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  1. Article ; Online: Protecting Privacy of Pregnant and LGBTQ+ Research Participants.

    Clayton, Ellen Wright / Bland, Harris T / Mittendorf, Kathleen F

    JAMA

    2024  

    Language English
    Publishing date 2024-04-15
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2958-0
    ISSN 1538-3598 ; 0254-9077 ; 0002-9955 ; 0098-7484
    ISSN (online) 1538-3598
    ISSN 0254-9077 ; 0002-9955 ; 0098-7484
    DOI 10.1001/jama.2024.4837
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  2. Article ; Online: Accelerated curation of checkpoint inhibitor-induced colitis cases from electronic health records.

    Rahman, Protiva / Ye, Cheng / Mittendorf, Kathleen F / Lenoue-Newton, Michele / Micheel, Christine / Wolber, Jan / Osterman, Travis / Fabbri, Daniel

    JAMIA open

    2023  Volume 6, Issue 1, Page(s) ooad017

    Abstract: Objective: Automatically identifying patients at risk of immune checkpoint inhibitor (ICI)-induced colitis allows physicians to improve patientcare. However, predictive models require training data curated from electronic health records (EHR). Our ... ...

    Abstract Objective: Automatically identifying patients at risk of immune checkpoint inhibitor (ICI)-induced colitis allows physicians to improve patientcare. However, predictive models require training data curated from electronic health records (EHR). Our objective is to automatically identify notes documenting ICI-colitis cases to accelerate data curation.
    Materials and methods: We present a data pipeline to automatically identify ICI-colitis from EHR notes, accelerating chart review. The pipeline relies on BERT, a state-of-the-art natural language processing (NLP) model. The first stage of the pipeline segments long notes using keywords identified through a logistic classifier and applies BERT to identify ICI-colitis notes. The next stage uses a second BERT model tuned to identify false positive notes and remove notes that were likely positive for mentioning colitis as a side-effect. The final stage further accelerates curation by highlighting the colitis-relevant portions of notes. Specifically, we use BERT's attention scores to find high-density regions describing colitis.
    Results: The overall pipeline identified colitis notes with 84% precision and reduced the curator note review load by 75%. The segment BERT classifier had a high recall of 0.98, which is crucial to identify the low incidence (<10%) of colitis.
    Discussion: Curation from EHR notes is a burdensome task, especially when the curation topic is complicated. Methods described in this work are not only useful for ICI colitis but can also be adapted for other domains.
    Conclusion: Our extraction pipeline reduces manual note review load and makes EHR data more accessible for research.
    Language English
    Publishing date 2023-04-01
    Publishing country United States
    Document type Journal Article
    ISSN 2574-2531
    ISSN (online) 2574-2531
    DOI 10.1093/jamiaopen/ooad017
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  3. Article ; Online: Incidence of Adolescent Syncope and Related Injuries Following Vaccination and Routine Venipuncture.

    Groom, Holly C / Brooks, Neon B / Weintraub, Eric S / Slaughter, Matthew T / Mittendorf, Kathleen F / Naleway, Allison L

    The Journal of adolescent health : official publication of the Society for Adolescent Medicine

    2023  Volume 74, Issue 4, Page(s) 696–702

    Abstract: Purpose: Vaccination is associated with syncope in adolescents. However, incidence of vaccine-associated syncope and resulting injury, and how it compares to syncope incidence following other medical procedures, is not known. Here, we describe the ... ...

