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1.
Int J Mol Sci ; 25(9)2024 Apr 27.
Article in English | MEDLINE | ID: mdl-38732007

ABSTRACT

Due to the high mortality rate in Western countries, pancreatic cancer is considered one of the big killers, leaving patients and their families with little hope upon diagnosis. Although surgical and drug therapies are critical for cancer patients to improve life expectancy and alleviation of suffering, nutrition plays a key role in improving cancer treatment outcomes. This narrative review, conducted as part of the activities of the Italian Society of Human Nutrition (SINU) working group in oncology, focuses on the prevalence of vitamin malnutrition among pancreatic cancer patients. The results of the literature search show that pancreatic cancer patients are at a heightened risk of water-soluble vitamin deficiencies, particularly of vitamins B1, B3, and B6. Additionally, they also face an increased risk of deficiency of fat-soluble vitamins. Among these vitamins, the potential role of vitamin D in pancreatic cancer has garnered the most attention, with its plasma levels being identified as a significant factor in patient survival. Investigating vitamin nutritional status could provide valuable insights for incorporating nutritional approaches into the prevention and treatment of pancreatic cancer, thereby reducing the exacerbation of symptoms associated with the diagnosis.


Subject(s)
Nutritional Status , Pancreatic Neoplasms , Humans , Pancreatic Neoplasms/complications , Pancreatic Neoplasms/blood , Vitamins/therapeutic use , Vitamins/blood , Vitamins/metabolism , Vitamin D/blood , Vitamin D/metabolism
2.
Clin Transl Radiat Oncol ; 46: 100774, 2024 May.
Article in English | MEDLINE | ID: mdl-38596818

ABSTRACT

This series introduces the clinical management of difficult-to-treat non-melanoma skin cancers (NMSCs) through a multidisciplinary approach, emphasizing the integration of dermoscopy and Ultra high-frequency ultrasound (UHFUS) for accurate diagnosis and treatment planning, particularly in cases referred for radiotherapy (RT). Dermoscopy aids in diagnosing both pigmented and non-pigmented skin lesions, guiding treatment margins and reducing the benign-to-malignant biopsy ratio. UHFUS provides valuable insights into tumor size, depth, and vascularity, complementing clinical evaluations and assisting in RT planning. Three challenging cases are presented, highlighting the pivotal role of dermoscopy and UHFUS in decision-making and treatment optimization. Collaboration between dermatologists, radiation oncologists, and radiologists enhances diagnostic accuracy, tailoring treatment plans to individual patient needs and preferences, ultimately improving patient outcomes and experience. The integration of these imaging techniques holds promise for optimizing non-surgical treatments like RT and monitoring treatment progress, offering a personalized approach to NMSC management.

3.
Clin Chem ; 70(6): 830-840, 2024 Jun 03.
Article in English | MEDLINE | ID: mdl-38581343

ABSTRACT

BACKGROUND: Microsatellite instability (MSI) indicates DNA mismatch repair deficiency in certain types of cancer, such as colorectal cancer. The current gold standard technique, PCR-capillary electrophoresis (CE), requires matching normal samples and specialized instrumentation. We developed VarTrace, a rapid and low-cost quantitative PCR (qPCR) assay, to evaluate MSI using solely the tumor sample DNA, obviating the requirement for matching normal samples. METHODS: One hundred and one formalin-fixed paraffin-embedded (FFPE) tumor samples were tested using VarTrace and compared with the Promega OncoMate assay utilizing PCR-CE. Tumor percentage limit of detection was evaluated on contrived samples derived from clinical high MSI (MSI-H) samples. Analytical sensitivity, specificity, limit of detection, and input requirements were assessed using synthetic commercial reference standards. RESULTS: VarTrace successfully analyzed all 101 clinical FFPE samples, demonstrating 100% sensitivity and 98% specificity compared to OncoMate. It detected MSI-H with 97% accuracy down to 10% tumor. Analytical studies using synthetic samples showed a limit of detection of 5% variant allele frequency and a limit of input of 0.5 ng. CONCLUSIONS: This study validates VarTrace as a swift, accurate, and economical assay for MSI detection in samples with low tumor percentages without the need for matching normal DNA. VarTrace's capacity for highly sensitive MSI analysis holds potential for enhancing the efficiency of clinical work flows and broadening the availability of this test.


