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1.  Association of total protein intake with bone mineral density (BMD) and bone loss in men and women from the Framingham Offspring Study 
Public health nutrition  2013;17(11):2570-2576.
Objective
To examine the association of % of total energy from protein (protein%) with bone mineral density (BMD, g/cm2) and bone loss at the femoral neck (FN), trochanter (TR); L2–L4 spine (LS). To examine calcium as an effect modifier.
Setting
The Framingham Offspring Study.
Subjects
1,280 men and 1,639 women completed an FFQ in 1992–95 or 1995–98 and baseline DXA-BMD measurement in 1996–2000. 495 men and 680 women had follow-up BMD measured in 2002–2005.
Design
Cohort study using multivariable regression to examine the association of protein% with each BMD, adjusting for covariates. Statistical interaction between protein% and calcium (total, dietary; supplemental) intake was examined.
Results
The mean age at baseline was 61y(±9). In the cross-sectional analyses, protein% was positively associated with all BMD sites (P:0.02–0.04) in women but not in men. Significant interactions were observed with total calcium intake (<800 vs. ≥800 mg/d) in women at all bone sites (P:0.002–0.02). Upon stratification, protein% was positively associated with all BMD sites (P:0.04–0.10) in women with low calcium intakes but not with high calcium intakes. In the longitudinal analyses, in men, higher protein% was associated with more TR-bone loss (P=0.01) while no associations were seen in women, regardless of calcium intake.
Conclusion
This suggests that greater protein intake benefits women especially those with lower calcium intakes. However, protein effects are not significant for short term changes in bone density. Contrastingly, in men, higher protein intakes lead to greater TR-bone loss. Longer follow-up is required to examine the impact of protein on bone loss.
doi:10.1017/S1368980013002875
PMCID: PMC4103961  PMID: 24168918
Protein; bone mineral density; bone loss; diet; calcium
3.  The Challenges of Genome-Wide Interaction Studies: Lessons to Learn from the Analysis of HDL Blood Levels 
PLoS ONE  2014;9(10):e109290.
Genome-wide association studies (GWAS) have revealed 74 single nucleotide polymorphisms (SNPs) associated with high-density lipoprotein cholesterol (HDL) blood levels. This study is, to our knowledge, the first genome-wide interaction study (GWIS) to identify SNP×SNP interactions associated with HDL levels. We performed a GWIS in the Rotterdam Study (RS) cohort I (RS-I) using the GLIDE tool which leverages the massively parallel computing power of Graphics Processing Units (GPUs) to perform linear regression on all genome-wide pairs of SNPs. By performing a meta-analysis together with Rotterdam Study cohorts II and III (RS-II and RS-III), we were able to filter 181 interaction terms with a p-value<1 · 10−8 that replicated in the two independent cohorts. We were not able to replicate any of these interaction term in the AGES, ARIC, CHS, ERF, FHS and NFBC-66 cohorts (Ntotal = 30,011) when adjusting for multiple testing. Our GWIS resulted in the consistent finding of a possible interaction between rs774801 in ARMC8 (ENSG00000114098) and rs12442098 in SPATA8 (ENSG00000185594) being associated with HDL levels. However, p-values do not reach the preset Bonferroni correction of the p-values. Our study suggest that even for highly genetically determined traits such as HDL the sample sizes needed to detect SNP×SNP interactions are large and the 2-step filtering approaches do not yield a solution. Here we present our analysis plan and our reservations concerning GWIS.
doi:10.1371/journal.pone.0109290
PMCID: PMC4203717  PMID: 25329471
4.  Performance of statistical methods on CHARGE targeted sequencing data 
BMC Genetics  2014;15(1):104.
Background
The CHARGE (Cohorts for Heart and Aging Research in Genomic Epidemiology) Sequencing Project is a national, collaborative effort from 3 studies: Framingham Heart Study (FHS), Cardiovascular Health Study (CHS), and Atherosclerosis Risk in Communities (ARIC). It uses a case-cohort design, whereby a random sample of study participants is enriched with participants in extremes of traits. Although statistical methods are available to investigate the role of rare variants, few have evaluated their performance in a case-cohort design.
Results
We evaluate several methods, including the sequence kernel association test (SKAT), Score-Seq, and weighted (Madsen and Browning) and unweighted burden tests. Using genotypes from the CHARGE targeted-sequencing project for FHS (n = 1096), we simulate phenotypes in a large population for 11 correlated traits and then sample individuals to mimic the CHARGE Sequencing study design. We evaluate type I error and power for 77 targeted regions.
