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PubMed1998

Accurate sequencing by hybridization for DNA diagnostics and individual genomics.

Medical DNA diagnostics will increasingly rely on an accurate and inexpensive identification of mutations that affect the function of a gene. To validate diagnostic sequencing by hybridization (SBH), a number of p53 samples were analyzed with the complete set of 8192 noncomplementary 7-mer oligonucleotides. In four repeated, blind experiments we accurately sequenced 1.1 kb per each of 12 homozygote and heterozygote samples possessing base substitutions, insertions, and deletions. This SBH variant offers a high throughput platform to inexpensively sequence individual gene or pathogen genome samples within the clinical laboratory setting.

DNA↗
PubMed1998

Fot 1 insertions in the Fusarium oxysporum f. sp. albedinis genome provide diagnostic PCR targets for detection of the date palm pathogen.

Populations of Fusarium oxysporum f. sp. albedinis, the causal agent of Bayoud disease of date palm, are derivatives of a single clonal lineage and exhibit very similar Fot 1 hybridization patterns. In order to develop a sensitive diagnostic tool for F. oxysporum f. sp. albedinis detection, we isolated several DNA clones containing a copy of the transposable element Fot 1 from a genomic library of the date palm pathogen. Regions flanking the insertion sites were sequenced, and these sequences were used to design PCR primers that amplify the DNA regions at several Fot 1 insertion sites. When tested on a large sample of Fusarium isolates, including 286 F. oxysporum f. sp. albedinis isolates, 17 other special forms, nonpathogenic F. oxysporum isolates from palm grove soils, and 8 other Fusarium species, the primer pair TL3-FOA28 allowed amplification of a 400-bp fragment found only in F. oxysporum f. sp. albedinis. Sequence analysis showed that one of the Fot 1 copies was truncated, lacking 182 bp at its 3' terminus. The primer pair BI03-FOA1 amplified a 204-bp fragment which overlapped the Fot 1 truncated copy and its 3' site of insertion in the F. oxysporum f. sp. albedinis genome and identified 95% of the isolates. The primer pairs BIO3-FOA1 and TL3-FOA28 used in PCR assays thus provide a useful diagnostic tool for F. oxysporum f. sp. albedinis isolates.

Cloning, Molecular↗
PubMed2001

MALDI TOF mass spectrometry: an emerging platform for genomics and diagnostics.

Matrix-assisted laser desorption/ionization-time of flight (MALDI TOF) mass spectrometry has become, in recent years, a tool of choice for large molecule analyses. The platform is ideal for analysis of protein and nucleic acid sequence, structure and purity. MALDI TOF is the method of choice for quality assurance in oligo and peptide synthesis. Exact mass measurements along with signal intensity detection provide a high level of quality assurance as to the accuracy of the measurement. This accuracy has the potential to significantly lower the level of indeterminate assays that require retest.

Genomics↗
PubMed2004

Post-genome molecular diagnostics in obstetrics.

PURPOSE OF REVIEW: The intention of this review is to familiarize the practicing clinician with the current status and future direction of molecular testing in obstetrics. As a discipline, obstetrics and gynecology is unique in that it deals with the full spectrum of molecular genetic testing. This spectrum includes infectious disease, neoplasia and inherited diseases. This review will focus on inherited conditions and complex diseases, as it is in this context that we may fully realize the true promise of the human genome and its application to the practice of medicine. RECENT FINDINGS: Despite the successful sequencing of the human genome, very few new molecular genetic tests have become available. The apparent reason for this lies in the relative paucity of information gleaned from examining the genes themselves. Two new avenues of investigation are presently underway to improve the 'infirmity' of this information archive. Rather than merely looking at differential gene expression, clinician scientists have begun to examine genetic polymorphisms of single and multiple genes within and between individuals in an attempt to explain biologic processes, including disease states. The second avenue involves the characterization of the products of gene expression--proteins. Proteomics, in conjunction with high throughput polymorphism analysis, may enable us to diagnose and treat complex multifactorial diseases. SUMMARY: Molecular diagnostics for multifactorial diseases will become conceptually and technologically more complex than present DNA testing modalities. The development and ultimate acceptance of these tests will require greater coordination between the medical and scientific communities to ensure that the right technologies are applied to the highest quality samples to answer the most relevant questions.

Female↗
PubMed2024

Offering complex genomic screening in acute pediatric settings: Family decision-making and outcomes.

