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PubMed2001

Accuracy of simple techniques for estimating fractional zinc absorption in humans.

The theoretical basis of the accuracy of a number of simple techniques for estimating fractional zinc absorption (FZA) in humans using stable isotopic tracers has not been evaluated. These techniques include fecal monitoring (FM), deconvolution analysis (DA), double isotopic tracer ratio (DITR) and indicator dilution methods. Using a compartmental model, we investigated the accuracy and logic of each of these techniques. Time-dependent estimates of FZA based on the simple techniques were simulated using the compartmental model and compared with the known FZA derived from the model. The analysis elucidated logical errors in some of the FM techniques, and even when these problems were corrected, the FM technique was still prone to errors due to incomplete fecal tracer recovery and variable gastrointestinal (GI) transit time. Although logically correct, the indicator dilution techniques were also highly sensitive to incomplete fecal tracer recovery and variable GI transit time. The DA and DITR techniques were the most robust in that they were logically correct and were insensitive to incomplete fecal tracer recovery and variable GI transit time. Although all of the DA and DITR methods provided similarly good estimates of FZA relative to the compartmental model, the DITR technique performed on a spot urine specimen obtained several days after tracer administration was the preferred choice because of its simplicity and minimal requirements for patient compliance.

Body Fluid Compartments↗

PubMed1994

Exposure efficacy and change in contact rates in evaluating prophylactic HIV vaccines in the field.

Field studies of the efficacy of prophylactic vaccines in reducing susceptibility rely on the assumption of equal exposure to infection in the vaccinated and unvaccinated groups. Differential exposure to infection could, however, be the goal of other types of intervention programme, or it could occur secondary to belief in the protective effects of a prophylactic measure, such as vaccination. We call this differential exposure the exposure efficacy, or behaviour efficacy. To study the relative contribution of unequal exposure to infection and differential susceptibility to the estimate of vaccine efficacy, we formulate a simple model that explicitly includes both susceptibility and exposure to infection. We illustrate this on the example of randomized field trials of prophylactic human immunodeficiency virus vaccines. Increased exposure to infection in the vaccinated group may bias the estimated reduction in susceptibility. The bias in the estimate depends on the choice of efficacy parameter, the amount of information used in the analysis, the distribution and level of protection in the population, and the imbalance in exposure to infection. Sufficient increase in contacts in the vaccinated could result in the vaccine being interpreted as having an immunosuppressive effect. Estimates of vaccine efficacy are generally more robust to imbalances in exposure to infection when the detailed history of exposure to infection can be used in the analysis or at high levels of protection. The bias also depends on the relationship between the distribution of vaccine protection and the distribution of behaviour change, which could differ between blinded and unblinded trials.

AIDS Vaccines↗

PubMed2004

Minimal haemodynamic system model including ventricular interaction and valve dynamics.

Characterising circulatory dysfunction and choosing a suitable treatment is often difficult and time consuming, and can result in a deterioration in patient condition, or unsuitable therapy choices. A stable minimal model of the human cardiovascular system (CVS) is developed with the ultimate specific aim of assisting medical staff for rapid, on site modelling to assist in diagnosis and treatment. Models found in the literature simulate specific areas of the CVS with limited direct usefulness to medical staff. Others model the full CVS as a closed loop system, but they were found to be very complex, difficult to solve, or unstable. This paper develops a model that uses a minimal number of governing equations with the primary goal of accurately capturing trends in the CVS dynamics in a simple, easily solved, robust model. The model is shown to have long term stability and consistency with non-specific initial conditions as a result. An "open on pressure close on flow" valve law is created to capture the effects of inertia and the resulting dynamics of blood flow through the cardiac valves. An accurate, stable solution is performed using a method that varies the number of states in the model depending on the specific phase of the cardiac cycle, better matching the real physiological conditions. Examples of results include a 9% drop in cardiac output when increasing the thoracic pressure from -4 to 0 mmHg, and an increase in blood pressure from 120/80 to 165/130 mmHg when the systemic resistance is doubled. These results show that the model adequately provides appropriate magnitudes and trends that are in agreement with existing data for a variety of physiologically verified test cases simulating human CVS function.

Blood Flow Velocity↗

PubMed2004

Robustness of case-control studies of genetic factors to population stratification: magnitude of bias and type I error.

