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Genetics of Personality Consortium (2015). Meta-analysis of genome-wide association studies for neuroticism, and the polygenic association with major depressive disorder. JAMA Psychiatry, 72(7), 642-650. doi:10.1001/jamapsychiatry.2015.0554.
Abstract
Importance
Neuroticism is a pervasive risk factor for psychiatric conditions. It genetically overlaps with major depressive disorder (MDD) and is therefore an important phenotype for psychiatric genetics. The Genetics of Personality Consortium has created a resource for genome-wide association analyses of personality traits in more than 63 000 participants (including MDD cases).Objectives
To identify genetic variants associated with neuroticism by performing a meta-analysis of genome-wide association results based on 1000 Genomes imputation; to evaluate whether common genetic variants as assessed by single-nucleotide polymorphisms (SNPs) explain variation in neuroticism by estimating SNP-based heritability; and to examine whether SNPs that predict neuroticism also predict MDD.Design, Setting, and Participants
Genome-wide association meta-analysis of 30 cohorts with genome-wide genotype, personality, and MDD data from the Genetics of Personality Consortium. The study included 63 661 participants from 29 discovery cohorts and 9786 participants from a replication cohort. Participants came from Europe, the United States, or Australia. Analyses were conducted between 2012 and 2014.Main Outcomes and Measures
Neuroticism scores harmonized across all 29 discovery cohorts by item response theory analysis, and clinical MDD case-control status in 2 of the cohorts.Results
A genome-wide significant SNP was found on 3p14 in MAGI1 (rs35855737; P = 9.26 × 10−9 in the discovery meta-analysis). This association was not replicated (P = .32), but the SNP was still genome-wide significant in the meta-analysis of all 30 cohorts (P = 2.38 × 10−8). Common genetic variants explain 15% of the variance in neuroticism. Polygenic scores based on the meta-analysis of neuroticism in 27 cohorts significantly predicted neuroticism (1.09 × 10−12 <} P {<} .05) and MDD (4.02 × 10−9 {<} P {< .05) in the 2 other cohorts.Conclusions and Relevance
This study identifies a novel locus for neuroticism. The variant is located in a known gene that has been associated with bipolar disorder and schizophrenia in previous studies. In addition, the study shows that neuroticism is influenced by many genetic variants of small effect that are either common or tagged by common variants. These genetic variants also influence MDD. Future studies should confirm the role of the MAGI1 locus for neuroticism and further investigate the association of MAGI1 and the polygenic association to a range of other psychiatric disorders that are phenotypically correlated with neuroticism.Additional information
http://archpsyc.jamanetwork.com/article.aspx?articleid=2294268#tab12Files private
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Guggenheim, J. A., St Pourcain, B., McMahon, G., Timpson, N. J., Evans, D. M., & Williams, C. (2015). Assumption-free estimation of the genetic contribution to refractive error across childhood. Molecular Vision, 21, 621-632. Retrieved from http://www.molvis.org/molvis/v21/621.
Abstract
Studies in relatives have generally yielded high heritability estimates for refractive error: twins 75–90%, families 15–70%. However, because related individuals often share a common environment, these estimates are inflated (via misallocation of unique/common environment variance). We calculated a lower-bound heritability estimate for refractive error free from such bias.
Between the ages 7 and 15 years, participants in the Avon Longitudinal Study of Parents and Children (ALSPAC) underwent non-cycloplegic autorefraction at regular research clinics. At each age, an estimate of the variance in refractive error explained by single nucleotide polymorphism (SNP) genetic variants was calculated using genome-wide complex trait analysis (GCTA) using high-density genome-wide SNP genotype information (minimum N at each age=3,404).
The variance in refractive error explained by the SNPs (“SNP heritability”) was stable over childhood: Across age 7–15 years, SNP heritability averaged 0.28 (SE=0.08, p<0.001). The genetic correlation for refractive error between visits varied from 0.77 to 1.00 (all p<0.001) demonstrating that a common set of SNPs was responsible for the genetic contribution to refractive error across this period of childhood. Simulations suggested lack of cycloplegia during autorefraction led to a small underestimation of SNP heritability (adjusted SNP heritability=0.35; SE=0.09). To put these results in context, the variance in refractive error explained (or predicted) by the time participants spent outdoors was <0.005 and by the time spent reading was <0.01, based on a parental questionnaire completed when the child was aged 8–9 years old.
Genetic variation captured by common SNPs explained approximately 35% of the variation in refractive error between unrelated subjects. This value sets an upper limit for predicting refractive error using existing SNP genotyping arrays, although higher-density genotyping in larger samples and inclusion of interaction effects is expected to raise this figure toward twin- and family-based heritability estimates. The same SNPs influenced refractive error across much of childhood. Notwithstanding the strong evidence of association between time outdoors and myopia, and time reading and myopia, less than 1% of the variance in myopia at age 15 was explained by crude measures of these two risk factors, indicating that their effects may be limited, at least when averaged over the whole population. -
St Pourcain, B., Haworth, C. M. A., Davis, O. S. P., Wang, K., Timpson, N. J., Evans, D. M., Kemp, J. P., Ronald, A., Price, T., Meaburn, E., Ring, S. M., Golding, J., Hakonarson, H., Plomin, R., & Davey Smith, G. (2015). Heritability and genome-wide analyses of problematic peer relationships during childhood and adolescence. Human Genetics, 134(6), 539-551. doi:10.1007/s00439-014-1514-5.
