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PubMed2005

Evaluation of linkage disequilibrium and its effect on non-parametric multipoint linkage analysis using two high density single-nucleotide polymorphism mapping panels.

Genotype data from the Illumina Linkage III SNP panel (n = 4,720 SNPs) and the Affymetrix 10 k mapping array (n = 11,120 SNPs) were used to test the effects of linkage disequilibrium (LD) between SNPs in a linkage analysis in the Collaborative Study on the Genetics of Alcoholism pedigree collection (143 pedigrees; 1,614 individuals). The average r2 between adjacent markers across the genetic map was 0.099 +/- 0.003 in the Illumina III panel and 0.17 +/- 0.003 in the Affymetrix 10 k array. In order to determine the effect of LD between marker loci in a nonparametric multipoint linkage analysis, markers in strong LD with another marker (r2 > 0.40) were removed (n = 471 loci in the Illumina panel; n = 1,804 loci in the Affymetrix panel) and the linkage analysis results were compared to the results using the entire marker sets. In all analyses using the ALDX1 phenotype, 8 linkage regions on 5 chromosomes (2, 7, 10, 11, X) were detected (peak markers p < 0.01), and the Illumina panel detected an additional region on chromosome 6. Analysis of the same pedigree set and ALDX1 phenotype using short tandem repeat markers (STRs) resulted in 3 linkage regions on 3 chromosomes (peak markers p < 0.01). These results suggest that in this pedigree set, LD between loci with spacing similar to the SNP panels tested may not significantly affect the overall detection of linkage regions in a genome scan. Moreover, since the data quality and information content are greatly improved in the SNP panels over STR genotyping methods, new linkage regions may be identified due to higher information content and data quality in a dense SNP linkage panel.

Alcoholism↗

PubMed1997

Improving information management in family practice: testing an adult learning model.

Information management training has been neglected in family practice in the UK in the past. An adult learning model for such training is introduced. A pilot study using the adult learning approach showed improvements in information management processes over the six-month study period. The research project described in this paper compares the effectiveness of on-site training using adult learning methods, written information, and no intervention, in 33 family practices in the UK. Nine of the eleven practices in the on-site training group completed the training sessions and eight provided full data, whereas only one of the eleven practices in the written information group, and only one of the eleven practices in the control group provided full data. Preliminary analysis demonstrates that on-site training practices made considerable changes to the information systems in their practices, and appreciated the importance of high-quality data, both for patient care and reporting requirements. Full comparisons of data quality and information management methods are presented, and an assessment of priority training needs for maximum benefit is made.

Adult↗

PubMed2005

Antioxidants for preventing pre-eclampsia.

BACKGROUND: Oxidative stress has been proposed as a key factor involved in the development of pre-eclampsia. Supplementing women with antioxidants during pregnancy may help to counteract oxidative stress and thereby prevent or delay the onset of pre-eclampsia. OBJECTIVES: To determine the effectiveness and safety of any antioxidant supplementation during pregnancy and the risk of developing pre-eclampsia and its related complications. SEARCH STRATEGY: We searched the Cochrane Pregnancy and Childbirth Group Trials Register (June 2004) and the Cochrane Central Register of Controlled Trials (The Cochrane Library, Issue 3, 2004). SELECTION CRITERIA: All randomised and quasi-randomised trials comparing one or more antioxidants with either placebo or no antioxidants during pregnancy for the prevention of pre-eclampsia, and trials comparing one or more antioxidants with another, or with other interventions. DATA COLLECTION AND ANALYSIS: Two review authors independently assessed trials for inclusion, data extraction and trial quality. Data were double-entered into the Review Manager software. MAIN RESULTS: Seven trials involving 6082 women are included in this review. The largest trial (5021 women) was quasi-random and only three of the seven included trials were rated high quality. Supplementing women with any antioxidants during pregnancy compared with control or placebo was associated with a 39% reduction in the risk of pre-eclampsia (relative risk (RR) 0.61, 95% confidence intervals (CI) 0.50 to 0.75, seven trials, 6082 women). Women receiving antioxidants compared with control or placebo also had a reduced risk of having a small-for-gestational-age infant (RR 0.64, 95% CI 0.47 to 0.87, three trials, 634 women), their infants had a greater mean birthweight (weighted mean difference 91.83 g, 95% CI 11.55 to 172.11, three trials, 451 women), but they were more likely to give birth preterm (RR 1.38, 95% CI 1.04 to 1.82, three trials, 583 women). There were insufficient data for reliable conclusions about possible effects on any other outcomes. AUTHORS' CONCLUSIONS: These results should be interpreted with caution, as most of the data come from poor quality studies. Nevertheless, antioxidant supplementation seems to reduce the risk of pre-eclampsia. There also appears to be a reduction in the risk of having a small-for-gestational-age baby associated with antioxidants, although there is an increase in the risk of preterm birth. Several large trials are ongoing, and the results of these are needed before antioxidants can be recommended for clinical practice.

