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An 8-year-old girl presented with precocious puberty and an otherwise normal examination. MRI of the pituitary was normal; however, an incidental oval, non-enhancing T2 hyperintense lesion in the right temporal subcortical white matter was identified ([figure 1][1]). The neuro-radiographic

A 31-year-old Caucasian woman underwent a standard workup as a potential kidney transplant donor. Kidney donor protocol CT showed a left para-aortic hypervascular mass suspicious for a paraganglioma. Biochemical workup revealed elevated urinary catecholamines, supporting this suspicion. The patient underwent surgical resection with histopathological evaluation that confirmed the diagnosis. Endocrine evaluation 2 years later revealed a family history of a cousin with a history of pheochromocytoma as a teenager. A genetic panel identified a missense mutation in succinate dehydrogenase C (c.202T>C; p.Ser68Pro), which was described as a variant of unknown significance. In silico analysis suggested that it may be a deleterious mutation. We concluded that this mutation may be pathogenic, considering these supporting pieces of evidence and her early-onset paraganglioma. This report highlights the importance of genetic screening in patients with paragangliomas/pheochromocytomas, since many cases are familial. Additionally, it underscores the importance of evaluating and documenting cases of variants of unknown significance.

AO_SCPLOWBSTRACTC_SCPLOWNon-pharmaceutical interventions (NPIs), such as social distancing and contact tracing, have been widely implemented during the COVID-19 pandemic. In addition to playing an important role in suppressing transmission, NPIs influence pathogen evolution by mediating mutation supply and altering the strength of selection for novel variants. However, it is unclear how NPIs might affect the emergence of novel variants of concern that are able to escape pre-existing immunity (partially or fully), are more transmissible, or cause greater mortality. Here, we analyse a stochastic two-strain epidemiological model to determine how the strength of NPIs affects the emergence of variants with similar or contrasting life-history characteristics to the wildtype. We show that, while stronger and timelier NPIs generally reduce the likelihood of variant emergence, it is possible for more transmissible variants with high cross immunity to have a greater probability of emerging at intermediate levels of NPIs. However, since one cannot predict the characteristics of a variant, the best strategy to prevent emergence is likely to be implementation of strong, timely NPIs. AO_SCPLOWUTHORC_SCPLOWO_SCPCAP C_SCPCAPO_SCPLOWSUMMARYC_SCPLOWDuring the COVID-19 pandemic, a wide range of non-pharmaceutical interventions, including mask wearing, quarantine, isolation, and lockdowns, have been used by governments around the world to suppress virus transmission. Although considerable efforts have been made to understand how such interventions affect transmission, much less attention has been paid to their effects on pathogen evolution. While vaccines are well-known to affect virus evolution, non-pharmaceutical interventions also influence mutation supply and the strength of selection, and hence play a key role in the emergence of novel variants. Here, we use a relatively simple mathematical model to explore how non-pharmaceutical interventions during an epidemic affect the emergence of a novel variant of a pathogen. We show that in general, it is important to implement effective transmission-reducing public health measures in a timely manner to prevent the emergence of novel variants, which may be more transmissible, more deadly, or able to escape immunity.

Compiler diagnostic warnings help developers identify potential programming mistakes during program compilation. However, these warnings could be erroneous due to the defects of compiler warning diagnostics. Although many techniques have been proposed to automatically generate test programs for compiler warning defect detection, the effectiveness of these techniques on defect-nding is still limited, due to their ability at generating warning-sensitive test program structures. Therefore, in this paper, we propose a DIversity-guided PROgram Mutation approach, called DIPROM, to construct diverse warning-sensitive programs for effective compiler warning defect detection. Given a seed test program, DIPROM rst removes its dead code to reduce false positive warning defects. Then, the abstract syntax tree (AST) of the test program is constructed; DIPROM iteratively mutates the structures of the AST to generate warning-sensitive program variants. To improve the diversity of program variants, DIPROM applies a novel diversity function to guide the selection of the best program variants in each iteration. With the selected program variants, differential testing is conducted to effectively detect warning defects in different compilers. In the experiments, we evaluate DIPROM with two popular C compilers (i.e., GCC and Clang). Experimental results show that DIPROM can detect 75.36% and 218.42% more warning defects than two state-of-the-art approaches (i.e., Epiphron and Csmith), respectively. Meanwhile, DIPROM is efcient, which only spends 61.14% of the time of comparative approaches on average in nding the same number of warning defects. We at last applied DIPROM on the latest development versions of GCC and Clang. After two months running, DIPROM reported 12 new warning defects; nine of them have been conrmed/xed by developers.

Hash bit selection determines an optimal subset of hash bits from a candidate bit pool. It is formulated as a zero-one quadratic programming problem subject to binary and cardinality constraints. In this article, the problem is equivalently reformulated as a global optimization problem. A collaborative neurodynamic optimization (CNO) approach is applied to solve the problem by using a group of neurodynamic models initialized with particle swarm optimization iteratively in the CNO. Lévy mutation is used in the CNO to avoid premature convergence by ensuring initial state diversity. A theoretical proof is given to show that the CNO with the Lévy mutation operator is almost surely convergent to global optima. Experimental results are discussed to substantiate the efficacy and superiority of the CNO-based hash bit selection method to the existing methods on three benchmarks.

Fabry disease (FD) is an X-linked, systemic lysosomal deposition disease caused by alpha-galactosidase A (AGAL) enzyme deficiency deriving out of changes on the GLA gene. Though several mutations have been described, one must consider that even a specific mutation may present with variable clinical expression within the same family. Typically described as a disease that affects hemizygous men with no residual AGAL activity, we describe a novel FD mutation (first case of GLA T194A variant worldwide) in a 49-year-old woman presenting with a classic phenotype of FD. The patient investigation highlighted a previously not described mutation in exon 4 of the GLA gene, as for the substitution of threonine for alanine. The same mutation was identified in her children, one of them presenting with end-stage kidney disease (ESKD) in early adulthood.