Conclusions
We provide some guidelines on the performance of these aggregate-based tests to detect associations with rare variants when applied to case-cohort study designs, using CHARGE targeted sequencing data. Type I error is conservative when we consider variants with minor allele frequency (MAF) < 1%. Power is generally low, although it is relatively larger for Score-Seq. Greater numbers of causal variants and a greater proportion of variance improve the power, but it tends to be lower in the presence of bi-directionality of effects of causal genotypes, especially for Score-Seq.
Electronic supplementary material
The online version of this article (doi:10.1186/s12863-014-0104-9) contains supplementary material, which is available to authorized users.
doi:10.1186/s12863-014-0104-9
PMCID: PMC4197341  PMID: 25277365
Case-cohort design; CHARGE targeted sequencing data; Rare variants; Type I error; Power; SKAT; Score-Seq; Madsen and browning; Burden tests
5.  Sequencing of SCN5A identifies rare and common variants associated with cardiac conduction 
Background
The cardiac sodium channel SCN5A regulates atrioventricular and ventricular conduction. Genetic variants in this gene are associated with PR and QRS intervals. We sought to further characterize the contribution of rare and common coding variation in SCN5A to cardiac conduction.
Methods and Results
In the Cohorts for Heart and Aging Research in Genomic Epidemiology Targeted Sequencing Study (CHARGE), we performed targeted exonic sequencing of SCN5A (n=3699, European-ancestry individuals) and identified 4 common (minor allele frequency >1%) and 157 rare variants. Common and rare SCN5A coding variants were examined for association with PR and QRS intervals through meta-analysis of European ancestry participants from CHARGE, NHLBI’s Exome Sequencing Project (ESP, n=607) and the UK10K (n=1275) and by examining ESP African-ancestry participants (N=972). Rare coding SCN5A variants in aggregate were associated with PR interval in European and African-ancestry participants (P=1.3×10−3). Three common variants were associated with PR and/or QRS interval duration among European-ancestry participants and one among African-ancestry participants. These included two well-known missense variants; rs1805124 (H558R) was associated with PR and QRS shortening in European-ancestry participants (P=6.25×10−4 and P=5.2×10−3 respectively) and rs7626962 (S1102Y) was associated with PR shortening in those of African ancestry (P=2.82×10−3). Among European-ancestry participants, two novel synonymous variants, rs1805126 and rs6599230, were associated with cardiac conduction. Our top signal, rs1805126 was associated with PR and QRS lengthening (P=3.35×10−7 and P=2.69×10−4 respectively), and rs6599230 was associated with PR shortening (P=2.67×10−5).
Conclusions
By sequencing SCN5A, we identified novel common and rare coding variants associated with cardiac conduction.
doi:10.1161/CIRCGENETICS.113.000098
PMCID: PMC4177904  PMID: 24951663
PR interval; QRS interval; genetics; sequencing; cohort
6.  Association of Distinct Variants in SORL1 With Cerebrovascular and Neurodegenerative Changes Related to Alzheimer Disease 
Archives of neurology  2008;65(12):1640-1648.
Background
Single-nucleotide polymorphisms (SNPs) in 2 distinct regions of the gene for the sortilin-related receptor (SORL1) (bounded by consecutively numbered SNPs 8−10 and 22−25) were shown to be associated with Alzheimer disease (AD) in multiple ethnically diverse samples.
Objective
To test the hypothesis that SORL1 is associated with brain magnetic resonance imaging (MRI) measurements of atrophy and/or vascular disease.
Design, Setting, and Patients
We evaluated the association of 30 SNPs spanning SORL1 with MRI measures of general cerebral atrophy, hippocampal atrophy, white matter hyperintensities, and overall cerebrovascular disease in 44 African American and 182 white sibships from the MIRAGE Study. We performed single-and 3-SNP haplotype association analyses using family-based tests. Haplotypes found to be significantly associated with at least 1 MRI trait were tested for association with 6 pathological traits in a separate sample of 69 white patients with autopsy-confirmed AD.
Results
In white patients, white matter hyperintensities were associated with multiple markers in the region encompassing SNPs 6 to 10, whereas cerebral and hippocampal atrophy were associated with markers from the region including SNPs 21 to 26. Examination of specific 3-SNP haplotypes from these 2 regions in the autopsy-confirmed cases of AD revealed association of white matter disease with SNPs 8 to 10 and association of hippocampal atrophy with SNPs 22 to 26. The haplotype CGC at SNPs 8 to 10 was associated with fewer white matter changes in the clinical (P<.001) and autopsy (P=.02) samples.