Antioxidants↗

PubMed2026

Comprehensive evaluation of new sequencer T20 and well-established T7 with 507 human samples.

The DNBSEQ-T20×2 (T20) sequencer, developed by MGI Tech, enables cost-effective human whole-genome sequencing (WGS) at 30× coverage for less than $100 per genome. Here, we evaluate the sequencing performance and data quality of the T20 platform by benchmarking it against the established DNBSEQ-T7 (T7) sequencer using 507 samples derived from blood (N = 75), stool (N = 242), and saliva (N = 190). The T20 exhibited lower sequencing quality metrics compared with the T7, with Q20 scores of 95.76%-95.83% and Q30 scores of 87.25%-87.40%, compared with 97.81%-97.93% and 93.26%-93.60%, respectively, for T7 data. Quality differences were more evident toward the end of reads, and PCR-free libraries sequenced on the T20 showed similar reductions in quality scores. The median empirical base error rate estimated from 102 ZymoBIOMICS samples was 0.33%. The T20 demonstrated comparable coverage uniformity to the T7 and showed high concordance in microbiome composition analysis, with a median Bray-Curtis dissimilarity of 0.02. Variant calling performance was highly consistent between the two platforms. Among variants with non-missing genotype calls on both platforms, 94.92% of SNPs and 87.20% of InDels showed concordant genotypes between T20 and T7. Overall, the T20 delivers reliable sequencing accuracy and reproducibility for large-scale genomic and microbiome studies, providing a cost-effective alternative for high-throughput sequencing applications.

Metagenomics↗

PubMed2003

Can patients with osteoporosis, who should benefit from implementation of the national service framework for older people, be identified from general practice computer records? A pilot study that illustrates the variability of computerized medical records and problems with searching them.

Although UK general practice is highly computerized, comprehensive use of these computers is often limited to registration data and the issue of repeat prescriptions. The recording of diagnostic data is patchy. This study examines whether patients with, or at risk of, osteoporosis can be readily identified from general practice computer records. It reports the findings of a pilot study designed to show the variability of recording the diagnosis of osteoporosis and osteopenia, as well as how useful surrogate markers might be to identify these patients. The study also illustrates the difficulties that even skilled practitioners in a primary care research network experience in extracting clinical data from practice information systems. Computer searches were carried out across six practices in a general practice research network in the south-east of England. Two of these practices had previously undertaken research projects in osteoporosis and were consequently expected to have excellent data quality in osteoporosis. These two practices had a combined list size of 27,500 and the remaining practices had a combined practice population of 43,000 patients. The data were found to be variable with over 10-fold differences between practices in the recorded prevalence of osteoporosis diagnosis as well as its surrogate markers-such as fragility fractures, long-term steroid prescription, etc. There was no difference in data quality between the two practices that had conducted osteoporosis research and the rest of the group, other than in the areas of diagnostic recording and prescribing for osteoporosis and recording of fractures. Issues were raised by the practices that struggled to identify patients at risk of osteoporosis about the limitations of Read classification in this disease area. Practices need further assistance if the patients at risk are to be identified. Without urgent action, it will be difficult for practices to identify the patients who are likely to benefit from Standard 6-'Falls' of the National Service Framework for Older People. These findings also have broader implications as UK general practice moves towards the implementation of a quality-based contract.

