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1.  Association of Variants at BCL11A and HBS1L-MYB with Hemoglobin F and Hospitalization Rates among Sickle Cell Patients in Cameroon 
PLoS ONE  2014;9(3):e92506.
Genetic variation at loci influencing adult levels of HbF have been shown to modify the clinical course of sickle cell disease (SCD). Data on this important aspect of SCD have not yet been reported from West Africa. We investigated the relationship between HbF levels and the relevant genetic loci in 610 patients with SCD (98% HbSS homozygotes) from Cameroon, and compared the results to a well-characterized African-American cohort.
Methods and Findings
Socio-demographic and clinical features were collected and medical records reviewed. Only patients >5 years old, who had not received a blood transfusion or treatment with hydroxyurea were included. Hemoglobin electrophoresis and a full blood count were conducted upon arrival at the hospital. RFLP-PCR was used to describe the HBB gene haplotypes. SNaPshot PCR, Capillary electrophoresis and cycle sequencing were used for the genotyping of 10 selected SNPs. Genetic analysis was performed with PLINK software and statistical models in the statistical package R. Allele frequencies of relevant variants at BCL11A were similar to those detected in African Americans; although the relationships with Hb F were significant (p <.001), they explained substantially less of the variance in HbF than was observed among African Americans (∼ 2% vs 10%). SNPs in HBS1L-MYB region (HMIP) likewise had a significant impact on HbF, however, we did not find an association between HbF and the variations in HBB cluster and OR51B5/6 locus on chromosome 11p, due in part to the virtual absence of the Senegal and Indian Arab haplotypes. We also found evidence that selected SNPs in HBS1L-MYB region (HMIP) and BCL11A affect both other hematological indices and rates of hospitalization.
This study has confirmed the associations of SNPs in BCL11A and HBS1L-MYB and fetal haemoglobin in Cameroonian SCA patients; hematological indices and hospitalization rates were also associated with specific allelic variants.
PMCID: PMC3965431  PMID: 24667352
2.  Effects of Rare and Common Blood Pressure Gene Variants on Essential Hypertension: Results from the FBPP, CLUE and ARIC Studies 
Circulation research  2012;112(2):318-326.
Hypertension (HTN) affects ~30% of adults in industrialized countries and is the major risk factor for cardiovascular disease.
We sought to study the genetic effect of coding and conserved non-coding variants in syndromic HTN genes on systolic (SBP) and diastolic (DBP) blood pressure to assess their overall impact on essential hypertension (EH).
Methods and Results
We resequenced 11 genes (AGT, CYP11B1, CYP17A1, HSD11B2, NR3C1, NR3C2, SCNN1A, SCNN1B, SCNN1G, WNK1 and WNK4) in 560 European (EA) and African (AA) ancestry GenNet participants with extreme SBP. We investigated genetic associations of 2,535 variants with BP in 19,997 EAs and 6,069 AAs in three types of analyses. First, we studied the combined effects of all variants in GenNet. Second, we studied 1000 Genomes imputed polymorphic variants in 9,747 EA and 3,207 AA ARIC subjects. Lastly, we genotyped 37 missense and common noncoding variants in 6,591 EAs and 6,521 individuals (3,659 EA/2,862 AA) from the CLUE and FBPP studies. None of the variants individually reached significant false-discovery rates (FDR≤0.05) for SBP and DBP. However, upon pooling all coding and non-coding variants we identified at least 5 loci (AGT, CYP11B1, NR3C2, SCNN1G and WNK1), with higher association at evolutionary conserved sites.
Both rare and common variants at these genes affect BP in the general population with modest effects sizes (<0.05 standard deviation units) and much larger sample sizes are required to assess the impact of individual genes. Collectively, conserved noncoding variants affect BP to a greater extent than missense mutations.
PMCID: PMC3548950  PMID: 23149595
essential hypertension; blood pressure; population genetics; sequencing; genotype
3.  The Nigerian Anti-Hypertensive Adherence Trial (NA-HAT): A Community-Based Randomized Trial 
Journal of hypertension  2013;31(1):201-207.
Research in industrialized countries has demonstrated that a key factor limiting the control of hypertension is poor patient adherence and that the most successful interventions for long-term adherence employ multiple strategies. Very little data exist on this question in low-income countries, where medication-taking behavior may be less well developed. We conducted a treatment adherence trial of 544 subjects (mean age ~63 years, mean BP ~168/92 mmHg) with previously untreated hypertension in urban and rural Nigeria. Eligible participants were randomized to one of two arms: clinic management only, or clinic management + home visits. Both interventions included three elements: a community based, nurse-led treatment program with physician backup; facilitation of clinic visits and health education; and the use of diuretics plus a beta blocker as needed. After initial diagnosis, the management protocol was implemented by a nurse with physician backup. Participants were evaluated monthly for 6 months. Medication adherence was assessed with pill count and urine testing. Dropout rates, by treatment group, ranged from 12% to 28%. Among participants who completed the 6 month trial, overall adherence was high (~77% of participants took > 98% of prescribed pills). Adherence did not differ by treatment arm, but was better at the rural than the urban site and among those with higher baseline BP. Hypertension control (BP < 140/90 mmHg) was achieved in ~66% of participants at 6 months. This community-based intervention confirms relatively modest default rates compared to industrialized societies, and suggests that medication adherence can be high in developing world settings in clinic attenders.
