ResearchPad - quality-control https://www.researchpad.co Default RSS Feed en-us © 2020 Newgen KnowledgeWorks <![CDATA[Proficiency based progression simulation training significantly reduces utility strikes; A prospective, randomized and blinded study]]> https://www.researchpad.co/article/elastic_article_7871 We evaluated a simulation-based training curriculum with quantitatively defined performance benchmarks for utility workers location and excavation of utility services.BackgroundDamaging buried utilities is associated with considerable safety risks to workers and substantial cost to employers.MethodsIn a prospective, randomized and blinded study we assessed the impact of Proficiency Based Progression (PBP) simulation training on the location and excavation of utility services work.ResultsPBP simulation training reduced performance errors (33%, p = 0.006) in comparison a standard trained group. When implemented across all workers in the same division there was a 35–61% reduction in utility strikes (p = 0.028) and an estimated cost saving of £116,000 –£2,175,000 in the 12 months (47,000 work hours) studied.ConclusionsThe magnitude of the training benefit of PBP simulation training in the utilities sector appears to be the same as it is in surgery, cardiology and procedure-based medicine.ApplicationQuality-assured utility worker simulation training significantly reduces utility damage and associated costs. ]]> <![CDATA[A field test on the effectiveness of male annihilation technique against Bactrocera dorsalis (Diptera: Tephritidae) at varying application densities]]> https://www.researchpad.co/article/5c8c1939d5eed0c484b4d1d4

Male Annihilation Technique (MAT) is a key tool to suppress or eradicate pestiferous tephritid fruit flies for which there exist powerful male lures. In the case of Bactrocera dorsalis (Hendel), a highly invasive and destructive species, current implementations of MAT utilize a combination of the male attractant methyl eugenol (ME) and a toxicant such as spinosad (“SPLAT-MAT-ME”) applied at a high density with the goal of attracting and killing an extremely high proportion of males. We conducted direct comparisons of trap captures of marked B. dorsalis males released under three experimental SPLAT-MAT-ME site densities (110, 220, and 440 per km2) near Hilo, Hawaii using both fresh and aged traps to evaluate the effectiveness of varying densities and how weathering of the SPLAT-MAT-ME formulation influenced any density effects observed. Counterintuitively, we observed decreasing effectiveness (percent kill) with increasing application density. We also estimated slightly higher average kill for any given density for weathered grids compared with fresh. Spatial analysis of the recapture patterns of the first trap service per replicate x treatment reveals similar positional effects for all grid densities despite differences in overall percent kill. This study suggests that benefits for control and eradication programs would result from reducing the application density of MAT against B. dorsalis through reduced material use, labor costs, and higher effectiveness. Additional research in areas where MAT programs are currently undertaken would be helpful to corroborate this study’s findings.

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<![CDATA[The Ayushman Bharat Pradhan Mantri Jan Arogya Yojana and the path to universal health coverage in India: Overcoming the challenges of stewardship and governance]]> https://www.researchpad.co/article/5c8acc3bd5eed0c48498f23f

In an Essay, Blake Angell and colleagues discuss ambitious reforms planned to expand coverage of the health system in India.

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<![CDATA[Late-life mortality is underestimated because of data errors]]> https://www.researchpad.co/article/5c65dcdbd5eed0c484dec3bf

Knowledge of true mortality trajectory at extreme old ages is important for biologists who test their theories of aging with demographic data. Studies using both simulation and direct age validation found that longevity records for ages 105 years and older are often incorrect and may lead to spurious mortality deceleration and mortality plateau. After age 105 years, longevity claims should be considered as extraordinary claims that require extraordinary evidence. Traditional methods of data cleaning and data quality control are just not sufficient. New, more strict methodologies of data quality control need to be developed and tested. Before this happens, all mortality estimates for ages above 105 years should be treated with caution.

