%0 Journal Article %J Neurology %D 2023 %T Association of Mitochondrial DNA Copy Number With Brain MRI Markers and Cognitive Function: A Meta-analysis of Community-Based Cohorts. %A Zhang, Yuankai %A Liu, Xue %A Wiggins, Kerri L %A Kurniansyah, Nuzulul %A Guo, Xiuqing %A Rodrigue, Amanda L %A Zhao, Wei %A Yanek, Lisa R %A Ratliff, Scott M %A Pitsillides, Achilleas %A Aguirre Patiño, Juan Sebastian %A Sofer, Tamar %A Arking, Dan E %A Austin, Thomas R %A Beiser, Alexa S %A Blangero, John %A Eric Boerwinkle %A Bressler, Jan %A Curran, Joanne E %A Hou, Lifang %A Hughes, Timothy M %A Kardia, Sharon L R %A Launer, Lenore J %A Levy, Daniel %A Mosley, Thomas H %A Nasrallah, Ilya M %A Rich, Stephen S %A Rotter, Jerome I %A Seshadri, Sudha %A Tarraf, Wassim %A González, Kevin A %A Ramachandran, Vasan %A Yaffe, Kristine %A Nyquist, Paul A %A Psaty, Bruce M %A DeCarli, Charles S %A Smith, Jennifer A %A Glahn, David C %A Gonzalez, Hector M %A Bis, Joshua C %A Fornage, Myriam %A Heckbert, Susan R %A Fitzpatrick, Annette L %A Liu, Chunyu %A Satizabal, Claudia L %K Aged %K Alzheimer Disease %K Brain %K Cognition %K Cross-Sectional Studies %K DNA Copy Number Variations %K DNA, Mitochondrial %K Female %K Humans %K Magnetic Resonance Imaging %K Male %K Middle Aged %K Prospective Studies %X

BACKGROUND AND OBJECTIVES: Previous studies suggest that lower mitochondrial DNA (mtDNA) copy number (CN) is associated with neurodegenerative diseases. However, whether mtDNA CN in whole blood is related to endophenotypes of Alzheimer disease (AD) and AD-related dementia (AD/ADRD) needs further investigation. We assessed the association of mtDNA CN with cognitive function and MRI measures in community-based samples of middle-aged to older adults.

METHODS: We included dementia-free participants from 9 diverse community-based cohorts with whole-genome sequencing in the Trans-Omics for Precision Medicine (TOPMed) program. Circulating mtDNA CN was estimated as twice the ratio of the average coverage of mtDNA to nuclear DNA. Brain MRI markers included total brain, hippocampal, and white matter hyperintensity volumes. General cognitive function was derived from distinct cognitive domains. We performed cohort-specific association analyses of mtDNA CN with AD/ADRD endophenotypes assessed within ±5 years (i.e., cross-sectional analyses) or 5-20 years after blood draw (i.e., prospective analyses) adjusting for potential confounders. We further explored associations stratified by sex and age (<60 vs ≥60 years). Fixed-effects or sample size-weighted meta-analyses were performed to combine results. Finally, we performed mendelian randomization (MR) analyses to assess causality.

RESULTS: We included up to 19,152 participants (mean age 59 years, 57% women). Higher mtDNA CN was cross-sectionally associated with better general cognitive function (β = 0.04; 95% CI 0.02-0.06) independent of age, sex, batch effects, race/ethnicity, time between blood draw and cognitive evaluation, cohort-specific variables, and education. Additional adjustment for blood cell counts or cardiometabolic traits led to slightly attenuated results. We observed similar significant associations with cognition in prospective analyses, although of reduced magnitude. We found no significant associations between mtDNA CN and brain MRI measures in meta-analyses. MR analyses did not reveal a causal relation between mtDNA CN in blood and cognition.

DISCUSSION: Higher mtDNA CN in blood is associated with better current and future general cognitive function in large and diverse communities across the United States. Although MR analyses did not support a causal role, additional research is needed to assess causality. Circulating mtDNA CN could serve nevertheless as a biomarker of current and future cognitive function in the community.

%B Neurology %V 100 %P e1930-e1943 %8 2023 May 02 %G eng %N 18 %1 https://www.ncbi.nlm.nih.gov/pubmed/36927883?dopt=Abstract %R 10.1212/WNL.0000000000207157 %0 Journal Article %J JAMA Cardiol %D 2023 %T Association of Rare Protein-Truncating DNA Variants in APOB or PCSK9 With Low-density Lipoprotein Cholesterol Level and Risk of Coronary Heart Disease. %A Dron, Jacqueline S %A Patel, Aniruddh P %A Zhang, Yiyi %A Jurgens, Sean J %A Maamari, Dimitri J %A Wang, Minxian %A Eric Boerwinkle %A Morrison, Alanna C %A de Vries, Paul S %A Fornage, Myriam %A Hou, Lifang %A Lloyd-Jones, Donald M %A Psaty, Bruce M %A Tracy, Russell P %A Bis, Joshua C %A Vasan, Ramachandran S %A Levy, Daniel %A Heard-Costa, Nancy %A Rich, Stephen S %A Guo, Xiuqing %A Taylor, Kent D %A Richard A Gibbs %A Rotter, Jerome I %A Willer, Cristen J %A Oelsner, Elizabeth C %A Moran, Andrew E %A Peloso, Gina M %A Natarajan, Pradeep %A Khera, Amit V %K Adult %K Aged %K Apolipoproteins B %K Cholesterol, LDL %K Coronary Disease %K DNA %K Female %K Humans %K Male %K Middle Aged %K Proprotein Convertase 9 %K Prospective Studies %X

IMPORTANCE: Protein-truncating variants (PTVs) in apolipoprotein B (APOB) and proprotein convertase subtilisin/kexin type 9 (PCSK9) are associated with significantly lower low-density lipoprotein (LDL) cholesterol concentrations. The association of these PTVs with coronary heart disease (CHD) warrants further characterization in large, multiracial prospective cohort studies.

OBJECTIVE: To evaluate the association of PTVs in APOB and PCSK9 with LDL cholesterol concentrations and CHD risk.

DESIGN, SETTING, AND PARTICIPANTS: This studied included participants from 5 National Heart, Lung, and Blood Institute (NHLBI) studies and the UK Biobank. NHLBI study participants aged 5 to 84 years were recruited between 1971 and 2002 across the US and underwent whole-genome sequencing. UK Biobank participants aged 40 to 69 years were recruited between 2006 and 2010 in the UK and underwent whole-exome sequencing. Data were analyzed from June 2021 to October 2022.

EXPOSURES: PTVs in APOB and PCSK9.

MAIN OUTCOMES AND MEASURES: Estimated untreated LDL cholesterol levels and CHD.

RESULTS: Among 19 073 NHLBI participants (10 598 [55.6%] female; mean [SD] age, 52 [17] years), 139 (0.7%) carried an APOB or PCSK9 PTV, which was associated with 49 mg/dL (95% CI, 43-56) lower estimated untreated LDL cholesterol level. Over a median (IQR) follow-up of 21.5 (13.9-29.4) years, incident CHD was observed in 12 of 139 carriers (8.6%) vs 3029 of 18 934 noncarriers (16.0%), corresponding to an adjusted hazard ratio of 0.51 (95% CI, 0.28-0.89; P = .02). Among 190 464 UK Biobank participants (104 831 [55.0%] female; mean [SD] age, 57 [8] years), 662 (0.4%) carried a PTV, which was associated with 45 mg/dL (95% CI, 42-47) lower estimated untreated LDL cholesterol level. Estimated CHD risk by age 75 years was 3.7% (95% CI, 2.0-5.3) in carriers vs 7.0% (95% CI, 6.9-7.2) in noncarriers, corresponding to an adjusted hazard ratio of 0.51 (95% CI, 0.32-0.81; P = .004).

CONCLUSIONS AND RELEVANCE: Among 209 537 individuals in this study, 0.4% carried an APOB or PCSK9 PTV that was associated with less exposure to LDL cholesterol and a 49% lower risk of CHD.

%B JAMA Cardiol %V 8 %P 258-267 %8 2023 Mar 01 %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/36723951?dopt=Abstract %R 10.1001/jamacardio.2022.5271 %0 Journal Article %J Hum Mol Genet %D 2021 %T Epigenome-wide association study of mitochondrial genome copy number. %A Wang, Penglong %A Castellani, Christina A %A Yao, Jie %A Huan, Tianxiao %A Bielak, Lawrence F %A Zhao, Wei %A Haessler, Jeffrey %A Joehanes, Roby %A Sun, Xianbang %A Guo, Xiuqing %A Longchamps, Ryan J %A Manson, JoAnn E %A Grove, Megan L %A Bressler, Jan %A Taylor, Kent D %A Lappalainen, Tuuli %A Kasela, Silva %A Van Den Berg, David J %A Hou, Lifang %A Reiner, Alexander %A Liu, Yongmei %A Eric Boerwinkle %A Smith, Jennifer A %A Peyser, Patricia A %A Fornage, Myriam %A Rich, Stephen S %A Rotter, Jerome I %A Kooperberg, Charles %A Arking, Dan E %A Levy, Daniel %A Liu, Chunyu %K Aged %K DNA Copy Number Variations %K DNA Methylation %K DNA, Mitochondrial %K Epigenome %K Female %K Genome, Mitochondrial %K Humans %K Male %K Middle Aged %X

We conducted cohort- and race-specific epigenome-wide association analyses of mitochondrial deoxyribonucleic acid (mtDNA) copy number (mtDNA CN) measured in whole blood from participants of African and European origins in five cohorts (n = 6182, mean age = 57-67 years, 65% women). In the meta-analysis of all the participants, we discovered 21 mtDNA CN-associated DNA methylation sites (CpG) (P < 1 × 10-7), with a 0.7-3.0 standard deviation increase (3 CpGs) or decrease (18 CpGs) in mtDNA CN corresponding to a 1% increase in DNA methylation. Several significant CpGs have been reported to be associated with at least two risk factors (e.g. chronological age or smoking) for cardiovascular disease (CVD). Five genes [PR/SET domain 16, nuclear receptor subfamily 1 group H member 3 (NR1H3), DNA repair protein, DNA polymerase kappa and decaprenyl-diphosphate synthase subunit 2], which harbor nine significant CpGs, are known to be involved in mitochondrial biosynthesis and functions. For example, NR1H3 encodes a transcription factor that is differentially expressed during an adipose tissue transition. The methylation level of cg09548275 in NR1H3 was negatively associated with mtDNA CN (effect size = -1.71, P = 4 × 10-8) and was positively associated with the NR1H3 expression level (effect size = 0.43, P = 0.0003), which indicates that the methylation level in NR1H3 may underlie the relationship between mtDNA CN, the NR1H3 transcription factor and energy expenditure. In summary, the study results suggest that mtDNA CN variation in whole blood is associated with DNA methylation levels in genes that are involved in a wide range of mitochondrial activities. These findings will help reveal molecular mechanisms between mtDNA CN and CVD.