PMCID: PMC3530610  PMID: 23137954
anti-hypertensive; adherence; compliance trial
4.  The difficult airway with recommendations for management – Part 1 – Difficult tracheal intubation encountered in an unconscious/induced patient 
Canadian Journal of Anaesthesia  2013;60:1089-1118.
Previously active in the mid-1990s, the Canadian Airway Focus Group (CAFG) studied the unanticipated difficult airway and made recommendations on management in a 1998 publication. The CAFG has since reconvened to examine more recent scientific literature on airway management. The Focus Group’s mandate for this article was to arrive at updated practice recommendations for management of the unconscious/induced patient in whom difficult or failed tracheal intubation is encountered.
Nineteen clinicians with backgrounds in anesthesia, emergency medicine, and intensive care joined this iteration of the CAFG. Each member was assigned topics and conducted reviews of Medline, EMBASE, and Cochrane databases. Results were presented and discussed during multiple teleconferences and two face-to-face meetings. When appropriate, evidence- or consensus-based recommendations were made together with assigned levels of evidence modelled after previously published criteria.
The clinician must be aware of the potential for harm to the patient that can occur with multiple attempts at tracheal intubation. This likelihood can be minimized by moving early from an unsuccessful primary intubation technique to an alternative “Plan B” technique if oxygenation by face mask or ventilation using a supraglottic device is non-problematic. Irrespective of the technique(s) used, failure to achieve successful tracheal intubation in a maximum of three attempts defines failed tracheal intubation and signals the need to engage an exit strategy. Failure to oxygenate by face mask or supraglottic device ventilation occurring in conjunction with failed tracheal intubation defines a failed oxygenation, “cannot intubate, cannot oxygenate” situation. Cricothyrotomy must then be undertaken without delay, although if not already tried, an expedited and concurrent attempt can be made to place a supraglottic device.
PMCID: PMC3825644  PMID: 24132407
5.  The difficult airway with recommendations for management – Part 2 – The anticipated difficult airway 
Canadian Journal of Anaesthesia  2013;60:1119-1138.
Appropriate planning is crucial to avoid morbidity and mortality when difficulty is anticipated with airway management. Many guidelines developed by national societies have focused on management of difficulty encountered in the unconscious patient; however, little guidance appears in the literature on how best to approach the patient with an anticipated difficult airway.
To review this and other subjects, the Canadian Airway Focus Group (CAFG) was re-formed. With representation from anesthesiology, emergency medicine, and critical care, CAFG members were assigned topics for review. As literature reviews were completed, results were presented and discussed during teleconferences and two face-to-face meetings. When appropriate, evidence- or consensus-based recommendations were made, and levels of evidence were assigned.
Principal findings
Previously published predictors of difficult direct laryngoscopy are widely known. More recent studies report predictors of difficult face mask ventilation, video laryngoscopy, use of a supraglottic device, and cricothyrotomy. All are important facets of a complete airway evaluation and must be considered when difficulty is anticipated with airway management. Many studies now document the increasing patient morbidity that occurs with multiple attempts at tracheal intubation. Therefore, when difficulty is anticipated, tracheal intubation after induction of general anesthesia should be considered only when success with the chosen device(s) can be predicted in a maximum of three attempts. Concomitant predicted difficulty using oxygenation by face mask or supraglottic device ventilation as a fallback makes an awake approach advisable. Contextual issues, such as patient cooperation, availability of additional skilled help, and the clinician’s experience, must also be considered in deciding the appropriate strategy.
With an appropriate airway evaluation and consideration of relevant contextual issues, a rational decision can be made on whether an awake approach to tracheal intubation will maximize patient safety or if airway management can safely proceed after induction of general anesthesia. With predicted difficulty, close attention should be paid to details of implementing the chosen approach. This should include having a plan in case of the failure of tracheal intubation or patient oxygenation.
PMCID: PMC3825645  PMID: 24132408
6.  ‘I can't be an addict. I am.’ Over-the-counter medicine abuse: a qualitative study 
BMJ Open  2013;3(6):e002913.
Over-the-counter (OTC) pharmacy medicines are considered relatively safe in contrast to prescribed and illicit substances, but their abuse and addiction potential is increasingly recognised. Those affected represent a hard to reach group, with little known about their experiences. Study objectives were to describe the experiences and views of those self-reporting OTC medicine abuse, and why medicines were taken, how they were obtained and associated treatment and support sought.
Qualitative study using in-depth mainly telephone interviews.
A purposive sample of 25 adults, aged 20–60s, 13 women.
UK, via two internet support groups.
