63 Vietnam provinces throughout 1995-2019. Case profiles were based on serology, symptoms, eosinophilia, imaging techniques, stool egg finding, and post-specific-treatment recovery. Radio broadcasting about symptoms and costless diagnosis/treatment led patients to hospitals after symptom onset. Yearly case numbers were modelled and spatio-temporally analyzed. Missing data and confounders were assessed. The countrywide spread has no precedent. It started in the central coast, including 53,109 patients, mostly adults and females. Seasonality, linked to vegetable consumption, peaks in June, although the intensity of this peak differs according to relief/climatic zones. Incidence data and logistic regression curves are obtained for the first time in human fascioliasis. Fasciolid hybrids accompanying the spreading F. gigantica flukes, and climate change assessed by risk index correlations, are both ruled out as outbreak causes. Human-guided movements of livestock from an original area prove to be the way used by fasciolids and lymnaeid vectors to expand geographically. Radix viridis, a highly efficient transmitting and colonizing vector, played a decisive role in the spread. The use of irrigated crop fields, widely inhabited by R. viridis, for livestock grazing facilitated the transmission and spread of the disease. General physician awareness and diagnostic capacity improvement proved the successful impact of such knowledge transfer in facilitating and increasing patient infection detection. Information, education and communication to the public by radio broadcasting demonstrated to be very helpful. Fasciola gigantica is able to cause epidemic and endemic situations similar to F. hepatica. The magnitude of the human outbreak in Vietnam is a health wake-up call for southern and southeastern countries of Asia which present the highest human population densities with increasing food demands, uncontrolled livestock inter-country exchange, foreign import practices, and monsoon's increasing climate change impact.

Clinical phenotype of the 16p.13.11 microdeletion: a case report with a mini review of the literature.

Background: Chromosome 16p13.11 microdeletion is a very rare copy number variant (CNV), associated with a clinical syndrome characterized by global development delay, neuropsychiatric conditions, facial dysmorphisms, microcephaly, gastroesophageal reflux disease, and congenital heart defects. The 16p13.11 locus is a very unstable genomic region, rich in low-copy number repeats, characterized by many homologous DNA sequences. Usually, the most common CNV of this region include microduplications/duplications, while the microdeletions are rare, and their clinical features are heterogeneous and poorly described so far. Case report: In this paper, we report the genetic and the clinical features of a patient diagnosed with chromosome 16p13.11 microdeletion, and a short review of the literature on this topic. Our patient was characterized by several facial dysmorphic features, autistic symptoms and language development delay. The genetic evaluation revealed and interstitial deletion of the long arm of the chromosome 16, approximately of 1.5 Mb. Conclusion: Interestingly, compared to previous cases, this patient was characterized by autistic symptoms, severe language and motor coordination disorder, without cognitive and cerebral malformations, frequently associated with this microdeletion syndrome.

Global stability and bifurcations in a mathematical model for the waste plastic management in the ocean.

The use of plastic is very widespread in the world and the spread of plastic waste has also reached the oceans. Observing marine debris is a serious threat to the management system of this pollution. Because it takes years to recycle the current wastes, while their amount increases every day. The importance of mathematical models for plastic waste management is that it provides a framework for understanding the dynamics of this waste in the ocean and helps to identify effective strategies for its management. A mathematical model consisting of three compartments plastic waste, marine debris, and recycle is studied in the form of a system of ordinary differential equations. After describing the formulation of the model, some properties of the model are given. Then the equilibria of the model and the basic reproduction number are obtained by the next generation matrix method. In addition, the global stability of the model are proved at the equilibria. The bifurcations of the model and sensitivity analysis are also used for better understanding of the dynamics of the model. Finally, the numerical simulations of discussed models are given and the model is examined in several aspects. It is proven that the solutions of the system are positive if initial values are positive. It is shown that there are two equilibria E 0 and E ∗ and if B R < 1 , it is proven that E 0 is globally stable, while when B R > 1 , the equilibrium E ∗ exists and it is globally stable. Also, at B R = 1 the model exhibits a forward bifurcation. The sensitivity analysis of B R concludes that the rates of waste to marine, new waste, and the recycle rate have most effect on the amount of marine debris.