    Abstract Purpose: Vaccination is associated with syncope in adolescents. However, incidence of vaccine-associated syncope and resulting injury, and how it compares to syncope incidence following other medical procedures, is not known. Here, we describe the incidence of syncope and syncope-related injury in adolescents following vaccination and routine venipuncture.
    Methods: We identified all Kaiser Permanente Northwest members ages 9-18 years with a vaccination or routine venipuncture and a same-day International Classification of Diseases diagnosis of syncope from 2013 through 2019. All cases were chart reviewed to establish chronology of events (vaccination, venipuncture, syncope, and injury, as applicable) and to attribute cause to vaccination or venipuncture. Incidence rates for vaccine-associated and venipuncture-associated syncope were calculated overall, by sex and age group. Syncope events resulting in injury were assessed for each event type.
    Results: Of 197,642 vaccination and 12,246 venipuncture events identified, 549 vaccination and 67 venipuncture events had same-day syncope codes. Chart validation confirmed 59/549 (10.7%) events as vaccine-associated syncope, for a rate of 2.99 per 10,000 vaccination events (95% confidence interval (CI): 2.27-3.85) and 20/67 (29.9%) events as venipuncture-associated syncope, for a rate of 16.33 per 10,000 venipuncture events (95% CI: 9.98-25.21). The incidence rate ratio of vaccine-associated to venipuncture-associated syncope events was 0.18 (95% CI: 0.11-0.31). The incidence of vaccine-associated syncope increased with each additional simultaneously administered vaccine, from 1.51 per 10,000 vaccination events (95% CI: 0.93-2.30) following a single vaccine to 9.94 per 10,000 vaccination events (95% CI: 6.43-14.67) following three or more vaccines. Syncope resulted in injury in about 15% of both vaccine and venipuncture events.
    Discussion: Syncope occurs more commonly following venipuncture than vaccination. The number of simultaneously administered vaccines is a risk factor for postvaccination syncope in adolescents.
    MeSH term(s) Adolescent ; Humans ; Incidence ; Phlebotomy/adverse effects ; Syncope/etiology ; Syncope/complications ; Vaccination/adverse effects ; Vaccines
    Chemical Substances Vaccines
    Language English
    Publishing date 2023-12-09
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1063374-1
    ISSN 1879-1972 ; 1054-139X
    ISSN (online) 1879-1972
    ISSN 1054-139X
    DOI 10.1016/j.jadohealth.2023.11.005
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  4. Article ; Online: Utilization of electronic health record data to evaluate the association of urban environment with systemic lupus erythematosus symptoms.

    Song, Janet / Forrest, Noah / Gordon, Adam / Kottyan, Leah / Mittendorf, Kathleen F / Wei, Wei-Qi / Ramsey-Goldman, Rosalind / Walunas, Theresa / Kho, Abel

    Rheumatology (Oxford, England)

    2022  Volume 62, Issue 6, Page(s) e180–e181

    MeSH term(s) Humans ; Electronic Health Records ; Lupus Erythematosus, Systemic
    Language English
    Publishing date 2022-11-16
    Publishing country England
    Document type Research Support, N.I.H., Extramural ; Letter
    ZDB-ID 1464822-2
    ISSN 1462-0332 ; 1462-0324
    ISSN (online) 1462-0332
    ISSN 1462-0324
    DOI 10.1093/rheumatology/keac647
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  5. Article ; Online: Epidemiology of Upper Limb Complex Regional Pain Syndrome in a Retrospective Cohort of Persons Aged 9-30 Years, 2002-2017.

    Naleway, Allison L / Henninger, Michelle L / Irving, Stephanie A / Bianca Salas, S / Kauffman, Tia L / Crane, Bradley / Mittendorf, Kathleen F / Harsh, Stacy / Elder, Charles / Gee, Julianne

    The Permanente journal

    2023  Volume 27, Issue 2, Page(s) 75–86

    Abstract: Introduction This paper describes the epidemiology and clinical presentation of complex regional pain syndrome (CRPS) in a large, integrated health care delivery system; and CRPS incidence rates (IRs) over a time period spanning human papillomavirus (HPV) ...

