Guidelines For Interpretation Research Articles

PRECAUTIONARY MEASURE AGAINST INDIGENOUS PERSONS IN ECUADOR: AN ANALYSIS OF ITS CULTURAL AND LEGAL APPROPRIATENESS

Objetive: This article analyzes the appropriateness of pretrial detention when used as a precautionary measure in criminal procedures against Indigenous persons in Ecuador. Theoretical structure: The theoretical framework is based on the doctrine of criminal guarantees and the conventional obligations of the Ecuadorian state, mainly from inter-American jurisprudence. The discussion is complemented by a critical analysis of positivism and the persistence of the colonialist vision in the institutionality of the criminal justice system. Method: A doctrinal and jurisprudential approach is carried out, which is complemented with an analysis based on the ethnographic approach and interpretation of the normative as discourse. Conclusion: With regard to pretrial detention, Inter-American law has developed standards that will be analyzed in the framework of cultural diversity, seeking to establish a few guidelines for an intercultural interpretation, in which Indigenous authorities may participate in the precautionary guarantees. Therefore, the Constitutional Court of Ecuador has rendered many judgments that adhere to intercultural guidelines for cases and trials against Indigenous peoples and nationalities.

Unsupervised Machine Learning‐Derived Anion‐Exchange Membrane Polymers Map: A Guideline for Polymers Exploration and Design

AbstractAlthough anion‐exchange membranes (AEMs) are commonly used in fuel cells and water electrolyzers, their widespread commercialization is hindered by problems such as low anion conductivity and durability. Moreover, the development of high‐performance AEMs remains complex and time consuming. Here, we address these challenges by proposing an innovative approach for the efficient design and screening of AEM polymers using unsupervised machine learning. Our model, which combines principal component analysis with uniform manifold approximation and projection, generates an intuitive map that clusters AEM polymers based on structural similarities without any predefined knowledge regarding anion conductivity or other experimentally derived variables. As a powerful navigation tool, this map provides insights into promising main‐chain structures, such as poly(arylene alkylene)s with consistently high conductivity and polyolefins with exceptional performance depending on the substituent. Furthermore, assisted by key molecular descriptors, inverse analysis with this model allows targeted design and property prediction before synthesis, which will significantly accelerate the discovery of novel AEM polymers. This work represents a paradigm shift not only in AEM research but also generally in materials research, moving from black‐box predictions toward interpretable guidelines that foster collaboration between researchers and machine learning for efficient and informed material development.

P-566 Addressing ethnic underrepresentation in carrier screening: prioritizing comprehensive variant curation over ClinVar-based automated analysis

Abstract Study question How does the use of a ClinVar-based approach in Carrier Genetic Screening (CGS) affect the efficiency and accuracy of carrier detection analysis? Summary answer For CGS, comprehensive variant curation, not automated analysis alone, addresses risk from under-representation of diverse populations in genetic databases. What is known already Next-generation sequencing (NGS) analyses in Carrier Screening (CS) yield numerous variants per patient requiring interpretation for pathogenicity assessment. Public variant databases aid in the curation process, clinical interpretation, and genomic data sharing, reducing error risks and diagnostic delays. Consequently, an increasing number of genetic laboratories are integrating these databases into their workflows. However, over-representation of certain ethnic groups persists due to genetic inequality, as these databases primarily contain variants previously reported in patients and manually recorded. This lack of ethnic diversity in human genomic studies and databases can lead to inaccurate risk assessment and inadequate interventions in under-studied populations. Study design, size, duration Retrospective analysis involved 3886 patients of various ethnicities examined between June 2021 and March 2023. They were grouped according to self-reported ethnicity: African(54), Asian(43), Mediterranean(689), European/Caucasian(2402), Latino(449) and not reported(249). Participants/materials, setting, methods Patients were categorized based on their self-reported ethnicity after undergoing analysis with a Carrier Screening (CS) panel of 300 genes, which included autosomal recessive and X-linked disorders, using Next-Generation Sequencing (NGS). Complete variant curation (CCV) was conducted using the American College of Medical Genetics and Genomics(ACMG) and ClinGen guidelines for variant interpretation. The average number of variants per patient was calculated for both the automated process using only the ClinVar database and the CCV performed. Main results and the role of chance Upon evaluating the number of variants identified per patient,, 1.51 variants/patient (v/p) were observed when CCV, while 1.27 v/p would have been detected using only ClinVar (automated process). In summary, ClinVar accounted for 88% of all variants identified with CCV. Significant differences in variant detection were observed across ethnicities. The percentage of variants not detected by the automatic process were as follows: 21.95% in Asian ethnicity, 17.84% in African, 13.99% in Latino, 11.88% in Mediterranean, 10.97% in European/Caucasian and 10.70% in patients who did not report ethnicity. Among these, Asian and African ethnic groups had the lowest percentage of variants detected by ClinVar 78.05% and 82.16%, respectively. In the Asian group, 0.95 v/p were identified, while in the African group, 1.70 v/p were identified. Limitations, reasons for caution Data was collected based on self-reported ethnicity, which may not always accurately reflect true ancestry. Additionally, the sample size for certain ethnicities was relatively small. Variant classification relied on information available in databases or literature at the time of the study, potentially subject to updates or revisions in the future. Wider implications of the findings This study underscores the limitations of automated analysis in detecting all variants identified by CCV across ethnicities, highlighting genetic disparities present in mutation databases like ClinVar. The findings emphasize the importance of implementing CCV in Carrier Screening tests to effectively mitigate reproductive risks across diverse ethnic groups. Trial registration number not applicable