Further diversity in the origins of fish antifreeze proteins.

Shifts in environmental conditions can impose strong selection for adaptive traits. During the Cenozoic era, as the oceans cooled, many marine teleost fish species were at risk of freezing. This led to the independent emergence of distinct ice-binding antifreeze proteins (AFPs). The report in this issue by Graham and Davies reveals the development of AFP genes in shorthorn and longhorn sculpin from a copy of the lunapark gene. The predicted sculpin AFP sequences are unrelated to that of lunapark; the coding sequences for the AFPs appear to have arisen from small portions of the lunapark gene by codon frameshifting along with a series of mutations.

A Novel Molecular-Genetic Approach to the Monitoring of Dynamics of Mitochondrial Function Improvement during Treatment.

Making a correct genetically based diagnosis in patients with diseases associated with mitochondrial dysfunction can be challenging both genetically and clinically, as can further management of such patients on the basis of molecular-genetic data assessing the state of their mitochondria. In this opinion article, we propose a novel approach (which may result in a clinical protocol) to the use of a precise molecular-genetic tool in order to monitor the state of mitochondria (which reflects their function) during treatment of certain conditions, by means of not only signs and symptoms but also the molecular-genetic basis of the current condition. This is an example of application of personalized genomic medicine at the intersection of a person's mitochondrial genome information and clinical care. Advantages of the proposed approach are its relatively low cost (compared to various types of sequencing), an ability to use samples with a low input amount of genetic material, and rapidness. When this approach receives positive outside reviews and gets an approval of experts in the field (in terms of the standards), it may then be picked up by other developers and introduced into clinical practice.

Spontaneous grip force fluctuations mirror semantic numerical magnitude processing: Larger numbers elicit larger forces.

This study investigated the relationship between semantic numerical magnitudes and motor magnitudes. We asked whether the processing of numbers can affect motor behavior such as the size of numbers affecting the size of motor actions. For this, we recorded continuous grip force fluctuations from 43 healthy adults during a symbolic magnitude comparison task. We found that numbers induced spontaneous grip force fluctuations during number processing. Smaller numbers induced lower grip forces, whereas larger numbers induced larger forces. This result constitutes strong behavioral support for a generalized magnitude processing by continuously quantifying the response that challenges binary accounts of cross-domain interactions.

Joint identity among loci under mutation and regular inbreeding.

This study describes a compact method for determining joint probabilities of identity-by-state (IBS) within and between loci in populations evolving under genetic drift, crossing-over, mutation, and regular inbreeding (partial self-fertilization). Analogues of classical indices of associations among loci arise as functions of these joint identities. This coalescence-based analysis indicates that multi-locus associations reflect simultaneous coalescence events across loci. Measures of association depend on genetic diversity rather than allelic frequencies, as do linkage disequilibrium and its relatives. Scaled indices designed to show monotonic dependence on rates of crossing-over, inbreeding, and mutation may prove useful for interpreting patterns of genome-scale variation.

A nomogram prediction of coronary artery dilation in Kawasaki diseases based on mtDNA copy number.

Objective: The level of mitochondrial DNA copy number (mtDNA-CN) in peripheral blood cells had been identified to be involved in several immune and cardiovascular diseases. Thus, the aim of this study is to evaluate the levels of mtDNA-CN in Kawasaki disease (KD) and to construct a nomogram prediction for coronary artery lesions in children with KD. Methods: One hundred and forty-four children with KD diagnosed from March 2020 to March 2022 were involved in the study. The clinical features and laboratory test parameters of these children were assessed between the KD and normal groups. Univariable and multivariable analyses were performed sequentially to identify the essential risk factors. Subsequently, a nomogram prediction was constructed. Results: A total of 274 children were included in the analysis. Of these, 144 (52.6%) represented the KD group. Peripheral blood DNA mtDNA qPCR showed that the -log value of mtDNA-CN in the KD group (6.67 ± 0.34) was significantly higher than that in the healthy group (6.40 ± 0.18) (P<0.001). The area under the ROC curve for mtDNA-CN in distinguishing KD was 0.757. MtDNA-CN (OR = 13.203, P = 0.009, 95% CI 1.888-92.305), RBC (OR = 5.135, P = 0.014, 95% CI 1.394-18.919), and PA (OR = 0.959, P = 0.014, 95% CI 0.927-0.991) were identified as independent risk factors for coronary artery dilation in children with KD. Finally, the nomogram predictive was established based on the results of multivariable analysis, demonstrating the satisfied prediction and calibration values. Conclusion: The results of this study revealed that mtDNA-CN could be used as a biomarker in predicting the development of KD. Furthermore, the higher the mtDNA-CN was significantly associated with coronary artery dilation in KD.

