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Article: Neighborhood-level COVID vaccination and booster disparities: A population-level analysis across California.

Oh, Debora L / Kemper, Kathryn E / Meltzer, Dan / Canchola, Alison J / Bibbins-Domingo, Kirsten / Lyles, Courtney R

SSM - population health

2023 Volume 22, Page(s) 101366

Abstract: Objectives: To describe vaccine and booster uptake by neighborhood-level factors in California.: Methods: We examined trends in COVID-19 vaccination up to September 21, 2021, and boosters up to March 29, 2022 using data from the California Department ...

Abstract	Objectives: To describe vaccine and booster uptake by neighborhood-level factors in California. Methods: We examined trends in COVID-19 vaccination up to September 21, 2021, and boosters up to March 29, 2022 using data from the California Department of Public Health. Quasi-Poisson regression was used to model the association between neighborhood-level factors and fully vaccinated and boosted among ZIP codes. Sub-analyses on booster rates were compared among the 10 census regions. Results: In a minimally adjusted model, a higher proportion of Black residents was associated with lower vaccination (HR = 0.97; 95%CI: 0.96-0.98). However, in a fully adjusted model, proportion of Black, Hispanic/Latinx, and Asian residents were associated with higher vaccination rates (HR = 1.02; 95%CI: 1.01-1.03 for all). The strongest predictor of low vaccine coverage was disability (HR = 0.89; 95%CI: 0.86-0.91). Similar trends persisted for booster doses. Factors associated with booster coverage varied by region. Conclusions: Examining neighborhood-level factors associated with COVID-19 vaccination and booster rates uncovered significant variation within the large and geographically and demographically diverse state of California. Equity-based approaches to vaccination must ensure a robust consideration of multiple social determinants of health.
Language	English
Publishing date	2023-02-21
Publishing country	England
Document type	Journal Article
ISSN	2352-8273
ISSN	2352-8273
DOI	10.1016/j.ssmph.2023.101366
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Article ; Online: Impacts of Individual Patient Language and Neighborhood Ethnic Enclave on COVID-19 Test Positivity Among Hispanic/Latinx Patients in San Francisco.

Nguyen, Kim Hanh / Rubinsky, Anna D / DeRouen, Mindy C / Kemper, Kathryn E / Bibbins-Domingo, Kirsten / Lyles, Courtney R

Medical care

2023 Volume 61, Issue 2, Page(s) 67–74

Abstract: Background: Given the known disparities in COVID-19 within the Hispanic/Latinx community, we sought to examine the interaction between individual-level and neighborhood-level social determinants of health using linked electronic health record data.: ... ...

Abstract	Background: Given the known disparities in COVID-19 within the Hispanic/Latinx community, we sought to examine the interaction between individual-level and neighborhood-level social determinants of health using linked electronic health record data. Methods: We examined electronic health record data linked to neighborhood data among Hispanic/Latinx patients tested for COVID-19 between March 1, 2020, and February 28, 2021, from 2 large health care systems in San Francisco. Hispanic/Latinx ethnic enclave is measured using an index of census-tract level indicators of ethnicity, nativity, and language. Multilevel logistic regression models examined associations between ethnic enclave and COVID-19 positivity (COVID-19+), adjusting for patient-level sociodemographic and clinical characteristics and health system. Cross-level interactions were used to test whether associations between ethnic enclave and COVID-19+ differed by patient language preference. Results: Among 26,871 patients, mean age was 37 years, 56% had Spanish-language preference, and 21% were COVID-19+. In unadjusted models, patients living in the highest versus lowest Hispanic/Latinx enclave had 3.2 higher odds of COVID-19+ (95% CI, 2.45-4.24). Adjusted, the relationship between ethnic enclave and COVID-19+ was attenuated, but not eliminated (odds ratio: 1.4; 95% CI, 1.13-1.17). Our results demonstrated a significant cross-level interaction, such that the influence of ethnic enclave was modified by patient language preference. For individuals with Spanish-language preference, risk of COVID-19+ was high regardless of neighborhood context, whereas for those with English preference, neighborhood ethnic enclave more than doubled the odds of infection. Conclusions: Findings suggest that a multilevel and intersectional approach to the study of COVID-19 inequities may illuminate dimensions of health inequity that affect marginalized communities and offer insights for targeted clinical and community-based interventions.
MeSH term(s)	Humans ; Adult ; San Francisco ; COVID-19 ; Hispanic or Latino ; Ethnicity ; Residence Characteristics
Language	English
Publishing date	2023-01-11
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	411646-x
ISSN	1537-1948 ; 0025-7079
ISSN (online)	1537-1948
ISSN	0025-7079
DOI	10.1097/MLR.0000000000001804
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Article ; Online: Advancing artificial intelligence to help feed the world.