The A-to-G point mutation at position 3243 in the human mitochondrial genome (m.3243A > G) is the most common pathogenic mtDNA variant responsible for disease in humans. It is widely accepted that m.3243A > G levels decrease in blood with age, and an age correction representing ~ 2% annual decline is often applied to account for this change in mutation level. Here we report that recent data indicate that the dynamics of m.3243A > G are more complex and depend on the mutation level in blood in a bi-phasic way. Consequently, the traditional 2% correction, which is adequate ‘on average’, creates opposite predictive biases at high and low mutation levels. Unbiased age correction is needed to circumvent these drawbacks of the standard model. We propose to eliminate both biases by using an approach where age correction depends on mutation level in a biphasic way to account for the dynamics of m.3243A > G in blood. The utility of this approach was further tested in estimating germline selection of m.3243A > G. The biphasic approach permitted us to uncover patterns consistent with the possibility of positive selection for m.3243A > G. Germline selection of m.3243A > G shows an ‘arching’ profile by which selection is positive at intermediate mutant fractions and declines at high and low mutant fractions. We conclude that use of this biphasic approach will greatly improve the accuracy of modelling changes in mtDNA mutation frequencies in the germline and in somatic cells during aging.

Hyperphosphatemic familial tumoral calcinosis (HFTC) is a rare autosomal recessive disorder. Topical sodium thiosulfate (STS) and acetazolamide can be a safe and effective treatment for the patients who do not respond to conventional therapy for ectopic calcifications. We report the successful treatment of deep soft-tissue calcifications with topical STS and acetazolamide in a boy diagnosed with HFTC due to a novel homozygous mutation of FGF23.

Previous research proposed the uniform mutation inside the sphere as a new mutation operator for evolution strategies (continuous evolutionary algorithms), with case study the elitist algorithm on the SPHERE. For that landscape, one-step success probability and expected progress were estimated analytically, and further proved to converge, as space dimension increases, to the corresponding asymptotics of the algorithm with normal mutation. This paper takes the analysis further by considering the RIDGE, an asymmetric landscape almost uncovered in literature. For the elitist algorithm, estimates of expected progress along the radial and longitudinal axes are derived, then tested numerically against the real behavior of the algorithm on several functions from this class. The global behavior of the algorithm is predicted correctly by iterating the one-step analytical formulas. Moreover, experiments show identical mean value dynamics for the algorithms with uniform and normal mutation, which implies that the derived formulas apply also to the normal case. Essential to the whole analysis is θ, the inclination angle of the RIDGE. The behavior of the algorithm on the SPHERE and HYPERPLANE is also obtained, at the limits of the θ interval (0∘,90∘.

BackgroundRecently, four Parkinson’s disease (PD)-linked mutations (Y92C, R141L, 184PGext*5 and 184Wext*5) in transmembrane protein 230 (TMEM230) were identified in PD patients, and these mutations have implications in protein trafficking and neurodegeneration. However, there is a lack of in vivo studies on the roles of PD-related variants of TMEM230 in PD pathogenesis.MethodsIn this study, we generated human wild-type (WT) and mutant TMEM230 (Y92C, R141L, 184PGext*5 and 184Wext*5) transgenic Drosophila using isoform Ⅱ cDNA. ResultsWe found that the expression of TMEM230 184PGext*5 in pan-neurons or dopaminergic neurons in Drosophila induced PD-like phenotypes, which included impaired locomotor ability, a shortened lifespan, reduced TH levels, and increased phosphorylated JNK and cleaved caspase-3 levels. Moreover, rotenone, a common pesticide, enhanced TMEM230-184PGext*5-induced PD-like phenotypes. In contrast, the overexpression of wild-type (WT) VPS35 rescued TMEM230-184PGext*5-induced PD-like phenotypes, while the knockdown of VPS35 by RNA interference (RNAi) or the expression of mutant VPS35 D620N worsened PD-like phenotypes. ConclusionThese results indicate that VPS35, as a downstream effector of TMEM230, plays a critical role in TMEM230-linked JNK/caspase-3 signalling pathways and that mutations in TMEM230 and VPS35 disrupt these pathways, resulting in dopaminergic neurodegeneration and PD-like phenotypes. These findings provide novel insight into the molecular mechanisms of mutant TME230- and VPS35-induced abnormalities underlying the pathogenesis of PD.

Hereditary ataxias are a group of devastating neurological disorders that affect coordination of gait and are often associated with poor coordination of hands, speech, and eye movements. Ataxia with Ocular Apraxia type 1 (AOA1) (OMIM: 606350.0006) is characterized by slowly progressive symptoms of childhood-onset and pathogenic mutations in APTX; the only known cause underpinning AOA1. APTX encodes the protein Aprataxin, composed of three domains sharing homology with proteins involved in DNA damage, signaling, and repair. We present four siblings from an endogamic family in a rural, isolated town of Colombia with ataxia and ocular apraxia of childhood-onset and confirmed molecular diagnosis of AOA1, homozygous for the W279* p.Trp279Ter mutation. We predicted the mutated APTX with Alpha Fold to demonstrate the effects of this stop-gain mutation that deletes three beta helices encoded by amino acid 270 to 339 rescinding the C2H2-type zinc fingers (Znf) (C2H2 Znf) DNA-binding and DNA-repair domain and the whole tridimensional structure of the APTX. All siblings exhibited different ages of onset (4, 6, 8, and 11 y/o) and heterogeneous patterns of dysarthria (ranging from absence to mild-moderate dysarthria). Neuropsychological evaluation showed no neurocognitive impairment in three siblings, but one sibling showed temporospatial disorientation, semantic and phonologic fluency impairment, episodic memory affection, constructional apraxia, moderate anomia, low executive function, and symptoms of depression. This heterogeneous phenotype suggests genetic interactions can shape the natural history of AOA1. To our knowledge, this report represents the most extensive series of siblings affected with AOA1 in Latin America, and the genetic analysis completed adds important knowledge to outline this family’s disease and general complex phenotype of hereditary ataxias.

