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  1. Book ; Online ; E-Book: The Applied Genomic Epidemiology Handbook

    Black, Allison / Dudas, Gytis

    A Practical Guide to Leveraging Pathogen Genomic Data in Public Health

    (Chapman and Hall/CRC Computational Biology Series)

    2024  

    Abstract: An Applied Genomic Epidemiology Handbook: A Practical Guide to Leveraging Pathogen Genomic Data in Public Health provides rationale, theory, and implementation guidance to help public health practitioners incorporate pathogen genomic data analysis into ... ...

    Series title Chapman and Hall/CRC Computational Biology Series
    Abstract An Applied Genomic Epidemiology Handbook: A Practical Guide to Leveraging Pathogen Genomic Data in Public Health provides rationale, theory, and implementation guidance to help public health practitioners incorporate pathogen genomic data analysis into their investigations.
    Language English
    Size 1 online resource (165 pages)
    Edition 1st ed.
    Publisher CRC Press LLC
    Publishing place Milton
    Document type Book ; Online ; E-Book
    Remark Zugriff für angemeldete ZB MED-Nutzerinnen und -Nutzer
    ISBN 1-003-85384-6 ; 9781032530260 ; 978-1-003-85384-8 ; 103253026X
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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  2. Article ; Online: Invited Commentary: Computational Flow Dynamics: The Future of Fontan Conduit Selection and Operative Planning?

    Black, Allison K / Alsoufi, Bahaaldin

    World journal for pediatric & congenital heart surgery

    2022  Volume 13, Issue 3, Page(s) 302–303

    MeSH term(s) Fontan Procedure ; Heart Defects, Congenital/surgery ; Hemodynamics ; Humans
    Language English
    Publishing date 2022-04-20
    Publishing country United States
    Document type Journal Article ; Comment
    ZDB-ID 2550261-X
    ISSN 2150-136X ; 2150-1351
    ISSN (online) 2150-136X
    ISSN 2150-1351
    DOI 10.1177/21501351221091341
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  3. Article ; Online: Dimensionality reduction distills complex evolutionary relationships in seasonal influenza and SARS-CoV-2

    Nanduri, Sravani / Black, Allison / Bedford, Trevor / Huddleston, John

    bioRxiv

    Abstract: Public health researchers and practitioners commonly infer phylogenies from viral genome sequences to understand transmission dynamics and identify clusters of genetically-related samples. However, viruses that reassort or recombine violate phylogenetic ... ...

    Abstract Public health researchers and practitioners commonly infer phylogenies from viral genome sequences to understand transmission dynamics and identify clusters of genetically-related samples. However, viruses that reassort or recombine violate phylogenetic assumptions and require more sophisticated methods. Even when phylogenies are appropriate, they can be unnecessary or difficult to interpret without specialty knowledge. For example, pairwise distances between sequences can be enough to identify clusters of related samples or assign new samples to existing phylogenetic clusters. In this work, we tested whether dimensionality reduction methods could capture known genetic groups within two human pathogenic viruses that cause substantial human morbidity and mortality and frequently reassort or recombine, respectively: seasonal influenza A/H3N2 and SARS-CoV-2. We applied principal component analysis (PCA), multidimensional scaling (MDS), t-distributed stochastic neighbor embedding (t-SNE), and uniform manifold approximation and projection (UMAP) to sequences with well-defined phylogenetic clades and either reassortment (H3N2) or recombination (SARS-CoV-2). For each low-dimensional embedding of sequences, we calculated the correlation between pairwise genetic and Euclidean distances in the embedding and applied a hierarchical clustering method to identify clusters in the embedding. We measured the accuracy of clusters compared to previously defined phylogenetic clades, reassortment clusters, or recombinant lineages. We found that MDS maintained the strongest correlation between pairwise genetic and Euclidean distances between sequences and best captured the intermediate placement of recombinant lineages between parental lineages. Clusters from t-SNE most accurately recapitulated known phylogenetic clades and recombinant lineages. Both MDS and t-SNE accurately identified reassortment groups. We show that simple statistical methods without a biological model can accurately represent known genetic relationships for relevant human pathogenic viruses. Our open source implementation of these methods for analysis of viral genome sequences can be easily applied when phylogenetic methods are either unnecessary or inappropriate.
    Keywords covid19
    Language English
    Publishing date 2024-02-08
    Publisher Cold Spring Harbor Laboratory
    Document type Article ; Online
    DOI 10.1101/2024.02.07.579374
    Database COVID19

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  4. Article ; Online: Comparison of Echocardiography and Multi-Planar Gated Acquisition Scans for Predicting Cancer-Treatment-Related Cardiovascular Dysfunction.