Hayes, Ben J / Chen, Chensong / Powell, Owen / Dinglasan, Eric / Villiers, Kira / Kemper, Kathryn E / Hickey, Lee T

Nature biotechnology

2023 Volume 41, Issue 9, Page(s) 1188–1189

MeSH term(s)	Artificial Intelligence ; Food Supply
Language	English
Publishing date	2023-07-31
Publishing country	United States
Document type	Letter ; Research Support, Non-U.S. Gov't
ZDB-ID	1311932-1
ISSN	1546-1696 ; 1087-0156
ISSN (online)	1546-1696
ISSN	1087-0156
DOI	10.1038/s41587-023-01898-2
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Article: Social Determinants of Health Documentation in Structured and Unstructured Clinical Data of Patients With Diabetes: Comparative Analysis.

Mehta, Shivani / Lyles, Courtney R / Rubinsky, Anna D / Kemper, Kathryn E / Auerbach, Judith / Sarkar, Urmimala / Gottlieb, Laura / Brown Iii, William

JMIR medical informatics

2023 Volume 11, Page(s) e46159

Abstract: Background: Electronic health records (EHRs) have yet to fully capture social determinants of health (SDOH) due to challenges such as nonexistent or inconsistent data capture tools across clinics, lack of time, and the burden of extra steps for the ... ...

Abstract	Background: Electronic health records (EHRs) have yet to fully capture social determinants of health (SDOH) due to challenges such as nonexistent or inconsistent data capture tools across clinics, lack of time, and the burden of extra steps for the clinician. However, patient clinical notes (unstructured data) may be a better source of patient-related SDOH information. Objective: It is unclear how accurately EHR data reflect patients' lived experience of SDOH. The manual process of retrieving SDOH information from clinical notes is time-consuming and not feasible. We leveraged two high-throughput tools to identify SDOH mappings to structured and unstructured patient data: PatientExploreR and Electronic Medical Record Search Engine (EMERSE). Methods: We included adult patients (≥18 years of age) receiving primary care for their diabetes at the University of California, San Francisco (UCSF), from January 1, 2018, to December 31, 2019. We used expert raters to develop a corpus using SDOH in the compendium as a knowledge base as targets for the natural language processing (NLP) text string mapping to find string stems, roots, and syntactic similarities in the clinical notes of patients with diabetes. We applied advanced built-in EMERSE NLP query parsers implemented with JavaCC. Results: We included 4283 adult patients receiving primary care for diabetes at UCSF. Our study revealed that SDOH may be more significant in the lives of patients with diabetes than is evident from structured data recorded on EHRs. With the application of EMERSE NLP rules, we uncovered additional information from patient clinical notes on problems related to social connectionsisolation, employment, financial insecurity, housing insecurity, food insecurity, education, and stress. Conclusions: We discovered more patient information related to SDOH in unstructured data than in structured data. The application of this technique and further investment in similar user-friendly tools and infrastructure to extract SDOH information from unstructured data may help to identify the range of social conditions that influence patients' disease experiences and inform clinical decision-making.
Language	English
Publishing date	2023-08-22
Publishing country	Canada
Document type	Journal Article
ZDB-ID	2798261-0
ISSN	2291-9694
ISSN	2291-9694
DOI	10.2196/46159
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Article ; Online: Genetic influence on within-person longitudinal change in anthropometric traits in the UK Biobank.

Kemper, Kathryn E / Sidorenko, Julia / Wang, Huanwei / Hayes, Ben J / Wray, Naomi R / Yengo, Loic / Keller, Matthew C / Goddard, Michael / Visscher, Peter M

Nature communications

2024 Volume 15, Issue 1, Page(s) 3776

Abstract: The causes of temporal fluctuations in adult traits are poorly understood. Here, we investigate the genetic determinants of within-person trait variability of 8 repeatedly measured anthropometric traits in 50,117 individuals from the UK Biobank. We found ...

