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Frontiers in Genetics 2024The clinical application of technological progress in the identification of DNA alterations has always led to improvements of diagnostic yields in genetic medicine. At... (Review)
Review
The clinical application of technological progress in the identification of DNA alterations has always led to improvements of diagnostic yields in genetic medicine. At chromosome side, from cytogenetic techniques evaluating number and gross structural defects to genomic microarrays detecting cryptic copy number variants, and at molecular level, from Sanger method studying the nucleotide sequence of single genes to the high-throughput next-generation sequencing (NGS) technologies, resolution and sensitivity progressively increased expanding considerably the range of detectable DNA anomalies and alongside of Mendelian disorders with known genetic causes. However, particular genomic regions (i.e., repetitive and GC-rich sequences) are inefficiently analyzed by standard genetic tests, still relying on laborious, time-consuming and low-sensitive approaches (i.e., southern-blot for repeat expansion or long-PCR for genes with highly homologous pseudogenes), accounting for at least part of the patients with undiagnosed genetic disorders. Third generation sequencing, generating long reads with improved mappability, is more suitable for the detection of structural alterations and defects in hardly accessible genomic regions. Although recently implemented and not yet clinically available, long read sequencing (LRS) technologies have already shown their potential in genetic medicine research that might greatly impact on diagnostic yield and reporting times, through their translation to clinical settings. The main investigated LRS application concerns the identification of structural variants and repeat expansions, probably because techniques for their detection have not evolved as rapidly as those dedicated to single nucleotide variants (SNV) identification: gold standard analyses are karyotyping and microarrays for balanced and unbalanced chromosome rearrangements, respectively, and southern blot and repeat-primed PCR for the amplification and sizing of expanded alleles, impaired by limited resolution and sensitivity that have not been significantly improved by the advent of NGS. Nevertheless, more recently, with the increased accuracy provided by the latest product releases, LRS has been tested also for SNV detection, especially in genes with highly homologous pseudogenes and for haplotype reconstruction to assess the parental origin of alleles with pathogenic variants. We provide a review of relevant recent scientific papers exploring LRS potential in the diagnosis of genetic diseases and its potential future applications in routine genetic testing.
PubMed: 38510277
DOI: 10.3389/fgene.2024.1374860 -
Orphanet Journal of Rare Diseases Jul 2023Intellectual disability (ID) has a prevalence of 1-3% and aproximately 30-50% of ID cases have a genetic cause. Development of next-generation sequencing has shown a... (Review)
Review
Intellectual disability (ID) has a prevalence of 1-3% and aproximately 30-50% of ID cases have a genetic cause. Development of next-generation sequencing has shown a high diagnostic potential. The aim of this work was to evaluate the diagnostic yield of clinical exome sequencing in 188 ID patients and the economic impact of its introduction in clinical practice. An analysis of diagnostic yield according to the different clinical variables was performed in order to establish an efficient diagnostic protocol for ID patients. Diagnostic yield of clinical exome sequencing was significant (34%) supporting its utility in diagnosis of ID patients. Wide genetic heterogeneity and predominance of autosomal dominant de novo variants in ID patients were observed. Time to diagnosis was shortened and diagnostic study costs decreased by 62% after implementation of clinical exome sequencing. No association was found between any of the variables analyzed and a higher diagnostic yield; added to the fact that many of the diagnoses weren't clinically detectable, the reduction of time to diagnosis and the economic savings with respect to classical diagnostic studies, strengthen the clinical and economical convenience of early implementation of clinical exome sequencing in the diagnostic workup of ID patients in clinical practice.
Topics: Humans; Intellectual Disability; Exome Sequencing; Exome; High-Throughput Nucleotide Sequencing
PubMed: 37480025
DOI: 10.1186/s13023-023-02809-z -
Biomedical Reports Sep 2023Gastric cancer (GC) remains a disease with poor prognosis despite increasing availability of more effective targeted treatment. This may be in part due to the difficulty... (Review)
Review
Gastric cancer (GC) remains a disease with poor prognosis despite increasing availability of more effective targeted treatment. This may be in part due to the difficulty in selecting patients for appropriate treatment. Conventional taxonomic classifications of GC are ill-suited to make full use of recent advances in personalised therapy. In the past decade a number of molecular classifications have been proposed to address this; however, to date, there has been little implementation in the diagnostic routine. The lack of harmonisation between these classifications, the complexity and unavailability of some of the tests required plus the demands on time and resources, all contribute to poor uptake in the diagnostic routine. In the present study, these classifications were reviewed and an inclusive working classification that includes their main points, focuses on prognosis and treatment options and can be delivered using four on-slide tests ( hybridization for Epstein-Barr encoding region and immunohistochemistry for mismatch repair, E-cadherin and p53) is proposed. These tests can be performed on paraffin-embedded tissue and could be available in the majority of histopathology laboratories. The proposed classification also includes reflex testing for specific biomarkers relevant to treatment selection.
