Sexual risk characteristics, social vulnerability, and anal cancer screening uptake among men living with HIV in the deep south

ABSTRACTWithout standard guidelines, there is a critical need to examine anal cancer screening uptake in the South which has the highest HIV incidence in the U.S. We identified factors associated with screening among men living with HIV (MLHIV) at a large academic HIV outpatient clinic in Alabama. Relationships between sociodemographic, clinical, sexual risk characteristics and screening were examined using T-tests, Fisher's exact, Chi-square, and logistic regression analyses. Unadjusted and adjusted odds ratios (AOR) were computed to estimate the odds of screening. Among 1,114 men, 52% had received annual anal cytology (pap) screening. Men who were screened were more likely to have multiple sexual partners compared to men who were not screened (22.8% vs. 14.8%, p = 0.002). Among men with one partner, the youngest were almost five times more likely to be screened compared to middle-aged men (AOR = 4.93, 95% CI: 2.34-10.39). Heterosexual men had lower odds and men who reported unprotected anal sex had higher odds of screening. Our findings suggest a racial disparity, with older black MLHIV being the least likely to be screened. In the South, MLHIV who are older, black, heterosexual, or live in high social vulnerability counties may be less likely to receive annual anal cancer screening.

Electronic health record reveals community-level cardiometabolic health benefits associated with 10 years of community-based participatory research

BACKGROUND

While a major goal of community-based participatory research (CBPR) is to improve community health; it is unclear how to measure longstanding success of CBPR.

OBJECTIVE

We sought to determine the impact of ongoing CBPR on cardiometabolic health of participating communities, including in people not directly participating in research.

METHODS

We used linear mixed-effects modelling with electronic medical records from 2002 to 2012 from the Yukon-Kuskokwim Health Corporation, which provides health care to all Alaska Native people in southwestern Alaska, to compare rates of change in cardiometabolic risk factors between communities that did and did not participate in ongoing CBPR beginning in 2003.

RESULTS

We analysed 1,262,035 medical records from 12,402 individuals from 10 study and 38 control communities. Blood pressure declined faster in study than in control communities: systolic blood pressure (0.04 mmHg/year; 95% confidence interval [CI]: 0.01, 0.08); diastolic blood pressure (DBP) (0.07 mmHg/year; 95% CI: 0.04, 0.09). Body mass index increased 0.04 units/year faster in study communities than in control communities (95% CI: 0.03, 0.05). More study visits were associated with faster reduction of DBP and triglyceride levels in study communities.

CONCLUSIONS

Ongoing CBPR may improve overall cardiometabolic health in communities, perhaps by increasing engagement in health and advocacy.

Socio-demographic and comorbid risk factors for poor prognosis in patients hospitalized with community-acquired bacterial pneumonia in southeastern US

BACKGROUND

How socio-demographic characteristics and comorbidities affect bacterial community-acquired pneumonia (CAP) prognosis during/after hospitalization is important in disease management.

OBJECTIVES

To identify predictors of medical intensive care unit (MICU) admission, length of hospital stay (LOS), in-hospital mortality, and bacterial CAP readmission in patients hospitalized with bacterial CAP.

METHODS

ICD-9/10 codes were used to query electronic medical records to identify a cohort of patients hospitalized for bacterial CAP at a tertiary hospital in Southeastern US between 01/01/2013-12/31/2019. Adjusted accelerated failure time and modified Poisson regression models were used to examine predictors of MICU admission, LOS, in-hospital mortality, and 1-year readmission.

RESULTS

There were 1956 adults hospitalized with bacterial CAP. Median (interquartile range) LOS was 11 days (6-23), and there were 26 % (513) MICU admission, 14 % (266) in-hospital mortality, and 6 % (117) 1-year readmission with recurrent CAP. MICU admission was associated with heart failure (RR 1.38; 95 % CI 1.17-1.62) and obesity (RR 1.26; 95 % CI 1.04-1.52). Longer LOS was associated with heart failure (adjusted time ratio[TR] 1.27;95 %CI 1.12-1.43), stroke (TR 1.90;95 %CI 1.54,2.35), type 2 diabetes (TR 1.20;95 %CI 1.07-1.36), obesity (TR 1.50;95 %CI 1.31-1.72), Black race (TR 1.17;95 %CI 1.04-1.31), and males (TR 1.24;95 %CI 1.10-1.39). In-hospital mortality was associated with stroke (RR 1.45;95 %CI 1.03-2.04) and age ≥65 years (RR 1.34;95 %CI 1.06-1.68). 1-year readmission was associated with COPD (RR 1.55;95 %CI 1.05-2.27) and underweight BMI (RR 1.74;95 %CI 1.04-2.90).

CONCLUSIONS

Comorbidities and socio-demographic characteristics have varying impacts on bacterial CAP in-hospital prognosis and readmission. More studies are warranted to confirm these findings to develop comprehensive care plans and inform public health interventions.

Pharmacogenomics of Coronary Artery Response to Intravenous Gamma Globulin in Kawasaki Disease

Background

Kawasaki disease (KD) is a multisystem inflammatory illness of infants and young children that can result in acute vasculitis. The pathological walls of afflicted coronary arteries show propensity for forming thrombosis and aneurysms. The mechanism of coronary artery aneurysms (CAA) despite intravenous gamma globulin (IVIG) treatment is not known.

Methods

We performed a Whole Genome Sequencing (WGS) association analysis in a racially diverse cohort of KD patients treated with IVIG, both using AHA guidelines. We defined coronary aneurysm (CAA) (N = 234) as coronary z>2.5 and large coronary aneurysm (CAA/L) (N = 92) as z>5.0. We conducted logistic regression models to examine the association of genetic variants with CAA/L during acute KD and with persistence >6 weeks using an additive model between cases and 238 controls with no CAA. We adjusted for age, gender and three principal components of genetic ancestry. We performed functional mapping and annotation (FUMA) analysis and further assessed the predictive risk score of genomic risk loci using the area under the receiver operating characteristic curve (AUC).

Results

The top significant variants associated with CAA/L were in the intergenic regions (rs62154092 p<6.32E-08 most significant). Variants in SMAT4, LOC100127 , PTPRD, TCAF2 and KLRC2 were the most significant non-intergenic SNPs. FUMA identified 12 genomic risk loci with eQTL or chromatin interactions mapped to 48 genes. Of these NDUFA5 has been implicated in KD CAA and MICU and ZMAT4 has potential functional implications. Genetic risk score using these 12 genomic risk loci yielded an AUC of 0.86.

Conclusions

This pharmacogenomics study provides insights into the pathogenesis of CAA/L in IVIG-treated KD patients. We have identified multiple novel SNPs associated with CAA/L and related genes with potential functional implications. The study shows that genomics can help define the cause of CAA/L to guide management and improve risk stratification of KD patients.

Pharmacogenomics of intravenous immunoglobulin response in Kawasaki disease

Introduction

Kawasaki disease (KD) is a diffuse vasculitis in children. Response to high dose intravenous gamma globulin (IVIG), the primary treatment, varies according to genetic background. We sought to identify genetic loci, which associate with treatment response using whole genome sequencing (WGS).

Method

We performed WGS in 472 KD patients with 305 IVIG responders and 167 non-responders defined by AHA clinical criteria. We conducted logistic regression models to test additive genetic effect in the entire cohort and in four subgroups defined by ancestry information markers (Whites, African Americans, Asians, and Hispanics). We performed functional mapping and annotation using FUMA to examine genetic variants that are potentially involved IVIG non-response. Further, we conducted SNP-set [Sequence] Kernel Association Test (SKAT) for all rare and common variants.

Results

Of the 43,288,336 SNPs (23,660,970 in intergenic regions, 16,764,594 in introns and 556,814 in the exons) identified, the top ten hits associated with IVIG non-response were in FANK1, MAP2K3:KCNJ12, CA10, FRG1DP, CWH43 regions. When analyzed separately in ancestry-based racial subgroups, SNPs in several novel genes were associated. A total of 23 possible causal genes were pinpointed by positional and chromatin mapping. SKAT analysis demonstrated association in the entire MANIA2, EDN1, SFMBT2, and PPP2R5E genes and segments of CSMD2, LINC01317, HIVEPI, HSP90AB1, and TTLL11 genes.

Conclusions

This WGS study identified multiple predominantly novel understudied genes associated with IVIG response. These data can serve to inform regarding pathogenesis of KD, as well as lay ground work for developing treatment response predictors.

RNA-seq analysis identifies transcriptomic profiles associated with anal cancer recurrence among people living with HIV

BACKGROUND

Chemoradiation therapy (CRT) is the standard of care for squamous cell carcinoma of the anus (SCCA), the most common type of anal cancer. However, approximately one fourth of patients still relapse after CRT.

METHODS

We used RNA-sequencing technology to characterize coding and non-coding transcripts in tumor tissues from CRT-treated SCCA patients and compare them between 9 non-recurrent and 3 recurrent cases. RNA was extracted from FFPE tissues. Library preparations for RNA-sequencing were created using SMARTer Stranded Total RNA-Seq Kit. All libraries were pooled and sequenced on a NovaSeq 6000. Function and pathway enrichment analysis was performed with Metascape and enrichment of gene ontology (GO) was performed with Gene Set Enrichment Analysis (GSEA).

RESULTS

There were 449 differentially expressed genes (DEGs) observed (390 mRNA, 12 miRNA, 17 lincRNA and 18 snRNA) between the two groups. We identified a core of upregulated genes (IL4, CD40LG, ICAM2, HLA-I (HLA-A, HLA-C) and HLA-II (HLA-DQA1, HLA-DRB5) in the non-recurrent SCCA tissue enriching to the gene ontology term 'allograft rejection', which suggests a CD4+ T cell driven immune response. Conversely, in the recurrent tissues, keratin (KRT1, 10, 12, 20) and hedgehog signaling pathway (PTCH2) genes involved in 'Epidermis Development,', were significantly upregulated. We identified miR-4316, that inhibit tumor proliferation and migration by repressing vascular endothelial growth factors, as being upregulated in non-recurrent SCCA. On the contrary, lncRNA-SOX21-AS1, implicated in the progression of many other cancers, was also found to be more common in our recurrent compared to non-recurrent SCCA.