Abstract	The causes of temporal fluctuations in adult traits are poorly understood. Here, we investigate the genetic determinants of within-person trait variability of 8 repeatedly measured anthropometric traits in 50,117 individuals from the UK Biobank. We found that within-person (non-directional) variability had a SNP-based heritability of 2-5% for height, sitting height, body mass index (BMI) and weight (P
MeSH term(s)	Humans ; United Kingdom ; Biological Specimen Banks ; Polymorphism, Single Nucleotide ; Male ; Female ; Body Mass Index ; Aged ; Quantitative Trait Loci ; Middle Aged ; Body Height/genetics ; Longitudinal Studies ; Apolipoproteins E/genetics ; Anthropometry ; Mendelian Randomization Analysis ; Bone Density/genetics ; Body Weight/genetics ; Adult ; Alzheimer Disease/genetics ; Genome-Wide Association Study ; Lumbar Vertebrae ; Alleles ; UK Biobank
Chemical Substances	Apolipoproteins E
Language	English
Publishing date	2024-05-06
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-024-47802-7
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Article: Parsimonious model for mass-univariate vertexwise analysis.

Couvy-Duchesne, Baptiste / Zhang, Futao / Kemper, Kathryn E / Sidorenko, Julia / Wray, Naomi R / Visscher, Peter M / Colliot, Olivier / Yang, Jian

Journal of medical imaging (Bellingham, Wash.)

2022 Volume 9, Issue 5, Page(s) 52404

Abstract: Purpose: ...

Abstract	Purpose:
Language	English
Publishing date	2022-05-20
Publishing country	United States
Document type	Journal Article
ISSN	2329-4302
ISSN	2329-4302
DOI	10.1117/1.JMI.9.5.052404
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Article ; Online: Cross-ancestry analyses identify new genetic loci associated with 25-hydroxyvitamin D.

Wang, Xiaotong / Hivert, Valentin / Groot, Shiane / Wang, Ying / Yengo, Loic / McGrath, John J / Kemper, Kathryn E / Visscher, Peter M / Wray, Naomi R / Revez, Joana A

PLoS genetics

2023 Volume 19, Issue 11, Page(s) e1011033

Abstract: Vitamin D status-a complex trait influenced by environmental and genetic factors-is tightly associated with skin colour and ancestry. Yet very few studies have investigated the genetic underpinnings of vitamin D levels across diverse ancestries, and the ... ...

Abstract	Vitamin D status-a complex trait influenced by environmental and genetic factors-is tightly associated with skin colour and ancestry. Yet very few studies have investigated the genetic underpinnings of vitamin D levels across diverse ancestries, and the ones that have, relied on small sample sizes, resulting in inconclusive results. Here, we conduct genome-wide association studies (GWAS) of 25 hydroxyvitamin D (25OHD)-the main circulating form of vitamin D-in 442,435 individuals from four broad genetically-determined ancestry groups represented in the UK Biobank: European (N = 421,867), South Asian (N = 9,983), African (N = 8,306) and East Asian (N = 2,279). We identify a new genetic determinant of 25OHD (rs146759773) in individuals of African ancestry, which was not detected in previous analysis of much larger European cohorts due to low minor allele frequency. We show genome-wide significant evidence of dominance effects in 25OHD that protect against vitamin D deficiency. Given that key events in the synthesis of 25OHD occur in the skin and are affected by pigmentation levels, we conduct GWAS of 25OHD stratified by skin colour and identify new associations. Lastly, we test the interaction between skin colour and variants associated with variance in 25OHD levels and identify two loci (rs10832254 and rs1352846) whose association with 25OHD differs in individuals of distinct complexions. Collectively, our results provide new insights into the complex relationship between 25OHD and skin colour and highlight the importance of diversity in genomic studies. Despite the much larger rates of vitamin D deficiency that we and others report for ancestry groups with dark skin (e.g., South Asian), our study highlights the importance of considering ancestral background and/or skin colour when assessing the implications of low vitamin D.
MeSH term(s)	Humans ; Genome-Wide Association Study ; Polymorphism, Single Nucleotide/genetics ; Vitamin D/genetics ; Vitamin D Deficiency/genetics
Chemical Substances	25-hydroxyvitamin D (A288AR3C9H) ; Vitamin D (1406-16-2)
Language	English
Publishing date	2023-11-14
Publishing country	United States
Document type	Journal Article
ZDB-ID	2186725-2
ISSN	1553-7404 ; 1553-7390
ISSN (online)	1553-7404
ISSN	1553-7390
DOI	10.1371/journal.pgen.1011033
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Article ; Online: Visit and Between-Visit Interaction Frequency Before and After COVID-19 Telehealth Implementation.