Individuals considered themselves ‘addicted’, but socially and economically active and different from illicit substance misusers. They blamed themselves for losing control over their medicine use, which usually began for genuine medical reasons and not experimentation and was often linked to the cessation of, or ongoing, medical prescribing. Codeine, in compound analgesics, was the main medicine implicated with three distinct dose ranges emerging with decongestant and sedative antihistamine abuse also being reported. Subsequent use was for the ‘buzz’ or similar effects of the opiate, which was obtained unproblematically by having lists of pharmacies to visit and occasionally using internet suppliers. Perceived withdrawal symptoms were described for all three dose ranges, and work and health problems were reported with higher doses. Mixed views about different treatment and support options emerged with standard drug treatment services being considered inappropriate for OTC medicines and concerns that this ‘hidden addiction’ was recorded in medical notes. Most supported the continued availability of OTC medicines with appropriate addiction warnings.
Greater awareness of the addiction potential of OTC medicines is needed for the public, pharmacists and medical prescribers, along with appropriate communication about, and reviews of, treatment and support options, for this distinct group.
PMCID: PMC3693421  PMID: 23794565
Qualitative Research; Primary Care
7.  A Canonical Theory of Dynamic Decision-Making 
Decision-making behavior is studied in many very different fields, from medicine and economics to psychology and neuroscience, with major contributions from mathematics and statistics, computer science, AI, and other technical disciplines. However the conceptualization of what decision-making is and methods for studying it vary greatly and this has resulted in fragmentation of the field. A theory that can accommodate various perspectives may facilitate interdisciplinary working. We present such a theory in which decision-making is articulated as a set of canonical functions that are sufficiently general to accommodate diverse viewpoints, yet sufficiently precise that they can be instantiated in different ways for specific theoretical or practical purposes. The canons cover the whole decision cycle, from the framing of a decision based on the goals, beliefs, and background knowledge of the decision-maker to the formulation of decision options, establishing preferences over them, and making commitments. Commitments can lead to the initiation of new decisions and any step in the cycle can incorporate reasoning about previous decisions and the rationales for them, and lead to revising or abandoning existing commitments. The theory situates decision-making with respect to other high-level cognitive capabilities like problem solving, planning, and collaborative decision-making. The canonical approach is assessed in three domains: cognitive and neuropsychology, artificial intelligence, and decision engineering.
PMCID: PMC3613596  PMID: 23565100
decision-making; autonomous agents; clinical decision-making; unified theories of cognition; cognitive systems
8.  Genetic variation in APOL1 and MYH9 genes is associated with chronic kidney disease among Nigerians 
A region of chromosome 22 which includes APOL1 and MYH9 genes was recently identified as a risk locus for non-diabetic forms of kidney disease, including idiopathic and HIV associated focal segmental glomerular sclerosis and kidney disease clinically attributed to hypertension among African Americans. The purpose of the current study was therefore to examine the frequency of these variants and to determine whether they are associated with chronic kidney disease (CKD) among native Africans.
To investigate possible evidence of association between variants in these genes and non-diabetic CKD among West Africans, we performed a case/control analysis in a sample of 166 Nigerians without history of European admixture. Our study included a total of 9 variants on APOL1 (n=4) and MYH9 (n=5) genes.
We observed significantly strong associations with previously reported APOL1 variants rs73885319 and rs60910145 and their two-allele “G1” haplotype (P < 0.005). We did not observe significant evidence of association between non-diabetic CKD and any of the MYH9 variants or haplotypes after accounting for multiple testing in our sample.
In conclusion, APOL1 risk variants are associated with non-diabetic forms of CKD among Nigerians of Yoruba ethnicity. Further information on APOL1/MYH9 variants may lead to screening programs which could lead to earlier detection and interventions for non-diabetic kidney disease.
PMCID: PMC3599169  PMID: 22956460
chronic kidney disease; APOL1; MYH9; genetic renal disease
9.  Over-the-counter medicine abuse – a review of the literature 
Journal of Substance Use  2011;18(2):82-107.
The sale of over-the-counter (OTC) medicines from pharmacies can help individuals self-manage symptoms. However, some OTC medicines may be abused, with addiction and harms being increasingly recognised. This review describes the current knowledge and understanding of OTC medicine abuse.
Comprehensive search of international empirical and review literature between 1990 and 2011.
OTC medicine abuse was identified in many countries and although implicated products varied, five key groups emerged: codeine-based (especially compound analgesic) medicines, cough products (particularly dextromethorphan), sedative antihistamines, decongestants and laxatives. No clear patterns relating to those affected or their experiences were identified and they may represent a hard-to-reach group, which coupled with heterogeneous data, makes estimating the scale of abuse problematic. Associated harms included direct physiological or psychological harm (e.g. opiate addiction), harm from another ingredient (e.g. ibuprofen-related gastric bleeding) and associated social and economic problems. Strategies and interventions included limiting supplies, raising public and professional awareness and using existing services and Internet support groups, although associated evaluations were lacking. Terminological variations were identified.
OTC medicine abuse is a recognised problem internationally but is currently incompletely understood. Research is needed to quantify scale of abuse, evaluate interventions and capture individual experiences, to inform policy, regulation and interventions.