    Nolan, Mark T / Pathan, Faraz / Nott, Louise / Black, Allison / Pointon, Owen / Marwick, Thomas H

    Heart, lung & circulation

    2024  

    Abstract: Background: Current guidelines recommend using sequential cardiac imaging to monitor for cancer treatment-related cardiac dysfunction (CTRCD) in patients undergoing potentially cardiotoxic chemotherapy. Multiple different imaging cardiac modalities are ... ...

    Abstract Background: Current guidelines recommend using sequential cardiac imaging to monitor for cancer treatment-related cardiac dysfunction (CTRCD) in patients undergoing potentially cardiotoxic chemotherapy. Multiple different imaging cardiac modalities are available and there are few prospective head-to-head comparative studies to help guide treatment.
    Objectives: To perform an exploratory prospective cohort study of "real-world" CTRCD comparing multigated acquisition nuclear ventriculography (MUGA) at the referring cancer specialist's discretion with a novel echocardiographic strategy at an Australian tertiary hospital.
    Method: Patients were recruited from haematology and oncology outpatient clinics if they were scheduled for treatment with anthracyclines and/or trastuzumab. Patients underwent simultaneous MUGA-based cardiac imaging (conventional strategy) at a frequency according to evidenced-based guidelines in addition to researcher-conducted echocardiographic imaging. The echocardiographic imaging was performed in all patients at time points recommended by international society guidelines. Outcomes included adherence to guideline recommendations, concordance between MUGA and echocardiographic left ventricular ejection fraction (LVEF) measurements, and detection of cardiac dysfunction (defined as >5% LVEF decrement from baseline by three-dimensional [3D]-LVEF). A secondary end point was accuracy of global longitudinal strain in predicting cardiac dysfunction.
    Results: In total, 35 patients were recruited, including 15 with breast cancer, 19 with haematological malignancy, and one with gastric cancer. MUGA and echocardiographic LVEF measurements correlated poorly with limits of agreement of 30% between 3D-LVEF and MUGA-LVEF and 37% for 3D-LVEF and MUGA-LVEF. Only one case (2.9%) of CTRCD was diagnosed by MUGA, compared with 12 (34.2%) cases by echocardiography. Four (4) patients had >10% decrement in 3D-LVEF that was not detected by MUGA. Global longitudinal strain at 2 months displayed significant ability to predict CTRCD (area under the curve, 0.75, 95% confidence interval, 0.55-0.94).
    Conclusions: The MUGA correlates poorly with echocardiographic assessment with substantial discrepancy between MUGA and echocardiography in CTRCD diagnosis. Echocardiographic and MUGA imaging strategies should not be considered equivalent for imaging cancer patients, and a single imaging modality should ideally be used per patient to prevent misdiagnosis by inter-modality variation These findings should be considered hypothesis-generating and require confirmation with larger studies.
    Language English
    Publishing date 2024-04-30
    Publishing country Australia
    Document type Journal Article
    ZDB-ID 2020980-0
    ISSN 1444-2892 ; 1443-9506
    ISSN (online) 1444-2892
    ISSN 1443-9506
    DOI 10.1016/j.hlc.2024.03.010
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    Zs.A 4988: Show issues Location:
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  5. Article ; Online: Identifying Food Insecurity in Cardiology Clinic and Connecting Families to Resources.

    Black, Allison K / Pantalone, Julia / Marrone, Anna-Claire / Morell, Evonne / Telles, Robin / DeBrunner, Mark

    Pediatrics

    2022  Volume 149, Issue 5

    Abstract: Background: Food insecurity (FI) increases children's risk for illness and developmental and behavioral problems, which are ongoing concerns for congenital heart disease (CHD) patients. In 2020, 14.8% of households with children suffered from FI. The ... ...