Our study identified key host factors which may drive the recurrence of SCCA and warrants further studies to understand the mechanism and evaluate their potential use in personalized treatment.Key MessageOur study used RNA sequencing (RNA-seq) to identify pivotal factors in coding and non-coding transcripts which differentiate between patients at risk for recurrent anal cancer after treatment. There were 449 differentially expressed genes (390 mRNA, 12 miRNA, 17 lincRNA and 18 snRNA) between 9 non-recurrent and 3 recurrent squamous cell carcinoma of anus (SCCA) tissues. The enrichment of genes related to allograft rejection was observed in the non-recurrent SCCA tissues, while the enrichment of genes related to epidermis development was positively linked with recurrent SCCA tissues.

HLA-DQB1*06 and Select Neighboring HLA Variants Predict Chlamydia Reinfection Risk

Associations of HLA class II alleles with genital chlamydial infection outcomes have been reported, especially HLA DQB1*06. However, the potential role of DQB1*06 in influencing reinfection risk has still not been established. The purpose of this study was to determine whether the association of DQB1*06 with chlamydia reinfection was impacted by any other nearby HLA class II variants that were also associated with reinfection. We used next-generation sequencing to map HLA class II variants spanning the HLA-DQ and -DR loci. DQB1*06 as well as DQB1*04 were confirmed as significant predictors of chlamydia reinfection, when controlling for age and percent African ancestry. SKAT analysis revealed one region each in DRB1, DRB5, DQA2, and three intergenic regions that had variants associated with reinfection. Further analyses of these variants revealed that rs112651494 within DRB5 and an intergenic SNP rs617058 in DRB1:DQA1 were significantly associated with reinfection, but this did not impact the significance of the association of DQB1*06 or DQB1*04 with reinfection.

Variations in Genes Encoding Human Papillomavirus Binding Receptors and Susceptibility to Cervical Precancer

BACKGROUND

Cervical cancer oncogenesis starts with human papillomavirus (HPV) cell entry after binding to host cell surface receptors; however, the mechanism is not fully known. We examined polymorphisms in receptor genes hypothesized to be necessary for HPV cell entry and assessed their associations with clinical progression to precancer.

METHODS

African American women (N = 1,728) from the MACS/WIHS Combined Cohort Study were included. Two case-control study designs were used-cases with histology-based precancer (CIN3+) and controls without; and cases with cytology-based precancer [high-grade squamous intraepithelial lesions (HSIL)] and controls without. SNPs in candidate genes (SDC1, SDC2, SDC3, SDC4, GPC1, GPC2, GPC3, GPC4, GPC5, GPC6, and ITGA6) were genotyped using an Illumina Omni2.5-quad beadchip. Logistic regression was used to assess the associations in all participants and by HPV genotypes, after adjusting for age, human immunodeficiency virus serostatus, CD4 T cells, and three principal components for ancestry.

RESULTS

Minor alleles in SNPs rs77122854 (SDC3), rs73971695, rs79336862 (ITGA6), rs57528020, rs201337456, rs11987725 (SDC2), rs115880588, rs115738853, and rs9301825 (GPC5) were associated with increased odds of both CIN3+ and HSIL, whereas, rs35927186 (GPC5) was found to decrease the odds for both outcomes (P value ≤ 0.01). Among those infected with Alpha-9 HPV types, rs722377 (SDC3), rs16860468, rs2356798 (ITGA6), rs11987725 (SDC2), and rs3848051 (GPC5) were associated with increased odds of both precancer outcomes.

CONCLUSIONS

Polymorphisms in genes that encode binding receptors for HPV cell entry may play a role in cervical precancer progression.

IMPACT

Our findings are hypothesis generating and support further exploration of mechanisms of HPV entry genes that may help prevent progression to cervical precancer.

Seasonality and geographical distribution of Kawasaki disease among Black children in the Southeast United States

Introduction

Kawasaki Disease (KD) is a leading cause of pediatric acquired heart disease in the United States, affecting up to 7,000 children annually. Seasonal variation, an epidemiological characteristic of KD, has previously been reported predominantly among Asian children; however, little is known about the epidemiology and seasonality of KD of Black children within the U.S.

Methods

Electronic medical records were abstracted from 529 hospitalized KD patients admitted to a single tertiary center in Alabama between 2005 and 2019. Medical charts were reviewed to confirm KD diagnosis following American Heart Association criteria. Cases were stratified by the month of diagnosis date to assess seasonality, and statewide distribution of incidence is reported at county level using geographical spatial analysis. Comparisons were performed between Black patients and White patients with KD.

Results

The average number of KD cases per year was 35. Approximately, 60% were males and 44% were White children (N = 234), 45% were Black children (N = 240) and 11% were other races (N = 55). Black children were younger than White children at KD admission (median age 32 vs. 41 months respectively, p = 0.02). Overall, the highest rates of cases occurred between January and April. When stratifying by race, cases started to rise in December among White children with the highest rates between February and April with a peak in March. Among Black children cases were high during the winter season (January-April) with a peak in April. Similarly high rates also occurred in June, July and November. There were no differences in geographical distribution of cases by race.

Conclusion

KD incidence among White children in Alabama follows a seasonal cycle similar to other regions in the U.S. However, sustained incidence and additional peaks outside of the usual KD seasonality were seen among Black children with KD. Further studies are needed to investigate differential triggers between races.

Traditional risk factors and cancer-related factors associated with cardiovascular disease risk in head and neck cancer patients

Background

Risk of incident cardiovascular disease (CVD) in head and neck squamous cell carcinoma (HNSCC) patients is under-reported. We assessed the association of HNSCC-related factors and traditional risk factors with 1- and 5-year CVD risk in HNSCC patients without prevalent CVD at cancer diagnosis.

Methods

A clinical cohort of 1,829 HNSCC patients diagnosed between 2012 and 2018, at a National Cancer Institute (NCI)-designated cancer center was included. Information on HNSCC-related factors [HNSCC anatomical subsite, stage at diagnosis, treatment, and tumor human papillomavirus (HPV) status] were extracted from the tumor registry. Data on traditional risk factors (hypertension, dyslipidemia, diabetes, tobacco smoking status, and obesity) were extracted from the electronic health records system (EHR) at baseline (HNSCC diagnosis). A composite of ischemic heart disease, heart failure, and ischemic stroke was the outcome of interest in time to event analysis. Hazard ratio (HR) (95% CI) were reported with death as a competing risk.

Results

In patients diagnosed with HNSCC, 10.61% developed incident CVD events by 1-year post cancer diagnosis. One-year CVD risk was lower in patients using antihypertensive medications at baseline, compared to patients without baseline hypertension [HR (95% CI): 0.41 (0.24-0.61)]. One-year CVD risk was high in patients receiving HNSCC surgery. Patients receiving radiation therapy had a higher 5-year CVD risk than surgery patients [HR (95% CI): 2.17 (1.31-3.04)]. Patients using antihypertensive medications had a lower 5-year CVD risk than patients without baseline hypertension [HR (95% CI): 0.45 (0.22-0.75)]. Older age and diabetes were associated with increased 1- and 5-year CVD risk. HPV-negative patients were older (p 0.006) and had a higher 5-year cumulative incidence of CVD (p 0.013) than HPV-positive patients.

Conclusion

Traditional risk factors and cancer-related factors are associated with CVD risk in HNSCC patients. Future research should investigate the role of antihypertensive medications in reducing CVD risk in HNSCC patients.

Obesity-Associated Dyslipidemia Is Moderated by Habitual Intake of Marine-Derived n-3 Polyunsaturated Fatty Acids in Yup'ik Alaska Native People: A Cross-Sectional Mediation-Moderation Analysis

BACKGROUND

Obesity leads to insulin resistance, altered lipoprotein metabolism, dyslipidemia, and cardiovascular disease. The relationship between long-term intake of n-3 polyunsaturated fatty acids (n-3 PUFAs) and prevention of cardiometabolic disease remains unresolved.

OBJECTIVES

The aim of this study was to explore direct and indirect pathways between adiposity and dyslipidemia, and the degree to which n-3 PUFAs moderate adiposity-induced dyslipidemia in a population with highly variable n-3 PUFA intake from marine foods.

METHODS

In total, 571 Yup'ik Alaska Native adults (18-87 y) were enrolled in this cross-sectional study. The red blood cell (RBC) nitrogen isotope ratio (15N/14N, or NIR) was used as a validated objective measure of n-3 PUFA intake. EPA and DHA were measured in RBCs. Insulin sensitivity and resistance were estimated by the HOMA2 method. Mediation analysis was conducted to evaluate the contribution of the indirect causal path between adiposity and dyslipidemia mediated through insulin resistance. Moderation analysis was used to assess the influence of dietary n-3 PUFAs on the direct and indirect paths between adiposity and dyslipidemia. Outcomes of primary interest included plasma total cholesterol (TC), LDL-cholesterol (LDL-C), HDL-cholesterol (HDL-C), non-HDL-C, and triglycerides (TG).

RESULTS

In this Yup'ik study population, we found that up to 21.6% of the total effects of adiposity on plasma TG, HDL-C, and non-HDL-C are mediated through measures of insulin resistance or sensitivity. Moreover, RBC DHA and EPA moderated the positive association between waist circumference (WC) and TC or non-HDL-C, whereas only DHA moderated the positive association between WC and TG. However, the indirect path between WC and plasma lipids was not significantly moderated by dietary n-3 PUFAs.

CONCLUSIONS

Intake of n-3 PUFAs may independently reduce dyslipidemia through the direct path resulting from excess adiposity in Yup'ik adults. NIR moderation effects suggest that additional nutrients contained in n-3 PUFA-rich foods may also reduce dyslipidemia.

Clinical risk factors for admission with Pseudomonas and multidrug-resistant Pseudomonas community-acquired pneumonia

Background

Microbial etiology for community-acquired pneumonia (CAP) is evolving with pathogens known for high CAP mortality e.g., Pseudomonas species. Chronic obstructive pulmonary disease (COPD) patients are at risk for hospitalization for CAP. Understanding regional patterns and risk factors for multidrug-resistant (MDR) Pseudomonas acquisition has implications for antimicrobial stewardship.

Objectives

To evaluate the regional epidemiology of MDR Pseudomonas CAP and its association with COPD.

Methods

We queried the electronic medical records of the University of Alabama at Birmingham Healthcare System to identify patients hospitalized for CAP with Pseudomonas positive respiratory samples between 01/01/2013–12/31/2019. Log binomial regression models were used to examine associations between COPD diagnosis and risk of Pseudomonas/MDR Pseudomonas CAP.