%B Hum Mol Genet %V 31 %P 309-319 %8 2021 Dec 27 %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/34415308?dopt=Abstract %R 10.1093/hmg/ddab240 %0 Journal Article %J EBioMedicine %D 2021 %T Whole genome sequence analyses of eGFR in 23,732 people representing multiple ancestries in the NHLBI trans-omics for precision medicine (TOPMed) consortium. %A Lin, Bridget M %A Grinde, Kelsey E %A Brody, Jennifer A %A Breeze, Charles E %A Raffield, Laura M %A Mychaleckyj, Josyf C %A Thornton, Timothy A %A Perry, James A %A Baier, Leslie J %A de Las Fuentes, Lisa %A Guo, Xiuqing %A Heavner, Benjamin D %A Hanson, Robert L %A Hung, Yi-Jen %A Qian, Huijun %A Hsiung, Chao A %A Hwang, Shih-Jen %A Irvin, Margaret R %A Jain, Deepti %A Kelly, Tanika N %A Kobes, Sayuko %A Lange, Leslie %A Lash, James P %A Li, Yun %A Liu, Xiaoming %A Mi, Xuenan %A Musani, Solomon K %A Papanicolaou, George J %A Parsa, Afshin %A Reiner, Alex P %A Salimi, Shabnam %A Sheu, Wayne H-H %A Shuldiner, Alan R %A Taylor, Kent D %A Smith, Albert V %A Smith, Jennifer A %A Tin, Adrienne %A Vaidya, Dhananjay %A Wallace, Robert B %A Yamamoto, Kenichi %A Sakaue, Saori %A Matsuda, Koichi %A Kamatani, Yoichiro %A Momozawa, Yukihide %A Yanek, Lisa R %A Young, Betsi A %A Zhao, Wei %A Okada, Yukinori %A Abecasis, Gonzalo %A Psaty, Bruce M %A Arnett, Donna K %A Eric Boerwinkle %A Cai, Jianwen %A Yii-Der Chen, Ida %A Correa, Adolfo %A Cupples, L Adrienne %A He, Jiang %A Kardia, Sharon Lr %A Kooperberg, Charles %A Mathias, Rasika A %A Mitchell, Braxton D %A Nickerson, Deborah A %A Turner, Steve T %A Vasan, Ramachandran S %A Rotter, Jerome I %A Levy, Daniel %A Kramer, Holly J %A Köttgen, Anna %A Rich, Stephen S %A Lin, Dan-Yu %A Browning, Sharon R %A Franceschini, Nora %K Alleles %K Gene Frequency %K Genetic Predisposition to Disease %K Genome-Wide Association Study %K Genomics %K Glomerular Filtration Rate %K Humans %K Male %K National Heart, Lung, and Blood Institute (U.S.) %K Polymorphism, Single Nucleotide %K Precision Medicine %K Public Health Surveillance %K Quantitative Trait, Heritable %K United States %K Whole Genome Sequencing %X

BACKGROUND: Genetic factors that influence kidney traits have been understudied for low frequency and ancestry-specific variants.

METHODS: We combined whole genome sequencing (WGS) data from 23,732 participants from 10 NHLBI Trans-Omics for Precision Medicine (TOPMed) Program multi-ethnic studies to identify novel loci for estimated glomerular filtration rate (eGFR). Participants included European, African, East Asian, and Hispanic ancestries. We applied linear mixed models using a genetic relationship matrix estimated from the WGS data and adjusted for age, sex, study, and ethnicity.

FINDINGS: When testing single variants, we identified three novel loci driven by low frequency variants more commonly observed in non-European ancestry (PRKAA2, rs180996919, minor allele frequency [MAF] 0.04%, P = 6.1 × 10; METTL8, rs116951054, MAF 0.09%, P = 4.5 × 10; and MATK, rs539182790, MAF 0.05%, P = 3.4 × 10). We also replicated two known loci for common variants (rs2461702, MAF=0.49, P = 1.2 × 10, nearest gene GATM, and rs71147340, MAF=0.34, P = 3.3 × 10, CDK12). Testing aggregated variants within a gene identified the MAF gene. A statistical approach based on local ancestry helped to identify replication samples for ancestry-specific variants.

INTERPRETATION: This study highlights challenges in studying variants influencing kidney traits that are low frequency in populations and more common in non-European ancestry.

%B EBioMedicine %V 63 %P 103157 %8 2021 Jan %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/33418499?dopt=Abstract %R 10.1016/j.ebiom.2020.103157 %0 Journal Article %J Nature %D 2020 %T Inherited causes of clonal haematopoiesis in 97,691 whole genomes. %A Bick, Alexander G %A Weinstock, Joshua S %A Nandakumar, Satish K %A Fulco, Charles P %A Bao, Erik L %A Zekavat, Seyedeh M %A Szeto, Mindy D %A Liao, Xiaotian %A Leventhal, Matthew J %A Nasser, Joseph %A Chang, Kyle %A Laurie, Cecelia %A Burugula, Bala Bharathi %A Gibson, Christopher J %A Lin, Amy E %A Taub, Margaret A %A Aguet, Francois %A Ardlie, Kristin %A Mitchell, Braxton D %A Barnes, Kathleen C %A Moscati, Arden %A Fornage, Myriam %A Redline, Susan %A Psaty, Bruce M %A Silverman, Edwin K %A Weiss, Scott T %A Palmer, Nicholette D %A Vasan, Ramachandran S %A Burchard, Esteban G %A Kardia, Sharon L R %A He, Jiang %A Kaplan, Robert C %A Smith, Nicholas L %A Arnett, Donna K %A Schwartz, David A %A Correa, Adolfo %A de Andrade, Mariza %A Guo, Xiuqing %A Konkle, Barbara A %A Custer, Brian %A Peralta, Juan M %A Gui, Hongsheng %A Meyers, Deborah A %A McGarvey, Stephen T %A Chen, Ida Yii-Der %A Shoemaker, M Benjamin %A Peyser, Patricia A %A Broome, Jai G %A Gogarten, Stephanie M %A Wang, Fei Fei %A Wong, Quenna %A Montasser, May E %A Daya, Michelle %A Kenny, Eimear E %A North, Kari E %A Launer, Lenore J %A Cade, Brian E %A Bis, Joshua C %A Cho, Michael H %A Lasky-Su, Jessica %A Bowden, Donald W %A Cupples, L Adrienne %A Mak, Angel C Y %A Becker, Lewis C %A Smith, Jennifer A %A Kelly, Tanika N %A Aslibekyan, Stella %A Heckbert, Susan R %A Tiwari, Hemant K %A Yang, Ivana V %A Heit, John A %A Lubitz, Steven A %A Johnsen, Jill M %A Curran, Joanne E %A Wenzel, Sally E %A Weeks, Daniel E %A Rao, Dabeeru C %A Darbar, Dawood %A Moon, Jee-Young %A Tracy, Russell P %A Buth, Erin J %A Rafaels, Nicholas %A Loos, Ruth J F %A Durda, Peter %A Liu, Yongmei %A Hou, Lifang %A Lee, Jiwon %A Kachroo, Priyadarshini %A Freedman, Barry I %A Levy, Daniel %A Bielak, Lawrence F %A Hixson, James E %A Floyd, James S %A Whitsel, Eric A %A Ellinor, Patrick T %A Irvin, Marguerite R %A Fingerlin, Tasha E %A Raffield, Laura M %A Armasu, Sebastian M %A Wheeler, Marsha M %A Sabino, Ester C %A Blangero, John %A Williams, L Keoki %A Levy, Bruce D %A Sheu, Wayne Huey-Herng %A Roden, Dan M %A Eric Boerwinkle %A Manson, JoAnn E %A Mathias, Rasika A %A Desai, Pinkal %A Taylor, Kent D %A Johnson, Andrew D %A Auer, Paul L %A Kooperberg, Charles %A Laurie, Cathy C %A Blackwell, Thomas W %A Smith, Albert V %A Zhao, Hongyu %A Lange, Ethan %A Lange, Leslie %A Rich, Stephen S %A Rotter, Jerome I %A Wilson, James G %A Scheet, Paul %A Kitzman, Jacob O %A Lander, Eric S %A Engreitz, Jesse M %A Ebert, Benjamin L %A Reiner, Alexander P %A Jaiswal, Siddhartha %A Abecasis, Goncalo %A Sankaran, Vijay G %A Kathiresan, Sekar %A Natarajan, Pradeep %K Adult %K Africa %K Aged %K Aged, 80 and over %K alpha Karyopherins %K Black People %K Cell Self Renewal %K Clonal Hematopoiesis %K Dioxygenases %K DNA-Binding Proteins %K Female %K Genetic Predisposition to Disease %K Genome, Human %K Germ-Line Mutation %K Hematopoietic Stem Cells %K Humans %K Intracellular Signaling Peptides and Proteins %K Male %K Middle Aged %K National Heart, Lung, and Blood Institute (U.S.) %K Phenotype %K Precision Medicine %K Proto-Oncogene Proteins %K Tripartite Motif Proteins %K United States %K Whole Genome Sequencing %X

Age is the dominant risk factor for most chronic human diseases, but the mechanisms through which ageing confers this risk are largely unknown. The age-related acquisition of somatic mutations that lead to clonal expansion in regenerating haematopoietic stem cell populations has recently been associated with both haematological cancer and coronary heart disease-this phenomenon is termed clonal haematopoiesis of indeterminate potential (CHIP). Simultaneous analyses of germline and somatic whole-genome sequences provide the opportunity to identify root causes of CHIP. Here we analyse high-coverage whole-genome sequences from 97,691 participants of diverse ancestries in the National Heart, Lung, and Blood Institute Trans-omics for Precision Medicine (TOPMed) programme, and identify 4,229 individuals with CHIP. We identify associations with blood cell, lipid and inflammatory traits that are specific to different CHIP driver genes. Association of a genome-wide set of germline genetic variants enabled the identification of three genetic loci associated with CHIP status, including one locus at TET2 that was specific to individuals of African ancestry. In silico-informed in vitro evaluation of the TET2 germline locus enabled the identification of a causal variant that disrupts a TET2 distal enhancer, resulting in increased self-renewal of haematopoietic stem cells. Overall, we observe that germline genetic variation shapes haematopoietic stem cell function, leading to CHIP through mechanisms that are specific to clonal haematopoiesis as well as shared mechanisms that lead to somatic mutations across tissues.

%B Nature %V 586 %P 763-768 %8 2020 Oct %G eng %N 7831 %1 https://www.ncbi.nlm.nih.gov/pubmed/33057201?dopt=Abstract %R 10.1038/s41586-020-2819-2 %0 Journal Article %J Circulation %D 2019 %T Blood Leukocyte DNA Methylation Predicts Risk of Future Myocardial Infarction and Coronary Heart Disease. %A Agha, Golareh %A Mendelson, Michael M %A Ward-Caviness, Cavin K %A Joehanes, Roby %A Huan, Tianxiao %A Gondalia, Rahul %A Salfati, Elias %A Brody, Jennifer A %A Fiorito, Giovanni %A Bressler, Jan %A Chen, Brian H %A Ligthart, Symen %A Guarrera, Simonetta %A Colicino, Elena %A Just, Allan C %A Wahl, Simone %A Gieger, Christian %A Vandiver, Amy R %A Tanaka, Toshiko %A Hernandez, Dena G %A Pilling, Luke C %A Singleton, Andrew B %A Sacerdote, Carlotta %A Krogh, Vittorio %A Panico, Salvatore %A Tumino, Rosario %A Li, Yun %A Zhang, Guosheng %A Stewart, James D %A Floyd, James S %A Wiggins, Kerri L %A Rotter, Jerome I %A Multhaup, Michael %A Bakulski, Kelly %A Horvath, Steven %A Tsao, Philip S %A Absher, Devin M %A Vokonas, Pantel %A Hirschhorn, Joel %A Fallin, M Daniele %A Liu, Chunyu %A Bandinelli, Stefania %A Eric Boerwinkle %A Dehghan, Abbas %A Schwartz, Joel D %A Psaty, Bruce M %A Feinberg, Andrew P %A Hou, Lifang %A Ferrucci, Luigi %A Sotoodehnia, Nona %A Matullo, Giuseppe %A Peters, Annette %A Fornage, Myriam %A Assimes, Themistocles L %A Whitsel, Eric A %A Levy, Daniel %A Baccarelli, Andrea A %K Adult %K Aged %K Cohort Studies %K Coronary Disease %K CpG Islands %K DNA Methylation %K Europe %K Female %K Genome-Wide Association Study %K Humans %K Incidence %K Leukocytes %K Male %K Middle Aged %K Myocardial Infarction %K Population Groups %K Prognosis %K Prospective Studies %K Risk %K United States %X

BACKGROUND: DNA methylation is implicated in coronary heart disease (CHD), but current evidence is based on small, cross-sectional studies. We examined blood DNA methylation in relation to incident CHD across multiple prospective cohorts.