PMCID: PMC3603170  PMID: 23525509
Over-the-counter; abuse; medicines
10.  Blacks and whites in the Cuba have equal prevalence of hypertension: confirmation from a new population survey 
BMC Public Health  2013;13:169.
The excess burden of hypertension among blacks has been a prominent feature of the heath disparities literature, and many scientists presume it to be a stable and inevitable phenomenon. The underlying causes of this disparity can only be disentangled in a setting in which the population does not experience racial stratification of socioeconomic opportunities. While such conditions of racial equality remain uncommon, they may be approximated in Cuba, a country with a persistent policy of social inclusion over the last 5 decades.
We report on a 2010–2011 stratified probability sample of those aged 15–74 years from the urban population of Cienfuegos in central Cuba. A total of 1496 adults (880 women and 616 men) were recruited and assessed for blood pressure and anthropometrics according to standardized protocols, as well as medication use, educational attainment and observed skin tone (dichotomized into “black” and “white”). Weighted tabular and regression analyses were conducted to estimate adjusted prevalences of hypertension (> 140/90 mmHg) and adjusted prevalence odds ratios for contrasts between the two skin color groups.
Mean pressures were higher for men than for women, but overall did not differ importantly between racial groups. About half of all diagnosed hypertensive men were on medication, a proportion that did not vary by racial group. For women, however, adjusted prevalence was somewhat higher among blacks, and treatment and control rates were also somewhat advantaged for white women.
Overall, skin color was unrelated to mean blood pressure or hypertensive status in this population, although among women specifically some racial advantage appears evident in adjusted prevalence and control, and should be investigated further. The overall null result suggests that Cuba may exemplify the social conditions in which racial excess in hypertension, characteristic of much of the western world, is not a necessary reality.
PMCID: PMC3635894  PMID: 23433343
Blood pressure; Cuba; Ethnic groups; Hypertension; Stress
11.  A Systematic Mapping Approach of 16q12.2/FTO and BMI in More Than 20,000 African Americans Narrows in on the Underlying Functional Variation: Results from the Population Architecture using Genomics and Epidemiology (PAGE) Study 
PLoS Genetics  2013;9(1):e1003171.
Genetic variants in intron 1 of the fat mass– and obesity-associated (FTO) gene have been consistently associated with body mass index (BMI) in Europeans. However, follow-up studies in African Americans (AA) have shown no support for some of the most consistently BMI–associated FTO index single nucleotide polymorphisms (SNPs). This is most likely explained by different race-specific linkage disequilibrium (LD) patterns and lower correlation overall in AA, which provides the opportunity to fine-map this region and narrow in on the functional variant. To comprehensively explore the 16q12.2/FTO locus and to search for second independent signals in the broader region, we fine-mapped a 646–kb region, encompassing the large FTO gene and the flanking gene RPGRIP1L by investigating a total of 3,756 variants (1,529 genotyped and 2,227 imputed variants) in 20,488 AAs across five studies. We observed associations between BMI and variants in the known FTO intron 1 locus: the SNP with the most significant p-value, rs56137030 (8.3×10−6) had not been highlighted in previous studies. While rs56137030was correlated at r2>0.5 with 103 SNPs in Europeans (including the GWAS index SNPs), this number was reduced to 28 SNPs in AA. Among rs56137030 and the 28 correlated SNPs, six were located within candidate intronic regulatory elements, including rs1421085, for which we predicted allele-specific binding affinity for the transcription factor CUX1, which has recently been implicated in the regulation of FTO. We did not find strong evidence for a second independent signal in the broader region. In summary, this large fine-mapping study in AA has substantially reduced the number of common alleles that are likely to be functional candidates of the known FTO locus. Importantly our study demonstrated that comprehensive fine-mapping in AA provides a powerful approach to narrow in on the functional candidate(s) underlying the initial GWAS findings in European populations.
Author Summary
Genetic variants within the fat mass– and obesity-associated (FTO) gene are associated with increased risk of obesity. To better understand which specific genetic variant(s) in this genetic region is associated with obesity risk, we attempt to genotype or impute all known genetic variants in the region and test for association with body mass index as a measurement of obesity in over 20,000 African Americans. We identified 29 potential candidate variants, of which one variant (rs1421085) is a particularly interesting candidate for future functional follow-up studies. Our example shows the powerful approach of studying a large African American population, substantially reducing the number of possible functional variants compared with European descent populations.
PMCID: PMC3547789  PMID: 23341774
13.  Patterns of Sodium and Potassium Excretion and Blood Pressure in the African Diaspora 
Journal of Human Hypertension  2011;26(5):315-324.