Results

Cohort consisted of 913 culture positive CAP cases aged 59-year (IQR:48–68), 61% (560) male, 60% (547) white, 65% (580) current/past smokers, and 42% (384) COPD. Prevalence of Pseudomonas CAP in culture positive CAP was 18% (167), MDR Pseudomonas CAP in Pseudomonas CAP was 22% (36), and yearly incidence of MDR Pseudomonas CAP was stable (p = 0.169). COPD was associated with Pseudomonas CAP (RR 1.39; 95% CI 1.01, 1.91; p = 0.041) but not with MDR Pseudomonas CAP (0.71; 95% CI 0.35, 1.45; p = 0.349). Stroke (RR 2.64; 95% CI 1.51, 4.61; p = 0.0006) and use of supplemental oxygen (RR 2.31; 95% CI 1.30, 4.12; p = 0.005) were associated with MDR Pseudomonas CAP.

Conclusion

Incidence of MDR Pseudomonas CAP was stable over time. COPD was associated with Pseudomonas CAP but not with MDR Pseudomonas CAP. Larger cohort studies are needed to confirm findings.

Racial and rural-urban disparities in cardiovascular risk factors among patients with head and neck cancer in a clinical cohort

BACKGROUND

Evidence on distribution of cardiovascular disease (CVD) risk factors in patients with head and neck squamous cell carcinoma (HNSCC) is limited. We assessed disparities in prevalence and incidence of CVD risk factors in patients with HNSCC.

METHODS

Electronic health records (EHR) data on 2262 patients with HNSCC diagnosed between 2012 and 2018 at a NCI-designated cancer center were included. Prevalence of CVD risk factors at baseline and incidence at 1-year post HNSCC diagnosis were assessed using logistic and robust Poisson regression, respectively.

RESULTS

At baseline, 31.72% white patients with HNSCC had dyslipidemia, compared to 24.29% blacks (p < 0.008); diabetes was more prevalent in blacks (p < 0.027). Odds of ≥1 prevalent CVD clinical risk factor at baseline was lower in blacks (OR, 95%CI: 0.71, 0.54-0.93) and in rural patients (OR, 95%CI: 0.70, 0.58-0.85). At 1 year, risk of incident diabetes was higher in rural patients (RR, 95%CI: 1.63, 1.21-2.19).

CONCLUSIONS

Demographic disparities were observed in distribution of CVD risk factors in patients with HNSCC.

Habitual Intake of Marine-Derived n-3 PUFAs is Inversely Associated with a Cardiometabolic Inflammatory Profile in Yup'ik Alaska Native People

BACKGROUND

The relationship between dietary n-3 PUFAs and the prevention of cardiometabolic diseases, including type 2 diabetes, is unresolved. Examination of the association between n-3 PUFAs and chronic low-grade inflammation in a population where many individuals have had an extremely high intake of marine mammals and fish throughout their lifespan may provide important clues regarding the impact of n-3 PUFAs on health.

OBJECTIVES

The aim of this study was to explore associations between concentrations of n-3 PUFAs resulting from habitual intake of natural food sources high in fish and marine mammals with immune biomarkers of metabolic inflammation and parameters of glucose regulation.

METHODS

A total of 569 Yup'ik Alaska Native adults (18-87 years old) were enrolled in this cross-sectional study between December 2016 and November 2019. The RBC nitrogen isotope ratio (NIR; 15N/14N) was used as a validated measure of n-3 PUFA intake to select 165 participant samples from the first and fourth quartiles of n-3 PUFA intakes. Outcomes included 38 pro- and anti-inflammatory cytokines and 8 measures of glucose homeostasis associated with type 2 diabetes risks. These outcomes were evaluated for their associations with direct measurements of EPA, DHA, and arachidonic acid in RBCs.

ANALYSIS

Linear regression was used to detect significant relationships with cytokines and n-3 PUFAs, adiposity, and glucose-related variables.

RESULTS

The DHA concentration in RBC membranes was inversely associated with IL-6 (β = -0.0066; P < 0.001); EPA was inversely associated with TNFα (β = -0.4925; P < 0.001); and the NIR was inversely associated with Monocyte chemoattractant protein-1 (MCP-1) (β = -0.8345; P < 0.001) and IL-10 (β = -1.2868; P < 0.001).

CONCLUSIONS

Habitual intake of marine mammals and fish rich in n-3 PUFAs in this study population of Yup'ik Alaska Native adults is associated with reduced systemic inflammation, which may contribute to the low prevalence of diseases in which inflammation plays an important role.

Estimates of West African Ancestry in African Americans Using Alleles of Iron-Related Genes HJV, SLC40A1, and TFR2

Background: Few studies have estimated African ancestry of African Americans (AA). In sub-Saharan West African (WA) Blacks, some nonancestral alleles of iron-related genes HJV, SLC40A1, and TFR2 are common, whereas in European Americans (EA) the same alleles are rare. These alleles have not been used to estimate WA Black ancestry in AA. Methods: We estimated WA Black ancestry in AA (M) using published HJV c.929C>G (rs7540883), SLC40A1 c.744G>T (rs11568350), and TFR2 c.713C>T (rs34242818) allele frequencies in WA Blacks, AA, and EA. We computed standard error (SE) and one-sided 95% confidence intervals (CI) for each M. Results: The combined representation of WA Blacks from The Gambia and Nigeria was 79-89%. Aggregate HJV, SLC40A1, and TFR2 allele frequencies in WA Blacks were 0.1025 [95% CI: 0.0835-0.1253] (n = 405), 0.0517 [0.0469-0.0569] (n = 3839), and 0.1432 [0.1202-0.1697] (n = 405), respectively. Aggregate HJV, SLC40A1, and TFR2 allele frequencies in AA were 0.0718 [0.0648-0.0797] (n = 2352), 0.0557 [0.0506-0.0613] (n = 3590), and 0.1224 [0.1132-0.1322] (n = 2352), respectively. Aggregate HJV, SLC40A1, and TFR2 allele frequencies in 4449 EA were 0.0002 [0-0.0009], 0.0003 [0.0001-0.0010], and 0.0004 [0.0001-0.0012], respectively. M (SE [one-sided 95% CI]) for HJV, SLC40A1, and TFR2 alleles was 0.7006 (0.0818 [0.5402-1.0000]), 1.0000 (0.0752 [0.9306-1.0000]), and 0.8546 (0.0810 [0.6959-1.0000]), respectively. Mean of these M is 0.8777 (87.8%). Conclusions: The mean proportional WA Black ancestry in AA of 87.8% using HJV c.929C>G, SLC40A1 c.744G>T, and TFR2 c.713C>T allele frequencies is consistent with that of previous studies that used other autosomal markers and methods.

Immunophenotype-associated gene signature in ductal breast tumors varies by receptor subtype, but the expression of individual signature genes remains consistent

BACKGROUND

In silico deconvolution of invasive immune cell infiltration in bulk breast tumors helps characterize immunophenotype, expands treatment options, and influences survival endpoints. In this study, we identify the differential expression (DE) of the LM22 signature to classify immune-rich and -poor breast tumors and evaluate immune infiltration by receptor subtype and lymph node metastasis.

METHODS

Using publicly available data, we applied the CIBERSORT algorithm to estimate immune cells infiltrating the tumor into immune-rich and immune-poor groups. We then tested the association of receptor subtype and nodal status with immune-rich/poor phenotype. We used DE to test individual signature genes and over-representation analysis for related pathways.

RESULTS

CCL19 and CXCL9 expression differed between rich/poor signature groups regardless of subtype. Overexpression of CHI3L2 and FES was observed in triple negative breast cancers (TNBCs) relative to other subtypes in immune-rich tumors. Non-signature genes, LYZ, C1QB, CORO1A, EVI2B, GBP1, PSMB9, and CD52 were consistently overexpressed in immune-rich tumors, and SCUBE2 and GRIA2 were associated with immune-poor tumors. Immune-rich tumors had significant upregulation of genes/pathways while none were identified in immune-poor tumors.

CONCLUSIONS

Overall, the proportion of immune-rich/poor tumors differed by subtype; however, a subset of 10 LM22 genes that marked immune-rich status remained the same across subtype. Non-LM22 genes differentially expressed between the phenotypes suggest that the biologic processes responsible for immune-poor phenotype are not yet well characterized.

Changes in lipidomic profile by anti-retroviral treatment regimen: An ACTG 5257 ancillary study

High cardiovascular disease risk in people living with HIV is partly attributed to antiretroviral therapy (ART). Lipid response to ART has been extensively studied, yet, little is known how small molecule lipids respond to Integrase inhibitor-based (INSTI-based) compared to Protease inhibitor-based (PI-based) ART regimens.Ancillary study to a phase 3, randomized, open-label trial [AIDS Clinical Trial Group A5257 Study] in treatment-naive HIV-infected patients randomized in a 1:1:1 ratio to receive ritonavir-boosted atazanavir (ATV/r), ritonavir-boosted darunavir (DRV/r) (both PI-based), or raltegravir with Tenofovir Disoproxil Fumarate-TDF plus emtricitabine (RAL, INSTI-based).We examined small molecule lipid response in a subcohort of 75 participants. Lipidomic assays of plasma samples collected pre- and post-ART treatment (48 weeks) were conducted using ultra-performance liquid chromatography coupled to time-of-flight mass spectrometry. The effect of ART regimens was regressed on lipid species response adjusting for the baseline covariates (lipids, age, sex, race, CD4 level, BMI, and smoking). Results were validated in the Centers for AIDS Research Network of Integrated Clinical Systems study (N = 16).Out of 417 annotated lipids, glycerophospholipids (P = .007) and sphingolipids (P = .028) had a higher response to ATV/r and DRV/r compared to RAL. The lysophosphatidylcholine (LPCs(16:1),(17:1),(20:3)) and phosphophatidylcholine species (PCs(40:7),(38:4)) had an opposite response to RAL versus ATV/r in the discovery and validation cohort. The INSTI-based regimen had an opposite response of ceramide species ((d38:1), (d42:2)), PCs((35:2), (38:4)), phosphatidylethanolamines (PEs(38:4), (38:6)), and sphingomyelin(SMd38:1) species compared with the PI-based regimens. There were no differences observed between 2 PI-based regimens.We observed differences in response of small molecule lipid species by ART regimens in treatment-naive people living with HIV.