CYP2D6 copy number determination using digital PCR.

Background: CYP2D6 testing is increasingly used to guide drug therapy and thus, reliable methods are needed to test this complex and polymorphic gene locus. A particular challenge arises from the detection and interpretation of structural variants (SVs) including gene deletions, duplications, and hybrids with the CYP2D7 pseudogene. This study validated the Absolute Q™ platform for digital PCR-based CYP2D6 copy number variation (CNV) determination by comparing results to those obtained with a previously established method using the QX200 platform. In addition, protocols for streamlining CYP2D6 CNV testing were established and validated including the "One-pot" single-step restriction enzyme digestion and a multiplex assay simultaneously targeting the CYP2D6 5'UTR, intron 6, and exon 9 regions. Methods: Genomic DNA (gDNA) samples from Coriell (n = 13) and from blood, saliva, and liver tissue (n = 17) representing 0-6 copies were tested on the Absolute Q and QX200 platforms. Custom TaqMan™ copy number (CN) assays targeting CYP2D6 the 5'UTR, intron 6, and exon 9 regions and a reference gene assay (TERT or RNaseP) were combined for multiplexing by optical channel. In addition, two digestion methods (One-pot digestion and traditional) were assessed. Inconclusive CN values on the Absolute Q were resolved using an alternate reference gene and/or diluting gDNA. Results: Overall, results between the two platforms and digestions methods were consistent. The "One-pot" digestion method and optically multiplexing up to three CYP2D6 regions yielded consistent result across DNA sample types and diverse SVs, reliably detecting up to 6 gene copies. Rare variation in reference genes were found to interfere with results and interpretation, which were resolved by using a different reference. Conclusion: The Absolute Q produced accurate and reliable CYP2D6 copy number results allowing for a streamlined and economical protocol using One-pot digestion and multiplexing three target regions. Protocols are currently being expanded to other pharmacogenes presenting with SVs/CNVs.

Real-time assessment of relative mitochondrial ATP synthesis response against inhibiting and stimulating substrates (MitoRAISE).

BACKGROUND: Mitochondria are known to synthesize adenosine triphosphate (ATP) through oxidative phosphorylation. Understanding and accurately measuring mitochondrial ATP synthesis rate can provide insights into the functional status of mitochondria and how it contributes to overall cellular energy homeostasis. Traditional methods only estimate mitochondrial function by measuring ATP levels at a single point in time or through oxygen consumption rates. This study introduced the relative mitochondrial ATP synthesis response against inhibiting and stimulating substrates (MitoRAISE), designed to detect real-time changes in ATP levels as the cells respond to substrates. METHODS: The sensitivity and specificity of the MitoRAISE assay were verified under various conditions, including the isolation of mitochondria, variations in cell numbers, cells exhibiting mitochondrial damage, and heterogeneous mixtures. Using peripheral blood mononuclear cells (PBMCs), we analyzed MitoRAISE data from 19 patients with breast cancer and 23 healthy women. RESULTS: The parameters observed in the MitoRAISE data increased depending on the quantity of isolated mitochondria and cell count, whereas it remained unmeasured in mitochondrial-damaged cell lines. Basal ATP, rotenone response, malonate response, and mitochondrial DNA copy numbers were lower in PBMCs from patients with breast cancer than in those from healthy women. CONCLUSIONS: The MitoRAISE assay has demonstrated its sensitivity and specificity by measuring relative ATP synthesis rates under various conditions. We propose MitoRAISE assay as a potential tool for monitoring changes in the mitochondrial metabolic status associated with various diseases.