Habitual levels of dietary sodium and potassium are correlated with age-related increases in blood pressure (BP) and likely play a role in this phenomenon. Although extensive published evidence exists from randomized trials, relatively few large-scale community surveys with multiple 24-hour urine collections have been reported. We obtained three 24-hour samples on 2,704 individuals from Nigeria, Jamaica and the US to evaluate patterns of intake and within-person relationships to blood pressure. The average (±s.d.) age and weight of participants across all three sites were 39.9±8.6 years and 76.1±21.2 kg, respectively, and 55% of the total participants were females. Sodium excretion increased across the East-West gradient (e.g., 123.9±54.6, 134.1±48.8, 176.6±71.0 (±s.d.) mmol, Nigeria, Jamaica and US, respectively), while potassium was essentially unchanged (e.g., 46.3±22.9, 40.7±16.1, 44.7±16.4 (±s.d.) mmol, respectively). In multivariate analyses both sodium (positively) and potassium (negatively) were strongly correlated with blood pressure (p < 0.001); quantitatively the association was stronger, and more consistent in each site individually, for potassium. Within-population day-to-day variation was also greater for sodium than for potassium. Among each population group a significant correlation was observed between sodium and urine volume, supporting the prior finding of sodium as a determinant of fluid intake in free-living individuals. These data confirm the consistency with the possible role of dietary electrolytes as hypertension risk factors, reinforcing the relevance of potassium in these populations.
PMCID: PMC3158967  PMID: 21593783
blood pressure; sodium excretion; potassium excretion; African Diaspora
14.  The efficacy of detecting variants with small effects on the Affymetrix 6.0 platform using pooled DNA 
Human genetics  2011;130(5):607-621.
Genome-wide genotyping of a cohort using pools rather than individual samples has long been proposed as a cost-saving alternative for performing genome-wide association (GWA) studies. However, successful disease gene mapping using pooled genotyping has thus far been limited to detecting common variants with large effect sizes, which tend not to exist for many complex common diseases or traits. Therefore, for DNA pooling to be a viable strategy for conducting GWA studies, it is important to determine whether commonly used genome-wide SNP array platforms such as the Affymetrix 6.0 array can reliably detect common variants of small effect sizes using pooled DNA. Taking obesity and age at menarche as examples of human complex traits, we assessed the feasibility of genome-wide genotyping of pooled DNA as a single-stage design for phenotype association. By individually genotyping the top associations identified by pooling, we obtained a 14- to 16-fold enrichment of SNPs nominally associated with the phenotype, but we likely missed the top true associations. In addition, we assessed whether genotyping pooled DNA can serve as an inexpensive screen as the second stage of a multi-stage design with a large number of samples by comparing the most cost-effective 3-stage designs with 80% power to detect common variants with genotypic relative risk of 1.1, with and without pooling. Given the current state of the specific technology we employed and the associated genotyping costs, we showed through simulation that a design involving pooling would be 1.07 times more expensive than a design without pooling. Thus, while a significant amount of information exists within the data from pooled DNA, our analysis does not support genotyping pooled DNA as a means to efficiently identify common variants contributing small effects to phenotypes of interest. While our conclusions were based on the specific technology and study design we employed, the approach presented here will be useful for evaluating the utility of other or future genome-wide genotyping platforms in pooled DNA studies.
PMCID: PMC3474315  PMID: 21424828
15.  Clinical Guidelines, the Politics of Value, and the Practice of Medicine: Physicians at the Crossroads 
Journal of Oncology Practice  2012;8(4):233-235.
Best practice guidelines are being used to an increasing degree, not only by physicians to improve the level of care, but also by bureaucrats to constrain reimbursement and guide the pathways of care.
PMCID: PMC3396820  PMID: 23180988
16.  Mortality Rates Across 25-Hydroxyvitamin D (25[OH]D) Levels among Adults with and without Estimated Glomerular Filtration Rate <60 ml/min/1.73 m2: The Third National Health and Nutrition Examination Survey 
PLoS ONE  2012;7(10):e47458.
Previous studies exploring the association between 25[OH]D levels and mortality in adults with and without kidney disease utilized 25[OH]D thresholds that have recently been scrutinized by the Institute of Medicine Committee to Review Dietary References Intakes for Vitamin D and Calcium.
We explored all-cause mortality rates across the spectrum of 25[OH]D levels over an eighteen-year follow-up among adults with and without an estimated glomerular filtration rate (eGFR) <60 ml/min/1.73 m2.
The study included 1,097 U.S. adults with eGFR <60 ml/min/1.73 m2 and 14, 002 adults with eGFR ≥60 ml/min/1.73 m2. Mortality rates and rate ratios (RR) across 25[OH]D groups were calculated with Poisson regression and restricted cubic splines while adjusting for covariates.
Prevalence of 25[OH]D levels <30 and <20 ng/ml among adults with eGFR <60 ml/min/1.73 m2 was 76.5% (population estimate 6.2 million) and 35.4% (population estimate 2.9 million), respectively. Among adults with eGFR ≥60 ml/min/1.73 m2, 70.5% had 25[OH]D levels <30 ng/ml (population estimate 132.2 million) while 30.3% had 25[OH]D levels <20 ng/ml (population estimate 56.8 million). Significantly higher mortality rates were noted among individuals with 25[OH]D levels <12 ng/ml compared to referent group (24 to <30 ng/ml): RR1.41 (95% CI 1.17, 1.71) among individuals with eGFR <60 ml/min/1.73 m2 and RR 1.32 (95% CI 1.13, 1.56) among individuals with eGFR ≥60 ml/min/1.73 m2 after adjustment for covariates including co-morbid conditions. Mortality rates were fairly similar across all 25[OH]D groups with levels >20 ng/ml after adjustment for all covariates.