Subject(s)
Microsatellite Instability , Humans , Paraffin Embedding , Neoplasms/genetics , Neoplasms/diagnosis , Multiplex Polymerase Chain Reaction/methods , Colorectal Neoplasms/genetics , Colorectal Neoplasms/diagnosis , Sensitivity and Specificity , Electrophoresis, Capillary/methods , Formaldehyde , DNA, Neoplasm/genetics , Limit of Detection , Polymerase Chain Reaction/methods
4.
Sci Rep ; 14(1): 6919, 2024 03 22.
Article in English | MEDLINE | ID: mdl-38519527

ABSTRACT

In order to tackle the global increase in overweight and obesity prevalence, several nutrient profiling systems have been developed; among others, Food Compass Score (FCS) has been designed to encompass multiple domains of food healthfulness. However, environmental sustainability of healthy diets is another crucial dimension which should not be overlooked in the context of human health. The aim of the present study is to assess the association between healthiness and environmental sustainability of food items, using the FCS and Agribalyse databases, respectively. A total of 806 matching food items were identified, grouped in 12 food categories; within each category, differences in median Z-scores between FCS and Single Environmental Footprint (EF) Score were assessed. While Fruits, Legumes and Nuts, Mixed foods, Meat Poultry and Eggs (MPE), Savory and Sweets, and Vegetables showed statistically significant differences (all p < 0.001), Beverages (p = 0.361), Dairy (p = 0.092), Fats and Oils (p = 0.594), Grains (p = 0.436), Sauce and Condiments (p = 0.093), and Seafood (p = 0.241) had similar Food Compass and Single EF Z-scores distributions. These findings underscore a relevant lack of difference between healthfulness and environmental impact of some prominent food categories, such as Grains and Seafood. Therefore, we suggest matching nutrient profiling systems with adequate environmental sustainability indices.


Subject(s)
Diet, Healthy , Diet , Humans , Vegetables , Fruit , Beverages
5.
Diagnostics (Basel) ; 14(2)2024 Jan 10.
Article in English | MEDLINE | ID: mdl-38248034

ABSTRACT

Our radiology department conducted an assessment of 300 neonatal radiographs in the neonatal intensive care unit over almost two years. The purpose was to evaluate the correct positioning of intravascular venous catheters. Our case series revealed that out of a total of 95 cases with misplaced devices, 59 were umbilical venous catheters and 36 were peripherally inserted central catheters. However, all of the central venous catheters were found to be properly positioned. Misplacements of neonatal intravascular devices were found to occur more frequently than expected. The scientific literature contains several articles highlighting the potential complications associated with misplaced devices. Our goal is to highlight the potential misplacements and associated complications that radiologists may encounter while reviewing conventional radiology imaging. Based on our experience, which primarily involved placing UVCs and PICCs, we discovered that conventional radiology is the most effective method for assessing proper device placement with the lowest possible radiation exposure. Given the high number of neonatal vascular device placement procedures, it is essential for radiologists to maintain a high level of vigilance and stay updated on the latest developments in this field.

6.
Front Clin Diabetes Healthc ; 4: 1292006, 2023.
Article in English | MEDLINE | ID: mdl-38047211

ABSTRACT

An emerging research niche has focused on the link between social determinants of health and diabetes mellitus, one of the most prevalent non-communicable diseases in modern society. The aim of the present mini-review is to explore and summarize current findings in this field targeting high-income countries. In the presence of disadvantaged neighborhood factors (including socioeconomic status, food environment, walkability and neighborhood aesthetics), diabetes prevention and care are affected at a multidimensional level. The vast majority of the included studies suggest that, besides individual risk factors, aggregated neighborhood inequalities should be tackled to implement effective evidence-based policies for diabetes mellitus.

