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PubMed2001

Towards high-throughput genotyping of SNPs by dynamic allele-specific hybridization.

Analysis of single nucleotide polymorphisms (SNPs)--the most common form of variation in the human genome--has become a popular strategy for discovering genes involved in complex diseases such as Alzheimer's disease, obesity and diabetes. It is also widely anticipated that SNPs will play a major role in pharmacogenomics, where the identification of variations in specific genes relevant to drug efficacy, toxicity and metabolism will help to establish optimal therapeutic strategies for individual patients. Reflecting these expectations, many new SNP-related technologies have appeared over the past few years, each with unique advantages, but all with the common goal of simplifying and expediting SNP analysis. We recently introduced a technique termed dynamic allele-specific hybridization (DASH), a convenient method for SNP (and insertion-deletion) genotyping, which is highly applicable to both basic research and clinical diagnostics. Commercial DASH devices are now available, making the technology affordably accessible for all laboratories.

Alleles↗

PubMed2002

Limited genetic diversity of Candida albicans in fecal flora of healthy volunteers and inpatients: a proposed basis for strain homogeneity in clinical isolates.

Molecular analysis of Candida albicans isolates from individual patients often yields a single strain at multiple sites. Whether this strain-limitation is due to virulence factors favoring the invasive strain or to lack of genetic diversity in the gastrointestinal reservoir is uncertain. We elected to study C. albicans genotypes in the fecal flora among healthy volunteers and inpatients. Self-obtained stool swabs or stool samples were cultured on inhibitory mold agar. From each subject with C. albicans, nine colonies were randomly selected, individually propagated, and typed utilizing random amplified polymorphic DNA. Colonies were considered identical (all bands matched), related variants (one to three unique bands), or distinct strains (more than three unique bands). Analysis showed a single clone in 33/43 (76.7%) volunteers and 6/18 (33.3%) inpatients (P = 0.018), two to four related variants in eight (18.6%) volunteers and 10 (55.6%) inpatients, and two distinct strains in two volunteers (4.6%) and two inpatients (11.1%). Strain variation was more common in females (33.5 versus 5.6%; P = 0.04) and tended to increase with age (r = 0.245, P = 0.06). These findings illustrate that most healthy subjects harbor a single strain of C. albicans in the fecal flora. This strain may undergo genetic evolution leading to minor clonal variations. The mechanisms for strain selection, maintenance and possible evolution remain to be delineated.

Candida albicans↗

PubMed2007

The future of pediatric cancer and complex diseases: aren't they all?

Over the past decade, the investigation of human genetics and disease has pursued both common and uncommon germ-line variation and shown that both can be associated with altered risk for cancer and its outcomes. This line of investigation has not only begun to generate markers for disease but also insights into the biological pathways that are altered in cancer. Already, there is emerging evidence that germ-line genetic variation can alter susceptibility to different types of cancers, including pediatric cancers. It is evident that common genetic variation has emerged as a key component of a comprehensive understanding of pediatric cancer and its outcome. Future studies should unravel the complex interaction between genes and the environment.

Child↗

PubMed1998

Variable number tandem repeat polymorphism of the mucin genes located in the complex on 11p15.5.

A family of four genes that encode major secreted mucins (MUC6, MUC2, MUC5AC and MUC5B) map to within 400 kb on chromosome 11p15.5. These genes contain long stretches of tandem repeats of sequence that encode serine- and threonine-rich domains but that otherwise show no similarity from gene to gene, and regions of unique sequence domains that do show evidence of sequence homology. We have previously reported the existence of polymorphism in three of these genes but the extent and nature of this allelic variation is now described here in detail. Variable number tandem repeat polymorphisms of MUC6, MUC2 and MUC5AC are predicted to encode mucin polypeptides that differ in length. In the case of MUC2 and MUC6 these length differences are substantial (up to twofold). MUC5B in contrast does not show common allele length variation. Three MUC2 mutations are reported, none of which are associated with the meiotic recombinations previously observed in this region of chromosome 11.

Child↗

PubMed2003

Multivariate group effect analysis in functional Magnetic Resonance Imaging.