Prediction of lateral neck metastasis in patients with papillary thyroid cancer with suspicious lateral lymph ultrasonic imaging based on central lymph node metastasis features.

Neck lymphatic metastasis is a common occurrence with thyroid cancers, and pre operative lateral lymph node metastasis (LLNM) and postoperative lateral lymph node recurrence (LLNR) are two independent risk factors that are negatively associated with the prognosis of patients with thyroid cancer. The aim of the present study was to investigate the relationship between central lymph node metastasis (CLNM) and LLNM in patients with papillary thyroid carcinoma (PTC) with sonographically suspected LLNM, such as those without lymph node fine-needle aspiration (FNA) cytological results or negative FNA results at the time of diagnosis. The predictive ability of CLNM regarding LLNR was also investigated. The present study retrospectively reviewed the clinical data of 1,061 patients that were surgically treated for PTC and 128 patients with sonographically suspected lateral lymph nodes that received central lymph node dissection and lateral lymph node dissection at the Thyroid Department of The First Affiliated Hospital of Anhui Medical University (Hefei, China) from June 2019 to June 2021. In patients with suspicious ultrasonic images suggesting LLNM, a significant association between the central lymph node ratio (CLNR), the number of positive central lymph nodes and LLNM was demonstrated. Otherwise, there were no statistically significant differences between the CLNR in patients with PTC and patients with PTC without evidence of lateral cervical metastasis. However, the rate of LLNR increased significantly when the number of positive central lymph nodes was >3. In conclusion, the CLNR and the number of positive central lymph nodes could be used to predict LLNM in patients with PTC with sonographically suspect lateral lymph nodes, including those with no FNA cytological results or negative FNA results, which may potentially support physicians in making personalized clinical decisions.

Theoretical and experimental investigation of the impact of oil functional groups on the performance of smart water in clay-rich sandstones.

This research investigated the effect of ion concentration on the performance of low salinity water under different conditions. First, the effect of injection water composition on interparticle forces in quartz-kaolinite, kaolinite-kaolinite, and quartz-oil complexes was tested and modeled. The study used two oil samples, one with a high total acid number (TAN) and the other with a low TAN. The results illustrated that reducing the concentration of divalent ions to 10 mM resulted in the electric double layer (EDL) around the clay and quartz particles and the high TAN oil droplets, expanding and intensifying the repulsive forces. Next, the study investigated the effect of injection water composition and formation oil type on wettability and oil/water interfacial tension (IFT). The results were consistent with the modeling of interparticle forces. Reducing the divalent cation concentration to 10 mM led to IFT reduction and wettability alteration in high TAN oil, but low TAN oil reacted less to this change, with the contact angle and IFT remaining almost constant. Sandpack flooding experiments demonstrated that reducing the concentration of divalent cations incremented the recovery factor (RF) in the presence of high TAN oil. However, the RF increment was minimal for the low TAN oil sample. Finally, different low salinity water scenarios were injected into sandpacks containing migrating fines. By comparing the results of high TAN oil and low TAN oil samples, the study observed that fine migration was more effective than wettability alteration and IFT reduction mechanisms for increasing the RF of sandstone reservoirs.

Large-scale copy number alterations are enriched for synthetic viability in BRCA1/BRCA2 tumors.