Abstract
Peer behaviour plays an important role in the development of social adjustment, though little is known about its genetic architecture. We conducted a twin study combined with a genome-wide complex trait analysis (GCTA) and a genome-wide screen to characterise genetic influences on problematic peer behaviour during childhood and adolescence. This included a series of longitudinal measures (parent-reported Strengths-and-Difficulties Questionnaire) from a UK population-based birth-cohort (ALSPAC, 4–17 years), and a UK twin sample (TEDS, 4–11 years). Longitudinal twin analysis (TEDS; N ≤ 7,366 twin pairs) showed that peer problems in childhood are heritable (4–11 years, 0.60 < twin-h 2 ≤ 0.71) but genetically heterogeneous from age to age (4–11 years, twin-r g = 0.30). GCTA (ALSPAC: N ≤ 5,608, TEDS: N ≤ 2,691) provided furthermore little support for the contribution of measured common genetic variants during childhood (4–12 years, 0.02 < GCTA-h 2(Meta) ≤ 0.11) though these influences become stronger in adolescence (13–17 years, 0.14 < GCTA-h 2(ALSPAC) ≤ 0.27). A subsequent cross-sectional genome-wide screen in ALSPAC (N ≤ 6,000) focussed on peer problems with the highest GCTA-heritability (10, 13 and 17 years, 0.0002 < GCTA-P ≤ 0.03). Single variant signals (P ≤ 10−5) were followed up in TEDS (N ≤ 2835, 9 and 11 years) and, in search for autism quantitative trait loci, explored within two autism samples (AGRE: N Pedigrees = 793; ACC: N Cases = 1,453/N Controls = 7,070). There was, however, no evidence for association in TEDS and little evidence for an overlap with the autistic continuum. In summary, our findings suggest that problematic peer relationships are heritable but genetically complex and heterogeneous from age to age, with an increase in common measurable genetic variation during adolescence. -
Stergiakouli, E., Martin, J., Hamshere, M. L., Langley, K., Evans, D. M., St Pourcain, B., Timpson, N. J., Owen, M. J., O'Donovan, M., Thapar, A., & Davey Smith, G. (2015). Shared Genetic Influences Between Attention-Deficit/Hyperactivity Disorder (ADHD) Traits in Children and Clinical ADHD. Journal of the American Academy of Child and Adolescent Psychiatry, 54(4), 322-327. doi:10.1016/j.jaac.2015.01.010.
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The UK10K Consortium (2015). The UK10K project identifies rare variants in health and disease. Nature, 526(7571), 82-89. doi:10.1038/nature14962.
Abstract
The contribution of rare and low-frequency variants to human traits is largely unexplored. Here we describe insights from sequencing whole genomes (low read depth, 7×) or exomes (high read depth, 80×) of nearly 10,000 individuals from population-based and disease collections. In extensively phenotyped cohorts we characterize over 24 million novel sequence variants, generate a highly accurate imputation reference panel and identify novel alleles associated with levels of triglycerides (APOB), adiponectin (ADIPOQ) and low-density lipoprotein cholesterol (LDLR and RGAG1) from single-marker and rare variant aggregation tests. We describe population structure and functional annotation of rare and low-frequency variants, use the data to estimate the benefits of sequencing for association studies, and summarize lessons from disease-specific collections. Finally, we make available an extensive resource, including individual-level genetic and phenotypic data and web-based tools to facilitate the exploration of association results.Additional information
http://www.nature.com/nature/journal/vaop/ncurrent/full/nature14962.html#supple… -
van der Valk, R. J. P., Kreiner-Møller, E., Kooijman, M. N., Guxens, M., Stergiakouli, E., Sääf, A., Bradfield, J. P., Geller, F., Hayes, M. G., Cousminer, D. L., Körner, A., Thiering, E., Curtin, J. A., Myhre, R., Huikari, V., Joro, R., Kerkhof, M., Warrington, N. M., Pitkänen, N., Ntalla, I. and 98 morevan der Valk, R. J. P., Kreiner-Møller, E., Kooijman, M. N., Guxens, M., Stergiakouli, E., Sääf, A., Bradfield, J. P., Geller, F., Hayes, M. G., Cousminer, D. L., Körner, A., Thiering, E., Curtin, J. A., Myhre, R., Huikari, V., Joro, R., Kerkhof, M., Warrington, N. M., Pitkänen, N., Ntalla, I., Horikoshi, M., Veijola, R., Freathy, R. M., Teo, Y.-Y., Barton, S. J., Evans, D. M., Kemp, J. P., St Pourcain, B., Ring, S. M., Davey Smith, G., Bergström, A., Kull, I., Hakonarson, H., Mentch, F. D., Bisgaard, H., Chawes, B., Stokholm, J., Waage, J., Eriksen, P., Sevelsted, A., Melbye, M., van Duijn, C. M., Medina-Gomez, C., Hofman, A., de Jongste, J. C., Taal, H. R., Uitterlinden, A. G., Armstrong, L. L., Eriksson, J., Palotie, A., Bustamante, M., Estivill, X., Gonzalez, J. R., Llop, S., Kiess, W., Mahajan, A., Flexeder, C., Tiesler, C. M. T., Murray, C. S., Simpson, A., Magnus, P., Sengpiel, V., Hartikainen, A.-L., Keinanen-Kiukaanniemi, S., Lewin, A., Da Silva Couto Alves, A., Blakemore, A. I., Buxton, J. L., Kaakinen, M., Rodriguez, A., Sebert, S., Vaarasmaki, M., Lakka, T., Lindi, V., Gehring, U., Postma, D. S., Ang, W., Newnham, J. P., Lyytikäinen, L.-P., Pahkala, K., Raitakari, O. T., Panoutsopoulou, K., Zeggini, E., Boomsma, D. I., Groen-Blokhuis, M., Ilonen, J., Franke, L., Hirschhorn, J. N., Pers, T. H., Liang, L., Huang, J., Hocher, B., Knip, M., Saw, S.-M., Holloway, J. W., Melén, E., Grant, S. F. A., Feenstra, B., Lowe, W. L., Widén, E., Sergeyev, E., Grallert, H., Custovic, A., Jacobsson, B., Jarvelin, M.-R., Atalay, M., Koppelman, G. H., Pennell, C. E., Niinikoski, H., Dedoussis, G. V., Mccarthy, M. I., Frayling, T. M., Sunyer, J., Timpson, N. J., Rivadeneira, F., Bønnelykke, K., Jaddoe, V. W. V., & Early Growth Genetics (EGG) Consortium (2015). A novel common variant in DCST2 is associated with length in early life and height in adulthood. Human Molecular Genetics, 24(4), 1155-1168. doi:10.1093/hmg/ddu510.