Conclusions
Variants of SORL1 previously associated with AD are also associated with MRI and neuropathological measures of neurodegenerative and cerebrovascular disease. These findings not only support the hypothesis that multiple areas in SORL1 are of functional importance but also raise the possibility that multiple SORL1 variants influence amyloid precursor protein or endothelial lipoprotein processing or both in different regions of the brain.
doi:10.1001/archneur.65.12.1640
PMCID: PMC2719762  PMID: 19064752
7.  Genome-wide analysis of BMI in adolescents and young adults reveals additional insight into the effects of genetic loci over the life course 
Human Molecular Genetics  2013;22(17):3597-3607.
Genetic loci for body mass index (BMI) in adolescence and young adulthood, a period of high risk for weight gain, are understudied, yet may yield important insight into the etiology of obesity and early intervention. To identify novel genetic loci and examine the influence of known loci on BMI during this critical time period in late adolescence and early adulthood, we performed a two-stage meta-analysis using 14 genome-wide association studies in populations of European ancestry with data on BMI between ages 16 and 25 in up to 29 880 individuals. We identified seven independent loci (P < 5.0 × 10−8) near FTO (P = 3.72 × 10−23), TMEM18 (P = 3.24 × 10−17), MC4R (P = 4.41 × 10−17), TNNI3K (P = 4.32 × 10−11), SEC16B (P = 6.24 × 10−9), GNPDA2 (P = 1.11 × 10−8) and POMC (P = 4.94 × 10−8) as well as a potential secondary signal at the POMC locus (rs2118404, P = 2.4 × 10−5 after conditioning on the established single-nucleotide polymorphism at this locus) in adolescents and young adults. To evaluate the impact of the established genetic loci on BMI at these young ages, we examined differences between the effect sizes of 32 published BMI loci in European adult populations (aged 18–90) and those observed in our adolescent and young adult meta-analysis. Four loci (near PRKD1, TNNI3K, SEC16B and CADM2) had larger effects and one locus (near SH2B1) had a smaller effect on BMI during adolescence and young adulthood compared with older adults (P < 0.05). These results suggest that genetic loci for BMI can vary in their effects across the life course, underlying the importance of evaluating BMI at different ages.
doi:10.1093/hmg/ddt205
PMCID: PMC3736869  PMID: 23669352
8.  Hallux Valgus and Lesser Toe Deformities are Highly Heritable in Adult Men and Women: the Framingham Foot Study 
Arthritis care & research  2013;65(9):1515-1521.
Objective
To estimate heritability of three common disorders affecting the forefoot: hallux valgus, lesser toe deformities and plantar forefoot soft tissue atrophy in adult Caucasian men and women.
Methods
Between 2002-2008, a trained examiner used a validated foot exam to document presence of hallux valgus, lesser toe deformities and plantar soft tissue atrophy in 2,446 adults from the Framingham Foot Study. Among these, 1,370 participants with available pedigree structure were included. Heritability (h2) was estimated using pedigree structures by Sequential Oligogenic Linkage Analysis Routines (SOLAR) package. Results were adjusted for age, sex and BMI.
Results
Mean age of participants was 66 years (range 39 to 99 years) and 57% were female. Prevalence of hallux valgus, lesser toe deformities and plantar soft tissue atrophy was 31%, 29.6% and 28.4%, respectively. Significant h2 was found for hallux valgus (0.29 ~ 0.89, depending on age and sex) and lesser toe deformity (0.49 ~ 0.90 depending on age and sex). The h2 for lesser toe deformity in men and women aged 70+ years was 0.65 (p= 9×10−7). Significant h2 was found for plantar soft tissue atrophy in men and women aged 70+ years (h2 = 0.37; p=3.8×10−3).
Conclusion
To our knowledge, these are the first findings of heritability of foot disorders in humans, and they confirm the widely-held view that hallux valgus and lesser toe deformities are highly heritable in European-descent Caucasian men and women, underscoring the importance of future work to identify genetic determinants of the underlying genetic susceptibility to these common foot disorders.
doi:10.1002/acr.22040
PMCID: PMC3775916  PMID: 23696165
hallux valgus; lesser toe deformities; heritability; fat pad atrophy; foot disorders; pedigree
9.  Trends in the Association of Parental History of Obesity over 60 Years 
Obesity (Silver Spring, Md.)  2014;22(3):919-924.
