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Science translational medicine 05/2013; 5(183):183fs15. · 7.80 Impact Factor
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ABSTRACT: OBJECTIVE: Genome-wide association studies have identified several genetic variants associated with coronary heart disease (CHD). The aim of this study was to evaluate the genetic risk discrimination and reclassification and apply the results for a 2-stage population risk screening strategy for CHD.Approach and Results-We genotyped 28 genetic variants in 24 124 participants in 4 Finnish population-based, prospective cohorts (recruitment years 1992-2002). We constructed a multilocus genetic risk score and evaluated its association with incident cardiovascular disease events. During the median follow-up time of 12 years (interquartile range 8.75-15.25 years), we observed 1093 CHD, 1552 cardiovascular disease, and 731 acute coronary syndrome events. Adding genetic information to conventional risk factors and family history improved risk discrimination of CHD (C-index 0.856 versus 0.851; P=0.0002) and other end points (cardiovascular disease: C-index 0.840 versus 0.837, P=0.0004; acute coronary syndrome: C-index 0.859 versus 0.855, P=0.001). In a standard population of 100 000 individuals, additional genetic screening of subjects at intermediate risk for CHD would reclassify 2144 subjects (12%) into high-risk category. Statin allocation for these subjects is estimated to prevent 135 CHD cases over 14 years. Similar results were obtained by external validation, where the effects were estimated from a training data set and applied for a test data set. CONCLUSIONS: Genetic risk score improves risk prediction of CHD and helps to identify individuals at high risk for the first CHD event. Genetic screening for individuals at intermediate cardiovascular risk could help to prevent future cases through better targeting of statins.
Arteriosclerosis Thrombosis and Vascular Biology 04/2013; · 6.37 Impact Factor
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Sonja I Berndt,
Stefan Gustafsson,
Reedik Mägi,
Andrea Ganna,
Eleanor Wheeler,
Mary F Feitosa,
Anne E Justice,
Keri L Monda,
Damien C Croteau-Chonka,
Felix R Day, [......],
Joel N Hirschhorn,
Cecilia M Lindgren,
Andrew P Morris,
David Meyre,
André Scherag,
Mark I McCarthy,
Elizabeth K Speliotes,
Kari E North,
Ruth J F Loos,
Erik Ingelsson
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ABSTRACT: Approaches exploiting trait distribution extremes may be used to identify loci associated with common traits, but it is unknown whether these loci are generalizable to the broader population. In a genome-wide search for loci associated with the upper versus the lower 5th percentiles of body mass index, height and waist-to-hip ratio, as well as clinical classes of obesity, including up to 263,407 individuals of European ancestry, we identified 4 new loci (IGFBP4, H6PD, RSRC1 and PPP2R2A) influencing height detected in the distribution tails and 7 new loci (HNF4G, RPTOR, GNAT2, MRPS33P4, ADCY9, HS6ST3 and ZZZ3) for clinical classes of obesity. Further, we find a large overlap in genetic structure and the distribution of variants between traits based on extremes and the general population and little etiological heterogeneity between obesity subgroups.
Nature Genetics 04/2013; · 35.53 Impact Factor
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Sonja I Berndt,
Stefan Gustafsson,
Reedik Magi,
Andrea Ganna,
Eleanor Wheeler,
Mary F Feitosa,
Anne E Justice,
Keri L Monda,
Damien C Croteau-Chonka,
Felix R Day, [......],
Joel N Hirschhorn,
Cecilia M Lindgren,
Andrew P Morris,
David Meyre,
Andre Scherag,
Mark I McCarthy,
Elizabeth K Speliotes,
Kari E North,
Ruth J F Loos,
Erik Ingelsson
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ABSTRACT: Approaches exploiting trait distribution extremes may be used to identify loci associated with common traits, but it is unknown whether these loci are generalizable to the broader population. In a genome-wide search for loci associated with the upper versus the lower 5th percentiles of body mass index, height and waist-to-hip ratio, as well as clinical classes of obesity, including up to 263,407 individuals of European ancestry, we identified 4 new loci (IGFBP4, H6PD, RSRC1 and PPP2R2A) influencing height detected in the distribution tails and 7 new loci (HNF4G, RPTOR, GNAT2, MRPS33P4, ADCY9, HS6ST3 and ZZZ3) for clinical classes of obesity. Further, we find a large overlap in genetic structure and the distribution of variants between traits based on extremes and the general population and little etiological heterogeneity between obesity subgroups.
