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At least 91 records · Page 5Linked to original sources
PubMed2026

Multigene testing to guide clinical adjuvant decisions in breast cancer: An overview focused on the assessment of the quality of evidence with the grading of recommendations assessment, development and evaluation (GRADE) approach.

Multigene tests have emerged as valuable tools in guiding adjuvant chemotherapy decisions for patients with ER-positive/HER2-negative early breast cancer. This study applied the Grading of Recommendations Assessment, Development and Evaluation (GRADE) approach to assess the quality of evidence supporting the clinical utility of these tests. We focused on OncotypeDX® and MammaPrint®, the two tests evaluated in prospective randomized trials. The analysis was structured around the clinical question of whether these tests should be recommended for patients with ER-positive, HER2-negative, lymph node-negative or up to 3 lymph nodes-positive invasive breast cancer to guide adjuvant chemotherapy decisions. Our findings reveal that OncotypeDX® demonstrates high clinical utility in sparing chemotherapy for older/postmenopausal patients, with convincing quality of evidence for both node-negative and node-positive patients. The clinical utility of MammaPrint® appears more controversial, with conflicting results between node-negative and node-positive patients. A particularly critical aspect remains the clinical usefulness of these tests in younger/premenopausal women, where the benefit of adjuvant chemotherapy was shown but with potential biases in the study designs. Despite the established role of multigene tests and their availability in Italy since 2021, their uptake in clinical practice remains suboptimal. This formal appraisal of the clinical utility of genomic tests, particularly OncotypeDX®, aims to reinforce their fundamental role in personalizing adjuvant treatment decisions and optimizing resource allocation. The study underscores the importance of these tests in sparing unnecessary chemotherapy toxicities and costs, while emphasizing the need for further research to address remaining uncertainties, especially in younger patient populations.

Humans↗
PubMed1996

Privacy and the Human Genome Project.

The Human Genome Project has raised many issues regarding the contributions of genetics to a variety of diseases and societal conditions. With genetic testing now easily conducted with lowered costs in nonmedical domains, a variety of privacy issues must be considered. Such testing will result in the loss of significant privacy rights for the individual. Society must now consider such issues as the ownership of genetic data, confidentiality rights to such information, limits placed on genetic screening, and legislation to control genetic testing and its applications. There is often a conflict between individual rights to privacy and the need for societal protection.

Confidentiality↗
PubMed1996

Capture and RT-PCR of hepatitis C virus RNA with safety primers.

The principle and practice of the polymerase chain reaction (PCR) has had a major impact on medical research. This is a powerful method but it does have its limitations, especially for clinical diagnostic work. We describe some improvements of hepatitis C virus (HCV) amplification such as simplification of specimen preparation, elimination of false negative reactions influenced by point mutations, and fluorimetric detection. The aim of the method is to make the procedure as easy and as inexpensive as possible for routine laboratories and for blood screening. After rapid chemical denaturation of the clinical specimen with guanidine thiocyanate and simultaneous hybridization of biotinylated primers to template HCV RNA, the product was fixed to streptavidin-coated magnetic beads and potential inhibitors were removed in easy washing steps. To eliminate the influence of point mutations within the primer binding sites, primer sets with different lengths at their 3'-end were developed for capture, reverse transcription, and amplification of genomic fragments by PCR. Positive results were identified by fluorescence staining. The low cost of the method allows the quantitation of templates by testing of dilution series as is common in microbiological laboratories.

DNA Primers↗
PubMed2026

Hospital transmission of methicillin-resistant Staphylococcus aureus driven by addictive mupA plasmids.

