@article {927, title = {African ancestry, socioeconomic status, and kidney function in elderly African Americans: a genetic admixture analysis.}, journal = {J Am Soc Nephrol}, volume = {17}, year = {2006}, month = {2006 Dec}, pages = {3491-6}, abstract = {

Kidney disease is a major public health problem in the United States that affects African Americans disproportionately. The relative contribution of environmental and genetic factors to the increased burden of kidney disease among African Americans is unknown. The associations of genetic African ancestry and socioeconomic status with kidney function were studied cross-sectionally and longitudinally among 736 community-dwelling African Americans who were aged >65 yr and participating in the Cardiovascular Health Study. Genetic African ancestry was determined by genotyping 24 biallelic ancestry-informative markers and combining this information statistically to generate an estimate of ancestry for each individual. Kidney function was evaluated by cystatin C and estimated GFR (eGFR) using the Modification of Diet in Renal Disease equation. Longitudinal changes in serum creatinine and eGFR were estimated using baseline and follow-up values. In cross-sectional analyses, there was no association between genetic African ancestry and either measure of kidney function (P = 0.36 for cystatin C and 0.68 for eGFR). African ancestry was not associated with change in serum creatinine > or =0.05 mg/dl per yr (odds ratio [OR] 0.94; 95\% confidence interval [CI] 0.83 to 1.06) or with change in eGFR > or =3 ml/min per 1.73 m(2) per yr (OR 1.02; 95\% CI 0.92 to 1.13). In contrast, self reported African-American race was strongly associated with increased risk for kidney disease progression compared with white individuals for change in creatinine (OR 1.77; 95\% CI 1.33 to 2.36) and for change in eGFR (OR 3.21; 95\% CI 2.54 to 4.06). Among self-identified African Americans, low income (< US dollars 8000/yr) was strongly associated with prevalent kidney dysfunction by cystatin C >1.29 g/dl (adjusted OR 2.7; 95\% CI 1.0 to 7.5) or by eGFR <60 ml/min per 1.73 m(2) (adjusted OR 3.2; 95\% CI 1.1 to 9.4) compared with those with incomes >US dollars 35,000/yr. Alleles that are known to be present more frequently in the African ancestral group were not associated with kidney dysfunction or kidney disease progression. Rather, kidney dysfunction in elderly African Americans seems more attributable to differences in environmental and social factors.

}, keywords = {African Americans, Aged, Creatinine, Cross-Sectional Studies, Cystatin C, Cystatins, Disease Progression, Female, Glomerular Filtration Rate, Humans, Kidney Diseases, Linear Models, Longitudinal Studies, Male, Social Class}, issn = {1046-6673}, doi = {10.1681/ASN.2006050493}, author = {Peralta, Carmen A and Ziv, Elad and Katz, Ronit and Reiner, Alex and Burchard, Esteban Gonz{\'a}lez and Fried, Linda and Kwok, Pui-Yan and Psaty, Bruce and Shlipak, Michael} } @article {982, title = {IL-6 gene variation is associated with IL-6 and C-reactive protein levels but not cardiovascular outcomes in the Cardiovascular Health Study.}, journal = {Hum Genet}, volume = {122}, year = {2007}, month = {2007 Dec}, pages = {485-94}, abstract = {

Interleukin-6 (IL-6) and C-reactive protein (CRP) levels increase with age and likely play a role in adverse health outcomes in older adults. The relationship between IL-6 gene tag single nucleotide polymorphisms (SNPs) and circulating IL-6 and CRP levels, cardiovascular disease (CVD) outcomes, and mortality in Caucasian (CA) and African American (AA) participants of the Cardiovascular Health Study (CHS) was evaluated using ANCOVA and Cox proportional hazards models. The minor allele of the promoter SNP 1510 and intronic SNP 3572 associates with significantly higher serum IL-6 and CRP levels in CA but not AA. The CRP association persisted after CA and AA populations were combined and after accounting for multiple comparisons. These associations did not carry through to cardiovascular disease outcomes. Decreased risk of stroke was identified in CA, with the minor allele of SNP 1111 (HRR 0.71, 95\% CI 0.52, 0.95), P = 0.02, and increased risk of CVD and all-cause mortality (HRR 1.31, 95\% CI 1.05-1.64) in AAs heterozygote for SNP 2989. While genetic variation in the IL-6 gene was associated with circulating IL-6 and especially with CRP concentrations in this study, there is little evidence for association between common IL-6 gene variation and adverse health outcomes in this population of older adults.

