Genotype Imputation for African Americans Using Data From HapMap Phase II Versus 1000 Genomes Projects

Background: Reference-based phasing and genotype imputation algorithms have been developed with sublinear theoretical runtime behaviour, but runtimes are still high in practice when large genome-wide reference datasets are used. Methods: We developed EagleImp, a software with algorithmic and technical improvements and new features for accurate and accelerated phasing and imputation in a single tool. Results: We compared accuracy and runtime of EagleImp with Eagle2, PBWT and prominent imputation servers using whole-genome sequencing data from the 1000 Genomes Project, the Haplotype Reference Consortium and simulated data with more than 1 million reference genomes. EagleImp is 2 to 10 times faster (depending on the single or multiprocessor configuration selected) than Eagle2/PBWT, with the same or better phasing and imputation quality in all tested scenarios. For common variants investigated in typical GWAS studies, EagleImp provides same or higher imputation accuracy than the Sanger Imputation Service, Michigan Imputation Server and the newly developed TOPMed Imputation Server, despite larger (not publicly available) reference panels. It has many new features, including automated chromosome splitting and memory management at runtime to avoid job aborts, fast reading and writing of large files, and various user-configurable algorithm and output options. Conclusions: Due to the technical optimisations, EagleImp can perform fast and accurate reference-based phasing and imputation for future very large reference panels with more than 1 million genomes. EagleImp is freely available for download from https://github.com/ikmb/eagleimp.

Download Full-text

BMI Trajectories in Adulthood: The Intersection of Skin Color, Gender, and Age among African Americans

Journal of Health and Social Behavior ◽

10.1177/0022146518802439 ◽

2018 ◽

Vol 59 (4) ◽

pp. 501-519 ◽

Cited By ~ 6

Author(s):

Taylor W. Hargrove

Keyword(s):

African Americans ◽

Skin Color ◽

Growth Curve Models ◽

Gender And Age ◽

Bmi Trajectories ◽

Research Questions ◽

And Gender ◽

Using Data ◽

Gender Groups ◽

Gender Specific

This study addresses three research questions critical to understanding if and how skin color shapes health among African Americans: (1) Does skin color predict trajectories of body mass index (BMI) among African Americans across ages 32 to 55? (2) To what extent is this relationship contingent on gender? (3) Do sociodemographic, psychosocial, and behavioral factors explain the skin color–BMI relationship? Using data from the Coronary Artery Risk Development in Young Adults Study and growth curve models, results indicate that dark-skinned women have the highest BMI across adulthood compared to all other skin color–gender groups. BMI differences between dark- and lighter-skinned women remain stable from ages 32 to 55. Among men, a BMI disadvantage emerges and widens between light- and dark-skinned men and their medium-skinned counterparts. Observed sociodemographic characteristics, stressors, and health behaviors do not explain these associations. Overall, findings suggest that skin color– and gender-specific experiences likely play an important role in generating BMI inequality.

Download Full-text

An Examination of John Henryism, Trust, and Medication Adherence Among African Americans With Hypertension

Health Education & Behavior ◽

10.1177/1090198119878778 ◽

2019 ◽

Vol 47 (1) ◽

pp. 162-169

Author(s):

Yendelela L. Cuffee ◽

Lee Hargraves ◽

Milagros Rosal ◽

Becky A. Briesacher ◽

Jeroan J. Allison ◽

...

Keyword(s):

Medication Adherence ◽

African Americans ◽

Confidence Interval ◽

Health Behaviors ◽

Safety Net ◽

The Body ◽

John Henryism ◽

Point Increase ◽

Safety Net Hospital ◽

Using Data

Background. John Henryism is defined as a measure of active coping in response to stressful experiences. John Henryism has been linked with health conditions such as diabetes, prostate cancer, and hypertension, but rarely with health behaviors. Aims. We hypothesized that reporting higher scores on the John Henryism Scale may be associated with poorer medication adherence, and trust in providers may mediate this relationship. Method. We tested this hypothesis using data from the TRUST study. The TRUST study included 787 African Americans with hypertension receiving care at a safety-net hospital. Ordinal logistic regression was used to examine the relationship between John Henryism and medication adherence. Results. Within our sample of African Americans with hypertension, lower John Henryism scores was associated with poorer self-reported adherence (low, 20.62; moderate, 19.19; high, 18.12; p < .001). Higher John Henryism scores were associated with lower trust scores (low John Henryism: 40.1; high John Henryism: 37.9; p < .001). In the adjusted model, each 1-point increase in the John Henryism score decreased the odds of being in a better cumulative medication adherence category by a factor of 4% (odds ratio = 0.96, p = .014, 95% confidence interval = 0.93-0.99). Twenty percent of the association between medication adherence and John Henryism was mediated by trust (standard deviation = 0.205, 95% confidence interval = 0.074-0.335). Discussion. This study provides important insights into the complex relationship between psychological responses and health behaviors. It also contributes to the body of literature examining the construct of John Henryism among African Americans with hypertension. Conclusion. The findings of this study support the need for interventions that promote healthful coping strategies and patient–provider trust.