BACKGROUND: Resistance to mupirocin, a cornerstone of Staphylococcus aureus decolonization, is a recognized cause of decolonization failure. Its role in hospital transmission is unknown. METHODS: We conducted genomic surveillance of >10,000 S. aureus isolates from adult patients at two urban hospitals where mupirocin decolonization is routine. Bacterial phenotypes and fitness were evaluated in vitro and in murine colonization models to interpret surveillance results. RESULTS: Genome sequencing identified 475 hospital transmission events; conventional surveillance detected none. The plasmid-mediated resistance determinant mupA ( ileS2 ) was enriched eightfold in methicillin-resistant S. aureus (MRSA) relative to methicillin-susceptible strains. mupA was associated with nearly threefold greater hospital transmission, especially within healthcare-associated MRSA lineages. Surprisingly, multiple independently evolved inactivating mutations in the essential chromosomal gene ileS1 co-occurred with mupA , creating plasmid addiction in which mupA became indispensable for bacterial survival. Plasmid carriage activated the stringent response and reduced colonization fitness, but also conferred collateral tolerance to disinfectants such as ethanol and peroxide. Although addiction further reduced S. aureus fitness, it increased plasmid transfer, promoting spread despite these costs. Unexpectedly, we found a mupirocin-dependent vulnerability to isoleucine limitation, revealing a potential strategy to target mupA -mediated resistance. CONCLUSIONS: Hospital transmission of mupirocin-resistant MRSA is promoted by plasmids that create an evolutionary trap in which mupirocin use selects for bacterial dependence on costly resistance elements. These findings suggest that reducing mupirocin use alone is unlikely to eliminate resistance, underscore the need for genomic surveillance and resistance testing, and provide a framework for strategies to preserve mupirocin effectiveness. MAJOR POINT: This work shows that mupirocin resistance promotes hospital transmission of MRSA, identifies a previously unappreciated mechanism of plasmid addiction, and exposes a collateral vulnerability. These findings underscore the need for genomic surveillance and provide a framework to preserve mupirocin effectiveness.

Journal Article↗
PubMed2026

A tiled amplicon protocol for culture-free whole-genome sequencing of M. tuberculosis from clinical specimens.

Whole-genome sequencing of Mycobacterium tuberculosis can be a valuable tool for TB surveillance and treatment, providing insights into transmission patterns and comprehensive drug susceptibility testing. However, the slow growth of M. tuberculosis means traditional culture-based sequencing methods can take weeks to return results, which has limited the widespread adoption of these techniques and limited their use in clinical decision-making. Tiled amplicon sequencing is a fast, reliable, and cost-effective method of whole-genome sequencing that can be done directly on clinical specimens and has been implemented at scale in academic and public health laboratories across the world; it was the cornerstone of SARS-CoV-2 sequencing and has been adapted for a wide range of viral pathogens. However, similar methods are not yet available for far larger bacterial genomes. Extending this approach to M. tuberculosis would significantly reduce the cost, labor, and turnaround time for whole-genome sequencing. We designed a tiled amplicon panel consisting of 5,128 primers that covers the entire M. tuberculosis genome, the largest tiled amplicon sequencing panel we are aware of to date. Applying our amplicon panels to clinical samples of sputum, we show the ability to recover whole-genome bacterial sequences without the need for culture. The resulting sequence data can be used to determine M. tuberculosis lineage and reliably identify markers of drug resistance. Using this approach in clinical settings could reduce the time needed for comprehensive drug susceptibility testing from weeks to days and enable genomic epidemiology to be performed at scale, even in resource-limited settings.IMPORTANCEWe have developed and tested an amplicon panel, TB-seq, for the priority pathogen Mycobacterium tuberculosis, demonstrating recovery of near-full genomes directly from patient sputum, including mixed and low-concentration samples. This approach significantly reduces the turnaround time for this slow-growing bacterium while maintaining high accuracy in detecting clinically relevant mutations, including those associated with drug resistance. Given the global burden of tuberculosis and the critical need for faster diagnostic solutions, we believe our method has the potential to improve clinical decision-making and public health strategies.

Mycobacterium tuberculosis↗
PubMed1991

Ethical issues in human genome research.