7.
Clim Change ; 176(8): 108, 2023.
Article in English | MEDLINE | ID: mdl-37520165

ABSTRACT

The geographic distribution of natural ecosystems is affected by both climate and cropland. Discussions of future land use/land cover usually focus on how cropland expands and displaces natural vegetation especially as climate change impacts become stronger. Less commonly considered is the direct influence of climate change on natural ecosystems simultaneously with cropland incursion. We combine a natural vegetation model responsive to climate with a cropland allocation algorithm to assess the relative importance of climate change compared to cropland incursion. Globally, the model indicates that climate change drives larger gains and losses than cropland incursion. For example, in the Amazonian rainforests, more than one sixth of the forest area could be lost due to climate change with cropland playing virtually no role. Our findings suggest that policies to protect specific ecosystems may be undercut by climate change and that localized analyses that fully account for the impacts of a changing climate on natural vegetation and agriculture are necessary to formulate policies that preserve natural ecosystems over the long term. Supplementary Information: The online version contains supplementary material available at 10.1007/s10584-023-03584-3.

9.
Nutrients ; 15(5)2023 Feb 26.
Article in English | MEDLINE | ID: mdl-36904175

ABSTRACT

Nutrient profiling and front-of-pack labeling (FOPL) have been developed to categorize food products as more or less healthy based on their nutrient content and to easily communicate this information to consumers. The goal is to change individual food choices toward a healthier diet. Since global climate change has recently become an urgent matter, this paper also aims to investigate the correlations between different food health scales, including some FOPLs currently adopted by one or more countries, and several sustainability indicators. For this purpose, a food sustainability composite index has been developed to summarize environmental indicators and compare food scales. Results indicate, as expected, that well-known healthy and sustainable diets are strongly correlated with both environmental indicators and the composite index, while FOPLs based on portions or on 100 g show moderate and weak correlation values, respectively. Within-category analysis has not found any associations that explain these results. Hence, 100 g standard, on which FOPLs are usually developed, seems not to be the ideal basis for developing a label that aspires to communicate healthiness and sustainability in a unique format, as required by the need for simple messaging. On the contrary, FOPLs based on portions appear to be more likely to achieve this goal.


Subject(s)
Consumer Behavior , Food Labeling , Food Labeling/methods , Choice Behavior , Nutritive Value , Food Preferences , Environment
10.
Biomedicines ; 11(2)2023 Feb 06.
Article in English | MEDLINE | ID: mdl-36831008

ABSTRACT

Accumulating evidence supports a connection between sarcopenic obesity (SO) and NAFLD. The extent to which fatty liver contributes to impaired muscle contractility is not yet well established. The aim of our study was to investigate the effect of NAFLD on dynapenia in patients with SO. In this study, 71 non-diabetic subjects (age 55 (7.8) years, BMI 35.2 kg/m2 (32.6-38.8)) were classified as having SO and non-sarcopenic obesity (NSO). SO patients displayed worse serum lipid profiles, higher body fat, and lower skeletal muscle mass (both total and appendicular) than NSO patients, despite the absence of any significant differences in body weight, glycometabolic parameters, and hepatic steatosis prevalence. A positive correlation between disposition index and muscle quality index (MQI) (r = 0.393, p = 0.013) emerged after controlling for menopause and body fat percentage. Based on multiple linear regression analysis, MQI was significantly positively associated with the disposition index (ß: 0.059, SE: 0.002, p = 0.006) after adjustment for menopause, body fat percentage, and the presence of hepatic steatosis according to the hepatorenal index (HRI). Similar findings emerged when including liver enzyme levels in place of hepatic steatosis. Muscle quality was positively associated with ß-cell function corrected for insulin resistance among patients with obesity and sarcopenic obesity, irrespective of the presence of fatty liver disease.

11.
Eat Weight Disord ; 28(1): 23, 2023 Feb 23.
Article in English | MEDLINE | ID: mdl-36813943

ABSTRACT

The aim of this Editorial is to give an overview on the multiple aspects of front-of-pack labels (FOPLs) and provide the readers a balanced view of the problems raised in this research field, placing them in a wider context. Furthermore, this editorial paper discusses whether and how the use of FOPLs can promote health status in relation to the individual eating pattern and which should be the next research scenarios to investigate to further improve and integrate these tools.