Objective
The association of familial as compared to genetic factors in the current obesogenic environment, compared to earlier, leaner time periods, is uncertain.
Design and Methods
Participants from the Framingham Heart Study were classified according to parental obesity status in the Original, Offspring, and Third Generation cohorts; mean BMI levels were estimated and we compared the association of parental history across generations. Finally, a genetic risk score comprised of 32 well-replicated single nucleotide polymorphisms for BMI was examined in association with BMI levels in 1948, 1971, and 2002.
Results
BMI was 1.49 kg/m2 higher per each affected parent among the Offspring, and increased to 2.09 kg/m2 higher among the Third Generation participants (p-value for the cohort comparison=0.007). Parental history of obesity was associated with increased weight gain (p<0.0001) and incident obesity (p=0.009). Despite a stronger association of parental obesity with offspring BMI in more contemporary time periods, we observed no change in the effect size of a BMI genetic risk score from 1948 to 2002 (p=0.11 for test of trend across the time periods).
Conclusions
The association of parental obesity has become stronger in more contemporary time period, whereas the association of a BMI genetic risk score has not changed.
doi:10.1002/oby.20564
PMCID: PMC3887126  PMID: 23836774
obesity; epidemiology; weight change; family history; Framingham Heart Study
10.  Vertebral Size, Bone Density, and Strength in Men and Women Matched for Age and Areal Spine BMD 
To explore the possible mechanisms underlying sex-specific differences in skeletal fragility that may be obscured by two-dimensional areal bone mineral density (aBMD) measures, we compared quantitative computed tomography (QCT)-based vertebral bone measures among pairs of men and women from the Framingham Heart Study Multidetector Computed Tomography Study who were matched for age and spine aBMD. Measurements included vertebral body cross-sectional area (CSA, cm2), trabecular volumetric BMD (Tb.vBMD, g/cm3), integral volumetric BMD (Int.vBMD, g/cm3), estimated vertebral compressive loading and strength (Newtons) at L3, the factor-of-risk (load-to-strength ratio), and vertebral fracture prevalence. We identified 981 male-female pairs (1:1 matching) matched on age (± 1 year) and QCT-derived aBMD of L3 (± 1%), with an average age of 51 years (range 34 to 81 years). Matched for aBMD and age, men had 20% larger vertebral CSA, lower Int.vBMD (−8%) and Tb.vBMD (−9%), 10% greater vertebral compressive strength, 24% greater vertebral compressive loading, and 12% greater factor-of-risk than women (p < 0.0001 for all), as well as higher prevalence of vertebral fracture. After adjusting for height and weight, the differences in CSA and volumetric bone mineral density (vBMD) between men and women were attenuated but remained significant, whereas compressive strength was no longer different. In conclusion, vertebral size, morphology, and density differ significantly between men and women matched for age and spine aBMD, suggesting that men and women attain the same aBMD by different mechanisms. These results provide novel information regarding sex-specific differences in mechanisms that underlie vertebral fragility.
doi:10.1002/jbmr.2067
PMCID: PMC4149904  PMID: 23955966
AGING; BONE MINERAL DENSITY; VERTEBRAL FRACTURE; BIOMECHANICS; OSTEOPOROSIS; POPULATION STUDIES
11.  Comparing baseline and longitudinal measures in association studies 
BMC Proceedings  2014;8(Suppl 1):S84.
In recent years, longitudinal family-based studies have had success in identifying genetic variants that influence complex traits in genome-wide association studies. In this paper, we suggest that longitudinal analyses may contain valuable information that can enable identification of additional associations compared to baseline analyses. Using Genetic Analysis Workshop 18 data, consisting of whole genome sequence data in a pedigree-based sample, we compared 3 methods for the genetic analysis of longitudinal data to an analysis that used baseline data only. These longitudinal methods were (a) longitudinal mixed-effects model; (b) analysis of the mean trait over time; and (c) a 2-stage analysis, with estimation of a random intercept in the first stage and regression of the random intercept on a single-nucleotide polymorphism at the second stage. All methods accounted for the familial correlation among subjects within a pedigree. The analyses considered common variants with minor allele frequency above 5% on chromosome 3. Analyses were performed without knowledge of the simulation model. The 3 longitudinal methods showed consistent results, which were generally different from those found by using only the baseline observation. The gene CACNA2D3, identified by both longitudinal and baseline approaches, had a stronger signal in the longitudinal analysis (p = 2.65 × 10−7) compared to that in the baseline analysis (p = 2.48 × 10−5). The effect size of the longitudinal mixed-effects model and mean trait were higher compared to the 2-stage approach. The longitudinal results provided stable results different from that using 1 observation at baseline and generally had lower p values.
doi:10.1186/1753-6561-8-S1-S84
PMCID: PMC4143666  PMID: 25519412
12.  Genome-wide meta-analysis of observational studies shows common genetic variants associated with macronutrient intake1234 
Background: Macronutrient intake varies substantially between individuals, and there is evidence that this variation is partly accounted for by genetic variants.
