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At least 217 records · Page 12Linked to original sources
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↗
PubMed2005

Detection and calibration of microdeletions and microduplications by array-based comparative genomic hybridization and its applicability to clinical genetic testing.

PURPOSE: Genome-wide telomere screening by fluorescence in situ hybridization (FISH) has revealed that approximately 6% of unexplained mental retardation is due to submicroscopic telomere imbalances. However, the use of FISH for telomere screening is labor intensive and time consuming, given that 41 telomeres are interrogated. We have evaluated the use of array-based Comparative Genomic Hybridization (aCGH) as a more efficient tool for identifying telomere rearrangements. METHODS: In this study, 102 individuals with unexplained mental retardation, with either normal or abnormal FISH results, were selected for a blinded retrospective study using aCGH. Results between the two methodologies were compared to ascertain the ability of aCGH to be used in a clinical diagnostics setting. RESULTS: We detected 100% of all imbalances previously identified by FISH (n = 17) and identified two additional abnormalities, a 10q telomere duplication and an interstitial duplication of 22q11. Interphase FISH analysis verified all abnormal array results. We also demonstrated that aCGH can accurately calibrate the size of telomere imbalances by using an array with "molecular rulers" for the telomeric regions of 1p, 16p, 17p, and 22q. CONCLUSION: This study demonstrates that aCGH is an equivalent methodology to telomere FISH for detecting submicroscopic deletions. In addition, small duplications that are not easily visible by FISH can be accurately detected using aCGH. Because aCGH allows simultaneous interrogation of hundreds to thousands of DNA probes and is more amenable to automation, it offers an efficient and high-throughput alternative for detecting and calibrating unbalanced rearrangements, both of the telomere region, as well as other genomic locations.

Chromosome Aberrations↗
PubMed2003

Genomic imprinting and linkage test for quantitative-trait Loci in extended pedigrees.

Genomic imprinting is a mechanism in which only one of the two copies of a gene is expressed. Some genes that affect development and behavior in mammals are known to be imprinted. Deregulation of imprinted genes has been found in a number of human diseases. Incorporating imprinting information into linkage analysis results in a more powerful test for linkage. Here, we propose an efficient method to test for linkage and imprinting of quantitative traits in extended pedigrees. We compared the results obtained by using the extended-pedigree-analysis approach proposed in this study with other existing approaches. We found that the proposed method is more powerful and uses extended-pedigree information most efficiently.

Female↗
PubMed2006

A statistical framework for genome-wide scanning and testing of imprinted quantitative trait loci.

Non-equivalent expression of alleles at a locus results in genomic imprinting. In this article, a statistical framework for genome-wide scanning and testing of imprinted quantitative trait loci (iQTL) underlying complex traits is developed based on experimental crosses of inbred line species in backcross populations. The joint likelihood function is composed of four component likelihood functions with each of them derived from one of four backcross families. The proposed approach models genomic imprinting effect as a probability measure with which one can test the degree of imprinting. Simulation results show that the model is robust for identifying iQTL with various degree of imprinting ranging from no imprinting, partial imprinting to complete imprinting. Under various simulation scenarios, the proposed model shows consistent parameter estimation with reasonable precision and high power in testing iQTL. When a QTL shows Mendelian effect, the proposed model also outperforms traditional Mendelian model. Extension to incorporate maternal effect is also given. The developed model, built within the maximum likelihood framework and implemented with the EM algorithm, provides a quantitative framework for testing and estimating iQTL involved in the genetic control of complex traits.

Algorithms↗
PubMed2003

Power of genome-wide linkage disequilibrium testing by using microsatellite markers.

Linkage disequilibrium (LD) testing is often used in the search for disease genes. In this study, we developed a method for calculating the expected power of genome-wide LD testing by using microsatellite markers under the following assumptions: (1) microsatellite markers have unequally frequent alleles, (2) markers are equally spaced through the human genome, (3) the degree of LD between the disease variant and the marker decays gradually because of recombination and mutation, (4) the population frequency of the disease variant is low (e.g., 0.05), (5) a single-marker test is performed in a case-control study, and (6) the significance level is adjusted by the number of tests to avoid inflation of the type I error. Our calculations revealed a markedly higher power for microsatellite markers than for single nucleotide polymorphism (SNP) markers, even if more SNPs are analyzed, suggesting that the use of microsatellite markers is preferable to the use of SNPs for genome-wide screening under the above assumptions. This method will be helpful to researchers who design genome-wide LD testing with microsatellite markers.