Abstract
Common genetic variants have been identified for adult height, but not much is known about the genetics of skeletal growth in early life. To identify common genetic variants that influence fetal skeletal growth, we meta-analyzed 22 genome-wide association studies (Stage 1; N = 28 459). We identified seven independent top single nucleotide polymorphisms (SNPs) (P < 1 × 10(-6)) for birth length, of which three were novel and four were in or near loci known to be associated with adult height (LCORL, PTCH1, GPR126 and HMGA2). The three novel SNPs were followed-up in nine replication studies (Stage 2; N = 11 995), with rs905938 in DC-STAMP domain containing 2 (DCST2) genome-wide significantly associated with birth length in a joint analysis (Stages 1 + 2; β = 0.046, SE = 0.008, P = 2.46 × 10(-8), explained variance = 0.05%). Rs905938 was also associated with infant length (N = 28 228; P = 5.54 × 10(-4)) and adult height (N = 127 513; P = 1.45 × 10(-5)). DCST2 is a DC-STAMP-like protein family member and DC-STAMP is an osteoclast cell-fusion regulator. Polygenic scores based on 180 SNPs previously associated with human adult stature explained 0.13% of variance in birth length. The same SNPs explained 2.95% of the variance of infant length. Of the 180 known adult height loci, 11 were genome-wide significantly associated with infant length (SF3B4, LCORL, SPAG17, C6orf173, PTCH1, GDF5, ZNFX1, HHIP, ACAN, HLA locus and HMGA2). This study highlights that common variation in DCST2 influences variation in early growth and adult height.Additional information
http://hmg.oxfordjournals.org/content/24/4/1155/suppl/DC1 -
Warrington, N. M., Howe, L. D., Paternoster, L., Kaakinen, M., Herrala, S., Huikari, V., Wu, Y. Y., Kemp, J. P., Timpson, N. J., St Pourcain, B., Smith, G. D., Tilling, K., Jarvelin, M.-R., Pennell, C. E., Evans, D. M., Lawlor, D. A., Briollais, L., & Palmer, L. J. (2015). A genome-wide association study of body mass index across early life and childhood. International Journal of Epidemiology, 44(2), 700-712. doi:10.1093/ije/dyv077.
Abstract
Background: Several studies have investigated the effect of known adult body mass index (BMI) associated single nucleotide polymorphisms (SNPs) on BMI in childhood. There has been no genome-wide association study (GWAS) of BMI trajectories over childhood.
Methods: We conducted a GWAS meta-analysis of BMI trajectories from 1 to 17 years of age in 9377 children (77 967 measurements) from the Avon Longitudinal Study of Parents and Children (ALSPAC) and the Western Australian Pregnancy Cohort (Raine) Study. Genome-wide significant loci were examined in a further 3918 individuals (48 530 measurements) from Northern Finland. Linear mixed effects models with smoothing splines were used in each cohort for longitudinal modelling of BMI.
Results: A novel SNP, downstream from the FAM120AOS gene on chromosome 9, was detected in the meta-analysis of ALSPAC and Raine. This association was driven by a difference in BMI at 8 years (T allele of rs944990 increased BMI; PSNP = 1.52 × 10−8), with a modest association with change in BMI over time (PWald(Change) = 0.006). Three known adult BMI-associated loci (FTO, MC4R and ADCY3) and one childhood obesity locus (OLFM4) reached genome-wide significance (PWald < 1.13 × 10−8) with BMI at 8 years and/or change over time.
Conclusions: This GWAS of BMI trajectories over childhood identified a novel locus that warrants further investigation. We also observed genome-wide significance with previously established obesity loci, making the novel observation that these loci affected both the level and the rate of change in BMI. We have demonstrated that the use of repeated measures data can increase power to allow detection of genetic loci with smaller sample sizes.Additional information
http://ije.oxfordjournals.org/content/44/2/700/suppl/DC1 -
Warrington, N. M., Zhu, G., Dy, V., Heath, A. C., Madden, P. A. F., Hemani, G., Kemp, J. P., McMahon, G., St Pourcain, B., Timpson, N. J., Taylor, C. M., Golding, J., Lawlor, D. A., Steer, C., Montgomery, G. W., Martin, N. G., Smith, G. D., Evans, D. M., & Whitfield, J. B. (2015). Genome-wide association study of blood lead shows multiple associations near ALAD. Human Molecular Genetics, 24(13), 3871-3879. doi:10.1093/hmg/ddv112.