Subject(s)
Food Preferences , Health Promotion , Humans , Health Behavior , Food Labeling , Consumer Behavior , Choice Behavior , Nutritive Value , Feeding Behavior
12.
J Appl Lab Med ; 8(3): 479-490, 2023 05 04.
Article in English | MEDLINE | ID: mdl-36759689

ABSTRACT

BACKGROUND: Key criteria in the diagnostic workup and risk stratification for myeloproliferative neoplasms (MPN) include molecular testing for JAK2V617F and other mutant alleles. Multiple methods for quantitatively detecting nucleotide sequence changes exist, but the lower limit of detection can limit identification of the low-level allele fraction of a variant. We evaluated a recently developed blocker displacement amplification (BDA)-based quantitative PCR platform for detection and quantitation of JAK2V617F variant allele fraction (VAF). METHODS: Clinical samples were tested using BDA, next-generation sequencing (NGS), and droplet digital PCR (ddPCR) in a head-to-head comparison of sensitivity and specificity in detecting the JAK2V617F variant. In total, 112 human genomic DNA specimens previously tested for JAK2V617F gene mutation status with NGS were analyzed, including 12 samples with low-level variants with VAF ≤2%, 6 samples with VAF >2%, and 94 samples with no variant previously identified by NGS. RESULTS: BDA and ddPCR results correlated well across a range of VAFs, with both methods identifying the JAK2V617F variant down to at least 0.05% VAF. NGS of routine sequencing depth was less sensitive, identifying JAK2V617F only at 0.6% VAF. CONCLUSIONS: BDA can provide a cost-effective alternative means to identify low-level variants using instrumentation commonly found in laboratories.


Subject(s)
Myeloproliferative Disorders , Humans , Myeloproliferative Disorders/diagnosis , Myeloproliferative Disorders/genetics , Mutation , Polymerase Chain Reaction/methods , Alleles , Nucleic Acid Amplification Techniques
13.
Radiol Case Rep ; 18(3): 1376-1379, 2023 Mar.
Article in English | MEDLINE | ID: mdl-36818997

ABSTRACT

Polydactyly, or hyperdactyly, is a frequent malformation, with a reported incidence between 0.37 and 1.2 per 1000 live births. Most cases encountered in medical practice are sporadic cases, usually presenting one-sided manifestations. More frequently, polydactyly can be detected prenatally through an ultrasound examination, if not, it is usually diagnosed at birth, during the first physical examination. Although the clinical diagnosis is relatively easy in patients with manifest cases, it can sometimes be present with mild or partial forms that are not clinically evident on physical examination, resulting in later diagnosis and treatment. We reported a particular case of polydactyly of the foot not clinically manifest, diagnosed in a 39-year-old Caucasian Male patient with a history of recurrent localized pain in the big toe often associated with subungual bleeding, since he was a child who came to our emergency room following a car accident. Polydactyly is a frequently reported congenital malformation which may present in many different varieties of deformities. In this case, the X-ray, which was required after a car accident, leads to the incidental diagnosis of polydactyly in an adult patient. As described, because of the functional limitations related to this malformation, as well as to limit recurrent pain, and subungual anomalies, the patient underwent to a surgical correction to improve its quality of life.

14.
Nutrients ; 15(2)2023 Jan 07.
Article in English | MEDLINE | ID: mdl-36678173

ABSTRACT

Digital anthropometry (DA) has been recently developed for body composition evaluation and for postural analysis. The aims of this review are to examine the current state of DA technology, as well as to verify the methods for identifying the best technology to be used in the field of DA by evaluating the reliability and accuracy of the available technologies on the market, and lay the groundwork for future technological developments. A literature search was performed and 28 studies met the inclusion criteria. The reliability and accuracy of DA was high in most studies, especially in the assessment of patients with obesity, although they varied according to the technology used; a good correlation was found between DA and conventional anthropometry (CA) and body composition estimates. DA is less time-consuming and less expensive and could be used as a screening tool before more expensive imaging techniques or as an alternative to other less affordable techniques. At present, DA could be useful in clinical practice, but the heterogeneity of the available studies (different devices used, laser technologies, population examined, etc.) necessitates caution in the interpretation of the obtained results. Furthermore, the need to develop integrated technologies for analyzing body composition according to multi-compartmental models is increasingly evident.