Interpretation and reporting considerations of low-level DNA profiles following MinElute® purification of PowerPlex® 21 amplified products

The generation of high-quality DNA profiles from trace amounts of DNA continues to be an issue in forensic casework. Several methods have been proposed over the years to increase recovery rates for low input DNA, including purification of PCR products, an increase in PCR cycle numbers and increasing injection time or voltage during electrophoresis. In this study, the characteristics of DNA profiles generated using QIAGEN MinElute® purification of Promega PowerPlex® 21 amplified products for low DNA input samples, ranging from 80 pg down to 4 pg, were evaluated. MinElute® purification was found to be a simple, effective and time efficient method, which can greatly improve the resolution of amplified PCR products, recovering 100% of donor concordant alleles from as little 16 pg of input template DNA and generating sufficient allelic information for interpretation from as low as 4 pg inputs. However, as is commonly observed with low template DNA samples, the results exhibited extensive disparity in the effects of stochastic variation in amplification, including increased heterozygote peak height imbalance, stutter ratios and instances of allelic drop-in and drop-out, both within and between replicates. As such, it is important that the extent and variability of these stochastic effects are appropriately incorporated in the development of robust profile interpretation guidelines for DNA profiles generated from purified PCR products.

Specifications of the ACMG/AMP Variant Curation Guidelines for Hereditary Hemorrhagic Telangiectasia Genes—ENG and ACVRL1

The 2015 ACMG/AMP standards and guidelines for interpretation of sequence variants are widely used by laboratories, including for variant curation of the hereditary hemorrhagic telangiectasia (HHT) genes. However, the need for gene- and disease-specific modifications and specifications of these general guidelines to optimize and standardize variant classification was recognized at the time of publication. With this goal, the ClinGen HHT variant curation expert panel was formed. Here, we describe our recommended HHT-specific variant classification criteria and the outcomes from pilot testing of 30 variants of the ENG and ACVRL1 genes. Eight of the original ACMG/AMP rules were determined to not be applicable for ENG- or ACVRL1-related HHT or were previously recommended by ClinGen for removal, two rules were unmodified, and the remaining 18 rules were modified according to HHT specifications or previous ClinGen general recommendations. This study demonstrates the importance of HHT-specific criteria in the optimization and standardization of HHT variant classification and conflicting classification resolution.

Image analysis of acoustic data and interpretation of rock stress orientations for geothermal exploration in Gothenburg borehole GE-1, SW Sweden