PURPOSE: Families of children in pediatric acute care who are offered ultrarapid genomic sequencing are making complex decisions during a high-stress period. To reduce complexity for families and clinicians, we offered genomic screening for the child and parents after the completion of diagnostic testing. We evaluated uptake, understanding, and service delivery preferences. METHODS: A cohort of 235 families who had completed ultrarapid diagnostic genomic sequencing at 17 Australian hospitals were offered up to 3 screens on their genomic data: pediatric-onset, adult-onset, and expanded couple carrier screening. We investigated decision making, understanding, and service delivery preferences using surveys at 3 time points (pre counseling, post counseling, and post result) and performed inductive content analysis of pretest genetic counseling transcripts. RESULTS: A total of 119 families (51%) attended genetic counseling with 115 (49%) accepting genomic screening. Survey respondents were more likely to find decisions about couple carrier screening easy (87%) compared with adult (68%; P = .002) or pediatric (71%; P = .01) screening decisions. All respondents with newly detected pathogenic variants accurately recalled this 1 month later. A delayed offer of screening was acceptable to most respondents (78%). CONCLUSION: Separating genomic screening from the stressful diagnostic period is supported by families who demonstrate good knowledge and recall. Our results suggest delaying genomic screening should be trialed more widely.

Humans↗
PubMed1994

[Summary and evaluation of genome and antibody diagnosis in hepatitis C virus infection].

Hepatitis C virus (HCV) infection can be diagnosed by antibody assay systems using recombinant antigens since the HCV genome has been identified. It is still impossible to detect viral antigens associated with HCV. Therefore, the polymerase chain reaction (PCR) has been widely used in practical laboratory examinations. Because HCV is an RNA virus and the reverse transcription process is required prior to the PCR reaction, the process of HCV RNA detection has a risk of contamination and the detection rate may differ with the PCR condition. There are several genome diagnostic methods for HCV infection; that is, genome detection by nested PCR, HCV subtyping using mixed primer, quantitation of HCV genome using competitive PCR, Quant-Amp and branched DNA probe. To clarify what factors are responsible, the efficacy of interferon therapy against chronic hepatitis C was examined. The normalization rate of serum ALT level and clearance rate of HCV RNA in serum at six months after the end of the treatment were correlated to the titer of HCV RNA genome and the HCV subtype. The patients with HCV RNA titers of less than 10(4) copies/50 microliters and with subtype group III showed a high response to interferon administration. On the other hand, the results of quantitation of the HCV core antibody titer were closely associated with the presence of HCV RNA using core protein with the recombinant vaccinia expression system or recombinant E. coli system (JCC-2). Especially, in the group of high responders to interferon treatment, the antibody titer against core protein was apparently decreased after the end of interferon therapy.(ABSTRACT TRUNCATED AT 250 WORDS)

Genome, Viral↗
PubMed2002

Recent developments in laboratory automation using magnetic particles for genome analysis.

The majority of research for genome analysis has shifted from nucleic acid sequencing to the biological functional analysis of each gene. Based on past success, it may not be long before genome diagnostics becomes a widespread tool in human, veterinary and botany research fields. Genome analysis involves the processes of nucleic acid purification, amplification, labeling and signal detection (specific reaction, separation and signal counting). Except for the purification of nucleic acids, the other processes cannot be achieved without instruments, resulting in the advancement of automation processes. Since purification of nucleic acids can be done manually, automating this process has been delayed. However, because the purification of nucleic acids using magnetic particles is suitable for automation, its development has also been accelerated. The need for full automation for other processes is not as great because the majority of genome analysis is to identify the nucleic acid sequence and analyze genome expression. However, once useful diagnostic tools are generated, the desire for full automation will significantly increase. In order to develop realistic and practical automation, various technologies developed for each process in genome analysis have to be evaluated and only a few technologies, useful for automation, selected. The other key factor in automation is the development of methods to manage reagents and reaction mixtures precisely without any risks specifically related to genome handling, such as cross-contamination. Methods using magnetic particles, which have been used for the automation of nucleic acid purification and immunoassay, appear to be the most promising way to automate processes used in biological research.

Animals↗
PubMed2026

Real-World Testing Landscape and Costs of Companion Diagnostics and Comprehensive Genomic Profiling Across Nine Solid Tumors in Japan: A 10-Year Analysis.