Estimates of European American Ancestry in African Americans Using HFE p.C282Y

Background: HFE p.C282Y (chromosome 6p22.2; exon 4, c.845G>A; rs1800562), a hemochromatosis-associated polymorphism in European Americans, is absent in sub-Saharan West African blacks. Methods: We estimated European American ancestry in African Americans (M) using published p.C282Y allele frequencies of sub-Saharan West African blacks; and ≥50 unselected African Americans and ≥50 unselected European Americans in the same city/region. Results: p.C282Y allele frequency in 870 West African blacks (The Gambia, Ghana, Nigeria, Senegal, Sierra Leone) was 0.0000 (confidence interval [95% CI 0.0000-0.0027]). p.C282Y allele frequencies in European Americans were 0.0600 (12,592 participants; five single-site studies) and 0.0673 (54,882 participants; two multisite studies). p.C282Y allele frequencies in African Americans were 0.0102 (3084 participants; five single-site studies) and 0.0122 (30,762 participants; two multisite studies). M for all data was 0.1803 (standard error 0.0049; [95% CI 0.1706-0.1900]). City/region estimates of M differed 1.8-fold: 0.1321, Rochester, NY; 0.1456, Birmingham, AL; 0.1569, Upper Savannah Region, SC; 0.1612, Portland, OR; 0.1746, San Diego, CA; 0.1780, Hartford, CT; 0.1957, District of Columbia; 0.2377, Oakland, CA; and 0.2429, Irvine, CA. Conclusions: Estimates of M using p.C282Y are consistent with those using other autosomal markers, differ across nine cities/regions, and reflect paternal and maternal contributions of European American ancestry in African Americans.

Genetic Admixture and Survival in Diverse Populations with Pulmonary Arterial Hypertension

Rationale: Limited information is available on racial/ethnic differences in pulmonary arterial hypertension (PAH).Objectives: Determine effects of race/ethnicity and ancestry on mortality and disease outcomes in diverse patients with PAH.Methods: Patients with Group 1 PAH were included from two national registries with genome-wide data and two local cohorts, and further incorporated in a global meta-analysis. Hazard ratios (HRs) and 95% confidence intervals (CIs) were calculated for transplant-free, all-cause mortality in Hispanic patients with non-Hispanic white (NHW) patients as the reference group. Odds ratios (ORs) for inpatient-specific mortality in patients with PAH were also calculated for race/ethnic groups from an additional National Inpatient Sample dataset not included in the meta-analysis.Measurements and Main Results: After covariate adjustment, self-reported Hispanic patients (n = 290) exhibited significantly reduced mortality versus NHW patients (n = 1,970) after global meta-analysis (HR, 0.60 [95% CI, 0.41-0.87]; P = 0.008). Although not significant, increasing Native American genetic ancestry appeared to account for part of the observed mortality benefit (HR, 0.48 [95% CI, 0.23-1.01]; P = 0.053) in the two national registries. Finally, in the National Inpatient Sample, an inpatient mortality benefit was also observed for Hispanic patients (n = 1,524) versus NHW patients (n = 8,829; OR, 0.65 [95% CI, 0.50-0.84]; P = 0.001). An inpatient mortality benefit was observed for Native American patients (n = 185; OR, 0.38 [95% CI, 0.15-0.93]; P = 0.034).Conclusions: This study demonstrates a reproducible survival benefit for Hispanic patients with Group 1 PAH in multiple clinical settings. Our results implicate contributions of genetic ancestry to differential survival in PAH.

Geographical and Racial Disparities in Head and Neck Cancer Diagnosis in South-Eastern United States: Using Real-World Electronic Medical Records Data

Background: Rurality, race, and age at diagnosis are important predictors in head and neck cancer (HNC) prognosis. However, literature on the associations of rurality and race with age at HNC diagnosis is limited. Data on geographical, racial, and gender disparities in young HNC patients (diagnosed ≤45 years) are also scarce.

Materials and Methods: This retrospective study assesses rural–urban, racial, and gender disparities in age at HNC diagnosis, using electronic medical records (Cerner) data of 4258 HNC patients (1538 residing in rural counties and 2720 in urban counties) from National Cancer Institute-designated cancer center in Alabama. Rurality was defined based on 2010 U.S. Census Bureau's rural–urban classification. Logistic regression was used to assess the association of young HNC diagnosis with demographical, behavioral, and clinical variables. ArcGIS 10.2 was used to map geospatial distribution of age and population-adjusted HNC case across rural and urban counties.

Results: Patients from rural counties were less likely to be diagnosed at younger age (≤45 years) compared with urban counties (odds ratio [OR] [95% confidence interval (CI)]: 0.74 [0.58–0.93]). Most patients present at stage III/IV (64.9% in rural and 60.2% in urban). Compared with white patients, black patients were 70% more likely to get diagnosed at a young age (95% CI: 1.23–2.35). Young patients were more likely to be females and blacks compared with older patients (p<0.0001). Among oral cavity cancer patients, rural patients were 51% less likely to get diagnosed at young age compared with urban patients (95% CI: 0.27–0.89).

Conclusions: Head and neck cancer screening is not routinely conducted so most show up at later stage of cancer. There is also evidence of disparities in age at HNC diagnosis based on rurality, race, and gender; targeted screening can help in reducing these disparities.

Comorbidities associated with HPV infection among people living with HIV-1 in the southeastern US: a retrospective clinical cohort study

Background

The southeastern US is an epicenter for incident HIV in the US with high prevalence of human papillomavirus (HPV) co-infections. However, epidemiologies of HPV-associated clinical conditions (CC) among people living with HIV-1 infection (PLWH) are not fully known.

Methods

Electronic medical records (EMR) of PLWH attending one of the leading HIV clinics in the southeastern US between 2006 and 2018 were reviewed and analyzed. The retrospective study was nested within the University of Alabama at Birmingham HIV clinical cohort, which has electronically collected over 7000 PLWH’s clinical and sociobehavioral data since 1999. Incidence rates of HPV-related CC including anogenital warts, penile, anal, cervical, and vaginal/vulvar low- and high-grade squamous intraepithelial lesions (LSIL and HSIL) were estimated per 10,000 person years. Joinpoint regressions were performed to examine temporal changes in the trends of incident CC. All rates and trends were stratified by gender and race.

Results

Of the 4484 PLWH included in the study (3429 men, 1031 women, and 24 transgender), we observed 1038 patients with HPV-related CC. The median nadir CD4 count (cells/uL) was higher in the HPV-condition free group than the case groups (P < 0.0001). Anogenital warts, anal LSIL, HSIL, and cancer were more likely to be diagnosed among HIV-infected men than women. White men presented more frequently with anal LSIL and anal and penile cancers than black men (P < 0.03). White women were also more likely to be diagnosed with cervical HSIL (P = 0.023) and cancer (P = 0.037) than black women.

Conclusions

There were significant differences between gender and race with incidence of HPV-related CC among HIV patients. EMR-based studies provide insights on understudied HPV-related anogenital conditions in PLWH; however, large-scale studies in other regions are needed to generalize current findings and draw public health attention to co-infection induced non-AIDS defining comorbidities among PLWH.

Protective HLA alleles are associated with reduced LPS levels in acute HIV infection with implications for immune activation and pathogenesis

Despite extensive research on the mechanisms of HLA-mediated immune control of HIV-1 pathogenesis, it is clear that much remains to be discovered, as exemplified by protective HLA alleles like HLA-B*81 which are associated with profound protection from CD4+ T cell decline without robust control of early plasma viremia. Here, we report on additional HLA class I (B*1401, B*57, B*5801, as well as B*81), and HLA class II (DQB1*02 and DRB1*15) alleles that display discordant virological and immunological phenotypes in a Zambian early infection cohort. HLA class I alleles of this nature were also associated with enhanced immune responses to conserved epitopes in Gag. Furthermore, these HLA class I alleles were associated with reduced levels of lipopolysaccharide (LPS) in the plasma during acute infection. Elevated LPS levels measured early in infection predicted accelerated CD4+ T cell decline, as well as immune activation and exhaustion. Taken together, these data suggest novel mechanisms for HLA-mediated immune control of HIV-1 pathogenesis that do not necessarily involve significant control of early viremia and point to microbial translocation as a direct driver of HIV-1 pathogenesis rather than simply a consequence.

During acute HIV infection, there exists a complex interplay between the host immune response and the virus, and the balance of these interactions dramatically affects disease trajectory in infected individuals. Variations in Human Leukocyte Antigen (HLA) alleles dictate the potency of the cellular immune response to HIV, and certain well-studied alleles (HLA-B*57, B*27) are associated with control of HIV viremia. However, though plasma viral load is indicative of disease progression, the number of CD4+ T cells in the blood is a better measurement of disease severity. Through analysis of a large Zambian acute infection cohort, we identified HLA alleles that were associated with protection for CD4+ T cell loss, without dramatic affect on early plasma viremia. We further link these favorable HLA alleles to reduction in a well-known contributor to HIV pathogenesis, the presence of microbial products in the blood, which is indicative of damage to the gastrointestinal tract, a process which accelerates disease progression in HIV infected individuals. Ultimately, these results suggest a new mechanism by which the cellular immune response can combat HIV-associated pathogenesis, and further highlight the contribution of gut damage and microbial translocation to accelerating disease progression, even at early stages in HIV infection.

Increasing Levels of Serum Heat Shock Protein 70 Precede the Development of AIDS-Defining Non-Hodgkin Lymphoma Among Carriers of HLA-B8-DR3

BACKGROUND

We hypothesized that carriage of presumably high Hsp70-producing gene variants on a specific human major histocompatibility complex haplotype, the 8.1 ancestral haplotype (8.1AH), may predispose HIV-infected individuals to AIDS-non-Hodgkin lymphoma (NHL).

SETTING

We compared serum Hsp70 levels in the years preceding the diagnosis of AIDS-NHL in a matched case-control study (n = 151 pairs) nested in the Multicenter AIDS Cohort Study.

METHODS

We tested the impact of 8.1AH-specific single-nucleotide polymorphism (SNP) and joint SNP-human leukocyte antigen extended haplotypes previously associated with AIDS-NHL in the Multicenter AIDS Cohort Study on the circulating Hsp70 levels in mixed linear models.