BACKGROUND: Pathogenic BRCA1 or BRCA2 germline mutations contribute to hereditary breast, ovarian, prostate, and pancreatic cancer. Paradoxically, bi-allelic inactivation of BRCA1 or BRCA2 (bBRCA1/2) is embryonically lethal and decreases cellular proliferation. The compensatory mechanisms that facilitate oncogenesis in bBRCA1/2 tumors remain unclear. METHODS: We identified recurrent genetic alterations enriched in human bBRCA1/2 tumors and experimentally validated if these improved proliferation in cellular models. We analyzed mutations and copy number alterations (CNAs) in bBRCA1/2 breast and ovarian cancer from the TCGA and ICGC. We used Fisher's exact test to identify CNAs enriched in bBRCA1/2 tumors compared to control tumors that lacked evidence of homologous recombination deficiency. Genes located in CNA regions enriched in bBRCA1/2 tumors were further screened by gene expression and their effects on proliferation in genome-wide CRISPR/Cas9 screens. A set of candidate genes was functionally validated with in vitro clonogenic survival and functional assays to validate their influence on proliferation in the setting of bBRCA1/2 mutations. RESULTS: We found that bBRCA1/2 tumors harbor recurrent large-scale genomic deletions significantly more frequently than histologically matched controls (n = 238 cytobands in breast and ovarian cancers). Within the deleted regions, we identified 277 BRCA1-related genes and 218 BRCA2-related genes that had reduced expression and increased proliferation in bBRCA1/2 but not in wild-type cells in genome-wide CRISPR screens. In vitro validation of 20 candidate genes with clonogenic proliferation assays validated 9 genes, including RIC8A and ATMIN (ATM-Interacting protein). We identified loss of RIC8A, which occurs frequently in both bBRCA1/2 tumors and is synthetically viable with loss of both BRCA1 and BRCA2. Furthermore, we found that metastatic homologous recombination deficient cancers acquire loss-of-function mutations in RIC8A. Lastly, we identified that RIC8A does not rescue homologous recombination deficiency but may influence mitosis in bBRCA1/2 tumors, potentially leading to increased micronuclei formation. CONCLUSIONS: This study provides a means to solve the tumor suppressor paradox by identifying synthetic viability interactions and causal driver genes affected by large-scale CNAs in human cancers.

Whole Exome Sequencing of Intermediate-Risk Acute Myeloid Leukemia without Recurrent Genetic Abnormalities Offers Deeper Insights into New Diagnostic Classifications.

Two new diagnostic classifications of acute myeloid leukemia (AML) were published in 2022 to update current knowledge on disease biology. In previous 2017-edition categories of AML with myelodysplasia-related changes, AML was not otherwise specified, but AML with mutated RUNX1 experienced profound changes. We performed whole exome sequencing on a cohort of 69 patients with cytogenetic intermediate-risk AML that belonged to these diagnostic categories to correlate their mutational pattern and copy-number alterations with their new diagnostic distribution. Our results show that 45% of patients changed their diagnostic category, being AML myelodysplasia-related the most enlarged, mainly due to a high frequency of myelodysplasia-related mutations (58% of patients). These showed a good correlation with multilineage dysplasia and/or myelodysplastic syndrome history, but at the same time, 21% of de novo patients without dysplasia also presented them. RUNX1 was the most frequently mutated gene, with a high co-occurrence rate with other myelodysplasia-related mutations. We found a high prevalence of copy-neutral loss of heterozygosity, frequently inducing a homozygous state in particular mutated genes. Mild differences in current classifications explain the diagnostic disparity in 10% of patients, claiming a forthcoming unified classification.

Chromosome-Level Assembly Reveals a Fifteen-Chromosome Aneuploid Genome and Environmental Adaptation Strategy of Chinese Traditional Medical Fungus Wolfiporia hoelen.

The sclerotia of Wolfiporia hoelen are one of the most important traditional Chinese medicines and foods commonly used in China, Japan, Korea, and other Asian countries. To provide a high-quality reference genome and deepen our understanding of the genome of W. hoelen to elucidate various biological phenomena. In this study, we assembled three genomes of W. hoelen using a combination of Nanopore and Illumina sequencing strategies. The fifteen-chromosome genome L7 of W. hoelen was assembled with two-sided telomere and rDNA sequences for the first time. The chromosome count was subsequently confirmed through collinearity analysis, correcting the previous belief that W. hoelen had only fourteen chromosomes. Moreover, the aneuploid genome was discovered in W. hoelen for the first time through sequencing depth analysis of different chromosomes, and only some strains of W. hoelen exhibit aneuploid genomes. According to the genome analysis of homokaryotic offspring and protoplast-isolated strains, a potential variation in chromosome allocation patterns was revealed. Moreover, the gene function enrichment analysis of genes on reduplicated chromosomes demonstrated that aneuploidy in the genome may be the result of environmental adaptation for W. hoelen. The discovery of an aneuploid genome also provides new ideas for genetic improvement of W. hoelen.

