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  • 1
    Online Resource
    Online Resource
    Oxford University Press (OUP) ; 2021
    In:  Clinical Infectious Diseases Vol. 73, No. 9 ( 2021-11-02), p. e3047-e3052
    In: Clinical Infectious Diseases, Oxford University Press (OUP), Vol. 73, No. 9 ( 2021-11-02), p. e3047-e3052
    Abstract: Coronavirus disease 2019 has highlighted deficiencies in the testing capacity of many developed countries during the early stages of pandemics. Here we describe a strategy using pan-family viral assays to improve early accessibility of large-scale nucleic acid testing. Methods Coronaviruses and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were used as a case study for assessing utility of pan-family viral assays during the early stages of a novel pandemic. Specificity of a pan-coronavirus (Pan-CoV) assay for a novel pathogen was assessed using the frequency of common human coronavirus (HCoV) species in key populations. A reported Pan-CoV assay was assessed to determine sensitivity to 60 reference coronaviruses, including SARS-CoV-2. The resilience of the primer target regions of this assay to mutation was assessed in 8893 high-quality SARS-CoV-2 genomes to predict ongoing utility during pandemic progression. Results Because of common HCoV species, a Pan-CoV assay would return false positives for as few as 1% of asymptomatic adults, but up to 30% of immunocompromised patients with respiratory disease. One-half of reported Pan-CoV assays identify SARS-CoV-2 and with small adjustments can accommodate diverse variation observed in animal coronaviruses. The target region of 1 well-established Pan-CoV assay is highly resistant to mutation compared to species-specific SARS-CoV-2 reverse transcriptase-polymerase chain reaction assays. Conclusions Despite cross-reactivity with common pathogens, pan-family assays may greatly assist management of emerging pandemics through prioritization of high-resolution testing or isolation measures. Targeting highly conserved genomic regions make pan-family assays robust and resilient to mutation. A strategic stockpile of pan-family assays may improve containment of novel diseases before the availability of species-specific assays.
    Type of Medium: Online Resource
    ISSN: 1058-4838 , 1537-6591
    RVK:
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
    detail.hit.zdb_id: 2002229-3
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  • 2
    In: Alzheimer's & Dementia, Wiley, Vol. 18, No. S5 ( 2022-12)
    Abstract: Amyloid beta ( Aβ ), measured using PET imaging, is a key biomarker for Alzheimer’s disease (AD) with the consequences of abnormally high Aβ levels ( Aβ +) well‐established from prospective research cohorts. A critical question is whether the prognostic capabilities of Aβ can be improved further, for example by refinement of optimal criteria for abnormality. To date, existing studies have explored such issues using association analyses, which may not reflect performance in prognostic settings due to potential overfitting. Here, the impact of different Aβ cut‐points is determined in a cross‐validation framework, providing performance estimates on data from individuals that were not used for model construction, which better reflects realworld prognostic application. Using data for cognitively normal individuals (CN) from ADNI and AIBL, we estimate time to i) MCI or AD diagnosis and ii) cognitive deficit, defined as MMSE≤26. Method We analyse measurements from 344 and 748 CN from ADNI and AIBL respectively who have available PET Aβ scans. PET Aβ SUVRs were transformed to the centiloid scale (CL). For each task, the Aβ cut‐point is varied from ‐10 to 65CL and Cox models are constructed within 10 repeats of 10‐fold cross‐validation. From the resulting 100 models, performance is quantified as the median concordance index (i.e. Harrell’s C). Result Details of the two cohorts are shown in Table 1. Across both AIBL and ADNI, a PET only model shows robust performance for cut‐points within a wide range (5 and 50CL) for predicting either time to diagnosis cognitive deficit (Figure 1), with performance dropping rapidly outside this range. When additional covariates are included 2, we see maximal performance for lower cutpoints (5‐20CL) for diagnosis in ADNI and cognitive deficit in ADNI, while remaining tasks show improved performance with higher cut‐point ranges (20‐50CL). Trends in cut‐point are consistent regardless of covariates. Leaving Aβ as a continuous variable yields near‐optimal performance across all tasks. Conclusion Our results suggest that within a range (5 and 50CL), prognostic performance is robust to the choice of cut‐point for Aβ , suggesting further refinement of a single cut‐point within this range may not yield substantial improvements for prognostic tasks for CN individuals.