RESULTS

We report elevated serum levels of Hsp70 in the 4 years preceding the diagnosis of AIDS-NHL in cases that carry 8.1AH, but not in noncarrier cases and not in carrier- or non-carrier-matched controls. The strongest predictor of higher serum Hsp70 was the haplotype A-G-A-C formed by SNPs rs537160(A) and rs1270942(G) in the complement factor CFB gene cluster, and rs2072633(A) and rs6467(C) in nearby RDBP and CYP21A2 located 70 Kb apart from the Hsp70 gene cluster. The association with A-G-A-C haplotype (beta = 0.718; standard error = 0.182; P = 0.0002) and with other 8.1AH-specific haplotypes including the high-producing tumor necrosis factor-alpha haplotype rs909253(G)-rs1800629(A) (beta = 0.308; standard error = 0.140; P = 0.032) were observed only with NHL identified as an AIDS-defining condition, but not as a post-AIDS condition, nor in combined AIDS and post-AIDS cases.

CONCLUSION

Our combined genetic and functional approach suggests that the altered level of Hsp70 is a correlate of 8.1AH-mediated AIDS-NHL. Further investigation of the Hsp70 gene cluster and nearby loci that are tagged by A-G-A-C could better elucidate the genetic determinants of the malignancy.

Illustration of Measurement Error Models for Reducing Bias in Nutrition and Obesity Research Using 2-D Body Composition Data

OBJECTIVE

This study aimed to illustrate the use and value of measurement error models for reducing bias when evaluating associations between body fat and having type 2 diabetes (T2D) or being physically active.

METHODS

Logistic regression models were used to evaluate T2D and physical activity among adults aged 19 to 80 years from the Photobody Study (n = 558). Self-reported T2D and physical activity were categorized as "yes" or "no." Body fat measured by two-dimensional photographs was adjusted for bias using dual-energy x-ray absorptiometry scans as a reference. Three approaches were applied: regression calibration (RC), simulation extrapolation (SIMEX), and multiple imputation (MI).

RESULTS

Unadjusted two-dimensional measures of body fat had upward biases of 30% and 233% for physical activity and T2D, respectively. For the physical activity model, RC-adjusted values had a 13% upward bias, whereas MI and SIMEX decreased the bias to 9% and 91%, respectively. For the T2D model, MI reduced the bias to 0%, whereas RC and SIMEX increased the upward bias to > 300%.

CONCLUSIONS

Of three statistical approaches to reducing bias due to measurement errors, MI performed best in comparison to RC and SIMEX. Measurement error methods can improve the reliability of analyses that look for relations between body fat measures and health outcomes.

A method for measuring human body composition using digital images

BACKGROUND/OBJECTIVES

Body mass index (BMI) is a proxy for obesity that is commonly used in spite of its limitation in estimating body fatness. Trained observers with repeated exposure to different body types can estimate body fat (BF) of individuals compared to criterion methods with reasonable accuracy. The purpose of this study was to develop and validate a computer algorithm to provide a valid estimate %BF using digital photographs.

SUBJECTS/METHODS

Our sample included 97 children and 226 adults (age in years: 11.3±3.3; 38.1±11.6, respectively). Measured height and weight were used (BMI in kg/m2: 20.4±4.4; 28.7±6.6 for children and adults, respectively). Dual x-ray absorptiometry (DXA) was the criterion method. Body volume (BVPHOTO) and body shape (BSPHOTO) were derived from two digital images. Final support vector regression (SVR) models were trained using age, sex, race, BMI for % BFNOPHOTO, plus BVPHOTO and BSPHOTO for %BFPHOTO. Separate validation models were used to evaluate the learning algorithm in children and adults. The differences in correlations between %BFDXA, %BFNOPHOTO and %BFPHOTO were tested using the Fisher's Z-score transformation.

RESULTS

Mean BFDXA and BFPHOTO were 27.0%±9.2 vs. 26.7%± 7.4 in children and 32.9± 10.4% vs. 32.8%±9.3 in adults. SVR models produced %BFPHOTO values strongly correlated with %BFDXA. Our final model produced correlations of rDP = 0.80 and rDP = 0.87 in children and adults, respectively for %BFPHOTO vs. %BFDXA. The correlation between %BFNOPHOTO and %BFDXA was moderate, yet statistically significant in both children rDB = 0.70; p <0.0001 and adults rDB = 0.86; p<0.0001. However, the correlations for rDP were statistically higher than rDB (%BFDXA vs. %BFNOPHOTO) in both children and adults (children: Z = 5.95, p<0.001; adults: Z = 3.27, p<0.0001).

CONCLUSIONS

Our photographic method produced valid estimates of BF in both children and adults. Further research is needed to create norms for subgroups by sex, race/ethnicity, and mobility status.

Identification of novel high-impact recessively inherited type 2 diabetes risk variants in the Greenlandic population

AIMS/HYPOTHESIS

In a recent study using a standard additive genetic model, we identified a TBC1D4 loss-of-function variant with a large recessive impact on risk of type 2 diabetes in Greenlanders. The aim of the current study was to identify additional genetic variation underlying type 2 diabetes using a recessive genetic model, thereby increasing the power to detect variants with recessive effects.

METHODS

We investigated three cohorts of Greenlanders (B99, n = 1401; IHIT, n = 3115; and BBH, n = 547), which were genotyped using Illumina MetaboChip. Of the 4674 genotyped individuals passing quality control, 4648 had phenotype data available, and type 2 diabetes association analyses were performed for 317 individuals with type 2 diabetes and 2631 participants with normal glucose tolerance. Statistical association analyses were performed using a linear mixed model.

RESULTS

Using a recessive genetic model, we identified two novel loci associated with type 2 diabetes in Greenlanders, namely rs870992 in ITGA1 on chromosome 5 (OR 2.79, p = 1.8 × 10-8), and rs16993330 upstream of LARGE1 on chromosome 22 (OR 3.52, p = 1.3 × 10-7). The LARGE1 variant did not reach the conventional threshold for genome-wide significance (p < 5 × 10-8) but did withstand a study-wide Bonferroni-corrected significance threshold. Both variants were common in Greenlanders, with minor allele frequencies of 23% and 16%, respectively, and were estimated to have large recessive effects on risk of type 2 diabetes in Greenlanders, compared with additively inherited variants previously observed in European populations.

CONCLUSIONS/INTERPRETATION

We demonstrate the value of using a recessive genetic model in a historically small and isolated population to identify genetic risk variants. Our findings give new insights into the genetic architecture of type 2 diabetes, and further support the existence of high-effect genetic risk factors of potential clinical relevance, particularly in isolated populations.

DATA AVAILABILITY

The Greenlandic MetaboChip-genotype data are available at European Genome-Phenome Archive (EGA; https://ega-archive.org/ ) under the accession EGAS00001002641.

Variants in immune-related genes and genital HPV 16 persistence in men

OBJECTIVES

While most human papillomavirus (HPV) infection clears on its own, persistent HPV infection can cause genital warts and anal, penile and oropharyngeal cancers in men. We conducted genetic analysis in a sub-cohort of the HPV infection in men (HIM) study to test the hypothesis that differences in host genes influence HPV persistence in men.

METHODS

Baseline and longitudinal genital HPV status at the genitals was measured every 6-months using the Linear Array assay amplified HPV L1 gene fragment using the PGMY09/11 L1 consensus primer system. DNA was extracted from peripheral blood and single nucleotide polymorphisms (SNPs) in the customized genome-wide genotyping array, the "TxArray," were examined using logistic regression in a case-control study design to assess the association with HPV16 persistence/clearance.

RESULTS

Of the total of 737,742 autosomal SNPs in the array, 605,885 passed basic quality control and were examined between 40 men (cases) with > 18 months persistent genital HPV 16 infection vs. 151 controls who were HPV 16-positive, but whose infections cleared in < 18 months. The logistic regression analysis from this case-control study showed variants in several gene regions associated with genital HPV 16 persistence, with the strongest association detected with SNPs on chromosomes 20 (p < 5.72 × 10^-6) and 15 (p < 5.89 × 10^-6), after adjusting for age, smoking status, number of sex partners and four principal components (ancestral background).

CONCLUSIONS

Our results provide a preliminary basis for understanding the biological mechanism of oncogenic HPV 16 pathogenesis at the genitals in men. Some of the genes flanking the top hit SNPs are consistent with previous findings in both HPV related and non-related cancers but further genetic studies in larger cohorts are warranted to confirm these and identify novel major susceptibility genes involved in the pathogenesis of genital HPV persistence in men.

Herpes Zoster in Persons Living with HIV-1 Infection: Viremia and Immunological Defects Are Strong Risk Factors in the Era of Combination Antiretroviral Therapy

In a cohort of 4,225 persons living with human immunodeficiency virus type 1 (HIV-1) infection (PLWH) enrolled at a southeastern US clinic, the overall rate of incident herpes zoster (HZ) was 101 per 10,000 person-years (PY) between January 1999 and 2017, which nearly quadruples the rate reported for the general US population. In the same cohort, the median age of HZ diagnosis was 39.5 years [interquartile range (IQR) 31.5–49.2] in African American (AA) and 39.1 years (IQR 34.9–45.2) in European American (EA) PLWH, with the highest incidence seen in PLWH who were over 50 years old (144 and 93 per 10,000 PY in AA and EA, respectively, P = 0.18), showing no bias between men (100 per 10,000 PY) and women (101 per 10,000 PY). In multivariable models that were applicable to 245 HZ cases and 3,713 controls, age, nadir CD4⁺ T-cell (CD4) count, plasma viral load (VL), and duration of combination antiretroviral therapy were independent correlates of incident HZ (adjusted P ≤ 0.006 for all). Regardless of other factors, viremic PLWH (VL > 50 copies/mL) was at the highest risk of HZ [adjusted odds ratio (OR) > 3.0, P < 0.0001]. PLWH with a nadir CD4 count of ≥500 cells/μL showed a relatively low risk (adjusted OR = 0.48, P = 0.003). By contrast, similar risk estimates were observed with three advancing age groups (30–39, 40–49, and ≥50) when compared with age <30 (adjusted OR = 1.86–2.17, P ≤ 0.010). These findings indicate that efforts for HZ diagnosis and prophylaxis should target viremic PLWH who are over 30 years old and with CD4 count <500 cells/μL.