Case-control studies of genetic factors are prone to a special form of confounding called population stratification, whenever the existence of one or more subpopulations may lead to a false association, be it positive or negative. We quantify both the bias (in terms of confounding risk ratio) and the probability of false association (type I error) in the most unfavorable situation in which only one high-risk subpopulation is hidden within the studied population, considering different scenarios of population structuring and varying sample sizes. In accord with previous work, we find that the bias is likely to be small in most cases. In addition, we show that the same applies to the associated type I error whenever the subpopulation is small in proportion. For instance, when the hidden subpopulation makes up 5% of the entire population, with an allelic frequency of 0.25 (versus 0.10) and a disease rate that is double, then the estimated bias is 1.07 and the type I error associated with a sample of 500 cases and 500 controls is 8% (instead of 5%). We also show that the type I error is substantially greater for a rare allele (frequency of 0.1) than for a common allele (frequency of 0.5) and analyze the pattern of increase of vulnerability to stratification bias with sample size. Based on our findings, we may therefore conclude that with moderate sample sizes the type I error associated with population stratification remains very limited in most realistic scenarios.

Bias↗

PubMed2004

Increasing hip fracture incidence in California Hispanics, 1983 to 2000.

BACKGROUND: Hip fracture incidence in non-Hispanic whites (NHW) has decreased nationwide for the past 20 years. Little is known regarding hip fracture incidence among Hispanics, the largest, fastest growing minority in the United States. OBJECTIVE: To assess the change in standardized hip fracture incidence from 1983 through 2000 in California Hispanics relative to other racial groups. DESIGN: Hospitalizations for individuals older than 55 years with hip fracture requiring repair in acute care hospitals. Annual population estimates based on US Census Bureau estimates. Incidence standardized to national gender-age strata. Change in annual incidence calculated by weighted linear regression with robust variance estimates. RESULTS: 372,078 hip fractures were identified. Age-adjusted annual incidence of hip fractures declined by 0.74% per year among women (655 to 568 per 100,000), but was unchanged among men (247 to 238 per 100,000). Among NHW women, the standardized annual incidence fell by 0.6% (4.0 fractures per 100,000) per year. Annual incidence among Hispanic women increased 4.9% (11.1 fractures per 100,000) per year. Annual incidence among Hispanic men increased by 4.2% (4.5 fractures per 100,000) per year and among NHW men by 0.5% (1.2 fractures per 100,000) per year. No significant change occurred among black or Asian women or men. CONCLUSIONS: Among California women, hip fracture incidence has doubled among Hispanics since 1983, while remaining unchanged or declining in other groups. Greater attention should be given to identification of individuals at risk for hip fracture and initiation of preventive measures in Hispanic populations.

Age Distribution↗

PubMed1990

Addition of lithium carbonate to carbamazepine: hematological and thyroid effects.

In view of the increasing use of lithium-carbamazepine combination therapy for refractory psychiatric disorders, the authors assessed the clinical laboratory effects of adding lithium to carbamazepine in 23 patients with affective disorders. Lithium produced a robust reversal of carbamazepine-induced leukopenia, increasing WBCs, predominantly neutrophils, to levels significantly above placebo baseline values. The combination produced additive antithyroidal effects, resulting in greater decreases in T4 and free T4 than with carbamazepine alone; the addition of lithium was associated with the emergence of a modestly higher TSH level. The authors discuss clinical and theoretical implications of these findings.

Adult↗

PubMed1996

Failure of ritanserin to block cocaine cue reactivity in humans.

As part of a double-blind placebo-controlled study of the effects of ritanserin on cocaine use and craving, reactivity to cocaine-related events was assessed both before and during medication. Twenty-two patients receiving ritanserin and 23 receiving placebo were exposed to cocaine cues while continuous measures of heart rate, skin temperature, and skin resistance were taken. Self-reports of high, withdrawal, and craving were also collected. The cues produced significant physiological responding as well as significant increases in high and craving during both sessions. Ritanserin reduced cue-elicited decreases in skin temperature, but had no effect on heart rate and skin resistance or on cue-induced high and craving. The results demonstrate that cue reactivity is a robust phenomenon across two assessment sessions but fail to support the use of ritanserin as a means of reducing cue-elicited drug states.

Arousal↗

PubMed2003

Phosphorylation site interdependence of human p53 post-translational modifications in response to stress.