    Type of Medium: Online Resource
    ISSN: 1552-5260 , 1552-5279
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2022
    detail.hit.zdb_id: 2201940-6
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  • 3
    Online Resource
    Online Resource
    Oxford University Press (OUP) ; 2021
    In:  Briefings in Bioinformatics Vol. 22, No. 4 ( 2021-07-20)
    In: Briefings in Bioinformatics, Oxford University Press (OUP), Vol. 22, No. 4 ( 2021-07-20)
    Abstract: Haplotype phasing is a critical step for many genetic applications but incorrect estimates of phase can negatively impact downstream analyses. One proposed strategy to improve phasing accuracy is to combine multiple independent phasing estimates to overcome the limitations of any individual estimate. However, such a strategy is yet to be thoroughly explored. This study provides a comprehensive evaluation of consensus strategies for haplotype phasing. We explore the performance of different consensus paradigms, and the effect of specific constituent tools, across several datasets with different characteristics and their impact on the downstream task of genotype imputation. Based on the outputs of existing phasing tools, we explore two different strategies to construct haplotype consensus estimators: voting across outputs from multiple phasing tools and multiple outputs of a single non-deterministic tool. We find that the consensus approach from multiple tools reduces SE by an average of 10% compared to any constituent tool when applied to European populations and has the highest accuracy regardless of population ethnicity, sample size, variant density or variant frequency. Furthermore, the consensus estimator improves the accuracy of the downstream task of genotype imputation carried out by the widely used Minimac3, pbwt and BEAGLE5 tools. Our results provide guidance on how to produce the most accurate phasing estimates and the trade-offs that a consensus approach may have. Our implementation of consensus haplotype phasing, consHap, is available freely at https://github.com/ziadbkh/consHap. Supplementary information: Supplementary data are available at Briefings in Bioinformatics online.
    Type of Medium: Online Resource
    ISSN: 1467-5463 , 1477-4054
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
    detail.hit.zdb_id: 2036055-1
    SSG: 12
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  • 4
    Online Resource
    Online Resource
    Oxford University Press (OUP) ; 2022
    In:  Bioinformatics Vol. 38, No. Supplement_1 ( 2022-06-24), p. i273-i281
    In: Bioinformatics, Oxford University Press (OUP), Vol. 38, No. Supplement_1 ( 2022-06-24), p. i273-i281
    Abstract: Literature-based gene ontology annotations (GOA) are biological database records that use controlled vocabulary to uniformly represent gene function information that is described in the primary literature. Assurance of the quality of GOA is crucial for supporting biological research. However, a range of different kinds of inconsistencies in between literature as evidence and annotated GO terms can be identified; these have not been systematically studied at record level. The existing manual-curation approach to GOA consistency assurance is inefficient and is unable to keep pace with the rate of updates to gene function knowledge. Automatic tools are therefore needed to assist with GOA consistency assurance. This article presents an exploration of different GOA inconsistencies and an early feasibility study of automatic inconsistency detection. Results We have created a reliable synthetic dataset to simulate four realistic types of GOA inconsistency in biological databases. Three automatic approaches are proposed. They provide reasonable performance on the task of distinguishing the four types of inconsistency and are directly applicable to detect inconsistencies in real-world GOA database records. Major challenges resulting from such inconsistencies in the context of several specific application settings are reported. This is the first study to introduce automatic approaches that are designed to address the challenges in current GOA quality assurance workflows. The data underlying this article are available in Github at https://github.com/jiyuc/AutoGOAConsistency.
    Type of Medium: Online Resource
    ISSN: 1367-4803 , 1367-4811
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 1468345-3
    SSG: 12
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  • 5
    In: NeuroImage, Elsevier BV, Vol. 278 ( 2023-09), p. 120279-
    Type of Medium: Online Resource
    ISSN: 1053-8119
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2023
    detail.hit.zdb_id: 1471418-8
    SSG: 5,2
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  • 6
    Online Resource
    Online Resource
    Springer Science and Business Media LLC ; 2020
    In:  European Journal of Human Genetics Vol. 28, No. 12 ( 2020-12), p. 1743-1752
    In: European Journal of Human Genetics, Springer Science and Business Media LLC, Vol. 28, No. 12 ( 2020-12), p. 1743-1752
    Type of Medium: Online Resource
    ISSN: 1018-4813 , 1476-5438
    RVK:
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2020
    detail.hit.zdb_id: 2005160-8
    SSG: 12
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  • 7
    Online Resource
    Online Resource
    Wiley ; 2022
    In:  Alzheimer's & Dementia Vol. 18, No. S6 ( 2022-12)
    In: Alzheimer's & Dementia, Wiley, Vol. 18, No. S6 ( 2022-12)
    Abstract: Alzheimer's Disease (AD) is a heterogeneous condition that can be viewed as a continuum involving multiple stages from cognitively normal to mild cognitive impairment and finally dementia. Recent works in Disease Progression Modelling (DPM) have attempted to use biomarkers to construct representations of progression that are more informative of patients' status than clinical diagnosis alone. However, there is no clear consensus (Figure 1) regarding the choice of evaluation methods or metrics to facilitate model comparison. We propose the use a simple, universally applicable biomarker‐based baseline to estimate patient‐realigning time‐shifts and subsequently evaluate it against multiple released DPM methods. Method We computed an abnormality score for 2439 patients from the Alzheimer's Disease Neuroimaging Initiative (ADNI) by averaging the normalised values collected for 12 biomarkers representative of amyloid, tau, neurodegeneration, and cognition. Abnormality ranges were determined from 251 amyloid‐positive patients. These scores were compared to values from published DPM models (Figure 3). Additionally, all methods were benchmarked in different ways, including diagnosis classification and cluster analysis. Result We found that, despite its simplicity, our abnormality score reasonably separated patients according to their diagnosis (Figure 2). Computed scores also correlated significantly with those of other methods (Figure 3, Pearson correlations up to 0.891). While our approach only required cross‐sectional information, other methods rely on longitudinal data. Our method performed similarly to others in the cutoff‐based disease classification task, with test F1‐scores of 0.734 and 0.890 in the harder tasks of CN/MCI and AD/MCI, respectively (Table 1). In a three‐class setting, all methods including our baseline showed a good level of agreement, with Rand indices all above 0.6 (Figure 4). Conclusion A significant challenge in DPM for AD lies in estimating a proxy for patient realignment, which is crucial to describe individuals on a common disease continuum. We have proposed a method to calculate an abnormality score at the baseline visit, which can be trivially extended to longitudinal data and help interpret progression in follow‐ups. We hope that future work considers more principled evaluation procedures, facilitating meaningful comparisons between DPMs.