In functional MRI (fMRI), analysis of multisubject data typically involves spatially normalizing (i.e. co-registering in a common standard space) all data sets and summarizing results in a single group activation map. This widely used approach does not explicitely account for between-subject anatomo-functional variability. Therefore, we propose a group effect analysis method which makes use of a multivariate model to select the main signal variations that are common to all subjects, while allowing final statistical inference on the individual scale. The normalization step is thus avoided and individual anatomo-functional features are preserved. The approach is evaluated by using simulated data and it is shown that sensitivity is drastically improved compared to more conventional individual analysis.

Algorithms↗

PubMed1979

Comparison of the genomes of simian, bovine, and human rotaviruses by gel electrophoresis and detection of genomic variation among bovine isolates.

By co-electrophoresis in polyacrylamide gels, the segmented double-standed RNA genome of the simian rotavirus, SA 11, was compared with those of human and bovine rotaviruses. A comparison between SA 11 virus and the Northern Ireland cell culture adapted bovine virus showed that the electrophoretic mobilities of each of the 11 corresponding segments differed. In other comparisons, four to seven segment variations were more common. When the genomes of various bovine rotaviruses were compared, eight different electropherotypes were detected. Four of these electropherotypes were obtained from one property during a single outbreak of disease. In view of such genetic diversity, a scheme for the systematic designation of different rotavirus samples is proposed. The significance of the variations in relation to the molecular epidemiology of bovine rotavirus infections is discussed.

Animals↗

PubMed1995

Factors shaping the tone level sensitivity of single neurons in posterior field of cat auditory cortex.

1. The posterior field (field P) of the cat's auditory cortex contains a higher proportion of neurons whose response/level functions for characteristic frequency (CF) tones are nonmonotonic than does the primary field (AI). The general purpose of the present study is to assess whether the response/level functions of field P neurons are generated by the same mechanisms as those of cells in AI. All of the data came from single neurons in the cortices of barbiturate-anesthetized cats, to which we presented tonal stimuli through sealed, calibrated stimulating systems. 2. We obtained quantitative data from 123 neurons, of which 108 were located in field P. Of the 108 field P cells, 70% had nonmonotonic response/level functions for 5-ms rise time tones of CF. For cells of any given CF, both CF thresholds and best SPLs (i.e., SPLs associated with maximal responses) varied widely. A correlation analysis revealed that a linear relation between best SPL and CF threshold accounted for 73% of the data variance in the association between those response variables. An analysis of data from 83 nonmonotonic cells in AI revealed a similar relation. 3. Field P neurons whose response/level functions were non-monotonic for 5-ms rise time CF tones became even more narrowly tuned to SPL when the rise time of the tone bursts was reduced to 1 ms. Lengthening the rise time to 20 ms reduced or eliminated the SPL tuning in almost all of these neurons. The general form of monotonic tone response/level functions was commonly unaffected by variation in signal rise time. In a few instances, cells with monotonic response/level functions for 5- and 20-ms rise time tones developed nonmonotonic functions for 1-ms rise time tones. 4. Field P neurons with nonmonotonic response/level functions for CF tones usually failed to respond to wideband noise pulses, or, less commonly, responded to noise only at low SPLs. In contrast, field P cells with a monotonic response to CF tones usually responded monotonically to noise. 5. The minimal mean first-spike latencies of field P neurons were generally longer than those of AI cells studied under similar conditions. The precision of first-spike timing, measured using the SD of the mean first-spike latency, was commonly poorer than that of AI cells. 6. The properties of field P cells followed the same rules as those seen in AI.(ABSTRACT TRUNCATED AT 400 WORDS)

Action Potentials↗

PubMed1976

Spinal cord vascularity. I. Extraspinal sources of spinal cord arteries in man.

The arrangement of extraspinal sources of the spinal cord arterial supply in man is more complicated than previously described, especially with regard to the origin and branching of the aortic segmental arteries. The fact that other arteries in the neck than the vertebral artery, such as the costo-cervical trunk and the ascending cervical artery may contribute to the supply of the cervical cord is confirmed, and also the occurrence of two or more spinal branches from different sources entering the same intervertebral foramen. Frequent occurrence of two or more segmental arteries arising from a common stem and variations in the branching of the subcostal arteries were found; their functional significance on the spinal cord circulation is not known. The fact that no significant anterior root artery was ever seen at the level of the vascular anomaly suggests that the anomaly is of no clinical importance. Nevertheless, obstruction of a common stem entail the risk of spinal cord infarction due to involvement of an important posterior root artery. On the other hand, the spinal cord seems to be fairly well protected against ischaemic injury following limited interference with the extraspinal arteries due to a profuse supply of intra- and extraspinal collaterals.

