克隆测序方法检测三核苷酸重复次数的可靠性

目的 探讨克隆测序技术用于检测三核苷酸(CAG)重复次数的可靠性.方法 对1例临床确诊的遗传性脊髓小脑性共济失调1型(SCA1)患者,PCR法扩增ATXN1基因的CAG重复次数,8%变性聚丙烯酰胺凝胶电泳(DPAGE)分离PCR产物以协助确诊.2.5%琼脂糖凝胶电泳分离PCR产物的大小片段,割胶回收大小片段测序.另外将割胶回收的大片段进行TA克隆测序.结果 DPAGE提示大片段存在CAG的异常扩增,故该患者可确诊为SCA1.PCR产物大小片段直接测序结果为:小片段为26次CAG重复,大片段为47次重复.而将大片段克隆测序后,则有50、47、46、41、32、28、27、26、25及24次共10种不同的CAG重复次数,而且出现了CCG、CGG、CTG、CAA、TAT等序列变异现象.结论 克隆测序检测CAG重复次数会造成重复次数变异,且存在各种碱基变异.因此不宜单用TA克隆测序检测CAG重复次数及筛查碱基变异,需联合应用多种方法以提高结果的可靠性.     

Reproducibility and robustness of metabolome analysis in rat plasma of 28-day repeated dose toxicity studies

BASF has developed a rat plasma metabolomics database (MetaMap^®Tox) containing the metabolome of more than 500 chemicals, agrochemicals and drugs, for which the toxicity is well known, derived from 28-day repeated dose toxicity studies in rats. The quality/reproducibility of data was assessed by comparing the metabolome of 16 reference compounds tested at least twice under identical experimental conditions at three time points (day 7, day 14 and day 28). Statistical correlation analysis showed that the repeated treatment induced very similar changes to the metabolome. For all repetitions the modes of action of the compounds were always correctly identified. Moreover, when compared against the metabolome of all compounds available in the MetaMap^®Tox database, the repetitions showed in most cases the highest degree of overall similarity with the metabolome of the original study. In addition, we also evaluated the robustness of our metabolomics technique, displayed by constancy of variability in control groups over time. Based on these results, it can be concluded, that metabolomics can reproducibly be applied during toxicological in vivo testing in rats under the conditions applied here.     

Are posterior default-mode networks more robust than anterior default-mode networks? Evidence from resting-state fMRI data analysis

Intrinsic brain activity known as default-mode networks (DMNs) has been observed predominantly within the medial/superior frontal areas, anterior/posterior cingulate gyri, and precuneus using blood-oxygenation-level-dependent (BOLD) functional MRI (fMRI). Despite anecdotal evidence of distinct spatial patterns reflecting neuropsychiatric conditions in these DMNs, rigorous analysis of the characteristic traits of DMNs has been limited in previous studies. In this letter, the reproducibility and potential variability of the anterior and posterior DMNs were evaluated based on individual-level variations in effect sizes, activated areas, and causal interactions. Our results indicated that the DMNs were indeed reproducible between sessions/subjects. Region-specific traits were also observed: the posterior DMN seemed more robust to individual-level variations than the anterior DMN. The proposed analytical methods and reported findings may be useful in the development of a wide range of applications, including those involving clinical populations, which utilize the characteristic traits of DMNs.     

Reproducibility of 24-Hour Combined Multiple Intraluminal Impedance (MII) and pH Measurements in Infants and Children. Evaluation of a Diagnostic Procedure for Gastroesophageal Reflux Disease