Regardless of presence of eGFR <60 ml/min/1.73 m2, mortality rates across groups with 25[OH]D levels 20–40 ng/ml are similar.
PMCID: PMC3480387  PMID: 23112816
17.  2-Acet­amido-4,5-di­nitro­toluene: a test mol­ecule for the CCDC ‘Blind Structure Prediction Test, 2004’. Corrigendum 
Corrigendum to Acta Cryst. (2004), E60, o2295–o2297.
The name of one of the authors in the paper by Watkin et al. [Acta Cryst. (2004), E60, o2295–o2297] is corrected.
PMCID: PMC3470118
18.  Genetic variation in APOL1 and MYH9 genes is associated with chronic kidney disease among Nigerians 
A region of chromosome 22 which includes APOL1 and MYH9 genes was recently identified as a risk locus for non-diabetic forms of kidney disease, including idiopathic and HIV-associated focal segmental glomerular sclerosis and kidney disease clinically attributed to hypertension among African Americans. The purposes of the current study were, therefore, to examine the frequency of these variants and to determine whether they are associated with chronic kidney disease (CKD) among native Africans.
To investigate the possible evidence of association between variants in these genes and non-diabetic CKD among West Africans, we performed a case/control analysis in a sample of 166 Nigerians without history of European admixture. Our study included a total of 9 variants on APOL1 (n = 4) and MYH9 (n = 5) genes.
We observed significantly strong associations with previously reported APOL1 variants rs73885319 and rs60910145, and their two-allele “G1” haplotype (P < 0.005). We did not observe significant evidence of association between non-diabetic CKD and any of the MYH9 variants or haplotypes after accounting for multiple testing in our sample.
In conclusion, APOL1 risk variants are associated with non-diabetic forms of CKD among Nigerians of Yoruba ethnicity. Further information on APOL1/MYH9 variants may lead to screening programs, which could lead to earlier detection and interventions for non-diabetic kidney disease.
PMCID: PMC3599169  PMID: 22956460
Chronic kidney disease; APOL1; MYH9; Genetic renal disease
19.  An Actor-Based Model of Social Network Influence on Adolescent Body Size, Screen Time, and Playing Sports 
PLoS ONE  2012;7(6):e39795.
Recent studies suggest that obesity may be “contagious” between individuals in social networks. Social contagion (influence), however, may not be identifiable using traditional statistical approaches because they cannot distinguish contagion from homophily (the propensity for individuals to select friends who are similar to themselves) or from shared environmental influences. In this paper, we apply the stochastic actor-based model (SABM) framework developed by Snijders and colleagues to data on adolescent body mass index (BMI), screen time, and playing active sports. Our primary hypothesis was that social influences on adolescent body size and related behaviors are independent of friend selection. Employing the SABM, we simultaneously modeled network dynamics (friendship selection based on homophily and structural characteristics of the network) and social influence. We focused on the 2 largest schools in the National Longitudinal Study of Adolescent Health (Add Health) and held the school environment constant by examining the 2 school networks separately (N = 624 and 1151). Results show support in both schools for homophily on BMI, but also for social influence on BMI. There was no evidence of homophily on screen time in either school, while only one of the schools showed homophily on playing active sports. There was, however, evidence of social influence on screen time in one of the schools, and playing active sports in both schools. These results suggest that both homophily and social influence are important in understanding patterns of adolescent obesity. Intervention efforts should take into consideration peers’ influence on one another, rather than treating “high risk” adolescents in isolation.
PMCID: PMC3387251  PMID: 22768124
20.  Combined admixture mapping and association analysis identifies a novel blood pressure genetic locus on 5p13: contributions from the CARe consortium 
Human Molecular Genetics  2011;20(11):2285-2295.
Admixture mapping based on recently admixed populations is a powerful method to detect disease variants with substantial allele frequency differences in ancestral populations. We performed admixture mapping analysis for systolic blood pressure (SBP) and diastolic blood pressure (DBP), followed by trait-marker association analysis, in 6303 unrelated African-American participants of the Candidate Gene Association Resource (CARe) consortium. We identified five genomic regions (P< 0.001) harboring genetic variants contributing to inter-individual BP variation. In follow-up association analyses, correcting for all tests performed in this study, three loci were significantly associated with SBP and one significantly associated with DBP (P< 10−5). Further analyses suggested that six independent single-nucleotide polymorphisms (SNPs) contributed to the phenotypic variation observed in the admixture mapping analysis. These six SNPs were examined for replication in multiple, large, independent studies of African-Americans [Women's Health Initiative (WHI), Maywood, Genetic Epidemiology Network of Arteriopathy (GENOA) and Howard University Family Study (HUFS)] as well as one native African sample (Nigerian study), with a total replication sample size of 11 882. Meta-analysis of the replication set identified a novel variant (rs7726475) on chromosome 5 between the SUB1 and NPR3 genes, as being associated with SBP and DBP (P< 0.0015 for both); in meta-analyses combining the CARe samples with the replication data, we observed P-values of 4.45 × 10−7 for SBP and 7.52 × 10−7 for DBP for rs7726475 that were significant after accounting for all the tests performed. Our study highlights that admixture mapping analysis can help identify genetic variants missed by genome-wide association studies because of drastically reduced number of tests in the whole genome.
