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1.  A genetic association study of activated partial thromboplastin time in European Americans and African Americans: the ARIC Study 
Human Molecular Genetics  2014;24(8):2401-2408.
Reduced activated partial thromboplastin time (aPTT) is a risk marker for incident and recurrent venous thromboembolism (VTE). Genetic factors influencing aPTT are not well understood, especially in populations of non-European ancestry. The present study aimed to identify aPTT-related gene variants in both European Americans (EAs) and African Americans (AAs). We conducted a genetic association study for aPTT in 9719 EAs and 2799 AAs from the Atherosclerosis Risk in Communities (ARIC) study. Using the Candidate Gene Association Resource (CARe) consortium candidate gene array, the analyses were based on ∼50 000 SNPs in ∼2000 candidate genes. In EAs, the analyses identified a new independent association for aPTT in F5 (rs2239852, P-value = 1.9 × 10−8), which clusters with a coding variant rs6030 (P-value = 7.8 × 10−7). The remaining significant signals were located on F5, HRG, KNG1, F11, F12 and ABO and have been previously reported in EA populations. In AAs, significant signals were identified in KNG1, HRG, F12, ABO and VWF, with the leading variants in KNG1, HRG and F12 being the same as in the EAs; the significant variant in VWF (rs2229446, P-value = 1.2 × 10−6) was specific to the AA sample (minor allele frequency = 19% in AAs and 0.2% in EAs) and has not been previously reported. This is the first study to report aPTT-related genetic variants in AAs. Our findings in AAs demonstrate transferability of previously reported associations with KNG1, HRG and F12 in EAs. We also identified new associations at F5 in EAs and VWF in AAs that have not been previously reported for aPTT.
doi:10.1093/hmg/ddu732
PMCID: PMC4375421  PMID: 25552651
2.  Comparison and integration of deleteriousness prediction methods for nonsynonymous SNVs in whole exome sequencing studies 
Human Molecular Genetics  2014;24(8):2125-2137.
Accurate deleteriousness prediction for nonsynonymous variants is crucial for distinguishing pathogenic mutations from background polymorphisms in whole exome sequencing (WES) studies. Although many deleteriousness prediction methods have been developed, their prediction results are sometimes inconsistent with each other and their relative merits are still unclear in practical applications. To address these issues, we comprehensively evaluated the predictive performance of 18 current deleteriousness-scoring methods, including 11 function prediction scores (PolyPhen-2, SIFT, MutationTaster, Mutation Assessor, FATHMM, LRT, PANTHER, PhD-SNP, SNAP, SNPs&GO and MutPred), 3 conservation scores (GERP++, SiPhy and PhyloP) and 4 ensemble scores (CADD, PON-P, KGGSeq and CONDEL). We found that FATHMM and KGGSeq had the highest discriminative power among independent scores and ensemble scores, respectively. Moreover, to ensure unbiased performance evaluation of these prediction scores, we manually collected three distinct testing datasets, on which no current prediction scores were tuned. In addition, we developed two new ensemble scores that integrate nine independent scores and allele frequency. Our scores achieved the highest discriminative power compared with all the deleteriousness prediction scores tested and showed low false-positive prediction rate for benign yet rare nonsynonymous variants, which demonstrated the value of combining information from multiple orthologous approaches. Finally, to facilitate variant prioritization in WES studies, we have pre-computed our ensemble scores for 87 347 044 possible variants in the whole-exome and made them publicly available through the ANNOVAR software and the dbNSFP database.
doi:10.1093/hmg/ddu733
PMCID: PMC4375422  PMID: 25552646
3.  Genome-wide Studies of Verbal Declarative Memory in Nondemented Older People: The Cohorts for Heart and Aging Research in Genomic Epidemiology Consortium 
Debette, Stéphanie | Ibrahim Verbaas, Carla A. | Bressler, Jan | Schuur, Maaike | Smith, Albert | Bis, Joshua C. | Davies, Gail | Wolf, Christiane | Gudnason, Vilmundur | Chibnik, Lori B. | Yang, Qiong | deStefano, Anita L. | de Quervain, Dominique J.F. | Srikanth, Velandai | Lahti, Jari | Grabe, Hans J. | Smith, Jennifer A. | Priebe, Lutz | Yu, Lei | Karbalai, Nazanin | Hayward, Caroline | Wilson, James F. | Campbell, Harry | Petrovic, Katja | Fornage, Myriam | Chauhan, Ganesh | Yeo, Robin | Boxall, Ruth | Becker, James | Stegle, Oliver | Mather, Karen A. | Chouraki, Vincent | Sun, Qi | Rose, Lynda M. | Resnick, Susan | Oldmeadow, Christopher | Kirin, Mirna | Wright, Alan F. | Jonsdottir, Maria K. | Au, Rhoda | Becker, Albert | Amin, Najaf | Nalls, Mike A. | Turner, Stephen T. | Kardia, Sharon L.R. | Oostra, Ben | Windham, Gwen | Coker, Laura H. | Zhao, Wei | Knopman, David S. | Heiss, Gerardo | Griswold, Michael E. | Gottesman, Rebecca F. | Vitart, Veronique | Hastie, Nicholas D. | Zgaga, Lina | Rudan, Igor | Polasek, Ozren | Holliday, Elizabeth G. | Schofield, Peter | Choi, Seung Hoan | Tanaka, Toshiko | An, Yang | Perry, Rodney T. | Kennedy, Richard E. | Sale, Michèle M. | Wang, Jing | Wadley, Virginia G. | Liewald, David C. | Ridker, Paul M. | Gow, Alan J. | Pattie, Alison | Starr, John M. | Porteous, David | Liu, Xuan | Thomson, Russell | Armstrong, Nicola J. | Eiriksdottir, Gudny | Assareh, Arezoo A. | Kochan, Nicole A. | Widen, Elisabeth | Palotie, Aarno | Hsieh, Yi-Chen | Eriksson, Johan G. | Vogler, Christian | van Swieten, John C. | Shulman, Joshua M. | Beiser, Alexa | Rotter, Jerome | Schmidt, Carsten O. | Hoffmann, Wolfgang | Nöthen, Markus M. | Ferrucci, Luigi | Attia, John | Uitterlinden, Andre G. | Amouyel, Philippe | Dartigues, Jean-François | Amieva, Hélène | Räikkönen, Katri | Garcia, Melissa | Wolf, Philip A. | Hofman, Albert | Longstreth, W.T. | Psaty, Bruce M. | Boerwinkle, Eric | DeJager, Philip L. | Sachdev, Perminder S. | Schmidt, Reinhold | Breteler, Monique M.B. | Teumer, Alexander | Lopez, Oscar L. | Cichon, Sven | Chasman, Daniel I. | Grodstein, Francine | Müller-Myhsok, Bertram | Tzourio, Christophe | Papassotiropoulos, Andreas | Bennett, David A. | Ikram, Arfan M. | Deary, Ian J. | van Duijn, Cornelia M. | Launer, Lenore | Fitzpatrick, Annette L. | Seshadri, Sudha | Mosley, Thomas H.