PubMed: 37614984
DOI: 10.3892/br.2023.1640 -
Journal of Analytical Methods in... 2023Carbapenem-resistant (CRE) infections constitute a threat to public health, and KPC and NDM are the major carbapenemases of concern. Rapid diagnostic tests are highly...
Carbapenem-resistant (CRE) infections constitute a threat to public health, and KPC and NDM are the major carbapenemases of concern. Rapid diagnostic tests are highly desirable in point-of-care (POC) and emergency laboratories with limited resources. Here, we developed a multiplex lateral flow assay based on asymmetric PCR and barcode capture probes for the simultaneous detection of KPC-2 and NDM-1. Biotinylated barcode capture probes corresponding to the KPC-2 and NDM-1 genes were designed and cast onto two different sensing zones of a nitrocellulose membrane after reacting with streptavidin to prepare a multiplex lateral flow strip. Streptavidin-coated gold nanoparticles (SA-AuNPs) were used as signal reporters. In response to the target carbapenemase genes, biotin-labelled ssDNA libraries were produced by asymmetric PCR, which bond to SA-AuNPs via biotin and hybridise with the barcode capture probe via a complementary sequence, thereby bridging SA-AuNPs and the barcode capture probe to form visible red lines on the detection zones. The signal intensities were proportional to the number of resistance genes tested. The strip sensor showed detection limits of 0.03 pM for the KPC-2 and 0.07 pM for NDM-1 genes, respectively, and could accurately distinguish between KPC-2 and NDM-1 genes in CRE strains. For the genotyping of clinical isolates, our strip exhibited excellent consistency with real-time fluorescent quantitative PCR and gene sequencing. Given its simplicity, cost-effectiveness, and rapid analysis accomplished by the naked eye, the multiplex strip is promising auxiliary diagnostic tool for KPC-2 and NDM-1 producers in routine clinical laboratories.
PubMed: 37520816
DOI: 10.1155/2023/9975620 -
Medicine Oct 2023To investigate the effect blood flow restriction (BFR) exercises on muscle size, strength and athletic performance in elite canoe athletes aged 18 to 25 years. (Randomized Controlled Trial)
Randomized Controlled Trial
BACKGROUND
To investigate the effect blood flow restriction (BFR) exercises on muscle size, strength and athletic performance in elite canoe athletes aged 18 to 25 years.
METHODS
This was a randomized controlled trial. The participants were divided into 2 groups: the intervention group (INT-gr) (n = 17, age: 18.59 ± 0.71 years) and the control group (CONT-gr) (n = 16, age: 18.81 ± 1.11 years). Anthropometric measurements, muscle size measured by ultrasound (US), strength measurements with an isokinetic dynamometer, and ergometer performance with an indoor ergometer were conducted before and after the exercise program. Knee flexion and extension and leg press one-repetition maximum (1 RM) tests were performed to determine the participants' training program. The INT-gr performed 1 RM 30% resistance training + BFR for 8 weeks, while the CONT-gr performed 1 RM 30% resistance training (RT) without BFR with their routine training program. US was used to measure the cross sectional area (CSA) and thickness of the quadriceps femoris (QF) and Hamstring (H) muscles in the pre-post design, and the isokinetic dynamometer was used to measure the strength of bilateral 60˚/s and 300˚/s peak torque (PT) values of the QF and H. Sports performance was tested on an indoor ergometer at distances of 200, 500, and 1000 m.
RESULTS
The changes in bilateral rectus femoris (RF) CSA and VL thickness measurements in the INT-gr were significant (P < .05). Ergometer performance measurements showed a significant improvement over CONT-gr at all distances (P < .05). In terms of strength scores measured by the isokinetic dynamometer, the right QF and H 300˚/s and the left QF 60˚/s PT values were significantly in favor of INT-gr.
CONCLUSION
BFR exercises are effective to increase strength, muscle size, and ergometer performance in elite canoe athletes.
Topics: Humans; Male; Adolescent; Young Adult; Adult; Muscle Strength; Blood Flow Restriction Therapy; Quadriceps Muscle; Resistance Training; Athletes
PubMed: 37832066
DOI: 10.1097/MD.0000000000035252 -
Journal of Medical Internet Research Jul 2023Deep learning (DL) prediction models hold great promise in the triage of COVID-19. (Meta-Analysis)
Meta-Analysis Review
BACKGROUND
Deep learning (DL) prediction models hold great promise in the triage of COVID-19.
OBJECTIVE
We aimed to evaluate the diagnostic test accuracy of DL prediction models for assessing and predicting the severity of COVID-19.