Alleles↗
PubMed2005

HEGESMA: genome search meta-analysis and heterogeneity testing.

SUMMARY: Heterogeneity and genome search meta-analysis (HEGESMA) is a comprehensive software for performing genome scan meta-analysis, a quantitative method to identify genetic regions (bins) with consistently increased linkage score across multiple genome scans, and for testing the heterogeneity of the results of each bin across scans. The program provides as an output the average of ranks and three heterogeneity statistics, as well as corresponding significance levels. Statistical inferences are based on Monte Carlo permutation tests. The program allows both unweighted and weighted analysis, with the weights for each study as specified by the user. Furthermore, the program performs heterogeneity analyses restricted to the bins with similar average ranks. AVAILABILITY: http://biomath.med.uth.gr.

Chromosome Mapping↗
PubMed2005

[The problem of multiple testing and solutions for genome-wide studies].

The problem of multiple testing and its solutions for genome-wide studies. Even if there is no real change, the traditional p = 0.05 can cause 5% of the investigated tests being reported significant. Multiple testing corrections have been developed to solve this problem. Here the authors describe the one-step (Bonferroni), multi-step (step-down and step-up) and graphical methods. However, sometimes a correction for multiple testing creates more problems, than it solves: the universal null hypothesis is of little interest, the exact number of investigations to be adjusted for can not determined and the probability of type II error increases. For these reasons the authors suggest not to perform multiple testing corrections routinely. The calculation of the false discovery rate is a new method for genome-wide studies. Here the p value is substituted by the q value, which also shows the level of significance. The q value belonging to a measurement is the proportion of false positive measurements when we accept it as significant. The authors propose using the q value instead of the p value in genome-wide studies.

Confidence Intervals↗
PubMedDate not supplied

[Detection of dsDNA antibodies in diagnosis of systemic lupus erythematosus--comparative studies of diagnostic effectiveness of 3 ELISA methods with different antigens and a Crithidia luciliae immunofluorescence test].

Antibodies to double-stranded DNA (anti-dsDNA, dsDNA-Ab) are frequently found in systemic lupus erythematosus (SLE), especially during active disease and differ with respect to immunoglobulin class and avidity. The detection of anti-dsDNA is one of the diagnostic criteria for SLE according to the American College of Rheumatology (ACR). Most of the commercial ELISA test systems have great advantages in routine laboratory testing but often detect dsDNA-Ab which are not specific for SLE and therefore give false positive results for non-SLE patients. The newly developed ELISA presented here, using human recombinant dsDNA (h-Rek) is compared to two commercial ELISA tests with genomic dsDNA from salmon testes (L-dsDNA) or plasmid dsDNA (P-dsDNA) and to the Chrithidia luciliae immunofluorescence test (CLIF) as well. In this study 143 sera were tested, 48 derived from patients with SLE, 40 from rheumatoid arthritis patients, 26 from non-rheumatoid patients whose sera were ANA-negative but L-dsDNA-Ab-positive and 30 from healthy volunteers. All patients were followed and clinically defined by the rheumatology outpatient clinic of our hospital. The prevalence for SLE of all sera was 32%. The sensitivity was 0.73 (h-Rek), 0.83 (L-dsDNA), 0.81 (P-dsDNA) and 0.57 (CLIF); specificity was determined 0.84 (h-Rek), 0.62 (L-dsDNA), 0.63 (P-dsDNA) and 0.98 (CLIF). The diagnostic efficiency of the L-dsDNA- and P-dsDNA-assay was identical, 0.69, and amounted to 0.81 for the h-Rek and 0.84 for the CLIF. Comparing all the ELISA tests and CLIF, the human recombinant dsDNA ELISA is much more sensitive than the CLIF, but considerably more specific than the ELISA assays using genomic or plasmid DNA, whereas the diagnostic efficiency is very close to that of the CLIF. This new generation of anti-dsDNA ELISA using human recombinant dsDNA seems to be a much better diagnostic tool for the detection of highly specific anti-dsDNA antibodies in the diagnosis of SLE than other commercial ELISAs. These results can only be explained by the use of a human recombinant antigen instead of undefined genomic or recombinant plasmid DNA for immobilization.