}, keywords = {African Americans, Aged, Alleles, C-Reactive Protein, Cardiovascular Diseases, Cohort Studies, European Continental Ancestry Group, Female, Gene Frequency, Genetic Predisposition to Disease, Genetic Variation, Humans, Interleukin-6, Introns, Longitudinal Studies, Male, Polymorphism, Single Nucleotide, Promoter Regions, Genetic}, issn = {1432-1203}, doi = {10.1007/s00439-007-0428-x}, author = {Walston, Jeremy D and Fallin, M Daniele and Cushman, Mary and Lange, Leslie and Psaty, Bruce and Jenny, Nancy and Browner, Warren and Tracy, Russell and Durda, Peter and Reiner, Alex} } @article {6610, title = {A low-frequency variant in MAPK14 provides mechanistic evidence of a link with myeloperoxidase: a prognostic cardiovascular risk marker.}, journal = {J Am Heart Assoc}, volume = {3}, year = {2014}, month = {2014 Aug}, abstract = {

BACKGROUND: Genetics can be used to predict drug effects and generate hypotheses around alternative indications. To support Losmapimod, a p38 mitogen-activated protein kinase inhibitor in development for acute coronary syndrome, we characterized gene variation in MAPK11/14 genes by exome sequencing and follow-up genotyping or imputation in participants well-phenotyped for cardiovascular and metabolic traits.

METHODS AND RESULTS: Investigation of genetic variation in MAPK11 and MAPK14 genes using additive genetic models in linear or logistic regression with cardiovascular, metabolic, and biomarker phenotypes highlighted an association of RS2859144 in MAPK14 with myeloperoxidase in a dyslipidemic population (Genetic Epidemiology of Metabolic Syndrome Study), P=2.3{\texttimes}10(-6)). This variant (or proxy) was consistently associated with myeloperoxidase in the Framingham Heart Study and Cardiovascular Health Study studies (replication meta-P=0.003), leading to a meta-P value of 9.96{\texttimes}10(-7) in the 3 dyslipidemic groups. The variant or its proxy was then profiled in additional population-based cohorts (up to a total of 58 930 subjects) including Cohorte Lausannoise, Ely, Fenland, European Prospective Investigation of Cancer, London Life Sciences Prospective Population Study, and the Genetics of Obesity Associations study obesity case-control for up to 40 cardiovascular and metabolic traits. Overall analysis identified the same single nucleotide polymorphisms to be nominally associated consistently with glomerular filtration rate (P=0.002) and risk of obesity (body mass index >=30 kg/m(2), P=0.004).

CONCLUSIONS: As myeloperoxidase is a prognostic marker of coronary events, the MAPK14 variant may provide a mechanistic link between p38 map kinase and these events, providing information consistent with current indication of Losmapimod for acute coronary syndrome. If replicated, the association with glomerular filtration rate, along with previous biological findings, also provides support for kidney diseases as alternative indications.

}, keywords = {Adult, Aged, Cardiovascular Diseases, Dyslipidemias, Exome, Female, Genotype, Humans, Linear Models, Logistic Models, Male, Metabolic Syndrome X, Middle Aged, Mitogen-Activated Protein Kinase 11, Mitogen-Activated Protein Kinase 14, Obesity, Peroxidase, Polymorphism, Single Nucleotide, Prognosis, Risk Factors, Sequence Analysis, DNA}, issn = {2047-9980}, doi = {10.1161/JAHA.114.001074}, author = {Waterworth, Dawn M and Li, Li and Scott, Robert and Warren, Liling and Gillson, Christopher and Aponte, Jennifer and Sarov-Blat, Lea and Sprecher, Dennis and Dupuis, Jos{\'e}e and Reiner, Alex and Psaty, Bruce M and Tracy, Russell P and Lin, Honghuang and McPherson, Ruth and Chissoe, Stephanie and Wareham, Nick and Ehm, Margaret G} } @article {6937, title = {Rare Exome Sequence Variants in CLCN6 Reduce Blood Pressure Levels and Hypertension Risk.}, journal = {Circ Cardiovasc Genet}, volume = {9}, year = {2016}, month = {2016 Feb}, pages = {64-70}, abstract = {

BACKGROUND: Rare genetic variants influence blood pressure (BP).

METHODS AND RESULTS: Whole-exome sequencing was performed on DNA samples from 17 956 individuals of European ancestry and African ancestry (14 497, first-stage discovery and 3459, second-stage discovery) to examine the effect of rare variants on hypertension and 4 BP traits: systolic BP, diastolic BP, pulse pressure, and mean arterial pressure. Tests of ≈170 000 common variants (minor allele frequency, >=1\%; statistical significance, P<=2.9{\texttimes}10(-7)) and gene-based tests of rare variants (minor allele frequency, <1\%; ≈17 000 genes; statistical significance, P<=1.5{\texttimes}10(-6)) were evaluated for each trait and ancestry, followed by multiethnic meta-analyses. In the first-stage discovery, rare coding variants (splicing, stop-gain, stop-loss, nonsynonymous variants, or indels) in CLCN6 were associated with lower diastolic BP (cumulative minor allele frequency, 1.3\%; β=-3.20; P=4.1{\texttimes}10(-6)) and were independent of a nearby common variant (rs17367504) previously associated with BP. CLCN6 rare variants were also associated with lower systolic BP (β=-4.11; P=2.8{\texttimes}10(-4)), mean arterial pressure (β=-3.50; P=8.9{\texttimes}10(-6)), and reduced hypertension risk (odds ratio, 0.72; P=0.017). Meta-analysis of the 2-stage discovery samples showed that CLCN6 was associated with lower diastolic BP at exome-wide significance (cumulative minor allele frequency, 1.1\%; β=-3.30; P=5.0{\texttimes}10(-7)).