Nouri, Sarah / Lyles, Courtney R / Sherwin, Elizabeth B / Kuznia, Magdalene / Rubinsky, Anna D / Kemper, Kathryn E / Nguyen, Oanh K / Sarkar, Urmimala / Schillinger, Dean / Khoong, Elaine C

JAMA network open

2023 Volume 6, Issue 9, Page(s) e2333944

Abstract: Importance: Telehealth implementation associated with the COVID-19 public health emergency (PHE) affected patient-clinical team interactions in numerous ways. Yet, studies have narrowly examined billed patient-clinician visits rather than including ... ...

Abstract	Importance: Telehealth implementation associated with the COVID-19 public health emergency (PHE) affected patient-clinical team interactions in numerous ways. Yet, studies have narrowly examined billed patient-clinician visits rather than including visits with other team members (eg, pharmacists) or between-visit interactions. Objective: To evaluate rates of change over time in visits (in-person, telehealth) and between-visit interactions (telephone calls, patient portal messages) overall and by key patient characteristics. Design, setting, and participants: This retrospective cohort study included adults with diabetes receiving primary care at urban academic (University of California San Francisco [UCSF]) and safety-net (San Francisco Health Network [SFHN]) health care systems. Encounters from April 2019 to March 2021 were analyzed. Exposure: Telehealth implementation over 3 periods: pre-PHE (April 2019 to March 2020), strict shelter-in-place (April to June 2020), and hybrid-PHE (July 2020 to March 2021). Main outcomes and measures: The main outcomes were rates of change in monthly mean number of total encounters, visits with any health care team member, visits with billing clinicians, and between-visit interactions. Key patient-level characteristics were age, race and ethnicity, language, and neighborhood socioeconomic status (nSES). Results: Of 15 148 patients (4976 UCSF; 8975 SFHN) included, 2464 (16%) were 75 years or older, 7734 (51%) were female patients, 9823 (65%) self-identified as racially or ethnically minoritized, 6223 (41%) had a non-English language preference, and 4618 (31%) lived in the lowest nSES quintile. After accounting for changes to care delivery through an interrupted time-series analysis, total encounters increased in the hybrid-PHE period (UCSF: 2.3% per patient/mo; 95% CI, 1.6%-2.9% per patient/mo; SFHN: 1.8% per patient/mo, 95% CI, 1.3%-2.2% per patient/mo), associated primarily with growth in between-visit interactions (UCSF: 3.1% per patient/mo, 95% CI, 2.3%-3.8% per patient/mo; SFHN: 2.9% per patient/mo, 95% CI, 2.3%-3.4% per patient/mo). In contrast, rates of visits were stable during the hybrid-PHE period. Although there were fewer differences in visit use by key patient-level characteristics during the hybrid-PHE period, pre-PHE differences in between-visit interactions persisted during the hybrid-PHE period at SFHN. Asian and Chinese-speaking patients at SFHN had fewer monthly mean between-visit interactions compared with White patients (0.46 [95% CI, 0.42-0.50] vs 0.59 [95% CI, 0.53-0.66] between-visit interactions/patient/mo; P < .001) and English-speaking patients (0.52 [95% CI, 0.47-0.58] vs 0.61 [95% CI, 0.56-0.66] between-visit interactions/patient/mo; P = .03). Conclusions and relevance: In this study, pre-PHE growth in overall patient-clinician encounters persisted after PHE-related telehealth implementation, driven in both periods by between-visit interactions. Differential utilization based on patient characteristics was observed, which may indicate disparities. The implications for health care team workload and patient outcomes are unknown, particularly regarding between-visit interactions. Therefore, to comprehensively understand care utilization for patients with chronic diseases, research should expand beyond billed visits.
MeSH term(s)	Adult ; Female ; Humans ; Male ; COVID-19 ; Retrospective Studies ; Telemedicine ; Diabetes Mellitus/therapy ; Delivery of Health Care ; Primary Health Care
Language	English
Publishing date	2023-09-05
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, P.H.S. ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ISSN	2574-3805
ISSN (online)	2574-3805
DOI	10.1001/jamanetworkopen.2023.33944
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Article ; Online: HIV viral load testing and monitoring in Côte d'Ivoire: A survival analysis of viral load testing and suppression, and evaluation of adherence to national recommendations.

Kemper, Kathryn E / Augusto, Orvalho / Gloyd, Stephen / Akoku, Derick A / Ouattara, Gbossouna / Perrone, Lucy A / Assoa, Paul Henri / Akoua-Koffi, Chantal / Adje-Toure, Christiane / Koné, Ahoua

PLOS global public health

2023 Volume 3, Issue 9, Page(s) e0001822

Abstract: Routine viral load (VL) monitoring is the standard of care in Côte d'Ivoire and allows for effective treatment guidance for people living with human immunodeficiency virus (HIV) to reach viral load suppression (VLS). For VL monitoring to be effective in ... ...