Animals↗
PubMed2006

Comparative isoschizomer profiling of cytosine methylation: the HELP assay.

The distribution of cytosine methylation in 6.2 Mb of the mouse genome was tested using cohybridization of genomic representations from a methylation-sensitive restriction enzyme and its methylation-insensitive isoschizomer. This assay, termed HELP (HpaII tiny fragment Enrichment by Ligation-mediated PCR), allows both intragenomic profiling and intergenomic comparisons of cytosine methylation. The intragenomic profile shows most of the genome to be contiguous methylated sequence with occasional clusters of hypomethylated loci, usually but not exclusively at promoters and CpG islands. Intergenomic comparison found marked differences in cytosine methylation between spermatogenic and brain cells, identifying 223 new candidate tissue-specific differentially methylated regions (T-DMRs). Bisulfite pyrosequencing confirmed the four candidates tested to be T-DMRs, while quantitative RT-PCR for two genes with T-DMRs located at their promoters showed the HELP data to be correlated with gene activity at these loci. The HELP assay is robust, quantitative, and accurate and is providing new insights into the distribution and dynamic nature of cytosine methylation in the genome.

Animals↗
PubMed2004

A graph-theoretic approach to testing associations between disparate sources of functional genomics data.

MOTIVATION: The last few years have seen the advent of high-throughput technologies to analyze various properties of the transcriptome and proteome of several organisms. The congruency of these different data sources, or lack thereof, can shed light on the mechanisms that govern cellular function. A central challenge for bioinformatics research is to develop a unified framework for combining the multiple sources of functional genomics information and testing associations between them, thus obtaining a robust and integrated view of the underlying biology. RESULTS: We present a graph-theoretic approach to test the significance of the association between multiple disparate sources of functional genomics data by proposing two statistical tests, namely edge permutation and node label permutation tests. We demonstrate the use of the proposed tests by finding significant association between a Gene Ontology-derived predictome and data obtained from mRNA expression and phenotypic experiments for Saccharomyces cerevisiae. Moreover, we employ the graph-theoretic framework to recast a surprising discrepancy presented elsewhere between gene expression and knockout phenotype, using expression data from a different set of experiments. AVAILABILITY: An R software package, GraphAT, containing the data and statistical procedures is available from Bioconductor: http://www.bioconductor.org.

Algorithms↗
PubMed1998

Genome screens using linkage disequilibrium tests: optimal marker characteristics and feasibility.

Linkage disequilibrium (LD) testing has become a popular and effective method of fine-scale disease-gene localization. It has been proposed that LD testing could also be used for genome screening, particularly as dense maps of diallelic markers become available and automation allows inexpensive genotyping of diallelic markers. We compare diallelic markers and multiallelic markers in terms of sample sizes required for detection of LD, by use of a single marker locus in a case-control study, for rare monophyletic diseases with Mendelian inheritance. We extrapolate from our results to discuss the feasibility of single-marker LD screening in more-complex situations. We have used a deterministic population genetic model to calculate the expected power to detect LD as a function of marker density, age of mutation, number of marker alleles, mode of inheritance of a rare disease, and sample size. Our calculations show that multiallelic markers always have more power to detect LD than do diallelic markers (under otherwise equivalent conditions) and that the ratio of the number of diallelic to the number of multiallelic markers needed for equivalent power increases with mutation age and complexity of mode of inheritance. Power equivalent to that achieved by a multiallelic screen can theoretically be achieved by use of a more dense diallelic screen, but mapping panels of the necessary resolution are not currently available and may be difficult to achieve. Genome screening that uses single-marker LD testing may therefore be feasible only for young (<20 generations), rare, monophyletic Mendelian diseases, such as may be found in rapidly growing genetic isolates.

Alleles↗
PubMed1987

Comparison of porcine parvovirus to other parvoviruses by restriction site mapping and hybridization analysis of Southern Blots.