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<![CDATA[Automated localization and quality control of the aorta in cine CMR can significantly accelerate processing of the UK Biobank population data]]> https://www.researchpad.co/article/5c6f151bd5eed0c48467adda

Introduction

Aortic distensibility can be calculated using semi-automated methods to segment the aortic lumen on cine CMR (Cardiovascular Magnetic Resonance) images. However, these methods require visual quality control and manual localization of the region of interest (ROI) of ascending (AA) and proximal descending (PDA) aorta, which limit the analysis in large-scale population-based studies. Using 5100 scans from UK Biobank, this study sought to develop and validate a fully automated method to 1) detect and locate the ROIs of AA and PDA, and 2) provide a quality control mechanism.

Methods

The automated AA and PDA detection-localization algorithm followed these steps: 1) foreground segmentation; 2) detection of candidate ROIs by Circular Hough Transform (CHT); 3) spatial, histogram and shape feature extraction for candidate ROIs; 4) AA and PDA detection using Random Forest (RF); 5) quality control based on RF detection probability. To provide the ground truth, overall image quality (IQ = 0–3 from poor to good) and aortic locations were visually assessed by 13 observers. The automated algorithm was trained on 1200 scans and Dice Similarity Coefficient (DSC) was used to calculate the agreement between ground truth and automatically detected ROIs.

Results

The automated algorithm was tested on 3900 scans. Detection accuracy was 99.4% for AA and 99.8% for PDA. Aorta localization showed excellent agreement with the ground truth, with DSC ≥ 0.9 in 94.8% of AA (DSC = 0.97 ± 0.04) and 99.5% of PDA cases (DSC = 0.98 ± 0.03). AA×PDA detection probabilities could discriminate scans with IQ ≥ 1 from those severely corrupted by artefacts (AUC = 90.6%). If scans with detection probability < 0.75 were excluded (350 scans), the algorithm was able to correctly detect and localize AA and PDA in all the remaining 3550 scans (100% accuracy).

Conclusion

The proposed method for automated AA and PDA localization was extremely accurate and the automatically derived detection probabilities provided a robust mechanism to detect low quality scans for further human review. Applying the proposed localization and quality control techniques promises at least a ten-fold reduction in human involvement without sacrificing any accuracy.

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<![CDATA[A proposal for the future of scientific publishing in the life sciences]]> https://www.researchpad.co/article/5c6c75c2d5eed0c4843d013c

Science advances through rich, scholarly discussion. More than ever before, digital tools allow us to take that dialogue online. To chart a new future for open publishing, we must consider alternatives to the core features of the legacy print publishing system, such as an access paywall and editorial selection before publication. Although journals have their strengths, the traditional approach of selecting articles before publication (“curate first, publish second”) forces a focus on “getting into the right journals,” which can delay dissemination of scientific work, create opportunity costs for pushing science forward, and promote undesirable behaviors among scientists and the institutions that evaluate them. We believe that a “publish first, curate second” approach with the following features would be a strong alternative: authors decide when and what to publish; peer review reports are published, either anonymously or with attribution; and curation occurs after publication, incorporating community feedback and expert judgment to select articles for target audiences and to evaluate whether scientific work has stood the test of time. These proposed changes could optimize publishing practices for the digital age, emphasizing transparency, peer-mediated improvement, and post-publication appraisal of scientific articles.

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<![CDATA[Developing a modern data workflow for regularly updated data]]> https://www.researchpad.co/article/5c59fef0d5eed0c4841357ed

Over the past decade, biology has undergone a data revolution in how researchers collect data and the amount of data being collected. An emerging challenge that has received limited attention in biology is managing, working with, and providing access to data under continual active collection. Regularly updated data present unique challenges in quality assurance and control, data publication, archiving, and reproducibility. We developed a workflow for a long-term ecological study that addresses many of the challenges associated with managing this type of data. We do this by leveraging existing tools to 1) perform quality assurance and control; 2) import, restructure, version, and archive data; 3) rapidly publish new data in ways that ensure appropriate credit to all contributors; and 4) automate most steps in the data pipeline to reduce the time and effort required by researchers. The workflow leverages tools from software development, including version control and continuous integration, to create a modern data management system that automates the pipeline.