Aged↗

PubMed2005

Scatterscore: a reconnaissance method to evaluate changes in water quality.

Water quality data collected in periodic monitoring programs are often difficult to evaluate, especially if the number of parameters is large, the sampling schedule varies, and values are of different orders of magnitude. The Scatterscore Water Quality Evaluation was developed to yield a quantitative score, based on all measured variables in periodic water quality reports, indicating positive, negative or random change. This new methodology calculates a reconnaissance score based on the differences between up-gradient (control) versus down-gradient (treatment) water quality data sets. All parameters measured over a period of time at two or more sampling points are compared. The relationship between the ranges of measured values and the ratio of the medians for each parameter produces a data point that falls into one of four sections on a scattergram. The number and average values of positive, negative and random change points is used to calculate a Scatterscore that indicates the magnitude and direction of overall change in water quality. The Scatterscore Water Quality Evaluation, a reconnaissance method to track general changes, has been applied to 20 sites at which coal utilization by-products (CUB) were used to control acid mine drainage (AMD).

Coal↗

PubMed2005

Top-down identification of endogenous peptides up to 9 kDa in cerebrospinal fluid and brain tissue by nanoelectrospray quadrupole time-of-flight tandem mass spectrometry.

Recent work on protein and peptide biomarker patterns revealed the difficulties in identifying their molecular components, which is indispensable for validation of the biological context. Cerebrospinal fluid and brain tissue are used as sources to discover new biomarkers, e.g. for neurodegenerative diseases. Many of these biomarker candidates are peptides with a molecular mass of <10 kDa. Their identification is favourably achieved with a 'top-down' approach, because this requires less purification and an enzymatic cleavage will often not yield enough specific fragments for successful database searches. Here, we describe an approach using quadrupole time-of-flight mass spectrometry (TOFMS) as a highly efficient mass spectrometric purification and identification tool after off-line decomplexation of biological samples by liquid chromatography. After initial peptidomic screening with matrix-assisted laser desorption/ionization (MALDI) TOFMS, the elution behaviour in chromatography and the exact molecular mass were used to locate the same signals in nanoelectrospray measurements. Most of the peaks detected in MALDI-TOFMS could be retrieved in nanoelectrospray quadrupole TOFMS. Suitable collision energies for informative fragment spectra were investigated for different parent ions, charge states and molecular masses. After collision-induced dissociation, the resulting fragmentation data of multiply charged ions can become much more complicated than those derived from tryptic peptide digests. However, the mass accuracy and resolution of quadrupole TOF instruments results in high-quality data suitable for determining peptide sequences. The protein precursor, proteolytic processing and post-translational modifications were identified by automated database searches. This is demonstrated by the exemplary identifications of thymosin beta-4 (5.0 kDa) and NPY (4.3 kDa) from rat hypothalamic tissue and ubiquitin (8.6 kDa) from human cerebrospinal fluid. The high data quality should also allow for de novo identification. This methodology is generally applicable for peptides up to a molecular mass of about 10 kDa from body fluids, tissues or other biological sources.

Amino Acid Sequence↗

PubMed1992

World Health Organization international intercalibration study on dioxins and furans in human milk and blood.

Under the sponsorship of the World Health Organization (WHO), an interlaboratory calibration on the analysis of PCDD/PCDFs in human milk and blood was carried out which included 19 laboratories from 14 countries. The study design involved the analysis of three samples of each matrix in triplicate. Selected samples were spiked with native standards of certain 2,3,7,8-substituted congeners at concentrations known only to WHO staff. The study design resulted in approximately 4000 individual pieces of PCDD/PCDF data generated by a variety of analytical methods, at various concentrations, and by laboratories of widely different experience. This was, by considerable margin, the largest study which allowed for the direct comparison of laboratory and method performance. The results of statistical analysis of this data base addresses the effect on data quality of clean up methods, instrumental methods, analyte concentration, laboratory QA programs, and laboratory experience. The study has shown that the laboratory is the single most important determinant of data precision and accuracy. The method of analyte enrichment (sample clean up), analyte measurement [gas chromatography/mass spectrometry (GC/MS) protocol], and analyte concentration have weaker correlations with data quality.