Essential thrombocythemia is a condition caused by a high platelet count and a positive JAK2 (V617F) mutation. There is an increasing occurrence of malignancy, such as oral squamous cell carcinoma (OSCC), in patients with essential thrombocythemia. The objective of this case report is to document the novel instance of a patient with OSCC after being diagnosed with essential thrombocythemia and a positive JAK2 (V617F) mutation. The patient was a 42-year-old female who complained of an ulcer and pain in the dextral lateral tongue for three months. After two weeks, the pain diminished; however, there was swelling and tenderness on the ulcer. The patient was diagnosed with essential thrombocythemia and a positive JAK2 (V617F) mutation and began undergoing hydroxyurea therapy three months ago. The diagnosis of OSCC was based on exfoliative cytology and MRI. The patient was treated with an antiseptic mouthwash to prevent secondary infection and referred to an oncologist to manage the OSCC. It is possible to use the suspected markers of thrombocytosis and a positive JAK2 (V617F) mutation to define the OSCC diagnosis.

Quantum-inspired differential evolution (QDE) is an evolutionary algorithm, which can effectively solve complex optimization problems. However, sometimes, it easily leads to premature convergence and low search ability and falls to local optima. To overcome these problems, based on the MSIQDE (improved QDE with multistrategies) algorithm, an enhanced MSIQDE algorithm based on mixing multiple strategies, namely, EMMSIQDE is proposed in this article. In the EMMSIQDE, a new differential mutation strategy of a difference vector is proposed to enhance the search ability and descent ability. Then, a new multipopulation mutation evolution mechanism is designed to ensure the relative independence of each subpopulation and the population diversity. The feasible solution space transformation strategy is used to achieve the optimal solution by mapping the quantum chromosome from a unit space to solution space. Finally, some multidimensional unimodal and multimodal functions are selected to demonstrate the optimization performance of EMMSIQDE. The results demonstrate that the EMMSIQDE is significantly better than the DE, QDE, QGA, and MSIQDE, and has better optimization ability, scalability, efficiency, and stability.

Contemporary evolution has the potential to significantly alter biotic responses to global change, including range expansion dynamics and biological invasions. However, predictive models often make highly simplifying assumptions about the genetic architecture underlying relevant traits. This can be problematic since genetic architecture defines evolvability, that is, evolutionary rates, and higher order evolutionary processes, which determine whether evolution will be able to keep up with environmental change or not. Therefore, we here study the impact of the genetic architecture of dispersal and local adaptation, two central traits of high relevance for range expansion dynamics, on the speed and variability of range expansions into an environmental gradient, such as temperature. In our theoretical model we assume that dispersal and local adaptation traits result from the products of two non-interacting gene-regulatory networks (GRNs). We compare our model to simpler quantitative genetics models and show that in the GRN model, range expansions are accelerated, faster and more variable. Increased variability implies that these evolutionary changes reduce predictability. We further find that acceleration in the GRN model is primarily driven by an increase in the rate of local adaptation to novel habitats which results from greater sensitivity to mutation (decreased robustness) and increased gene expression. Our results highlight how processes at microscopic scales, here, within genomes, can impact the predictions of large scale, macroscopic phenomena, such as range expansions, by modulating the rate of evolution.

Background: NADH dehydrogenase 5 (ND5) is one of 44 subunits forming Complex I in the mitochondrial respiratory chain. Therefore, a mitochondrially encoded ND5 (MT-ND5) gene mutation causes mitochondrial oxidative phosphorylation (OXPHOS) disorder, resulting in the development of mitochondrial diseases, such as mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes. Although focal segmental glomerulosclerosis (FSGS) is induced by several mitochondrial diseases, no reports have yet confirmed that an MT-ND5 mutation causes FSGS. Case presentation: A Japanese woman at 29 years old was found to have proteinuria and renal dysfunction in an annual health check-up for the first time. Because her proteinuria and renal dysfunction were persistent, she was admitted for a kidney biopsy to investigate the reason at 33 years of age. Although there were no abnormal neurological findings, she was diagnosed with sensorineural hearing loss by an otolaryngologist. Renal histology showed perihilar variant-type FSGS with podocytes filled with abnormal mitochondria. In addition, the renal pathological findings showed granular swollen epithelial cells (GSECs) in tubular cells, age-inappropriately disarranged and irregularly sized vascular smooth muscle cells (AiDIVs), and red-colored podocytes (ReCPos) by acidic dye, which are assumed to be characteristic changes of mitochondrial nephropathy. Genetic analysis using peripheral mononuclear blood cells and urine sediment cells detected the m.13513 G>A variant, which has already been confirmed as a pathogenic variant of the MT-ND5 gene. The heteroplasmy rates of the blood cells and urine sediments were 10.3% and 62.2%, respectively. Therefore, this patient was diagnosed with FSGS due to an MT-ND5 mutation. Conclusion: This is the first case report to show that a gene mutation encoding subunits of Complex I causes FSGS with podocytes filled with abnormal mitochondria. The routine evaluation of GSECs, AiDIVs, and ReCPos is expected to be useful for detecting mitochondrial nephropathies, which could be latent in etiology-unknown FSGS or glomerulosclerosis cases.