Biological psychiatry  2014;77(8):749-763.
BACKGROUND
Memory performance in older persons can reflect genetic influences on cognitive function and dementing processes. We aimed to identify genetic contributions to verbal declarative memory in a community setting.
METHODS
We conducted genome-wide association studies for paragraph or word list delayed recall in 19 cohorts from the Cohorts for Heart and Aging Research in Genomic Epidemiology consortium, comprising 29,076 dementia-and stroke-free individuals of European descent, aged ≥45 years. Replication of suggestive associations (p < 5 × 10−6) was sought in 10,617 participants of European descent, 3811 African-Americans, and 1561 young adults.
RESULTS
rs4420638, near APOE, was associated with poorer delayed recall performance in discovery (p = 5.57 × 10−10) and replication cohorts (p = 5.65 × 10−8). This association was stronger for paragraph than word list delayed recall and in the oldest persons. Two associations with specific tests, in subsets of the total sample, reached genome-wide significance in combined analyses of discovery and replication (rs11074779 [HS3ST4], p = 3.11 × 10−8, and rs6813517 [SPOCK3], p = 2.58 × 10−8) near genes involved in immune response. A genetic score combining 58 independent suggestive memory risk variants was associated with increasing Alzheimer disease pathology in 725 autopsy samples. Association of memory risk loci with gene expression in 138 human hippocampus samples showed cis-associations with WDR48 and CLDN5, both related to ubiquitin metabolism.
CONCLUSIONS
This largest study to date exploring the genetics of memory function in ~ 40,000 older individuals revealed genome-wide associations and suggested an involvement of immune and ubiquitin pathways.
doi:10.1016/j.biopsych.2014.08.027
PMCID: PMC4513651  PMID: 25648963
Alzheimer disease; Dementia; Epidemiology; Genetics; Population-based; Verbal declarative memory
4.  Interaction between GSTT1 and GSTP1 allele variants as a risk modulating-factor for autism spectrum disorders 
We investigated the role of glutathione S-transferase (GST) genes in Autism Spectrum Disorder (ASD). We used data from 111 pairs of age- and sex-matched ASD cases and typically developing (TD) controls between 2–8 years of age from Jamaica to investigate the role of GST pi 1 (GSTP1), GST theta 1 (GSTT1), and GST mu 1 (GSTM1) polymorphisms in susceptibility to ASD. In univariable conditional logistic regression models we did not observe significant associations between ASD status and GSTT1, GSTM1, or GSTP1 genotype (all P > 0.15). However, in multivariable conditional logistic regression models, we identified a significant interaction between GSTP1 and GSTT1 in relation to ASD. Specifically, in children heterozygous for the GSTP1 Ile105Val polymorphism, the odds of ASD was significantly higher in those with the null GSTT1 genotype than those with the other genotypes [Matched Odds Ratio (MOR) = 2.97, 95% CI (1.09, 8.01), P = 0.03]. Replication in other populations is warranted.
doi:10.1016/j.rasd.2014.12.008
PMCID: PMC4322427  PMID: 25685181
Autism spectrum disorder; Oxidative stress; glutathione S-transferase (GST) genes; Modulating-factor; gene-gene interaction
5.  Transethnic meta-analysis suggests genetic variation in the HEME pathway influences potassium response in patients treated with hydrochlorothiazide 
The pharmacogenomics journal  2014;15(2):153-157.
Hypokalemia is a recognized adverse effect of thiazide diuretic treatment. This phenomenon, which may impair insulin secretion, has been suggested to be a reason for the adverse effects on glucose metabolism associated with thiazide diuretic treatment of hypertension. However, the mechanisms underlying thiazide diuretic induced hypokalemia are not well-understood. In an effort to identify, genes or genomic regions associated with potassium response to hydrochlorothiazide, without a priori knowledge of biologic effects; we performed a genome-wide association study and a Multi-Ethnic Meta-Analysis in 718 European- and African-American hypertensive participants from two different pharmacogenetic studies. SNPs rs10845697 (Bayes Factor=5.560) on chromosome 12, near to the HEME binding protein 1 gene, and rs11135740 (Bayes Factor= 5.258) on chromosome 8 near the Mitoferrin-1 gene reached GWAS significance (Bayes Factor > 5). These results, if replicated, suggest a novel mechanism involving effects of genes in the HEME pathway influencing hydrochlorothiazide-induced renal potassium loss.