METHODS: Nine population-based cohorts from the United States and Europe profiled epigenome-wide blood leukocyte DNA methylation using the Illumina Infinium 450k microarray, and prospectively ascertained CHD events including coronary insufficiency/unstable angina, recognized myocardial infarction, coronary revascularization, and coronary death. Cohorts conducted race-specific analyses adjusted for age, sex, smoking, education, body mass index, blood cell type proportions, and technical variables. We conducted fixed-effect meta-analyses across cohorts.

RESULTS: Among 11 461 individuals (mean age 64 years, 67% women, 35% African American) free of CHD at baseline, 1895 developed CHD during a mean follow-up of 11.2 years. Methylation levels at 52 CpG (cytosine-phosphate-guanine) sites were associated with incident CHD or myocardial infarction (false discovery rate<0.05). These CpGs map to genes with key roles in calcium regulation (ATP2B2, CASR, GUCA1B, HPCAL1), and genes identified in genome- and epigenome-wide studies of serum calcium (CASR), serum calcium-related risk of CHD (CASR), coronary artery calcified plaque (PTPRN2), and kidney function (CDH23, HPCAL1), among others. Mendelian randomization analyses supported a causal effect of DNA methylation on incident CHD; these CpGs map to active regulatory regions proximal to long non-coding RNA transcripts.

CONCLUSION: Methylation of blood-derived DNA is associated with risk of future CHD across diverse populations and may serve as an informative tool for gaining further insight on the development of CHD.

%B Circulation %V 140 %P 645-657 %8 2019 Aug 20 %G eng %N 8 %1 https://www.ncbi.nlm.nih.gov/pubmed/31424985?dopt=Abstract %R 10.1161/CIRCULATIONAHA.118.039357 %0 Journal Article %J Hum Genet %D 2019 %T Leveraging linkage evidence to identify low-frequency and rare variants on 16p13 associated with blood pressure using TOPMed whole genome sequencing data. %A He, Karen Y %A Li, Xiaoyin %A Kelly, Tanika N %A Liang, Jingjing %A Cade, Brian E %A Assimes, Themistocles L %A Becker, Lewis C %A Beitelshees, Amber L %A Bress, Adam P %A Chang, Yen-Pei Christy %A Chen, Yii-Der Ida %A de Vries, Paul S %A Fox, Ervin R %A Franceschini, Nora %A Furniss, Anna %A Gao, Yan %A Guo, Xiuqing %A Haessler, Jeffrey %A Hwang, Shih-Jen %A Irvin, Marguerite Ryan %A Kalyani, Rita R %A Liu, Ching-Ti %A Liu, Chunyu %A Martin, Lisa Warsinger %A Montasser, May E %A Muntner, Paul M %A Mwasongwe, Stanford %A Palmas, Walter %A Reiner, Alex P %A Shimbo, Daichi %A Smith, Jennifer A %A Snively, Beverly M %A Yanek, Lisa R %A Eric Boerwinkle %A Correa, Adolfo %A Cupples, L Adrienne %A He, Jiang %A Kardia, Sharon L R %A Kooperberg, Charles %A Mathias, Rasika A %A Mitchell, Braxton D %A Psaty, Bruce M %A Vasan, Ramachandran S %A Rao, D C %A Rich, Stephen S %A Rotter, Jerome I %A Wilson, James G %A Chakravarti, Aravinda %A Morrison, Alanna C %A Levy, Daniel %A Arnett, Donna K %A Redline, Susan %A Zhu, Xiaofeng %K Alternative Splicing %K Blood Pressure %K Chromosomes, Human, Pair 16 %K Exome %K Female %K Follow-Up Studies %K Genetic Linkage %K Genetic Variation %K Genome, Human %K Genome-Wide Association Study %K High-Throughput Nucleotide Sequencing %K Humans %K Male %K Recombinases %K RNA Splicing Factors %X

In this study, we investigated low-frequency and rare variants associated with blood pressure (BP) by focusing on a linkage region on chromosome 16p13. We used whole genome sequencing (WGS) data obtained through the NHLBI Trans-Omics for Precision Medicine (TOPMed) program on 395 Cleveland Family Study (CFS) European Americans (CFS-EA). By analyzing functional coding variants and non-coding rare variants with CADD score > 10 residing within the chromosomal region in families with linkage evidence, we observed 25 genes with nominal statistical evidence (burden or SKAT p < 0.05). One of the genes is RBFOX1, an evolutionarily conserved RNA-binding protein that regulates tissue-specific alternative splicing that we previously reported to be associated with BP using exome array data in CFS. After follow-up analysis of the 25 genes in ten independent TOPMed studies with individuals of European, African, and East Asian ancestry, and Hispanics (N = 29,988), we identified variants in SLX4 (p = 2.19 × 10) to be significantly associated with BP traits when accounting for multiple testing. We also replicated the associations previously reported for RBFOX1 (p = 0.007). Follow-up analysis with GTEx eQTL data shows SLX4 variants are associated with gene expression in coronary artery, multiple brain tissues, and right atrial appendage of the heart. Our study demonstrates that linkage analysis of family data can provide an efficient approach for detecting rare variants associated with complex traits in WGS data.

%B Hum Genet %V 138 %P 199-210 %8 2019 Feb %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/30671673?dopt=Abstract %R 10.1007/s00439-019-01975-0 %0 Journal Article %J Hum Mol Genet %D 2019 %T A multi-ancestry genome-wide study incorporating gene-smoking interactions identifies multiple new loci for pulse pressure and mean arterial pressure. %A Sung, Yun Ju %A de Las Fuentes, Lisa %A Winkler, Thomas W %A Chasman, Daniel I %A Bentley, Amy R %A Kraja, Aldi T %A Ntalla, Ioanna %A Warren, Helen R %A Guo, Xiuqing %A Schwander, Karen %A Manning, Alisa K %A Brown, Michael R %A Aschard, Hugues %A Feitosa, Mary F %A Franceschini, Nora %A Lu, Yingchang %A Cheng, Ching-Yu %A Sim, Xueling %A Vojinovic, Dina %A Marten, Jonathan %A Musani, Solomon K %A Kilpeläinen, Tuomas O %A Richard, Melissa A %A Aslibekyan, Stella %A Bartz, Traci M %A Dorajoo, Rajkumar %A Li, Changwei %A Liu, Yongmei %A Rankinen, Tuomo %A Smith, Albert Vernon %A Tajuddin, Salman M %A Tayo, Bamidele O %A Zhao, Wei %A Zhou, Yanhua %A Matoba, Nana %A Sofer, Tamar %A Alver, Maris %A Amini, Marzyeh %A Boissel, Mathilde %A Chai, Jin Fang %A Chen, Xu %A Divers, Jasmin %A Gandin, Ilaria %A Gao, Chuan %A Giulianini, Franco %A Goel, Anuj %A Harris, Sarah E %A Hartwig, Fernando P %A He, Meian %A Horimoto, Andrea R V R %A Hsu, Fang-Chi %A Jackson, Anne U %A Kammerer, Candace M %A Kasturiratne, Anuradhani %A Komulainen, Pirjo %A Kühnel, Brigitte %A Leander, Karin %A Lee, Wen-Jane %A Lin, Keng-Hung %A Luan, Jian'an %A Lyytikäinen, Leo-Pekka %A McKenzie, Colin A %A Nelson, Christopher P %A Noordam, Raymond %A Scott, Robert A %A Sheu, Wayne H H %A Stančáková, Alena %A Takeuchi, Fumihiko %A van der Most, Peter J %A Varga, Tibor V %A Waken, Robert J %A Wang, Heming %A Wang, Yajuan %A Ware, Erin B %A Weiss, Stefan %A Wen, Wanqing %A Yanek, Lisa R %A Zhang, Weihua %A Zhao, Jing Hua %A Afaq, Saima %A Alfred, Tamuno %A Amin, Najaf %A Arking, Dan E %A Aung, Tin %A Barr, R Graham %A Bielak, Lawrence F %A Eric Boerwinkle %A Bottinger, Erwin P %A Braund, Peter S %A Brody, Jennifer A %A Broeckel, Ulrich %A Cade, Brian %A Campbell, Archie %A Canouil, Mickaël %A Chakravarti, Aravinda %A Cocca, Massimiliano %A Collins, Francis S %A Connell, John M %A de Mutsert, Renée %A de Silva, H Janaka %A Dörr, Marcus %A Duan, Qing %A Eaton, Charles B %A Ehret, Georg %A Evangelou, Evangelos %A Faul, Jessica D %A Forouhi, Nita G %A Franco, Oscar H %A Friedlander, Yechiel %A Gao, He %A Gigante, Bruna %A Gu, C Charles %A Gupta, Preeti %A Hagenaars, Saskia P %A Harris, Tamara B %A He, Jiang %A Heikkinen, Sami %A Heng, Chew-Kiat %A Hofman, Albert %A Howard, Barbara V %A Hunt, Steven C %A Irvin, Marguerite R %A Jia, Yucheng %A Katsuya, Tomohiro %A Kaufman, Joel %A Kerrison, Nicola D %A Khor, Chiea Chuen %A Koh, Woon-Puay %A Koistinen, Heikki A %A Kooperberg, Charles B %A Krieger, Jose E %A Kubo, Michiaki %A Kutalik, Zoltán %A Kuusisto, Johanna %A Lakka, Timo A %A Langefeld, Carl D %A Langenberg, Claudia %A Launer, Lenore J %A Lee, Joseph H %A Lehne, Benjamin %A Levy, Daniel %A Lewis, Cora E %A Li, Yize %A Lim, Sing Hui %A Liu, Ching-Ti %A Liu, Jianjun %A Liu, Jingmin %A Liu, Yeheng %A Loh, Marie %A Lohman, Kurt K %A Louie, Tin %A Mägi, Reedik %A Matsuda, Koichi %A Meitinger, Thomas %A Metspalu, Andres %A Milani, Lili %A Momozawa, Yukihide %A Mosley, Thomas H %A Nalls, Mike A %A Nasri, Ubaydah %A O'Connell, Jeff R %A Ogunniyi, Adesola %A Palmas, Walter R %A Palmer, Nicholette D %A Pankow, James S %A Pedersen, Nancy L %A Peters, Annette %A Peyser, Patricia A %A Polasek, Ozren %A Porteous, David %A Raitakari, Olli T %A Renstrom, Frida %A Rice, Treva K %A Ridker, Paul M %A Robino, Antonietta %A Robinson, Jennifer G %A Rose, Lynda M %A Rudan, Igor %A Sabanayagam, Charumathi %A Salako, Babatunde L %A Sandow, Kevin %A Schmidt, Carsten O %A Schreiner, Pamela J %A Scott, William R %A Sever, Peter %A Sims, Mario %A Sitlani, Colleen M %A Smith, Blair H %A Smith, Jennifer A %A Snieder, Harold %A Starr, John M %A Strauch, Konstantin %A Tang, Hua %A Taylor, Kent D %A Teo, Yik Ying %A Tham, Yih Chung %A Uitterlinden, André G %A Waldenberger, Melanie %A Wang, Lihua %A Wang, Ya Xing %A Wei, Wen Bin %A Wilson, Gregory %A Wojczynski, Mary K %A Xiang, Yong-Bing %A Yao, Jie %A Yuan, Jian-Min %A Zonderman, Alan B %A Becker, Diane M %A Boehnke, Michael %A Bowden, Donald W %A Chambers, John C %A Chen, Yii-Der Ida %A Weir, David R %A de Faire, Ulf %A Deary, Ian J %A Esko, Tõnu %A Farrall, Martin %A Forrester, Terrence %A Freedman, Barry I %A Froguel, Philippe %A Gasparini, Paolo %A Gieger, Christian %A Horta, Bernardo Lessa %A Hung, Yi-Jen %A Jonas, Jost Bruno %A Kato, Norihiro %A Kooner, Jaspal S %A Laakso, Markku %A Lehtimäki, Terho %A Liang, Kae-Woei %A Magnusson, Patrik K E %A Oldehinkel, Albertine J %A Pereira, Alexandre C %A Perls, Thomas %A Rauramaa, Rainer %A Redline, Susan %A Rettig, Rainer %A Samani, Nilesh J %A Scott, James %A Shu, Xiao-Ou %A van der Harst, Pim %A Wagenknecht, Lynne E %A Wareham, Nicholas J %A Watkins, Hugh %A Wickremasinghe, Ananda R %A Wu, Tangchun %A Kamatani, Yoichiro %A Laurie, Cathy C %A Bouchard, Claude %A Cooper, Richard S %A Evans, Michele K %A Gudnason, Vilmundur %A Hixson, James %A Kardia, Sharon L R %A Kritchevsky, Stephen B %A Psaty, Bruce M %A van Dam, Rob M %A Arnett, Donna K %A Mook-Kanamori, Dennis O %A Fornage, Myriam %A Fox, Ervin R %A Hayward, Caroline %A van Duijn, Cornelia M %A Tai, E Shyong %A Wong, Tien Yin %A Loos, Ruth J F %A Reiner, Alex P %A Rotimi, Charles N %A Bierut, Laura J %A Zhu, Xiaofeng %A Cupples, L Adrienne %A Province, Michael A %A Rotter, Jerome I %A Franks, Paul W %A Rice, Kenneth %A Elliott, Paul %A Caulfield, Mark J %A Gauderman, W James %A Munroe, Patricia B %A Rao, Dabeeru C %A Morrison, Alanna C %K Adolescent %K Adult %K Aged %K Aged, 80 and over %K Antiporters %K Arterial Pressure %K Blood Pressure %K Caspase 9 %K Ethnicity %K Female %K Gene-Environment Interaction %K Genome-Wide Association Study %K Humans %K Hypertension %K Male %K Membrane Proteins %K Middle Aged %K Polymorphism, Genetic %K Racial Groups %K Receptors, Vasopressin %K Smoking %K Sulfate Transporters %K Tumor Suppressor Proteins %K Young Adult %X