Angiography↗

PubMed1993

Variation in duration of hospital stay between hospitals and between doctors within hospitals.

Whether one examines the average length of hospital stay at the level of geographic areas, at the level of hospitals, or at the level of doctors, length-of-stay figures are known to vary widely. Even for hospital admissions for comparable surgical procedures among comparable groups of patients, significant length-of-stay variations have been reported. As is the case for variations in the occurrence of common surgical procedures, the overall conclusion is that large variations in duration of hospital stay associated with these common surgical procedures are the rule rather than the exception. The objective of the study is to examine whether variations in hospital medical practice, indicated by the duration of hospital stay in this study, can be reduced to differences in practice style between individual doctors within the same institutional setting or to differences in practice style between groups of doctors within the same institutional setting. The latter is assumed to be the combined effect of restrictions on the (hospital) supply side and the predilection of doctors to conform to the practice of immediate colleagues. It was found out that the variation in length of hospital stay, adjusted for patient case-mix, within hospitals is much smaller than the length-of-stay variation between different hospitals. The within hospital variation between (partnership of) doctors is in most of the cases statistically insignificant. Doctors working in more than one hospital on average choose a length of stay close to the average length of stay prevailing in the different hospitals.

Appendectomy↗

PubMed2002

Effect of a common reference plasma on the inter-laboratory variation of the measurement of total and free protein S: a collaborative study of the Dutch Working Group on Haemostasis Laboratory Diagnosis.

The comparability of test results for protein S between laboratories is hampered by a high inter-laboratory variability. The effect of the use and type of common reference plasma on the inter-laboratory variability of the total and free protein S measurement was evaluated. The results of 10 plasma samples measured against a centrally distributed frozen plasma and a centrally distributed lyophilized plasma were compared with those of various local reference plasmas regularly used by the 11 participating laboratories. The mean intra-assay coefficient of variation for total protein S in each laboratory varied from 3.8 to 12.8% (mean intra-assay CV of all laboratories: 7.4+/-2.3%); for free protein S this range was 3.1 to 13.3% (mean intra-assay CV of all laboratories: 6.6+/-2.7%). We confirmed the high inter-laboratory coefficient of variation (mean+/-SD) with the several local reference plasmas for both total protein S (13.4+/-5.6%; n = 10) and free protein S (17.1+/-7.5%: n = 11). For total protein S, the inter-laboratory CV was reduced to 11.5+/-4.8%, (p=0.05) by using a common frozen reference plasma, while it was increased to 16.8+/-3.4%, (p=0.022) using a common lyophilized reference plasma. For free protein S, these values decreased only statistically significantly for the common lyophilized reference plasma, to 15.1+/-6.0%, (p = 0.008). For free protein S, the dilution factor used was identified as a factor influencing the inter-laboratory variability. This study shows that, for both types of protein S measurements, using one frozen reference plasma shows a slight decrease in inter-laboratory variability, while a common lyophilized plasma shows inconsistent results. It is concluded that further investigation is necessary to examine other sources of variability to increase the comparability of laboratory results for both total and free protein S.

Adult↗

PubMed1999

Laparoscopic visualization of the cystic artery anatomy.

Uncontrolled bleeding from the cystic artery and its branches is a serious problem that may increase the risk of intraoperative lesions to vital vascular and biliary structures. On laparoscopic visualization anatomic relations are seen differently than during conventional surgery, so proper knowledge of the hepatobiliary triangle anatomic structures under the conditions of laparoscopic visualization is required. We present an original classification of the anatomic variations of the cystic artery into two main groups based on our experience with 200 laparoscopic cholecystectomies, with due consideration of the known anatomicotopographic relations. Group I designates a cystic artery situated within the hepatobiliary triangle on laparoscopic visualization. This group included three types: (1) normally lying cystic artery, found in 147 (73.5%) patients; (2) most common cystic artery variation, manifesting as its doubling, present in 31 (15.5%) patients; and (3) the cystic artery originating from the aberrant right hepatic artery, observed in 11 (5.5%) patients. Group II designates a cystic artery that could not be found within the hepatobiliary triangle on laparoscopic dissection. This group included two types of variation: (1) cystic artery originating from the gastroduodenal artery, found in nine (4. 5%) patients; and (2) cystic artery originating from the left hepatic artery, recorded in two (1%) patients.