doi:10.1038/tpj.2014.46
PMCID: PMC4362777  PMID: 25201287
Pharmacogenomics; hydrochlorothiazide; hypokalemia; HEME
6.  FBN1 Contributing to Familial Congenital Diaphragmatic Hernia 
Congenital diaphragmatic hernia (CDH) is a relatively common, life-threatening birth defect. We present a family with recurrent CDH—paraesophageal and central—for whom exome sequencing (ES) revealed a frameshift mutation (c.4969_4970insA, p. Ile1657Asnfs*30) in the fibrillin 1 gene (FBN1) that causes Marfan syndrome. A diagnosis of Marfan syndrome had not been considered previously in this family. However, a review of the literature demonstrated that FBN1 mutations have an unusual pattern of CDH in which paraesophageal hernias are particularly common. Subsequent clinical evaluations revealed evidence for ectopia lentis in affected family members supporting a clinical diagnosis of Marfan syndrome. Since only two other cases of familial CDH have been described in association with FBN1 mutations, we investigated an oligogenic hypothesis by examining ES data for deleterious sequence changes in other CDH-related genes. This search revealed putatively deleterious sequence changes in four other genes that have been shown to cause diaphragm defects in humans and/or mice—FREM1, DES, PAX3 and MET. It is unclear whether these changes, alone or in aggregate, are contributing to the development of CDH in this family. However, their individual contribution is likely to be small compared to that of the frameshift mutation in FBN1. We conclude that ES can be used to identify both major and minor genetic factors that may contribute to CDH. These results also suggest that ES should be considered in the diagnostic evaluation of individuals and families with CDH, particularly when other diagnostic modalities have failed to reveal a molecular etiology.
doi:10.1002/ajmg.a.36960
PMCID: PMC4522925  PMID: 25736269
congenital diaphragmatic hernia; exome sequencing; oligogenic inheritance; Marfan syndrome; FBN1; FREM1; PAX3; DES; MET
7.  Pathway analysis with next-generation sequencing data 
Although pathway analysis methods have been developed and successfully applied to association studies of common variants, the statistical methods for pathway-based association analysis of rare variants have not been well developed. Many investigators observed highly inflated false-positive rates and low power in pathway-based tests of association of rare variants. The inflated false-positive rates and low true-positive rates of the current methods are mainly due to their lack of ability to account for gametic phase disequilibrium. To overcome these serious limitations, we develop a novel statistic that is based on the smoothed functional principal component analysis (SFPCA) for pathway association tests with next-generation sequencing data. The developed statistic has the ability to capture position-level variant information and account for gametic phase disequilibrium. By intensive simulations, we demonstrate that the SFPCA-based statistic for testing pathway association with either rare or common or both rare and common variants has the correct type 1 error rates. Also the power of the SFPCA-based statistic and 22 additional existing statistics are evaluated. We found that the SFPCA-based statistic has a much higher power than other existing statistics in all the scenarios considered. To further evaluate its performance, the SFPCA-based statistic is applied to pathway analysis of exome sequencing data in the early-onset myocardial infarction (EOMI) project. We identify three pathways significantly associated with EOMI after the Bonferroni correction. In addition, our preliminary results show that the SFPCA-based statistic has much smaller P-values to identify pathway association than other existing methods.
doi:10.1038/ejhg.2014.121
PMCID: PMC4666565  PMID: 24986826
8.  Association of Rare Loss-Of-Function Alleles in HAL, Serum Histidine Levels and Incident Coronary Heart Disease 
Background
Histidine is a semi-essential amino acid with anti-oxidant and anti-inflammatory properties. Few data are available on the associations between genetic variants, histidine levels and incident coronary heart disease (CHD) in a population-based sample.
Methods and Results
By conducting whole-exome sequencing on 1,152 African Americans in the Atherosclerosis Risk in Communities (ARIC) study and focusing on loss-of-function (LoF) variants, we identified three novel rare LoF variants in HAL, a gene which encodes histidine ammonia-lyase in the first step of histidine catabolism. These LoF variants had large effects on blood histidine levels (β = 0.26, p = 1.2 × 10-13). The positive association with histidine levels was replicated by genotyping an independent sample of 718 ARIC African Americans (MAF = 1%, p = 1.2 × 10-4). In addition, high blood histidine levels were associated with reduced risk of developing incident CHD with an average of 21.5 years follow-up among African Americans (HR = 0.18, p = 1.9 × 10-4). This finding was validated in an independent sample of European-Americans from the Framingham Heart Study (FHS) Offspring Cohort. However, LoF variants in HAL were not directly significantly associated with incident CHD after meta-analyzing results from the CHARGE Consortium.
Conclusions
Three LoF mutations in HAL were associated with increased histidine levels, which in turn were shown to be inversely related to the risk of CHD among both African- and European-Americans. Future investigations on the association between HAL gene variation and CHD are warranted.
doi:10.1161/CIRCGENETICS.114.000697
PMCID: PMC4406800  PMID: 25575548
coronary heart disease; loss-of-function variants; histidine; HAL
9.  Using genetics to test the causal relationship of total adiposity and periodontitis: Mendelian randomization analyses in the Gene-Lifestyle Interactions and Dental Endpoints (GLIDE) Consortium 
Background: The observational relationship between obesity and periodontitis is widely known, yet causal evidence is lacking. Our objective was to investigate causal associations between periodontitis and body mass index (BMI).
Methods: We performed Mendelian randomization analyses with BMI-associated loci combined in a genetic risk score (GRS) as the instrument for BMI. All analyses were conducted within the Gene-Lifestyle Interactions and Dental Endpoints (GLIDE) Consortium in 13 studies from Europe and the USA, including 49 066 participants with clinically assessed (seven studies, 42.1% of participants) and self-reported (six studies, 57.9% of participants) periodontitis and genotype data (17 672/31 394 with/without periodontitis); 68 761 participants with BMI and genotype data; and 57 871 participants (18 881/38 990 with/without periodontitis) with data on BMI and periodontitis.
Results: In the observational meta-analysis of all participants, the pooled crude observational odds ratio (OR) for periodontitis was 1.13 [95% confidence interval (CI): 1.03, 1.24] per standard deviation increase of BMI. Controlling for potential confounders attenuated this estimate (OR = 1.08; 95% CI:1.03, 1.12). For clinically assessed periodontitis, corresponding ORs were 1.25 (95% CI: 1.10, 1.42) and 1.13 (95% CI: 1.10, 1.17), respectively. In the genetic association meta-analysis, the OR for periodontitis was 1.01 (95% CI: 0.99, 1.03) per GRS unit (per one effect allele) in all participants and 1.00 (95% CI: 0.97, 1.03) in participants with clinically assessed periodontitis. The instrumental variable meta-analysis of all participants yielded an OR of 1.05 (95% CI: 0.80, 1.38) per BMI standard deviation, and 0.90 (95% CI: 0.56, 1.46) in participants with clinical data.
