@article {1204, title = {Common genetic determinants of vitamin D insufficiency: a genome-wide association study.}, journal = {Lancet}, volume = {376}, year = {2010}, month = {2010 Jul 17}, pages = {180-8}, abstract = {

BACKGROUND: Vitamin D is crucial for maintenance of musculoskeletal health, and might also have a role in extraskeletal tissues. Determinants of circulating 25-hydroxyvitamin D concentrations include sun exposure and diet, but high heritability suggests that genetic factors could also play a part. We aimed to identify common genetic variants affecting vitamin D concentrations and risk of insufficiency.

METHODS: We undertook a genome-wide association study of 25-hydroxyvitamin D concentrations in 33 996 individuals of European descent from 15 cohorts. Five epidemiological cohorts were designated as discovery cohorts (n=16 125), five as in-silico replication cohorts (n=9367), and five as de-novo replication cohorts (n=8504). 25-hydroxyvitamin D concentrations were measured by radioimmunoassay, chemiluminescent assay, ELISA, or mass spectrometry. Vitamin D insufficiency was defined as concentrations lower than 75 nmol/L or 50 nmol/L. We combined results of genome-wide analyses across cohorts using Z-score-weighted meta-analysis. Genotype scores were constructed for confirmed variants.

FINDINGS: Variants at three loci reached genome-wide significance in discovery cohorts for association with 25-hydroxyvitamin D concentrations, and were confirmed in replication cohorts: 4p12 (overall p=1.9x10(-109) for rs2282679, in GC); 11q12 (p=2.1x10(-27) for rs12785878, near DHCR7); and 11p15 (p=3.3x10(-20) for rs10741657, near CYP2R1). Variants at an additional locus (20q13, CYP24A1) were genome-wide significant in the pooled sample (p=6.0x10(-10) for rs6013897). Participants with a genotype score (combining the three confirmed variants) in the highest quartile were at increased risk of having 25-hydroxyvitamin D concentrations lower than 75 nmol/L (OR 2.47, 95\% CI 2.20-2.78, p=2.3x10(-48)) or lower than 50 nmol/L (1.92, 1.70-2.16, p=1.0x10(-26)) compared with those in the lowest quartile.

INTERPRETATION: Variants near genes involved in cholesterol synthesis, hydroxylation, and vitamin D transport affect vitamin D status. Genetic variation at these loci identifies individuals who have substantially raised risk of vitamin D insufficiency.

FUNDING: Full funding sources listed at end of paper (see Acknowledgments).

}, keywords = {Canada, Chromosomes, Human, Pair 11, Chromosomes, Human, Pair 4, Cohort Studies, Dietary Supplements, Europe, European Continental Ancestry Group, Genetic Predisposition to Disease, Genome-Wide Association Study, Heterozygote, Homozygote, Humans, Immunoassay, International Cooperation, Linkage Disequilibrium, Polymorphism, Single Nucleotide, Seasons, United States, Vitamin D, Vitamin D Deficiency}, issn = {1474-547X}, doi = {10.1016/S0140-6736(10)60588-0}, author = {Wang, Thomas J and Zhang, Feng and Richards, J Brent and Kestenbaum, Bryan and van Meurs, Joyce B and Berry, Diane and Kiel, Douglas P and Streeten, Elizabeth A and Ohlsson, Claes and Koller, Daniel L and Peltonen, Leena and Cooper, Jason D and O{\textquoteright}Reilly, Paul F and Houston, Denise K and Glazer, Nicole L and Vandenput, Liesbeth and Peacock, Munro and Shi, Julia and Rivadeneira, Fernando and McCarthy, Mark I and Anneli, Pouta and de Boer, Ian H and Mangino, Massimo and Kato, Bernet and Smyth, Deborah J and Booth, Sarah L and Jacques, Paul F and Burke, Greg L and Goodarzi, Mark and Cheung, Ching-Lung and Wolf, Myles and Rice, Kenneth and Goltzman, David and Hidiroglou, Nick and Ladouceur, Martin and Wareham, Nicholas J and Hocking, Lynne J and Hart, Deborah and Arden, Nigel K and Cooper, Cyrus and Malik, Suneil and Fraser, William D and Hartikainen, Anna-Liisa and Zhai, Guangju and Macdonald, Helen M and Forouhi, Nita G and Loos, Ruth J F and Reid, David M and Hakim, Alan and Dennison, Elaine and Liu, Yongmei and Power, Chris and Stevens, Helen E and Jaana, Laitinen and Vasan, Ramachandran S and Soranzo, Nicole and Bojunga, J{\"o}rg and Psaty, Bruce M and Lorentzon, Mattias and Foroud, Tatiana and Harris, Tamara B and Hofman, Albert and Jansson, John-Olov and Cauley, Jane A and Uitterlinden, Andr{\'e} G and Gibson, Quince and Jarvelin, Marjo-Riitta and Karasik, David and Siscovick, David S and Econs, Michael J and Kritchevsky, Stephen B and Florez, Jose C and Todd, John A and Dupuis, Jos{\'e}e and Hypp{\"o}nen, Elina and Spector, Timothy D} } @article {7144, title = {Discovery of Genetic Variation on Chromosome 5q22 Associated with Mortality in Heart Failure.}, journal = {PLoS Genet}, volume = {12}, year = {2016}, month = {2016 May}, pages = {e1006034}, abstract = {

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.