In addition to provocative questions about science policy, research on the human genome will generate important ethical questions in at least three categories. First, the possibility of greatly increased genetic information about individuals and populations will require choices to be made about what that information should be and about who should control the generation and dissemination of genetic information. Presymptomatic testing, carrier screening, workplace genetic screening, and testing by insurance companies pose significant ethical problems. Second, the burgeoning ability to manipulate human genotypes and phenotypes raises a number of important ethical questions. Third, increasing knowledge about genetic contributions to ethically and politically significant traits and behaviors will challenge our self-understanding and social institutions.

Bioethics↗
PubMed2003

Molecular diagnosis of leishmaniasis.

This review describes the worldwide situation of visceral and tegumentary leishmaniasis with an emphasis on diagnosis, including methods for the detection of antibodies, antigens, parasite DNA and of skin testing. The advantages and problems of each method are discussed and the need for a rapid, sensitive and low-cost diagnostic method for use in field conditions is highlighted. Recent advances in Leishmania genome sequencing, the use of DNA microarrays and protein microarray methodologies and their potential use for leishmaniasis diagnosis are presented.

Animals↗
PubMed2026

Phylogenomic subsampling and upsampling for efficient evolutionary analyses of big data.

Long runtimes, high memory demands, and reliance on high-performance computing impede phylogenomic analyses. We review a scalable phylogenomic subsampling with upsampling (PSU) framework to address this challenge, which reduces runtime and memory requirements by orders of magnitude. In PSU, small subsamples of sites from a concatenated alignment are analyzed, which are expanded by upsampling before inference, and the resulting inferences are aggregated to obtain evolutionary estimates. PSU harnesses the fact that the computational cost of maximum likelihood analysis is strongly influenced by the number of distinct site patterns in the concatenated alignment, whereas statistical power depends primarily on the amount of evolutionary information represented by the total number of sites and substitutions. By reducing the former while restoring the latter through upsampling, PSU can approximate many full-alignment analyses at substantially lower computational cost. Analysis of simulated and empirical datasets shows that PSU can accurately estimate bootstrap support values, select the optimal substitution model, test evolutionary hypotheses, and infer branch lengths, divergence times, and associated uncertainty measures. PSU also provides distributions of inferred clade support across independent subsamples, enabling detection of conflicting phylogenetic signals that may remain hidden in conventional bootstrap analysis of concatenated alignments. Automated tuning of subsample size, the number of subsamples, and the number of upsampling replicates make PSU practical. We suggest that PSU is a general approach for scalable phylogenomic inference using a broad range of statistical methods. By enabling analyses of genome-scale alignments on commodity hardware, PSU broadens research access and reduces environmental and infrastructural costs of big-data phylogenomics.

Phylogeny↗
PubMed2026

Sequencing approaches in hereditary cancer testing: strengths, limitations and future directions.

Over the past three decades, Hereditary Cancer Testing (HCT) has evolved from single gene assays into multigene panel testing (MGPT), which allows for the screening of all known hereditary cancer genes in a single assay. MGPT is currently the standard approach for clinical HCT. However, with decreasing sequencing costs and increased instrument throughput, the scalability of exome sequencing (ES) and genome sequencing (GS) for HCT indications is becoming more viable. These methods provide broader insights into the coding exons and/or the entire genome, respectively. ES/GS data can also be reanalyzed to identify variants in novel genes that were not characterized at the time of initial testing, or to support research efforts aimed at uncovering additional associations between germline variants and cancer predisposition. Additionally, the emerging use of long-read sequencing (LRS) is noteworthy, enabling improved variant detection compared to short-read sequencing, especially for complex/structural variants and variation in difficult-to-sequence or paralogous regions in genes such as PMS2. This has the potential to increase the accuracy of HCT, reduce the turnaround time, find previously unidentifiable cancer risk variants, and ultimately increase the diagnostic yield. This article provides a comprehensive summary of the sequencing approaches used in HCT, discussing their strengths and limitations. We also highlight the added value of complementing DNA-only testing with RNA and tumor sequencing. Furthermore, we explore LRS-based approaches and discuss opportunities for their implementation in routine genetic testing for hereditary cancer.