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<![CDATA[Cryopreservation of the Mediterranean fruit fly (Diptera: Tephritidae) VIENNA 8 genetic sexing strain: No effect on large scale production of high quality sterile males for SIT applications]]> https://www.researchpad.co/article/5c57e685d5eed0c484ef3571

The sterile insect technique (SIT) integrated in area-wide integrated pest management (AW-IPM) programmes is being used for the successful management of the Mediterranean fruit fly Ceratitis capitata (Wiedemann) (Diptera: Tephritidae) which is a horticultural pest of economic importance in tropical and subtropical countries. All programmes with an SIT component are using the VIENNA genetic sexing strains (GSS), mainly the VIENNA 8 GSS, which have been developed by applying classical genetic approaches. The VIENNA 8 GSS carries two selectable markers, the white pupae and the temperature sensitive lethal genes, which allows the production and release of only males thus increasing the biological efficiency and cost effectiveness of SIT applications. However, mass rearing may affect quality traits of the GSS, in which case replenishment of the colony with wild flies is recommended, a process which is tedious and time consuming. We previously reported the development of a cryopreservation protocol for the VIENNA 8D53+ strain. In the present study, we report on the evaluation of the cryopreserved strain VIENNA 8D53+/Cryo-228L, reared under semi mass rearing conditions, for production parameters, quality control indices and mating competitiveness of males, in a comparative way with the non-cryopreserved VIENNA 8D53+ strain, against wild type males. The VIENNA 8D53+ and VIENNA 8D53+/Cryo-228L strains were similar for production parameters viz. egg production, pupal production, pupal recovery, and quality control indices like fly emergence, sex ratio and flight ability. Males from both strains were equally competitive with males of the wild type strain in achieving mating with wild type females under field cage conditions. Results are discussed in the context of cryopreservation as a potential backup strategy for refreshing the mass rearing colony with biological material from a cryopreserved stock.

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<![CDATA[Deterministic column subset selection for single-cell RNA-Seq]]> https://www.researchpad.co/article/5c64493fd5eed0c484c2f93e

Analysis of single-cell RNA sequencing (scRNA-Seq) data often involves filtering out uninteresting or poorly measured genes and dimensionality reduction to reduce noise and simplify data visualization. However, techniques such as principal components analysis (PCA) fail to preserve non-negativity and sparsity structures present in the original matrices, and the coordinates of projected cells are not easily interpretable. Commonly used thresholding methods to filter genes avoid those pitfalls, but ignore collinearity and covariance in the original matrix. We show that a deterministic column subset selection (DCSS) method possesses many of the favorable properties of common thresholding methods and PCA, while avoiding pitfalls from both. We derive new spectral bounds for DCSS. We apply DCSS to two measures of gene expression from two scRNA-Seq experiments with different clustering workflows, and compare to three thresholding methods. In each case study, the clusters based on the small subset of the complete gene expression profile selected by DCSS are similar to clusters produced from the full set. The resulting clusters are informative for cell type.

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<![CDATA[Determination of blood dexmedetomidine in dried blood spots by LC-MS/MS to screen therapeutic levels in paediatric patients]]> https://www.researchpad.co/article/5c46655ed5eed0c484518d3c

Dexmedetomidine is an imidazole derivative, with high affinity for α2 adrenergic receptors, used for sedation, analgesia and adjuvant anaesthesia. In this study, an analytical method for the quantification of dexmedetomidine in dried blood spots was developed, validated and applied. The drug was extracted from dried blood spot by liquid extraction; the separation was carried out by ultra high-resolution liquid chromatography in reverse phase coupled to tandem mass spectrometry method. An X Select cyano 5 μm HSS column (2.1 X 150 mm, Waters) and a mobile phase composed of 0.1% formic acid: acetonitrile [50:50 v/v], were used. The test was linear over the concentration range of 50 to 2000 pg/mL. The coefficients of variation for the intra and interday trials were less than 15%. The drug was stable under the conditions tested. The method was successfully applied for the quantification of 6 patients, aged 0 to 2 years, with classification ASA I, who underwent ambulatory surgeries, receiving a dose of 1 μg/Kg dexmedetomidine IV. The drug concentrations in the different sampling times were in the range of 76 to 868 pg/mL.