PMCID: PMC3090198  PMID: 21422096
21.  Adrenergic Alpha-1 Pathway Is Associated with Hypertension among Nigerians in a Pathway-focused Analysis 
PLoS ONE  2012;7(5):e37145.
The pathway-focused association approach offers a hypothesis driven alternative to the agnostic genome-wide association study. Here we apply the pathway-focused approach to an association study of hypertension, systolic blood pressure (SBP), and diastolic blood pressure (DBP) in 1614 Nigerians with genome-wide data.
Methods and Results
Testing of 28 pathways with biological relevance to hypertension, selected a priori, containing a total of 101 unique genes and 4,349 unique single-nucleotide polymorphisms (SNPs) showed an association for the adrenergic alpha 1 (ADRA1) receptor pathway with hypertension (p<0.0009) and diastolic blood pressure (p<0.0007). Within the ADRA1 pathway, the genes PNMT (hypertension Pgene<0.004, DBP Pgene<0.004, and SBP Pgene<0.009, and ADRA1B (hypertension Pgene<0.005, DBP Pgene<0.02, and SBP Pgene<0.02) displayed the strongest associations. Neither ADRA1B nor PNMT could be the sole mediator of the observed pathway association as the ADRA1 pathway remained significant after removing ADRA1B, and other pathways involving PNMT did not reach pathway significance.
We conclude that multiple variants in several genes in the ADRA1 pathway led to associations with hypertension and DBP. SNPs in ADRA1B and PNMT have not previously been linked to hypertension in a genome-wide association study, but both genes have shown associations with hypertension through linkage or model organism studies. The identification of moderately significant (10−2>p>10−5) SNPs offers a novel method for detecting the “missing heritability” of hypertension. These findings warrant further studies in similar and other populations to assess the generalizability of our results, and illustrate the potential of the pathway-focused approach to investigate genetic variation in hypertension.
PMCID: PMC3353888  PMID: 22615923
22.  Poverty, Wealth, and Health Care Utilization: A Geographic Assessment 
Geographic variation has been of interest to both health planners and social epidemiologists. However, while the major focus of interest of planners has been on variation in health care spending, social epidemiologists have focused on health; and while social epidemiologists have observed strong associations between poor health and poverty, planners have concluded that income is not an important determinant of variation in spending. These different conclusions stem, at least in part, from differences in approach. Health planners have generally studied variation among large regions, such as states, counties, or hospital referral regions (HRRs), while epidemiologists have tended to study local areas, such as ZIP codes and census tracts. To better understand the basis for geographic variation in hospital utilization, we drew upon both approaches. Counties and HRRs were disaggregated into their constituent ZIP codes and census tracts and examined the interrelationships between income, disability, and hospital utilization that were examined at both the regional and local levels, using statistical and geomapping tools. Our studies centered on the Milwaukee and Los Angeles HRRs, where per capita health care utilization has been greater than elsewhere in their states. We compared Milwaukee to other HRRs in Wisconsin and Los Angeles to the other populous counties of California and to a region in California of comparable size and diversity, stretching from San Francisco to Sacramento (termed “San-Framento”). When studied at the ZIP code level, we found steep, curvilinear relationships between lower income and both increased hospital utilization and increasing percentages of individuals reporting disabilities. These associations were also evident on geomaps. They were strongest among populations of working-age adults but weaker among seniors, for whom income proved to be a poor proxy for poverty and whose residential locations deviated from the major underlying income patterns. Among working-age adults, virtually all of the excess utilization in Milwaukee was attributable to very high utilization in Milwaukee’s segregated “poverty corridor.” Similarly, the greater rate of hospital use in Los Angeles than in San-Framento could be explained by proportionately more low-income ZIP codes in Los Angeles and fewer in San-Framento. Indeed, when only high-income ZIP codes were assessed, there was little variation in hospital utilization among California’s 18 most populous counties. We estimated that had utilization within each region been at the rate of its high-income ZIP codes, overall utilization would have been 35 % less among working-age adults and 20 % less among seniors. These studies reveal the importance of disaggregating large geographic units into their constituent ZIP codes in order to understand variation in health care utilization among them. They demonstrate the strong association between low ZIP code income and both higher percentages of disability and greater hospital utilization. And they suggest that, given the large contribution of the poorest neighborhoods to aggregate utilization, it will be difficult to curb the growth of health care spending without addressing the underlying social determinants of health.