Abdominal Muscles↗

PubMed1997

Variations of hepatitis B virus core gene sequence in Western patients with chronic hepatitis B virus infection.

Heterogeneity of the hepatitis B virus (HBV) core gene has been reported to be associated with the presence of active liver disease in Japanese patients with chronic HBV infection. This study evaluated the significance of HBV core gene heterogeneity in Western patients with chronic HBV infection. The hepatitis B virus precore/core gene from 45 patients (inactive:active liver disease ratio 16:29) was amplified from serum by polymerase chain reaction (PCR). Gel electrophoresis was employed to detect large deletions. The PCR amplicons from 13 patients (all HBV serotype adw but with a different spectrum of liver disease) were cloned and sequenced. Hepatitis B surface antigen (HBsAg) serotypes were tested by enzyme immunoassay (EIA) and hepatic expression of HBV antigens was assessed by immunohistochemistry. The HBV core gene was amplified from the serum of all 45 patients. Three patients had mixed infection with both precore mutant and wild-type HBV and all three had active liver disease. No patient had a large deletion of the HBV core gene. Hepatitis B virus core gene sequence variations were more common in the midcore region and there was no difference in the number of silent and missense substitutions between those with inactive and active liver disease. There was no correlation between the nucleotide or encoded amino acid substitutions and the clinical and biochemical parameters, including the subsequent response to interferon-alpha therapy (n = 37) or hepatic HBV antigen expression. Variation of the HBV core gene was not found to be preferentially associated with active liver disease in Western patients with chronic HBV infection. The pattern of hepatitis B core gene variation is in accord with the genomic organization of HBV.

Adult↗

PubMed2005

A comparison of bilateral breast cancers in BRCA carriers.

BACKGROUND: Women with breast cancer and a BRCA mutation have a high risk of developing a contralateral breast cancer. It is generally believed that the two cancers represent independent events. However, the extent of concordance between the first and second tumors with respect to hormone receptor expression and other pathologic features is unknown. PURPOSE: To determine the degree of concordance of estrogen receptor (ER) status, tumor grade, and histology in tumors from women with bilateral breast cancer and a BRCA mutation. SUBJECTS AND METHODS: Women with a history of bilateral invasive breast cancers were selected from an international registry of women with BRCA1 or BRCA2 mutations. Medical records were reviewed to document the characteristics of each cancer and the treatments received. RESULTS: Data were available for 286 women with bilateral breast cancer and a BRCA mutation (211 BRCA1; 75 BRCA2). The mean interval between first and second tumor was 5.1 years. The two tumors were concordant more often than expected for ER status (P < 0.0001) and for grade (P < 0.0001), but not for histology (P = 0.55). The ER status of the first tumor was highly predictive of the ER status of the second tumor (odds ratio, 8.7; 95% confidence interval, 3.5-21.5; P < 0.0001). Neither age, menopausal status, oophorectomy nor tamoxifen use was predictive of the ER status of the second tumor. CONCLUSIONS: There is strong concordance in ER status and tumor grade between independent primary breast tumors in women with a BRCA mutation. The excess concordance may be due to common risk factors, genetic variation, or the existence of a preneoplastic lesion that is common to both tumors.

Adult↗

PubMed1992

A variant of flexor carpi ulnaris causing ulnar nerve compression.

Anatomical variations of the muscles and nerves around the wrist are common. Knowledge of such variations is derived from 2 sources: anatomical dissections and clinically reported cases. We present a case of duplication of the tendon of flexor carpi ulnaris with splitting of the ulnar nerve. The ulnar slip of the tendon was inserted into the pisiform bone and the radial slip into the proximal phalanx of the ring finger. The anatomical literature and the clinically reported cases of variations of the flexor carpi ulnaris are reviewed.

Adult↗

PubMed1987

Restriction-map variation in natural populations of Drosophila melanogaster: white-locus region.

Restriction-map variation among 38 chromosomes collected from natural populations from around the world was surveyed using probes for a 45-kb region containing and surrounding the white locus. Insertion and deletion variation was more common in the regions flanking the white transcriptional unit, and restriction-site polymorphism appears to be most common 5' of the white locus. The frequencies of individual large insertions (suspected transposable elements) were low, although 37% of the chromosomes had at least one insertion in the white-locus region. The estimated level of nucleotide heterozygosity over the whole region was 0.012. There was little linkage disequilibrium among the polymorphic sites. In contrast to earlier reports of the variation in other regions of the Drosophila melanogaster genome, there seemed to be less linkage disequilibrium and perhaps more nucleotide polymorphism.