Elevated blood pressure (BP), a leading cause of global morbidity and mortality, is influenced by both genetic and lifestyle factors. Cigarette smoking is one such lifestyle factor. Across five ancestries, we performed a genome-wide gene-smoking interaction study of mean arterial pressure (MAP) and pulse pressure (PP) in 129 913 individuals in stage 1 and follow-up analysis in 480 178 additional individuals in stage 2. We report here 136 loci significantly associated with MAP and/or PP. Of these, 61 were previously published through main-effect analysis of BP traits, 37 were recently reported by us for systolic BP and/or diastolic BP through gene-smoking interaction analysis and 38 were newly identified (P < 5 × 10-8, false discovery rate < 0.05). We also identified nine new signals near known loci. Of the 136 loci, 8 showed significant interaction with smoking status. They include CSMD1 previously reported for insulin resistance and BP in the spontaneously hypertensive rats. Many of the 38 new loci show biologic plausibility for a role in BP regulation. SLC26A7 encodes a chloride/bicarbonate exchanger expressed in the renal outer medullary collecting duct. AVPR1A is widely expressed, including in vascular smooth muscle cells, kidney, myocardium and brain. FHAD1 is a long non-coding RNA overexpressed in heart failure. TMEM51 was associated with contractile function in cardiomyocytes. CASP9 plays a central role in cardiomyocyte apoptosis. Identified only in African ancestry were 30 novel loci. Our findings highlight the value of multi-ancestry investigations, particularly in studies of interaction with lifestyle factors, where genomic and lifestyle differences may contribute to novel findings.

%B Hum Mol Genet %V 28 %P 2615-2633 %8 2019 Aug 01 %G eng %N 15 %1 https://www.ncbi.nlm.nih.gov/pubmed/31127295?dopt=Abstract %R 10.1093/hmg/ddz070 %0 Journal Article %J Nat Genet %D 2018 %T Genetic analysis of over 1 million people identifies 535 new loci associated with blood pressure traits. %A Evangelou, Evangelos %A Warren, Helen R %A Mosen-Ansorena, David %A Mifsud, Borbala %A Pazoki, Raha %A Gao, He %A Ntritsos, Georgios %A Dimou, Niki %A Cabrera, Claudia P %A Karaman, Ibrahim %A Ng, Fu Liang %A Evangelou, Marina %A Witkowska, Katarzyna %A Tzanis, Evan %A Hellwege, Jacklyn N %A Giri, Ayush %A Velez Edwards, Digna R %A Sun, Yan V %A Cho, Kelly %A Gaziano, J Michael %A Wilson, Peter W F %A Tsao, Philip S %A Kovesdy, Csaba P %A Esko, Tõnu %A Mägi, Reedik %A Milani, Lili %A Almgren, Peter %A Boutin, Thibaud %A Debette, Stephanie %A Ding, Jun %A Giulianini, Franco %A Holliday, Elizabeth G %A Jackson, Anne U %A Li-Gao, Ruifang %A Lin, Wei-Yu %A Luan, Jian'an %A Mangino, Massimo %A Oldmeadow, Christopher %A Prins, Bram Peter %A Qian, Yong %A Sargurupremraj, Muralidharan %A Shah, Nabi %A Surendran, Praveen %A Thériault, Sébastien %A Verweij, Niek %A Willems, Sara M %A Zhao, Jing-Hua %A Amouyel, Philippe %A Connell, John %A de Mutsert, Renée %A Doney, Alex S F %A Farrall, Martin %A Menni, Cristina %A Morris, Andrew D %A Noordam, Raymond %A Paré, Guillaume %A Poulter, Neil R %A Shields, Denis C %A Stanton, Alice %A Thom, Simon %A Abecasis, Goncalo %A Amin, Najaf %A Arking, Dan E %A Ayers, Kristin L %A Barbieri, Caterina M %A Batini, Chiara %A Bis, Joshua C %A Blake, Tineka %A Bochud, Murielle %A Boehnke, Michael %A Eric Boerwinkle %A Boomsma, Dorret I %A Bottinger, Erwin P %A Braund, Peter S %A Brumat, Marco %A Campbell, Archie %A Campbell, Harry %A Chakravarti, Aravinda %A Chambers, John C %A Chauhan, Ganesh %A Ciullo, Marina %A Cocca, Massimiliano %A Collins, Francis %A Cordell, Heather J %A Davies, Gail %A de Borst, Martin H %A de Geus, Eco J %A Deary, Ian J %A Deelen, Joris %A Del Greco M, Fabiola %A Demirkale, Cumhur Yusuf %A Dörr, Marcus %A Ehret, Georg B %A Elosua, Roberto %A Enroth, Stefan %A Erzurumluoglu, A Mesut %A Ferreira, Teresa %A Frånberg, Mattias %A Franco, Oscar H %A Gandin, Ilaria %A Gasparini, Paolo %A Giedraitis, Vilmantas %A Gieger, Christian %A Girotto, Giorgia %A Goel, Anuj %A Gow, Alan J %A Gudnason, Vilmundur %A Guo, Xiuqing %A Gyllensten, Ulf %A Hamsten, Anders %A Harris, Tamara B %A Harris, Sarah E %A Hartman, Catharina A %A Havulinna, Aki S %A Hicks, Andrew A %A Hofer, Edith %A Hofman, Albert %A Hottenga, Jouke-Jan %A Huffman, Jennifer E %A Hwang, Shih-Jen %A Ingelsson, Erik %A James, Alan %A Jansen, Rick %A Jarvelin, Marjo-Riitta %A Joehanes, Roby %A Johansson, Åsa %A Johnson, Andrew D %A Joshi, Peter K %A Jousilahti, Pekka %A Jukema, J Wouter %A Jula, Antti %A Kähönen, Mika %A Kathiresan, Sekar %A Keavney, Bernard D %A Khaw, Kay-Tee %A Knekt, Paul %A Knight, Joanne %A Kolcic, Ivana %A Kooner, Jaspal S %A Koskinen, Seppo %A Kristiansson, Kati %A Kutalik, Zoltán %A Laan, Maris %A Larson, Marty %A Launer, Lenore J %A Lehne, Benjamin %A Lehtimäki, Terho %A Liewald, David C M %A Lin, Li %A Lind, Lars %A Lindgren, Cecilia M %A Liu, Yongmei %A Loos, Ruth J F %A Lopez, Lorna M %A Lu, Yingchang %A Lyytikäinen, Leo-Pekka %A Mahajan, Anubha %A Mamasoula, Chrysovalanto %A Marrugat, Jaume %A Marten, Jonathan %A Milaneschi, Yuri %A Morgan, Anna %A Morris, Andrew P %A Morrison, Alanna C %A Munson, Peter J %A Nalls, Mike A %A Nandakumar, Priyanka %A Nelson, Christopher P %A Niiranen, Teemu %A Nolte, Ilja M %A Nutile, Teresa %A Oldehinkel, Albertine J %A Oostra, Ben A %A O'Reilly, Paul F %A Org, Elin %A Padmanabhan, Sandosh %A Palmas, Walter %A Palotie, Aarno %A Pattie, Alison %A Penninx, Brenda W J H %A Perola, Markus %A Peters, Annette %A Polasek, Ozren %A Pramstaller, Peter P %A Nguyen, Quang Tri %A Raitakari, Olli T %A Ren, Meixia %A Rettig, Rainer %A Rice, Kenneth %A Ridker, Paul M %A Ried, Janina S %A Riese, Harriëtte %A Ripatti, Samuli %A Robino, Antonietta %A Rose, Lynda M %A Rotter, Jerome I %A Rudan, Igor %A Ruggiero, Daniela %A Saba, Yasaman %A Sala, Cinzia F %A Salomaa, Veikko %A Samani, Nilesh J %A Sarin, Antti-Pekka %A Schmidt, Reinhold %A Schmidt, Helena %A Shrine, Nick %A Siscovick, David %A Smith, Albert V %A Snieder, Harold %A Sõber, Siim %A Sorice, Rossella %A Starr, John M %A Stott, David J %A Strachan, David P %A Strawbridge, Rona J %A Sundström, Johan %A Swertz, Morris A %A Taylor, Kent D %A Teumer, Alexander %A Tobin, Martin D %A Tomaszewski, Maciej %A Toniolo, Daniela %A Traglia, Michela %A Trompet, Stella %A Tuomilehto, Jaakko %A Tzourio, Christophe %A Uitterlinden, André G %A Vaez, Ahmad %A van der Most, Peter J %A van Duijn, Cornelia M %A Vergnaud, Anne-Claire %A Verwoert, Germaine C %A Vitart, Veronique %A Völker, Uwe %A Vollenweider, Peter %A Vuckovic, Dragana %A Watkins, Hugh %A Wild, Sarah H %A Willemsen, Gonneke %A Wilson, James F %A Wright, Alan F %A Yao, Jie %A Zemunik, Tatijana %A Zhang, Weihua %A Attia, John R %A Butterworth, Adam S %A Chasman, Daniel I %A Conen, David %A Cucca, Francesco %A Danesh, John %A Hayward, Caroline %A Howson, Joanna M M %A Laakso, Markku %A Lakatta, Edward G %A Langenberg, Claudia %A Melander, Olle %A Mook-Kanamori, Dennis O %A Palmer, Colin N A %A Risch, Lorenz %A Scott, Robert A %A Scott, Rodney J %A Sever, Peter %A Spector, Tim D %A van der Harst, Pim %A Wareham, Nicholas J %A Zeggini, Eleftheria %A Levy, Daniel %A Munroe, Patricia B %A Newton-Cheh, Christopher %A Brown, Morris J %A Metspalu, Andres %A Hung, Adriana M %A O'Donnell, Christopher J %A Edwards, Todd L %A Psaty, Bruce M %A Tzoulaki, Ioanna %A Barnes, Michael R %A Wain, Louise V %A Elliott, Paul %A Caulfield, Mark J %K Adult %K Aged %K Aged, 80 and over %K Blood Pressure %K Cardiovascular Diseases %K Cells, Cultured %K Female %K Genetic Loci %K Genetic Predisposition to Disease %K Genetic Testing %K Genetics, Population %K Genome-Wide Association Study %K Human Umbilical Vein Endothelial Cells %K Humans %K Hypertension %K Life Style %K Male %K Middle Aged %K Polymorphism, Single Nucleotide %K Quantitative Trait Loci %K Risk Factors %X