Humans↗
PubMed2004

Restriction fragment length polymorphism of L1 amplicon using Rsa 1 detects five different human papillomavirus types and their co-infections among women attending a gynaecological outpatient department.

Detection of human papillomavirus (HPV) types 6, 11, 16, 18, and 33 including co-infections among females attending gynaecological outpatient department and cancer clinics, was done by restriction fragment length polymorphism (using Rsa-1), of approximately 450bp amplicon, obtained by the amplification of the L1 region of HPV genome with consensus primers MY09/11 [Cancer Cells 7 (1989) 209]. The results were further tested with HPV type specific primers [J. Med. Virol. 29 (1989) 20]. The technique was found to be low-cost and less time consuming. The advantage of Rsa 1 over other enzymes was that it detects the five most prevalent HPV types commonly associated with warts, cervical dysplasia, and cancer.

Bacteriophage phi X 174↗
PubMed1991

Genetic discrimination: the use of genetically based diagnostic and prognostic tests by employers and insurers.

Genetic discrimination is detrimental to public health programs, as well as to society generally. Advances in genetic testing and screening, accelerated and prompted by the Human Genome Initiative, increase society's ability to detect and monitor chromosomal differences. These technologies and their resulting genomic data will enhance medical science, but may also encourage discrimination. Although few employers or insurers currently utilize genetic screening, testing or data, rising employee benefit costs and market forces create powerful incentives for usage. Current municipal, state and federal laws, including the Americans with Disabilities Act (ADA), may not sufficiently protect employees and insureds from genetic discrimination. While municipal and state protections should not be overlooked, the ADA's sweeping scope may currently provide the most comprehensive safeguard. Federal laws banning discrimination on the basis of race or sex might also successfully redress some forms of genetic discrimination. Genetic technologies' advent necessitates efforts to rectify state and federal statutory coverage gaps, strictly regulate employers and produce comprehensive guidelines regarding its use.

Persons with Disabilities↗
PubMed2000

The future of male infertility management and assisted reproduction technology.

Intracytoplasmic sperm injection (ICSI) is undoubtedly a powerful, and sometimes the only effective, form of infertility treatment. Nonetheless, it is a non-specific treatment that, combined with increasingly heroic techniques to recover male germinal cells, has led to perceptions of men as just providers of gametes in the infertility equation. In response to this nihilist attitude, where women are investigated extensively and scant attention is paid to men, there is a re-emerging awareness of andrology--particularly in countries with limited healthcare resources. Structured management strategies, using diagnostic information to recognize causative factors amenable to simpler, even systemic, therapies with reasonable chances of pregnancy rather than resorting prematurely to assisted reproduction technology, represent rational, cost-effective approaches to infertility management. Furthermore, genetic testing (particularly cystic fibrosis gene defects and Y-chromosome microdeletions) is essential for couples to make fully informed decisions on their options. Recognition that free radical-induced damage to the sperm genome (e.g. from smoking or in-vitro sperm manipulation) underlies deleterious paternal effects on preimplantation development promotes further synergy between andrology and embryology. Although societies strike different balances between considerations of affordability and cost-effectiveness of assisted reproduction technology, ICSI represents a last resort, to be used when less-invasive, lower-cost treatments have been deemed inappropriate or have failed. Consequently, rather than assisted reproduction technology eliminating the need for andrology, the future will see increasingly tighter integration of multidisciplinary infertility care, embracing careful diagnosis and patient education before obtaining truly informed consent and embarking upon cost-effective treatment.

Delivery of Health Care↗
PubMed1998

Screening blood donations for viral genomes: multicenter study of real-time simulation using pooled samples on the model of hepatitis C virus RNA detection.