Download Full-text

Multitrial evaluation of progression-free survival (PFS) as a surrogate endpoint for overall survival (OS) in previously untreated extensive-stage small cell lung cancer (ES-SCLC): An Alliance-led analysis.

Journal of Clinical Oncology ◽

10.1200/jco.2013.31.15_suppl.7510 ◽

2013 ◽

Vol 31 (15_suppl) ◽

pp. 7510-7510 ◽

Cited By ~ 2

Author(s):

Nathan R. Foster ◽

Lindsay A. Renfro ◽

Steven E. Schild ◽

Mary Weber Redman ◽

Xiaofei F. Wang ◽

...

Keyword(s):

Phase Ii ◽

Primary Endpoint ◽

Cox Model ◽

Progression Free Survival ◽

Surrogate Endpoint ◽

Phase Iii ◽

Least Squares Regression ◽

Patient Level ◽

Phase Iii Trials ◽

Using Data

7510 Background: We previously demonstrated that PFS may be a candidate surrogate endpoint for OS in ES-SCLC using data from 3 randomized trials (Foster, Cancer 2011). Here, we sought to formally assess the patient- and trial-level surrogacy of PFS using data from 9 additional randomized phase II and III trials conducted by the NCI-funded cancer cooperative groups since 1986. Methods: Individual patient data from all 12 trials (3178 patients: 9 phase III and 3 phase II) were pooled. OS was the primary endpoint in all phase III trials; 3 phase III and 1 phase II trial were positive per protocol. Patient-level surrogacy (Kendall’s tau) was assessed using the Clayton copula bivariate survival model. Trial-level surrogacy was assessed via association of the log hazard ratios on OS and PFS across trials, including: weighted (by trial size) least squares regression of Cox model effects (R² WLS) and weighted (by trial size) correlation of the copula effects (R² Copula). One trial had 4 treatment arms thus 14 total two-arm comparisons were made. Results: With a median follow-up of 41.8 months in the 106 patients still alive, the median OS and PFS across trials were 9.7 months (95% CI: 9.5, 9.9) and 5.7 months (95% CI: 5.5, 5.8), respectively. There were 3120 PFS events in total (2564 disease progressions and 556 deaths without progression). The median time from progression to death was 4.1 months (95% CI: 3.9, 4.3). PFS showed modest association with OS at the patient-level (tau= 0.56) and at the trial-level (R² WLS = 0.58; R² Copula (standard error) = 0.55 (0.29)). The 95% CIs for the predicted HR for OS given observed HR on PFS under a weighted leave-one-out prediction always included the observed HR for OS; however such intervals were wide, suggesting uncertainty on the practical use of PFS as a surrogate for OS in this setting. Conclusions: PFS failed to demonstrate surrogacy for OS in ES-SCLC based on this large pooled analysis. Given that the difference in the median PFS and OS is less than 6 months, we recommend using OS as the primary endpoint in phase III trials of previously untreated ES-SCLC.

Download Full-text

Assessment of Genotype Imputation Performance Using 1000 Genomes in African American Studies

PLoS ONE ◽

10.1371/journal.pone.0050610 ◽

2012 ◽

Vol 7 (11) ◽

pp. e50610 ◽

Cited By ~ 35

Author(s):

Dana B. Hancock ◽

Joshua L. Levy ◽

Nathan C. Gaddis ◽

Laura J. Bierut ◽

Nancy L. Saccone ◽

...

Keyword(s):

African American ◽

American Studies ◽

African American Studies ◽

Genotype Imputation ◽

1000 Genomes

Download Full-text

Racial Differences in Multigenerational Living Arrangements in 1910

Social Science History ◽

10.1017/s014555320001155x ◽

2011 ◽

Vol 35 (3) ◽

pp. 275-322 ◽

Cited By ~ 1

Author(s):

Cheryl Elman ◽

Andrew S. London

Keyword(s):