High blood pressure is a highly heritable and modifiable risk factor for cardiovascular disease. We report the largest genetic association study of blood pressure traits (systolic, diastolic and pulse pressure) to date in over 1 million people of European ancestry. We identify 535 novel blood pressure loci that not only offer new biological insights into blood pressure regulation but also highlight shared genetic architecture between blood pressure and lifestyle exposures. Our findings identify new biological pathways for blood pressure regulation with potential for improved cardiovascular disease prevention in the future.

%B Nat Genet %V 50 %P 1412-1425 %8 2018 Oct %G eng %N 10 %1 https://www.ncbi.nlm.nih.gov/pubmed/30224653?dopt=Abstract %R 10.1038/s41588-018-0205-x %0 Journal Article %J PLoS One %D 2018 %T Novel genetic associations for blood pressure identified via gene-alcohol interaction in up to 570K individuals across multiple ancestries. %A Feitosa, Mary F %A Kraja, Aldi T %A Chasman, Daniel I %A Sung, Yun J %A Winkler, Thomas W %A Ntalla, Ioanna %A Guo, Xiuqing %A Franceschini, Nora %A Cheng, Ching-Yu %A Sim, Xueling %A Vojinovic, Dina %A Marten, Jonathan %A Musani, Solomon K %A Li, Changwei %A Bentley, Amy R %A Brown, Michael R %A Schwander, Karen %A Richard, Melissa A %A Noordam, Raymond %A Aschard, Hugues %A Bartz, Traci M %A Bielak, Lawrence F %A Dorajoo, Rajkumar %A Fisher, Virginia %A Hartwig, Fernando P %A Horimoto, Andrea R V R %A Lohman, Kurt K %A Manning, Alisa K %A Rankinen, Tuomo %A Smith, Albert V %A Tajuddin, Salman M %A Wojczynski, Mary K %A Alver, Maris %A Boissel, Mathilde %A Cai, Qiuyin %A Campbell, Archie %A Chai, Jin Fang %A Chen, Xu %A Divers, Jasmin %A Gao, Chuan %A Goel, Anuj %A Hagemeijer, Yanick %A Harris, Sarah E %A He, Meian %A Hsu, Fang-Chi %A Jackson, Anne U %A Kähönen, Mika %A Kasturiratne, Anuradhani %A Komulainen, Pirjo %A Kühnel, Brigitte %A Laguzzi, Federica %A Luan, Jian'an %A Matoba, Nana %A Nolte, Ilja M %A Padmanabhan, Sandosh %A Riaz, Muhammad %A Rueedi, Rico %A Robino, Antonietta %A Said, M Abdullah %A Scott, Robert A %A Sofer, Tamar %A Stančáková, Alena %A Takeuchi, Fumihiko %A Tayo, Bamidele O %A van der Most, Peter J %A Varga, Tibor V %A Vitart, Veronique %A Wang, Yajuan %A Ware, Erin B %A Warren, Helen R %A Weiss, Stefan %A Wen, Wanqing %A Yanek, Lisa R %A Zhang, Weihua %A Zhao, Jing Hua %A Afaq, Saima %A Amin, Najaf %A Amini, Marzyeh %A Arking, Dan E %A Aung, Tin %A Boerwinkle, Eric %A Borecki, Ingrid %A Broeckel, Ulrich %A Brown, Morris %A Brumat, Marco %A Burke, Gregory L %A Canouil, Mickaël %A Chakravarti, Aravinda %A Charumathi, Sabanayagam %A Ida Chen, Yii-Der %A Connell, John M %A Correa, Adolfo %A de Las Fuentes, Lisa %A de Mutsert, Renée %A de Silva, H Janaka %A Deng, Xuan %A Ding, Jingzhong %A Duan, Qing %A Eaton, Charles B %A Ehret, Georg %A Eppinga, Ruben N %A Evangelou, Evangelos %A Faul, Jessica D %A Felix, Stephan B %A Forouhi, Nita G %A Forrester, Terrence %A Franco, Oscar H %A Friedlander, Yechiel %A Gandin, Ilaria %A Gao, He %A Ghanbari, Mohsen %A Gigante, Bruna %A Gu, C Charles %A Gu, Dongfeng %A Hagenaars, Saskia P %A Hallmans, Goran %A Harris, Tamara B %A He, Jiang %A Heikkinen, Sami %A Heng, Chew-Kiat %A Hirata, Makoto %A Howard, Barbara V %A Ikram, M Arfan %A John, Ulrich %A Katsuya, Tomohiro %A Khor, Chiea Chuen %A Kilpeläinen, Tuomas O %A Koh, Woon-Puay %A Krieger, Jose E %A Kritchevsky, Stephen B %A Kubo, Michiaki %A Kuusisto, Johanna %A Lakka, Timo A %A Langefeld, Carl D %A Langenberg, Claudia %A Launer, Lenore J %A Lehne, Benjamin %A Lewis, Cora E %A Li, Yize %A Lin, Shiow %A Liu, Jianjun %A Liu, Jingmin %A Loh, Marie %A Louie, Tin %A Mägi, Reedik %A McKenzie, Colin A %A Meitinger, Thomas %A Metspalu, Andres %A Milaneschi, Yuri %A Milani, Lili %A Mohlke, Karen L %A Momozawa, Yukihide %A Nalls, Mike A %A Nelson, Christopher P %A Sotoodehnia, Nona %A Norris, Jill M %A O'Connell, Jeff R %A Palmer, Nicholette D %A Perls, Thomas %A Pedersen, Nancy L %A Peters, Annette %A Peyser, Patricia A %A Poulter, Neil %A Raffel, Leslie J %A Raitakari, Olli T %A Roll, Kathryn %A Rose, Lynda M %A Rosendaal, Frits R %A Rotter, Jerome I %A Schmidt, Carsten O %A Schreiner, Pamela J %A Schupf, Nicole %A Scott, William R %A Sever, Peter S %A Shi, Yuan %A Sidney, Stephen %A Sims, Mario %A Sitlani, Colleen M %A Smith, Jennifer A %A Snieder, Harold %A Starr, John M %A Strauch, Konstantin %A Stringham, Heather M %A Tan, Nicholas Y Q %A Tang, Hua %A Taylor, Kent D %A Teo, Yik Ying %A Tham, Yih Chung %A Turner, Stephen T %A Uitterlinden, André G %A Vollenweider, Peter %A Waldenberger, Melanie %A Wang, Lihua %A Wang, Ya Xing %A Wei, Wen Bin %A Williams, Christine %A Yao, Jie %A Yu, Caizheng %A Yuan, Jian-Min %A Zhao, Wei %A Zonderman, Alan B %A Becker, Diane M %A Boehnke, Michael %A Bowden, Donald W %A Chambers, John C %A Deary, Ian J %A Esko, Tõnu %A Farrall, Martin %A Franks, Paul W %A Freedman, Barry I %A Froguel, Philippe %A Gasparini, Paolo %A Gieger, Christian %A Jonas, Jost Bruno %A Kamatani, Yoichiro %A Kato, Norihiro %A Kooner, Jaspal S %A Kutalik, Zoltán %A Laakso, Markku %A Laurie, Cathy C %A Leander, Karin %A Lehtimäki, Terho %A Study, Lifelines Cohort %A Magnusson, Patrik K E %A Oldehinkel, Albertine J %A Penninx, Brenda W J H %A Polasek, Ozren %A Porteous, David J %A Rauramaa, Rainer %A Samani, Nilesh J %A Scott, James %A Shu, Xiao-Ou %A van der Harst, Pim %A Wagenknecht, Lynne E %A Wareham, Nicholas J %A Watkins, Hugh %A Weir, David R %A Wickremasinghe, Ananda R %A Wu, Tangchun %A Zheng, Wei %A Bouchard, Claude %A Christensen, Kaare %A Evans, Michele K %A Gudnason, Vilmundur %A Horta, Bernardo L %A Kardia, Sharon L R %A Liu, Yongmei %A Pereira, Alexandre C %A Psaty, Bruce M %A Ridker, Paul M %A van Dam, Rob M %A Gauderman, W James %A Zhu, Xiaofeng %A Mook-Kanamori, Dennis O %A Fornage, Myriam %A Rotimi, Charles N %A Cupples, L Adrienne %A Kelly, Tanika N %A Fox, Ervin R %A Hayward, Caroline %A van Duijn, Cornelia M %A Tai, E Shyong %A Wong, Tien Yin %A Kooperberg, Charles %A Palmas, Walter %A Rice, Kenneth %A Morrison, Alanna C %A Elliott, Paul %A Caulfield, Mark J %A Munroe, Patricia B %A Rao, Dabeeru C %A Province, Michael A %A Levy, Daniel %K Adolescent %K Adult %K Aged %K Aged, 80 and over %K Alcohol Drinking %K Blood Pressure %K Cohort Studies %K Female %K Gene-Environment Interaction %K Genetic Predisposition to Disease %K Genome-Wide Association Study %K Humans %K Hypertension %K Male %K Middle Aged %K Pedigree %K Polymorphism, Single Nucleotide %K Racial Groups %K Young Adult %X

Heavy alcohol consumption is an established risk factor for hypertension; the mechanism by which alcohol consumption impact blood pressure (BP) regulation remains unknown. We hypothesized that a genome-wide association study accounting for gene-alcohol consumption interaction for BP might identify additional BP loci and contribute to the understanding of alcohol-related BP regulation. We conducted a large two-stage investigation incorporating joint testing of main genetic effects and single nucleotide variant (SNV)-alcohol consumption interactions. In Stage 1, genome-wide discovery meta-analyses in ≈131K individuals across several ancestry groups yielded 3,514 SNVs (245 loci) with suggestive evidence of association (P < 1.0 x 10-5). In Stage 2, these SNVs were tested for independent external replication in ≈440K individuals across multiple ancestries. We identified and replicated (at Bonferroni correction threshold) five novel BP loci (380 SNVs in 21 genes) and 49 previously reported BP loci (2,159 SNVs in 109 genes) in European ancestry, and in multi-ancestry meta-analyses (P < 5.0 x 10-8). For African ancestry samples, we detected 18 potentially novel BP loci (P < 5.0 x 10-8) in Stage 1 that warrant further replication. Additionally, correlated meta-analysis identified eight novel BP loci (11 genes). Several genes in these loci (e.g., PINX1, GATA4, BLK, FTO and GABBR2) have been previously reported to be associated with alcohol consumption. These findings provide insights into the role of alcohol consumption in the genetic architecture of hypertension.