CONCLUSIONS: These findings implicate the effect of rare coding variants in CLCN6 in BP variation and offer new insights into BP regulation.

}, issn = {1942-3268}, doi = {10.1161/CIRCGENETICS.115.001215}, author = {Yu, Bing and Pulit, Sara L and Hwang, Shih-Jen and Brody, Jennifer A and Amin, Najaf and Auer, Paul L and Bis, Joshua C and Boerwinkle, Eric and Burke, Gregory L and Chakravarti, Aravinda and Correa, Adolfo and Dreisbach, Albert W and Franco, Oscar H and Ehret, Georg B and Franceschini, Nora and Hofman, Albert and Lin, Dan-Yu and Metcalf, Ginger A and Musani, Solomon K and Muzny, Donna and Palmas, Walter and Raffel, Leslie and Reiner, Alex and Rice, Ken and Rotter, Jerome I and Veeraraghavan, Narayanan and Fox, Ervin and Guo, Xiuqing and North, Kari E and Gibbs, Richard A and van Duijn, Cornelia M and Psaty, Bruce M and Levy, Daniel and Newton-Cheh, Christopher and Morrison, Alanna C} } @article {7552, title = {The GH receptor exon 3 deletion is a marker of male-specific exceptional longevity associated with increased GH sensitivity and taller stature.}, journal = {Sci Adv}, volume = {3}, year = {2017}, month = {2017 Jun}, pages = {e1602025}, abstract = {

Although both growth hormone (GH) and insulin-like growth factor 1 (IGF-1) signaling were shown to regulate life span in lower organisms, the role of GH signaling in human longevity remains unclear. Because a GH receptor exon 3 deletion (d3-GHR) appears to modulate GH sensitivity in humans, we hypothesized that this polymorphism could play a role in human longevity. We report a linear increased prevalence of d3-GHR homozygosity with age in four independent cohorts of long-lived individuals: 841 participants [567 of the Longevity Genes Project (LGP) (8\% increase; P = 0.01), 152 of the Old Order Amish (16\% increase; P = 0.02), 61 of the Cardiovascular Health Study (14.2\% increase; P = 0.14), and 61 of the French Long-Lived Study (23.5\% increase; P = 0.02)]. In addition, mega analysis of males in all cohorts resulted in a significant positive trend with age (26\% increase; P = 0.007), suggesting sexual dimorphism for GH action in longevity. Further, on average, LGP d3/d3 homozygotes were 1 inch taller than the wild-type (WT) allele carriers (P = 0.05) and also showed lower serum IGF-1 levels (P = 0.003). Multivariate regression analysis indicated that the presence of d3/d3 genotype adds approximately 10 years to life span. The LGP d3/d3-GHR transformed lymphocytes exhibited superior growth and extracellular signal-regulated kinase activation, to GH treatment relative to WT GHR lymphocytes (P < 0.01), indicating a GH dose response. The d3-GHR variant is a common genetic polymorphism that modulates GH responsiveness throughout the life span and positively affects male longevity.

}, issn = {2375-2548}, doi = {10.1126/sciadv.1602025}, author = {Ben-Avraham, Danny and Govindaraju, Diddahally R and Budagov, Temuri and Fradin, Delphine and Durda, Peter and Liu, Bing and Ott, Sandy and Gutman, Danielle and Sharvit, Lital and Kaplan, Robert and Bougn{\`e}res, Pierre and Reiner, Alex and Shuldiner, Alan R and Cohen, Pinchas and Barzilai, Nir and Atzmon, Gil} } @article {9588, title = {Determinants of mosaic chromosomal alteration fitness.}, journal = {medRxiv}, year = {2023}, month = {2023 Oct 21}, abstract = {

Clonal hematopoiesis (CH) is characterized by the acquisition of a somatic mutation in a hematopoietic stem cell that results in a clonal expansion. These driver mutations can be single nucleotide variants in cancer driver genes or larger structural rearrangements called mosaic chromosomal alterations (mCAs). The factors that influence the variations in mCA fitness and ultimately result in different clonal expansion rates are not well-understood. We used the Passenger-Approximated Clonal Expansion Rate (PACER) method to estimate clonal expansion rate for 6,381 individuals in the NHLBI TOPMed cohort with gain, loss, and copy-neutral loss of heterozygosity mCAs. Our estimates of mCA fitness were correlated (R = 0.49) with an alternative approach that estimated fitness of mCAs in the UK Biobank using a theoretical probability distribution. Individuals with lymphoid-associated mCAs had a significantly higher white blood cell count and faster clonal expansion rate. In a cross-sectional analysis, genome-wide association study of estimates of mCA expansion rate identified , , and locus variants as modulators of mCA clonal expansion rate.

