Fine genetic association map of body mass index on chromosome 1q43 in NIEHS uterine fibroid study.

<p>The plot shows the significance level of SNP associations (expressed as minus log₁₀ of p-value) with the body mass index (BMI) in a sample of 525 African American (EA) and 391 European American (EA) women participants in NIEHS-UFS (National Institute of Environmental Health Science-Uterine Fibroid Study). P-values were obtained from general linear models adjusted for age, physical activity and uterine fibroid affection status. The results were obtained under the assumption of a recessive genetic model in race-stratified analyses and in meta-analysis using beta coefficient and standard error estimates from the latter models. <i>RGS7</i> (regulator of G-protein 7); <i>FH</i> (fumarate hydratase); <i>KMO</i> (kynurenine 3-monooxygenase); <i>OPN3</i> (opsin 3); <i>WDR64</i> (WD repeat domain 64); <i>EXO1</i> (exonuclease 1); <i>MAP1LC3C (</i>microtubule-associated protein 1 light chain 3 gamma); <i>PLD5</i> (phospholipase D family, member 5).</p

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

<div><p>Introduction</p><p>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.</p><p>Methods</p><p>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 <i>RGS7</i> (regulator of G-protein signaling 7) and <i>PLD5</i> (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.</p><p>Results</p><p>The strongest associations were observed in a recessive genetic model and peaked in the 3’ end of <i>RGS7</i> 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 <i>RGS7</i>. 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 <i>PLD5</i> in meta-analysis (3.2 x 10⁻⁴ ≤ p ≤ 5.8 x 10⁻⁴).</p><p>Conclusion</p><p>We report replication data suggesting that <i>RGS7</i>, 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 <i>RGS7</i> region.</p></div

Linkage disequilibrium pattern across the 5’end and upstream sequence of <i>RGS7</i> in the 1,000 genome project reference populations for the European ancestry.

<p>The plot shows the pairwise linkage disequilibrium (LD) and haploblock structure across a 157 Kb-long interval overlapping the first translated exon of <i>RGS7</i> (regulator of G protein signaling 7) on human chromosome 1q43. The haploblock structure was obtained using D’ measures of pairwise LD determined for single nucleotide polymorphism (SNP) genotypes available in reference populations of the 1,000 genomes project for the European ancestry (super European population). The genetic analysis program Haploview was used to estimate D’ and to visualize the structure of haploblocks in the region associated with BMI and body fat in populations of European descent. Note that because the LD pattern may be distorted in the presence of founder effect, the Finish reference population (FIN) was not included in the superpopulation sample used for the construction of the LD plot. Haploblock 4 is located in the 2-Kb upstream sequence of <i>RGS7</i> and includes candidate body fat SNP rs1341467 in the Quebec Family Study, which is in strong LD (D’ = 0.94) with the candidate BMI SNP rs6429264 in NIEHS-UFS. Note also that the last four SNPs map to the 20 Kb upstream sequence of <i>RGS7</i>; these SNPs are candidates for uterine fibroids that were added to the LD plot to check for potential correlations with the candidate obesity SNPs.</p

Association of body mass index with SNP variants in the <i>RGS7-PLD5</i> genomic interval in NIEHS-UFS.

<p>Association of body mass index with SNP variants in the <i>RGS7-PLD5</i> genomic interval in NIEHS-UFS.</p

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

<p>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 (<i>P<</i>1.03E-7) and exhibited changing rates of DNAm change with age (<i>P<</i>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 (<i>P<5.0</i>E-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<<i>P<</i>0.039). cg07955995 and cg22285878 reside in the promoter region of <i>KLF14</i>, 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.</p

Genomic Copy Number Variants: Evidence for Association with Antibody Response to Anthrax Vaccine Adsorbed