Subject(s)
Body Composition , Technology , Humans , Reproducibility of Results , Anthropometry/methods , Digital Technology
15.
Eat Weight Disord ; 27(8): 3037-3051, 2022 Dec.
Article in English | MEDLINE | ID: mdl-36369593

ABSTRACT

BACKGROUND: Front-of-Pack Nutritional Labels are considered a useful tool to help consumers orient themselves in their food choices and direct their behavior toward a healthier diet. FOPNL development and use are part of a framework that includes cognitive, biological, hedonic and cultural aspects, able to affect consumers' eating and purchasing behavior. AIM: Given the complexity of the matter, the aim of this narrative review is to analyze the combination of different factors that drive food choices and eating behaviors and to highlight some aspects that are not fully studied. METHODS: The authors conducted the research using a top-down approach at first, followed by a bottom-up approach; starting with general considerations about the purchasing process, gradually narrowing the discussion to a specific sub-population, and finally extending the discussion back to more general reasonings about the direction to adopt in future, or at least to evaluate, for effective communication. RESULTS: Biases and attitudes toward food products were found to regularly interfere with buying behavior patterns, making it impossible to standardize an average consumer. This reflects in current research, increasing the complexity of the topic. All determinants influencing food choices are often assessed individually rather than in a synergistic and multidimensional context, while the purchasing scenario is characterized by multiple stimuli to which the consumer is subjected. FOPNLs' impact on perceived healthiness has been studied in different conditions, but some population subgroups have not been sufficiently represented. In particular, the effect of FOPNLs on consumers suffering from eating disorders is understudied and needs further attention. Furthermore, some approaches can be compared to "negative nutrition" or "loss-framed communication", putting nutrients out of context, emphasizing losses more than gains and risking promoting negative feelings in consumers. CONCLUSION: Due to the heterogeneity of studies, evidence on what works best in driving people to adopt lasting lifestyle changes is still mixed. Science communicators and policymakers should consider the possibility that a multi-component approach incorporating nutrition information and education may be a key strategy to promote consumers' self-consciousness and to support them in their cognitive efforts toward a healthy and sustainable diet. LEVEL OF EVIDENCE: Level V, narrative review.


Subject(s)
Choice Behavior , Diet , Humans , Nutritive Value , Food Preferences/psychology , Nutritional Status
16.
Nutrition ; 102: 111770, 2022 10.
Article in English | MEDLINE | ID: mdl-35816811

ABSTRACT

Nutrition labels advise consumers about the nutritional value of packaged foods and their contribution to the overall composition of the diet. They have been proposed as an instrument for the promotion of healthy diets and as a fundamental tool in the prevention of obesity and diet-related non-communicable diseases (NCDs). The aim of this review is to discuss the effectiveness of front-of-pack nutrition labels (FOPNLs) in improving health status, the concern about focusing on single nutrients/foods rather than on eating patterns to prevent obesity and NCDs, and the strength of positive rather than negative messages to promote a healthy and sustainable diet. Although nutrition science investigates individual foods or nutrients, when communicating to the public most of the significant evidence of the favorable health effect largely depends on dietary patterns and not on a single food component or individual nutrient. Therefore, we suggest that a new tool based on positive communication should be developed and implemented to highlight the importance of the diet as a complex matrix.


Subject(s)
Food Labeling , Noncommunicable Diseases , Consumer Behavior , Diet, Healthy , Humans , Noncommunicable Diseases/prevention & control , Nutritional Status , Nutritive Value , Obesity/prevention & control
17.
Rev. Enferm. Atual In Derme ; 96(39): 1-15, Jul-Set. 2022.
Article in Portuguese | BDENF - Nursing | ID: biblio-1417038