Nature Genetics 04/2013; · 35.53 Impact Factor
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Veryan Codd,
Christopher P Nelson,
Eva Albrecht,
Massimo Mangino,
Joris Deelen,
Jessica L Buxton,
Jouke Jan Hottenga,
Krista Fischer,
Tõnu Esko,
Ida Surakka, [......],
Iiris Hovatta,
Christian Gieger,
Andres Metspalu,
Dorret I Boomsma,
Marjo-Riitta Jarvelin,
P Eline Slagboom,
John R Thompson,
Tim D Spector,
Pim van der Harst,
Nilesh J Samani
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ABSTRACT: Interindividual variation in mean leukocyte telomere length (LTL) is associated with cancer and several age-associated diseases. We report here a genome-wide meta-analysis of 37,684 individuals with replication of selected variants in an additional 10,739 individuals. We identified seven loci, including five new loci, associated with mean LTL (P < 5 × 10(-8)). Five of the loci contain candidate genes (TERC, TERT, NAF1, OBFC1 and RTEL1) that are known to be involved in telomere biology. Lead SNPs at two loci (TERC and TERT) associate with several cancers and other diseases, including idiopathic pulmonary fibrosis. Moreover, a genetic risk score analysis combining lead variants at all 7 loci in 22,233 coronary artery disease cases and 64,762 controls showed an association of the alleles associated with shorter LTL with increased risk of coronary artery disease (21% (95% confidence interval, 5-35%) per standard deviation in LTL, P = 0.014). Our findings support a causal role of telomere-length variation in some age-related diseases.
Nature Genetics 03/2013; 45(4):422-427. · 35.53 Impact Factor
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Diana L Cousminer,
Diane J Berry,
Nicholas J Timpson,
Wei Ang,
Elisabeth Thiering,
Enda Byrne,
H Rob Taal,
Ville Huikari,
Jonathan P Bradfield,
Marjan Kerkhof, [......],
Joachim Heinrich,
Craig E Pennell,
Olli Raitakari,
Johan G Eriksson,
George Davey Smith,
Elina Hyppönen,
Marjo-Riitta Järvelin,
Mark I McCarthy,
Samuli Ripatti,
Elisabeth Widén
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ABSTRACT: The pubertal height growth spurt is a distinctive feature of childhood growth reflecting both the central onset of puberty and local growth factors. While little is known about the underlying genetics, growth variability during puberty correlates with adult risks for hormone-dependent cancer and adverse cardiometabolic health. The only gene so far associated with pubertal height growth, LIN28B, pleiotropically influences childhood growth, puberty, and cancer progression, pointing to shared underlying mechanisms.To discover genetic loci influencing pubertal height and growth and place them in context of overall growth and maturation, we performed genome-wide association (GWA) meta-analyses in up to 18,737 European samples utilizing longitudinally collected height measurements. We found significant associations (P<1.67 x 10-8) at 10 loci, including LIN28B. Five loci associated with pubertal timing, all impacting multiple aspects of growth. In particular, a novel variant correlated with expression of MAPK3, and associated both with increased prepubertal growth and earlier menarche. Another variant near ADCY3-POMC associated with increased BMI, reduced pubertal growth, and earlier puberty.While epidemiological correlations suggest that early puberty marks a pathway from rapid prepubertal growth to reduced final height and adult obesity, our study shows that individual loci associating with pubertal growth have variable longitudinal growth patterns that may differ from epidemiological observations. Overall this study uncovers part of the complex genetic architecture linking pubertal height growth, the timing of puberty, and childhood obesity, and provides new information to pinpoint processes linking these traits.