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<![CDATA[Genome wide association study to identify predictors for severe skin toxicity in colorectal cancer patients treated with cetuximab]]> https://www.researchpad.co/article/5c21513cd5eed0c4843f9470

EGFR-antibodies are associated with significant skin toxicity, including acneiform rash and folliculitis. It remains impossible to predict the occurrence of severe skin toxicity due to the lack of predictive markers. Here, we present the first genome-wide association study (GWAS) to find single nucleotide polymorphisms (SNPs) associated with EGFR inhibitor-induced skin toxicity using data of the multicentre randomized phase III CAIRO2 trial (clinicaltrials.gov NCT00208546). In this study, advanced or metastatic colorectal cancer patients were treated with capecitabine, oxaliplatin and bevacizumab with or without cetuximab. Germline DNA was available in 282 of the 368 patients in the cetuximab arm. Mild skin toxicity occurred in 195 patients (i.e. CTC grade 1 or 2, respectively 91 and 104 patients) and severe skin toxicity (i.e. grade 3) in 36 patients. Grade 4 skin toxicity did not occur. None of the SNPs reached the formal genome wide threshold for significance of 5x10-8, though SNPs of at least 8 loci did show moderate association (p-value between 5x10-7 and 5x10-5) with the occurrence of grade 3 (severe) skin toxicity. These SNPs did not overlap with SNPs associated with cetuximab efficacy as found in a previous GWAS in the same CAIRO2 cohort. If formally proven by replication, the SNPs associated with severe EGFR induced skin toxicity may be helpful to predict the occurrence and severity of skin toxicity in patients that will receive cetuximab and allow for adequate information on the risk of skin toxicity and prophylactic measurements.

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<![CDATA[Loop-mediated isothermal amplification (LAMP) and Polymerase Chain Reaction (PCR) as quality assurance tools for Rapid Diagnostic Test (RDT) malaria diagnosis in Northern Namibia]]> https://www.researchpad.co/article/5c1ab81bd5eed0c484026b67

Malaria cases sometimes go undetected using RDTs due to their inaccurate use, poor storage conditions and failure to detect low parasitaemia (<50parasites/μL). This could result in continuous transmission of malaria and sustenance of parasite reservoirs. Molecular diagnostic tools are more sensitive and specific than RDTs in the detection of plasmodium parasites. However, the Polymerase Chain Reaction (PCR) is not routinely used because equipment and reagents are expensive and requires highly skilled personnel. Loop-mediated isothermal amplification (LAMP) is a relatively new molecular diagnostic tool for malaria with all the advantages of PCR (sensitive and specific) without the mentioned disadvantages. However, it has not been evaluated extensively as a point of care diagnostic in the field. One hundred and fifteen used RDTs were collected from health facilities in Northern Namibia in a blind study and PCR and LAMP were used to determine the presence of Plasmodium DNA. The sensitivities and PPV were 40.91% and 90% respectively for RDTs, 72.73% and 100% respectively for PCR with LAMP as the golden standard. In low malaria transmission settings, LAMP can be also be considered for use as a surveillance tool to detect all sources of malaria and determine proportion of low parasitaemia infections in order to eliminate them.

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<![CDATA[Improving the calling of non-invasive prenatal testing on 13-/18-/21-trisomy by support vector machine discrimination]]> https://www.researchpad.co/article/5c117b86d5eed0c48469989c

With the advance of next-generation sequencing (NGS) technologies, non-invasive prenatal testing (NIPT) has been developed and employed in fetal aneuploidy screening on 13-/18-/21-trisomies through detecting cell-free fetal DNA (cffDNA) in maternal blood. Although Z-test is widely used in NIPT NGS data analysis, there is still necessity to improve its accuracy for reducing a) false negatives and false positives, and b) the ratio of unclassified data, so as to lower the potential harm to patients as well as the induced cost of retests. Combining the multiple Z-tests with indexes of clinical signs and quality control, features were collected from the known samples and scaled for model training using support vector machine (SVM). We trained SVM models from the qualified NIPT NGS data that Z-test can discriminate and tested the performance on the data that Z-test cannot discriminate. On screenings of 13-/18-/21-trisomies, the trained SVM models achieved 100% accuracies in both internal validations and unknown sample predictions. It is shown that other machine learning (ML) models can also achieve similar high accuracy, and SVM model is most robust in this study. Moreover, four false positives and four false negatives caused by Z-test were corrected by using the SVM models. To our knowledge, this is one of the earliest studies to employ SVM in NIPT NGS data analysis. It is expected to replace Z-test in clinical practice.