ABSTRACT

Objetivo: Descrever a experiência do desenvolvimento do Processo de Enfermagem, com base nas demandas terapêuticas de uma paciente com diagnósticos de sequelas neuropsiquiátricas de acordo com a Teoria do Cuidar Transpessoal e a CIPE® em um hospital no extremo norte do Brasil. Método: Trata-se de um relato de experiência, realizado em maio de 2022 em uma Instituição Pública de Saúde de Boa Vista-RR, a partir da produção do Processo de Enfermagem à uma paciente com diagnósticos de sequelas neuropsiquiátricas decorrentes da COVID-19. Na etapa Coleta de Dados foi realizada entrevista clínica e exame físico, seguindo-se roteiro norteador da instituição. Para as etapas de Diagnóstico, Planejamento e Implementação, utilizou-se a Taxonomia da CIPE®, respeitando os aspectos éticos. Resultados: Paciente do sexo feminino, 19 anos, brasileira, natural e residente de Boa Vista-RR, com os diagnósticos de transtorno funcional, síndrome do pânico com pseudocrises convulsivas e depressão, sequelas da COVID-19. A partir da Coleta de Dados foram elencados os seguintes Diagnósticos: Convulsão alta; Fraqueza parcial; Desorientação simples; Memória prejudicada; Dor aguda moderada; Risco de queda aumentada; Marcha (caminhada) prejudicada; Risco de infecção; Recuperação física lenta; Delírio leve; Problema emocional real; Resposta psicológica prejudicada; Resiliência prejudicada; Medo moderado, os quais fundamentaram as demais etapas. Considerações finais: A experiência permitiu a aplicação da teoria científica na prática de enfermagem, aprimorando as habilidades dos pensamentos crítico, reflexivo e clínico, e a implementação do Processo de Enfermagem no contexto das sequelas neuropsiquiátricas pós COVID-19.


Objective:To describe the experience of developing the Nursing Process, based on the therapeutic demands of a patient diagnosed with neuropsychiatric sequelae according to the Transpersonal Caring Theory and ICNP® in a hospital in the extreme north of Brazil. Method:This is an experience report, carried out in May 2022 in a Public Health Institution in Boa Vista-RR, from the production of the Nursing Process to a patient with diagnoses of neuropsychiatric sequelae resulting from COVID-19. In the Data Collection stage, a clinical interview and physical examination were carried out, following the guiding script of the institution. For the stages of Diagnosis, Planning and Implementation, the ICNP® Taxonomy was used, respecting ethical aspects. Results:Female patient, 19 years old, Brazilian, born and resident of Boa Vista-RR, with diagnoses of functional disorder, panic syndrome with pseudoseizures and depression, sequelae of COVID-19. From the Data Collection, the following diagnoses were listed: High seizure; partial weakness; Simple disorientation; Impaired memory; Moderate acute pain; Increased risk of falling; Impaired gait (walking); Risk of infection; Slow physical recovery; Mild delirium; Actual emotional problem; Impaired psychological response; Impaired resilience; Moderate fear, which underpinned the other stages. Final considerations: The experience allowed the application of scientific theory in nursing practice, improving critical, reflective and clinical thinkingskills, and the implementation of the Nursing Process in the context of post-COVID-19 neuropsychiatric sequelae.


Objetivo:Describir la experiencia de desarrollo del Procesode Enfermería, a partir de las demandas terapéuticas de un paciente diagnosticado con secuelas neuropsiquiátricas según la Teoría del Cuidado Transpersonal y la CIPE® en un hospital del extremo norte de Brasil. Método:Se trata de un relato de experiencia, realizado en mayo de 2022 en una Institución de Salud Pública de Boa Vista-RR, a partir de la elaboración del Proceso de Enfermería a un paciente con diagnósticos de secuelas neuropsiquiátricas resultantes de la COVID-19. En la etapa de Recolección de Datos, se realizó entrevista clínica y examen físico, siguiendo el guión rector de la institución. Para las etapas de Diagnóstico, Planificación e Implementación se utilizó la Taxonomía CIPE®, respetando los aspectos éticos. Resultados: Paciente femenina, de19 años, brasileña, nacida y residente de Boa Vista-RR, con diagnósticos de trastorno funcional, síndrome de pánico con pseudocrisis y depresión, secuelas de la COVID-19. A partir de la Recolección de Datos, fueron listados los siguientes diagnósticos: Convulsión alta; debilidad parcial; Desorientación simple; Deterioro de la memoria; dolor agudo moderado; Mayor riesgo de caídas; Alteración de la marcha (caminar); Riesgo de infección; Lenta recuperación física; delirio leve; Problema emocional real; Deterioro de la respuesta psicológica; Deterioro de la resiliencia; Miedo moderado, que sustentaba las otras etapas. Consideraciones finales:La experiencia permitió la aplicación de la teoría científica en la práctica de enfermería, mejorando las habilidades depensamiento crítico, reflexivo y clínico, y la implementación del Proceso de Enfermería en el contexto de las secuelas neuropsiquiátricas post-COVID-19.