Abstract
Exposure to high levels of environmental lead, or biomarker evidence of high body lead content, is associated with anaemia, developmental and neurological deficits in children, and increased mortality in adults. Adverse effects of lead still occur despite substantial reduction in environmental exposure. There is genetic variation between individuals in blood lead concentration but the polymorphisms contributing to this have not been defined. We measured blood or erythrocyte lead content, and carried out genome-wide association analysis, on population-based cohorts of adult volunteers from Australia and UK (N = 5433). Samples from Australia were collected in two studies, in 1993–1996 and 2002–2005 and from UK in 1991–1992. One locus, at ALAD on chromosome 9, showed consistent association with blood lead across countries and evidence for multiple independent allelic effects. The most significant single nucleotide polymorphism (SNP), rs1805313 (P = 3.91 × 10−14 for lead concentration in a meta-analysis of all data), is known to have effects on ALAD expression in blood cells but other SNPs affecting ALAD expression did not affect blood lead. Variants at 12 other loci, including ABO, showed suggestive associations (5 × 10−6 >} P {> 5 × 10−8). Identification of genetic polymorphisms affecting blood lead reinforces the view that genetic factors, as well as environmental ones, are important in determining blood lead levels. The ways in which ALAD variation affects lead uptake or distribution are still to be determined.Additional information
http://hmg.oxfordjournals.org/content/24/13/3871/suppl/DC1 -
Li, Q., Wojciechowski, R., Simpson, C. L., Hysi, P. G., Verhoeven, V. J. M., Ikram, M. K., Höhn, R., Vitart, V., Hewitt, A. W., Oexle, K., Mäkelä, K.-M., MacGregor, S., Pirastu, M., Fan, Q., Cheng, C.-Y., St Pourcain, B., McMahon, G., Kemp, J. P., Northstone, K., Rahi, J. S. and 69 moreLi, Q., Wojciechowski, R., Simpson, C. L., Hysi, P. G., Verhoeven, V. J. M., Ikram, M. K., Höhn, R., Vitart, V., Hewitt, A. W., Oexle, K., Mäkelä, K.-M., MacGregor, S., Pirastu, M., Fan, Q., Cheng, C.-Y., St Pourcain, B., McMahon, G., Kemp, J. P., Northstone, K., Rahi, J. S., Cumberland, P. M., Martin, N. G., Sanfilippo, P. G., Lu, Y., Wang, Y. X., Hayward, C., Polašek, O., Campbell, H., Bencic, G., Wright, A. F., Wedenoja, J., Zeller, T., Schillert, A., Mirshahi, A., Lackner, K., Yip, S. P., Yap, M. K. H., Ried, J. S., Gieger, C., Murgia, F., Wilson, J. F., Fleck, B., Yazar, S., Vingerling, J. R., Hofman, A., Uitterlinden, A., Rivadeneira, F., Amin, N., Karssen, L., Oostra, B. A., Zhou, X., Teo, Y.-Y., Tai, E. S., Vithana, E., Barathi, V., Zheng, Y., Siantar, R. G., Neelam, K., Shin, Y., Lam, J., Yonova-Doing, E., Venturini, C., Hosseini, S. M., Wong, H.-S., Lehtimäki, T., Kähönen, M., Raitakari, O., Timpson, N. J., Evans, D. M., Khor, C.-C., Aung, T., Young, T. L., Mitchell, P., Klein, B., van Duijn, C. M., Meitinger, T., Jonas, J. B., Baird, P. N., Mackey, D. A., Wong, T. Y., Saw, S.-M., Pärssinen, O., Stambolian, D., Hammond, C. J., Klaver, C. C. W., Williams, C., Paterson, A. D., Bailey-Wilson, J. E., & Guggenheim, J. A. (2015). Genome-wide association study for refractive astigmatism reveals genetic co-determination with spherical equivalent refractive error: the CREAM consortium. Human Genetics, 134, 131-146. doi:10.1007/s00439-014-1500-y.
Abstract
To identify genetic variants associated with refractive astigmatism in the general population, meta-analyses of genome-wide association studies were performed for: White Europeans aged at least 25 years (20 cohorts, N = 31,968); Asian subjects aged at least 25 years (7 cohorts, N = 9,295); White Europeans aged <25 years (4 cohorts, N = 5,640); and all independent individuals from the above three samples combined with a sample of Chinese subjects aged <25 years (N = 45,931). Participants were classified as cases with refractive astigmatism if the average cylinder power in their two eyes was at least 1.00 diopter and as controls otherwise. Genome-wide association analysis was carried out for each cohort separately using logistic regression. Meta-analysis was conducted using a fixed effects model. In the older European group the most strongly associated marker was downstream of the neurexin-1 (NRXN1) gene (rs1401327, P = 3.92E−8). No other region reached genome-wide significance, and association signals were lower for the younger European group and Asian group. In the meta-analysis of all cohorts, no marker reached genome-wide significance: The most strongly associated regions were, NRXN1 (rs1401327, P = 2.93E−07), TOX (rs7823467, P = 3.47E−07) and LINC00340 (rs12212674, P = 1.49E−06). For 34 markers identified in prior GWAS for spherical equivalent refractive error, the beta coefficients for genotype versus spherical equivalent, and genotype versus refractive astigmatism, were highly correlated (r = −0.59, P = 2.10E−04). This work revealed no consistent or strong genetic signals for refractive astigmatism; however, the TOX gene region previously identified in GWAS for spherical equivalent refractive error was the second most strongly associated region. Analysis of additional markers provided evidence supporting widespread genetic co-susceptibility for spherical and astigmatic refractive errors. -
Benyamin, B., St Pourcain, B., Davis, O. S., Davies, G., Hansell, N. K., Brion, M.-J., Kirkpatrick, R. M., Cents, R. A. M., Franić, S., Miller, M. B., Haworth, C. M. A., Meaburn, E., Price, T. S., Evans, D. M., Timpson, N., Kemp, J., Ring, S., McArdle, W., Medland, S. E., Yang, J. and 23 moreBenyamin, B., St Pourcain, B., Davis, O. S., Davies, G., Hansell, N. K., Brion, M.-J., Kirkpatrick, R. M., Cents, R. A. M., Franić, S., Miller, M. B., Haworth, C. M. A., Meaburn, E., Price, T. S., Evans, D. M., Timpson, N., Kemp, J., Ring, S., McArdle, W., Medland, S. E., Yang, J., Harris, S. E., Liewald, D. C., Scheet, P., Xiao, X., Hudziak, J. J., de Geus, E. J. C., Jaddoe, V. W. V., Starr, J. M., Verhulst, F. C., Pennell, C., Tiemeier, H., Iacono, W. G., Palmer, L. J., Montgomery, G. W., Martin, N. G., Boomsma, D. I., Posthuma, D., McGue, M., Wright, M. J., Davey Smith, G., Deary, I. J., Plomin, R., & Visscher, P. M. (2014). Childhood intelligence is heritable, highly polygenic and associated with FNBP1L. Molecular Psychiatry, 19(2), 253-258. doi:10.1038/mp.2012.184.