The genomic relationship between porcine parvovirus (PPV) and several other autonomous parvoviruses was examined by restriction site and hybridization analysis. Restriction site maps of the PPV genome were prepared by digesting the double-stranded replicative form of the viral DNA with each of eight restriction enzymes. Subsequent comparison of such maps with those previously reported for PPV, canine parvovirus (CPV), feline panleukopenia virus (FPV), minute virus of mice (MVM), H-1 virus (H-1) and bovine parvovirus (BPV) revealed that while the maps of CPV, FPV, MVM and H-1 had a number of features in common, those of PPV and BPV were substantially different. For hybridization analysis radioactive probes prepared by nick translation of PPV, CPV and BPV genomes were tested under conditions of both low and high stringency for homologous hybridization and for heterologous hybridization with each of the other two viruses and with FPV. The results of these tests indicated homology among the genomes of PPV, CPV and FPV, but little or no homology between the genome of BPV and those of any of the other viruses tested. Additional tests with restriction fragments of PPV and a CPV probe indicated that heterologous hybridization was confined primarily to a segment of the genome between 1.85 and 2.7 kb from the 3' end. Based on transcriptional maps previously determined for several of the rodent parvoviruses, this interval is likely to include part of the coding sequences for both non-structural and structural proteins and may be the genetic basis for the replicative as well as the antigenic similarities between PPV and both CPV and FPV.

Animals↗
PubMedDate not supplied

Proteomics, genomics and the future of medical education.

The completion of the human genome project in 2003 ushered in the era of genomics, the systematic study of our DNA sequence. Proteomics, the study of the full complement of proteins present in a cell, is a natural extension of genomics. Together, the information obtainable through genomics and proteomics has tremendous potential to change clinical practice. The application of such information to medical diagnosis and treatment will require significant changes in the training of physicians. All students and physicians in training will need to acquire enough knowledge of the underlying science, including medical genetics, epidemiology, bioinformatics and statistics, so they will intuitively understand the technology and recognize the strengths and limitations of genomic/proteomic tests. Because genomic or proteomic testing may yield extensive information about a person's genetic makeup and disease risks, consideration will need to be given throughout the medical curriculum to the ethical issues raised by the application of this new technology to the diagnosis and treatment of patients.

Clinical Medicine↗
PubMed1999

Genome scans for genetic predisposition to alcoholism by use of transmission disequilibrium test analyses.

We report the results of the analysis of three measures of alcoholism and six associated symptoms using transmission disequilibrium (TDT) analysis on data from the Collaborative Study on the Genetics of Alcoholism data set. Implementation of identity-by-state (IBS) routines for error checking revealed 10 reported full siblings that were rejected as a full sibling to all of their purported full siblings with p < 0.05. TDT analysis revealed two loci with significant transmission disequilibrium (p < 0.001) on chromosomes 1 and 7. Analysis by parental origin found alleles at three loci displaying significant disequilibrium in the transmission of the paternal alleles for at least three of the nine tested traits. These loci are on chromosomes 6, 9, and 13. Analyses of Caucasian families alone and the use of a single affected individual from each family also yielded significant results for the loci on chromosomes 6, 9, and 13.

Alcoholism↗
PubMed2001

A family of Tc1-like transposons from the genomes of fishes and frogs: evidence for horizontal transmission.

Tc1-like transposons are very widely distributed within the genomes of animal species. They consist of an inverted repeat sequence flanking a transposase gene with homology to the mobile DNA element, Tc1 of the nematode Caenorhabditis elegans. These elements seem particularly to infest the genomes of fish and amphibian species where they can account for 1% of the total genome. However, all vertebrate Tc1-like elements isolated so far are non-functional in that they contain multiple frameshifts within their transposase coding regions. Here I describe a Tc1-like transposon (PPTN) from the genome of a marine flatfish species (Pleuronectes platessa) which bears conserved inverted repeats flanking an apparently intact transposase gene. Closely related, although degenerate, Tc1-like transposons were also isolated from the genomes of Atlantic salmon (SSTN, Salmo salar) and frog (RTTN, Rana temporaria). Consensual nucleic acid sequences were derived by comparing several individual isolates from each species and conceptual amino acid sequences were thence derived for their transposases. Phylogenetic analysis of these sequences with previously isolated Tc1-like transposases shows that the elements from plaice, salmon and frog comprise a new subfamily of Tc1-like transposons. Each member is distinct in that it is not found in the genomes of the other species tested. Plaice genomes contain about 300 copies of PPTN, salmon 1200 copies of SSTN and frog genomes about 500 copies of RTTN. The presence of these closely related elements in the genomes of fish and frog species, representing evolutionary lines, which diverged more than 400 million years ago, is not consistent with a vertical transmission model for their distributions.

Amino Acid Sequence↗