African Americans ◽

Life Course ◽

Racial Differences ◽

Living Arrangements ◽

Living Arrangement ◽

Future Research ◽

European Americans ◽

Kin Support ◽

Using Data ◽

The Life Course

We explore racial differences in multigenerational living arrangements in 1910, focusing on trigenerational kin structures. Coresidence across generations represents a public function of the family, and we observe this across different ages or life-course stages through which adults came to be at risk for providing simultaneous household support for multiple generations of kin dependents. Using data from the 1.4 percent 1910 Integrated Public Use Microdata Sample, our comparisons adjust for marital turnover, including widow(er)hood/divorce and remarriage, as rates are known to be historically higher among African Americans in this period. Across subgroups defined by age and sex, we find that African Americans are virtually always as likely as or more likely than European Americans (of both native and foreign parentage) to live as grandparents in trigenerational households. Widow(er)hood/divorce generally increased the likelihood of trigenerational coresidence, while remarriage sometimes increased, sometimes decreased, and sometimes had no association with this living arrangement. Also, we find that the life-course staging of household kin support in 1910 differed across race/generation partly due to different economic and demographic circumstances, suggesting more complexity in kin support than previously considered. We discuss these findings in relation to the histories of African American and European American families as well as their implications for future research.

Download Full-text

Efficient analysis of large datasets and sex bias with ADMIXTURE

10.1101/039347 ◽

2016 ◽

Cited By ~ 1

Author(s):

Suyash S. Shringarpure ◽

Carlos D. Bustamante ◽

Kenneth L. Lange ◽

David H. Alexander

Keyword(s):

Large Datasets ◽

Allele Frequencies ◽

Sex Bias ◽

1000 Genomes Project ◽

1000 Genomes ◽

Males And Females ◽

Related Individuals ◽

Using Data ◽

Human Ancestry ◽

Individual Ancestry

Background: A number of large genomic datasets are being generated for studies of human ancestry and diseases. The ADMIXTURE program is commonly used to infer individual ancestry from genomic data. Results: We describe two improvements to the ADMIXTURE software. The first enables ADMIXTURE to infer ancestry for a new set of individuals using cluster allele frequencies from a reference set of individuals. Using data from the 1000 Genomes Project, we show that this allows ADMIXTURE to infer ancestry for 10,920 individuals in a few hours (a 5x speedup). This mode also allows ADMIXTURE to correctly estimate individual ancestry and allele frequencies from a set of related individuals. The second modification allows ADMIXTURE to correctly handle X-chromosome (and other haploid) data from both males and females. We demonstrate increased power to detect sex-biased admixture in African-American individuals from the 1000 Genomes project using this extension. Conclusions: These modifications make ADMIXTURE more efficient and versatile, allowing users to extract more information from large genomic datasets.

Download Full-text

Racial and Age Group Disparities in the Effect of Social Distancing on Health Status

Innovation in Aging ◽

10.1093/geroni/igab046.749 ◽

2021 ◽

Vol 5 (Supplement_1) ◽

pp. 197-198

Author(s):

Karen Lincoln

Keyword(s):

Public Health ◽

Health Disparities ◽

African Americans ◽

Protective Factors ◽

Living Arrangements ◽

Health Conditions ◽

Age Group ◽

Work Demands ◽

Social Distancing ◽

Using Data

Abstract African Americans are dying from COVID-19 at younger ages than Whites. Social distancing (SD) prevents the spread of the virus, but because of work demands, transportation needs, and living arrangements SD may be difficult for many African Americans, many of whom are experiencing higher unemployment, poverty, food insufficiency, and social isolation. This study will determine if the health of African Americans and Whites are differentially impacted by SD measures. SD rules can increase or decrease health disparities by: (a) directly impacting the symptoms and progression of chronic health conditions; (b) influencing availability of protective factors and exposure to risk factors; and (c) mitigating or exacerbating the effects of sources of disparities. These hypotheses will be tested using data from the Understanding America’s COVID Study. Findings can advance understanding of how public health requirements can reduce or increase health disparities and identify protective factors to facilitate adherence to public health guidelines.

Download Full-text

The effect of aspirin on colorectal cancer incidence in African Americans.

Journal of Clinical Oncology ◽

10.1200/jco.2020.38.15_suppl.4085 ◽

2020 ◽

Vol 38 (15_suppl) ◽

pp. 4085-4085

Author(s):

Oluwadunni Emiloju ◽

Djeneba Audrey Djibo ◽

Jean G Ford

Keyword(s):