Abstract This study contributes to geothermal exploration in 1660–1520 Ma old, reworked bedrock in Sweden. Our primary objectives are to constrain the orientation of horizontal stresses, and to discuss implications for geothermal exploration. High-resolution acoustic televiewer image data reveal the downhole distribution of stress indicators (borehole breakouts, drilling-induced fractures and petal centreline fractures) and pre-existing structures (natural fractures, foliation). About 135 m of stress indicators are measured from 0.2–1.0 km. The results suggest a uniform NNW–SSE mean maximum horizontal stress orientation. A total of 1525 pre-existing structures (natural fractures, foliation) are mapped in borehole GE-1. The prevailing stress regime controls whether natural fractures and foliation are well-oriented for stimulation. For strike-slip and normal faulting stress regimes, well-oriented fractures steeply dip towards the WSW. For a reverse faulting stress regime, shallow dipping fractures are well-oriented for stimulation. The downhole distribution of stress indicators and other stress measurements in the region and other parts of Fennoscandia tentatively suggest a strike-slip stress regime, but additional studies are needed to constrain the complete stress field at study depth and towards engineered geothermal systems reservoir target depths. Our secondary objective is to highlight that interpretation of high-resolution acoustic data, particularly in metamorphic crystalline rocks, is subjective and that more guidelines for data interpretation are needed. The interactive interpretation of the images is based on visual analyses of complex pre-existing structures and stress indicators with highly variable shapes. The application of three methods for data analyses in the GE-1 borehole proposes that drilling-induced fractures are little influenced by the method applied. Interpretations on individual borehole breakout azimuths may, however, result in over 10° differences in orientation.

Analysis of measurable residual disease by IG/TR gene rearrangements: quality assurance and updated EuroMRD guidelines.

Minimal/measurable residual disease (MRD) diagnostics using real-time quantitative PCR analysis of rearranged immunoglobulin and T-cell receptor gene rearrangements are nowadays implemented in most treatment protocols for patients with acute lymphoblastic leukemia (ALL). Within the EuroMRD Consortium, we aim to provide comparable, high-quality MRD diagnostics, allowing appropriate risk-group classification for patients and inter-protocol comparisons. To this end, we set up a quality assessment scheme, that was gradually optimized and updated over the last 20 years, and that now includes participants from around 70 laboratories worldwide. We here describe the design and analysis of our quality assessment scheme. In addition, we here report revised data interpretation guidelines, based on our newly generated data and extensive discussions between experts. The main novelty is the partial re-definition of the "positive below quantitative range" category by two new categories, "MRD low positive, below quantitative range" and "MRD of uncertain significance". The quality assessment program and revised guidelines will ensure reproducible and accurate MRD data for ALL patients. Within the Consortium, similar programs and guidelines have been introduced for other lymphoid diseases (e.g., B-cell lymphoma), for new technological platforms (e.g., digital droplet PCR or Next-Generation Sequencing), and for other patient-specific MRD PCR-based targets (e.g., fusion genes).

The updates of the ACMG variant interpretation guidelines affect the pathogenicity determination of OTOF gene variations in patients with auditory neuropathy

Objective: To compare the differences between the variation interpretation standards and guidelines issued by the American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) in 2015 (The 2015ACMG/AMP guideline) and the Deafness Specialist Group of the Clinical Genome Resource (ClinGen) in 2018 for hereditary hearing loss (Healing loss, HL) issued the expert specification of the variation interpretation guide (The 2018 HL-EP guideline) in evaluating the pathogenicity of OTOF gene variation in patients with auditory neuropathy. Methods: Thirty-eight auditory neuropathy patients with OTOF gene variant were selected as the study subjects (23 males and 15 females, aged 0.3-25.9 years). Using whole-genome sequencing, whole exome sequencing or target region sequencing (Panel) combined with Sanger sequencing, 38 cases were found to carry more than two OTOF mutation sites. A total of 59 candidate variants were independently interpreted based on the 2015 ACMG/AMP guideline and 2018 HL-EP guideline. Compared with the judgment results in 2015 ACMG/AMP guideline, the variants interpreted as lower pathogenic classifications in the 2018 HL-EP guideline were defined as downgraded variants, and the variants regarded as higher pathogenic classifications were defined as upgraded variants. Statistical analysis was conducted using SPSS 20.0. Results: The concordance rate of variant classification between the guidelines was 72.9%(43/59). The 13.6%(8/59) of variants were upgraded and 13.6% (8/59) of variants downgraded in the classifications of the 2018 HL-EP guideline. A couple of rules saw significant differences between the guidelines (PVS1, PM3, PP2, PP3 and PP5). The distribution of pathogenicity of splicing mutation was statistically different (P=0.013). Conclusions: The 2018 HL-EP guideline is inconsistent with the 2015 ACMG/AMP guideline, when judging the pathogenicity of OTOF gene variants in patients with auditory neuropathy. Through the deletion and refinement of evidence and the breaking of solidification thinking, the 2018 HL-EP guideline makes the pathogenicity grading more traceable and improves the credibility.