INTRODUCTION: This study aimed to examine utilization, testing sequences, and associated genomic testing costs of companion diagnostics (CDx) and comprehensive genomic profiling (CGP) among Japanese patients with nine representative solid tumors. METHODS: This retrospective study used anonymized data, from Medical Data Vision Co., Ltd. (MDV; January 2015-March 2025) and JMDC Inc. (JMDC; January 2015-January 2025), for patients with solid tumors of nine cancer types who underwent CDx and/or CGP testing or received any cancer treatment. Patient demographics, distribution and testing sequences of CDx and CGP, and associated genomic testing costs per patient were evaluated. RESULTS: Proportions of CDx and CGP testing varied across nine cancer types. Most patients underwent CDx testing once or twice, although some cohorts, particularly with non-small cell lung cancer (NSCLC), were tested thrice or more. Biliary tract cancer demonstrated the highest proportions for CGP testing alone, and both CDx and CGP testing. For both CDx and CGP testing, the greatest median costs were observed for ovarian and breast cancers, with bimodal peaks near US dollars (USD) 4000 and USD 5000. Median CDx costs were equal to or higher for patients who underwent both CDx and CGP testing compared with those who had CDx testing alone, particularly in breast, pancreatic, prostate, and ovarian cancers. For CDx testing alone, NSCLC, ovarian cancer, and prostate cancer had the highest costs, with a small peak near USD 1333. These results were mostly consistent across databases. CONCLUSIONS: Multiple CDx testing followed by CGP testing increased genomic testing costs per patient. Early implementation of CGP testing could reduce redundant testing and associated delays in treatment, thereby contributing to lower overall healthcare costs and more efficient treatment selection amid rapid advances in targeted therapies.

Administrative claims database↗
PubMed2002

Patents, genomics, research, and diagnostics.

Two kinds of currently available genomic patents may significantly interfere with medical research: (1) patents such as those on specific single nucleotide polymorphisms (SNPs), which may include claims that control the inference of phenotypic characteristics from specific genotypes, and (2) patents on computer-based genomic information, databases, or manipulation procedures. These will create more serious encumbrances than will patents on expressed sequence tags (ESTs). Two approaches should be considered vis-à-vis these genomic patents: (1) Reconsideration and redefinition of the recent extensions of patentable subject matter into more and more intangible areas. This could be pursued by legislation or by test litigation to seek Supreme Court reversal of certain of the decisions of the Court of Appeals for the Federal Circuit (CAFC). (2) A narrow legislative exemption protecting the ability to use SNPs and phenotypic-genotypic relationships in medical research, including contexts in which medical research and clinical practice are substantially intertwined.

Databases, Nucleic Acid↗
PubMed1990

[Wilson's disease in East Germany: in retrospect and perspectives -- an evaluation].

Wilson's disease is an autosomal recessive inherited metabolic disorder due to a disturbance of copper metabolism. Although the primary genetic defect is not known a longlife treatment is necessary for establishing a negative copper balance by removing the metal of the abnormal body stores. Experiences in handling with this disease in our country over a period of 20 years are reported. Especially epidemiologic findings, the diagnostic procedures and the strategies in therapeutic regimes are discussed. Future advances in genomic diagnostics are mentioned.

Adolescent↗
PubMed2004

Anthrax molecular epidemiology and forensics: using the appropriate marker for different evolutionary scales.

Precise identification of Bacillus anthracis isolates has aided forensic and epidemiological analyses of natural anthrax cases, bioterrorism acts and industrial scale accidents by state-sponsored bioweapons programs. Because there is little molecular variation among B. anthracis isolates, identifying and using rare variation is crucial for precise strain identification. We think that mutation is the primary diversifying force in a clonal, recently emerged pathogen, such as B. anthracis, since mutation rate is correlated with diversity on a per locus basis. While single nucleotide polymorphisms (SNPs) are rare, their detection is facilitated by whole genome discovery approaches. As highly stable phylogenetic markers, SNPs are useful for identifying long branches or key phylogenetic positions. Selection of single, diagnostic "Canonical SNPs" (canSNPs) for these phylogenetic positions allows for efficient and defining assays. We have taken a nested hierarchal strategy for subtyping B. anthracis, which is consistent with traditional diagnostics and applicable to a wide range of pathogens. Progressive hierarchical resolving assays using nucleic acids (PHRANA) uses a progression of diagnostic genomic loci that are initially highly stable but with low resolution and, ultimately, very unstable but with high resolution. This approach mitigates the need for data weighting and provides both a deeply rooted phylogenetic hypothesis and high resolution discrimination among closely related isolates.

Animals↗
PubMed2004

GENOSENSE Diagnostics GmbH.