Conclusions: Our study does not support total adiposity as a causal risk factor for periodontitis, as the point estimate is very close to the null in the causal inference analysis, with wide confidence intervals.
doi:10.1093/ije/dyv075
PMCID: PMC4817600  PMID: 26050256
Mendelian randomization; BMI; periodontitis; casual inference; confounding
10.  Strategic Transformation of Population Studies: Recommendations of the Working Group on Epidemiology and Population Sciences From the National Heart, Lung, and Blood Advisory Council and Board of External Experts 
American Journal of Epidemiology  2015;181(6):363-368.
In 2013, the National Heart, Lung, and Blood Institute assembled a working group on epidemiology and population sciences from its Advisory Council and Board of External Experts. The working group was charged with making recommendations to the National Heart, Lung, and Blood Advisory Council about how the National Heart, Lung, and Blood Institute could take advantage of new scientific opportunities and delineate future directions for the epidemiology of heart, lung, blood, and sleep diseases. Seven actionable recommendations were proposed for consideration. The themes included 1) defining the compelling scientific questions and challenges in population sciences and epidemiology of heart, lung, blood, and sleep diseases; 2) developing methods and training mechanisms to integrate “big data” science into the practice of epidemiology; 3) creating a cohort consortium and inventory of major studies to optimize the efficient use of data and specimens; and 4) fostering a more open, competitive approach to evaluating large-scale longitudinal epidemiology and population studies. By building on the track record of success of the heart, lung, blood, and sleep cohorts to leverage new data science opportunities and encourage broad research and training partnerships, these recommendations lay a strong foundation for the transformation of heart, lung, blood, and sleep epidemiology.
doi:10.1093/aje/kwv011
PMCID: PMC4375403  PMID: 25743324
big data; clinical trials; cohort studies; epidemiology; public health; training
12.  Genome-Wide Association Study for Incident Myocardial Infarction and Coronary Heart Disease in Prospective Cohort Studies: The CHARGE Consortium 
PLoS ONE  2016;11(3):e0144997.
Background
Data are limited on genome-wide association studies (GWAS) for incident coronary heart disease (CHD). Moreover, it is not known whether genetic variants identified to date also associate with risk of CHD in a prospective setting.
Methods
We performed a two-stage GWAS analysis of incident myocardial infarction (MI) and CHD in a total of 64,297 individuals (including 3898 MI cases, 5465 CHD cases). SNPs that passed an arbitrary threshold of 5×10−6 in Stage I were taken to Stage II for further discovery. Furthermore, in an analysis of prognosis, we studied whether known SNPs from former GWAS were associated with total mortality in individuals who experienced MI during follow-up.
Results
In Stage I 15 loci passed the threshold of 5×10−6; 8 loci for MI and 8 loci for CHD, for which one locus overlapped and none were reported in previous GWAS meta-analyses. We took 60 SNPs representing these 15 loci to Stage II of discovery. Four SNPs near QKI showed nominally significant association with MI (p-value<8.8×10−3) and three exceeded the genome-wide significance threshold when Stage I and Stage II results were combined (top SNP rs6941513: p = 6.2×10−9). Despite excellent power, the 9p21 locus SNP (rs1333049) was only modestly associated with MI (HR = 1.09, p-value = 0.02) and marginally with CHD (HR = 1.06, p-value = 0.08). Among an inception cohort of those who experienced MI during follow-up, the risk allele of rs1333049 was associated with a decreased risk of subsequent mortality (HR = 0.90, p-value = 3.2×10−3).
Conclusions
QKI represents a novel locus that may serve as a predictor of incident CHD in prospective studies. The association of the 9p21 locus both with increased risk of first myocardial infarction and longer survival after MI highlights the importance of study design in investigating genetic determinants of complex disorders.
doi:10.1371/journal.pone.0144997
PMCID: PMC4780701  PMID: 26950853
13.  Genetic overlap between diagnostic subtypes of ischemic stroke 
Background and Purpose
Despite moderate heritability, the phenotypic heterogeneity of ischemic stroke has hampered gene discovery, motivating analyses of diagnostic subtypes with reduced sample sizes. We assessed evidence for shared genetic etiology among the three major subtypes: large artery atherosclerosis (LAA), cardioembolism (CE) and small vessel disease (SVD), to inform potential cross-subtype analyses.
Methods
Analyses used genome-wide summary data for 12,389 ischemic stroke cases (including 2,167 LAA, 2,405 CE and 1,854 SVD) and 62,004 controls from the Metastroke consortium. For 4,561 cases and 7,094 controls, individual-level genotype data were also available. Genetic correlations between subtypes were estimated using linear mixed models (LMM) and polygenic profile scores. Meta-analysis of a combined LAA-SVD phenotype (4,021 cases, 51,976 controls) was performed to identify shared risk alleles.
Results
High genetic correlation was identified between LAA and SVD using LMM (rg=0.96, SE=0.47, P=9×10−4) and profile scores (rg=0.72; 95% CI: 0.52 – 0.93). Between LAA and CE, and SVD and CE, correlation was moderate using LMM but not significantly different from zero for profile scoring. Joint meta-analysis of LAA and SVD identified strong association (P=1×10−7) for SNPs near the opioid receptor μ1 (OPRM1) gene.
Conclusions
Our results suggest that LAA and SVD, which have been hitherto treated as genetically distinct, may share a substantial genetic component. Combined analyses of LAA and SVD may increase power to identify small-effect alleles influencing shared pathophysiological processes.
doi:10.1161/STROKEAHA.114.007930
PMCID: PMC4342266  PMID: 25613305
ischemic stroke; genetic epidemiology; atherosclerosis; lacunar stroke
14.  Mutations in the nuclear bile acid receptor FXR cause progressive familial intrahepatic cholestasis 
Nature Communications  2016;7:10713.