Abstract
Intelligence in childhood, as measured by psychometric cognitive tests, is a strong predictor of many important life outcomes, including educational attainment, income, health and lifespan. Results from twin, family and adoption studies are consistent with general intelligence being highly heritable and genetically stable throughout the life course. No robustly associated genetic loci or variants for childhood intelligence have been reported. Here, we report the first genome-wide association study (GWAS) on childhood intelligence (age range 6–18 years) from 17 989 individuals in six discovery and three replication samples. Although no individual single-nucleotide polymorphisms (SNPs) were detected with genome-wide significance, we show that the aggregate effects of common SNPs explain 22–46% of phenotypic variation in childhood intelligence in the three largest cohorts (P=3.9 × 10−15, 0.014 and 0.028). FNBP1L, previously reported to be the most significantly associated gene for adult intelligence, was also significantly associated with childhood intelligence (P=0.003). Polygenic prediction analyses resulted in a significant correlation between predictor and outcome in all replication cohorts. The proportion of childhood intelligence explained by the predictor reached 1.2% (P=6 × 10−5), 3.5% (P=10−3) and 0.5% (P=6 × 10−5) in three independent validation cohorts. Given the sample sizes, these genetic prediction results are consistent with expectations if the genetic architecture of childhood intelligence is like that of body mass index or height. Our study provides molecular support for the heritability and polygenic nature of childhood intelligence. Larger sample sizes will be required to detect individual variants with genome-wide significance.Additional information
http://www.nature.com/mp/journal/v19/n2/suppinfo/mp2012184s1.html?url=/mp/journ… -
Bolton, J. L., Hayward, C., Direk, N., Lewis, J. G., Hammond, G. L., Hill, L. A., Anderson, A., Huffman, J., Wilson, J. F., Campbell, H., Rudan, I., Wright, A., Hastie, N., Wild, S. H., Velders, F. P., Hofman, A., Uitterlinden, A. G., Lahti, J., Räikkönen, K., Kajantie, E. and 37 moreBolton, J. L., Hayward, C., Direk, N., Lewis, J. G., Hammond, G. L., Hill, L. A., Anderson, A., Huffman, J., Wilson, J. F., Campbell, H., Rudan, I., Wright, A., Hastie, N., Wild, S. H., Velders, F. P., Hofman, A., Uitterlinden, A. G., Lahti, J., Räikkönen, K., Kajantie, E., Widen, E., Palotie, A., Eriksson, J. G., Kaakinen, M., Järvelin, M.-R., Timpson, N. J., Davey Smith, G., Ring, S. M., Evans, D. M., St Pourcain, B., Tanaka, T., Milaneschi, Y., Bandinelli, S., Ferrucci, L., van der Harst, P., Rosmalen, J. G. M., Bakker, S. J. L., Verweij, N., Dullaart, R. P. F., Mahajan, A., Lindgren, C. M., Morris, A., Lind, L., Ingelsson, E., Anderson, L. N., Pennell, C. E., Lye, S. J., Matthews, S. G., Eriksson, J., Mellstrom, D., Ohlsson, C., Price, J. F., Strachan, M. W. J., Reynolds, R. M., Tiemeier, H., Walker, B. R., & CORtisol NETwork (CORNET) Consortium (2014). Genome Wide Association Identifies Common Variants at the SERPINA6/SERPINA1 Locus Influencing Plasma Cortisol and Corticosteroid Binding Globulin. PLoS Genetics, 10(7): e1004474. doi:10.1371/journal.pgen.1004474.
Abstract
Variation in plasma levels of cortisol, an essential hormone in the stress response, is associated in population-based studies with cardio-metabolic, inflammatory and neuro-cognitive traits and diseases. Heritability of plasma cortisol is estimated at 30-60% but no common genetic contribution has been identified. The CORtisol NETwork (CORNET) consortium undertook genome wide association meta-analysis for plasma cortisol in 12,597 Caucasian participants, replicated in 2,795 participants. The results indicate that <1% of variance in plasma cortisol is accounted for by genetic variation in a single region of chromosome 14. This locus spans SERPINA6, encoding corticosteroid binding globulin (CBG, the major cortisol-binding protein in plasma), and SERPINA1, encoding α1-antitrypsin (which inhibits cleavage of the reactive centre loop that releases cortisol from CBG). Three partially independent signals were identified within the region, represented by common SNPs; detailed biochemical investigation in a nested sub-cohort showed all these SNPs were associated with variation in total cortisol binding activity in plasma, but some variants influenced total CBG concentrations while the top hit (rs12589136) influenced the immunoreactivity of the reactive centre loop of CBG. Exome chip and 1000 Genomes imputation analysis of this locus in the CROATIA-Korcula cohort identified missense mutations in SERPINA6 and SERPINA1 that did not account for the effects of common variants. These findings reveal a novel common genetic source of variation in binding of cortisol by CBG, and reinforce the key role of CBG in determining plasma cortisol levels. In turn this genetic variation may contribute to cortisol-associated degenerative diseases. -
Eaves, L. J., St Pourcain, B., Smith, G. D., York, T. P., & Evans, D. M. (2014). Resolving the Effects of Maternal and Offspring Genotype on Dyadic Outcomes in Genome Wide Complex Trait Analysis (“M-GCTA”). Behavior Genetics, 44(5), 445-455. doi:10.1007/s10519-014-9666-6.