Recreational Therapists’ Usability Perceptions of the Meta Quest 2 VR System

This study used survey methods to examine recreational therapists’ perceptions of the usability of the Meta Quest 2, a popular commercial virtual reality (VR) system, for recreational therapy (RT) practice. Participants (N = 22) completed the System Usability Scale (SUS) following attendance at a six-hour continuing education workshop that included didactic education and experiential learning with the Meta Quest 2 and eight different VR applications. The SUS scores ranged from 37.50–97.50 (M = 64.31, SD = 17.93) which corresponds with a “high marginal” acceptability rating, a letter grade of C-, and an adjective rating of “good” based on three separate SUS interpretation guidelines. There were no significant differences in SUS scores across several personal (age, gender, race) and professional (years of RT practice experience, primary service setting, client diagnostic characteristics, age of clients served) demographic groups. Findings add to the evidence-base in the emerging area of VR use in RT practice, and suggest opportunities for future research.

Developing an interpretation model for body fluid identification

Criminal investigations, particularly sexual assaults, frequently require the identification of body fluid type in addition to body fluid donor to provide context. In most cases this can be achieved by conventional methods, however, in certain scenarios, alternative molecular methods are required. An example of this is the detection of menstrual fluid and vaginal material, which are not able to be identified using conventional techniques. Endpoint reverse-transcription PCR (RT-PCR) is currently used for this purpose to amplify body fluid specific messenger RNA (mRNA) transcripts in forensic casework. Real-time quantitative reverse-transcription PCR (RT-qPCR) is a similar method but utilises fluorescent markers to generate quantitative results in the form of threshold cycle (Cq) values. Despite the uncertainty surrounding body fluid identification, most interpretation guidelines utilise categorical statements. Probabilistic modelling is more realistic as it reflects biological variation as well as the known performance of the method. This research describes the application of various machine learning models to single-source mRNA profiles obtained by RT-qPCR and assesses their performance. Multinomial logistic regression (MLR), Naïve Bayes (NB), and linear discriminant analysis (LDA) were used to discriminate between the following body fluid categories: saliva, circulatory blood, menstrual fluid, vaginal material, and semen. We identified that the performance of MLR was somewhat improved when the quantitative dataset of the original Cq values was used (overall accuracy of approximately 0.95) rather than presence/absence coded data (overall accuracy of approximately 0.94). This indicates that the quantitative information obtained by RT-qPCR amplification is useful in assigning body fluid class. Of the three classification methods, MLR performed the best. When we utilised receiver operating characteristic curves to observe performance by body fluid class, it was clear that all methods found difficulty in classifying menstrual blood samples. Future work will involve the modelling of body fluid mixtures, which are common in samples analysed as part of sexual assault investigations.

Undiagnosed RASopathies in infertile men.

RASopathies are syndromes caused by congenital defects in the Ras/mitogen-activated protein kinase (MAPK) pathway genes, with a population prevalence of 1 in 1,000. Patients are typically identified in childhood based on diverse characteristic features, including cryptorchidism (CR) in >50% of affected men. As CR predisposes to spermatogenic failure (SPGF; total sperm count per ejaculate 0-39 million), we hypothesized that men seeking infertility management include cases with undiagnosed RASopathies. Likely pathogenic or pathogenic (LP/P) variants in 22 RASopathy-linked genes were screened in 521 idiopathic SPGF patients (including 155 CR cases) and 323 normozoospermic controls using exome sequencing. All 844 men were recruited to the ESTonian ANDrology (ESTAND) cohort and underwent identical andrological phenotyping. RASopathy-specific variant interpretation guidelines were used for pathogenicity assessment. LP/P variants were identified in PTPN11 (two), SOS1 (three), SOS2 (one), LZTR1 (one), SPRED1 (one), NF1 (one), and MAP2K1 (one). The findings affected six of 155 cases with CR and SPGF, three of 366 men with SPGF only, and one (of 323) normozoospermic subfertile man. The subgroup "CR and SPGF" had over 13-fold enrichment of findings compared to controls (3.9% vs. 0.3%; Fisher's exact test, p = 5.5 × 10-3). All ESTAND subjects with LP/P variants in the Ras/MAPK pathway genes presented congenital genitourinary anomalies, skeletal and joint conditions, and other RASopathy-linked health concerns. Rare forms of malignancies (schwannomatosis and pancreatic and testicular cancer) were reported on four occasions. The Genetics of Male Infertility Initiative (GEMINI) cohort (1,416 SPGF cases and 317 fertile men) was used to validate the outcome. LP/P variants in PTPN11 (three), LZTR1 (three), and MRAS (one) were identified in six SPGF cases (including 4/31 GEMINI cases with CR) and one normozoospermic man. Undiagnosed RASopathies were detected in total for 17 ESTAND and GEMINI subjects, 15 SPGF patients (10 with CR), and two fertile men. Affected RASopathy genes showed high expression in spermatogenic and testicular somatic cells. In conclusion, congenital defects in the Ras/MAPK pathway genes represent a new congenital etiology of syndromic male infertility. Undiagnosed RASopathies were especially enriched among patients with a history of cryptorchidism. Given the relationship between RASopathies and other conditions, infertile men found to have this molecular diagnosis should be evaluated for known RASopathy-linked health concerns, including specific rare malignancies.