%B PLoS One %V 13 %P e0198166 %8 2018 %G eng %N 6 %1 https://www.ncbi.nlm.nih.gov/pubmed/29912962?dopt=Abstract %R 10.1371/journal.pone.0198166 %0 Journal Article %J PLoS Med %D 2017 %T Association of Body Mass Index with DNA Methylation and Gene Expression in Blood Cells and Relations to Cardiometabolic Disease: A Mendelian Randomization Approach. %A Mendelson, Michael M %A Marioni, Riccardo E %A Joehanes, Roby %A Liu, Chunyu %A Hedman, Åsa K %A Aslibekyan, Stella %A Demerath, Ellen W %A Guan, Weihua %A Zhi, Degui %A Yao, Chen %A Huan, Tianxiao %A Willinger, Christine %A Chen, Brian %A Courchesne, Paul %A Multhaup, Michael %A Irvin, Marguerite R %A Cohain, Ariella %A Schadt, Eric E %A Grove, Megan L %A Bressler, Jan %A North, Kari %A Sundström, Johan %A Gustafsson, Stefan %A Shah, Sonia %A McRae, Allan F %A Harris, Sarah E %A Gibson, Jude %A Redmond, Paul %A Corley, Janie %A Murphy, Lee %A Starr, John M %A Kleinbrink, Erica %A Lipovich, Leonard %A Visscher, Peter M %A Wray, Naomi R %A Krauss, Ronald M %A Fallin, Daniele %A Feinberg, Andrew %A Absher, Devin M %A Fornage, Myriam %A Pankow, James S %A Lind, Lars %A Fox, Caroline %A Ingelsson, Erik %A Arnett, Donna K %A Boerwinkle, Eric %A Liang, Liming %A Levy, Daniel %A Deary, Ian J %K Aged %K Body Mass Index %K Coronary Artery Disease %K DNA Methylation %K Epigenesis, Genetic %K Female %K Gene Expression Regulation %K Genome-Wide Association Study %K Humans %K Leukocytes %K Lipid Metabolism %K Male %K Mendelian Randomization Analysis %K Obesity %K Oligonucleotide Array Sequence Analysis %X

BACKGROUND: The link between DNA methylation, obesity, and adiposity-related diseases in the general population remains uncertain.

METHODS AND FINDINGS: We conducted an association study of body mass index (BMI) and differential methylation for over 400,000 CpGs assayed by microarray in whole-blood-derived DNA from 3,743 participants in the Framingham Heart Study and the Lothian Birth Cohorts, with independent replication in three external cohorts of 4,055 participants. We examined variations in whole blood gene expression and conducted Mendelian randomization analyses to investigate the functional and clinical relevance of the findings. We identified novel and previously reported BMI-related differential methylation at 83 CpGs that replicated across cohorts; BMI-related differential methylation was associated with concurrent changes in the expression of genes in lipid metabolism pathways. Genetic instrumental variable analysis of alterations in methylation at one of the 83 replicated CpGs, cg11024682 (intronic to sterol regulatory element binding transcription factor 1 [SREBF1]), demonstrated links to BMI, adiposity-related traits, and coronary artery disease. Independent genetic instruments for expression of SREBF1 supported the findings linking methylation to adiposity and cardiometabolic disease. Methylation at a substantial proportion (16 of 83) of the identified loci was found to be secondary to differences in BMI. However, the cross-sectional nature of the data limits definitive causal determination.

CONCLUSIONS: We present robust associations of BMI with differential DNA methylation at numerous loci in blood cells. BMI-related DNA methylation and gene expression provide mechanistic insights into the relationship between DNA methylation, obesity, and adiposity-related diseases.

%B PLoS Med %V 14 %P e1002215 %8 2017 Jan %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/28095459?dopt=Abstract %R 10.1371/journal.pmed.1002215 %0 Journal Article %J PLoS Genet %D 2016 %T Discovery of Genetic Variation on Chromosome 5q22 Associated with Mortality in Heart Failure. %A Smith, J Gustav %A Felix, Janine F %A Morrison, Alanna C %A Kalogeropoulos, Andreas %A Trompet, Stella %A Wilk, Jemma B %A Gidlöf, Olof %A Wang, Xinchen %A Morley, Michael %A Mendelson, Michael %A Joehanes, Roby %A Ligthart, Symen %A Shan, Xiaoyin %A Bis, Joshua C %A Wang, Ying A %A Sjögren, Marketa %A Ngwa, Julius %A Brandimarto, Jeffrey %A Stott, David J %A Aguilar, David %A Rice, Kenneth M %A Sesso, Howard D %A Demissie, Serkalem %A Buckley, Brendan M %A Taylor, Kent D %A Ford, Ian %A Yao, Chen %A Liu, Chunyu %A Sotoodehnia, Nona %A van der Harst, Pim %A Stricker, Bruno H Ch %A Kritchevsky, Stephen B %A Liu, Yongmei %A Gaziano, J Michael %A Hofman, Albert %A Moravec, Christine S %A Uitterlinden, André G %A Kellis, Manolis %A van Meurs, Joyce B %A Margulies, Kenneth B %A Dehghan, Abbas %A Levy, Daniel %A Olde, Björn %A Psaty, Bruce M %A Cupples, L Adrienne %A Jukema, J Wouter %A Djousse, Luc %A Franco, Oscar H %A Boerwinkle, Eric %A Boyer, Laurie A %A Newton-Cheh, Christopher %A Butler, Javed %A Vasan, Ramachandran S %A Cappola, Thomas P %A Smith, Nicholas L %K Alleles %K Basic Helix-Loop-Helix Transcription Factors %K Black or African American %K Chromosomes, Human, Pair 5 %K DNA Methylation %K Female %K Gene Expression Regulation %K Gene Knockdown Techniques %K Genetic Predisposition to Disease %K Genetic Variation %K Genome-Wide Association Study %K Genotype %K Heart Failure %K HEK293 Cells %K Humans %K Male %K Middle Aged %K Polymorphism, Single Nucleotide %K Receptors, Cytokine %X

Failure of the human heart to maintain sufficient output of blood for the demands of the body, heart failure, is a common condition with high mortality even with modern therapeutic alternatives. To identify molecular determinants of mortality in patients with new-onset heart failure, we performed a meta-analysis of genome-wide association studies and follow-up genotyping in independent populations. We identified and replicated an association for a genetic variant on chromosome 5q22 with 36% increased risk of death in subjects with heart failure (rs9885413, P = 2.7x10-9). We provide evidence from reporter gene assays, computational predictions and epigenomic marks that this polymorphism increases activity of an enhancer region active in multiple human tissues. The polymorphism was further reproducibly associated with a DNA methylation signature in whole blood (P = 4.5x10-40) that also associated with allergic sensitization and expression in blood of the cytokine TSLP (P = 1.1x10-4). Knockdown of the transcription factor predicted to bind the enhancer region (NHLH1) in a human cell line (HEK293) expressing NHLH1 resulted in lower TSLP expression. In addition, we observed evidence of recent positive selection acting on the risk allele in populations of African descent. Our findings provide novel genetic leads to factors that influence mortality in patients with heart failure.

%B PLoS Genet %V 12 %P e1006034 %8 2016 May %G eng %N 5 %1 https://www.ncbi.nlm.nih.gov/pubmed/27149122?dopt=Abstract %R 10.1371/journal.pgen.1006034 %0 Journal Article %J Aging (Albany NY) %D 2016 %T DNA methylation-based measures of biological age: meta-analysis predicting time to death. %A Chen, Brian H %A Marioni, Riccardo E %A Colicino, Elena %A Peters, Marjolein J %A Ward-Caviness, Cavin K %A Tsai, Pei-Chien %A Roetker, Nicholas S %A Just, Allan C %A Demerath, Ellen W %A Guan, Weihua %A Bressler, Jan %A Fornage, Myriam %A Studenski, Stephanie %A Vandiver, Amy R %A Moore, Ann Zenobia %A Tanaka, Toshiko %A Kiel, Douglas P %A Liang, Liming %A Vokonas, Pantel %A Schwartz, Joel %A Lunetta, Kathryn L %A Murabito, Joanne M %A Bandinelli, Stefania %A Hernandez, Dena G %A Melzer, David %A Nalls, Michael %A Pilling, Luke C %A Price, Timothy R %A Singleton, Andrew B %A Gieger, Christian %A Holle, Rolf %A Kretschmer, Anja %A Kronenberg, Florian %A Kunze, Sonja %A Linseisen, Jakob %A Meisinger, Christine %A Rathmann, Wolfgang %A Waldenberger, Melanie %A Visscher, Peter M %A Shah, Sonia %A Wray, Naomi R %A McRae, Allan F %A Franco, Oscar H %A Hofman, Albert %A Uitterlinden, André G %A Absher, Devin %A Assimes, Themistocles %A Levine, Morgan E %A Lu, Ake T %A Tsao, Philip S %A Hou, Lifang %A Manson, JoAnn E %A Carty, Cara L %A LaCroix, Andrea Z %A Reiner, Alexander P %A Spector, Tim D %A Feinberg, Andrew P %A Levy, Daniel %A Baccarelli, Andrea %A van Meurs, Joyce %A Bell, Jordana T %A Peters, Annette %A Deary, Ian J %A Pankow, James S %A Ferrucci, Luigi %A Horvath, Steve %K Aging %K DNA Methylation %K Epigenesis, Genetic %K Female %K Humans %K Logistic Models %K Male %K Mortality %K Racial Groups %K Risk Factors %K Survival Analysis %K T-Lymphocyte Subsets %X

Estimates of biological age based on DNA methylation patterns, often referred to as "epigenetic age", "DNAm age", have been shown to be robust biomarkers of age in humans. We previously demonstrated that independent of chronological age, epigenetic age assessed in blood predicted all-cause mortality in four human cohorts. Here, we expanded our original observation to 13 different cohorts for a total sample size of 13,089 individuals, including three racial/ethnic groups. In addition, we examined whether incorporating information on blood cell composition into the epigenetic age metrics improves their predictive power for mortality. All considered measures of epigenetic age acceleration were predictive of mortality (p≤8.2x10, independent of chronological age, even after adjusting for additional risk factors (p<5.4x10, and within the racial/ethnic groups that we examined (non-Hispanic whites, Hispanics, African Americans). Epigenetic age estimates that incorporated information on blood cell composition led to the smallest p-values for time to death (p=7.5x10). Overall, this study a) strengthens the evidence that epigenetic age predicts all-cause mortality above and beyond chronological age and traditional risk factors, and b) demonstrates that epigenetic age estimates that incorporate information on blood cell counts lead to highly significant associations with all-cause mortality.