Abstract
Genome wide complex trait analysis (GCTA) is extended to include environmental effects of the maternal genotype on offspring phenotype (“maternal effects”, M-GCTA). The model includes parameters for the direct effects of the offspring genotype, maternal effects and the covariance between direct and maternal effects. Analysis of simulated data, conducted in OpenMx, confirmed that model parameters could be recovered by full information maximum likelihood (FIML) and evaluated the biases that arise in conventional GCTA when indirect genetic effects are ignored. Estimates derived from FIML in OpenMx showed very close agreement to those obtained by restricted maximum likelihood using the published algorithm for GCTA. The method was also applied to illustrative perinatal phenotypes from ~4,000 mother-offspring pairs from the Avon Longitudinal Study of Parents and Children. The relative merits of extended GCTA in contrast to quantitative genetic approaches based on analyzing the phenotypic covariance structure of kinships are considered. -
Guggenheim, J. A., Williams, C., Northstone, K., Howe, L. D., Tilling, K., St Pourcain, B., McMahon, G., & Lawlor, D. A. (2014). Does Vitamin D Mediate the Protective Effects of Time Outdoors On Myopia? Findings From a Prospective Birth Cohort. Investigative Ophthalmology & Visual Science, 55(12), 8550-8558. doi:10.1167/iovs.14-15839.
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Kemp, J. P., Sayers, A., Paternoster, L., Evans, D. M., Deere, K., St Pourcain, B., Timpson, N. J., Ring, S. M., Lorentzon, M., Lehtimäki, T., Eriksson, J., Kähönen, M., Raitakari, O., Laaksonen, M., Sievänen, H., Viikari, J., Lyytikäinen, L.-P., Smith, G. D., Fraser, W. D., Vandenput, L. and 2 moreKemp, J. P., Sayers, A., Paternoster, L., Evans, D. M., Deere, K., St Pourcain, B., Timpson, N. J., Ring, S. M., Lorentzon, M., Lehtimäki, T., Eriksson, J., Kähönen, M., Raitakari, O., Laaksonen, M., Sievänen, H., Viikari, J., Lyytikäinen, L.-P., Smith, G. D., Fraser, W. D., Vandenput, L., Ohlsson, C., & Tobias, J. H. (2014). Does Bone Resorption Stimulate Periosteal Expansion? A Cross-Sectional Analysis of β-C-telopeptides of Type I Collagen (CTX), Genetic Markers of the RANKL Pathway, and Periosteal Circumference as Measured by pQCT. Journal of Bone and Mineral Research, 29(4), 1015-1024. doi:10.1002/jbmr.2093.
Abstract
We hypothesized that bone resorption acts to increase bone strength through stimulation of periosteal expansion. Hence, we examined whether bone resorption, as reflected by serum β-C-telopeptides of type I collagen (CTX), is positively associated with periosteal circumference (PC), in contrast to inverse associations with parameters related to bone remodeling such as cortical bone mineral density (BMDC ). CTX and mid-tibial peripheral quantitative computed tomography (pQCT) scans were available in 1130 adolescents (mean age 15.5 years) from the Avon Longitudinal Study of Parents and Children (ALSPAC). Analyses were adjusted for age, gender, time of sampling, tanner stage, lean mass, fat mass, and height. CTX was positively related to PC (β=0.19 [0.13, 0.24]) (coefficient=SD change per SD increase in CTX, 95% confidence interval)] but inversely associated with BMDC (β=-0.46 [-0.52,-0.40]) and cortical thickness [β=-0.11 (-0.18, -0.03)]. CTX was positively related to bone strength as reflected by the strength-strain index (SSI) (β=0.09 [0.03, 0.14]). To examine the causal nature of this relationship, we then analyzed whether single-nucleotide polymorphisms (SNPs) within key osteoclast regulatory genes, known to reduce areal/cortical BMD, conversely increase PC. Fifteen such genetic variants within or proximal to genes encoding receptor activator of NF-κB (RANK), RANK ligand (RANKL), and osteoprotegerin (OPG) were identified by literature search. Six of the 15 alleles that were inversely related to BMD were positively related to CTX (p<}0.05 cut-off) (n=2379). Subsequently, we performed a meta-analysis of associations between these SNPs and PC in ALSPAC (n=3382), Gothenburg Osteoporosis and Obesity Determinants (GOOD) (n=938), and the Young Finns Study (YFS) (n=1558). Five of the 15 alleles that were inversely related to BMD were positively related to PC (p{<0.05 cut-off). We conclude that despite having lower BMD, individuals with a genetic predisposition to higher bone resorption have greater bone size, suggesting that higher bone resorption is permissive for greater periosteal expansion.Additional information
http://onlinelibrary.wiley.com/doi/10.1002/jbmr.2093/suppinfo -
Kemp, J. P., Medina-Gomez, C., Estrada, K., St Pourcain, B., Heppe, D. H. M., Warrington, N. M., Oei, L., Ring, S. M., Kruithof, C. J., Timpson, N. J., Wolber, L. E., Reppe, S., Gautvik, K., Grundberg, E., Ge, B., van der Eerden, B., van de Peppel, J., Hibbs, M. A., Ackert-Bicknell, C. L., Choi, K. and 13 moreKemp, J. P., Medina-Gomez, C., Estrada, K., St Pourcain, B., Heppe, D. H. M., Warrington, N. M., Oei, L., Ring, S. M., Kruithof, C. J., Timpson, N. J., Wolber, L. E., Reppe, S., Gautvik, K., Grundberg, E., Ge, B., van der Eerden, B., van de Peppel, J., Hibbs, M. A., Ackert-Bicknell, C. L., Choi, K., Koller, D. L., Econs, M. J., Williams, F. M. K., Foroud, T., Zillikens, M. C., Ohlsson, C., Hofman, A., Uitterlinden, A. G., Davey Smith, G., Jaddoe, V. W. V., Tobias, J. H., Rivadeneira, F., & Evans, D. M. (2014). Phenotypic dissection of bone mineral density reveals skeletal site specificity and facilitates the identification of novel loci in the genetic regulation of bone mass attainment. PLoS Genetics, 10(6): e1004423. doi:10.1371/journal.pgen.1004423.