Neonatal cholestasis is a potentially life-threatening condition requiring prompt diagnosis. Mutations in several different genes can cause progressive familial intrahepatic cholestasis, but known genes cannot account for all familial cases. Here we report four individuals from two unrelated families with neonatal cholestasis and mutations in NR1H4, which encodes the farnesoid X receptor (FXR), a bile acid-activated nuclear hormone receptor that regulates bile acid metabolism. Clinical features of severe, persistent NR1H4-related cholestasis include neonatal onset with rapid progression to end-stage liver disease, vitamin K-independent coagulopathy, low-to-normal serum gamma-glutamyl transferase activity, elevated serum alpha-fetoprotein and undetectable liver bile salt export pump (ABCB11) expression. Our findings demonstrate a pivotal function for FXR in bile acid homeostasis and liver protection.
Neonatal cholestasis is a result of elevated bile acid levels, and is associated with mutations in genes regulating bile acid homeostasis. Here the authors identify mutations in the bile acid sensing farnesoid X receptor in four individuals with neonatal cholestasis from two unrelated families.
doi:10.1038/ncomms10713
PMCID: PMC4759630  PMID: 26888176
15.  Causal Role of Alcohol Consumption in an Improved Lipid Profile: The Atherosclerosis Risk in Communities (ARIC) Study 
PLoS ONE  2016;11(2):e0148765.
Introduction
Health benefits of low-to-moderate alcohol consumption may operate through an improved lipid profile. A Mendelian randomization (MR) approach was used to examine whether alcohol consumption causally affects lipid levels.
Methods
This analysis involved 10,893 European Americans (EA) from the Atherosclerosis Risk in Communities (ARIC) study. Common and rare variants in alcohol dehydrogenase and acetaldehyde dehydrogenase genes were evaluated for MR assumptions. Five variants, residing in the ADH1B, ADH1C, and ADH4 genes, were selected as genetic instruments and were combined into an unweighted genetic score. Triglycerides (TG), total cholesterol, high-density lipoprotein cholesterol (HDL-c) and its subfractions (HDL2-c and HDL3-c), low-density lipoprotein cholesterol (LDL-c), small dense LDL-c (sdLDL-c), apolipoprotein B (apoB), and lipoprotein (a) (Lp(a)) levels were analyzed.
Results
Alcohol consumption significantly increased HDL2-c and reduced TG, total cholesterol, LDL-c, sdLDL-c, and apoB levels. For each of these lipids a non-linear trend was observed. Compared to the first quartile of alcohol consumption, the third quartile had a 12.3% lower level of TG (p < 0.001), a 7.71 mg/dL lower level of total cholesterol (p = 0.007), a 10.3% higher level of HDL2-c (p = 0.007), a 6.87 mg/dL lower level of LDL-c (p = 0.012), a 7.4% lower level of sdLDL-c (p = 0.037), and a 3.5% lower level of apoB (p = 0.058, poverall = 0.022).
Conclusions
This study supports the causal role of regular low-to-moderate alcohol consumption in increasing HDL2-c, reducing TG, total cholesterol, and LDL-c, and provides evidence for the novel finding that low-to-moderate consumption of alcohol reduces apoB and sdLDL-c levels among EA. However, given the nonlinearity of the effect of alcohol consumption, even within the range of low-to-moderate drinking, increased consumption does not always result in a larger benefit.
doi:10.1371/journal.pone.0148765
PMCID: PMC4744040  PMID: 26849558
16.  Rare coding variants and X-linked loci associated with age at menarche 
Lunetta, Kathryn L. | Day, Felix R. | Sulem, Patrick | Ruth, Katherine S. | Tung, Joyce Y. | Hinds, David A. | Esko, Tõnu | Elks, Cathy E | Altmaier, Elisabeth | He, Chunyan | Huffman, Jennifer E. | Mihailov, Evelin | Porcu, Eleonora | Robino, Antonietta | Rose, Lynda M. | Schick, Ursula M. | Stolk, Lisette | Teumer, Alexander | Thompson, Deborah J. | Traglia, Michela | Wang, Carol A. | Yerges-Armstrong, Laura M. | Antoniou, Antonis C. | Barbieri, Caterina | Coviello, Andrea D. | Cucca, Francesco | Demerath, Ellen W. | Dunning, Alison M. | Gandin, Ilaria | Grove, Megan L. | Gudbjartsson, Daniel F. | Hocking, Lynne J. | Hofman, Albert | Huang, Jinyan | Jackson, Rebecca D. | Karasik, David | Kriebel, Jennifer | Lange, Ethan M. | Lange, Leslie A. | Langenberg, Claudia | Li, Xin | Luan, Jian’an | Mägi, Reedik | Morrison, Alanna C. | Padmanabhan, Sandosh | Pirie, Ailith | Polasek, Ozren | Porteous, David | Reiner, Alex P. | Rivadeneira, Fernando | Rudan, Igor | Sala, Cinzia F. | Schlessinger, David | Scott, Robert A. | Stöckl, Doris | Visser, Jenny A. | Völker, Uwe | Vozzi, Diego | Wilson, James G. | Zygmunt, Marek | Boerwinkle, Eric | Buring, Julie E. | Crisponi, Laura | Easton, Douglas F. | Hayward, Caroline | Hu, Frank B. | Liu, Simin | Metspalu, Andres | Pennell, Craig E. | Ridker, Paul M. | Strauch, Konstantin | Streeten, Elizabeth A. | Toniolo, Daniela | Uitterlinden, André G. | Ulivi, Sheila | Völzke, Henry | Wareham, Nicholas J. | Wellons, Melissa | Franceschini, Nora | Chasman, Daniel I. | Thorsteinsdottir, Unnur | Murray, Anna | Stefansson, Kari | Murabito, Joanne M. | Ong, Ken K. | Perry, John R.B.
Nature communications  2015;6:7756.