Human Molecular Genetics 02/2013; · 7.64 Impact Factor
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Pirkka-Pekka Laurila,
Ida Surakka,
Antti-Pekka Sarin,
Laxman Yetukuri,
Tuulia Hyötyläinen,
Sanni Söderlund,
Jussi Naukkarinen,
Jing Tang,
Johannes Kettunen,
Daniel B Mirel, [......],
Veikko Salomaa,
Antti Jula,
Olli T Raitakari,
Marjo-Riitta Järvelin, Aarno Palotie,
Leena Peltonen,
Matej Oresic,
Matti Jauhiainen,
Marja-Riitta Taskinen,
Samuli Ripatti
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ABSTRACT: OBJECTIVE: Low high-density lipoprotein cholesterol (HDL-C) is associated with cardiometabolic pathologies. In this study, we investigate the biological pathways and individual genes behind low HDL-C by integrating results from 3 high-throughput data sources: adipose tissue transcriptomics, HDL lipidomics, and dense marker genotypes from Finnish individuals with low or high HDL-C (n=450).Approach and Results-In the pathway analysis of genetic data, we demonstrate that genetic variants within inflammatory pathways were enriched among low HDL-C associated single-nucleotide polymorphisms, and the expression of these pathways upregulated in the adipose tissue of low HDL-C subjects. The lipidomic analysis highlighted the change in HDL particle quality toward putatively more inflammatory and less vasoprotective state in subjects with low HDL-C, as evidenced by their decreased antioxidative plasmalogen contents. We show that the focal point of these inflammatory pathways seems to be the human leukocyte antigen region with its low HDL-associated alleles also associating with more abundant local transcript levels in adipose tissue, increased plasma vascular cell adhesion molecule 1 levels, and decreased HDL particle plasmalogen contents, markers of adipose tissue inflammation, vascular inflammation, and HDL antioxidative potential, respectively. In a population-based look-up of the inflammatory pathway single-nucleotide polymorphisms in a large Finnish cohorts (n=11 211), no association of the human leukocyte antigen region was detected for HDL-C as quantitative trait, but with extreme HDL-C phenotypes, implying the presence of low or high HDL genes in addition to the population-genomewide association studies-identified HDL genes. CONCLUSIONS: Our study highlights the role of inflammation with a genetic component in subjects with low HDL-C and identifies novel cis-expression quantitative trait loci variants in human leukocyte antigen region to be associated with low HDL-C.
Arteriosclerosis Thrombosis and Vascular Biology 02/2013; · 6.37 Impact Factor
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Eleonora Porcu,
Marco Medici,
Giorgio Pistis,
Claudia B Volpato,
Scott G Wilson,
Anne R Cappola,
Steffan D Bos,
Joris Deelen,
Martin den Heijer,
Rachel M Freathy, [......],
Theo J Visser,
Bruce H R Wolffenbuttel,
Ingrid Meulenbelt,
Jerome I Rotter,
Tim D Spector,
Andrew A Hicks,
Daniela Toniolo,
Serena Sanna,
Robin P Peeters,
Silvia Naitza
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ABSTRACT: Thyroid hormone is essential for normal metabolism and development, and overt abnormalities in thyroid function lead to common endocrine disorders affecting approximately 10% of individuals over their life span. In addition, even mild alterations in thyroid function are associated with weight changes, atrial fibrillation, osteoporosis, and psychiatric disorders. To identify novel variants underlying thyroid function, we performed a large meta-analysis of genome-wide association studies for serum levels of the highly heritable thyroid function markers TSH and FT4, in up to 26,420 and 17,520 euthyroid subjects, respectively. Here we report 26 independent associations, including several novel loci for TSH (PDE10A, VEGFA, IGFBP5, NFIA, SOX9, PRDM11, FGF7, INSR, ABO, MIR1179, NRG1, MBIP, ITPK1, SASH1, GLIS3) and FT4 (LHX3, FOXE1, AADAT, NETO1/FBXO15, LPCAT2/CAPNS2). Notably, only limited overlap was detected between TSH and FT4 associated signals, in spite of the feedback regulation of their circulating levels by the hypothalamic-pituitary-thyroid axis. Five of the reported loci (PDE8B, PDE10A, MAF/LOC440389, NETO1/FBXO15, and LPCAT2/CAPNS2) show strong gender-specific differences, which offer clues for the known sexual dimorphism in thyroid function and related pathologies. Importantly, the TSH-associated loci contribute not only to variation within the normal range, but also to TSH values outside the reference range, suggesting that they may be involved in thyroid dysfunction. Overall, our findings explain, respectively, 5.64% and 2.30% of total TSH and FT4 trait variance, and they improve the current knowledge of the regulation of hypothalamic-pituitary-thyroid axis function and the consequences of genetic variation for hypo- or hyperthyroidism.