Recent theoretical research has shown that self-adjusting and self-adaptive mechanisms can provably outperform static settings in evolutionary algorithms for binary search spaces. However, the vast majority of these studies focuses on unimodal functions which do not require the algorithm to flip several bits simultaneously to make progress. In fact, existing self-adjusting algorithms are not designed to detect local optima and do not have any obvious benefit to cross large Hamming gaps. We suggest a mechanism called stagnation detection that can be added as a module to existing evolutionary algorithms (both with and without prior self-adjusting algorithms). Added to a simple (1+1) EA, we prove an expected runtime on the well-known Jump benchmark that corresponds to an asymptotically optimal parameter setting and outperforms other mechanisms for multimodal optimization like heavy-tailed mutation. We also investigate the module in the context of a self-adjusting (1+$\lambda$) EA and show that it combines the previous benefits of this algorithm on unimodal problems with more efficient multimodal optimization. To explore the limitations of the approach, we additionally present an example where both self-adjusting mechanisms, including stagnation detection, do not help to find a beneficial setting of the mutation rate. Finally, we investigate our module for stagnation detection experimentally., Comment: 26 pages. Full version of a paper appearing at GECCO 2020

Spastic paraplegia (SPG) is a syndrome characterised by lower limb spasticity, occurring alone or in association with other neurological manifestations. Despite of the new molecular technologies, many patients remain yet undiagnosed. The purpose of this study was to describe the clinical presentation and molecular characteristics of a cohort of 27 patients from 18 different families with SPG in the south of Spain. We used a targeted next-generation sequencing (NGS) approach to study a proband from each family. Variants in SPG11 gene were the most common cause of SPG in our area. We made a genetic diagnosis in 52% of cases, identified 3 novel variants and reclassified one uncertain variant in SPG11 gene as pathogenic variant. We identified a patient with two truncanting mutation in SPG11 gene and late onset disease and report another missense mutation outside of motor domain of KIF1A gene in a family with pure SPG. Our study contributes to enhance the scientific knowledge of SPG. It is important to note the large group of cases (48%) that were not genetically diagnosed in our cohort. Therefore NGS approach is an efficient diagnostic tool, but it still large the number of non-diagnosed subjects, suggesting further genetic heterogeneity.

This paper presents spacecraft trajectory optimizations for deep-space missions requiring multiple gravity-assists (MGA). The main algorithm is based on a self-adaptive/self-learning differential evolution (DE). In the process of improving the performance of DE for optimizing the MGA trajectory, the proposed algorithm alleviates the dependence on predetermined mutation strategy and control parameters in DE; as evolution progresses, the mutation strategy and the control parameters switch adaptively to more promising ones by reflecting experiences in previous evolution steps. Furthermore, the proposed algorithm is equipped with a re-initialization technique to directly mollify the issue of converging to a local optimum, which is often observed when optimizing the MGA trajectory. In order to demonstrate these favorable characteristics, the proposed algorithm is implemented to solve six well-known MGA trajectory optimization problems designed by the European space agency (ESA). Compared with the latest representative evolutionary algorithms, the proposed algorithm can successfully converge to the currently known best solutions of five MGA problems; our solutions to four of those MGA problems are better than currently known solutions. The proposed algorithm also performs well as a local/auxiliary search algorithm to improve the performance of other evolutionary algorithms. In addition to describing the algorithms and solutions characteristics, sensitivity analysis is presented to quantitatively investigate the search capability of finding the optimal solutions of MGA problems. The overall results show that our self-learning DE is competitively compared with other representative algorithms in terms of convergences to the global optimum, reliable search capability, and applicability to a variety of deep-space trajectory optimizations.

K-mer-based methods are widely used in bioinformatics, but there are many gaps in our understanding of their statistical properties. Here, we consider the simple model where a sequence S (e.g. a genome or a read) undergoes a simple mutation process whereby each nucleotide is mutated independently with some probability r, under the assumption that there are no spurious k-mer matches. How does this process affect the k-mers of S? We derive the expectation and variance of the number of mutated k-mers and of the number of islands (a maximal interval of mutated k-mers) and oceans (a maximal interval of non-mutated k-mers). We then derive hypothesis tests and confidence intervals for r given an observed number of mutated k-mers, or, alternatively, given the Jaccard similarity (with or without minhash). We demonstrate the usefulness of our results using a few select applications: obtaining a confidence interval to supplement the Mash distance point estimate, filtering out reads during alignment by Minimap2, and rating long read alignments to a de Bruijn graph by Jabba.

Background Individuals with intellectual and developmental disabilities (IDD) living in congregated settings have increased risk of COVID-19 infection and mortality. Little is known about variant B.1.1.519 with spike mutation T478K, dominant in Mexico. We describe a linked SARS-CoV-2 B.1.1.519 outbreak in three IDD facilities in the Netherlands. Methods Following notification of the index, subsequent cases were identified through serial PCR group testing. Positive specimens were submitted for whole-genome-sequencing. Clinical information was gathered through interviews with staff members of the three facilities. Results Attack rate (AR) in clients of the index facility was 92% (23/25), total AR in clients 45% (33/73) and in staff members 24% (8/34). 55% (18/33) of client cases were asymptomatic, versus 25% (2/8) of staff members. Five client cases (15%) were hospitalized, two died (6%). Sequencing yielded the same specific B.1.1.519 genotype in all three facilities. No significant difference in median viral load was established comparing the B.1.1.519 variant with other circulating variants. The index of the linked outbreak reported no travel history or link to suspected or confirmed cases suggesting regional surveillance. Observed peak regional prevalence of B.1.1.519 during the outbreak supports this. Conclusion AR, morbidity and mortality prior to control measures taking effect were high, probably related to the specific characteristics of the IDD setting and its clients. We assessed no evidence for intrinsic contributing properties of variant B.1.1.519. Our study argues for enhanced infection prevention protocols in the IDD setting, and prioritization of this group for vaccination against COVID-19.