Towards facilitated interpretation of shotgun metagenomics long-read sequencing data analyzed with KMA for the detection of bacterial pathogens and their antimicrobial resistance genes.

Metagenomic sequencing is a promising method that has the potential to revolutionize the world of pathogen detection and antimicrobial resistance (AMR) surveillance in food-producing environments. However, the analysis of the huge amount of data obtained requires performant bioinformatics tools and databases, with intuitive and straightforward interpretation. In this study, based on long-read metagenomics data of chicken fecal samples with a spike-in mock community, we proposed confidence levels for taxonomic identification and AMR gene detection, with interpretation guidelines, to help with the analysis of the output data generated by KMA, a popular k-mer read alignment tool. Additionally, we demonstrated that the completeness and diversity of the genomes present in the reference databases are key parameters for accurate and easy interpretation of the sequencing data. Finally, we explored whether KMA, in a two-step procedure, can be used to link the detected AMR genes to their bacterial host chromosome, both detected within the same long-reads. The confidence levels were successfully tested on 28 metagenomics datasets which were obtained with sequencing of real and spiked samples from fecal (chicken, pig, and buffalo) or food (minced beef and food enzyme products) origin. The methodology proposed in this study will facilitate the analysis of metagenomics sequencing datasets for KMA users. Ultimately, this will contribute to improvements in the rapid diagnosis and surveillance of pathogens and AMR genes in food-producing environments, as prioritized by the EU.

An AI-based approach driven by genotypes and phenotypes to uplift the diagnostic yield of genetic diseases.

Identifying disease-causing variants in Rare Disease patients' genome is a challenging problem. To accomplish this task, we describe a machine learning framework, that we called "Suggested Diagnosis", whose aim is to prioritize genetic variants in an exome/genome based on the probability of being disease-causing. To do so, our method leverages standard guidelines for germline variant interpretation as defined by the American College of Human Genomics (ACMG) and the Association for Molecular Pathology (AMP), inheritance information, phenotypic similarity, and variant quality. Starting from (1) the VCF file containing proband's variants, (2) the list of proband's phenotypes encoded in Human Phenotype Ontology terms, and optionally (3) the information about family members (if available), the "Suggested Diagnosis" ranks all the variants according to their machine learning prediction. This method significantly reduces the number of variants that need to be evaluated by geneticists by pinpointing causative variants in the very first positions of the prioritized list. Most importantly, our approach proved to be among the top performers within the CAGI6 Rare Genome Project Challenge, where it was able to rank the true causative variant among the first positions and, uniquely among all the challenge participants, increased the diagnostic yield of 12.5% by solving 2 undiagnosed cases.