Immunogenetic factors in early immune control of human immunodeficiency virus type 1 (HIV-1) infection: Evaluation of HLA class I amino acid variants in two African populations

Immune control of HIV-1 infection depends heavily on cytotoxic T-lymphocyte responses restricted by diverse HLA class I molecules. Recent work has uncovered specific amino acid residues (AARs) that seem to dictate the extent of immune control in African Americans, which prompted us to test these emerging hypotheses in seroconverters (SCs) from southern and eastern Africa. Based on data from 196 Zambians and 76 Rwandans with fully resolved HLA alleles and pre-therapy HIV-1 viral loads (VL) in the first 3- to 36-month of infection (>2300 person-visits), four AARs of primary interest (positions 63, 97, 116 and 245 in the mature HLA-B protein) were found to explain 8.1% and 15.8% of variance in set-point VL for these cohorts (P = .024 and 7.5 × 10^-6, respectively). Two AARs not reported previously (167S in HLA-B and 116F in HLA-C) also showed relatively consistent associations with VL (adjusted P = .009-.069), while many population-specific associations were also noted (false discovery rate <0.05). Extensive and often strong linkage disequilibrium among neighboring AAR variants called for more extensive analyses of AAR haplotypes in diverse cohorts before the structural basis of antigen presentation can be fully comprehended.

Genome-wide admixture and association study of subclinical atherosclerosis in the Women's Interagency HIV Study (WIHS)

Cardiovascular disease (CVD) is a major comorbidity among HIV-infected individuals. Common carotid artery intima-media thickness (cCIMT) is a valid and reliable subclinical measure of atherosclerosis and is known to predict CVD. We performed genome-wide association (GWA) and admixture analysis among 682 HIV-positive and 288 HIV-negative Black, non-Hispanic women from the Women’s Interagency HIV study (WIHS) cohort using a combined and stratified analysis approach. We found some suggestive associations but none of the SNPs reached genome-wide statistical significance in our GWAS analysis. The top GWAS SNPs were rs2280828 in the region intergenic to mediator complex subunit 30 and exostosin glycosyltransferase 1 (MED30 | EXT1) among all women, rs2907092 in the catenin delta 2 (CTNND2) gene among HIV-positive women, and rs7529733 in the region intergenic to family with sequence similarity 5, member C and regulator of G-protein signaling 18 (FAM5C | RGS18) genes among HIV-negative women. The most significant local European ancestry associations were in the region intergenic to the zinc finger and SCAN domain containing 5D gene and NADH: ubiquinone oxidoreductase complex assembly factor 1 (ZSCAN5D | NDUF1) pseudogene on chromosome 19 among all women, in the region intergenic to vomeronasal 1 receptor 6 pseudogene and zinc finger protein 845 (VN1R6P | ZNF845) gene on chromosome 19 among HIV-positive women, and in the region intergenic to the SEC23-interacting protein and phosphatidic acid phosphatase type 2 domain containing 1A (SEC23IP | PPAPDC1A) genes located on chromosome 10 among HIV-negative women. A number of previously identified SNP associations with cCIMT were also observed and included rs2572204 in the ryanodine receptor 3 (RYR3) and an admixture region in the secretion-regulating guanine nucleotide exchange factor (SERGEF) gene. We report several SNPs and gene regions in the GWAS and admixture analysis, some of which are common across HIV-positive and HIV-negative women as demonstrated using meta-analysis, and also across the two analytic approaches (i.e., GWA and admixture). These findings suggest that local European ancestry plays an important role in genetic associations of cCIMT among black women from WIHS along with other environmental factors that are related to CVD and may also be triggered by HIV. These findings warrant confirmation in independent samples.

Non-linear patterns in age-related DNA methylation may reflect CD4+ T cell differentiation

DNA methylation (DNAm) is an important epigenetic process involved in the regulation of gene expression. While many studies have identified thousands of loci associated with age, few have differentiated between linear and non-linear DNAm trends with age. Non-linear trends could indicate early- or late-life gene regulatory processes. Using data from the Illumina 450K array on 336 human peripheral blood samples, we identified 21 CpG sites that associated with age (P<1.03E-7) and exhibited changing rates of DNAm change with age (P<1.94E-6). For 2 of these CpG sites (cg07955995 and cg22285878), DNAm increased with age at an increasing rate, indicating that differential DNAm was greatest among elderly individuals. We observed significant replication for both CpG sites (P<5.0E-8) in a second set of peripheral blood samples. In 8 of 9 additional data sets comprising samples of monocytes, T cell subtypes, and brain tissue, we observed a pattern directionally consistent with DNAm increasing with age at an increasing rate, which was nominally significant in the 3 largest data sets (4.3E-15<P<0.039). cg07955995 and cg22285878 reside in the promoter region of KLF14, which encodes a protein involved in immune cell differentiation via the repression of FOXP3. These findings may suggest a possible role for cg07955995 and cg22285878 in immunosenescence.

Association Between Early Childhood Caries and Colonization with Streptococcus mutans Genotypes From Mothers

PURPOSE

The purpose of this study was to evaluate Streptococcus mutans genotypes (GT) between mother and child (M-C) in a high caries risk cohort to explore the association with early childhood caries (ECC).

METHODS

Sixty-nine infants (each approximately one year old) had periodic oral examinations (dmfs) and microbial samples collected from dental plaque, saliva, and other oral surfaces. Their mothers had an examination and plaque collected. S mutans isolates were genotyped using repetitive extragenic palindromic-PCR (rep-PCR). Statistical analyses were conducted for associations of S mutans in M-C dyads with caries outcomes.

RESULTS

Twenty-seven S mutans genotypes (GT) from 3,414 isolates were identified. M-C were categorized as GT match (n equals 40) or no-match (n equals 29). When modeling the severity of ECC at 36 months (approximately four years old), the estimated dmfs in the match group was 2.61 times that of the no-match group (P=.014).

CONCLUSIONS

Colonization of children with Streptococcus mutans genotypes that matched with mothers was shown to be highly associated with early childhood caries. Although the data suggest vertical transmission of S mutans in 40 of 69 children that shared GT with their mother, it is possible that other individuals transmitted the S mutans. Nonetheless, these findings support the importance of the mother's oral microbial status as a contributing influence to their children's oral health.

Genomic diversity and phylogenetic relationships of human papillomavirus 16 (HPV16) in Nepal

OBJECTIVES/BACKGROUND

Sequence variants in HPV16 confer differences in oncogenic potential; however, to date there have not been any HPV sequence studies performed in Nepal. The objective of this study was to characterize HPV16 viral genome sequences from Nepal compared to a reference sequence in order to determine their lineages. Additionally, we sought to determine if five High-grade Squamous Intraepithelial Lesion (HSIL) subjects were genetically distinct from the non-HSIL subjects.

METHODS

DNA was isolated from exfoliated cervical cells from 17 individuals in Nepal who were previously identified to be HPV16-positive. A custom HPV16 Ion Ampliseq panel of multiplexed degenerate primers was designed that generated 47 overlapping amplicons and covered 99% of the viral genome for all known HPV16 variant lineages. All sequence data were processed through a custom quality control and analysis pipeline of sequence comparisons and phylogenetic analysis.

RESULTS

There were high similarities across the genomes, with two major indels observed in the non-coding region between E5 and L2. Compared to the PAVE reference HPV16 genome, there were up to 9, 4, 38, 27, 8, 7, 52, and 32 nucleotide variants in the E6, E7, E1, E2, E4, E5, L2, and L1 genes in the Nepalese samples, respectively. Based on sequence variation, HPV16 from Nepal falls across the A, C, and D lineages in this study. We found no evidence of genetic distinctness between HSIL and non-HSIL subjects.

CONCLUSIONS

The evolutionary and pathological characteristics of the representative HPV16 genomes from Nepal seem similar to results from other parts of the world and provide the basis for further studies.

Polymorphisms in stearoyl coa desaturase and sterol regulatory element binding protein interact with N-3 polyunsaturated fatty acid intake to modify associations with anthropometric variables and metabolic phenotypes in Yup'ik people

SCOPE

n-3 polyunsaturated fatty acid (n-3 PUFA) intake is associated with protection from obesity; however, the mechanisms of protection remain poorly characterized. The stearoyl CoA desaturase (SCD), insulin-sensitive glucose transporter (SLC2A4), and sterol regulatory element binding protein (SREBF1) genes are transcriptionally regulated by n-3 PUFA intake and harbor polymorphisms associated with obesity. The present study investigated how consumption of n-3 PUFA modifies associations between SCD, SLC2A4, and SREBF1 polymorphisms and anthropometric variables and metabolic phenotypes.

MATERIALS AND METHODS

Anthropometric variables and metabolic phenotypes were measured in a cross-sectional sample of Yup'ik individuals (n = 1135) and 33 polymorphisms were tested for main effects and interactions using linear models that account for familial correlations. n-3 PUFA intake was estimated using red blood cell nitrogen stable isotope ratios. SCD polymorphisms were associated with ApoA1 concentration and n-3 PUFA interactions with SCD polymorphisms were associated with reduced fasting cholesterol levels and waist-to-hip ratio. SLC2A4 polymorphisms were associated with hip circumference, high-density lipoprotein and ApoA1 concentrations. SREBF1 polymorphisms were associated with low-density lipoprotein and HOMA-IR and n-3 PUFA interactions were associated with reduced fasting insulin and HOMA-IR levels.

CONCLUSION

The results suggest that an individual's genotype may interact with dietary n-3 PUFAs in ways that are associated with protection from obesity-related diseases in Yup'ik people.

Linkage and association analysis of circulating vitamin D and parathyroid hormone identifies novel loci in Alaska Native Yup'ik people

Background

Vitamin D deficiency is a well-documented public health issue with both genetic and environmental determinants. Populations living at far northern latitudes are vulnerable to vitamin D deficiency and its health sequelae, although consumption of traditional native dietary pattern rich in fish and marine mammals may buffer the effects of reduced sunlight exposure. To date, few studies have investigated the genetics of vitamin D metabolism in circumpolar populations or considered genediet interactions with fish and n-3 fatty acid intake.

Methods

We searched for genomic regions exhibiting linkage and association with circulating levels of vitamin D and parathyroid hormone (PTH) in 982 Yup’ik individuals from the Center for Alaska Native Health Research Study. We also investigated potential interactions between genetic variants and a biomarker of traditional dietary intake, the δ15N value.