PMCID: PMC3462827  PMID: 22566148
Poverty; Urban; Health care; Geographic variation
American Journal of Hypertension  2010;24(2):187-193.
The reasons for racial/ethnic disparities in hypertension prevalence in the U.S are poorly understood.
Using data from the Multi-Ethnic Study of Atherosclerosis (MESA), we investigated whether individual and neighborhood-level chronic stressors contribute to these disparities in cross-sectional analyses. The sample consisted of 2679 MESA participants (45–84yrs) residing in Baltimore, New York, and North Carolina. Hypertension was defined as systolic or diastolic blood pressure ≥140 or 90mmHg, or taking anti-hypertensive medications. Individual-level chronic stress was measured by self-reported chronic burden and perceived major and everyday discrimination. A measure of neighborhood (census tract) chronic stressors (i.e. physical disorder, violence) was developed using data from a telephone survey conducted with other residents of MESA neighborhoods. Binomial regression was used to estimate associations between hypertension and race/ethnicity before and after adjustment for individual and neighborhood stressors.
The prevalence of hypertension was 59.5% in African Americans (AA), 43.9% in Hispanics, and 42.0% in whites. Age and sex adjusted relative prevalences of hypertension (compared to whites) were 1.30 [95% Confidence Interval (CI): 1.22–1.38] for AA and 1.16 [95% CI: 1.04–1.31] for Hispanics. Adjustment for neighborhood stressors reduced these to 1.17 [95% CI: 1.11–1.22] and 1.09 [95% CI: 1.00–1.18] respectively. Additional adjustment for individual-level stressors, acculturation, income, education, and other neighborhood features only slightly reduced these associations.
Neighborhood chronic stressors may contribute to race/ethnic differences in hypertension prevalence in the U.S.
PMCID: PMC3319083  PMID: 20847728
neighborhoods; race; ethnicity; chronic stress; discrimination
24.  Adjustment for local ancestry in genetic association analysis of admixed populations 
Bioinformatics  2010;27(5):670-677.
Motivation: Admixed populations offer a unique opportunity for mapping diseases that have large disease allele frequency differences between ancestral populations. However, association analysis in such populations is challenging because population stratification may lead to association with loci unlinked to the disease locus.
Methods and results: We show that local ancestry at a test single nucleotide polymorphism (SNP) may confound with the association signal and ignoring it can lead to spurious association. We demonstrate theoretically that adjustment for local ancestry at the test SNP is sufficient to remove the spurious association regardless of the mechanism of population stratification, whether due to local or global ancestry differences among study subjects; however, global ancestry adjustment procedures may not be effective. We further develop two novel association tests that adjust for local ancestry. Our first test is based on a conditional likelihood framework which models the distribution of the test SNP given disease status and flanking marker genotypes. A key advantage of this test lies in its ability to incorporate different directions of association in the ancestral populations. Our second test, which is computationally simpler, is based on logistic regression, with adjustment for local ancestry proportion. We conducted extensive simulations and found that the Type I error rates of our tests are under control; however, the global adjustment procedures yielded inflated Type I error rates when stratification is due to local ancestry difference.
Supplementary information: Supplementary data are available at Bioinformatics online.
PMCID: PMC3042179  PMID: 21169375
25.  Protocol for the modeling the epidemiologic transition study: a longitudinal observational study of energy balance and change in body weight, diabetes and cardiovascular disease risk 
BMC Public Health  2011;11:927.
The prevalence of obesity has increased in societies of all socio-cultural backgrounds. To date, guidelines set forward to prevent obesity have universally emphasized optimal levels of physical activity. However there are few empirical data to support the assertion that low levels of energy expenditure in activity is a causal factor in the current obesity epidemic are very limited.
The Modeling the Epidemiologic Transition Study (METS) is a cohort study designed to assess the association between physical activity levels and relative weight, weight gain and diabetes and cardiovascular disease risk in five population-based samples at different stages of economic development. Twenty-five hundred young adults, ages 25-45, were enrolled in the study; 500 from sites in Ghana, South Africa, Seychelles, Jamaica and the United States. At baseline, physical activity levels were assessed using accelerometry and a questionnaire in all participants and by doubly labeled water in a subsample of 75 per site. We assessed dietary intake using two separate 24-hour recalls, body composition using bioelectrical impedance analysis, and health history, social and economic indicators by questionnaire. Blood pressure was measured and blood samples collected for measurement of lipids, glucose, insulin and adipokines. Full examination including physical activity using accelerometry, anthropometric data and fasting glucose will take place at 12 and 24 months. The distribution of the main variables and the associations between physical activity, independent of energy intake, glucose metabolism and anthropometric measures will be assessed using cross-section and longitudinal analysis within and between sites.
METS will provide insight on the relative contribution of physical activity and diet to excess weight, age-related weight gain and incident glucose impairment in five populations' samples of young adults at different stages of economic development. These data should be useful for the development of empirically-based public health policy aimed at the prevention of obesity and associated chronic diseases.
PMCID: PMC3297543  PMID: 22168992

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