Chromatography, Gas↗

PubMed2005

Validation of surgical site infection surveillance data in Scotland.

Validation of surveillance data is necessary to ensure its scientific credibility, to identify methodological problems within the surveillance programme, to help increase compliance and participation in the surveillance programme, and to identify data quality issues at local level. Surgical site infection surveillance (SSIS) in Scotland has been implemented in collaboration between Health Protection Scotland (HPS) and staff in acute divisions in Scotland. A team at HPS carried out a study to validate the SSIS data reported to them. The aims of the validation study were: (i) to measure the completeness of the denominator data; (ii) to measure the accuracy of all SSIS data items reported to HPS; and (iii) to determine the sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of the SSIs reported to HPS against the SSIs validated as part of this study. The methodology utilized for validation of SSIS data was based on an evaluation research approach. The evaluation research approach involves a range of investigative activities, aimed at judging the worth of a programme or practice, and measures SSIS in terms of structure, process and outcome. The completeness of the denominator and the means of identifying eligible patients was identified. Descriptive information about how SSIS data were collected and managed at hospital level was collated, and the accuracy and completeness of the reported SSIS data were measured by case note review of selected cases. SSIS data from 27 hospitals in 15 acute divisions and one special health board were validated. The results indicated that a total of 91% of the procedures carried out (denominator) during a specified three-month period were reported to HPS. The case notes validated over 90% of records reported to HPS; however, there was variation in data quality between hospitals. The sensitivity, specificity, PPV and NPV of the SSIs reported to HPS were 96.7, 99.0, 94.6 and 99.4%, respectively. Where problems with data were identified at local level, hospitals have been offered guidance to improve their data. As a result of this study, HPS are confident that the Scottish SSIS data are reliable and robust.

Cross Infection↗

PubMed2000

Method enabling pyrosequencing on double-stranded DNA.

Pyrosequencing is a new nonelectrophoretic, single-tube DNA sequencing method that takes advantage of co-operativity between four enzymes to monitor DNA synthesis (M. Ronaghi, M. Uhlén, and P. Nyrén, Science 281, 363-365). Pyrosequencing has so far only been performed on single-stranded DNA. In this paper different enzymatic strategies for template preparation enabling pyrosequencing on double-stranded DNA were studied. High quality data were obtained with several different enzyme combinations: (i) shrimp alkaline phosphatase and exonuclease I, (ii) calf intestine alkaline phosphatase and exonuclease I, (iii) apyrase and inorganic pyrophosphatase together with exonuclease I, and (iv) apyrase and ATP sulfurylase together with exonuclease I. In many cases, when the polymerase chain reaction was efficient exonuclease I could be omitted. In certain cases, additives such as dimethyl sulfoxide, single-stranded DNA-binding protein, and Klenow DNA polymerase improved the sequence quality. Apyrase was the fastest and most efficient of the three different nucleotide degrading enzymes tested. The data quality obtained on double-stranded DNA was comparable with that on single-stranded DNA. Pyrosequencing data for more than 30 bases could be generated on both long and short templates, as well as on templates with high GC content.

Alkaline Phosphatase↗

PubMed1993

[Structured documentation of findings and user acceptance--results of a study of abdominal ultrasound].

Structured reporting of medical findings is known to have positive effects on data quality, whereas user acceptance tends to be low because of time requirements. This paper presents the results of a survey among 19 physicians who worked for 14 months with a computer system using structured data input for abdominal ultrasonography. During this time, they prepared 8.827 reports. The two most important results are that it is feasible to realize well accepted documentation systems with high data quality by using modern computer technology, and that graphic user interfaces tend to increase user acceptance. For comparable systems, evaluation studies are suggested.

Attitude of Health Personnel↗

PubMed2000

Assessing the potential carcinogenic activity of magnetic fields using animal models.