Results

We identified several novel regions linked with circulating vitamin D and PTH as well as replicated a previous linkage finding on 2p16.2 for vitamin D. Bioinformatic analysis revealed multiple candidate genes for both PTH and vitamin D, including CUBN, MGAT3, and NFKBIA. Targeted association analysis identified NEBL as a candidate gene for vitamin D and FNDC3B for PTH. We observed significant associations between a variant in MXD1 and vitamin D only when an interaction with the δ15N value was included. Finally, we integrated pathway level information to illustrate the biological validity of the proposed candidate genes.

Conclusion

We provide evidence of linkage between several biologically plausible genomic regions and vitamin D metabolism in a circumpolar population. Additionally, these findings suggest that a traditional dietary pattern may modulate genetic effects on circulating vitamin D.

Electronic supplementary material

The online version of this article (doi:10.1186/s12263-016-0538-y) contains supplementary material, which is available to authorized users.

Fine Mapping of the Body Fat QTL on Human Chromosome 1q43

Introduction

Evidence for linkage and association of obesity-related quantitative traits to chromosome 1q43 has been reported in the Quebec Family Study (QFS) and in populations of Caribbean Hispanic ancestries yet no specific candidate locus has been replicated to date.

Methods

Using a set of 1,902 single nucleotide polymorphisms (SNPs) genotyped in 525 African American (AA) and 391 European American (EA) women enrolled in the NIEHS uterine fibroid study (NIEHS-UFS), we generated a fine association map for the body mass index (BMI) across a 2.3 megabase-long interval delimited by RGS7 (regulator of G-protein signaling 7) and PLD5 (Phospholipase D, member 5). Multivariable-adjusted linear regression models were fitted to the data to evaluate the association in race-stratified analyses and meta-analysis.

Results

The strongest associations were observed in a recessive genetic model and peaked in the 3’ end of RGS7 at intronic rs261802 variant in the AA group (p = 1.0 x 10⁻⁴) and in meta-analysis of AA and EA samples (p = 9.0 x 10⁻⁵). In the EA group, moderate associations peaked at rs6429264 (p = 2.0 x 10⁻³) in the 2 Kb upstream sequence of RGS7. In the reference populations for the European ancestry in the 1,000 genomes project, rs6429264 occurs in strong linkage disequilibrium (D’ = 0.94) with rs1341467, the strongest candidate SNP for total body fat in QFS that failed genotyping in the present study. Additionally we report moderate associations at the 3’ end of PLD5 in meta-analysis (3.2 x 10⁻⁴ ≤ p ≤ 5.8 x 10⁻⁴).

Conclusion

We report replication data suggesting that RGS7, a gene abundantly expressed in the brain, might be a putative body fat QTL on human chromosome 1q43. Future genetic and functional studies are required to substantiate our observations and to potentially link them to the neurobehavioral phenotypes associated with the RGS7 region.

Endothelin-1 Pathway Polymorphisms and Outcomes in Pulmonary Arterial Hypertension

RATIONALE

Pulmonary arterial hypertension (PAH) is a progressive fatal disease. Variable response and tolerability to PAH therapeutics suggests that genetic differences may influence outcomes. The endothelin pathway is central to pulmonary vascular function, and several polymorphisms and/or mutations in the genes coding for endothelin (ET)-1 and its receptors correlate with the clinical manifestations of other diseases.

OBJECTIVES

To examine the interaction of ET-1 pathway polymorphisms and treatment responses of patients with PAH treated with ET receptor antagonists (ERAs).

METHODS

A total of 1,198 patients with PAH were prospectively enrolled from 45 U.S. and Canadian pulmonary hypertension centers or retrospectively from global sites participating in the STRIDE (Sitaxsentan To Relieve Impaired Exercise) trials. Comprehensive objective measures including a 6-minute-walk test, Borg dyspnea score, functional class, and laboratory studies were completed at baseline, before the initiation of ERAs, and repeated serially. Single-nucleotide polymorphisms from ET-1 pathway candidate genes were selected from a completed genome-wide association study performed on the study cohort.

MEASUREMENTS AND MAIN RESULTS

Patient efficacy outcomes were analyzed for a relationship between ET-1 pathway polymorphisms and clinical efficacy using predefined, composite positive and negative outcome measures in 715 European descent samples. A single-nucleotide polymorphism (rs11157866) in the G-protein alpha and gamma subunits gene was significantly associated, accounting for multiple testing, with a combined improvement in functional class and 6-minute-walk distance at 12 and 18 months and marginally significant at 24 months.

CONCLUSIONS

ET-1 pathway associated polymorphisms may influence the clinical efficacy of ERA therapy for PAH. Further prospective studies are needed.

Genetics, Diet, and Season Are Associated with Serum 25-Hydroxycholecalciferol Concentration in a Yup'ik Study Population from Southwestern Alaska

BACKGROUND

Low blood vitamin D concentration is a concern for people living in circumpolar regions, where sunlight is insufficient for vitamin D synthesis in winter months and the consumption of traditional dietary sources of vitamin D is decreasing.

OBJECTIVE

The objective was to characterize the effects of diet, genetic variation, and season on serum 25-hydroxycholecalciferol [25(OH)D3] concentrations in Yup'ik Alaska Native people living in rural southwest Alaska.

METHODS

This study was a cross-sectional design that assessed the associations of traditional diet (via a biomarker, the RBC δ(15)N value), age, gender, body mass index (BMI), community location, and genotype of select single nucleotide polymorphisms (SNPs) in cytochrome P450 family 2, subfamily R, peptide 1 (CYP2R1), 7-dehydrocholesterol reductase (DHCR7), and vitamin D binding protein (GC) with serum 25(OH)D3 concentrations in 743 Yup'ik male and female participants, aged 14-93 y, recruited between September 2009 and December 2013.

RESULTS

Yup'ik participants, on average, had adequate concentrations of serum 25(OH)D3 (31.1 ± 1.0 ng/mL). Variations in diet, BMI, age, gender, season of sample collection, and inland or coastal community geography were all significantly associated with serum 25(OH)D3 concentration. In models not adjusting for other covariates, age, diet, and seasonal effects explained 33.7%, 20.7%, and 9.8%, respectively, of variability in serum 25(OH)D3 concentrations. Of the 8 SNPs interrogated in CYP2R1 and DHCR7, only rs11023374 in CYP2R1 was significantly associated with serum 25(OH)D3, explaining 1.5% of variability. The GC haplotype explained an additional 2.8% of variability. Together, age, diet, gender, season of sample collection, BMI, geography of the community, and genotype at rs11023374 explained 52.5% of the variability in serum 25(OH)D3 concentrations.

CONCLUSIONS

Lower consumption of the traditional diet was associated with lower serum concentrations of 25(OH)D3. Younger adults and youth in this community may be at increased risk of adverse outcomes associated with vitamin D insufficiency compared with older members of the community, especially during seasons of low sunlight exposure, because of lower consumption of dietary sources of vitamin D.

A family-specific linkage analysis of blood lipid response to fenofibrate in the Genetics of Lipid Lowering Drug and Diet Network

Cost-effective identification of novel pharmacogenetic variants remains a pressing need in the field. Using data from the Genetics of Lipid Lowering Drugs and Diet Network, we identified genomic regions of relevance to fenofibrate response in a sample of 173 families. Our approach included a multipoint linkage scan, followed by selection of the families showing evidence of linkage. We identified a strong signal for changes in LDL-cholesterol (LDL-C) on chromosome 7 (peak logarithm of odds score = 4.76) in the full sample (n = 821). The signal for LDL-C response remained even after adjusting for baseline LDL-C. Restricting analyses only to the families contributing to the linkage signal for LDL-C (N = 19), we observed a peak logarithm of odds score of 5.17 for chromosome 7. Two genes under this peak (ABCB4 and CD36) were of biological interest. These results suggest that linked family analyses might be a useful approach to gene discovery in the presence of a complex (e.g. multigenic) phenotype.

Fine mapping of the uterine leiomyoma locus on 1q43 close to a lncRNA in the RGS7-FH interval

Mutations in fumarate hydratase (FH) on chromosome 1q43 cause a rare cancer syndrome, hereditary leiomyomatosis and renal cell cancer (HLRCC), but are rare in nonsyndromic and common uterine leiomyoma (UL) or fibroids. Studies suggested that variants in FH or in a linked gene may also predispose to UL. We re-sequenced 2.3 Mb of DNA spanning FH in 96 UL cases and controls from the multiethnic NIEHS-uterine fibroid study, and in 18 HLRCC-associated UL probands from European families then selected 221 informative SNPs for follow-up genotyping. We report promising susceptibility associations with UL peaking at rs78220092 (P=7.0×10(-5)) in the RGS7-FH interval in African Americans. In race-combined analyses and in meta-analyses (n=916), we identified promising associations with risk peaking upstream of a non-protein coding RNA (lncRNA) locus located in the RGS7-FH interval closer to RGS7, and associations with tumor size peaking in the distal phospholipase D family, member 5 (PLD5) gene at rs2654879 (P=1.7×10(-4)). We corroborated previously reported FH mutations in nine out of the 18 HLRCC-associated UL cases and identified two missense mutations in FH in only two nonsyndromic UL cases and one control. Our fine association mapping and integration of existing gene profiling data showing upregulated expression of the lncRNA and downregulation of PLD5 in fibroids, as compared to matched myometrium, suggest a potential role of this genomic region in UL pathogenesis. While the identified variations at 1q43 represent a potential risk locus for UL, future replication analyses are required to substantiate our observation.

Linkage and association analysis of obesity traits reveals novel loci and interactions with dietary n-3 fatty acids in an Alaska Native (Yup'ik) population

OBJECTIVE

To identify novel genetic markers of obesity-related traits and to identify gene-diet interactions with n-3 polyunsaturated fatty acid (n-3 PUFA) intake in Yup'ik people.

MATERIAL AND METHODS

We measured body composition, plasma adipokines and ghrelin in 982 participants enrolled in the Center for Alaska Native Health Research (CANHR) Study. We conducted a genome-wide SNP linkage scan and targeted association analysis, fitting additional models to investigate putative gene-diet interactions. Finally, we performed bioinformatic analysis to uncover likely candidate genes within the identified linkage peaks.