}, doi = {10.1101/2023.10.20.23297280}, author = {Pershad, Yash and Mack, Taralynn and Poisner, Hannah and Jakubek, Yasminka A and Stilp, Adrienne M and Mitchell, Braxton D and Lewis, Joshua P and Boerwinkle, Eric and Loos, Ruth J and Chami, Nathalie and Wang, Zhe and Barnes, Kathleen and Pankratz, Nathan and Fornage, Myriam and Redline, Susan and Psaty, Bruce M and Bis, Joshua C and Shojaie, Ali and Silverman, Edwin K and Cho, Michael H and Yun, Jeong and DeMeo, Dawn and Levy, Daniel and Johnson, Andrew and Mathias, Rasika and Taub, Margaret and Arnett, Donna and North, Kari and Raffield, Laura M and Carson, April and Doyle, Margaret F and Rich, Stephen S and Rotter, Jerome I and Guo, Xiuqing and Cox, Nancy and Roden, Dan M and Franceschini, Nora and Desai, Pinkal and Reiner, Alex and Auer, Paul L and Scheet, Paul and Jaiswal, Siddhartha and Weinstock, Joshua S and Bick, Alexander G} } @article {9646, title = {Methylation patterns associated with C-reactive protein in racially and ethnically diverse populations.}, journal = {Epigenetics}, volume = {19}, year = {2024}, month = {2024 Dec}, pages = {2333668}, abstract = {

Systemic low-grade inflammation is a feature of chronic disease. C-reactive protein (CRP) is a common biomarker of inflammation and used as an indicator of disease risk; however, the role of inflammation in disease is not completely understood. Methylation is an epigenetic modification in the DNA which plays a pivotal role in gene expression. In this study we evaluated differential DNA methylation patterns associated with blood CRP level to elucidate biological pathways and genetic regulatory mechanisms to improve the understanding of chronic inflammation. The racially and ethnically diverse participants in this study were included as 50\% White, 41\% Black or African American, 7\% Hispanic or Latino/a, and 2\% Native Hawaiian, Asian American, American Indian, or Alaska Native (total = 13,433) individuals. We replicated 113 CpG sites from 87 unique loci, of which five were novel (, , and cg03282312), across a discovery set of 1,150 CpG sites associated with CRP level ( < 1.2E-7). The downstream pathways affected by DNA methylation included the identification of and CpG-gene transcript pairs which contributed to the innate immune response gene enrichment pathway along with , , and . Gene enrichment analysis also identified the nuclear factor-kappaB transcription pathway. Using two-sample Mendelian randomization (MR) we inferred methylation at three CpG sites as causal for CRP levels using both White and Black or African American MR instrument variables. Overall, we identified novel CpG sites and gene transcripts that could be valuable in understanding the specific cellular processes and pathogenic mechanisms involved in inflammation.

}, keywords = {C-Reactive Protein, CpG Islands, DNA, DNA Methylation, Epigenesis, Genetic, Genome-Wide Association Study, Humans, Inflammation, Intracellular Signaling Peptides and Proteins}, issn = {1559-2308}, doi = {10.1080/15592294.2024.2333668}, author = {Lundin, Jessica I and Peters, Ulrike and Hu, Yao and Ammous, Farah and Avery, Christy L and Benjamin, Emelia J and Bis, Joshua C and Brody, Jennifer A and Carlson, Chris and Cushman, Mary and Gignoux, Chris and Guo, Xiuqing and Haessler, Jeff and Haiman, Chris and Joehanes, Roby and Kasela, Silva and Kenny, Eimear and Lapalainien, Tuuli and Levy, Daniel and Liu, Chunyu and Liu, Yongmei and Loos, Ruth J F and Lu, Ake and Matise, Tara and North, Kari E and Park, Sungshim L and Ratliff, Scott M and Reiner, Alex and Rich, Stephen S and Rotter, Jerome I and Smith, Jennifer A and Sotoodehnia, Nona and Tracy, Russell and Van den Berg, David and Xu, Huichun and Ye, Ting and Zhao, Wei and Raffield, Laura M and Kooperberg, Charles} }