    Abstract Background: Food insecurity (FI) increases children's risk for illness and developmental and behavioral problems, which are ongoing concerns for congenital heart disease (CHD) patients. In 2020, 14.8% of households with children suffered from FI. The Hunger Vital Signs (HVS) asks 2 questions to assess FI. The global aim of the project is to implement HVS and connect FI families to resources.
    Methods: Stakeholders identified 6 critical drivers in implementing FI screening at an outpatient cardiology clinic and conducted plan-do-study-act (PDSA) cycles to implement HVS. Over the 13-month study period, time series analyses were performed to assess our process measure (FI screening) and outcome measure (connection of FI families to resources). Demographics and severity of CHD were analyzed for FI families.
    Results: Screening rates increased from 0% to >85%, screening 5064 families. Process evaluations revealed roadblocks including screening discomfort. FI families were more likely to identify as Black or multiple or other ethnicity. Severe CHD patients were at higher risk for FI (n = 106, odds ratio [OR] 1.67 [1.21-2.29], P = .002). Face-to-face meetings with social work and community partnerships reduced loss to follow-up and our ability to offer all FI families individualized FI resources.
    Conclusion: HVS screening can be implemented in a cardiology clinic to improve identification of FI families. A written tool can combat screening discomfort and improve identification of FI families. Children with severe CHD may be at increased risk for FI. A multidisciplinary team and community partnerships can improve individualized resource distribution.
    MeSH term(s) Ambulatory Care Facilities ; Cardiology ; Child ; Food Insecurity ; Food Supply ; Humans ; Mass Screening
    Language English
    Publishing date 2022-04-20
    Publishing country United States
    Document type Journal Article
    ZDB-ID 207677-9
    ISSN 1098-4275 ; 0031-4005
    ISSN (online) 1098-4275
    ISSN 0031-4005
    DOI 10.1542/peds.2020-011718
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    Um IV Zs.131: Show issues Location:
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    Zs.MO 357: Show issues

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  6. Article ; Online: Joint visualization of seasonal influenza serology and phylogeny to inform vaccine composition.

    Lee, Jover / Hadfield, James / Black, Allison / Sibley, Thomas R / Neher, Richard A / Bedford, Trevor / Huddleston, John

    Frontiers in bioinformatics

    2023  Volume 3, Page(s) 1069487

    Abstract: Seasonal influenza vaccines must be updated regularly to account for mutations that allow influenza viruses to escape our existing immunity. A successful vaccine should represent the genetic diversity of recently circulating viruses and induce antibodies ...

    Abstract Seasonal influenza vaccines must be updated regularly to account for mutations that allow influenza viruses to escape our existing immunity. A successful vaccine should represent the genetic diversity of recently circulating viruses and induce antibodies that effectively prevent infection by those recent viruses. Thus, linking the genetic composition of circulating viruses and the serological experimental results measuring antibody efficacy is crucial to the vaccine design decision. Historically, genetic and serological data have been presented separately in the form of static visualizations of phylogenetic trees and tabular serological results to identify vaccine candidates. To simplify this decision-making process, we have created an interactive tool for visualizing serological data that has been integrated into Nextstrain's real-time phylogenetic visualization framework, Auspice. We show how the combined interactive visualizations may be used by decision makers to explore the relationships between complex data sets for both prospective vaccine virus selection and retrospectively exploring the performance of vaccine viruses.
    Language English
    Publishing date 2023-03-22
    Publishing country Switzerland
    Document type Journal Article
    ISSN 2673-7647
    ISSN (online) 2673-7647
    DOI 10.3389/fbinf.2023.1069487
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  7. Article ; Online: Changing genomic epidemiology of COVID-19 in long-term care facilities during the 2020-2022 pandemic, Washington State.