GENOSENSE Diagnostics GmbH, a company specialized in preventive genetic diagnostics, has committed itself to applying molecular medical knowledge to realizing the vision of individual, preventive and patient-tailored medicine. GENOSENSE offers a unique line of preventive genomic diagnostic profiles. Each profile focuses on a carefully selected set of polymorphisms associated with particular diseases or physiologic imbalances. GENOSENSE does not only provide the genetic test results, but highly capable medical experts 'translate' the results into a clinical language and assist the customer with established support regarding their medical interpretation. In addition, the company provides academic institutions and pharmaceutical companies with turnkey solutions for research-based projects.

Drug Industry↗
PubMed1990

Methodical and ethical aspects of nucleic acid diagnostics. A review.

Aside from the established enzymatic and immunodiagnostic procedures, an increasing number of diagnostic procedures for nucleic acid detection--i.e. for the detection of the primary genetic information--has been developed in recent years. For the routine use of these diagnostic procedures in central analytical laboratories or by the general practitioner, automated DNA analysis methods with integrated highly sensitive detection systems have been developed. The most important objective of these developments--aside from the elucidation of the type of genetic defect on the molecular level through basic research--is the generation of a quantitative nonradioactive signal in corresponding analyzers. Detection methods using the ELISA principle as quantifiable reporter system--analogous to the automatic immunodiagnostic procedures--have hence been developed in recent years. Owing to the increasing importance of this analysis procedure alternative to the detection of bioactive low molecular weight substances or proteins--i.e. nucleic acid diagnostics--the following is an attempt to provide a survey of the methods and possibilities of application. Moreover, possibilities for nonradioactive signal generation and amplification will be presented. The chances and risks of genome diagnostics will be discussed in a final section.

Animals↗
PubMed2026

Genetic Testing in Cystic Kidney Disease.

Genomic investigation is playing an increasing role in the management of cystic kidney diseases, reflecting a broader shift toward precision medicine in nephrology. Recent updates to the Kidney Disease Improving Global Outcomes Clinical Practice Guideline emphasize diagnostic genomics as a core component of autosomal dominant polycystic kidney disease care in particular, recognizing its utility across a range of clinical scenarios. Traditionally, diagnosis of autosomal dominant polycystic kidney disease has been clinical, using age-dependent imaging criteria for at-risk individuals via ultrasound and magnetic resonance imaging. Although these imaging modalities have good sensitivity, there are pitfalls in clinical diagnosis, particularly in patients with atypical clinical features, those without family history, or those at a young age. A confirmed genetic diagnosis can guide screening of at-risk family members, inform reproductive decisions, support safe selection of living related kidney donors, and provide the opportunity to use genotype-specific prognostication tools. In addition, as genotype-specific therapies enter the landscape, accurate genotyping will become essential for identifying which patients will benefit from treatment. This narrative review aims to provide a practical approach for the general nephrologist of when to offer genetic testing to patients with cystic kidney disease and outline the technical and genetic counseling considerations in the provision of patient-centered genetic investigation.

Humans↗
PubMed2026

Precision periodontology in clinical practice: bridging omics and clinical decision-making.

BACKGROUND: Precision periodontology integrates molecular diagnostics, genomics, and advanced imaging into clinical decision-making. Despite major advances in microbiome characterisation, host genetics, and inflammatory biomarkers, their translation into routine care remains limited. OBJECTIVES: To critically appraise current evidence on microbiome-based profiling, genetic and epigenetic markers, host-response biomarkers, and three-dimensional imaging in periodontology, and to propose a conceptual decision-support framework linking diagnostic outputs to potential therapeutic actions and future implementation research. MATERIALS AND METHODS: A narrative review searching PubMed/MEDLINE, Scopus, Embase, and the Cochrane Library (2010-2025) using terms related to precision periodontology, subgingival microbiome, periodontitis genetics and epigenetics, salivary and GCF biomarkers, aMMP-8, CBCT, risk assessment, and artificial intelligence. Priority was given to meta-analyses, systematic reviews, longitudinal studies, and guideline documents. RESULTS: Microbiological testing has defined but narrow indications; single-SNP genotyping has not demonstrated clinical utility commensurate with cost; aMMP-8 point-of-care testing is among the most extensively investigated host-response tools and may have adjunctive value in selected monitoring and peri-implant scenarios; however, current evidence remains insufficient to support routine diagnostic implementation. CBCT may directly influence surgical decision-making through defect morphology characterisation. AI-based models show promise but lack prospective clinical validation. These conclusions are consistent with the 20th EFP Workshop Consensus Report. CONCLUSIONS: Precision periodontology currently operates in addition to, rather than in replacement of, conventional staging and grading. We propose a conceptual decision-threshold framework for the selective consideration of molecular and advanced imaging tools when their additive contribution may meaningfully inform management. This framework should be regarded as a research-oriented decision-support model rather than a validated clinical algorithm. CLINICAL RELEVANCE: Clinicians are provided with a structured, evidence-based framework that identifies specific clinical scenarios where molecular diagnostics, host-response biomarkers, and three-dimensional imaging may meaningfully modify periodontal treatment decisions, supporting the operationalisation of precision approaches in daily practice.