We update our 1997 publication by reviewing 29 new reports of tests of magnetic fields (MFs) in six different in vivo animal models of carcinogenesis: 2-year, lifetime, or multigeneration exposure studies in rats or mice; and promotion/progression models (rat mammary carcinoma, rat liver focus, mouse skin, several models of human leukemia/lymphoma in rats and mice, and brain cancer in rats). Individual experiments are evaluated using a set of data quality criteria, and summary judgments are made across multiple experiments by applying a criterion of rough reproducibility. The potential for carcinogenicity of MFs is discussed in light of the significant body of carcinogenesis data from animal bioassays that now exists. Excluding abstracts, approximately 80% of the 41 completed studies identified in this and our previous review roughly satisfy data quality criteria. Among these studies, the criterion for independent reproducibility is not satisfied for any positive results but is satisfied for negative results in chronic bioassays in rats and mice and for negative results in both promotion and co-promotion assays using the SENCAR mouse skin model. Results of independent replication studies using the rat mammary carcinoma model were conflicting. We conclude that long-term exposure to continuous 50- or 60-Hz MFs in the range of 0.002-5 mT is unlikely to result in carcinogenesis in rats or mice. Though results of most promotion/progression assays are negative, a weak promoting effect of MFs under certain exposure conditions cannot be ruled out based on available data.

Animals↗

PubMed2002

Comparing hospital discharge records with death certificates: can the differences be explained?

STUDY OBJECTIVE: The quality of mortality statistics is important for epidemiological research. Considerable discrepancies have been reported between death certificates and corresponding hospital discharge records. This study examines whether differences between the death certificate's underlying cause of death and the main condition from the final hospital discharge record can be explained by differences in ICD selection procedures. The authors also discuss the implications of unexplained differences for mortality data quality. DESIGN: Using ACME, a standard software for the selection of underlying cause of death, the compatibility between the underlying cause of death and the final main condition was examined. The study also investigates whether data available in the hospital discharge record, but not reported on the death certificate, influence the selection of the underlying cause of death. SETTING: Swedish death certificates for 1995 were linked to the national hospital discharge register. The resulting database comprised 69 818 people who had been hospitalised during their final year of life. MAIN RESULTS: The underlying cause of death and the main condition differed at Basic Tabulation List level in 54% of the deaths. One third of the differences could not be explained by ICD selection procedures. Adding hospital discharge data changed the underlying cause in 11% of deaths. For some causes of death, including medical misadventures and accidental falls, the effect was substantial. CONCLUSION: Most differences between underlying cause of death and final main condition can be explained by differences in ICD selection procedures. Further research is needed to investigate whether unexplained differences indicate lower data quality.

Adolescent↗

PubMed1979

A comparison of mail, telephone, and home interview strategies for household health surveys.

The method of data collection in household health surveys can be a major determinant of cost and data quality. A survey strategy can comprise mail, telephone, or home interview methods, individually or in combination to follow up non-respondents. The purpose of this study in Montreal was to compare cost and data quality of various strategies. Strategies which began with mail or telephone contact, followed by the two other methods, provided response rates as high as a home interview strategy (all between 80 and 90 per cent), for one-half the cost of home interviews when used as the sole method. The telephone response rate was higher than the mail response rate. Comparing different follow-up approaches to strategies beginning with mail or telephone, it proved less costly, and equally effective, to use home interviewing as a last resort for persistent non-respondents. Validity of response (comparing individual responses with records of a government health insurance data bank) and willingness to answer sensitive questions were greatest in mail strategy.

Canada↗

PubMed1999

Quality of HMO vaccination databases used to monitor childhood vaccine safety. Vaccine Safety DataLink Team.

The availability of large, population-based, automated, medical care databases provides unique opportunities for monitoring the safety of childhood vaccines. The authors assessed the quality of automated vaccination databases by comparing them with vaccinations documented in paper-based medical records at three large US West Coast health maintenance organizations (HMOs) participating in the Vaccine Safety DataLink (VSD) study, a Centers for Disease Control and Prevention collaborative study of childhood vaccine safety. The authors randomly selected 1% or 2% samples of VSD study populations (n = 1,224-2,577) for data quality analyses. Agreement between automated and abstracted vaccinations required identical triads of child identification number, vaccination date, and vaccine type. Separate analyses were conducted for each HMO and for each vaccine type administered between 1991 and 1995. Agreement was measured by three matching proportions: 1) the proportion of automated vaccinations present in the abstracted source, 2) the proportion of abstracted vaccinations present in the automated source, and 3) the proportion of vaccinations from either source present in both sources. Overall, for common childhood vaccines, proportion 1 ranged from 83% to 99%, proportion 2 ranged from 82% to 98%, and proportion 3 ranged from 70% to 97%. Lack of automated data was the most frequent type of discrepancy, followed by date mismatches and vaccine type mismatches. Vaccination exposure classification errors in the range reported here were found by mathematical modeling to only modestly bias measured medical outcome rate ratios toward the null hypothesis. The results of the data quality analyses support the usefulness of vaccination exposure data derived from these automated HMO vaccination databases.