    Oltean, Hanna N / Black, Allison / Lunn, Stephanie M / Smith, Nailah / Templeton, Allison / Bevers, Elyse / Kibiger, Lynae / Sixberry, Melissa / Bickel, Josina B / Hughes, James P / Lindquist, Scott / Baseman, Janet G / Bedford, Trevor

    BMC public health

    2024  Volume 24, Issue 1, Page(s) 182

    Abstract: Background: Long-term care facilities (LTCFs) are vulnerable to disease outbreaks. Here, we jointly analyze SARS-CoV-2 genomic and paired epidemiologic data from LTCFs and surrounding communities in Washington state (WA) to assess transmission patterns ... ...

    Abstract Background: Long-term care facilities (LTCFs) are vulnerable to disease outbreaks. Here, we jointly analyze SARS-CoV-2 genomic and paired epidemiologic data from LTCFs and surrounding communities in Washington state (WA) to assess transmission patterns during 2020-2022, in a setting of changing policy. We describe sequencing efforts and genomic epidemiologic findings across LTCFs and perform in-depth analysis in a single county.
    Methods: We assessed genomic data representativeness, built phylogenetic trees, and conducted discrete trait analysis to estimate introduction sizes over time, and explored selected outbreaks to further characterize transmission events.
    Results: We found that transmission dynamics among cases associated with LTCFs in WA changed over the course of the COVID-19 pandemic, with variable introduction rates into LTCFs, but decreasing amplification within LTCFs. SARS-CoV-2 lineages circulating in LTCFs were similar to those circulating in communities at the same time. Transmission between staff and residents was bi-directional.
    Conclusions: Understanding transmission dynamics within and between LTCFs using genomic epidemiology on a broad scale can assist in targeting policies and prevention efforts. Tracking facility-level outbreaks can help differentiate intra-facility outbreaks from high community transmission with repeated introduction events. Based on our study findings, methods for routine tree building and overlay of epidemiologic data for hypothesis generation by public health practitioners are recommended. Discrete trait analysis added valuable insight and can be considered when representative sequencing is performed. Cluster detection tools, especially those that rely on distance thresholds, may be of more limited use given current data capture and timeliness. Importantly, we noted a decrease in data capture from LTCFs over time. Depending on goals for use of genomic data, sentinel surveillance should be increased or targeted surveillance implemented to ensure available data for analysis.
    MeSH term(s) Humans ; COVID-19/epidemiology ; Pandemics/prevention & control ; SARS-CoV-2/genetics ; Washington/epidemiology ; Long-Term Care/methods ; Phylogeny ; Genomics
    Language English
    Publishing date 2024-01-15
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, P.H.S.
    ZDB-ID 2041338-5
    ISSN 1471-2458 ; 1471-2458
    ISSN (online) 1471-2458
    ISSN 1471-2458
    DOI 10.1186/s12889-023-17461-2
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  8. Article ; Online: Ten recommendations for supporting open pathogen genomic analysis in public health.

    Black, Allison / MacCannell, Duncan R / Sibley, Thomas R / Bedford, Trevor

    Nature medicine

    2020  Volume 26, Issue 6, Page(s) 832–841

    Abstract: Increasingly, public-health agencies are using pathogen genomic sequence data to support surveillance and epidemiological investigations. As access to whole-genome sequencing has grown, greater amounts of molecular data have helped improve the ability to ...

    Abstract Increasingly, public-health agencies are using pathogen genomic sequence data to support surveillance and epidemiological investigations. As access to whole-genome sequencing has grown, greater amounts of molecular data have helped improve the ability to detect and track outbreaks of diseases such as COVID-19, investigate transmission chains and explore large-scale population dynamics, such as the spread of antibiotic resistance. However, the wide adoption of whole-genome sequencing also poses new challenges for public-health agencies that must adapt to support a new set of expertise, which means that the capacity to perform genomic data assembly and analysis has not expanded as widely as the adoption of sequencing itself. In this Perspective, we make recommendations for developing an accessible, unified informatic ecosystem to support pathogen genomic analysis in public-health agencies across income settings. We hope that the creation of this ecosystem will allow agencies to effectively and efficiently share data, workflows and analyses and thereby increase the reproducibility, accessibility and auditability of pathogen genomic analysis while also supporting agency autonomy.
    MeSH term(s) Betacoronavirus/genetics ; Betacoronavirus/pathogenicity ; COVID-19 ; Coronavirus Infections/epidemiology ; Coronavirus Infections/genetics ; Coronavirus Infections/transmission ; Coronavirus Infections/virology ; Disease Outbreaks ; Drug Resistance, Microbial/genetics ; Genomics ; Humans ; Pandemics ; Pneumonia, Viral/epidemiology ; Pneumonia, Viral/genetics ; Pneumonia, Viral/transmission ; Pneumonia, Viral/virology ; Population Dynamics ; SARS-CoV-2 ; Whole Genome Sequencing
    Keywords covid19
    Language English
    Publishing date 2020-06-11
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
    ZDB-ID 1220066-9
    ISSN 1546-170X ; 1078-8956
    ISSN (online) 1546-170X
    ISSN 1078-8956
    DOI 10.1038/s41591-020-0935-z
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    Zs.A 4212: Show issues Location:
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    Zs.MG 39: Show issues