Abstract 2351: Genomics annotation and interpretation in somatic oncology using structured data from a clinical knowledgebase

Abstract Accurate and comprehensive interpretation of genomic variants has become a bottleneck in clinical sequencing applications due to the accelerating precision oncology and biomedical information explosion. This motivated us to build Ephesus, a framework enabling curation of predictive, prognostic and diagnostic evidence for clinical biomarkers in cancers. Currently Ephesus is the primary content source for Roche navify Mutation Profiler (nMP). The Ephesus’ data model ensures adherence to best practices in clinical genomic content curation. Variant classification follows the AMP guidelines for somatic variant interpretation. Variant interpretations are derived from international regulatory approvals and clinical practice guidelines (FDA, EMA, TGA, eVIQ, etc.) and recommendations (NCCN, ESMO). The data model is mapped to a set of relational tables. To enforce data integrity and validity, strategies such as data normalization based on standard nomenclatural ontologies, a submit-review-approval workflow, and biological constraints are adopted. Ephesus is deployed as a web application used by curators inside and outside Roche. The UI allows users to conduct edits, filtering, sorting and bulk operations on entities by attributes. In order to minimize manual effort and maximize content coverage, inference rules are applied before ingesting into nMP. Currently Ephesus is developed for data collection, browsing and summarizing primary entities such as biomarkers, evidence items, genes, variants, variant groups, and drugs. The content from the 2023-Aug snapshot contains 11,596 directly curated biomarker profiles (including biomarker combinations), and 6M+ expanded profiles for 41 major cancer types. To evaluate the clinical reporting value of the curated knowledge, ~160k real cancer patient samples of the AACR GENIE project were queried on Ephesus. Compared with three other major knowledgebases, Ephesus/NMP is observed showing the highest performance. Table 1. Percentage of patients or biomarkers with at least one interpretation from each knowledgebase CGI (2022-10-17) CIVIC(2023-09-01) ClinVar(2023-09-09) NMP(2023-08-11) AACR-Genie-v14.0 Total patient % with any interpretation 25% (40,545) 46% (73,835) 81% (130,882) 89% (142,905) 160,965 biomarker % (including combos) with any interpretation 0.03% (256) 0.06% (526) 13.26% (122,424) 73.79% (681,128) 923,093 Citation Format: Jian Li, Lili Niu, Shuba krishna, Fnu Kinshuk, Martin Jones, Carlos Hernandez, Michael Clark, Sandra Balladares. Genomics annotation and interpretation in somatic oncology using structured data from a clinical knowledgebase [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2351.

Explicable prioritization of genetic variants by integration of rule-based and machine learning algorithms for diagnosis of rare Mendelian disorders

BackgroundIn the process of finding the causative variant of rare diseases, accurate assessment and prioritization of genetic variants is essential. Previous variant prioritization tools mainly depend on the in-silico prediction of the pathogenicity of variants, which results in low sensitivity and difficulty in interpreting the prioritization result. In this study, we propose an explainable algorithm for variant prioritization, named 3ASC, with higher sensitivity and ability to annotate evidence used for prioritization. 3ASC annotates each variant with the 28 criteria defined by the ACMG/AMP genome interpretation guidelines and features related to the clinical interpretation of the variants. The system can explain the result based on annotated evidence and feature contributions.ResultsWe trained various machine learning algorithms using in-house patient data. The performance of variant ranking was assessed using the recall rate of identifying causative variants in the top-ranked variants. The best practice model was a random forest classifier that showed top 1 recall of 85.6% and top 3 recall of 94.4%. The 3ASC annotates the ACMG/AMP criteria for each genetic variant of a patient so that clinical geneticists can interpret the result as in the CAGI6 SickKids challenge. In the challenge, 3ASC identified causal genes for 10 out of 14 patient cases, with evidence of decreased gene expression for 6 cases. Among them, two genes (HDAC8 and CASK) had decreased gene expression profiles confirmed by transcriptome data.Conclusions3ASC can prioritize genetic variants with higher sensitivity compared to previous methods by integrating various features related to clinical interpretation, including features related to false positive risk such as quality control and disease inheritance pattern. The system allows interpretation of each variant based on the ACMG/AMP criteria and feature contribution assessed using explainable AI techniques.

Fosfomycin susceptibility testing and resistance mechanisms in Enterobacterales in South Africa.