}, issn = {1553-7404}, doi = {10.1371/journal.pgen.1006034}, author = {Smith, J Gustav and Felix, Janine F and Morrison, Alanna C and Kalogeropoulos, Andreas and Trompet, Stella and Wilk, Jemma B and Gidl{\"o}f, Olof and Wang, Xinchen and Morley, Michael and Mendelson, Michael and Joehanes, Roby and Ligthart, Symen and Shan, Xiaoyin and Bis, Joshua C and Wang, Ying A and Sj{\"o}gren, Marketa and Ngwa, Julius and Brandimarto, Jeffrey and Stott, David J and Aguilar, David and Rice, Kenneth M and Sesso, Howard D and Demissie, Serkalem and Buckley, Brendan M and Taylor, Kent D and Ford, Ian and Yao, Chen and Liu, Chunyu and Sotoodehnia, Nona and van der Harst, Pim and Stricker, Bruno H Ch and Kritchevsky, Stephen B and Liu, Yongmei and Gaziano, J Michael and Hofman, Albert and Moravec, Christine S and Uitterlinden, Andr{\'e} G and Kellis, Manolis and van Meurs, Joyce B and Margulies, Kenneth B and Dehghan, Abbas and Levy, Daniel and Olde, Bj{\"o}rn and Psaty, Bruce M and Cupples, L Adrienne and Jukema, J Wouter and Djouss{\'e}, Luc and Franco, Oscar H and Boerwinkle, Eric and Boyer, Laurie A and Newton-Cheh, Christopher and Butler, Javed and Vasan, Ramachandran S and Cappola, Thomas P and Smith, Nicholas L} } @article {7583, title = {DNA Methylation Analysis Identifies Loci for Blood Pressure Regulation.}, journal = {Am J Hum Genet}, volume = {101}, year = {2017}, month = {2017 Dec 07}, pages = {888-902}, abstract = {

Genome-wide association studies have identified hundreds of genetic variants associated with blood pressure (BP), but sequence variation accounts for a small fraction of the phenotypic variance. Epigenetic changes may alter the expression of genes involved in BP regulation and explain part of the missing heritability. We therefore conducted a two-stage meta-analysis of the cross-sectional associations of systolic and diastolic BP with blood-derived genome-wide DNA methylation measured on the Infinium HumanMethylation450 BeadChip in 17,010 individuals of European, African American, and Hispanic ancestry. Of 31 discovery-stage cytosine-phosphate-guanine (CpG) dinucleotides, 13 replicated after Bonferroni correction (discovery: N = 9,828, p < 1.0~{\texttimes} 10-7; replication: N = 7,182, p~<~1.6~{\texttimes} 10-3). The replicated methylation sites are heritable (h2 > 30\%) and independent of known BP genetic variants, explaining an additional 1.4\% and 2.0\% of the interindividual variation in systolic and diastolic BP, respectively. Bidirectional Mendelian randomization among up to 4,513 individuals of European ancestry from 4 cohorts suggested that methylation at cg08035323 (TAF1B-YWHAQ) influences BP, while BP influences methylation at cg00533891 (ZMIZ1), cg00574958 (CPT1A), and cg02711608 (SLC1A5). Gene expression analyses further identified six genes (TSPAN2, SLC7A11, UNC93B1, CPT1A, PTMS, and LPCAT3) with evidence of triangular associations between methylation, gene expression, and BP. Additional integrative Mendelian randomization analyses of gene expression and DNA methylation suggested that the expression of TSPAN2 is a putative mediator of association between DNA methylation at cg23999170 and BP. These findings suggest that heritable DNA methylation plays a role in regulating BP independently of previously known genetic variants.

}, keywords = {Aged, Blood Pressure, CpG Islands, Cross-Sectional Studies, DNA Methylation, Epigenesis, Genetic, Genetic Variation, Genome-Wide Association Study, Humans, Mendelian Randomization Analysis, Middle Aged, Nerve Tissue Proteins, Quantitative Trait Loci, Tetraspanins}, issn = {1537-6605}, doi = {10.1016/j.ajhg.2017.09.028}, author = {Richard, Melissa A and Huan, Tianxiao and Ligthart, Symen and Gondalia, Rahul and Jhun, Min A and Brody, Jennifer A and Irvin, Marguerite R and Marioni, Riccardo and Shen, Jincheng and Tsai, Pei-Chien and Montasser, May E and Jia, Yucheng and Syme, Catriona and Salfati, Elias L and Boerwinkle, Eric and Guan, Weihua and Mosley, Thomas H and Bressler, Jan and Morrison, Alanna C and Liu, Chunyu and Mendelson, Michael M and Uitterlinden, Andr{\'e} G and van Meurs, Joyce B and Franco, Oscar H and Zhang, Guosheng and Li, Yun and Stewart, James D and Bis, Joshua C and Psaty, Bruce M and Chen, Yii-Der Ida and Kardia, Sharon L R and Zhao, Wei and Turner, Stephen T and Absher, Devin and Aslibekyan, Stella and Starr, John M and McRae, Allan F and Hou, Lifang and Just, Allan C and Schwartz, Joel D and Vokonas, Pantel S and Menni, Cristina and Spector, Tim D and Shuldiner, Alan and Damcott, Coleen M and Rotter, Jerome I and Palmas, Walter and Liu, Yongmei and Paus, Tom{\'a}{\v s} and Horvath, Steve and O{\textquoteright}Connell, Jeffrey R and Guo, Xiuqing and Pausova, Zdenka and Assimes, Themistocles L and Sotoodehnia, Nona and Smith, Jennifer A and Arnett, Donna K and Deary, Ian J and Baccarelli, Andrea A and Bell, Jordana T and Whitsel, Eric and Dehghan, Abbas and Levy, Daniel and Fornage, Myriam} }