More than one hundred loci have been identified for age at menarche by genome-wide association studies (GWAS), but collectively these explain only ~3% of the trait variance. Here, we test two overlooked sources of variation in 192,974 European ancestry women: low-frequency protein-coding variants and X-chromosome variants. Five missense/nonsense variants (in ALMS1/LAMB2/TNRC6A/TACR3/PRKAG1) are associated with age at menarche (minor allele frequencies 0.08%-4.6%; effect sizes 0.08-1.25 years/allele; P<5×10−8). Additionally, we identify common X-chromosome loci at IGSF1 (rs762080, P=9.4×10−13) and FAAH2 (rs5914101, P=4.9×10−10). Highlighted genes implicate cellular energy homeostasis, post-transcriptional gene silencing and fatty acid amide signalling. A frequently reported mutation in TACR3 for idiopathic hypogonatrophic hypogonadism (p.W275X) is associated with 1.25-years later menarche (P=2.8×10−11), illustrating the utility of population studies to estimate the penetrance of reportedly pathogenic mutations. Collectively these novel variants explain ~0.5% variance, indicating these overlooked sources of variation do not substantially explain the ‘missing heritability’ of this complex trait.
doi:10.1038/ncomms8756
PMCID: PMC4538850  PMID: 26239645
17.  Association of Mitochondrial DNA levels with Frailty and All-Cause Mortality 
Mitochondrial function is altered with age, and variants in mitochondrial DNA (mtDNA) modulate risk for several age-related disease states. However, the association of mtDNA copy number, a readily available marker which reflects mitochondrial depletion, energy reserves and oxidative stress, on aging and mortality in the general population has not been addressed. To assess the association between mtDNA copy number and two primary outcomes—prevalent frailty and all-cause mortality, we utilize data from participants were from two multi-center, multi-ethnic, community-based, prospective studies—the Cardiovascular Health Study (CHS) (1989-2006) and the Atherosclerosis Risk in Communities study (ARIC) (1987-2013). A total of 4,892 participants (43.3% men) from CHS and 11,509 participants (44.9% men) from ARIC self-identifying as white or black were included in the analysis. mtDNA copy number, the trait of interest, was measured using a qPCR-based method in CHS and an array-based method in ARIC from DNA isolated from whole blood in participants from both cohorts.
In race-stratified meta-analyses, we observe a significant inverse association of mtDNA copy number with age, and higher mtDNA copy number in women relative to men. Lower mtDNA copy number was also significantly associated with prevalent frailty in white participants from CHS (OR 0.91, 95% CI, 0.85-0.97). Additionally, mtDNA copy number was a strong independent predictor of all-cause mortality in an age and sex-adjusted, race-stratified analysis of 16,401 participants from both cohorts with a pooled hazard ratio of 1.47 (95% CI, 1.33-1.62) for the lowest quintile of mtDNA copy number relative to the highest quintile.
doi:10.1007/s00109-014-1233-3
PMCID: PMC4319988  PMID: 25471480
Mitochondria; Mortality; Aging; Frailty
18.  New Mutations in the RAB28 Gene in 2 Spanish Families With Cone-Rod Dystrophy 
JAMA ophthalmology  2015;133(2):133-139.
IMPORTANCE
The families evaluated in this study represent the second report of cone-rod dystrophy (CRD) cases caused by mutations in RAB28, a recently discovered gene associated with CRD.
OBJECTIVE
To determine the disease-causing gene in 2 families of Spanish descent presenting with CRD who do not have ABCA4 mutations.
DESIGN, SETTING, AND PARTICIPANTS
Molecular genetics and observational case studies of 2 families, each with 1 affected proband with CRD and 3 or 5 unaffected family members. The affected individual from each family received a complete ophthalmic examination including assessment of refractive errors and best-corrected visual acuity, biomicroscopy, color fundus photography, electroretinography analysis, and visual-evoked potential analysis. After complete sequencing of the ABCA4 gene with negative results, the screening for disease-causing mutations was performed by whole-exome sequencing. Possible disease-associated variants were determined by filtering based on minor allele frequency, predicted pathogenicity, and segregation analysis in all family members.
MAIN OUTCOMES AND MEASURES
The appearance of the macula was evaluated by clinical examination, fundus photography, and fundus autofluorescence imaging, and visual function was assessed by electroretinography. Disease-causing mutations were assessed by sequence analyses.
RESULTS
Ophthalmologic findings included markedly reduced visual acuity, bull’s eye maculopathy, foveal hyperpigmentation, peripapillary atrophy, dyschromatopsia, extinguished photopic responses, and reduced scotopic responses observed on electroretinography consistent with the CRD phenotype often associated with ABCA4 mutations. Although no ABCA4 mutations were detected in either patient, whole-exome sequencing analysis identified 2 new homozygous mutations in the recently described RAB28 gene, the c.172 + 1G>C splice site variant in IVS2 and the missense c.T651G:p.C217W substitution. Both variants were determined as deleterious by predictive programs and were segregated with the disease in both families. Sequencing of 107 additional patients of Spanish descent with CRD did not reveal other cases with RAB28 mutations.
CONCLUSIONS AND RELEVANCE
Deleterious mutations in RAB28 result in a classic CRD phenotype and are an infrequent cause of CRD in the Spanish population.
doi:10.1001/jamaophthalmol.2014.4266
PMCID: PMC4351871  PMID: 25356532
19.  Variants for HDL-C, LDL-C and Triglycerides Identified from Admixture Mapping and Fine-Mapping Analysis in African-American Families 
Background
Admixture mapping of lipids was followed-up by family-based association analysis to identify variants for cardiovascular disease in African-Americans.
Methods and Results
The present study conducted admixture mapping analysis for total cholesterol, high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C) and triglycerides. The analysis was performed in 1,905 unrelated African-American subjects from the National Heart, Lung and Blood Institute’s Family Blood Pressure Program. Regions showing admixture evidence were followed-up with family-based association analysis in 3,556 African-American subjects from the FBPP. The admixture mapping and family-based association analyses were adjusted for age, age2, sex, body-mass-index, and genome-wide mean ancestry to minimize the confounding due to population stratification. Regions that were suggestive of local ancestry association evidence were found on chromosomes 7 (LDL-C), 8 (HDL-C), 14 (triglycerides) and 19 (total cholesterol and triglycerides). In the fine-mapping analysis, 52,939 SNPs were tested and 11 SNPs (8 independent SNPs) showed nominal significant association with HDL-C (2 SNPs), LDL-C (4 SNPs) and triglycerides (5 SNPs). The family data was used in the fine-mapping to identify SNPs that showed novel associations with lipids and regions including genes with known associations for cardiovascular disease.