    Abstract Introduction This paper describes the epidemiology and clinical presentation of complex regional pain syndrome (CRPS) in a large, integrated health care delivery system; and CRPS incidence rates (IRs) over a time period spanning human papillomavirus (HPV) vaccine licensure and published case reports of CRPS following HPV vaccination. Methods The authors examined CRPS diagnoses in patients aged 9-30 years between January 2002 and December 2017 using electronic medical records, excluding patients with lower limb diagnoses only. Medical record abstraction and adjudication were conducted to verify diagnoses and describe clinical characteristics. CRPS IRs were calculated for 3 periods: Period 1 (2002-2006: before HPV vaccine licensure), Period 2 (2007-2012: after licensure but before published case reports), and Period 3 (2013-2017: after published case reports). Results A total of 231 individuals received an upper limb or unspecified CRPS diagnosis code during the study period; 113 cases were verified through abstraction and adjudication. Most verified cases (73%) were associated with a clear precipitating event (eg, non-vaccine-related injury, surgical procedure). The authors identified only 1 case in which a practitioner attributed CRPS onset to HPV vaccination. Twenty-five incident cases occurred in Period 1 (IR = 4.35/100,000 person-years (PY), 95% confidence interval (CI) = 2.94-6.44), 42 in Period 2 (IR = 5.94/100,000 PY, 95% CI = 4.39-8.04), and 29 in Period 3 (IR = 4.53/100,000 PY, 95% CI = 3.15-6.52); differences between periods were not statistically significant. Conclusion These data provide a comprehensive assessment of the epidemiology and characteristics of CRPS in children and young adults and provide further reassurance about the safety of HPV vaccination.
    MeSH term(s) Child ; Humans ; Young Adult ; Complex Regional Pain Syndromes/epidemiology ; Complex Regional Pain Syndromes/diagnosis ; Papillomavirus Infections/prevention & control ; Papillomavirus Vaccines ; Retrospective Studies ; Upper Extremity ; Vaccination
    Chemical Substances Papillomavirus Vaccines
    Language English
    Publishing date 2023-05-08
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2062823-7
    ISSN 1552-5775 ; 1552-5775
    ISSN (online) 1552-5775
    ISSN 1552-5775
    DOI 10.7812/TPP/22.170
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  6. Article ; Online: Creating accessible Spanish language materials for Clinical Sequencing Evidence-Generating Research consortium genomic projects: challenges and lessons learned.

    Lindberg, Nangel M / Gutierrez, Amanda M / Mittendorf, Kathleen F / Ramos, Michelle A / Anguiano, Beatriz / Angelo, Frank / Joseph, Galen

    Personalized medicine

    2021  Volume 18, Issue 5, Page(s) 441–454

    Abstract: Aim: ...

    Abstract Aim:
    MeSH term(s) Genomics ; Hispanic or Latino ; Humans ; Language ; Surveys and Questionnaires ; Translating
    Language English
    Publishing date 2021-08-27
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2299146-3
    ISSN 1744-828X ; 1741-0541
    ISSN (online) 1744-828X
    ISSN 1741-0541
    DOI 10.2217/pme-2020-0075
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  7. Article ; Online: Prediction of Effectiveness and Toxicities of Immune Checkpoint Inhibitors Using Real-World Patient Data.

    Lippenszky, Levente / Mittendorf, Kathleen F / Kiss, Zoltán / LeNoue-Newton, Michele L / Napan-Molina, Pablo / Rahman, Protiva / Ye, Cheng / Laczi, Balázs / Csernai, Eszter / Jain, Neha M / Holt, Marilyn E / Maxwell, Christina N / Ball, Madeleine / Ma, Yufang / Mitchell, Margaret B / Johnson, Douglas B / Smith, David S / Park, Ben H / Micheel, Christine M /
    Fabbri, Daniel / Wolber, Jan / Osterman, Travis J

    JCO clinical cancer informatics

    2024  Volume 8, Page(s) e2300207

    Abstract: Purpose: Although immune checkpoint inhibitors (ICIs) have improved outcomes in certain patients with cancer, they can also cause life-threatening immunotoxicities. Predicting immunotoxicity risks alongside response could provide a personalized risk- ... ...