Modification-specific antibodies were used to characterize the phosphorylation and acetylation of human p53 in response to genotoxic (UV, IR, and adriamycin) and non-genotoxic (PALA, taxol, nocodazole) stress in cultured human cells at 14 known modification sites. In A549 cells, phosphorylation or acetylation was induced at most sites by the three DNA damage-inducing agents, but significant differences between agents were observed. IR-induced phosphorylation reached a maximum 2 h after treatment and returned to near pretreatment levels by 72 h; UV light and adriamycin induced a less rapid but more robust and prolonged p53 phosphorylation, which reached a maximum between 8 and 24 h, but persisted (UV) even 96 h after treatment. Ser33, Ser37, Ser46, and Ser392 were more efficiently phosphorylated after exposure to UV light than after IR. The non-genotoxic agents PALA, taxol and nocodazole induced p53 accumulation and phosphorylation at Ser6, Ser33, Ser46, and Ser392. Some phosphorylation at Ser15 also was observed. Modifications occurred similarly in the HCT116 human colon carcinoma cell line. Analysis of single site mutant p53s indicated clear interdependences between N-terminal phosphorylation sites, which could be classified in four clusters: Ser6 and Ser9; Ser9, Ser15, Thr18 and Ser20; Ser33 and Ser37; and Ser46. We suggest that p53 phosphorylation is regulated through a double cascade involving both the activation of secondary, effector protein kinases as well as intermolecular phosphorylation site interdependencies that check inappropriate p53 inactivation while allowing for signal amplification and the integration of signals from multiple stress pathways.

Animals↗

PubMed2002

The reinforcing efficacy of the dopamine reuptake inhibitor 2beta-propanoyl-3beta-(4-tolyl)-tropane (PTT) as measured by a progressive-ratio schedule and a choice procedure in rhesus monkeys.

The present series of experiments was undertaken to investigate the variables that influence the reinforcing efficacy of psychostimulants. The time of onset for dopamine transporter (DAT) occupancy of the long-acting, high-affinity DAT blocker 2beta-propanoyl-3beta-(4-tolyl)-tropane (PTT) was measured using an ex vivo binding assay in rodents and was determined to be significantly longer than for cocaine (30 min versus 2 min). To assess the reinforcing efficacy of PTT relative to cocaine, a discrete-trials drug-drug choice procedure (n = 3) and a progressive-ratio (PR) schedule (n = 4) were used in rhesus monkeys. Cocaine (0.003-0.56 mg/kg/injection) and PTT (0.003-0.03 mg/kg/injection) maintained responding greater than saline under the PR schedule. Maximal breaking points were significantly higher for cocaine compared with PTT. A separate group of monkeys prepared with double-lumen catheters was allowed to choose between cocaine (saline and 0.03-0.3 mg/kg/injection) and PTT (saline, and 0.01 and 0.03 mg/kg/injection). Under these conditions, PTT was not preferred over saline. When saline or 0.01 mg/kg/injection PTT was available as alternatives to cocaine, the highest dose of cocaine maintained greater than 80% choice. When 0.03 mg/kg/injection PTT was the alternative to cocaine, cocaine choice declined to approximately 50%, and total cocaine intake was decreased by ~70% at the highest cocaine dose. These results suggest that the reinforcing efficacy of PTT is less than cocaine in nonhuman primates. Data from studies with PTT indicate that slow-onset, long-acting DAT inhibitors can decrease cocaine self-administration while not functioning robustly as reinforcers, and support the further investigation of these drugs as treatment for cocaine addiction.

Animals↗

PubMed2003

Chromosomal deletion formation system based on Tn5 double transposition: use for making minimal genomes and essential gene analysis.

In this communication, we describe the use of specialized transposons (Tn5 derivatives) to create deletions in the Escherichia coli K-12 chromosome. These transposons are essentially rearranged composite transposons that have been assembled to promote the use of the internal transposon ends, resulting in intramolecular transposition events. Two similar transposons were developed. The first deletion transposon was utilized to create a consecutive set of deletions in the E. coli chromosome. The deletion procedure has been repeated 20 serial times to reduce the genome an average of 200 kb (averaging 10 kb per deletion). The second deletion transposon contains a conditional origin of replication that allows deleted chromosomal DNA to be captured as a complementary plasmid. By plating cells on media that do not support plasmid replication, the deleted chromosomal material is lost and if it is essential, the cells do not survive. This methodology was used to analyze 15 chromosomal regions and more than 100 open reading frames (ORFs). This provides a robust technology for identifying essential and dispensable genes.

Chromosome Deletion↗

PubMed2005

Multiple testing procedures based on weighted Kaplan-Meier statistics for right-censored survival data.