Conclusions
This study identified regions on chromosomes 7, 8, 14 and 19 and 11 SNPs from the fine-mapping analysis that were associated with HDL-C, LDL-C and triglycerides for further studies of cardiovascular disease in African-Americans.
doi:10.1161/CIRCGENETICS.114.000481
PMCID: PMC4378661  PMID: 25552592
lipids; genetics; association studies; African-Americans; admixture mapping analysis
20.  Association of exome sequences with plasma C-reactive protein levels in >9000 participants 
Human Molecular Genetics  2014;24(2):559-571.
C-reactive protein (CRP) concentration is a heritable systemic marker of inflammation that is associated with cardiovascular disease risk. Genome-wide association studies have identified CRP-associated common variants associated in ∼25 genes. Our aims were to apply exome sequencing to (1) assess whether the candidate loci contain rare coding variants associated with CRP levels and (2) perform an exome-wide search for rare variants in novel genes associated with CRP levels. We exome-sequenced 6050 European-Americans (EAs) and 3109 African-Americans (AAs) from the NHLBI-ESP and the CHARGE consortia, and performed association tests of sequence data with measured CRP levels. In single-variant tests across candidate loci, a novel rare (minor allele frequency = 0.16%) CRP-coding variant (rs77832441-A; p.Thr59Met) was associated with 53% lower mean CRP levels (P = 2.9 × 10−6). We replicated the association of rs77832441 in an exome array analysis of 11 414 EAs (P = 3.0 × 10−15). Despite a strong effect on CRP levels, rs77832441 was not associated with inflammation-related phenotypes including coronary heart disease. We also found evidence for an AA-specific association of APOE-ε2 rs7214 with higher CRP levels. At the exome-wide significance level (P < 5.0 × 10−8), we confirmed associations for reported common variants of HNF1A, CRP, IL6R and TOMM40-APOE. In gene-based tests, a burden of rare/lower frequency variation in CRP in EAs (P ≤ 6.8 × 10−4) and in retinoic acid receptor-related orphan receptor α (RORA) in AAs (P = 1.7 × 10−3) were associated with CRP levels at the candidate gene level (P < 2.0 × 10−3). This inquiry did not elucidate novel genes, but instead demonstrated that variants distributed across the allele frequency spectrum within candidate genes contribute to CRP levels.
doi:10.1093/hmg/ddu450
PMCID: PMC4334838  PMID: 25187575
21.  Corrigendum: Rare coding variants and X-linked loci associated with age at menarche 
Lunetta, Kathryn L. | Day, Felix R. | Sulem, Patrick | Ruth, Katherine S. | Tung, Joyce Y. | Hinds, David A. | Esko, Tõnu | Elks, Cathy E. | Altmaier, Elisabeth | He, Chunyan | Huffman, Jennifer E. | Mihailov, Evelin | Porcu, Eleonora | Robino, Antonietta | Rose, Lynda M. | Schick, Ursula M. | Stolk, Lisette | Teumer, Alexander | Thompson, Deborah J. | Traglia, Michela | Wang, Carol A. | Yerges-Armstrong, Laura M. | Antoniou, Antonis C. | Barbieri, Caterina | Coviello, Andrea D. | Cucca, Francesco | Demerath, Ellen W. | Dunning, Alison M. | Gandin, Ilaria | Grove, Megan L. | Gudbjartsson, Daniel F. | Hocking, Lynne J. | Hofman, Albert | Huang, Jinyan | Jackson, Rebecca D. | Karasik, David | Kriebel, Jennifer | Lange, Ethan M. | Lange, Leslie A. | Langenberg, Claudia | Li, Xin | Luan, Jian'an | Mägi, Reedik | Morrison, Alanna C. | Padmanabhan, Sandosh | Pirie, Ailith | Polasek, Ozren | Porteous, David | Reiner, Alex P. | Rivadeneira, Fernando | Rudan, Igor | Sala, Cinzia F. | Schlessinger, David | Scott, Robert A. | Stöckl, Doris | Visser, Jenny A. | Völker, Uwe | Vozzi, Diego | Wilson, James G. | Zygmunt, Marek | Boerwinkle, Eric | Buring, Julie E. | Crisponi, Laura | Easton, Douglas F. | Hayward, Caroline | Hu, Frank B. | Liu, Simin | Metspalu, Andres | Pennell, Craig E. | Ridker, Paul M. | Strauch, Konstantin | Streeten, Elizabeth A. | Toniolo, Daniela | Uitterlinden, André G. | Ulivi, Sheila | Völzke, Henry | Wareham, Nicholas J. | Wellons, Melissa | Franceschini, Nora | Chasman, Daniel I. | Thorsteinsdottir, Unnur | Murray, Anna | Stefansson, Kari | Murabito, Joanne M. | Ong, Ken K. | Perry, John R. B.
Nature Communications  2015;6:10257.
doi:10.1038/ncomms10257
PMCID: PMC4703878  PMID: 26674845
22.  POGZ truncating alleles cause syndromic intellectual disability 
Genome Medicine  2016;8:3.
Background
Large-scale cohort-based whole exome sequencing of individuals with neurodevelopmental disorders (NDDs) has identified numerous novel candidate disease genes; however, detailed phenotypic information is often lacking in such studies. De novo mutations in pogo transposable element with zinc finger domain (POGZ) have been identified in six independent and diverse cohorts of individuals with NDDs ranging from autism spectrum disorder to developmental delay.
Methods
Whole exome sequencing was performed on five unrelated individuals. Sanger sequencing was used to validate variants and segregate mutations with the phenotype in available family members.
Results
We identified heterozygous truncating mutations in POGZ in five unrelated individuals, which were confirmed to be de novo or not present in available parental samples. Careful review of the phenotypes revealed shared features that included developmental delay, intellectual disability, hypotonia, behavioral abnormalities, and similar facial characteristics. Variable features included short stature, microcephaly, strabismus and hearing loss.