Abstract
Heritability of bone mineral density (BMD) varies across skeletal sites, reflecting different relative contributions of genetic and environmental influences. To quantify the degree to which common genetic variants tag and environmental factors influence BMD, at different sites, we estimated the genetic (rg) and residual (re) correlations between BMD measured at the upper limbs (UL-BMD), lower limbs (LL-BMD) and skull (SK-BMD), using total-body DXA scans of ∼ 4,890 participants recruited by the Avon Longitudinal Study of Parents and their Children (ALSPAC). Point estimates of rg indicated that appendicular sites have a greater proportion of shared genetic architecture (LL-/UL-BMD rg = 0.78) between them, than with the skull (UL-/SK-BMD rg = 0.58 and LL-/SK-BMD rg = 0.43). Likewise, the residual correlation between BMD at appendicular sites (r(e) = 0.55) was higher than the residual correlation between SK-BMD and BMD at appendicular sites (r(e) = 0.20-0.24). To explore the basis for the observed differences in rg and re, genome-wide association meta-analyses were performed (n ∼ 9,395), combining data from ALSPAC and the Generation R Study identifying 15 independent signals from 13 loci associated at genome-wide significant level across different skeletal regions. Results suggested that previously identified BMD-associated variants may exert site-specific effects (i.e. differ in the strength of their association and magnitude of effect across different skeletal sites). In particular, variants at CPED1 exerted a larger influence on SK-BMD and UL-BMD when compared to LL-BMD (P = 2.01 × 10(-37)), whilst variants at WNT16 influenced UL-BMD to a greater degree when compared to SK- and LL-BMD (P = 2.31 × 10(-14)). In addition, we report a novel association between RIN3 (previously associated with Paget's disease) and LL-BMD (rs754388: β = 0.13, SE = 0.02, P = 1.4 × 10(-10)). Our results suggest that BMD at different skeletal sites is under a mixture of shared and specific genetic and environmental influences. Allowing for these differences by performing genome-wide association at different skeletal sites may help uncover new genetic influences on BMD.Additional information
http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1004423#s5 -
St Pourcain, B., Cents, R. A., Whitehouse, A. J., Haworth, C. M., Davis, O. S., O’Reilly, P. F., Roulstone, S., Wren, Y., Ang, Q. W., Velders, F. P., Evans, D. M., Kemp, J. P., Warrington, N. M., Miller, L., Timpson, N. J., Ring, S. M., Verhulst, F. C., Hofman, A., Rivadeneira, F., Meaburn, E. L. and 12 moreSt Pourcain, B., Cents, R. A., Whitehouse, A. J., Haworth, C. M., Davis, O. S., O’Reilly, P. F., Roulstone, S., Wren, Y., Ang, Q. W., Velders, F. P., Evans, D. M., Kemp, J. P., Warrington, N. M., Miller, L., Timpson, N. J., Ring, S. M., Verhulst, F. C., Hofman, A., Rivadeneira, F., Meaburn, E. L., Price, T. S., Dale, P. S., Pillas, D., Yliherva, A., Rodriguez, A., Golding, J., Jaddoe, V. W., Jarvelin, M.-R., Plomin, R., Pennell, C. E., Tiemeier, H., & Davey Smith, G. (2014). Common variation near ROBO2 is associated with expressive vocabulary in infancy. Nature Communications, 5: 4831. doi:10.1038/ncomms5831.
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St Pourcain, B., Skuse, D. H., Mandy, W. P., Wang, K., Hakonarson, H., Timpson, N. J., Evans, D. M., Kemp, J. P., Ring, S. M., McArdle, W. L., Golding, J., & Smith, G. D. (2014). Variability in the common genetic architecture of social-communication spectrum phenotypes during childhood and adolescence. Molecular Autism, 5: 18. doi:10.1186/2040-2392-5-18.