%B Aging (Albany NY) %V 8 %P 1844-1865 %8 2016 Sep 28 %G eng %N 9 %1 https://www.ncbi.nlm.nih.gov/pubmed/27690265?dopt=Abstract %R 10.18632/aging.101020 %0 Journal Article %J Nat Commun %D 2016 %T An exome array study of the plasma metabolome. %A Rhee, Eugene P %A Yang, Qiong %A Yu, Bing %A Liu, Xuan %A Cheng, Susan %A Deik, Amy %A Pierce, Kerry A %A Bullock, Kevin %A Ho, Jennifer E %A Levy, Daniel %A Florez, Jose C %A Kathiresan, Sek %A Larson, Martin G %A Vasan, Ramachandran S %A Clish, Clary B %A Wang, Thomas J %A Boerwinkle, Eric %A O'Donnell, Christopher J %A Gerszten, Robert E %K Exome %K Female %K Gene Frequency %K Genome-Wide Association Study %K Humans %K Male %K Metabolome %K Middle Aged %K Plasma %K Polymorphism, Single Nucleotide %K Ribonucleosides %K Xanthines %X

The study of rare variants may enhance our understanding of the genetic determinants of the metabolome. Here, we analyze the association between 217 plasma metabolites and exome variants on the Illumina HumanExome Beadchip in 2,076 participants in the Framingham Heart Study, with replication in 1,528 participants of the Atherosclerosis Risk in Communities Study. We identify an association between GMPS and xanthosine using single variant analysis and associations between HAL and histidine, PAH and phenylalanine, and UPB1 and ureidopropionate using gene-based tests (P<5 × 10(-8) in meta-analysis), highlighting novel coding variants that may underlie inborn errors of metabolism. Further, we show how an examination of variants across the spectrum of allele frequency highlights independent association signals at select loci and generates a more integrated view of metabolite heritability. These studies build on prior metabolomics genome wide association studies to provide a more complete picture of the genetic architecture of the plasma metabolome.

%B Nat Commun %V 7 %P 12360 %8 2016 Jul 25 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/27453504?dopt=Abstract %R 10.1038/ncomms12360 %0 Journal Article %J Circ Cardiovasc Genet %D 2016 %T Rare Exome Sequence Variants in CLCN6 Reduce Blood Pressure Levels and Hypertension Risk. %A Yu, Bing %A Pulit, Sara L %A Hwang, Shih-Jen %A Brody, Jennifer A %A Amin, Najaf %A Auer, Paul L %A Bis, Joshua C %A Boerwinkle, Eric %A Burke, Gregory L %A Chakravarti, Aravinda %A Correa, Adolfo %A Dreisbach, Albert W %A Franco, Oscar H %A Ehret, Georg B %A Franceschini, Nora %A Hofman, Albert %A Lin, Dan-Yu %A Metcalf, Ginger A %A Musani, Solomon K %A Muzny, Donna %A Palmas, Walter %A Raffel, Leslie %A Reiner, Alex %A Rice, Ken %A Rotter, Jerome I %A Veeraraghavan, Narayanan %A Fox, Ervin %A Guo, Xiuqing %A North, Kari E %A Gibbs, Richard A %A van Duijn, Cornelia M %A Psaty, Bruce M %A Levy, Daniel %A Newton-Cheh, Christopher %A Morrison, Alanna C %K Alleles %K Black People %K Blood Pressure %K Chloride Channels %K Exome %K Female %K Gene Frequency %K Humans %K Hypertension %K Male %K Risk Factors %K White People %X

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≤2.9×10(-7)) and gene-based tests of rare variants (minor allele frequency, <1%; ≈17 000 genes; statistical significance, P≤1.5×10(-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=4.1×10(-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=2.8×10(-4)), mean arterial pressure (β=-3.50; P=8.9×10(-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=5.0×10(-7)).

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

%B Circ Cardiovasc Genet %V 9 %P 64-70 %8 2016 Feb %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/26658788?dopt=Abstract %R 10.1161/CIRCGENETICS.115.001215 %0 Journal Article %J PLoS Genet %D 2016 %T Rare Functional Variant in TM2D3 is Associated with Late-Onset Alzheimer's Disease. %A Jakobsdottir, Johanna %A van der Lee, Sven J %A Bis, Joshua C %A Chouraki, Vincent %A Li-Kroeger, David %A Yamamoto, Shinya %A Grove, Megan L %A Naj, Adam %A Vronskaya, Maria %A Salazar, Jose L %A DeStefano, Anita L %A Brody, Jennifer A %A Smith, Albert V %A Amin, Najaf %A Sims, Rebecca %A Ibrahim-Verbaas, Carla A %A Choi, Seung-Hoan %A Satizabal, Claudia L %A Lopez, Oscar L %A Beiser, Alexa %A Ikram, M Arfan %A Garcia, Melissa E %A Hayward, Caroline %A Varga, Tibor V %A Ripatti, Samuli %A Franks, Paul W %A Hallmans, Goran %A Rolandsson, Olov %A Jansson, Jan-Håkon %A Porteous, David J %A Salomaa, Veikko %A Eiriksdottir, Gudny %A Rice, Kenneth M %A Bellen, Hugo J %A Levy, Daniel %A Uitterlinden, André G %A Emilsson, Valur %A Rotter, Jerome I %A Aspelund, Thor %A O'Donnell, Christopher J %A Fitzpatrick, Annette L %A Launer, Lenore J %A Hofman, Albert %A Wang, Li-San %A Williams, Julie %A Schellenberg, Gerard D %A Boerwinkle, Eric %A Psaty, Bruce M %A Seshadri, Sudha %A Shulman, Joshua M %A Gudnason, Vilmundur %A van Duijn, Cornelia M %K Age of Onset %K Aged %K Alleles %K Alzheimer Disease %K Amyloid beta-Protein Precursor %K Animals %K Apolipoproteins E %K Drosophila melanogaster %K Drosophila Proteins %K Exome %K Female %K Genome-Wide Association Study %K Genomics %K Humans %K Iceland %K Intracellular Signaling Peptides and Proteins %K Male %K Membrane Proteins %K Mutation %K Phenotype %K Receptors, Notch %K Tropomyosin %K White People %X

We performed an exome-wide association analysis in 1393 late-onset Alzheimer's disease (LOAD) cases and 8141 controls from the CHARGE consortium. We found that a rare variant (P155L) in TM2D3 was enriched in Icelanders (~0.5% versus <0.05% in other European populations). In 433 LOAD cases and 3903 controls from the Icelandic AGES sub-study, P155L was associated with increased risk and earlier onset of LOAD [odds ratio (95% CI) = 7.5 (3.5-15.9), p = 6.6x10-9]. Mutation in the Drosophila TM2D3 homolog, almondex, causes a phenotype similar to loss of Notch/Presenilin signaling. Human TM2D3 is capable of rescuing these phenotypes, but this activity is abolished by P155L, establishing it as a functionally damaging allele. Our results establish a rare TM2D3 variant in association with LOAD susceptibility, and together with prior work suggests possible links to the β-amyloid cascade.

%B PLoS Genet %V 12 %P e1006327 %8 2016 Oct %G eng %N 10 %1 https://www.ncbi.nlm.nih.gov/pubmed/27764101?dopt=Abstract %R 10.1371/journal.pgen.1006327 %0 Journal Article %J Hum Mol Genet %D 2015 %T Epigenome-wide association study (EWAS) of BMI, BMI change and waist circumference in African American adults identifies multiple replicated loci. %A Demerath, Ellen W %A Guan, Weihua %A Grove, Megan L %A Aslibekyan, Stella %A Mendelson, Michael %A Zhou, Yi-Hui %A Hedman, Åsa K %A Sandling, Johanna K %A Li, Li-An %A Irvin, Marguerite R %A Zhi, Degui %A Deloukas, Panos %A Liang, Liming %A Liu, Chunyu %A Bressler, Jan %A Spector, Tim D %A North, Kari %A Li, Yun %A Absher, Devin M %A Levy, Daniel %A Arnett, Donna K %A Fornage, Myriam %A Pankow, James S %A Boerwinkle, Eric %K Aged %K Atherosclerosis %K Black or African American %K Body Mass Index %K DNA Methylation %K Epigenesis, Genetic %K Female %K Genome-Wide Association Study %K Humans %K Lipid Metabolism %K Male %K Metabolic Networks and Pathways %K Middle Aged %K Obesity %K Waist Circumference %K White People %X

Obesity is an important component of the pathophysiology of chronic diseases. Identifying epigenetic modifications associated with elevated adiposity, including DNA methylation variation, may point to genomic pathways that are dysregulated in numerous conditions. The Illumina 450K Bead Chip array was used to assay DNA methylation in leukocyte DNA obtained from 2097 African American adults in the Atherosclerosis Risk in Communities (ARIC) study. Mixed-effects regression models were used to test the association of methylation beta value with concurrent body mass index (BMI) and waist circumference (WC), and BMI change, adjusting for batch effects and potential confounders. Replication using whole-blood DNA from 2377 White adults in the Framingham Heart Study and CD4+ T cell DNA from 991 Whites in the Genetics of Lipid Lowering Drugs and Diet Network Study was followed by testing using adipose tissue DNA from 648 women in the Multiple Tissue Human Expression Resource cohort. Seventy-six BMI-related probes, 164 WC-related probes and 8 BMI change-related probes passed the threshold for significance in ARIC (P < 1 × 10(-7); Bonferroni), including probes in the recently reported HIF3A, CPT1A and ABCG1 regions. Replication using blood DNA was achieved for 37 BMI probes and 1 additional WC probe. Sixteen of these also replicated in adipose tissue, including 15 novel methylation findings near genes involved in lipid metabolism, immune response/cytokine signaling and other diverse pathways, including LGALS3BP, KDM2B, PBX1 and BBS2, among others. Adiposity traits are associated with DNA methylation at numerous CpG sites that replicate across studies despite variation in tissue type, ethnicity and analytic approaches.