    Type of Medium: Online Resource
    ISSN: 1552-5260 , 1552-5279
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2022
    detail.hit.zdb_id: 2201940-6
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  • 8
    In: Trends in Hearing, SAGE Publications, Vol. 25 ( 2021-01), p. 233121652110375-
    Abstract: While the majority of cochlear implant recipients benefit from the device, it remains difficult to estimate the degree of benefit for a specific patient prior to implantation. Using data from 2,735 cochlear-implant recipients from across three clinics, the largest retrospective study of cochlear-implant outcomes to date, we investigate the association between 21 preoperative factors and speech recognition approximately one year after implantation and explore the consistency of their effects across the three constituent datasets. We provide evidence of 17 statistically significant associations, in either univariate or multivariate analysis, including confirmation of associations for several predictive factors, which have only been examined in prior smaller studies. Despite the large sample size, a multivariate analysis shows that the variance explained by our models remains modest across the datasets ([Formula: see text]–0.21). Finally, we report a novel statistical interaction indicating that the duration of deafness in the implanted ear has a stronger impact on hearing outcome when considered relative to a candidate’s age. Our multicenter study highlights several real-world complexities that impact the clinical translation of predictive factors for cochlear implantation outcome. We suggest several directions to overcome these challenges and further improve our ability to model patient outcomes with increased accuracy.
    Type of Medium: Online Resource
    ISSN: 2331-2165 , 2331-2165
    Language: English
    Publisher: SAGE Publications
    Publication Date: 2021
    detail.hit.zdb_id: 2778755-2
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  • 9
    In: Genetic Epidemiology, Wiley
    Abstract: Young breast and bowel cancers (e.g., those diagnosed before age 40 or 50 years) have far greater morbidity and mortality in terms of years of life lost, and are increasing in incidence, but have been less studied. For breast and bowel cancers, the familial relative risks, and therefore the familial variances in age‐specific log(incidence), are much greater at younger ages, but little of these familial variances has been explained. Studies of families and twins can address questions not easily answered by studies of unrelated individuals alone. We describe existing and emerging family and twin data that can provide special opportunities for discovery. We present designs and statistical analyses, including novel ideas such as the VALID (Variance in Age‐specific Log Incidence Decomposition) model for causes of variation in risk, the DEPTH (DEPendency of association on the number of Top Hits) and other approaches to analyse genome‐wide association study data, and the within‐pair, ICE FALCON (Inference about Causation from Examining FAmiliaL CONfounding) and ICE CRISTAL (Inference about Causation from Examining Changes in Regression coefficients and Innovative STatistical AnaLysis) approaches to causation and familial confounding. Example applications to breast and colorectal cancer are presented. Motivated by the availability of the resources of the Breast and Colon Cancer Family Registries, we also present some ideas for future studies that could be applied to, and compared with, cancers diagnosed at older ages and address the challenges posed by young breast and bowel cancers.
    Type of Medium: Online Resource
    ISSN: 0741-0395 , 1098-2272
    Language: English
    Publisher: Wiley
    Publication Date: 2024
    detail.hit.zdb_id: 1492643-X
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  • 10
    Online Resource
    Online Resource
    Wiley ; 2021
    In:  Alimentary Pharmacology & Therapeutics Vol. 53, No. 6 ( 2021-03), p. 759-760
    In: Alimentary Pharmacology & Therapeutics, Wiley, Vol. 53, No. 6 ( 2021-03), p. 759-760
    Abstract: LINKED CONTENT This article is linked to Sharp et al paper. To view this article, visit https://doi.org/10.1111/apt.15826
    Type of Medium: Online Resource
    ISSN: 0269-2813 , 1365-2036
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2021
    detail.hit.zdb_id: 2003094-0
    SSG: 15,3
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