Fosfomycin treatment of urinary tract infections is increasingly attractive due to escalating antibiotic resistance rates among urinary pathogens. Standard antibiotic susceptibility testing methods perform poorly for fosfomycin as there is poor correlation between susceptibility results and clinical outcomes in urinary pathogens other than Escherichia coli. We evaluated the performance of fosfomycin susceptibility testing in E. coli and Klebsiella pneumoniae to determine whether fosfomycin susceptibility is associated with molecular resistance mechanisms. Forty-six each of E. coli and K. pneumoniae clinical isolates were obtained from a tertiary hospital in South Africa, from 01 June 2017 to 31 January 2018. Agar dilution, disk diffusion, and gradient diffusion were performed and interpreted using the Clinical Laboratory Standards Institute and European Committee on Antimicrobial Susceptibility Testing guidelines. Molecular resistance mechanisms were identified by whole genome sequence analysis. Disk diffusion and gradient diffusion were accurate alternatives for fosfomycin susceptibility testing in E. coli (98% categorical agreement), but not in K. pneumoniae (47% categorical agreement). All E. coli isolates contained at least one resistance mechanism, but only one isolate with a fosA gene was resistant. In K. pneumoniae, 63% (29/46) and 70% (32/46) of isolates were susceptible to fosfomycin, using Clinical Laboratory Standards Institute and European Committee on Antimicrobial Susceptibility Testing breakpoints, respectively, despite all isolates containing a fosA gene and a uhpT mutation. A better understanding of fosfomycin susceptibility and improved antibiotic susceptibility testing tools could improve diagnostic capability and clinical guidelines for fosfomycin treatment of urinary tract infections. This study highlights the importance of adhering to interpretive guidelines when performing antimicrobial susceptibility testing and the need for simplified, accurate and standardised susceptibility testing methodology and interpretation for fosfomycin in Enterobacterales organisms.

Disease-specific variant interpretation highlighted the genetic findings in 2325 Japanese patients with retinitis pigmentosa and allied diseases

BackgroundAs gene-specific therapy for inherited retinal dystrophy (IRD) advances, unified variant interpretation across institutes is becoming increasingly important. This study aims to update the genetic findings of 86 retinitis pigmentosa...

Assessment of prevalence and risk factors associated with Hepatitis B virus infection among blood donors in Mogadishu Somalia

BackgroundThe Hepatitis B virus (HBV) is transmitted through contaminated blood or bodily fluids. Globally, over 81 million blood units are donated annually, a crucial therapeutic procedure without alternatives. However, blood-borne infections, including HBV, pose a significant hurdle to safe transfusions, especially in HBV-endemic regions like Somalia with limited screening. Therefore, this study aims to estimate the prevalence of Hepatitis B virus infection and identify risk factors associated with it among blood donors in Mogadishu, Somalia.MethodA hospital-based cross-sectional study was conducted between February and April 2023. Research tools included a 5-ml blood sample and a structured questionnaire. The presence or absence of HB markers was determined using a multi-HB rapid test and CDC’s HB marker interpretation guideline. Logistic regression was used in univariate and multivariate models to identify risk factors associated with HBV infection, with significance set at a p-value < 0.05 in the final model.ResultA total of 494 blood donors were recruited for this study; 93.9% were male, with a mean age of 31.5 (SD = 8.11). The prevalence of Hepatitis B virus (HBV) infection among blood donors was 9.7%, with a 95% CI of 7.1–12.3. In multivariable logistic regression, those with a monthly income of less than 200 USD (AOR = 5.20, 95% CI = 1.61–16.79), those with an income between 200 and 400 (AOR = 3.59, 95% CI = 1.38–9.34), Jobless blood donors (AOR = 3.78, 95% CI = 1.17–12.20), those in business occupations (AOR = 3.35, 95% CI = 1.24–9.08), those with a history of STDs (AOR = 4.83, 95% CI = 2.03–11.50), those without a history of HB vaccine (AOR = 13.81, 95% CI = 2.46–77.41), those with a history of tooth extraction (AOR = 6.90, 95% CI = 2.66–17.88), and those who shared sharp equipment (AOR = 2.90, 95% CI = 1.07–7.82) were more likely to become infected with the Hepatitis B virus (HBV) compared to their counterparts.ConclusionThis study highlights a high prevalence of Hepatitis B virus (HBV) infection. Implementation efforts against HBV infection should specifically focus on low-income individuals, the jobless, and donors with a history of STD to mitigate the burden of HBV infection and promote safer blood donation. In addition, discouraging the sharing of sharp equipment, improving infection control practices during tooth extraction procedures, and enhancing HB vaccination uptake, particularly among individuals lacking a history of HB vaccine, is highly recommended.