Pitfalls When Determining HNA-1 Genotypes and Finding Novel Alleles.

Genetic variation in the FCGR3B gene is responsible for different variants of human neutrophil antigen 1 (HNA-1). Laboratory techniques currently utilized for routine HNA-1 genotyping, predominantly PCR-sequence-specific primer (PCR-SSP) and PCR-sequence-based typing (PCR-SBT), lack specificity for FCGR3B. This study compares the capabilities and limitations of existing technologies including an in-house TaqMan PCR, a commercial PCR-SSP test, PCR-SBT and multiplex ligation-dependent probe amplification (MLPA) with those of a long-read nanopore sequencing assay. Testing was performed with both related and unrelated Danish samples with different copy numbers and/or rare alleles. Long-read nanopore sequencing was validated by blind testing of ten English samples. The results showed that FCGR3B copy numbers correlate with a dose-dependent distribution of alleles that complicates genotyping by TaqMan PCR, PCR-SSP and PCR-SBT, due to co-amplification of the homologous FCGR3A gene. MLPA can correctly quantify the dose-dependent distribution but not detect novel variants. Long-read nanopore sequencing showed high specificity for FCGR3B and was able to detect dosage-dependent distribution, and rare and novel variants that were previously not described. Current HNA-1 genotyping methods cannot produce unambiguous allele-level results, whereas long-read nanopore sequencing has shown the potential to resolve observed ambiguities, identify new HNA-1 variants and allow definitive allele assignment.

Identification of QTNs and Their Candidate Genes for Boll Number and Boll Weight in Upland Cotton.

Genome-wide association study (GWAS) has identified numerous significant loci for boll number (BN) and boll weight (BW), which play an essential role in cotton (Gossypium spp.) yield. The North Carolina design II (NC II) genetic mating population exhibits a greater number of genetic variations than other populations, which may facilitate the identification of additional genes. Accordingly, the 3VmrMLM method was employed for the analysis of upland cotton (Gossypium hirsutum L.) in an incomplete NC II genetic mating population across three environments. A total of 204 quantitative trait nucleotides (QTNs) were identified, of which 25 (24.75%) BN and 30 (29.13%) BW QTNs were of small effect (<1%) and 24 (23.76%) BN and 20 (19.42%) BW QTNs were rare (<10%). In the vicinity of these QTNs, two BN-related genes and two BW-related genes reported in previous studies were identified, in addition to five BN candidate genes and six BW candidate genes, which were obtained using differential expression analysis, gene function annotation, and haplotype analysis. Among these, six candidate genes were identified as homologs of Arabidopsis genes. The present study addresses the limitation of heritability missing and uncovers several new candidate genes. The findings of this study can provide a basis for further research and marker-assisted selection in upland cotton.

The Phenotypic Spectrum of 16p11.2 Recurrent Chromosomal Rearrangements.

The human 16p11.2 chromosomal region is rich in segmental duplications which mediate the formation of recurrent CNVs. CNVs affecting the 16p11.2 region are associated with an increased risk for developing neuropsychiatric disorders, including autism spectrum disorder (ASD), schizophrenia, and intellectual disability (ID), as well as abnormal body weight and head circumference and dysmorphic features, with marked phenotypic variability and reduced penetrance. CNVs affecting the 16p11.2 region mainly affect a distal interval of ~220 Kb, between Breakpoints 2 and 3 (BP2-BP3), and a proximal interval of ~593 Kb (BP4-BP5). Here, we report on 15 patients with recurrent 16p11.2 rearrangements that were identified among a cohort of 1600 patients (0.9%) with neurodevelopmental disorders. A total of 13 deletions and two duplications were identified, of which eight deletions included the proximal 16p11.2 region (BP4-BP5) and five included the distal 16p11.2 region (BP2-BP3). Of the two duplications that were identified, one affected the proximal and one the distal 16p11.2 region; however, both patients had additional CNVs contributing to phenotypic severity. The features observed and their severity varied greatly, even between patients within the same family. This article aims to further delineate the clinical spectrum of patients with 16p11.2 recurrent rearrangements in order to aid the counselling of patients and their families.