A computational grid needs to be cost-effective and highly reliable. It must have the ability to transfer maximum amount of data for end-to-end delivery. Many research works on computational grids conclude with a binary state of operation. Although some research reveals that, the grids operate with multiple states of connections and operations, they are silent about the mentioned constraints. Since there are multi-state operations, the reliability depends on the load, bandwidth and cost. This paper proposes a Genetic Algorithm (GA) based approach for optimization of reliability of computational grid with desired reliability under cost and bandwidth constraints. The method is well explained through illustration and its implementation on some Grid networks. The efficient encoding, cross-over, mutation and selection operation of the proposed scheme ensures the fast convergence to the optimal solution. On comparison, the proposed method is observed to be more efficient than the existing ones.

Patients with cancer present with an elevated risk of thrombosis, which entails high morbidity and mortality. Various predictive scales that incorporate clinical and biological data have been developed to identify those at high risk of thrombosis, but, in general, they do not allow for the optimal selection of subjects who are candidates for thromboprophylaxis. Recent studies have demonstrated that the mutation profile has a high impact on the risk of thrombosis; this will facilitate developing new predictive models of thrombosis in patients with cancer.

Orphan syndromes — a group of diseases that are extremely rare, with an incidence of 10 cases per 100,000 people. Doctors in different fields should pay considerable attention to orphan syndromes with endocrine disorders. Phenotypically, these syndromes begin to manifest since birth or they occur in childhood. The article presents short phenotypic and genetic characteristics of certain orphan endocrine syndromes, such as Perlman, Proteus, Sotos 1, Sotos 2 and Berardinelli, which are associated with gigantism.Above-mentioned syndromes are caused by different gene mutations, namely Perlman syndrome — by homozygous or heterozygous mutation in DIS3L2 gene on the chromosome 2q37, Proteus syndrome — mutation in AKT1 gene on chromosome 14q32.3, Sotos syndrome 1 is caused by heterozygous mutation in NSD1 gene in the 5q35 region, Sotos syndrome 2 — by heterozygous mutation in NFIX gene on chromosome 19p13.3. Berardinelli syndrome, which is divided into four types, has four different mutations, namely: type 1 is caused by mutations in AGPAT2 gene in locus 9q34, type 2 — in BSCα2gene in locus 11q13, type 3 — by mutations in CAV1 gene (locus 7q31), type 4 — by mutation in PTRF gene located on the chromosome 17.

Multiple myeloma (MM) measurable residual disease (MRD) persisting after treatment is an adverse prognostic factor for progression free survival (PFS) and overall survival.1Genomic mutations occurred in the remaining clonal aberrant plasma cells (A-PCs) are linked to the development of drug resistance and disease relapse.2 Thus, personalised treatment based on the genomic profile of MRD could be highly beneficial and ultimately increase patients’ survival. However, while large-scale sequencing studies have characterised the genome of many malignancies including MM,3–8 the genomic mutations present in MM MRD are at the beginning of investigation.9 Here, we set up an exome sequencing analysis to identify genomic mutations characteristic for MM MRD and explore if they could mediate drug response, resistance or disease progression.

Introduction In acute myeloid leukemia (AML), FMS-like tyrosine kinase 3-internal tandem duplication (FLT3-ITD) is a common driver mutation associated with high tumor burden and poor prognosis. This mutation is common in normal karyotype AML and such patients have high leukocyte count. The presence of this mutation can be predicted by certain hematological and immunophenotypic characteristics in day-to-day practice. Objective This study was undertaken to assess the strength of association between FLT3 gene mutation and hematological and immunophenotypic characteristics. Materials and Methods Morphological, hematological, immunophenotypic, and cytogenetic characteristics of FLT3 mutations recorded in 424 patients of AML in adults and children between 2016 and 2019 in a tertiary care cancer center in Western India. Blasts were classified according to French-American-British method. Tumor burden was assessed by serum lactate dehydrogenase (LDH) levels, leucocyte count, and peripheral smear blast percentage. Results Out of 424 cases, FLT3-ITD and FLT3-tyrosine kinase domain mutation were found in 72 and 25 AML patients, respectively. Patients with FLT3 mutation had high tumor burden, characterized by high leukocyte count (p < 0.001), peripheral blood (p = 0.01) and bone marrow (p = 0.03) blast percentage, and high serum LDH (mean 777.8 vs. 586; p = 0.10) compared with FLT3-negative patients. They also featured high platelet count (p < 0.001). Morphological, immunophenotypic, and cytogenetic characteristics also have been presented in the study. Conclusion Observations of the study suggest the presence of definitive hematological and immunophenotypic characteristics along with raised serum LDH levels serve as surrogate markers and indicators of FLT3 mutation in AML patients.