Animals↗

PubMed2003

[Atypical forms of atrioventricular nodal reentrant tachycardia].

The concept of functional dissociation of atrioventricular nodal conduction on an underlying structure with different nodal inputs is well established. In the common form of AVNRT, the circuit comprises the slow pathway for antegrade conduction and the fast pathway for retrograde conduction. However, the tachycardia circuit may be slightly or totally different as it is not based on discrete anatomical pathways but on functional pathways due to non-uniform anisotropy of the perinodal atrial tissue involved in the circuit. First, there are variations of the common form. The fast retrograde pathway may be posterior or left instead of being anteriorly-located. The so-called uncommon forms of AVNRT consist in slow-slow and fast-slow forms. The slow-slow form uses two different slow pathways as antegrade and retrograde limb of the circuit. These pathways may be posterior or left. The fast-slow form appears to be complex and heterogeneous. The retrograde slow pathway may be located posteriorly, anteriorly, in-between or sometimes left-sided. Whatever the circuit, targeting the antegrade or retrograde slow pathway remains the aim of ablation and the only therapeutic issue. However, a 1%-AV block rate has to be kept in mind.

Atrioventricular Node↗

PubMedDate not supplied

Variation in physician opinion about scheduling of return visits for common ambulatory care conditions.

OBJECTIVE: To determine whether there is consensus about intervals between visits for adult general medicine patients with common ambulatory care conditions. DESIGN: Survey of practicing physicians and residents. SETTING: Ambulatory care at a hospital clinic, a group practice, and a physician office. PARTICIPANTS: 153 physicians, including residents, fellows, and staff from The University of Iowa Hospitals and Clinics, internists and family practitioners from three Iowa towns, and internists from Atlantic City, New Jersey. INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: There was wide variation in responses, with greater consensus for more acute conditions than for chronic conditions or preventive care. CONCLUSIONS: 1) Wide variation exists in proposed intervals between visits for care of patients with common ambulatory conditions. 2) Variation occurs within the same geographic area and is unassociated with year of graduation from medical school, year in training, or academic appointment 3) Further study is needed to assess the significance of this variation.

Adult↗

PubMed2000

Differences between urologists in the United States and Canada in the approach to prostate cancer.

PURPOSE: We examine differences in screening, detection, staging and treatment of prostate cancer between urologists in the United States and Canada. MATERIALS AND METHODS: An anonymous questionnaire was developed and mailed to 700 randomly selected American and 350 Canadian urologists. The 7 domains of prostate cancer management comprised screening/case identification, radical prostatectomy indications, staging evaluations, neoadjuvant therapy, nerve sparing techniques, postoperative management and treatment of biochemical recurrence. The Dillman method of questionnaire administration was used. All data were stratified by country and analyzed using the generalized chi-square test. RESULTS: Surveys were adequately completed by 45% and 79% of American and Canadian urologists, respectively. Practice experience and clinical volumes were not significantly different between the 2 cohorts. Overall, there were few differences in prostate cancer screening, staging, postoperative management, biochemical failure and use of neoadjuvant therapy. However, practicing American urologists tended to pursue more aggressive case finding practices, such as a higher age cutoff for prostate specific antigen testing (p = 0.0001) and more frequent use of transition zone biopsies (p = 0.0001). American urologists also displayed a tendency toward more liberal indication for extirpative surgery. They were more likely to perform radical prostatectomy in men older than 70 years, those with higher prostate specific antigen and those with node positive disease. Among both national cohorts there was considerable variation in management patterns for all domains of prostate cancer. Variation was most common among treatment of patients with adverse pathological conditions (positive margins, seminal vesicle involvement) and postoperative biochemical failure. Even when credible evidence exists (biopsy technique, preoperative staging) significant proportions of urologists in both countries continued to practice contrary to existing data. CONCLUSIONS: American and Canadian practice patterns for prostate cancer differ significantly only in the domains of case identification and surgical indications. In addition, considerable intra-national variation in practice patterns exists. These data highlight the necessity to support randomized clinical trials in prostate cancer.

Canada↗