PLoS Genetics 02/2013; 9(2):e1003266. · 8.69 Impact Factor
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Karin Hek,
Ayse Demirkan,
Jari Lahti,
Antonio Terracciano,
Alexander Teumer,
Marilyn C Cornelis,
Najaf Amin,
Erin Bakshis,
Jens Baumert,
Jingzhong Ding, [......],
Katri Räikkönen,
Toshiko Tanaka,
Cornelia M van Duijn,
Hans J Grabe,
Lenore J Launer,
Kathryn L Lunetta,
Thomas H Mosley,
Anne B Newman,
Henning Tiemeier,
Joanne Murabito
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ABSTRACT: BACKGROUND: Depression is a heritable trait that exists on a continuum of varying severity and duration. Yet, the search for genetic variants associated with depression has had few successes. We exploit the entire continuum of depression to find common variants for depressive symptoms. METHODS: In this genome-wide association study, we combined the results of 17 population-based studies assessing depressive symptoms with the Center for Epidemiological Studies Depression Scale. Replication of the independent top hits (p<1×10(-5)) was performed in five studies assessing depressive symptoms with other instruments. In addition, we performed a combined meta-analysis of all 22 discovery and replication studies. RESULTS: The discovery sample comprised 34,549 individuals (mean age of 66.5) and no loci reached genome-wide significance (lowest p = 1.05×10(-7)). Seven independent single nucleotide polymorphisms were considered for replication. In the replication set (n = 16,709), we found suggestive association of one single nucleotide polymorphism with depressive symptoms (rs161645, 5q21, p = 9.19×10(-3)). This 5q21 region reached genome-wide significance (p = 4.78×10(-8)) in the overall meta-analysis combining discovery and replication studies (n = 51,258). CONCLUSIONS: The results suggest that only a large sample comprising more than 50,000 subjects may be sufficiently powered to detect genes for depressive symptoms.
Biological psychiatry 01/2013; · 8.93 Impact Factor
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Frances M K Williams,
Angela M Carter,
Pirro G Hysi,
Gabriela Surdulescu,
Dylan Hodgkiss,
Nicole Soranzo,
Matthew Traylor,
Steve Bevan,
Martin Dichgans,
Peter M W Rothwell, [......],
Karen L Furie,
Jonathan Rosand,
Mike Nalls,
James Meschia,
Thomas H Mosely,
Alun Evans, Aarno Palotie,
Hugh S Markus,
Peter J Grant,
Tim D Spector
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ABSTRACT: Objective: End-stage coagulation and the structure/function of fibrin are implicated in the pathogenesis of ischemic stroke. We explored whether genetic variants associated with end-stage coagulation in healthy REFVIDunteers account for the genetic predisposition to ischemic stroke and examined their influence on stroke subtype. Methods: Common genetic variants identified through genome-wide association studies of coagulation factors and fibrin structure/function in healthy twins (n = 2,100, Stage 1) were examined in ischemic stroke (n = 4,200 cases) using 2 independent samples of European ancestry (Stage 2). A third clinical collection having stroke subtyping (total 8,900 cases, 55,000 controls) was used for replication (Stage 3). Results: Stage 1 identified 524 single nucleotide polymorphisms (SNPs) from 23 linkage disequilibrium blocks having significant association (p < 5 × 10(-8) ) with 1 or more coagulation/fibrin phenotypes. The most striking associations included SNP rs5985 with factor XIII activity (p = 2.6 × 10(-186) ), rs10665 with FVII (p = 2.4 × 10(-47) ), and rs505922 in the ABO gene with both von Willebrand factor (p = 4.7 × 10(-57) ) and factor VIII (p = 1.2 × 10(-36) ). In Stage 2, the 23 independent SNPs were examined in stroke cases/noncases using MOnica Risk, Genetics, Archiving and Monograph (MORGAM) and Wellcome Trust Case Control Consortium 2 collections. SNP rs505922 was nominally associated with ischemic stroke (odds ratio = 0.94, 95% confidence interval = 0.88-0.99, p = 0.023). Independent replication in Meta-Stroke confirmed the rs505922 association with stroke, beta (standard error, SE) = 0.066 (0.02), p = 0.001, a finding specific to large-vessel and cardioembolic stroke (p = 0.001 and p = < 0.001, respectively) but not seen with small-vessel stroke (p = 0.811). Interpretation: ABO gene variants are associated with large-vessel and cardioembolic stroke but not small-vessel disease. This work sheds light on the different pathogenic mechanisms underpinning stroke subtype. Ann Neurol 2013.