RESULTS

We observed evidence of linkage for all obesity-related traits, replicating previous results and identifying novel regions of interest for adiponectin (10q26.13-2) and thigh circumference (8q21.11-13). Bioinformatic analysis revealed DOCK1, PTPRE (10q26.13-2) and FABP4 (8q21.11-13) as putative candidate genes in the newly identified regions. Targeted SNP analysis under the linkage peaks identified associations between three SNPs and obesity-related traits: rs1007750 on chromosome 8 and thigh circumference (P=0.0005), rs878953 on chromosome 5 and thigh skinfold (P=0.0004), and rs1596854 on chromosome 11 for waist circumference (P=0.0003). Finally, we showed that n-3 PUFA modified the association between obesity related traits and two additional variants (rs2048417 on chromosome 3 for adiponectin, P for interaction=0.0006 and rs730414 on chromosome 11 for percentage body fat, P for interaction=0.0004).

CONCLUSIONS

This study presents evidence of novel genomic regions and gene-diet interactions that may contribute to the pathophysiology of obesity-related traits among Yup'ik people.

Imputation of class I and II HLA loci using high-density SNPs from ImmunoChip and their associations with Kawasaki disease in family-based study

Kawasaki disease (KD) is the leading cause of acquired heart disease in children in most developed countries including the United States. The etiology of KD is not known; however, epidemiological and immunological data suggest infectious or immune-related factors in the manifestation of the disease. Further, KD has several hereditary features that strongly suggest a genetic component to disease pathogenesis. Human leucocyte antigen (HLA) loci have also been reported to be associated with KD, but results have been inconsistent, in part, because of small study samples and varying linkage disequilibrium (LD) patterns observed across different ethnic groups. To maximize the informativeness of single nucleotide polymorphism (SNP) genotypes in the major histocompatibility (MHC) region, we imputed classical HLA I (A, B, C) and HLA II (DRB1, DQA1, DQB1) alleles using SNP2HLA method from genotypes of 6700 SNPs within the extended MHC region contained in the ImmunoChip among 112 White patients with KD and their biological parents from North America and tested their association with KD susceptibility using the transmission disequilibrium test. Mendelian consistency in the trios suggested high accuracy and reliability of the imputed alleles (class I = 97.5%, class II = 96.6%). While several SNPs in the MHC region were individually associated with KD susceptibility, we report over-transmission of HLA-C*15 (z = +2.19, P = 0.03) and under-transmission of HLA-B*44 (z = -2.49, P = 0.01) alleles from parents to patients with KD. HLA-B*44 has been associated with KD in other smaller studies, and both HLA-C*15 and HLA-B*44 have biological mechanisms that could potentially be involved in KD pathogenesis. Overall, inferring HLA loci within the same ethnic group, using family-based information is a powerful approach. However, studies with larger sample sizes are warranted to evaluate the correlations of the strength and directions between the SNPs in MHC region and the imputed HLA alleles with KD.

Factors associated with early childhood caries incidence among high caries-risk children

OBJECTIVES

To assess the relationships between different behavioral factors and Early Childhood Caries (ECC) in African-American pre-school children.

METHODS

Ninety-six African-American children aged 3-22 months old at baseline were recruited from a high caries risk, non-fluoridated African-American community in Uniontown, Alabama. The children had dental examinations annually following World Health Organization (WHO) criteria at mean ages 1.1, 2.0, 3.1 and 4.0 years. All children received fluoride varnish application at each study visit. Parents provided oral hygiene and dietary information semiannually by completing questionnaires. Area-under-the-curve (AUC) with the trapezoidal rule was used to summarize longitudinal exposure data. Bivariate and multivariable relationships between ECC incidence and behavioral risk factors were assessed using logistic regression and negative binomial modeling for dichotomous and count dependent variables, respectively, with the independent variables defined at age 1, age 3 and as the AUC.

RESULTS

Greater frequency of toothbrushing and greater AUC composite of daily frequency of consumption of 100% juices were associated with lower incidence of dental caries (P-values = 0.01 and 0.049, ORs = 0.34 and 0.37, respectively). Greater AUC of daily frequency of consumption of sweetened foods and history of a previous visit to a dentist by age 3 were associated with greater incidence of ECC (ORs = 9.22 and 4.57, P-values = 0.002 and 0.03, respectively).

CONCLUSION

For these children living in a non-fluoridated community, more frequent consumption of sweetened food, less frequent consumption of 100% juice, less frequent toothbrushing, and reporting a previous visit to a dentist were significantly associated with greater ECC incidence.

High-density genotyping of immune loci in Kawasaki disease and IVIG treatment response in European-American case-parent trio study

Kawasaki disease (KD) is a diffuse and acute small-vessel vasculitis observed in children, and has genetic and autoimmune components. We genotyped 112 case-parent trios of European decent (confirmed by ancestry informative markers) using the immunoChip array, and performed association analyses with susceptibility to KD and intravenous immunoglobulin (IVIG) non-response. KD susceptibility was assessed using the transmission disequilibrium test, whereas IVIG non-response was evaluated using multivariable logistic regression analysis. We replicated single-nucleotide polymorphisms (SNPs) in three gene regions (FCGR, CD40/CDH22 and HLA-DQB2/HLA-DOB) that have been previously associated with KD and provide support to other findings of several novel SNPs in genes with a potential pathway in KD pathogenesis. SNP rs838143 in the 3'-untranslated region of the FUT1 gene (2.7 × 10(-5)) and rs9847915 in the intergenic region of LOC730109 | BRD7P2 (6.81 × 10(-7)) were the top hits for KD susceptibility in additive and dominant models, respectively. The top hits for IVIG responsiveness were rs1200332 in the intergenic region of BAZ1A | C14orf19 (1.4 × 10(-4)) and rs4889606 in the intron of the STX1B gene (6.95 × 10(-5)) in additive and dominant models, respectively. Our study suggests that genes and biological pathways involved in autoimmune diseases have an important role in the pathogenesis of KD and IVIG response mechanism.

Prevalence and incidence of early childhood caries among African-American children in Alabama

OBJECTIVES

This study aims to assess the prevalence and incidence of early childhood caries (ECC) in African-American children.

METHODS

A cohort of 96 African-American children approximately 1 year of age at baseline were recruited in Uniontown, Alabama, and followed for 3 years. Oral examinations were conducted annually by one of three trained/calibrated dentists using portable equipment, without radiographs, following WHO criteria.

RESULTS

The prevalence of decayed/missing/filled surfaces (dmfs) was: 1.1 percent (all d) at approximately age 1 (n = 90, six children were excluded for having no erupted teeth); 12.8 percent (d = 10.5 percent & f = 4.7 percent) at age 2 (n = 86); 39.3 percent (d = 21.4 percent, m = 2.4 percent & f = 22.6 percent) at age 3 (n = 84); and 65.8 percent (d = 28.8 percent, m = 5.5 & f = 46.6 percent) at age 4 (n = 73). The percentages of incisors, canines, first molars, and second molars with dmfs were: 0.1 percent, 0.0 percent, 0.0 percent, and 0.0 percent, at age 1; 2.4 percent, 0.1 percent, 0.8 percent, and 0.6 percent at age 2; 8.2 percent, 0.8 percent, 7.6 percent, and 6.3 percent at age 3; and 10.2 percent, 2.2 percent, 12.6 percent and 16.7 percent at age 4, respectively. The three, 1-year, person-level incidence rates were 12.8 percent (age 1 to age 2), 38.6 percent (age 2 to age 3), and 56.2 percent (age 3 to age 4). From baseline, the 2-year incidence was 39.3 percent and 3-year incidence was 65.8 percent, whereas the 2-year caries incidence from age 1 to age 3 was 66.7 percent (n = 72).

CONCLUSION

The majority of children developed caries during the 3-year follow-up, which is much higher than the 32 percent prevalence of caries among African-American children under age 6 years in National Health and Nutrition Examination Survey from 1999 to 2002.

SNP screening of central MHC-identified HLA-DMB as a candidate susceptibility gene for HIV-related Kaposi's sarcoma

The major histocompatibility complex (MHC) region on chromosome 6p21.3 is suspected to host susceptibility loci for HIV-related Kaposi’s sarcoma (HIV-KS). A nested case-control study in the Multicenter AIDS Cohort Study was designed to conduct fine genetic association mapping across central MHC. Individuals co-infected with HIV-1 and HHV-8 who later developed KS were defined as cases (n=354) and were matched 1:1 with co-infected KS-free controls.

We report data for new independent MHC class II and III susceptibility loci. In particular, class II HLA-DMB emerged as a strong candidate, with the intronic variant rs6902982 A>G associated with a 4-fold increase of risk (OR= 4.09; 95% CI: 1.90–8.80; p= 0.0003). A striking multiplicative effect on the estimated risk was associated with further carriage of two non-synonymous variants, rs1800453 A>G (Asp697Gly) and rs4148880 A>G (Ile393Val), in the linked TAP1 gene (OR=10.5; 95% CI: 2.54–43.6; p=0.0012). The class III susceptibility variant is moderately associated with HIV-KS and lies within a 120 Kb-long haplotype (OR=1.52; 95% CI: 1.01–2.28; p=0.047) formed by rs7029 A>G (GPANK1 3’UTR), rs1065356 G>A (LY6G6C), rs3749953 A>G (MSH5-SAPCD1 readthrough) and rs707926 G>A (VARS). Our data suggest that antigen processing by MHC class II molecules is a target pathway in the pathogenesis of HIV-KS.

Estimating proportions of explained variance: a comparison of whole genome subsets

Following the publication of the ENCODE project results, there has been increasing interest in investigating different areas of the chromosome and evaluating the relative contribution of each area to expressed phenotypes. This study aims to evaluate the contribution of variants, classified by minor allele frequency and gene annotation, to the observed interindividual differences. In this study, we fitted Bayesian linear regression models to data from Genetic Analysis Workshop 18 (n = 395) to estimate the variance of standardized and log-transformed systolic blood pressure that can be explained by subsets of genetic markers. Rare and very rare variants explained an overall higher proportion of the variance, as did markers located within a gene rather than flanking regions. The proportion of variance explained by rare and very rare variants decreased when we controlled for the number of markers, suggesting that the number of contributing rare alleles plays an important role in the genetic architecture of chronic disease traits. Our findings lend support to the "common disease, rare variant" hypothesis for systolic blood pressure and highlight allele frequency and functional annotation of a polymorphism as potentially crucial considerations in whole genome study designs.