‘Candidatus Liberibacter asiaticus’ (Las) is the prominent species of Liberibacter associated with huanglongbing, a devastating disease of citrus worldwide. In this study, we report the identification of an ∼8.3-kb DNA region of the Las genome containing eight putative open reading frames flanked by two inverted repeats, which was not present in the Las str. psy62 genome. Comparisons with other genome sequences established this region as a unique genetic element associated with genome plasticity/instability. Primers specific for both the presence (Las wild type) and absence (Las mutant) of this region were designed to study the population dynamics and host adaptation of the two strains. Las populations with and/or without the wild-type strain were detected and differentiated in >2,300 samples that included psyllids, periwinkle, and several species of citrus. In psyllids, although a mixed population of the wild type and mutant was observed in most samples (88%), the wild-type Las was detected alone at a rate of 11%. In contrast, none of the infected citrus plants were positive for the wild type alone, which harbored either the mutant strain alone (8%) or a mixed population of the mutant and wild type (92%). Furthermore, the dynamics of these two major Las populations varied with different citrus hosts, whereas an in-depth study on grapefruit that did not rapidly succumb to disease revealed that the population of mutant alone increased with time, indicating that the absence of this genetic element is associated with the fitness of Las in planta under the selection pressure of its host.

Background Pathologic evidence of Alzheimer disease (AD) is detectable years before onset of clinical symptoms. Imaging-based identification of structural changes of the brain in people at genetic risk for early-onset AD may provide insights into how genes influence the pathologic cascade that leads to dementia. Purpose To assess structural connectivity differences in cortical networks between cognitively normal autosomal dominant Alzheimer disease (ADAD) mutation carriers versus noncarriers and to determine the cross-sectional relationship of structural connectivity and cortical amyloid burden with estimated years to symptom onset (EYO) of dementia in carriers. Materials and Methods In this exploratory analysis of a prospective trial, all participants enrolled in the Dominantly Inherited Alzheimer Network between January 2009 and July 2014 who had normal cognition at baseline, T1-weighted MRI scans, and diffusion tensor imaging (DTI) were analyzed. Amyloid PET imaging using Pittsburgh compound B was also analyzed for mutation carriers. Areas of the cerebral cortex were parcellated into three cortical networks: the default mode network, frontoparietal control network, and ventral attention network. The structural connectivity of the three networks was calculated from DTI. General linear models were used to examine differences in structural connectivity between mutation carriers and noncarriers and the relationship between structural connectivity, amyloid burden, and EYO in mutation carriers. Correlation network analysis was performed to identify clusters of related clinical and imaging markers. Results There were 30 mutation carriers (mean age ± standard deviation, 34 years ± 10; 17 women) and 38 noncarriers (mean age, 37 years ± 10; 20 women). There was lower structural connectivity in the frontoparietal control network in mutation carriers compared with noncarriers (estimated effect of mutation-positive status, -0.0266; P = .04). Among mutation carriers, there was a correlation between EYO and white matter structural connectivity in the frontoparietal control network (estimated effect of EYO, -0.0015, P = .01). There was no significant relationship between cortical global amyloid burden and EYO among mutation carriers (P > .05). Conclusion White matter structural connectivity was lower in autosomal dominant Alzheimer disease mutation carriers compared with noncarriers and correlated with estimated years to symptom onset. Clinical trial registration no. NCT00869817 © RSNA, 2021 Online supplemental material is available for this article. See also the editorial by McEvoy in this issue.

Alkaptonuria (AKU), a rare genetic disorder, is characterized by the accumulation of homogentisic acid (HGA) in the body. Affected individuals lack enough functional levels of an enzyme required to breakdown HGA. Mutations in the HGD gene cause AKU and they are responsible for deficient levels of functional homogentisate 1,2-dioxygenase (HGD), which, in turn, leads to excess levels of HGA. Although HGA is rapidly cleared from the body by the kidneys, in the long term it starts accumulating in various tissues, especially cartilage. Over time (rarely before adulthood), it eventually changes the color of affected tissue to slate blue or black. Here we report a comprehensive mutation analysis of 111 pathogenic and 190 non-pathogenic HGD missense mutations using protein structural information. Using our comprehensive suite of graph-based signature methods, mCSM complemented with sequence-based tools, we studied the functional and molecular consequences of each mutation on protein stability, interaction and evolutionary conservation. The scores generated from the structure and sequence-based tools were used to train a supervised machine learning algorithm with 84% accuracy. The empirical classifier was used to generate the variant phenotype for novel HGD missense mutations. All this information is deployed as a user friendly freely available web server called HGDiscovery (http://biosig.unimelb.edu.au/hgdiscovery/).

We consider a model of stochastic evolution in symmetric coordination games with \begin{document}$ K\ge 2 $\end{document} strategies played by myopic agents. Agents employ the best response with mutations choice rule and simultaneously revise strategies in each period. We form the dynamic process as a Markov chain with state space being the set of best responses in order to overcome difficulties that arise with the large population. We examine the long run equilibria for both orders of limits where the small noise limit and the large population limit are taken sequentially. We characterize an equilibrium refinement criterion that is common among both orders of limits.

For a nationwide real-word data study on the application of predictive mutation testing of patients with colorectal cancer (CRC) for anti-epidermal growth factor receptor (EGFR) therapy stratification, pathology data were collected from the Dutch Pathology Registry from October 2017 until June 2019 (N=4060) and linked with the Netherlands Cancer Registry. Mutation testing rates increased from 24% at diagnosis of stage IV disease to 60% after 20–23 months of follow-up (pKRAS/NRAS wild-type patients was mainly observed from the third treatment line onwards (65% vs 17% in first/second treatment line (pKRAS/NRAS/BRAF mutation rate was 63.9%, being similar for next-generation sequencing (NGS)-based approaches and single gene tests (64.4% vs 61.2%, p=ns). NGS-based approaches detected more additional potential biomarkers, for example, ERBB2 amplifications (p

COVID orchitis (testicular pain) is reported in 10-15% of men with long COVID. We identified two siblings with COVID orchitis and hypothesized that genetic mutations are associated with susceptibility. Blood samples from five COVID-19 (+) men, three of whom had orchitis were evaluated by whole-exome-sequencing. A rare deletion on chromosome 7 was found in NACAD among the three men with orchitis. Interestingly, circulating ACE2 levels was decreased in men with COVID orchitis. This pilot study generated the hypothesis that men who develop COVID orchitis could have underlying genetic variants and altered levels in circulating ACE2 that may increase their risk.