<div><p>Background</p><p>Anthrax and its etiologic agent remain a biological threat. Anthrax vaccine is highly effective, but vaccine-induced IgG antibody responses vary widely following required doses of vaccinations. Such variation can be related to genetic factors, especially genomic copy number variants (CNVs) that are known to be enriched among genes with immunologic function. We have tested this hypothesis in two study populations from a clinical trial of anthrax vaccination.</p><p>Methods</p><p>We performed CNV-based genome-wide association analyses separately on 794 European Americans and 200 African-Americans. Antibodies to protective antigen were measured at week 8 (early response) and week 30 (peak response) using an enzyme-linked immunosorbent assay. We used DNA microarray data (Affymetrix 6.0) and two CNV detection algorithms, hidden markov model (PennCNV) and circular binary segmentation (GeneSpring) to determine CNVs in all individuals. Multivariable regression analyses were used to identify CNV-specific associations after adjusting for relevant non-genetic covariates.</p><p>Results</p><p>Within the 22 autosomal chromosomes, 2,943 non-overlapping CNV regions were detected by both algorithms. Genomic insertions containing <i>HLA-DRB5, DRB1</i> and <i>DQA1/DRA</i> genes in the major histocompatibility complex (MHC) region (chromosome 6p21.3) were moderately associated with elevated early antibody response (β = 0.14, p = 1.78×10⁻³) among European Americans, and the strongest association was observed between peak antibody response and a segmental insertion on chromosome 1, containing <i>NBPF4, NBPF5, STXMP3, CLCC1</i>, and <i>GPSM2</i> genes (β = 1.66, p = 6.06×10⁻⁵). For African-Americans, segmental deletions spanning <i>PRR20, PCDH17</i> and <i>PCH68</i> genes on chromosome 13 were associated with elevated early antibody production (β = 0.18, p = 4.47×10⁻⁵). Population-specific findings aside, one genomic insertion on chromosome 17 (containing <i>NSF, ARL17</i> and <i>LRRC37A</i> genes) was associated with elevated peak antibody response in both populations.</p><p>Conclusion</p><p>Multiple CNV regions, including the one consisting of MHC genes that is consistent with earlier research, can be important to humoral immune responses to anthrax vaccine adsorbed.</p></div

Dense Genotyping of Immune-Related Loci Identifies Variants Associated with Clearance of HPV among HIV-Positive Women in the HIV Epidemiology Research Study (HERS)

<div><p>Persistent high-risk human papillomavirus (HR-HPV) is a necessary and causal factor of cervical cancer. Most women naturally clear HPV infections; however, the biological mechanisms related to HPV pathogenesis have not been clearly elucidated. Host genetic factors that specifically regulate immune response could play an important role. All HIV-positive women in the HIV Epidemiology Research Study (HERS) with a HR-HPV infection and at least one follow-up biannual visit were included in the study. Cervicovaginal lavage samples were tested for HPV using type-specific HPV hybridization assays. Type-specific HPV clearance was defined as two consecutive HPV-negative tests after a positive test. DNA from participants was genotyped for 196,524 variants within 186 known immune related loci using the custom ImmunoChip microarray. To assess the influence of each single-nucleotide polymorphism (SNP) with HR-HPV clearance, the Cox proportional hazards model with the Wei-Lin-Weissfeld approach was used, adjusting for CD4+ count, low risk HPV (LR-HPV) co-infection, and relevant confounders. Three analytical models were performed: race-specific (African Americans (n = 258), European Americans (n = 87), Hispanics (n = 55), race-adjusted combined analysis, and meta-analysis of pooled independent race-specific analyses. Women were followed for a median time of 1,617 days. Overall, three SNPs (rs1112085, rs11102637, and rs12030900) in the <i>MAGI-3</i> gene and one SNP (rs8031627) in the <i>SMAD3</i> gene were associated with HR-HPV clearance (p<10⁻⁶). A variant (rs1633038) in <i>HLA-G</i> were also significantly associated in African American. Results from this study support associations of immune-related genes, having potential biological mechanism, with differential cervical HR-HPV infection outcomes.</p> </div

Manhattan plot showing the association P-values of single nucleotide polymorphisms (SNPs) in the ImmunoChip with the time to clearance of HR-HPV.

<p>The X-axes display the chromosome on which the SNP is located, the Y-axes display −log₁₀ P-value. The dashed black line represents a significance level needed for multiple testing using the K effective method. Panel A.) Race-adjusted analysis B.) African Americans only C.) European Americans only, and D.) Hispanics only.</p

Cox proportional Hazard Ratios (HR) for the SNPS associated with time to clearance of high-risk (HR-HPV) HPV infection in the race-adjusted analysis, individual race-specific analysis, and pooled analysis of the three races separately.

<p>Cox proportional Hazard Ratios (HR) for the SNPS associated with time to clearance of high-risk (HR-HPV) HPV infection in the race-adjusted analysis, individual race-specific analysis, and pooled analysis of the three races separately.</p

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

<div><p>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 (<i>MED30</i> | <i>EXT1</i>) among all women, rs2907092 in the catenin delta 2 (<i>CTNND2</i>) 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 (<i>FAM5C</i> | <i>RGS18</i>) 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 (<i>ZSCAN5D</i> | <i>NDUF1</i>) pseudogene on chromosome 19 among all women, in the region intergenic to vomeronasal 1 receptor 6 pseudogene and zinc finger protein 845 (<i>VN1R6P</i> | <i>ZNF845</i>) 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 (<i>SEC23IP</i> | <i>PPAPDC1A</i>) 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 (<i>RYR3</i>) and an admixture region in the secretion-regulating guanine nucleotide exchange factor (<i>SERGEF</i>) 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.</p></div