Annals of Neurology 01/2013; 73(1):16-31. · 11.09 Impact Factor
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ABSTRACT: During the past ten years the field of human disease genetics has made major leaps, including the completion of the Human Genome Project, the HapMap Project, the development of the genome-wide association (GWA) studies to identify common disease-predisposing variants, and the introduction of large- scale whole-genome and whole-exome sequencing studies. The introduction of new technologies has enabled researchers to utilize novel study designs to tackle previously unexplored research questions in human genomics. These new types of studies typically need large sample sizes to overcome the multiple testing challenges caused by the huge number of interrogated genetic variants. As a consequence, large consortia-studies are at present the default in disease genetics research. The systematic planning of the GWA-studies was a key element in the success of the approach. Similar planning and rigor in statistical inferences will likely be beneficial also to future sequencing studies. Already today, the next-generation exome sequencing has lead to the identification of a number of genes underlying Mendelian diseases. In spite of the clear benefits, the method has proven more challenging than anticipated. In the case of complex diseases, next-generation sequencing aims to identify disease-associated low-frequency alleles. However, their robust detection will require very large study samples, even larger than in the case of the GWA-studies. This has stimulated study designs that capitalize on enriching sets of low-frequency alleles, e.g studies focusing on population isolates such as Finland or Iceland. One example is the collaborative SISu Project (Sequencing Initiative Suomi) that aims to provide near complete genome variation information from Finnish study samples and pave the way for large, nationwide genome health initiative studies.
New Biotechnology 11/2012; · 2.76 Impact Factor
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Ida Surakka,
John B Whitfield,
Markus Perola,
Peter M Visscher,
Grant W Montgomery,
Mario Falchi,
Gonneke Willemsen,
Eco J C de Geus,
Patrik K E Magnusson,
Kaare Christensen, [......],
Ann-Christine Syvänen, Aarno Palotie,
Jaakko Kaprio,
Kirsten O Kyvik,
Nancy L Pedersen,
Dorret I Boomsma,
Tim Spector,
Nicholas G Martin,
Samuli Ripatti,
Leena Peltonen
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ABSTRACT: Genome-wide association analysis on monozygotic twin-pairs offers a route to discovery of gene-environment interactions through testing for variability loci associated with sensitivity to individual environment/lifestyle. We present a genome-wide scan of loci associated with intra-pair differences in serum lipid and apolipoprotein levels. We report data for 1,720 monozygotic female twin-pairs from GenomEUtwin project with 2.5 million SNPs, imputed or genotyped, and measured serum lipid fractions for both twins. We found one locus associated with intra-pair differences in high-density lipoprotein cholesterol, rs2483058 in an intron of SRGAP2, where twins carrying the C allele are more sensitive to environmental factors (P = 3.98 × 10-8). We followed up the association in further genotyped monozygotic twins (N = 1,261), which showed a moderate association for the variant (P = 0.200, same direction of an effect). In addition, we report a new association on the level of apolipoprotein A-II (P = 4.03 × 10-8).
Twin Research and Human Genetics 10/2012; · 1.70 Impact Factor
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ABSTRACT: Balanced chromosomal rearrangements occasionally have strong phenotypic effects, which may be useful in understanding pathobiology. However, conventional strategies for characterising breakpoints are laborious and inaccurate. We present here a proband with a thoracic aortic aneurysm (TAA) and a balanced translocation t(10;11) (q23.2;q24.2). Our purpose was to sequence the chromosomal breaks in this family to reveal a novel candidate gene for aneurysm.