Gastroesophageal reflux disease (GERD) is a common disease in infants and children. Prolonged (24-hr) pH monitoring in the esophagus for determination of increased acid exposure has, together with endoscopy, been the only routinely implemented method for GERD diagnosis. The recently introduced multiple intraluminal impedance (MII) provides additional information about the number of both acid and nonacid episodes of retrograde bolus movement in the esophagus. The aim of this study was to investigate the day-to-day reproducibility and the interobserver variability of 24-hr combined MII (number of nonacid and acidic reflux episodes) and pH in the esophagus in infants and children. Upper endoscopy followed by 2 × 24-hr consecutive combined MII and pH monitoring was performed in 33 infants and children referred to a tertiary center for evaluation of GERD. The study was performed in a hospital setting without dietary restrictions. Bland-Altman difference versus mean plots and calculation of the limits of agreement (LOA) were used for assessment of the reproducibility of the total number of acidic and nonacidic reflux episodes. LOA for the number of acidic reflux episodes on day 2 were 0.2–5.3 times the value obtained on day 1. For the total number of nonacidic reflux episodes, LOA were 0.04–8.6; for the total number of reflux episodes, 0.3–3.3. An abnormal reflux index on one or both recording days was found in 7 of 30 patients. In conclusion, considerable day-to-day variability was found for nonacidic reflux episodes. Less variability was found for acidic reflux episodes. This variability must be taken into consideration for the use of MII in the clinical evaluation of infants and children with GERD.     

Assessment of intra- and interobserver reproducibility of rest and cold pressor test-stimulated myocardial blood flow with <Superscript>13</Superscript>N-ammonia and PET

Purpose We investigated the intraobserver reproducibility of myocardial blood flow (MBF) measurements with PET at rest and during cold pressor test (CPT), and the interobserver agreement. Methods Twenty normal volunteers were studied. Using ¹³N-ammonia, MBF was measured at rest and during CPT and measurement was repeated in a 1-day session (short-term reproducibility; SR). After a follow-up of 2 weeks, MBF was measured again at rest and during CPT and compared with the initial baseline measurement (long-term reproducibility; LR). In addition, adenosine-induced hyperemic MBF increases were assessed. Results Assessment of the SR did not show a significant absolute difference in MBF at rest, MBF during CPT or the endothelium-related change in MBF from rest to CPT (ΔMBF) (0.09 ± 0.10, 0.11 ± 0.09, and 0.08 ± 0.05 ml/g/min; p = NS), and they were linearly correlated (r = 0.72, r = 0.76 and r = 0.84; p < 0.0001). Corresponding values for standard error of the estimate (SEE), as indicative for the range of MBF measurement error, were 0.14, 0.14, and 0.09 ml/g/min. The LR yielded relatively higher but non-significant absolute differences in the MBF at rest, MBF during CPT and ΔMBF (0.10 ± 0.10, 0.14 ± 0.10, and 0.19 ± 0.10 ml/g/min; p = NS), and paired MBFs significantly correlated (r = 0.75, r = 0.71, and r = 0.60; p < 0.001). Corresponding SEEs were 0.13, 0.15, and 0.16 ml/g/min. The interobserver analysis yielded a high correlation for MBF at rest, MBF during CPT, and hyperemic MBF (r = 0.96, SEE=0.04; r = 0.78, SEE=0.11; and r = 0.87, SEE=0.28; p < 0.0001, respectively), and also a good interobserver correlation for ΔMBF (r = 0.62, SEE=0.09; p < 0.003). Conclusion Short- and long-term MBF responses to CPT, as an index for endothelium-related coronary vasomotion, can be measured reproducibly with ¹³N-ammonia PET. In addition, the high interobserver reproducibility for repeat analysis of MBF values suggests the measurements to be largely operator independent. Thomas H. Schindler and Xiao-Li Zhang contributed equally to this paper.     

Within-person variability in urinary bisphenol A concentrations: Measurements from specimens after long-term frozen storage

Background

Bisphenol A (BPA) is an estrogenic contaminant of food and water associated with adverse developmental effects in laboratory animals. BPA has recently been linked to morbidity in adult humans, but studies of developmental effects in humans are methodologically more difficult. The ability to measure BPA in urine samples after long-term storage could aid in such studies. Because the half-life of BPA is <6 h, a single measurement would be useful only if the environmental exposure is relatively constant over weeks or months. Our aims were to evaluate the stability of BPA in specimens after 22-24 years of storage and to measure within-person temporal variability in urinary BPA.

Methods

We measured total BPA concentration by mass spectrometry in first-morning urine samples from 60 premenopausal women. We selected from each woman's stored daily collections three urine samples approximately 2 and 4 weeks apart. Samples were selected from both the follicular and luteal phases of the menstrual cycle to assess cycle effects. Temporal variability was assessed with mixed model regression and correlations.