ClinGen variant curation expert panel recommendations for classification of variants in GAMT, GATM and SLC6A8 for cerebral creatine deficiency syndromes

Cerebral creatine deficiency syndromes (CCDS) are inherited metabolic phenotypes of creatine synthesis and transport. There are two enzyme deficiencies, guanidinoacetate methyltransferase (GAMT), encoded by GAMT and arginine-glycine amidinotransferase (AGAT), encoded by GATM, which are involved in the synthesis of creatine. After synthesis, creatine is taken up by a sodium-dependent membrane bound creatine transporter (CRTR), encoded by SLC6A8, into all organs. Creatine uptake is very important especially in high energy demanding organs such as the brain, and muscle. To classify the pathogenicity of variants in GAMT, GATM, and SLC6A8, we developed the CCDS Variant Curation Expert Panel (VCEP) in 2018, supported by The Clinical Genome Resource (ClinGen), a National Institutes of Health (NIH)-funded resource. We developed disease-specific variant classification guidelines for GAMT-, GATM-, and SLC6A8-related CCDS, adapted from the American College of Medical Genetics/Association of Molecular Pathology (ACMG/AMP) variant interpretation guidelines. We applied specific variant classification guidelines to 30 pilot variants in each of the three genes that have variants associated with CCDS. Our CCDS VCEP was approved by the ClinGen Sequence Variant Interpretation Working Group (SVI WG) and Clinical Domain Oversight Committee in July 2022. We curated 181 variants including 72 variants in GAMT, 45 variants in GATM, and 64 variants in SLC6A8 and submitted these classifications to ClinVar, a public variant database supported by the National Center for Biotechnology Information. Missense variants were the most common variant type in all three genes. We submitted 32 new variants and reclassified 34 variants with conflicting interpretations. We report specific phenotype (PP4) using a points system based on the urine and plasma guanidinoacetate and creatine levels, brain magnetic resonance spectroscopy (MRS) creatine level, and enzyme activity or creatine uptake in fibroblasts ranging from PP4, PP4_Moderate and PP4_Strong. Our CCDS VCEP is one of the first panels applying disease specific variant classification algorithms for an X-linked disease. The availability of these guidelines and classifications can guide molecular genetics and genomic laboratories and health care providers to assess the molecular diagnosis of individuals with a CCDS phenotype.

Changes in Spirometry Interpretative Strategies: Implications for Classifying COPD and Predicting Exacerbations

Recent guidelines for spirometry interpretation recommend both race-neutral reference equations and use of z score thresholds to define severity of airflow obstruction. How does the transition from race-specific to race-neutral equations impact severity classifications for patients with COPD when using %predicted vsz score thresholds, and do changes in severity correspond to clinical risk? This retrospective cohort study included Black and White patients with COPD and available spirometry from the Johns Hopkins Health System. Global Lung Function Initiative (GLI) 2012 (race-specific) equations and GLI Global (race-neutral) equations were used to determine FEV1 %predicted and z score values. Patients were classified as having mild, moderate, or severe disease according to %predicted or z score thresholds. Associations between a change in severity classification from race-specific to race-neutral with COPD exacerbations and all-cause hospitalizations were evaluated using logistic regression. This cohort included 13,324 patients, of whom 9,232 patients (69.3%) were White (mean age, 65.7 years) and 4,092 patients (30.7%) were Black (mean age, 61.1 years). More Black than White patients showed a change in severity classification between approaches when using %predicted thresholds (20.2%vs6.1%; P< .001), but not with z score thresholds (12.6%vs12.3%; P= .68). An increased severity classification with a race-neutral approach was associated with increased risk of exacerbation when using z score thresholds (OR, 2.34; 95%CI, 1.51-3.63), but not when using %predicted thresholds (OR, 1.08; 95%CI, 0.61-1.93). A decreased severity classification with a race-neutral approach was associated with lower risk of exacerbation with both %predicted (OR, 0.49; 95%CI, 0.28-0.87) and z score (OR 0.67; 95%CI, 0.50-0.90) thresholds. The proportions of Black and White individuals reclassified were similar with z score thresholds, and changes in severity corresponded to clinical risk with z scores. These results support recent recommendations for use of race-neutral equations and z score thresholds for spirometry interpretation.