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<![CDATA[Genome-Wide Association Studies of Multiple Keratinocyte Cancers]]> https://www.researchpad.co/article/5989da13ab0ee8fa60b7a4e8

There is strong evidence for a role of environmental risk factors involved in susceptibility to develop multiple keratinocyte cancers (mKCs), but whether genes are also involved in mKCs susceptibility has not been thoroughly investigated. We investigated whether single nucleotide polymorphisms (SNPs) are associated with susceptibility for mKCs. A genome-wide association study (GWAS) of 1,666 cases with mKCs and 1,950 cases with single KC (sKCs; controls) from Harvard cohorts (the Nurses' Health Study [NHS], NHS II, and the Health Professionals Follow-Up Study) and the Framingham Heart Study was carried-out using over 8 million SNPs (stage-1). We sought to replicate the most significant statistical associations (p-value≤ 5.5x10-6) in an independent cohort of 574 mKCs and 872 sKCs from the Rotterdam Study. In the discovery stage, 40 SNPs with suggestive associations (p-value ≤5.5x10-6) were identified, with eight independent SNPs tagging all 40 SNPs. The most significant SNP was located at chromosome 9 (rs7468390; p-value = 3.92x10-7). In stage-2, none of these SNPs replicated and only two of them were associated with mKCs in the same direction in the combined meta-analysis. We tested the associations for 19 previously reported basal cell carcinoma-related SNPs (candidate gene association analysis), and found that rs1805007 (MC1R locus) was significantly associated with risk of mKCs (p-value = 2.80x10-4). Although the suggestive SNPs with susceptibility for mKCs were not replicated, we found that previously identified BCC variants may also be associated with mKC, which the most significant association (rs1805007) located at the MC1R gene.

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<![CDATA[An attribute control chart for a Weibull distribution under accelerated hybrid censoring]]> https://www.researchpad.co/article/5989db4fab0ee8fa60bdbc3a

In this article, an attribute control chart has been proposed using the accelerated hybrid censoring logic for the monitoring of defective items whose life follows a Weibull distribution. The product can be tested by introducing the acceleration factor based on different pressurized conditions such as stress, load, strain, temperature, etc. The control limits are derived based on the binomial distribution, but the fraction defective is expressed only through the shape parameter, the acceleration factor and the test duration constant. Tables of the average run lengths have been generated for different process parameters to assess the performance of the proposed control chart. Simulation studies have been performed for the practical use, where the proposed chart is compared with the Shewhart np chart for demonstration of the detection power of a process shift.

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<![CDATA[Performance Evaluation of the Becton Dickinson FACSPresto™ Near-Patient CD4 Instrument in a Laboratory and Typical Field Clinic Setting in South Africa]]> https://www.researchpad.co/article/5989d9e0ab0ee8fa60b6952f

Background

The BD-FACSPresto CD4 is a new, point-of-care (POC) instrument utilising finger-stick capillary blood sampling. This study evaluated its performance against predicate CD4 testing in South Africa.

Methods

Phase-I testing: HIV+ patient samples (n = 214) were analysed on the Presto under ideal laboratory conditions using venous blood. During Phase-II, 135 patients were capillary-bled for CD4 testing on FACSPresto, performed according to manufacturer instruction. Comparative statistical analyses against predicate PLG/CD4 method and industry standards were done using GraphPad Prism 6. It included Bland-Altman with 95% limits of agreement (LOA) and percentage similarity with coefficient of variation (%CV) analyses for absolute CD4 count (cells/μl) and CD4 percentage of lymphocytes (CD4%).

Results

In Phase-I, 179/217 samples yielded reportable results with Presto using venous blood filled cartridges. Compared to predicate, a mean bias of 40.4±45.8 (LOA of -49.2 to 130.2) and %similarity (%CV) of 106.1%±7.75 (7.3%) was noted for CD4 absolute counts. In Phase-2 field study, 118/135 capillary-bled Presto samples resulted CD4 parameters. Compared to predicate, a mean bias of 50.2±92.8 (LOA of -131.7 to 232) with %similarity (%CV) 105%±10.8 (10.3%), and 2.87±2.7 (LOA of -8.2 to 2.5) with similarity of 94.7±6.5% (6.83%) noted for absolute CD4 and CD4% respectively. No significant clinical differences were indicated for either parameter using two sampling methods.