Results

BPA levels had an inter-quartile range from 1.1 to 3.1 ng/mg creatinine, slightly higher than levels in specimens from NHANES collected 3-11 years later. The Spearman correlation was approximately 0.5 for samples 2 weeks apart and 0.3 for samples 4 weeks apart. Menstrual cycle phase did not influence levels. BPA tended to increase during the three-year collection period, but not significantly.

Conclusions

The similar distribution to NHANES samples and correlation of BPA levels taken at 2-week intervals provide indirect evidence that BPA is relatively stable during long-term freezer storage. The correlations indicate generally stable exposures over periods of weeks. These findings suggest that developmental effects of BPA exposure could be investigated with measurements from stored urine.     

Reproducibility and Angle Independence of Electromechanical Wave Imaging for the Measurement of Electromechanical Activation during Sinus Rhythm in Healthy Humans

Electromechanical wave imaging (EWI) is an ultrasound-based technique that can non-invasively map the transmural electromechanical activation in all four cardiac chambers in vivo. The objective of this study was to determine the reproducibility and angle independence of EWI for the assessment of electromechanical activation during normal sinus rhythm (NSR) in healthy humans. Acquisitions were performed transthoracically at 2000 frames/s on seven healthy human hearts in parasternal long-axis, apical four- and two-chamber views. EWI data was collected twice successively in each view in all subjects, while four successive acquisitions were obtained in one case. Activation maps were generated and compared (i) within the same acquisition across consecutive cardiac cycles; (ii) within same view across successive acquisitions; and (iii) within equivalent left-ventricular regions across different views. EWI was capable of characterizing electromechanical activation during NSR and of reliably obtaining similar patterns of activation. For consecutive heart cycles, the average 2-D correlation coefficient between the two isochrones across the seven subjects was 0.9893, with a mean average activation time fluctuation in LV wall segments across acquisitions of 6.19%. A mean activation time variability of 12% was obtained across different views with a measurement bias of only 3.2 ms. These findings indicate that EWI can map the electromechanical activation during NSR in human hearts in transthoracic echocardiography in vivo and results in reproducible and angle-independent activation maps.     

Reproducibility of bone mineral density measurements using dual X-ray absorptiometry in daily clinical practice

Bone mineral density (BMD) measurements are frequently performed repeatedly for each patient. Subsequent BMD measurements allow reproducibility to be assessed. Previous studies have suggested that reproducibility may be influenced by age and clinical status. The purpose of the study was to examine the reproducibility of BMD by dual energy X-ray absorptiometry (DXA) and to investigate the practical value of different measures of reproducibility in three distinct groups of subjects: healthy young volunteers, postmenopausal women and patients with chronic rheumatic diseases. Two hundred twenty-two subjects underwent two subsequent BMD measurements of the spine and hip. There were 60 young healthy subjects, 102 postmenopausal women and 60 patients with chronic rheumatic diseases (33 rheumatoid arthritis, 10 ankylosing spondylitis and 10 other systemic diseases). Forty-five patients (75%) among the third group were receiving corticosteroids. Reproducibility was expressed as the smallest detectable difference (SDD), coefficient of variation (CV), least significant change (LSC) and intraclass correlation coefficient (ICC). Sources of variation were investigated by linear regression analysis. The median interval between measurements was 0 days (range 0–7). The mean difference (SD) between the measurements (g/cm²) was –0.0001 (±0.003) and –0.0004 (±0.002) at L1-L4 and the total hip, respectively. At L1-L4 and the total hip, SDD (g/cm²) was ±0.04 and ±0.02, CV (%) was 2.02 and 1.29, and LSC (%) 5.60 and 3.56, respectively. The ICC at the spine and hip was 0.99 and 0.99, respectively. Only a minimal difference existed between the groups. Reproducibility in the three groups studied was good. In a repeated DXA scan, a BMD change, the least significant change (LSC) or the SDD should be regarded as significant. Use of the SDD is preferable to use of the CV and LSC because of its independence from BMD and its expression in absolute units. Expressed as SDD, a BMD change of at least ±0.04 g/cm² at L1-L4 and ±0.02 g/cm² at the total hip should be considered significant. This reproducibility seems independent from age and clinical status and improved in the hips by measuring the dual femur.