%B Hum Mol Genet %V 24 %P 4464-79 %8 2015 Aug 01 %G eng %N 15 %1 https://www.ncbi.nlm.nih.gov/pubmed/25935004?dopt=Abstract %R 10.1093/hmg/ddv161 %0 Journal Article %J Nature %D 2015 %T PLD3 variants in population studies. %A van der Lee, Sven J %A Holstege, Henne %A Wong, Tsz Hang %A Jakobsdottir, Johanna %A Bis, Joshua C %A Chouraki, Vincent %A van Rooij, Jeroen G J %A Grove, Megan L %A Smith, Albert V %A Amin, Najaf %A Choi, Seung-Hoan %A Beiser, Alexa S %A Garcia, Melissa E %A van IJcken, Wilfred F J %A Pijnenburg, Yolande A L %A Louwersheimer, Eva %A Brouwer, Rutger W W %A van den Hout, Mirjam C G N %A Oole, Edwin %A Eirkisdottir, Gudny %A Levy, Daniel %A Rotter, Jerome I %A Emilsson, Valur %A O'Donnell, Christopher J %A Aspelund, Thor %A Uitterlinden, André G %A Launer, Lenore J %A Hofman, Albert %A Boerwinkle, Eric %A Psaty, Bruce M %A DeStefano, Anita L %A Scheltens, Philip %A Seshadri, Sudha %A van Swieten, John C %A Gudnason, Vilmundur %A van der Flier, Wiesje M %A Ikram, M Arfan %A van Duijn, Cornelia M %K Alzheimer Disease %K Female %K Genetic Predisposition to Disease %K Genetic Variation %K Humans %K Male %K Phospholipase D %B Nature %V 520 %P E2-3 %8 2015 Apr 02 %G eng %N 7545 %1 https://www.ncbi.nlm.nih.gov/pubmed/25832410?dopt=Abstract %R 10.1038/nature14038 %0 Journal Article %J Am J Hum Genet %D 2014 %T Association of low-frequency and rare coding-sequence variants with blood lipids and coronary heart disease in 56,000 whites and blacks. %A Peloso, Gina M %A Auer, Paul L %A Bis, Joshua C %A Voorman, Arend %A Morrison, Alanna C %A Stitziel, Nathan O %A Brody, Jennifer A %A Khetarpal, Sumeet A %A Crosby, Jacy R %A Fornage, Myriam %A Isaacs, Aaron %A Jakobsdottir, Johanna %A Feitosa, Mary F %A Davies, Gail %A Huffman, Jennifer E %A Manichaikul, Ani %A Davis, Brian %A Lohman, Kurt %A Joon, Aron Y %A Smith, Albert V %A Grove, Megan L %A Zanoni, Paolo %A Redon, Valeska %A Demissie, Serkalem %A Lawson, Kim %A Peters, Ulrike %A Carlson, Christopher %A Jackson, Rebecca D %A Ryckman, Kelli K %A Mackey, Rachel H %A Robinson, Jennifer G %A Siscovick, David S %A Schreiner, Pamela J %A Mychaleckyj, Josyf C %A Pankow, James S %A Hofman, Albert %A Uitterlinden, André G %A Harris, Tamara B %A Taylor, Kent D %A Stafford, Jeanette M %A Reynolds, Lindsay M %A Marioni, Riccardo E %A Dehghan, Abbas %A Franco, Oscar H %A Patel, Aniruddh P %A Lu, Yingchang %A Hindy, George %A Gottesman, Omri %A Bottinger, Erwin P %A Melander, Olle %A Orho-Melander, Marju %A Loos, Ruth J F %A Duga, Stefano %A Merlini, Piera Angelica %A Farrall, Martin %A Goel, Anuj %A Asselta, Rosanna %A Girelli, Domenico %A Martinelli, Nicola %A Shah, Svati H %A Kraus, William E %A Li, Mingyao %A Rader, Daniel J %A Reilly, Muredach P %A McPherson, Ruth %A Watkins, Hugh %A Ardissino, Diego %A Zhang, Qunyuan %A Wang, Judy %A Tsai, Michael Y %A Taylor, Herman A %A Correa, Adolfo %A Griswold, Michael E %A Lange, Leslie A %A Starr, John M %A Rudan, Igor %A Eiriksdottir, Gudny %A Launer, Lenore J %A Ordovas, Jose M %A Levy, Daniel %A Chen, Y-D Ida %A Reiner, Alexander P %A Hayward, Caroline %A Polasek, Ozren %A Deary, Ian J %A Borecki, Ingrid B %A Liu, Yongmei %A Gudnason, Vilmundur %A Wilson, James G %A van Duijn, Cornelia M %A Kooperberg, Charles %A Rich, Stephen S %A Psaty, Bruce M %A Rotter, Jerome I %A O'Donnell, Christopher J %A Rice, Kenneth %A Boerwinkle, Eric %A Kathiresan, Sekar %A Cupples, L Adrienne %K 1-Alkyl-2-acetylglycerophosphocholine Esterase %K Adult %K Aged %K Alleles %K Animals %K Black People %K Cholesterol, HDL %K Cholesterol, LDL %K Cohort Studies %K Coronary Disease %K Female %K Gene Frequency %K Genetic Association Studies %K Genetic Code %K Genetic Variation %K Humans %K Linear Models %K Male %K Mice %K Mice, Inbred C57BL %K Microtubule-Associated Proteins %K Middle Aged %K Phenotype %K Sequence Analysis, DNA %K Subtilisins %K Triglycerides %K White People %X

Low-frequency coding DNA sequence variants in the proprotein convertase subtilisin/kexin type 9 gene (PCSK9) lower plasma low-density lipoprotein cholesterol (LDL-C), protect against risk of coronary heart disease (CHD), and have prompted the development of a new class of therapeutics. It is uncertain whether the PCSK9 example represents a paradigm or an isolated exception. We used the "Exome Array" to genotype >200,000 low-frequency and rare coding sequence variants across the genome in 56,538 individuals (42,208 European ancestry [EA] and 14,330 African ancestry [AA]) and tested these variants for association with LDL-C, high-density lipoprotein cholesterol (HDL-C), and triglycerides. Although we did not identify new genes associated with LDL-C, we did identify four low-frequency (frequencies between 0.1% and 2%) variants (ANGPTL8 rs145464906 [c.361C>T; p.Gln121*], PAFAH1B2 rs186808413 [c.482C>T; p.Ser161Leu], COL18A1 rs114139997 [c.331G>A; p.Gly111Arg], and PCSK7 rs142953140 [c.1511G>A; p.Arg504His]) with large effects on HDL-C and/or triglycerides. None of these four variants was associated with risk for CHD, suggesting that examples of low-frequency coding variants with robust effects on both lipids and CHD will be limited.

%B Am J Hum Genet %V 94 %P 223-32 %8 2014 Feb 06 %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/24507774?dopt=Abstract %R 10.1016/j.ajhg.2014.01.009 %0 Journal Article %J PLoS One %D 2013 %T Best practices and joint calling of the HumanExome BeadChip: the CHARGE Consortium. %A Grove, Megan L %A Yu, Bing %A Cochran, Barbara J %A Haritunians, Talin %A Bis, Joshua C %A Taylor, Kent D %A Hansen, Mark %A Borecki, Ingrid B %A Cupples, L Adrienne %A Fornage, Myriam %A Gudnason, Vilmundur %A Harris, Tamara B %A Kathiresan, Sekar %A Kraaij, Robert %A Launer, Lenore J %A Levy, Daniel %A Liu, Yongmei %A Mosley, Thomas %A Peloso, Gina M %A Psaty, Bruce M %A Rich, Stephen S %A Rivadeneira, Fernando %A Siscovick, David S %A Smith, Albert V %A Uitterlinden, Andre %A van Duijn, Cornelia M %A Wilson, James G %A O'Donnell, Christopher J %A Rotter, Jerome I %A Boerwinkle, Eric %K Aging %K Alleles %K Cluster Analysis %K Cohort Studies %K Exome %K Female %K Gene Frequency %K Genomics %K Genotype %K Heart %K Humans %K Male %K Oligonucleotide Array Sequence Analysis %K Polymorphism, Single Nucleotide %K Racial Groups %K Sample Size %K Self Report %K Sequence Analysis, DNA %X

Genotyping arrays are a cost effective approach when typing previously-identified genetic polymorphisms in large numbers of samples. One limitation of genotyping arrays with rare variants (e.g., minor allele frequency [MAF] <0.01) is the difficulty that automated clustering algorithms have to accurately detect and assign genotype calls. Combining intensity data from large numbers of samples may increase the ability to accurately call the genotypes of rare variants. Approximately 62,000 ethnically diverse samples from eleven Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium cohorts were genotyped with the Illumina HumanExome BeadChip across seven genotyping centers. The raw data files for the samples were assembled into a single project for joint calling. To assess the quality of the joint calling, concordance of genotypes in a subset of individuals having both exome chip and exome sequence data was analyzed. After exclusion of low performing SNPs on the exome chip and non-overlap of SNPs derived from sequence data, genotypes of 185,119 variants (11,356 were monomorphic) were compared in 530 individuals that had whole exome sequence data. A total of 98,113,070 pairs of genotypes were tested and 99.77% were concordant, 0.14% had missing data, and 0.09% were discordant. We report that joint calling allows the ability to accurately genotype rare variation using array technology when large sample sizes are available and best practices are followed. The cluster file from this experiment is available at www.chargeconsortium.com/main/exomechip.

%B PLoS One %V 8 %P e68095 %8 2013 %G eng %N 7 %1 https://www.ncbi.nlm.nih.gov/pubmed/23874508?dopt=Abstract %R 10.1371/journal.pone.0068095 %0 Journal Article %J Circ Cardiovasc Genet %D 2010 %T Genomic variation associated with mortality among adults of European and African ancestry with heart failure: the cohorts for heart and aging research in genomic epidemiology consortium. %A Morrison, Alanna C %A Felix, Janine F %A Cupples, L Adrienne %A Glazer, Nicole L %A Loehr, Laura R %A Dehghan, Abbas %A Demissie, Serkalem %A Bis, Joshua C %A Rosamond, Wayne D %A Aulchenko, Yurii S %A Wang, Ying A %A Haritunians, Talin %A Folsom, Aaron R %A Rivadeneira, Fernando %A Benjamin, Emelia J %A Lumley, Thomas %A Couper, David %A Stricker, Bruno H %A O'Donnell, Christopher J %A Rice, Kenneth M %A Chang, Patricia P %A Hofman, Albert %A Levy, Daniel %A Rotter, Jerome I %A Fox, Ervin R %A Uitterlinden, André G %A Wang, Thomas J %A Psaty, Bruce M %A Willerson, James T %A van Duijn, Cornelia M %A Boerwinkle, Eric %A Witteman, Jacqueline C M %A Vasan, Ramachandran S %A Smith, Nicholas L %K Aged %K Aged, 80 and over %K Black or African American %K Chemokines %K Cohort Studies %K Female %K Genome-Wide Association Study %K Genotype %K Heart Failure %K Humans %K Introns %K Male %K MARVEL Domain-Containing Proteins %K Membrane Proteins %K Middle Aged %K Polymorphism, Single Nucleotide %K Risk Factors %K White People %X

BACKGROUND: Prognosis and survival are significant concerns for individuals with heart failure (HF). To better understand the pathophysiology of HF prognosis, the association between 2,366,858 single-nucleotide polymorphisms (SNPs) and all-cause mortality was evaluated among individuals with incident HF from 4 community-based prospective cohorts: the Atherosclerosis Risk in Communities Study, the Cardiovascular Health Study, the Framingham Heart Study, and the Rotterdam Study.

METHODS AND RESULTS: Participants were 2526 individuals of European ancestry and 466 individuals of African ancestry who experienced an incident HF event during follow-up in the respective cohorts. Within each study, the association between genetic variants and time to mortality among individuals with HF was assessed by Cox proportional hazards models that included adjustment for sex and age at the time of the HF event. Prospective fixed-effect meta-analyses were conducted for the 4 study populations of European ancestry (N=1645 deaths) and for the 2 populations of African ancestry (N=281 deaths). Genome-wide significance was set at P=5.0x10(-7). Meta-analytic findings among individuals of European ancestry revealed 1 genome-wide significant locus on chromosome 3p22 in an intron of CKLF-like MARVEL transmembrane domain containing 7 (CMTM7, P=3.2x10(-7)). Eight additional loci in individuals of European ancestry and 4 loci in individuals of African ancestry were identified by high-signal SNPs (P<1.0x10(-5)) but did not meet genome-wide significance.

CONCLUSIONS: This study identified a novel locus associated with all-cause mortality among individuals of European ancestry with HF. This finding warrants additional investigation, including replication, in other studies of HF.

%B Circ Cardiovasc Genet %V 3 %P 248-55 %8 2010 Jun %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/20400778?dopt=Abstract %R 10.1161/CIRCGENETICS.109.895995