Conclusion

The Presto produced remarkable precision to predicate methods, irrespective of venous or capillary blood sampling. A consistent, clinically insignificant over-estimation (5–7%) of counts against PLG/CD4 and equivalency to FACSCount was noted. Further field studies are awaited to confirm longer-term use.

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<![CDATA[An Efficient Microarray-Based Genotyping Platform for the Identification of Drug-Resistance Mutations in Majority and Minority Subpopulations of HIV-1 Quasispecies]]> https://www.researchpad.co/article/5989db07ab0ee8fa60bc8c07

The response of human immunodeficiency virus type 1 (HIV-1) quasispecies to antiretroviral therapy is influenced by the ensemble of mutants that composes the evolving population. Low-abundance subpopulations within HIV-1 quasispecies may determine the viral response to the administered drug combinations. However, routine sequencing assays available to clinical laboratories do not recognize HIV-1 minority variants representing less than 25% of the population. Although several alternative and more sensitive genotyping techniques have been developed, including next-generation sequencing (NGS) methods, they are usually very time consuming, expensive and require highly trained personnel, thus becoming unrealistic approaches in daily clinical practice. Here we describe the development and testing of a HIV-1 genotyping DNA microarray that detects and quantifies, in majority and minority viral subpopulations, relevant mutations and amino acid insertions in 42 codons of the pol gene associated with drug- and multidrug-resistance to protease (PR) and reverse transcriptase (RT) inhibitors. A customized bioinformatics protocol has been implemented to analyze the microarray hybridization data by including a new normalization procedure and a stepwise filtering algorithm, which resulted in the highly accurate (96.33%) detection of positive/negative signals. This microarray has been tested with 57 subtype B HIV-1 clinical samples extracted from multi-treated patients, showing an overall identification of 95.53% and 89.24% of the queried PR and RT codons, respectively, and enough sensitivity to detect minority subpopulations representing as low as 5–10% of the total quasispecies. The developed genotyping platform represents an efficient diagnostic and prognostic tool useful to personalize antiviral treatments in clinical practice.

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<![CDATA[Rare Variants in NOD1 Associated with Carotid Bifurcation Intima-Media Thickness in Dominican Republic Families]]> https://www.researchpad.co/article/5989db16ab0ee8fa60bcd2ac

Cardiovascular disorders including ischemic stroke (IS) and myocardial infarction (MI) are heritable; however, few replicated loci have been identified. One strategy to identify loci influencing these complex disorders is to study subclinical phenotypes, such as carotid bifurcation intima-media thickness (bIMT). We have previously shown bIMT to be heritable and found evidence for linkage and association with common variants on chromosome 7p for bIMT. In this study, we aimed to characterize contributions of rare variants (RVs) in 7p to bIMT. To achieve this aim, we sequenced the 1 LOD unit down region on 7p in nine extended families from the Dominican Republic (DR) with strong evidence for linkage to bIMT. We then performed the family-based sequence kernel association test (famSKAT) on genes within the 7p region. Analyses were restricted to single nucleotide variants (SNVs) with population based minor allele frequency (MAF) <5%. We first analyzed all exonic RVs and then the subset of only non-synonymous RVs. There were 68 genes in our analyses. Nucleotide-binding oligomerization domain (NOD1) was the most significantly associated gene when analyzing exonic RVs (famSKAT p = 9.2x10-4; number of SNVs = 14). We achieved suggestive replication of NOD1 in an independent sample of twelve extended families from the DR (p = 0.055). Our study provides suggestive statistical evidence for a role of rare variants in NOD1 in bIMT. Studies in mice have shown Nod1 to play a role in heart function and atherosclerosis, providing biologic plausibility for a role in bIMT thus making NOD1 an excellent bIMT candidate.