In clinical trials or drug development studies, researchers are often interested in identifying which treatments or dosages are more effective than the standard one. Recently, several multiple testing procedures based on weighted logrank tests have been proposed to compare several treatments with a control in a one-way layout where survival data are subject to random right-censorship. However, weighted logrank tests are based on ranks, and these tests might not be sensitive to the magnitude of the difference in survival times against a specific alternative. Therefore, it is desirable to develop a more robust and powerful multiple testing procedure. This paper proposes multiple testing procedures based on two-sample weighted Kaplan-Meier statistics, each comparing an individual treatment with the control, to determine which treatments are more effective than the control. The comparative results from a simulation study are presented and the implementation of these methods to the prostate cancer clinical trial and the renal carcinoma tumour study are presented.

Administration, Oral↗

PubMed2006

Effects of baclofen on cocaine self-administration: opioid- and nonopioid-dependent volunteers.

Preclinical and clinical studies suggest that GABAB receptor agonists selectively decrease cocaine use. The behavioral mechanism for the interaction between baclofen and cocaine in humans is not known, nor have its effects been characterized in individuals dependent on both cocaine and methadone. The objective of this study is to determine how maintenance on baclofen influences smoked cocaine's reinforcing and subjective effects, mood and cocaine craving prior to and after the initiation of cocaine use in cocaine-dependent volunteers with and without concurrent opioid dependence. Nontreatment-seeking volunteers (10 nonopioid dependent; seven methadone maintained), residing on an in-patient research unit for 21 days, were maintained on each baclofen dose (0, 30, 60 mg po) for 7 days. A smoked cocaine dose-response curve (0, 12, 25, 50 mg) was determined twice: on days 3-4 and days 6-7 of each baclofen maintenance condition. Cocaine sessions began with a sample trial, when participants smoked the cocaine dose available that session, and five choice trials, when participants chose between smoking the available cocaine dose or receiving one 5 dollars merchandise voucher. The results show that in the nonmethadone group, baclofen (60 mg) decreased self-administration of a low cocaine dose (12 mg). In the methadone group, baclofen decreased craving for cocaine. In both groups, baclofen decreased cocaine's effects on heart rate. Baclofen did not alter cocaine's robust subjective effects (eg 'High,' 'Stimulated') for either group. The results from this laboratory study appear consistent with clinical evidence showing that baclofen decreases cocaine use in nonopioid-dependent patients seeking treatment for cocaine dependence. The distinct pattern of effects in methadone-maintained participants suggests baclofen may not be effective in opioid-dependent cocaine users.

Adult↗

PubMed2004

A prospective, double-blind, community-controlled comparison of three doses of galantamine in the treatment of mild to moderate Alzheimer's disease in a Korean population.

BACKGROUND: With the Korean population rapidly aging and the number of Koreans with Alzheimer's disease(AD) steadily growing, treatment of AD is becoming an increasing concern. Galantamine hydrobromide, a dual acetylcholinesterase inhibitor and allosteric modulator of nicotinic receptors, is being studied in the treatment of the disease. OBJECTIVE: This study compared the efficacy and tolerability of 3 doses of galantamine in a Korean population with mild to moderate AD. METHODS: In this prospective, multicenter, double-blind, community-controlled, comparative study, patients with mild to moderate AD were randomized to receive galantamine 8, 16, or 24 mg/d; patients were evaluated at baseline (week 0) and after 4, 8, and 16 weeks of treatment. A 4-week dose-titration schedule was used in the 16-and 24-mg/d groups. Also included were patients with AD from a community control group who were untreated and assessed at baseline and week 16. The primary efficacy outcome was change in cognitive function, as measured with the Korean version of the AD Assessment Scale-11-item cognitive subscale (ADAS-cog/11-K); secondary efficacy measures included changes in functional capacity, behavioral symptoms, and global impression (clinical response), as measured with the Korean versions of the Disability Assessment for Dementia Scale (DAD-K), Behavior Pathology in AD Rating Scale (BEHAVE-AD-K), and Clinician's Interview-Based Impression of Change plus Caregiver Input (CIBIC-plus-K). RESULTS: A total of 300 patients (228 women, 72 men) were enrolled (76, 78, 80, and 66 patients in the 8-, 16-,24-mg/d and community control groups, respectively). Significant differences in demographic characteristics were found between the galantamine and community control groups for age, sex, and duration of formal education (P = 0.042, P = 0.049, and P < 0.001, respectively). Results demonstrated a robust dose-response relationship between ADAS-cog/11-K and galantamine dosage compared with baseline and controls at 16 weeks. Mean (SE) improvements ranged from 3.7 (0.8) to 5.6 (0.8) points in the galantamine groups, whereas the control group deteriorated by 4.7 (0.5) points (P < 0.001). Similarly, significant improvements in all 3 treatment groups were observed in mean DAD-K, BEHAVE-AD-K, and CIBIC-plus-K scores (P < 0.001, P < 0.005, and P < 0.001, respectively). Galantamine was relatively well tolerated. CONCLUSIONS: This study found that galantamine effected significant benefits on the cognitive, functional, and behavioral symptoms of mild to moderate AD in this population of Korean patients. The tolerability results suggest that galantamine is well tolerated in these patients. Inc.