Vaccines against SARS-CoV-2 are very effective, but some mutations could reduce protection. Here we report a case of SARS-CoV-2 infection with a P.1.1 variant lacking the Y501 mutation in a vaccinated individual in Italy. Carefully monitoring breakthrough infections is important for assessing viral spreading of potential vaccine-resistant variants.

The success of genetically depauperate populations in the face of environmental change is contrary to the expectation that high genetic diversity is required for rapid adaptation. Alternative pathways such as environmentally induced genetic modifications and non-genetic heritable phenotypes have been proposed mechanisms for heritable adaptation within an ecologically relevant time frame. However, experimental evidence is currently lacking to establish if, and to what extent, these sources of phenotypic variation can produce a response. To test if adaptation can rapidly occur in the absence of initial standing genetic variation and recombination in small populations, we (a) exposed replicate monoclonal populations of the microzooplankton Brachionus calyciflorus to a culturing regime that selected for phenotypic variants with elevated population growth with either high or low phosphorus food for a period of 55 days and (b) examined population level response in two fully factorial common garden experiments at day 15 and 35 of the exposure experiment. Within six generations, we observed heritable local adaptation to nutrient limitation. More specifically, populations with a history of exposure to low P food exhibited higher population growth rates under low P food conditions than populations with a high P exposure history. However, the capacity for such a response was found to vary among clones. Our study finds that although standing genetic variation is considered essential for rapid heritable adaptation, the rapid emergence of de novo genetic variation or alternative sources of phenotypic variation could aid in the establishment and persistence of low-diversity populations.

Mitochondrial DNA (mtDNA) associated mitochondrial diseases hold a crucial position but comprehensive and systematic studies are relatively rare. Among the 262 patients of four children's hospitals in China, 96%-point mutations (30 alleles in 11 genes encoding tRNA, rRNA, Complex I and V) and 4%-deletions (seven of ten had not been reported before) were identified as the cause of 14 phenotypes. MILS presented the highest genetic heterogeneity, while the m.3243A G mutation was the only "hotspot" mutation with a wide range of phenotypes. The degrees of heteroplasmy in the leukocytes of MM were higher than MELAS. The heteroplasmy level of patients was higher than that in mild and carrier group, while we found low-level heteroplasmy pathogenic mutations as well. Some homoplasmic variations (e.g., m.9176 T C mutation) are having high incomplete penetrance. For a suspected MELAS, m.3243A G mutation was recommended to detect first; while for a suspected LS, trios-WES and mtDNA genome sequencing by NGS were recommended first in both blood and urine.

RNA-binding proteins (RBPs) play a significant part in several biological processes in the living cell, such as gene regulation and mRNA localization . The research indicates that the mutation of RBPs will lead to some serious diseases. Several deep learning methods , especially the model based on convolutional neural network (CNN), have been used to predict the binding sites. However, these methods only use single-scale filters to extract a fixed length of motifs features, which restricts the performance of prediction. For the sequence data, different sizes of filters may learn different biological information of the RNA sequence. Therefore, a deep multi-scale attention network (DeepMSA) based on convolutional neural network is proposed to predict the sequence-binding preferences of RBPs. DeepMSA extracts features by multi-scale CNNs and integrates these features with an attention model to predict the RBPs and binding motifs. Experiments demonstrate DeepMSA outperforms several state-of-the-art methods on the invivo and invitro datasets. The results indicate that attention can make the model learn the consistent pattern of candidate motifs, which can provide some important guiding advice for RBP motifs.

Germline heterozygous gain-of-function (GOF) mutation of NFKBIA, encoding IκBα, would affect the activation of NF-κB pathway and cause an autosomal dominant (AD) form of anhidrotic ectodermal dysplasia with immunodeficiency (EDA-ID). Here we reported a Chinese patient with a heterozygous N-terminal truncation mutation of NFKBIA/IκBα, she presented recurrent fever, infectious pneumonia and chronic diarrhea with EDA-ID. Impaired NF-κB translocation and IL1R and TLR4 pathway activation were revealed in this patient. The findings suggested that the truncation mutation of IκBα caused medium impaired of activation of NF-κB but the early death. Furthermore, we reviewed all the reported patients with NFKBIA mutation to learn more about this disease.

The zona pellucida (ZP) is an extracellular matrix surrounding mammalian oocytes. It is composed of three to four glycoproteins, ZP1-ZP4. ZP3 is essential for sperm binding and zona matrix formation. Here, we identified a novel heterozygous mutation (NM_001110354.2:c.502_504delGAG) of ZP3, occurring in a pair of sisters with empty follicle syndrome (EFS). A mouse model with the same mutation was established using the CRISPR/Cas9 gene-editing system. As in the above family, F0 -, F1 -, and F2 -generation female mice with the mutation were all infertile. Further analysis using the Chinese hamster ovary cells (CHO-K1) also showed that this mutation weakens the strength of binding between ZP3 and ZP2, which hinders the assembly of ZP and results in unstable ZP formation. Immunohistochemical analysis using ovarian serial sections in both humans and mice demonstrated that the ZP of preantral follicles was thinner than normal control, or even absent. Our study presents a new gene mutation that leads to EFS, providing new evidence and support for the genetic diagnosis of infertile individuals with similar phenotypes. Our results also show that the loop of ZP3 is not only a linker between two amphiphilic helices but may play a critical role in specifying the correct heterodimerization partner. This article is protected by copyright. All rights reserved.