Intracranial aneurysm (IA) and TAAs appear to run in the family in an autosomal dominant manner: After exploring the family history, we observed that the proband's two siblings both died from cerebral haemorrhage, and the proband's parent and parent's sibling died from aortic rupture. After application of a genome-wide paired-end DNA sequencing method for breakpoint mapping, we demonstrate that this translocation breaks intron 1 of a splicing isoform of Neurotrimin at 11q25 in a previously implicated candidate region for IAs and AAs (OMIM 612161).
Our results demonstrate the feasibility of genome-wide paired-end sequencing for the characterisation of balanced rearrangements and identification of candidate genes in patients with potentially disease-associated chromosome rearrangements. The family samples were gathered as a part of our recently launched National Registry of Reciprocal Balanced Translocations and Inversions in Finland (n=2575), and we believe that such a registry will be a powerful resource for the localisation of chromosomal aberrations, which can bring insight into the aetiology of related phenotypes.
Journal of Medical Genetics 10/2012; 49(10):621-9. · 6.36 Impact Factor
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Karin J H Verweij,
Jian Yang,
Jari Lahti,
Juha Veijola,
Mirka Hintsanen,
Laura Pulkki-Råback,
Kati Heinonen,
Anneli Pouta,
Anu-Katriina Pesonen,
Elisabeth Widen, [......],
Jorma Viikari,
Katri Räikkönen,
Johan G Eriksson,
Liisa Keltikangas-Järvinen,
Terho Lehtimäki,
Nicholas G Martin,
Marjo-Riitta Järvelin,
Peter M Visscher,
Matthew C Keller,
Brendan P Zietsch
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ABSTRACT: Personality traits are basic dimensions of behavioral variation, and twin, family, and adoption studies show that around 30% of the between-individual variation is due to genetic variation. There is rapidly growing interest in understanding the evolutionary basis of this genetic variation. Several evolutionary mechanisms could explain how genetic variation is maintained in traits, and each of these makes predictions in terms of the relative contribution of rare and common genetic variants to personality variation, the magnitude of nonadditive genetic influences, and whether personality is affected by inbreeding. Using genome-wide single nucleotide polymorphism (SNP) data from > 8000 individuals, we estimated that little variation in the Cloninger personality dimensions (7.2% on average) is due to the combined effect of common, additive genetic variants across the genome, suggesting that most heritable variation in personality is due to rare variant effects and/or a combination of dominance and epistasis. Furthermore, higher levels of inbreeding were associated with less socially desirable personality trait levels in three of the four personality dimensions. These findings are consistent with genetic variation in personality traits having been maintained by mutation-selection balance.
Evolution 10/2012; 66(10):3238-3251. · 5.15 Impact Factor
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ABSTRACT: Personalised medicine promises prediction, prevention and treatment of illness that is targeted to individuals’ needs. New technologies for detailed biological profiling of individuals at the molecular level have been crucial in initiating the move to personalised medicine; further novel technologies will be necessary if the vision is to become a reality. We will need to develop new technologies to collect and analyse data in a way that is not just linear but integrated (understanding system level functioning) and dynamic (understanding system in flux). Key factors in the development of technologies for personalised medicine are standardisation, integration and harmonisation. For example, the tools and processes for data collection and analysis must be standardised across research sites. Research activity at different sites must be integrated to maximise synergies, and scientific research must be integrated with healthcare to ensure effective translation. There must also be harmonisation between scientific practices in different research sites, between science and healthcare and between science, healthcare and wider society, including the ethical and regulatory frameworks, the prevailing political and cultural ethos and the expectations of patients/citizens.