Colorectal Cancer ◽

African Americans ◽

Secondary Analysis ◽

Mortality Data ◽

Atherosclerosis Risk In Communities ◽

Incidence And Mortality ◽

Using Data ◽

Cox Proportional Hazard Regression ◽

The Relationship

4085 Background: From 2011 to 2016, the incidence and mortality rate of colorectal cancer(CRC) were highest among African Americans(AA), compared to other US racial/ethnic groups. Long-term aspirin use is recommended as a strategy to reduce the risk of CRC. Yet, there is scant information on the chemopreventive effect of aspirin among AA. It is imperative to assess whether the reported chemo-preventive effect also occurs in AA. Our central hypothesis is that aspirin use in AA is associated with a lower incidence of CRC, irrespective of race/ethnicity. Methods: We conducted a secondary analysis, using data from AA participants in the Atherosclerosis Risk in Communities(ARIC) longitudinal study, who did not have CRC at enrollment, from 1987 to 1998. We extracted demographic, clinical and mortality data to compare the incidence of CRC among participants taking aspirin compared to those who were not taking aspirin, stratified by age, tobacco use, and body mass index. All-cause mortality and CRC mortality will also be assessed, and we will use Cox proportional hazard regression to determine the relationship between aspirin use and CRC incidence, and mortality. Results: At baseline in 1987, 15,026 participants enrolled in the ARIC study, 25% of whom were AA, median age 54(range 44-66), including 46.7% who reported using aspirin. We analyzed follow-up data from 10,960 participants in 1996-1998, 20% of whom were AA, and 56.9% of whom were taking aspirin. Non-AA participants were more likely to report using aspirin at baseline and follow-up, compared to AA, 53% vs 30% and 59% vs 50% respectively. After 10years, the total incidence of CRC in AA participants was 1% compared with 1.1% in non-AA(p = 0.7). There was no difference in CRC incidence by aspirin use among all participants, and when stratified by race(among all participants p = 0.81, amongAA p = 0.68, among non-AA p = 0.94). Conclusions: We found no difference in the incidence of CRC among AA compared to Caucasians, by aspirin use. Investigation of consistency and/or dose of aspirin use by race may provide further insights on the relationship between aspirin use and CRC incidence, comparing AA to Caucasians.

Download Full-text

Abstract P311: Individual Characteristics of Resilience Are Associated With Lower-Than-Expected Neighborhood Rates of Cardiovascular Disease in African-Americans: Results From the Morehouse-Emory Cardiovascular (MECA) Center for Health Equity Study

Circulation ◽

10.1161/circ.137.suppl_1.p311 ◽

2018 ◽

Vol 137 (suppl_1) ◽

Author(s):

Matthew L Topel ◽

Junjun Xu ◽

Peter Baltrus ◽

Viola Vaccarino ◽

Mahasin S Mujahid ◽

...

Keyword(s):

High Risk ◽

African Americans ◽

Well Being ◽

Individual Characteristics ◽

Low Risk ◽

Morbidity And Mortality ◽

Neighborhood Quality ◽

Aesthetic Quality ◽

Using Data ◽

Cv Disease

Background: Excess rates of cardiovascular (CV) disease in African-Americans, relative to Whites, have been well-documented. However, factors promoting CV health in the face of high risk, i.e. CV resilience, are unknown and may identify novel areas for intervention in reducing racial health disparities. Methods: Using data obtained from the Georgia Hospital Association, we identified age-, sex-, and income-matched neighborhoods (census tracts) in Atlanta, GA, with higher-than-expected (“high risk") or lower-than-expected (“low risk") rates of CV morbidity and mortality for African-Americans from 2010-2014. African-Americans from low risk (N = 742) and high risk (N = 753) neighborhoods were surveyed. Several domains of psychosocial well-being and neighborhood quality were assessed as features of resilience, in addition to individual demographic, socioeconomic and medical history variables. Ordinal logistic regression was used to determine odds of resilient characteristics among individuals living in neighborhoods at low versus high risk. Results: After adjustment for age, sex, household income, education, marital status and occupation, African-Americans living in low compared to high risk neighborhoods reported better overall neighborhood quality (odds ratio [OR] 1.25; 95% confidence interval [CI] 1.01, 1.57), driven by better aesthetic quality (OR 1.42; CI 1.17, 1.73), more safety (OR 1.34; CI 1.10, 1.62), absence of violence (OR 1.42; CI 1.10, 1.83) and better access to healthy foods (OR 1.50; CI 1.24, 1.82). Additionally, individuals from low compared to high risk neighborhoods reported greater environmental mastery (OR 1.33; CI 1.03, 1.71), purpose in life (OR 1.22, CI 1.01, 1.48), optimism (OR 1.28; CI 1.05, 1.55) and resilient coping (OR 1.33; CI 1.04, 1.70), while also reporting less depressive symptoms (OR 0.78; CI 0.63, 0.98). There were no reported differences in CV risk factors or disease, religious practices, spirituality or experiences of discrimination between low and high risk neighborhoods. Conclusions: African-Americans living in neighborhoods at lower risk for CVD morbidity and mortality reported better neighborhood quality and psychosocial well-being than individuals from neighborhoods at higher risk. Neighborhood and personal psychosocial determinants of health may confer resilience to CVD in African-American individuals and communities.

Download Full-text