Charcot-Marie-Tooth disease type 4H (CMT4H) is an autosomal recessive inherited demyelinating neuropathy caused by an FYVE, RhoGEF, and a PH domain-containing protein 4 (FGD4) gene mutation. CMT4H is characterized by an early onset, slow progression, scoliosis, distal muscle atrophy, and foot deformities. We herein present sibling cases of CMT4H with a homozygous mutation in the FGD4 gene. Both patients exhibited cauda equina thickening on magnetic resonance imaging, which had not been reported among the previous CMT4H cases. This is the first report of CMT4H with a homozygous FGD4 c.1730G>A (p.Arg577Gln) mutation showing mild progression and cauda equina thickening.

We herein describe a Charcot-Marie-Tooth disease (CMT) family with a MFN2 mutation with atypical ocular manifestations. The proband, his mother, his third daughter, and his deceased maternal grandfather all had symptoms of CMT and a visual impairment (either cataracts or severe astigmatism). On whole-exome sequencing for the proband having CMT and congenital cataracts, we identified a c.314C>T (p.Thr105Met) mutation in MFN2, but no mutation in the causative genes associated with cataracts. This missense mutation in MFN2 co-segregated with CMT and the atypical ocular manifestations in this family. The findings of this study might help to expand the clinical phenotype of heterogeneous MFN2-related CMT.

Autosomal primary microcephaly (MCPH) is a heterogenetic disorder that affects brain's cerebral cortex size and leads to a reduction in the cranial vault. Along with the hallmark feature of reduced head circumference, microcephalic patients also exhibit a variable degree of intellectual disability as well. Genetic studies have reported 28 MCPH genes, most of which produce microtubule-associated proteins and are involved in cell division. Herein this study, 14 patients from seven Pashtun origin Pakistani families of primary microcephaly were analyzed. Mutation analysis was performed through targeted Sanger DNA sequencing on the basis of phenotype-linked genetic makeup. Genetic analysis in one family found a novel pathogenic DNA change in the abnormal spindle microtubule assembly (ASPM) gene (NM_018136.4:c.3871dupGA), while the rest of the families revealed recurrent nonsense mutation c.3978GA (p.Trp1326*) in the same gene. The novel reported frameshift insertion presumably truncates the protein p.(Lys1291Glyfs*14) and deletes the N-terminus domains. Identification of novel ASPM-truncating mutation expands the mutational spectrum of the ASPM gene, while mapping of recurrent mutation c.3978GA (p.Trp1326*) will aid in establishing its founder effect in the Khyber Pakhtunkhwa (KPK) inhabitant population of Pakistan and should be suggestively screened for premarital counseling of MCPH susceptible families. Most of the recruited families are related to first-degree consanguinity. Hence, all the family elders were counseled to avoid intrafamilial marriages.

BACKGROUND AND PURPOSE: Pathogenic variants in the ACTA2 gene cause a distinctive arterial phenotype that has recently been described to be associated with brain malformation. Our objective was to further characterize gyral abnormalities in patients with ACTA2 pathogenic variants as per the 2020 consensus recommendations for the definition and classification of malformations of cortical development. MATERIALS AND METHODS: We performed a retrospective, multicentric review of patients with proved ACTA2 pathogenic variants, searching for the presence of malformations of cortical development. A consensus read was performed for all patients, and the type and location of cortical malformation were noted in each. The presence of the typical ACTA2 arterial phenotype as well as demographic and relevant clinical data was obtained. RESULTS: We included 13 patients with ACTA2 pathogenic variants (Arg179His mutation, n = 11, and Arg179Cys mutation, n = 2). Ninety-two percent (12/13) of patients had peri-Sylvian dysgyria, 77% (10/13) had frontal dysgyria, and 15% (2/13) had generalized dysgyria. The peri-Sylvian location was involved in all patients with dysgyria (12/12). All patients with dysgyria had a characteristic arterial phenotype described in ACTA2 pathogenic variants. One patient did not have dysgyria or the characteristic arterial phenotype. CONCLUSIONS: Dysgyria is common in patients with ACTA2 pathogenic variants, with a peri-Sylvian and frontal predominance, and was seen in all our patients who also had the typical ACTA2 arterial phenotype.

Multi-nucleotide variants (MNVs) represent an important type of genetic variation and have biological and clinical significance. To simulate MNVs, we designed four dual-mutation base editors combining hA3A(Y130F), TadA8e(V106W), and protospacer adjacent motif (PAM)-flexible SpRY and selected cytosine and adenine base editor-SpRY (CABE-RY), which had the best editing performance, for further study. Characterization and comparison showed that CABE-RY had a smaller DNA editing window and lower RNA off-target edits than the corresponding single base editors. Thus, we have established a versatile tool to efficiently simulate MNVs over the genome, which could be very useful for functional studies on MNVs in humans., Graphical abstract, Tao et al. established a new dual-mutation base editor (CABE-RY) to efficiently simulate multi-nucleotide variants (MNVs). Further characterization and comparison showed that CABE-RY had a smaller DNA editing window and lower RNA off-target edits than the corresponding single base editors, providing a new tool for functional studies on MNVs in humans.

Proposition 5.16 of the author's paper ‘Mutations of frozen Jacobian algebras’ [11] is false. We give several possible remedies with different applications.