METHODS
We searched PubMed, Scopus, LitCovid, Embase, Ovid, and the Cochrane Library for studies published from December 1, 2019, to April 30, 2022. Studies that used DL prediction models to assess or predict COVID-19 severity were included, while those without diagnostic test accuracy analysis or severity dichotomies were excluded. QUADAS-2 (Quality Assessment of Diagnostic Accuracy Studies 2), PROBAST (Prediction Model Risk of Bias Assessment Tool), and funnel plots were used to estimate the bias and applicability.
RESULTS
A total of 12 retrospective studies involving 2006 patients reported the cross-sectionally assessed value of DL on COVID-19 severity. The pooled sensitivity and area under the curve were 0.92 (95% CI 0.89-0.94; I=0.00%) and 0.95 (95% CI 0.92-0.96), respectively. A total of 13 retrospective studies involving 3951 patients reported the longitudinal predictive value of DL for disease severity. The pooled sensitivity and area under the curve were 0.76 (95% CI 0.74-0.79; I=0.00%) and 0.80 (95% CI 0.76-0.83), respectively.
CONCLUSIONS
DL prediction models can help clinicians identify potentially severe cases for early triage. However, high-quality research is lacking.
TRIAL REGISTRATION
PROSPERO CRD42022329252; https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD 42022329252.
Topics: Humans; COVID-19; Deep Learning; Retrospective Studies; PubMed; Diagnostic Tests, Routine; COVID-19 Testing
PubMed: 37477951
DOI: 10.2196/46340 -
PloS One 2023Postmenopausal bleeding (PMB) is a common gynecologic condition. Although it can be a sign of uterine cancer, most patients have benign etiology. However, research on...
BACKGROUND
Postmenopausal bleeding (PMB) is a common gynecologic condition. Although it can be a sign of uterine cancer, most patients have benign etiology. However, research on quality of diagnostic evaluation for PMB has been limited to cancer patients. To extend this research, we examined the timeliness of diagnostic evaluation for PMB among patients with benign conditions.
METHODS
Using the 2008-2019 MarketScan Research Databases, we identified 499176 patients (456741 with commercial insurance and 42435 with Medicaid insurance) who presented with PMB but did not have gynecologic cancer. For each patient, we measured the time from their PMB reporting to the date of their first diagnostic procedure. The association between patient characteristics and time to first diagnostic procedure was examined using Cox proportional hazards models (for the overall sample and then stratified by insurance type).
RESULTS
Overall, 54.3% of patients received a diagnostic procedure on the same day when they reported PMB and 86.6% received a diagnostic procedure within 12 months after reporting PMB. These percentages were 39.4% and 77.1%, respectively, for Medicaid patients, compared to 55.7% and 87.4%, respectively, for commercially insured patients (p<0.001 for both). Medicaid patients had an 18% lower rate of receiving a diagnostic procedure at any given time point than commercially insured patients (adjusted hazard ratio = 0.82, 95% CI: 0.81-0.83). Meanwhile, older age and non-gynecologic comorbidities were associated with a lower rate whereas concomitant gynecologic conditions and recent use of preventive care were associated with a higher rate of receiving diagnostic procedures. Analysis stratified by insurance type identified additional risk factors for delayed diagnostic procedures (e.g., non-metropolitan versus metropolitan location for commercially insured patients and Black versus White race for Medicaid patients).
CONCLUSION
A sizable proportion of patients did not receive prompt diagnostic evaluation for PMB. Both clinical and non-clinical factors could affect timeliness of evaluation.
Topics: United States; Female; Humans; Postmenopause; Retrospective Studies; Databases, Factual; Genital Neoplasms, Female; Insurance; Uterine Hemorrhage
PubMed: 37682914
DOI: 10.1371/journal.pone.0289692 -
Genes Mar 2024Neurodevelopmental disorders are a group of complex multifactorial disorders characterized by cognitive impairment, communication deficits, abnormal behaviour, and/or...
Neurodevelopmental disorders are a group of complex multifactorial disorders characterized by cognitive impairment, communication deficits, abnormal behaviour, and/or motor skills resulting from abnormal neural development. Copy number variants (CNVs) are genetic alterations often associated with neurodevelopmental disorders. We evaluated the diagnostic efficacy of the array-comparative genomic hybridization (a-CGH) method and its relevance as a routine diagnostic test in patients with neurodevelopmental disorders for the identification of the molecular alterations underlying or contributing to the clinical manifestations. In the present study, we analysed 1800 subjects with neurodevelopmental disorders using a CGH microarray. We identified 208 (7%) pathogenetic CNVs, 2202 (78%) variants of uncertain significance (VOUS), and 504 (18%) benign CNVs in the 1800 patients analysed. Some alterations contain genes potentially related to neurodevelopmental disorders including , , , , , , , , , , , , , and . The identification of interesting significant genes related to neurological disorders with a-CGH is therefore an essential step in the diagnostic procedure, allowing a better understanding of both the pathophysiology of these disorders and the mechanisms underlying their clinical manifestations.