Conclusions
While POGZ has been associated with neurodevelopmental disorders in large cohort studies, our data suggest that loss of function variants in POGZ lead to an identifiable syndrome of NDD with specific phenotypic traits. This study exemplifies the era of human reverse clinical genomics ushered in by large disease-directed cohort studies; first defining a new syndrome molecularly and, only subsequently, phenotypically.
doi:10.1186/s13073-015-0253-0
PMCID: PMC4702300  PMID: 26739615
23.  Essential Hypertension vs. Secondary Hypertension Among Children 
BACKGROUND
The aim was to determine the proportions and correlates of essential hypertension among children in a tertiary pediatric hypertension clinic.
METHODS
We evaluated 423 consecutive children and collected demographic and clinical history by retrospective chart review.
RESULTS
We identified 275 (65%) hypertensive children (blood pressure >95th percentile per the “Fourth Report on the Diagnosis, Evaluation, and Treatment of High Blood Pressure in Children and Adolescents”) from 423 children referred to the clinic for history of elevated blood pressure. The remainder of the patients had normotension (11%), white coat hypertension (11%), prehypertension (10%), and pending diagnosis (3%). Among the 275 hypertensive children, 43% (n = 119; boys = 56%; median age = 12 years; range = 3–17 years) had essential hypertension and 57% (n = 156; boys = 66%; median age = 9 years; range = 0.08–19 years) had secondary hypertension. When compared with those with secondary hypertension, those with essential hypertension had a significantly older age at diagnosis (P = 0.0002), stronger family history of hypertension (94% vs. 68%; P < 0.0001), and lower prevalence of preterm birth (20% vs. 46%; P < 0.001). There was a bimodal distribution of age of diagnosis in those with secondary hypertension.
CONCLUSIONS
The phenotype of essential hypertension can present as early as 3 years of age and is the predominant form of hypertension in children after age of 6 years. Among children with hypertension, those with essential hypertension present at an older age, have a stronger family history of hypertension, and have lower prevalence of preterm birth.
doi:10.1093/ajh/hpu083
PMCID: PMC4318949  PMID: 24842390
blood pressure; etiology; hypertension; pediatrics; primary hypertension; secondary hypertension.
24.  Factors associated with blood lead concentrations of children in Jamaica 
Lead is a heavy metal known to be detrimental to neurologic, physiologic, and behavioral health of children. Previous studies from Jamaica reported that mean lead levels in soil are four times that of lead levels in some other parts of the world. Other studies detected lead levels in fruits and root vegetables, which were grown in areas with lead contaminated soil. In this study, we investigate environmental factors associated with blood lead concentrations in Jamaican children. The participants in this study comprised 125 typically developing (TD) children (ages 2–8 years) who served as controls in an age- and sex-matched case-control study that enrolled children from 2009 – 2012 in Jamaica. We administered a questionnaire to assess demographic and socioeconomic information as well as potential exposures to lead through food. Using General Linear Models (GLMs), we identified factors associated with blood lead concentrations in Jamaican children. The geometric mean blood lead concentration (GMBLC) in the sample of children in this study was 2.80 μg/dL. In univariable GLM analyses, GMBLC was higher for children whose parents did not have education beyond high school compared to those whose parents had attained this level (3.00 μg/dL vs. 2.31 μg/dL; P = 0.05), children living near a high traffic road compared to those who did not (3.43 μg/dL vs. 2.52 μg/dL; P < 0.01), and children who reported eating ackee compared to those who did not eat this fruit (2.89 μg/dL vs. 1.65 μg/dL; P < 0.05). In multivariable analysis, living near a high traffic road was identified as an independent risk factor for higher adjusted GMBLC (3.05 μg/dL vs. 2.19 μg/dL; P = 0.01). While our findings indicate that GMBLC in Jamaican children has dropped by at least 62% during the past two decades, children living in Jamaica still have GMBLC that is twice that of children in more developed countries. In addition, we have identified significant risk factors for higher blood lead concentrations in Jamaican children. We believe increasing awareness among parents regarding these risk factors could potentially lead to a lower level of lead exposure in Jamaican children.
doi:10.1080/10934529.2015.994932
PMCID: PMC4659644  PMID: 25837555
Lead; children; risk factors; road traffic; food; Jamaica
25.  High Sensitivity Troponin T and Cardiovascular Events in Systolic Blood Pressure Categories: Atherosclerosis Risk In Communities Study 
Hypertension  2014;65(1):78-84.
Based on observational studies there is a linear increase in cardiovascular risk with higher systolic blood pressure, yet clinical trials have not shown benefit across all systolic blood pressure categories. We assessed if troponin-T measured using high-sensitivity assay was associated with cardiovascular disease within systolic blood pressure categories in 11191 Atherosclerosis Risk in Communities study participants. Rested sitting systolic blood pressure by 10-mmHg increments and troponin categories were identified. Incident heart failure hospitalization, coronary heart disease and stroke were ascertained over a median of 12 years after excluding individuals with corresponding disease. Approximately 53% of each type of cardiovascular event occurred in individuals with systolic blood pressure<140 mmHg and troponin-T≥3ng/L. Higher troponin-T was associated with increasing cardiovascular events across most systolic blood pressure categories. The association was strongest for heart failure and least strong for stroke. There was no similar association of systolic blood pressure with cardiovascular events across troponin-T categories. Individuals with troponin-T≥3ng/L and systolic blood pressure<140mmHg had higher cardiovascular risk compared to those with troponin-T<3ng/L and systolic blood pressure 140-159 mmHg.
Higher troponin-T levels within narrow systolic blood pressure categories portend increased cardiovascular risk, particularly for heart failure. Individuals with lower systolic blood pressure but measurable troponin-T had greater cardiovascular risk compared to those with suboptimal systolic blood pressure but undetectable troponin-T. Future trials of systolic hypertension may benefit by using high-sensitivity troponin-T to target high-risk patients.
doi:10.1161/HYPERTENSIONAHA.114.04206
PMCID: PMC4268376  PMID: 25350984
High-sensitivity troponin-T; Hypertension; Atherosclerosis Risk In Communities (ARIC) Study; Cardiovascular disease; Heart failure

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