Aged↗

PubMed2003

Development of an interleukin-12-deficient mouse model that is permissive for colonization by a motile KE26695 strain of Helicobacter pylori.

The identification of genes associated with colonization and persistence of Helicobacter pylori in the gastric mucosa has been limited by the lack of robust animal models that support infection by strains whose genomes have been completely sequenced. Here we report that an interleukin-12 (IL-12)-deficient mouse (IL-12(-/-) p40 subunit knockout in C57BL/6 mouse) is permissive for infection by a motile variant (KE88-3887) of The Institute For Genomic Research-sequenced strain (KE26695) of H. pylori. The IL-12-deficient mouse was also more permissive for colonization by the mouse-colonizing Sydney 1 strain of H. pylori than were wild-type C57BL/6 mice. Differences in colonization efficiency were demonstrated by mouse challenge with SS1 strains containing loss-of-function mutations in two genes (hspR and hrcA), whose products negatively regulate several heat shock genes. At 5 weeks postinfection, double-knockout mutants (SS1 hspR hrcA) efficiently colonized IL-12-deficient mice (5 of 5 animals compared to 4 of 10 for C57BL6 mice) and bacterial counts were higher in stomachs of IL-12-deficient mice (10(6) versus 10(5) CFU/g of stomach, respectively). IL-12-deficient mice were efficiently colonized by KE88-3887 (29 of 30), but not by nonmotile KE26695, and bacterial numbers (10(4) to 10(5) CFU/g of stomach) were unchanged over an 8-week period postinfection. In contrast, C57BL/6 mice were inefficiently colonized by KE88-3887 (8 of 20 animals with bacterial loads at the limit of detection, approximately 10(3) CFU/g), and infection did not persist much beyond 5 weeks. Cytokine responses (tumor necrosis factor alpha and gamma interferon), pathology, and antral-predominant infection were indistinguishable between IL-12-deficient and C57BL/6 mice. The increased permissiveness of the IL-12-deficient mouse for infection with H. pylori should facilitate whole-genome-based strategies to study genes associated with virulence and immune modulation.

Animals↗

PubMed2004

Action-specific extrapolation of target motion in human visual system.

Neuropsychological studies have indicated two distinct visual pathways in our brain, one dedicated to conscious perception and one to visuomotor control. Some psychophysical results support this idea with normal subjects, but they are still controversial. This study provides new psychophysical evidence for the dissociation by showing action-specific extrapolation of the visual target trajectory. When a moving target disappears, the perceived final position is liable to be shifted forward (representational momentum). In experiment 1, larger and more robust forward shifts were found when the position was directly touched without seeing the screen (open-loop pointing) than when the position was judged perceptually. The most striking dissociation was that fixation did not affect the forward shift in open-loop pointing while it almost abolished the shifts in perceptual judgements. In experiment 2, this action-specific result was found to disappear after a response delay of 4000 ms. Experiments 3 and 4 confirmed that the results were not affected by the external reference frames. The specific forward shifts found in open-loop pointing suggest that the visuomotor system compensates for the neural delays by extrapolating the target motion. The results, together with earlier findings, lead to a psychophysical double dissociation of the two visual pathways.

Adult↗

PubMed2005

The Nkx6.1 homeodomain transcription factor suppresses glucagon expression and regulates glucose-stimulated insulin secretion in islet beta cells.