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<![CDATA[Extending the use of GWAS data by combining data from different genetic platforms]]> https://www.researchpad.co/article/5989db53ab0ee8fa60bdcbc9

Background

In the past decade many Genome-wide Association Studies (GWAS) were performed that discovered new associations between single-nucleotide polymorphisms (SNPs) and various phenotypes. Imputation methods are widely used in GWAS. They facilitate the phenotype association with variants that are not directly genotyped. Imputation methods can also be used to combine and analyse data genotyped on different genotyping arrays. In this study we investigated the imputation quality and efficiency of two different approaches of combining GWAS data from different genotyping platforms. We investigated whether combining data from different platforms before the actual imputation performs better than combining the data from different platforms after imputation.

Methods

In total 979 unique individuals from the AMC-PAS cohort were genotyped on 3 different platforms. A total of 706 individuals were genotyped on the MetaboChip, a total of 757 individuals were genotyped on the 50K gene-centric Human CVD BeadChip, and a total of 955 individuals were genotyped on the HumanExome chip. A total of 397 individuals were genotyped on all 3 individual platforms. After pre-imputation quality control (QC), Minimac in combination with MaCH was used for the imputation of all samples with the 1,000 genomes reference panel. All imputed markers with an r2 value of <0.3 were excluded in our post-imputation QC.

Results

A total of 397 individuals were genotyped on all three platforms. All three datasets were carefully matched on strand, SNP ID and genomic coordinates. This resulted in a dataset of 979 unique individuals and a total of 258,925 unique markers. A total of 4,117,036 SNPs were available when imputation was performed before merging the three datasets. A total of 3,933,494 SNPs were available when imputation was done on the combined set. Our results suggest that imputation of individual datasets before merging performs slightly better than after combining the different datasets.

Conclusions

Imputation of datasets genotyped by different platforms before merging generates more SNPs than imputation after putting the datasets together.

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<![CDATA[Genome-Wide Pharmacogenomic Study on Methadone Maintenance Treatment Identifies SNP rs17180299 and Multiple Haplotypes on CYP2B6, SPON1, and GSG1L Associated with Plasma Concentrations of Methadone R- and S-enantiomers in Heroin-Dependent Patients]]> https://www.researchpad.co/article/5989db40ab0ee8fa60bd6944

Methadone maintenance treatment (MMT) is commonly used for controlling opioid dependence, preventing withdrawal symptoms, and improving the quality of life of heroin-dependent patients. A steady-state plasma concentration of methadone enantiomers, a measure of methadone metabolism, is an index of treatment response and efficacy of MMT. Although the methadone metabolism pathway has been partially revealed, no genome-wide pharmacogenomic study has been performed to identify genetic determinants and characterize genetic mechanisms for the plasma concentrations of methadone R- and S-enantiomers. This study was the first genome-wide pharmacogenomic study to identify genes associated with the plasma concentrations of methadone R- and S-enantiomers and their respective metabolites in a methadone maintenance cohort. After data quality control was ensured, a dataset of 344 heroin-dependent patients in the Han Chinese population of Taiwan who underwent MMT was analyzed. Genome-wide single-locus and haplotype-based association tests were performed to analyze four quantitative traits: the plasma concentrations of methadone R- and S-enantiomers and their respective metabolites. A significant single nucleotide polymorphism (SNP), rs17180299 (raw p = 2.24 × 10−8), was identified, accounting for 9.541% of the variation in the plasma concentration of the methadone R-enantiomer. In addition, 17 haplotypes were identified on SPON1, GSG1L, and CYP450 genes associated with the plasma concentration of methadone S-enantiomer. These haplotypes accounted for approximately one-fourth of the variation of the overall S-methadone plasma concentration. The association between the S-methadone plasma concentration and CYP2B6, SPON1, and GSG1L were replicated in another independent study. A gene expression experiment revealed that CYP2B6, SPON1, and GSG1L can be activated concomitantly through a constitutive androstane receptor (CAR) activation pathway. In conclusion, this study revealed new genes associated with the plasma concentration of methadone, providing insight into the genetic foundation of methadone metabolism. The results can be applied to predict treatment responses and methadone-related deaths for individualized MMTs.

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