New Biotechnology 09/2012; 29(6):625-33. · 2.76 Impact Factor
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Michael Inouye,
Samuli Ripatti,
Johannes Kettunen,
Leo-Pekka Lyytikäinen,
Niku Oksala,
Pirkka-Pekka Laurila,
Antti J Kangas,
Pasi Soininen,
Markku J Savolainen,
Jorma Viikari,
Mika Kähönen,
Markus Perola,
Veikko Salomaa,
Olli Raitakari,
Terho Lehtimäki,
Marja-Riitta Taskinen,
Marjo-Riitta Järvelin,
Mika Ala-Korpela, Aarno Palotie,
Paul I W de Bakker
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ABSTRACT: Association testing of multiple correlated phenotypes offers better power than univariate analysis of single traits. We analyzed 6,600 individuals from two population-based cohorts with both genome-wide SNP data and serum metabolomic profiles. From the observed correlation structure of 130 metabolites measured by nuclear magnetic resonance, we identified 11 metabolic networks and performed a multivariate genome-wide association analysis. We identified 34 genomic loci at genome-wide significance, of which 7 are novel. In comparison to univariate tests, multivariate association analysis identified nearly twice as many significant associations in total. Multi-tissue gene expression studies identified variants in our top loci, SERPINA1 and AQP9, as eQTLs and showed that SERPINA1 and AQP9 expression in human blood was associated with metabolites from their corresponding metabolic networks. Finally, liver expression of AQP9 was associated with atherosclerotic lesion area in mice, and in human arterial tissue both SERPINA1 and AQP9 were shown to be upregulated (6.3-fold and 4.6-fold, respectively) in atherosclerotic plaques. Our study illustrates the power of multi-phenotype GWAS and highlights candidate genes for atherosclerosis.
PLoS Genetics 08/2012; 8(8):e1002907. · 8.69 Impact Factor
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Vesna Boraska,
Ana Jeroncic,
Vincenza Colonna,
Lorraine Southam,
Dale R Nyholt,
Nigel William Rayner,
John R B Perry,
Daniela Toniolo,
Eva Albrecht,
Wei Ang, [......],
Sheila Ulivi,
Pim van der Harst,
Peter Vollenweider,
Henry Völzke,
Nicholas J Wareham,
H-Erich Wichmann,
James F Wilson,
Igor Rudan,
Yali Xue,
Eleftheria Zeggini
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ABSTRACT: The male-to-female sex ratio at birth is constant across world populations with an average of 1.06 (106 male to 100 female live births) for populations of European descent. The sex ratio is considered to be affected by numerous biological and environmental factors and to have a heritable component. The aim of this study was to investigate the presence of common allele modest effects at autosomal and chromosome X variants that could explain the observed sex ratio at birth. We conducted a large-scale genome-wide association scan (GWAS) meta-analysis across 51 studies, comprising overall 114 863 individuals (61 094 women and 53 769 men) of European ancestry and 2 623 828 common (minor allele frequency >0.05) single-nucleotide polymorphisms (SNPs). Allele frequencies were compared between men and women for directly-typed and imputed variants within each study. Forward-time simulations for unlinked, neutral, autosomal, common loci were performed under the demographic model for European populations with a fixed sex ratio and a random mating scheme to assess the probability of detecting significant allele frequency differences. We do not detect any genome-wide significant (P < 5 × 10(-8)) common SNP differences between men and women in this well-powered meta-analysis. The simulated data provided results entirely consistent with these findings. This large-scale investigation across ∼115 000 individuals shows no detectable contribution from common genetic variants to the observed skew in the sex ratio. The absence of sex-specific differences is useful in guiding genetic association study design, for example when using mixed controls for sex-biased traits.
Human Molecular Genetics 07/2012; 21(21):4805-15. · 7.64 Impact Factor
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Tobias Freilinger,
Verneri Anttila,
Boukje de Vries,
Rainer Malik,
Mikko Kallela,
Gisela M Terwindt,
Patricia Pozo-Rosich,
Bendik Winsvold,
Dale R Nyholt,
Willebrordus P J van Oosterhout, [......],
Thomas Meitinger,
Bertram Müller-Myhsok,
John-Anker Zwart,
Markus Färkkilä,
Alfons Macaya,
Michel D Ferrari,
Christian Kubisch, Aarno Palotie,
Martin Dichgans,
Arn M J M van den Maagdenberg
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ABSTRACT: Migraine without aura is the most common form of migraine, characterized by recurrent disabling headache and associated autonomic symptoms. To identify common genetic variants associated with this migraine type, we analyzed genome-wide association data of 2,326 clinic-based German and Dutch individuals with migraine without aura and 4,580 population-matched controls. We selected SNPs from 12 loci with 2 or more SNPs associated with P values of <1 × 10(-5) for replication testing in 2,508 individuals with migraine without aura and 2,652 controls. SNPs at two of these loci showed convincing replication: at 1q22 (in MEF2D; replication P = 4.9 × 10(-4); combined P = 7.06 × 10(-11)) and at 3p24 (near TGFBR2; replication P = 1.0 × 10(-4); combined P = 1.17 × 10(-9)). In addition, SNPs at the PHACTR1 and ASTN2 loci showed suggestive evidence of replication (P = 0.01; combined P = 3.20 × 10(-8) and P = 0.02; combined P = 3.86 × 10(-8), respectively). We also replicated associations at two previously reported migraine loci in or near TRPM8 and LRP1. This study identifies the first susceptibility loci for migraine without aura, thereby expanding our knowledge of this debilitating neurological disorder.