We have previously described rat insulinoma INS-1-derived cell lines with robust or poor glucose-stimulated insulin secretion (GSIS). In the current study, we have further resolved these lines into three classes: class 1, glucose-unresponsive/glucagon-expressing; class 2, glucose-unresponsive/glucagon-negative; and class 3, glucose-responsive/glucagon-negative. The transcription factor Nkx2.2 was expressed with relative abundance of 3.3, 1.0, and 1.0 in class 1, class 2, and class 3 cells, respectively, whereas Nkx6.1 expression had the opposite trend: 1.0, 2.6, and 6.4 in class 1, class 2, and class 3 cells, respectively. In class 1 cells, overexpressed Nkx6.1 suppressed glucagon expression but did not affect the levels of several other prominent beta cell transcription factors. RNA interference (RNAi)-mediated suppression of Nkx6.1 in class 3 cells resulted in a doubling of glucagon mRNA, with no effect on Pdx1 levels, whereas suppression of Pdx1 in class 3 cells caused a 12-fold increase in glucagon transcript levels, demonstrating independent effects of Nkx6.1 and Pdx1 on glucagon expression in beta cell lines. RNAi-mediated suppression of Nkx6.1 expression in class 3 cells also caused a decrease in GSIS from 13.9- to 3.7-fold, whereas suppression of Pdx1 reduced absolute amounts of insulin secretion without affecting fold response. Finally, RNAi-mediated suppression of Nkx6.1 mRNA in primary rat islets was accompanied by a significant decrease in GSIS relative to control cells. In sum, our studies have revealed roles for Nkx6.1 in suppression of glucagon expression and control of GSIS in islet beta cells.

Adenoviridae↗

PubMed2005

Economic evaluation of levetiracetam as an add-on therapy in patients with refractory epilepsy.

OBJECTIVES: This study provides the results of a cost-effectiveness analysis of levetiracetam as an adjunctive treatment for refractory epilepsy from the Canadian Ministry of Health perspective. The main objective is to estimate the expected cost-effectiveness ratio expressed as the incremental cost per seizure-free day gained when using levetiracetam. In addition, this study examines the potential savings that might result by reducing the number of surgical evaluations and surgery when using levetiracetam. METHODS: A 1-year dose escalation decision-tree model comparing levetiracetam plus standard therapy with standard therapy alone was designed in order to combine probability, resource use and unit cost data (1999 Canadian dollars [$Can]). The short-term outcomes were derived from three phase III randomised, double-blind, placebo-controlled trials performed in 904 patients, aged 16-70 years, with at least 1 year history of epilepsy, two to four partial seizures per month, and receiving a maximum of two classic antiepileptic drugs. RESULTS: The average gain in seizure-free days attributed to levetiracetam was 19 days per patient per year and the incremental cost-effectiveness ratio (ICER) for levetiracetam add-on in the base-case scenario was $Can80.7 per seizure-free day gained per patient per year. Moreover, when surgical investigation and surgery are considered in the model, the use of levetiracetam may be dominant, with substantial savings to the overall healthcare budget. All univariate sensitivity analyses show that the model was robust to the assumptions made. CONCLUSIONS: The economic analysis presented in this paper suggests, given a wide range of assumptions, that the increased cost of treating patients (with refractory epilepsy) with levetiracetam may be partially offset by a reduction in other direct medical costs (from the Canadian Ministry of Health perspective), as a consequence of an increase in the number of seizure-free days. Moreover, potential cost savings may be foreseen when it is assumed that levetiracetam may reduce the number of candidates for surgical evaluation and surgery through a reduction of seizure frequency.

Anticonvulsants↗

PubMed2026

DNA-FISH Metaphase Spreads to Distinguish Extrachromosomal DNA from Homogeneously Staining Regions in Human Cancer Cell Lines.

Whole-genome sequencing identifies focal DNA amplifications with base-pair resolution but cannot determine whether amplified sequences reside on extrachromosomal DNA (ecDNA, also known as double minutes) or within chromosomally integrated homogeneously staining regions (HSRs). DNA fluorescence in situ hybridization (DNA-FISH) metaphase spreads remain the gold standard for distinguishing these amplification states at single-cell resolution. Here, we present a detailed protocol for DNA-FISH metaphase spreads using human cancer cell lines, encompassing cell culture, metaphase arrest, hypotonic treatment, fixation, chromosome spreading, fluorescent probe hybridization, and fluorescence imaging. The protocol incorporates intermediate quality-control steps to verify successful chromosome dispersion and optimize metaphase spread quality, making the workflow accessible to laboratories without specialized cytogenetics expertise. Results demonstrate clear visualization of ecDNA and HSR amplification states using locus-specific probes and illustrate common technical artifacts that can affect interpretation. This protocol provides a robust and reproducible approach for studying the structural organization of oncogene amplification in cancer cells.

Humans↗