    Abstract Purpose: Although immune checkpoint inhibitors (ICIs) have improved outcomes in certain patients with cancer, they can also cause life-threatening immunotoxicities. Predicting immunotoxicity risks alongside response could provide a personalized risk-benefit profile, inform therapeutic decision making, and improve clinical trial cohort selection. We aimed to build a machine learning (ML) framework using routine electronic health record (EHR) data to predict hepatitis, colitis, pneumonitis, and 1-year overall survival.
    Methods: Real-world EHR data of more than 2,200 patients treated with ICI through December 31, 2018, were used to develop predictive models. Using a prediction time point of ICI initiation, a 1-year prediction time window was applied to create binary labels for the four outcomes for each patient. Feature engineering involved aggregating laboratory measurements over appropriate time windows (60-365 days). Patients were randomly partitioned into training (80%) and test (20%) sets. Random forest classifiers were developed using a rigorous model development framework.
    Results: The patient cohort had a median age of 63 years and was 61.8% male. Patients predominantly had melanoma (37.8%), lung cancer (27.3%), or genitourinary cancer (16.4%). They were treated with PD-1 (60.4%), PD-L1 (9.0%), and CTLA-4 (19.7%) ICIs. Our models demonstrate reasonably strong performance, with AUCs of 0.739, 0.729, 0.755, and 0.752 for the pneumonitis, hepatitis, colitis, and 1-year overall survival models, respectively. Each model relies on an outcome-specific feature set, though some features are shared among models.
    Conclusion: To our knowledge, this is the first ML solution that assesses individual ICI risk-benefit profiles based predominantly on routine structured EHR data. As such, use of our ML solution will not require additional data collection or documentation in the clinic.
    MeSH term(s) Humans ; Male ; Middle Aged ; Female ; Immune Checkpoint Inhibitors ; Ambulatory Care Facilities ; Colitis ; Hepatitis ; Pneumonia/chemically induced ; Pneumonia/diagnosis
    Chemical Substances Immune Checkpoint Inhibitors
    Language English
    Publishing date 2024-03-01
    Publishing country United States
    Document type Journal Article
    ISSN 2473-4276
    ISSN (online) 2473-4276
    DOI 10.1200/CCI.23.00207
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  8. Article ; Online: Participant-guided development of bilingual genomic educational infographics for Electronic Medical Records and Genomics Phase IV study.

    Casillan, Aimiel / Florido, Michelle E / Galarza-Cornejo, Jamie / Bakken, Suzanne / Lynch, John A / Chung, Wendy K / Mittendorf, Kathleen F / Berner, Eta S / Connolly, John J / Weng, Chunhua / Holm, Ingrid A / Khan, Atlas / Kiryluk, Krzysztof / Limdi, Nita A / Petukhova, Lynn / Sabatello, Maya / Wynn, Julia

    Journal of the American Medical Informatics Association : JAMIA

    2023  Volume 31, Issue 2, Page(s) 306–316

    Abstract: Objective: Developing targeted, culturally competent educational materials is critical for participant understanding of engagement in a large genomic study that uses computational pipelines to produce genome-informed risk assessments.: Materials and ... ...

    Abstract Objective: Developing targeted, culturally competent educational materials is critical for participant understanding of engagement in a large genomic study that uses computational pipelines to produce genome-informed risk assessments.
    Materials and methods: Guided by the Smerecnik framework that theorizes understanding of multifactorial genetic disease through 3 knowledge types, we developed English and Spanish infographics for individuals enrolled in the Electronic Medical Records and Genomics Network. Infographics were developed to explain concepts in lay language and visualizations. We conducted iterative sessions using a modified "think-aloud" process with 10 participants (6 English, 4 Spanish-speaking) to explore comprehension of and attitudes towards the infographics.
    Results: We found that all but one participant had "awareness knowledge" of genetic disease risk factors upon viewing the infographics. Many participants had difficulty with "how-to" knowledge of applying genetic risk factors to specific monogenic and polygenic risks. Participant attitudes towards the iteratively-refined infographics indicated that design saturation was reached.
    Discussion: There were several elements that contributed to the participants' comprehension (or misunderstanding) of the infographics. Visualization and iconography techniques best resonated with those who could draw on prior experiences or knowledge and were absent in those without. Limited graphicacy interfered with the understanding of absolute and relative risks when presented in graph format. Notably, narrative and storytelling theory that informed the creation of a vignette infographic was most accessible to all participants.
    Conclusion: Engagement with the intended audience who can identify strengths and points for improvement of the intervention is necessary to the development of effective infographics.
    MeSH term(s) Humans ; Communication ; Data Visualization ; Electronic Health Records ; Genomics ; Health Education/methods
    Language English
    Publishing date 2023-10-04
    Publishing country England
    Document type Journal Article
    ZDB-ID 1205156-1
    ISSN 1527-974X ; 1067-5027
    ISSN (online) 1527-974X
    ISSN 1067-5027
    DOI 10.1093/jamia/ocad207
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    Zs.A 4128: Show issues Location:
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  9. Article: Evaluating cancer genetic services in a safety net system: overcoming barriers for a lasting impact beyond the CHARM research project.