Abstract
Background Social-communication abilities are heritable traits, and their impairments overlap with the autism continuum. To characterise the genetic architecture of social-communication difficulties developmentally and identify genetic links with the autistic dimension, we conducted a genome-wide screen of social-communication problems at multiple time-points during childhood and adolescence. Methods Social-communication difficulties were ascertained at ages 8, 11, 14 and 17 years in a UK population-based birth cohort (Avon Longitudinal Study of Parents and Children; N ≤ 5,628) using mother-reported Social Communication Disorder Checklist scores. Genome-wide Complex Trait Analysis (GCTA) was conducted for all phenotypes. The time-points with the highest GCTA heritability were subsequently analysed for single SNP association genome-wide. Type I error in the presence of measurement relatedness and the likelihood of observing SNP signals near known autism susceptibility loci (co-location) were assessed via large-scale, genome-wide permutations. Association signals (P ≤ 10−5) were also followed up in Autism Genetic Resource Exchange pedigrees (N = 793) and the Autism Case Control cohort (Ncases/Ncontrols = 1,204/6,491). Results GCTA heritability was strongest in childhood (h2(8 years) = 0.24) and especially in later adolescence (h2(17 years) = 0.45), with a marked drop during early to middle adolescence (h2(11 years) = 0.16 and h2(14 years) = 0.08). Genome-wide screens at ages 8 and 17 years identified for the latter time-point evidence for association at 3p22.2 near SCN11A (rs4453791, P = 9.3 × 10−9; genome-wide empirical P = 0.011) and suggestive evidence at 20p12.3 at PLCB1 (rs3761168, P = 7.9 × 10−8; genome-wide empirical P = 0.085). None of these signals contributed to risk for autism. However, the co-location of population-based signals and autism susceptibility loci harbouring rare mutations, such as PLCB1, is unlikely to be due to chance (genome-wide empirical Pco-location = 0.007). Conclusions Our findings suggest that measurable common genetic effects for social-communication difficulties vary developmentally and that these changes may affect detectable overlaps with the autism spectrum.Additional information
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Stergiakouli, E., Gaillard, R., Tavaré, J. M., Balthasar, N., Loos, R. J., Taal, H. R., Evans, D. M., Rivadeneira, F., St Pourcain, B., Uitterlinden, A. G., Kemp, J. P., Hofman, A., Ring, S. M., Cole, T. J., Jaddoe, V. W. V., Davey Smith, G., & Timpson, N. J. (2014). Genome-wide association study of height-adjusted BMI in childhood identifies functional variant in ADCY3. Obesity, 22(10), 2252-2259. doi:10.1002/oby.20840.
Abstract
OBJECTIVE: Genome-wide association studies (GWAS) of BMI are mostly undertaken under the assumption that "kg/m(2) " is an index of weight fully adjusted for height, but in general this is not true. The aim here was to assess the contribution of common genetic variation to a adjusted version of that phenotype which appropriately accounts for covariation in height in children. METHODS: A GWAS of height-adjusted BMI (BMI[x] = weight/height(x) ), calculated to be uncorrelated with height, in 5809 participants (mean age 9.9 years) from the Avon Longitudinal Study of Parents and Children (ALSPAC) was performed. RESULTS: GWAS based on BMI[x] yielded marked differences in genomewide results profile. SNPs in ADCY3 (adenylate cyclase 3) were associated at genome-wide significance level (rs11676272 (0.28 kg/m(3.1) change per allele G (0.19, 0.38), P = 6 × 10(-9) ). In contrast, they showed marginal evidence of association with conventional BMI [rs11676272 (0.25 kg/m(2) (0.15, 0.35), P = 6 × 10(-7) )]. Results were replicated in an independent sample, the Generation R study. CONCLUSIONS: Analysis of BMI[x] showed differences to that of conventional BMI. The association signal at ADCY3 appeared to be driven by a missense variant and it was strongly correlated with expression of this gene. Our work highlights the importance of well understood phenotype use (and the danger of convention) in characterising genetic contributions to complex traits.Additional information
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Ward, M. E., McMahon, G., St Pourcain, B., Evans, D. M., Rietveld, C. A., Benjamin, D. J., Koellinger, P. D., Cesarini, D., Smith, G. D., Timpson, N. J., & Consortium}, {. S. G. A. (2014). Genetic variation associated with differential educational attainment in adults has anticipated associations with school performance in children. PLoS ONE, 9(7): e100248. doi:10.1371/journal.pone.0100248.
Abstract
Genome-wide association study results have yielded evidence for the association of common genetic variants with crude measures of completed educational attainment in adults. Whilst informative, these results do not inform as to the mechanism of these effects or their presence at earlier ages and where educational performance is more routinely and more precisely assessed. Single nucleotide polymorphisms exhibiting genome-wide significant associations with adult educational attainment were combined to derive an unweighted allele score in 5,979 and 6,145 young participants from the Avon Longitudinal Study of Parents and Children with key stage 3 national curriculum test results (SATS results) available at age 13 to 14 years in English and mathematics respectively. Standardised (z-scored) results for English and mathematics showed an expected relationship with sex, with girls exhibiting an advantage over boys in English (0.433 SD (95%CI 0.395, 0.470), p<10-10) with more similar results (though in the opposite direction) in mathematics (0.042 SD (95%CI 0.004, 0.080), p = 0.030). Each additional adult educational attainment increasing allele was associated with 0.041 SD (95%CI 0.020, 0.063), p = 1.79×10-04 and 0.028 SD (95%CI 0.007, 0.050), p = 0.01 increases in standardised SATS score for English and mathematics respectively. Educational attainment is a complex multifactorial behavioural trait which has not had heritable contributions to it fully characterised. We were able to apply the results from a large study of adult educational attainment to a study of child exam performance marking events in the process of learning rather than realised adult end product. Our results support evidence for common, small genetic contributions to educational attainment, but also emphasise the likely lifecourse nature of this genetic effect. Results here also, by an alternative route, suggest that existing methods for child examination are able to recognise early life variation likely to be related to ultimate educational attainment.Additional information
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0100248#s5
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