Abstract	Routine viral load (VL) monitoring is the standard of care in Côte d'Ivoire and allows for effective treatment guidance for people living with human immunodeficiency virus (HIV) to reach viral load suppression (VLS). For VL monitoring to be effective in reducing the impact of HIV, it must be provided in accordance with national guidance. This study aimed to evaluate VL testing, VLS rates and adherence to national guidance for VL testing using data collected from three national laboratories. We collected data on VL testing between 2015-2018 from OpenELIS (OE), an open-source electronic laboratory information system. We merged data by unique patient ID for patients (0-80 years old) who received multiple VL tests to calculate time between tests. We defined VLS as HIV RNA ≤1,000 copies/mL based on Côte d'Ivoire national and WHO guidance at the time of data collection. We used the Kaplan-Meier survival estimator to estimate time between ART (antiretroviral therapy) initiation and the first VL test, time between subsequent VL tests, and to estimate the proportion of people living with HIV (PLHIV) who were virally suppressed within 12 months of ART initiation. At the first documented VL test, 79.6% of patients were virally suppressed (95% CI: 78.9-80.3). Children under 15 were the least likely to be virally suppressed (55.2%, 95% CI: 51.5-58.8). The median time from ART initiation to the first VL sample collection for testing was 7.8 months (IQR:6.2-13.4). 72.4% of patients were virally suppressed within one year of treatment initiation (95% CI:71.5-73.3). Approximately 30% of patients received a second VL test during the 4-year study period. The median time between the first and second VL tests was 24.9 months (IQR: 4.7->40). Most PLHIV received their first VL test within the recommended 12 months of ART initiation but did not receive subsequent VL monitoring tests within the recommended time frame, reducing the benefits of VL monitoring. While VLS was fairly high, children were least likely to be virally suppressed. Our findings highlight the importance of regular VL monitoring after the first VL test, especially for children.
Language	English
Publishing date	2023-09-14
Publishing country	United States
Document type	Journal Article
ISSN	2767-3375
ISSN (online)	2767-3375
DOI	10.1371/journal.pgph.0001822
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Article ; Online: Comparison of Genotypic and Phenotypic Correlations: Cheverud's Conjecture in Humans.

Sodini, Sebastian M / Kemper, Kathryn E / Wray, Naomi R / Trzaskowski, Maciej

Genetics

2018 Volume 209, Issue 3, Page(s) 941–948

Abstract: Accurate estimation of genetic correlation requires large sample sizes and access to genetically informative data, which are not always available. Accordingly, phenotypic correlations are often assumed to reflect genotypic correlations in evolutionary ... ...

Abstract	Accurate estimation of genetic correlation requires large sample sizes and access to genetically informative data, which are not always available. Accordingly, phenotypic correlations are often assumed to reflect genotypic correlations in evolutionary biology. Cheverud's conjecture asserts that the use of phenotypic correlations as proxies for genetic correlations is appropriate. Empirical evidence of the conjecture has been found across plant and animal species, with results suggesting that there is indeed a robust relationship between the two. Here, we investigate the conjecture in human populations, an analysis made possible by recent developments in availability of human genomic data and computing resources. A sample of 108,035 British European individuals from the UK Biobank was split equally into discovery and replication datasets. Seventeen traits were selected based on sample size, distribution, and heritability. Genetic correlations were calculated using linkage disequilibrium score regression applied to the genome-wide association summary statistics of pairs of traits, and compared within and across datasets. Strong and significant correlations were found for the between-dataset comparison, suggesting that the genetic correlations from one independent sample were able to predict the phenotypic correlations from another independent sample within the same population. Designating the selected traits as morphological or nonmorphological indicated little difference in correlation. The results of this study support the existence of a relationship between genetic and phenotypic correlations in humans. This finding is of specific interest in anthropological studies, which use measured phenotypic correlations to make inferences about the genetics of ancient human populations.
MeSH term(s)	Anthropology ; Biological Evolution ; Biological Specimen Banks ; European Continental Ancestry Group/genetics ; Genetic Variation ; Genetics, Population ; Genome-Wide Association Study/methods ; Genotype ; Humans ; Linkage Disequilibrium ; Phenotype ; Quantitative Trait Loci ; United Kingdom
Language	English
Publishing date	2018-05-08
Publishing country	United States
Document type	Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2167-2
ISSN	1943-2631 ; 0016-6731
ISSN (online)	1943-2631
ISSN	0016-6731
DOI	10.1534/genetics.117.300630
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