Humans↗
PubMed2006

[Clinical research within the German competence net "acute and chronic leukemias"].

BACKGROUND: Leukemias are a challenge and a cost factor to society because of their frequency in all age groups. They also serve as a model for a variety of diseases and possess exemplary relevance for basic research and patient care. Leukemia research and therapy have achieved high standards and even a leading position in Germany with regard to clinical trials, standardization of diagnostics and molecular studies of prognostic factors, signal transduction and gene expression. Progress is hampered, however, by fragmentation of leukemia trial groups, diagnostic approaches and treatment research activities. GOALS: A network was therefore created to integrate the leading leukemia trial groups on chronic myeloid leukemia (CML), acute myeloid leukemia (AML), acute lymphatic leukemia (ALL), myelodysplastic syndromes (MDS) and chronic myeloproliferative diseases (CMPD) and their interdisciplinary partners (diagnostics, treatment research, biometry) in cooperation with basic research and pharmaceutical industry to foster advancements in leukemiarelated research and health care through clinical trials, promotion of translational research, introduction of standards for diagnostics and therapy, and development of evidence-based guidelines. ACHIEVEMENTS: Achievements include establishment of central information, communication and management structures, creation of an AML intergroup comprising five study groups, formation of an MDS study group and establishment of platforms for diagnostics, genomics and proteomics, and medical informatics. Exchange of scientific progress is mediated by intra- and internet, biannual newsletters, regular project group meetings, and annual network symposia. PERSPECTIVES: On the basis of experience with the Competence Network "Acute and chronic leukemias" with its management, communication and information structures, the "European LeukemiaNet" (ELN) has been established within the 6th Framework Program of the European Union. The ELN integrates 78 leading leukemia trial groups (AML, ALL, CML, CLL, MDS, and CMPD), their 83 interdisciplinary partner groups (diagnostics, treatment research, registry, guidelines), industry and SMEs (small- and medium-sized enterprises) across Europe to form a cooperative network for advancements in leukemia-related research and health care.

Acute Disease↗
PubMed1994

Follow-up of a report of a potential linkage for schizophrenia on chromosome 22q12-q13.1: Part 2.

A collaboration involving four groups of investigators (Johns Hopkins University/Massachusetts Institute of Technology; Medical College of Virginia/The Health Research Board, Dublin; Institute of Psychiatry, London/University of Wales, Cardiff; Centre National de la Recherche Scientifique, Paris) was organized to confirm results suggestive of a schizophrenia susceptibility locus on chromosome 22 identified by the JHU/MIT group after a random search of the genome. Diagnostic, laboratory, and analytical reliability exercises were conducted among the groups to ensure uniformity of procedures. Data from genotyping of 3 dinucleotide repeat polymorphisms (at the loci D22S268, IL2RB, D22S307) for a combined replication sample of 256 families, each having 2 or more affected individuals with DNA, were analysed using a complex autosomal dominant model. This study provided no evidence for linkage or heterogeneity for the region 22q12-q13 under this model. We conclude that if this region confers susceptibility to schizophrenia, it must be in only a small proportion of families. Collaborative efforts to obtain large samples must continue to play an important role in the genetic search for clues to complex psychiatric disorders such as schizophrenia.

Adult↗
PubMed2026

The application of the CRISPR-Cas system in Pseudomonas aeruginosa infections.

Due to the extensive drug resistance of Pseudomonas aeruginosa (P. aeruginosa), it is still a great clinical challenge. The clustered regularly interspaced short palindromic repeats and associated proteins (CRISPR-Cas) system has become a promising strategy against this pathogen. This review critically evaluates the multifaceted applications of CRISPR-Cas technology in P. aeruginosa, including its role in antimicrobial resistance, diagnostics, genome editing, and emerging therapeutic and vaccine strategies. In addition to conducting a comprehensive analysis of various studies, we also compared the performance and limitations of various CRISPR platforms, and discussed the main technologies and transformation obstacles in this field. Finally, we look forward to the direction of applying these experimental tools to clinical research in the future.

Pseudomonas aeruginosa↗