    Okuyama, Sonia / White, Larissa L / Anderson, Katherine P / Medina, Elizabeth / Deutsch, Sonia / Ransom, Chelese / Jackson, Paige / Kauffman, Tia L / Mittendorf, Kathleen F / Leo, Michael C / Bulkley, Joanna E / Wilfond, Benjamin S / Goddard, Katrina Ab / Feigelson, Heather Spencer

    Journal of community genetics

    2023  Volume 14, Issue 3, Page(s) 329–336

    Abstract: Underserved patients face substantial barriers to receiving cancer genetic services. The Cancer Health Assessments Reaching Many (CHARM) study evaluated ways to increase access to genetic testing for individuals in underserved populations at risk for ... ...

    Abstract Underserved patients face substantial barriers to receiving cancer genetic services. The Cancer Health Assessments Reaching Many (CHARM) study evaluated ways to increase access to genetic testing for individuals in underserved populations at risk for hereditary cancer syndromes (HCS). Here, we report the successful implementation of CHARM in a low-resource environment and the development of sustainable processes to continue genetic risk assessment in this setting. The research team involved key clinical personnel and patient advisors at Denver Health to provide input on study methods and materials. Through iterative and collaborative stakeholder engagement, the team identified barriers and developed solutions that would both facilitate participation in CHARM and be feasible to implement and sustain long term in clinical care. With a focus on infrastructure building, educational modules were developed to increase awareness among referring providers, and standard methods of identifying and managing HCS patients were implemented in the electronic medical record. Three hundred sixty-four DH patients successfully completed the risk assessment tool within the study, and we observed a sustained increase in referrals to genetics for HCS (from 179 in 2017 to 427 in 2021 post-intervention). Implementation of the CHARM study at a low-resourced safety net health system resulted in sustainable improvements in access to cancer genetic risk assessment and services that continue even after the study ended.Trial registration NCT03426878.
    Language English
    Publishing date 2023-05-01
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 2543127-4
    ISSN 1868-6001 ; 1868-310X
    ISSN (online) 1868-6001
    ISSN 1868-310X
    DOI 10.1007/s12687-023-00647-x
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  10. Article ; Online: Conducting inclusive research in genetics for transgender, gender-diverse, and sex-diverse individuals: Case analyses and recommendations from a clinical genomics study.

    Bland, Harris T / Gilmore, Marian J / Andujar, Justin / Martin, Makenna A / Celaya-Cobbs, Natasha / Edwards, Clasherrol / Gerhart, Meredith / Hooker, Gillian W / Kraft, Stephanie A / Marshall, Dana R / Orlando, Lori A / Paul, Natalie A / Pratap, Siddharth / Rosenbloom, S Trent / Wiesner, Georgia L / Mittendorf, Kathleen F

    Journal of genetic counseling

    2023  

    Abstract: A person's phenotypic sex (i.e., endogenous expression of primary, secondary, and endocrinological sex characteristics) can impact crucial aspects of genetic assessment and resulting clinical care recommendations. In studies with genetics components, it ... ...

    Abstract A person's phenotypic sex (i.e., endogenous expression of primary, secondary, and endocrinological sex characteristics) can impact crucial aspects of genetic assessment and resulting clinical care recommendations. In studies with genetics components, it is critical to collect phenotypic sex, information about current organ/tissue inventory and hormonal milieu, and gender identity. If researchers do not carefully construct data models, transgender, gender diverse, and sex diverse (TGSD) individuals may be given inappropriate care recommendations and/or be subjected to misgendering, inflicting medical and psychosocial harms. The recognized need for an inclusive care experience should not be limited to clinical practice but should extend to the research setting, where researchers must build an inclusive experience for TGSD participants. Here, we review three TGSD participants in the Family History and Cancer Risk Study (FOREST) to critically evaluate sex- and gender-related survey measures and associated data models in a study seeking to identify patients at risk for hereditary cancer syndromes. Furthermore, we leverage these participants' responses to sex- and gender identity-related questions in FOREST to inform needed changes to the FOREST data model and to make recommendations for TGSD-inclusive genetics research design, data models, and processes.
    Language English
    Publishing date 2023-09-04
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1117799-8
    ISSN 1573-3599 ; 1059-7700
    ISSN (online) 1573-3599
    ISSN 1059-7700
    DOI 10.1002/jgc4.1785
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