BACKGROUND: The systematic screening for several blood-borne viral genomes in blood donations is a complementary safety measure planned or discussed by the national authorities of several countries. STUDY DESIGN AND METHODS: To appreciate the feasibility of such screening using pooled samples, a multicenter study of real-time simulation has been performed on the model of hepatitis C virus (HCV) infection. Four blood transfusion center laboratories and two research and diagnosis laboratories simultaneously screened, by several HCV RNA polymerase chain reaction assays, a panel of plasma sample pools of different sizes (500, 100, and 10 samples), collected from HCV-infected or HCV-uninfected blood donors. One viremic plasma was introduced in each pool. HCV RNA was detected by in-house polymerase chain reaction procedures or by standardized manual or semi-automated polymerase chain reaction assays. RESULTS: The results indicate the feasibility of sample pooling, which renders the screening for viral genomes by molecular biology techniques applicable in the short term and the importance of the experience of laboratory personnel in the use of molecular biology tools. CONCLUSION: The improvement of standardized assays needs to be continued, and training of laboratory staff members appears to be a crucial step before systematic screening of blood donations for viral genomes by molecular biology techniques can occur.

Blood Donors↗
PubMed2001

Detection of mutations in the dystrophin gene via automated DHPLC screening and direct sequencing.

BACKGROUND: Currently molecular diagnostic laboratories focus only on the identification of large deletion and duplication mutations (spanning one exon or more) for Duchenne Muscular Dystrophy (DMD) yielding 65% of causative mutations. These mutations are detected by an existing set of multiplexed polymerase chain reaction (PCR) primer pairs. Due to the large size of the dystrophin gene (79 exons), finding point mutations (substitutions, deletions or insertions of one or several nucleotides) has been prohibitively expensive and laborious. The aim of this project was to develop an effective and convenient method of finding all, or most, mutations in the dystrophin gene with only a moderate increase in cost. RESULTS: Using denaturing high performance liquid chromatography (DHPLC) screening and direct sequencing, 86 PCR amplicons of genomic DNA from the dystrophin gene were screened for mutations in eight patients diagnosed with DMD who had tested negative for large DNA rearragements. Mutations likely to be disease-causative were found in six of the eight patients. All 86 amplicons from the two patients in whom no likely disease-causative mutations were found were completely sequenced and only polymorphisms were found. CONCLUSIONS: We have shown that it is now feasible for clinical laboratories to begin testing for both point mutations and large deletions/duplications in the dystrophin gene. The detection rate will rise from 65% to greater than 92% with only a moderate increase in cost.

Automation↗
PubMed2025

Detection and characterization of neonatal cytomegalovirus through nanopore sequencing using flongle flow cells: Pilot study in Philadelphia, Pennsylvania.

BACKGROUND: Cytomegalovirus (CMV) remains a significant infection in neonates and its early detection can aid with further treatment (antiviral, audiology). However, current diagnostics do not provide genetic information. OBJECTIVE: We explored the use of the portable and comprehensive sequencing method from Oxford Nanopore Technologies, utilizing low-cost Flongle flow cells to detect and perform sequence-level characterization of neonatal urine samples that tested positive for CMV by PCR. STUDY DESIGN: We performed a pilot study based on a retrospective cohort study of neonates who were positive for CMV by PCR, who were admitted at two birth hospitals in Philadelphia, PA. We leveraged deep and long-read sequencing results to analyze the reads in two forms: by comparing them against a reference-based strain and by reconstructing the genome through de novo assembly with phylogenetic tree analysis. RESULTS: We assayed seven clinical samples, including a positive and negative control sample, from newborns ranging from 23 weeks' gestation to term, with testing performed for microcephaly, hearing test results, small gestational age, and thrombocytopenia. Each sample showed multiple differences compared to the reference strain, and the phylogenetic tree analysis of the de novo assembly depicted the genetic diversity of the samples. CONCLUSION: This pilot study shows that nanopore sequencing with low-cost Flongle flow cells can detect and characterize CMV strains from clinical neonatal urine samples. This, coupled with current screening and diagnostic criteria, could further our genomic understanding of neonatal CMV, such as viral genome diversity, genotype-phenotype associations, and spread of strains.