Subject(s)
Humans , Male , Female , Neuropsychiatry , COVID-19 , Nursing Care , Nursing Process
18.
Anal Chem ; 94(27): 9586-9594, 2022 07 12.
Article in English | MEDLINE | ID: mdl-35749270

ABSTRACT

Clinically and biologically, it is essential to detect rare DNA-sequence variants for early cancer diagnosis or drug-resistance mutation identification. Some of the common quantitative polymerase chain reaction (qPCR)-based variant detection methods are restricted in the limit of detection (LoD) because the DNA polymerases used for these methods have a high polymerase misincorporation rate; thus, the detection sensitivity is sometimes unsatisfactory. With the proofreading activity, high-fidelity (HiFi) DNA polymerases have a 50- to 250-fold higher fidelity. However, there are currently no proper probe-based designs functioning as the fluorescence indicator allowing multiplexed HiFi qPCR reactions, thus restricting the application of HiFi DNA polymerases like the variant detection. We presented the occlusion system, composed of a 5'-overhanged primer with a fluorophore modification and a probe with a short-stem hairpin and a 3' quencher modification. We demonstrated that the occlusion system allowed multiplexing HiFi qPCR reaction, and it was compatible with the current variant-enrichment method to improve the LoD up to 10-fold. Thus, the occlusion system satisfactorily functioned as an efficient fluorescence indicator in HiFi qPCR reactions and allowed the application of HiFi DNA polymerases in variant detection methods to improve detection sensitivity.


Subject(s)
DNA-Directed DNA Polymerase , DNA , DNA/genetics , DNA Primers/genetics , Multiplex Polymerase Chain Reaction/methods , Mutation , Real-Time Polymerase Chain Reaction
19.
Nutrients ; 14(10)2022 May 23.
Article in English | MEDLINE | ID: mdl-35631307

ABSTRACT

As a team of scientists who believe that exchanging views is one of the prerequisites of the scientific method, we welcome the comments from Aguenaou H et al. [...].


Subject(s)
Food Labeling , Physicians , Health Policy , Humans , Nutrients
20.
ACS Sens ; 7(4): 1165-1174, 2022 04 22.
Article in English | MEDLINE | ID: mdl-35418222

ABSTRACT

Molecular detection of disease-associated mutations, especially those with low abundance, is essential for academic research and clinical diagnosis. Certain variant detection methods reach satisfactory sensitivity and specificity in detecting rare mutations based on the introduction of blocking oligos to prevent the amplification of wild-type or unwanted templates, thus selectively amplifying and enriching the mutations. These blocking oligos usually suppress PCR amplification through the 3' chemical modifications, with high price, slow synthesis, and reduced purity. Herein, we introduce chemistry-free designs to block enzymatic extension during PCR by the steric hindrance from the secondary structures attached to the 3' end of the oligos (nonextensible oligonucleotide, NEO). We demonstrated that NEO efficiently prohibited the extension of both Taq and high-fidelity DNA polymerases. By further applying NEO as blockers in blocker displacement amplification (BDA) qPCR, multiplex BDA (mBDA) NGS, and quantitative BDA (QBDA) NGS methods, we showed that NEO blockers had performance comparable with previously validated chemical modifications. Comparison experiments using QBDA with NEO blockers and droplet digital PCR (ddPCR) on clinical formalin-fixed paraffin-embedded (FFPE) samples exhibited 100% concordance. Lastly, the ability of NEO to adjust plex uniformity through changes of PCR amplification efficiency was demonstrated in an 80-plex NGS panel.


Subject(s)
High-Throughput Nucleotide Sequencing , Oligonucleotides , High-Throughput Nucleotide Sequencing/methods , Mutation , Oligonucleotides/genetics , Real-Time Polymerase Chain Reaction/methods , Sensitivity and Specificity
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