Nature Genetics 06/2012; 44(7):777-82. · 35.53 Impact Factor
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Alisa K Manning,
Marie-France Hivert,
Robert A Scott,
Jonna L Grimsby,
Nabila Bouatia-Naji,
Han Chen,
Denis Rybin,
Ching-Ti Liu,
Lawrence F Bielak,
Inga Prokopenko, [......],
Tatijana Zemunik,
Lina Zgaga,
Nicholas J Wareham,
Mark I McCarthy,
Ines Barroso,
Richard M Watanabe,
Jose C Florez,
Josée Dupuis,
James B Meigs,
Claudia Langenberg
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ABSTRACT: Recent genome-wide association studies have described many loci implicated in type 2 diabetes (T2D) pathophysiology and β-cell dysfunction but have contributed little to the understanding of the genetic basis of insulin resistance. We hypothesized that genes implicated in insulin resistance pathways might be uncovered by accounting for differences in body mass index (BMI) and potential interactions between BMI and genetic variants. We applied a joint meta-analysis approach to test associations with fasting insulin and glucose on a genome-wide scale. We present six previously unknown loci associated with fasting insulin at P < 5 × 10(-8) in combined discovery and follow-up analyses of 52 studies comprising up to 96,496 non-diabetic individuals. Risk variants were associated with higher triglyceride and lower high-density lipoprotein (HDL) cholesterol levels, suggesting a role for these loci in insulin resistance pathways. The discovery of these loci will aid further characterization of the role of insulin resistance in T2D pathophysiology.
Nature Genetics 05/2012; 44(6):659-69. · 35.53 Impact Factor
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H Rob Taal,
Beate St Pourcain,
Elisabeth Thiering,
Shikta Das,
Dennis O Mook-Kanamori,
Nicole M Warrington,
Marika Kaakinen,
Eskil Kreiner-Møller,
Jonathan P Bradfield,
Rachel M Freathy, [......],
Andrew T Hattersley,
Mads Melbye,
Hans Bisgaard,
Craig E Pennell,
Elisabeth Widen,
Hakon Hakonarson,
George Davey Smith,
Joachim Heinrich,
Marjo-Riitta Jarvelin,
Vincent W V Jaddoe
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ABSTRACT: To identify genetic variants associated with head circumference in infancy, we performed a meta-analysis of seven genome-wide association studies (GWAS) (N = 10,768 individuals of European ancestry enrolled in pregnancy and/or birth cohorts) and followed up three lead signals in six replication studies (combined N = 19,089). rs7980687 on chromosome 12q24 (P = 8.1 × 10(-9)) and rs1042725 on chromosome 12q15 (P = 2.8 × 10(-10)) were robustly associated with head circumference in infancy. Although these loci have previously been associated with adult height, their effects on infant head circumference were largely independent of height (P = 3.8 × 10(-7) for rs7980687 and P = 1.3 × 10(-7) for rs1042725 after adjustment for infant height). A third signal, rs11655470 on chromosome 17q21, showed suggestive evidence of association with head circumference (P = 3.9 × 10(-6)). SNPs correlated to the 17q21 signal have shown genome-wide association with adult intracranial volume, Parkinson's disease and other neurodegenerative diseases, indicating that a common genetic variant in this region might link early brain growth with neurological disease in later life.
Nature Genetics 04/2012; 44(5):532-8. · 35.53 Impact Factor