Abstracting and Indexing↗

PubMed2001

Web survey design and administration.

Many claims are being made about the advantages of conducting surveys on the Web. However, there has been little research on the effects of format or design on the levels of unit and item response or on data quality. In a study conducted at the University of Michigan, a number of experiments were added to a survey of the student population to assess the impact of design features on resulting data quality. A sample of 1,602 students was sent an e-mail invitation to participate in a Web survey on attitudes toward affirmative action. Three experiments on design approaches were added to the survey application. One experiment varied whether respondents were reminded of their progress through the instrument. In a second experiment, one version presented several related items on one screen, while the other version presented one question per screen. In a third experiment, for one series of questions a random half of the sample clicked radio buttons to indicate their answers, while the other half entered a numeric response in a box. This article discusses the overall implementation and outcome of the survey, and it describes the results of the imbedded design experiments.

Journal Article↗

PubMed2001

Validation of satellite data for quality assurance in lake monitoring applications.

The operational application of remote sensing technologies to lake water quality monitoring requires products derived from remote sensing to be quantitatively self-consistent and have a certified accuracy. Fundamental elements in this quality assurance framework are sensor radiometric calibration and atmospheric correction models, which are briefly discussed in the paper. In order to evaluate the accuracy of present operational techniques to retrieve basic parameters from satellite data, such as water-leaving radiance and reflectance, an experiment was organised in the frame of SAtellite remote sensing for Lake MONitoring (SALMON), a European Union co-funded research project. A series of ship-based radiometric and atmospheric measuring campaigns were conducted on Lake Iseo and Lake Garda (Italy) together with limnological sampling. Four Landsat-5 Thematic Mapper (TM) scenes were acquired during different seasons and simultaneous in situ measurements were made. After the radiometric calibration procedure, satellite digital images were processed by applying two entirely image-based atmospheric correction models. These models account for the effects of both additive scattering and multiplicative transmittance effects in the atmosphere on the at-satellite measured signal. The results achieved using these procedures were evaluated by comparing satellite-based estimates with in situ measurements of water reflectance. The root mean square difference between Landsat TM-derived reflectance values and ground measurements was close to 0.010 reflectance for each TM spectral band. Such image-based correction models, requiring no in situ field measurements during the satellite overpass, constitute a valid method of lake water monitoring.

Atmosphere↗

PubMed2004

Validation study of the TrueAllele automated data review system.

The New York State Convicted Offender DNA Databank is the first U.S. lab to complete an internal validation of the TrueAllele expert data review system. TrueAllele is designed to assess short tandem repeat (STR) DNA data based on several key features such as peak height, shape, area, and position relative to a standard ladder and use this information to make accurate allele calls. The software then prioritizes the allele calls based on several user-defined rules. As a result, the user need only review low-quality data. The validation of this system consisted of an extensive optimization phase and a large concordance phase. During optimization, the rule settings were tailored to minimize the amount of high-quality data viewed by the user. In the concordance phase, a large dataset was typed in parallel with the ABI software Gene Scan and Genotyper (manual review) and TrueAllele (automated review) for comparison of allele calls and sample state assignment. Only one significant difference was discovered out of 2048 samples in the concordance study. In this case, TrueAllele revealed a spike in the profile that was interpreted as a DNA peak by the analyst in Genotyper. TrueAllele was designed to focus the review on poor data and to eliminate the need for complete reanalysis technical review. This validation project proved TrueAllele to be dependable for use at the NYS Convicted Offender DNA Databank.

Alleles↗