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  9. Article ; Online: Use of abatacept in steroid refractory, immune checkpoint-induced myocarditis.

    Kalapurackal Mathai, Vinod / Black, Allison / Lovibond, Sam / Binny, Simon / Lipton, Jonathan / Moldovan, Cristina

    Internal medicine journal

    2021  Volume 51, Issue 11, Page(s) 1971–1972

    MeSH term(s) Abatacept ; Humans ; Myocarditis/chemically induced ; Myocarditis/drug therapy ; Nivolumab ; Steroids
    Chemical Substances Steroids ; Nivolumab (31YO63LBSN) ; Abatacept (7D0YB67S97)
    Language English
    Publishing date 2021-11-19
    Publishing country Australia
    Document type Letter
    ZDB-ID 2045436-3
    ISSN 1445-5994 ; 1444-0903
    ISSN (online) 1445-5994
    ISSN 1444-0903
    DOI 10.1111/imj.15566
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    Zs.A 792: Show issues Location:
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    Zs.MO 424: Show issues

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  10. Article ; Online: Infection clusters can elevate risk of diagnostic target failure for detection of SARS-CoV-2.

    Lopez, Denise / Roberts, Jill / Bourgeois, Marie / Kootstra, Joshua / Minnick, Sharon / Black, Allison / Mauss, Joshua / Flores, Nick

    PloS one

    2022  Volume 17, Issue 2, Page(s) e0264008

    Abstract: The C29197T mutation is one of 4 point mutations known to cause N-gene target failure (NGTF) in the Xpert Xpress SARS-CoV-2 and Xpert Omni SARS-CoV-2 assays from Cepheid (Sunnyvale, CA). We describe a high local prevalence in January of 8.5% (CI 4.9-14.2% ...

    Abstract The C29197T mutation is one of 4 point mutations known to cause N-gene target failure (NGTF) in the Xpert Xpress SARS-CoV-2 and Xpert Omni SARS-CoV-2 assays from Cepheid (Sunnyvale, CA). We describe a high local prevalence in January of 8.5% (CI 4.9-14.2%) for the C29197T mutation, which was over 3-fold higher than the prevalence estimated statewide in California during the same time frame, 2.5% (CI 2.1-2.8%). Using phylogenetic analysis, we discovered that this increase in prevalence was due, at least in part, to a disproportionately large infection cluster of unknown origin. This study emphasizes the importance of sequencing at the local jurisdictional level and demonstrates the impact that regional variation can have when assessing risk due to point mutations that impact clinical test performance. It also reinforces the need for diligent reporting of abnormal test results by clinical laboratories, especially during Emergency Use Authorization (EUA) periods, as additional information is gathered about the target organism and the performance of EUA-authorized tests over time.
    MeSH term(s) COVID-19/diagnosis ; COVID-19 Testing/methods ; Genes, Viral ; Humans ; Molecular Diagnostic Techniques/methods ; Mutation ; Phylogeny ; Prevalence ; SARS-CoV-2/genetics ; SARS-CoV-2/isolation & purification ; Sensitivity and Specificity
    Language English
    Publishing date 2022-02-16
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2267670-3
    ISSN 1932-6203 ; 1932-6203
    ISSN (online) 1932-6203
    ISSN 1932-6203
    DOI 10.1371/journal.pone.0264008
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