Humans↗
PubMed2026

Aligning awareness, systems and policy to increase equitable access to genomically driven cancer care.

Genomic testing has the potential to transform cancer care across the patient pathway. However, its benefits remain unevenly realised across populations and health systems. Precision oncology is characterised by a strong promissory discourse, with expectations of improved outcomes and cost-effectiveness, yet real-world implementation remains variable and context dependent. This review examines how patient and public awareness interacts with, and is constrained by, structural, organisational and political-economic factors that shape equitable access to genomically driven cancer care across five themes: (1) the power of patient and public advocacy; (2) learning from the patient perspective; (3) culturally responsive communication; (4) structural and personal barriers and facilitators and (5) political economy of health. Examples are mapped across global regions to highlight how health system, structural and societal factors continue to limit the universal realisation of genomic medicine's benefits. We present four recommendations to strengthen the translation of awareness into equitable access and clinical impact: (1) expand and adequately power genomic studies in underserved populations; (2) improve risk communication and decision-making across the cancer pathway; (3) equitable validation and interpretation of emerging genomic technologies and (4) generate real-world evidence on access, uptake and outcomes of genome-matched therapies. Embedding awareness, trust, access and equity in future initiatives is imperative to realise the promise of precision medicine for all patients.

Biomarkers↗
PubMed2026

The curious case of sporadic nematode susceptibility in "Tifguard" peanut (Arachis hypogaea): seed mixture or genetic instability?

The Runner-type peanut (Arachis hypogaea L.) cultivar "Tifguard" carries an introgressed chromosomal segment on chromosome A09 from A. cardenasii that confers resistance to root-knot nematode (RKN). Despite this, a proportion of "Tifguard" plants show RKN symptoms, which could plausibly be attributed to seed mixture or outcrossing. However, recent work has shown that cultivated peanut exhibits surprisingly frequent large-scale chromosomal instability (1% to 5%); suggesting that resistance loss could arise from spontaneous structural genomic change. To test these possibilities, we grew foundation seed in an RKN-infested field and collected symptomatic and asymptomatic plants. Lineages derived by single-seed descent were genotyped using the Axiom Arachis 48K SNP array v2 and whole-genome sequencing. Symptomatic lineages lacked the A. cardenasii introgression on chromosome A09 and instead carried the complete endogenous A. hypogaea A09 region at the expected dosage. There was no evidence of large-scale homoeologous exchange, deletion, or other genomic instability affecting this chromosome. Most susceptible plants were closely related to resistant "Tifguard" but lacked the A09 introgression, with a smaller proportion assignable to known nematode-susceptible cultivars, implicating seed mixture with a possible contribution from cross-pollination rather than genomic instability. Because resistance depends on a single major-effect segment, rare events have disproportionate phenotypic impact, placing high demands on genetic purity. For important traits conferred by major loci, marker-based testing across seed-increase stages could verify trait retention directly, and is increasingly practical as marker costs decline.

Arachis↗
PubMed2004

Microbiology of nosocomial infections: progress and challenges.

Technological advances have expanded the role of the clinical microbiology laboratory in supporting management and control of health-care-associated infections (HAI). Diagnostic capabilities have been complemented by new methods for characterisation of microbial antigens and nucleic acids. Genomic "fingerprinting" enables the study of transmission of nosocomial pathogens. Monitoring of their antimicrobial resistance patterns has gained critical importance. However, cost-effective application of microbiological testing for improved treatment and prevention of HAI requires further study.

Antigens↗