Topics: Humans; Neurodevelopmental Disorders; DNA Copy Number Variations; Female; Male; Comparative Genomic Hybridization; Italy; Child; Adolescent; Child, Preschool
PubMed: 38674362
DOI: 10.3390/genes15040427 -
World Journal of Hepatology Jan 2024Hepatitis C virus (HCV) remains a significant public health problem as it can cause acute and chronic hepatitis. Chronic HCV infection is a major cause of liver...
Hepatitis C virus (HCV) remains a significant public health problem as it can cause acute and chronic hepatitis. Chronic HCV infection is a major cause of liver fibrosis, and evaluation of liver fibrosis is essential because the prognosis of patients with chronic HCV infection is closely related to the stage of fibrosis. Liver fibrosis is traditionally evaluated based on pathological analysis of biopsy specimens, which is considered the gold standard. Nevertheless, liver biopsy is invasive and susceptible to sampling error and inter- and intraobserver variation in pathological interpretation; it is also costly. Therefore, noninvasive diagnostic investigations have been developed, including the use of fibrotic markers, scoring systems based on routine blood tests, and transient elastography with magnetic resonance imaging or ultrasonography. Recently, metabolomics, an emerging technology, has been used to detect the fibrosis stage. In this editorial, I comment on the article titled "Metabolomics in chronic hepatitis C: Decoding fibrosis grading and underlying pathways" by Ferrasi published in the recent issue of the . I discuss previous studies on the use of metabolome analysis for the diagnosis of HCV-related liver fibrosis and the potential development of biopsy-free diagnostic techniques.
PubMed: 38313246
DOI: 10.4254/wjh.v16.i1.12 -
World Journal of Gastroenterology May 2024Increased lipase level is a serological hallmark of the diagnosis of acute pancreatitis (AP) but can be detected in various other diseases associated with lipase leakage... (Observational Study)
Observational Study
BACKGROUND
Increased lipase level is a serological hallmark of the diagnosis of acute pancreatitis (AP) but can be detected in various other diseases associated with lipase leakage due to inflammation of organs surrounding the pancreas or reduced renal clearance and/or hepatic metabolism. This non-pancreatic hyperlipasemia (NPHL) is puzzling for attending physicians during the diagnostic procedure for AP. It would be clinically beneficial to identify the clinical and laboratory variables that hinder the accuracy of lipase diagnosis with the aim of improve it. A more precise description of the NPHL condition could potentially provide prognostic factors for adverse outcomes which is currently lacking.
AIM
To perform a detailed clinical and laboratory characterization of NPHL in a large prospective patient cohort with an assessment of parameters determining disease outcomes.
METHODS
A Hungarian patient cohort with serum lipase levels at least three times higher than the upper limit of normal (ULN) was prospectively evaluated over 31 months. Patients were identified using daily electronic laboratory reports developed to support an ongoing observational, multicenter, prospective cohort study called the EASY trial (ISRCTN10525246) to establish a simple, easy, and accurate clinical scoring system for early prognostication of AP. Diagnosis of NPHL was established based on ≥ 3 × ULN serum lipase level in the absence of abdominal pain or abdominal imaging results characteristic of pancreatitis.
RESULTS
A total of 808 patients [male, = 420 (52%); median age (IQR): 65 (51-75) years] were diagnosed with ≥ 3 × ULN serum lipase levels. A total of 392 patients had AP, whereas 401 had NPHL with more than 20 different etiologies. Sepsis and acute kidney injury (AKI) were the most prevalent etiologies of NPHL (27.7% and 33.2%, respectively). The best discriminative cut-off value for lipase was ≥ 666 U/L (sensitivity, 71.4%; specificity, 88.8%). The presence of AKI or sepsis negatively affected the diagnostic performance of lipase. NPHL was associated with a higher in-hospital mortality than AP (22.4% 5.1%, < 0.001). In multivariate binary logistic regression, not lipase but increased amylase level (> 244 U/L) and neutrophil-to-lymphocyte ratio (NLR) (> 10.37, OR: 3.71, 95%CI: 2.006-6.863, < 0.001), decreased albumin level, age, and presence of sepsis were independent risk factors for in-hospital mortality in NPHL.
CONCLUSION
NPHL is a common cause of lipase elevation and is associated with high mortality rates. Increased NLR value was associated with the highest mortality risk. The presence of sepsis/AKI significantly deteriorates the serological differentiation of AP from NPHL.
Topics: Humans; Lipase; Male; Female; Middle Aged; Prospective Studies; Pancreatitis; Aged; Prognosis; Hungary; Biomarkers; Adult
PubMed: 38817657
DOI: 10.3748/wjg.v30.i19.2538