Objective: The objective of the study was to identify common genetic variants that are associated with macronutrient intake.
Design: We performed 2-stage genome-wide association (GWA) meta-analysis of macronutrient intake in populations of European descent. Macronutrients were assessed by using food-frequency questionnaires and analyzed as percentages of total energy consumption from total fat, protein, and carbohydrate. From the discovery GWA (n = 38,360), 35 independent loci associated with macronutrient intake at P < 5 × 10−6 were identified and taken forward to replication in 3 additional cohorts (n = 33,533) from the DietGen Consortium. For one locus, fat mass obesity-associated protein (FTO), cohorts with Illumina MetaboChip genotype data (n = 7724) provided additional replication data.
Results: A variant in the chromosome 19 locus (rs838145) was associated with higher carbohydrate (β ± SE: 0.25 ± 0.04%; P = 1.68 × 10−8) and lower fat (β ± SE: −0.21 ± 0.04%; P = 1.57 × 10−9) consumption. A candidate gene in this region, fibroblast growth factor 21 (FGF21), encodes a fibroblast growth factor involved in glucose and lipid metabolism. The variants in this locus were associated with circulating FGF21 protein concentrations (P < 0.05) but not mRNA concentrations in blood or brain. The body mass index (BMI)–increasing allele of the FTO variant (rs1421085) was associated with higher protein intake (β ± SE: 0.10 ± 0.02%; P = 9.96 × 10−10), independent of BMI (after adjustment for BMI, β ± SE: 0.08 ± 0.02%; P = 3.15 × 10−7).
Conclusion: Our results indicate that variants in genes involved in nutrient metabolism and obesity are associated with macronutrient consumption in humans. Trials related to this study were registered at clinicaltrials.gov as NCT00005131 (Atherosclerosis Risk in Communities), NCT00005133 (Cardiovascular Health Study), NCT00005136 (Family Heart Study), NCT00005121 (Framingham Heart Study), NCT00083369 (Genetic and Environmental Determinants of Triglycerides), NCT01331512 (InCHIANTI Study), and NCT00005487 (Multi-Ethnic Study of Atherosclerosis).
doi:10.3945/ajcn.112.052183
PMCID: PMC3652928  PMID: 23636237
13.  Whole Genome Sequence-Based Analysis of a Model Complex Trait, High Density Lipoprotein Cholesterol 
Nature genetics  2013;45(8):899-901.
We describe initial steps for interrogating whole genome sequence (WGS) data to characterize the genetic architecture of a complex trait, such as high density lipoprotein cholesterol (HDL-C). We estimate that common variation contributes more to HDL-C heritability than rare variation, and screening for Mendelian dyslipidemia variants identified individuals with extreme HDL-C. WGS analyses highlight the value of regulatory and non-protein coding regions of the genome in addition to protein coding regions.
doi:10.1038/ng.2671
PMCID: PMC4030301  PMID: 23770607
14.  Genetic variation associated with circulating monocyte count in the eMERGE Network 
Human Molecular Genetics  2013;22(10):2119-2127.
With white blood cell count emerging as an important risk factor for chronic inflammatory diseases, genetic associations of differential leukocyte types, specifically monocyte count, are providing novel candidate genes and pathways to further investigate. Circulating monocytes play a critical role in vascular diseases such as in the formation of atherosclerotic plaque. We performed a joint and ancestry-stratified genome-wide association analyses to identify variants specifically associated with monocyte count in 11 014 subjects in the electronic Medical Records and Genomics Network. In the joint and European ancestry samples, we identified novel associations in the chromosome 16 interferon regulatory factor 8 (IRF8) gene (P-value = 2.78×10(−16), β = −0.22). Other monocyte associations include novel missense variants in the chemokine-binding protein 2 (CCBP2) gene (P-value = 1.88×10(−7), β = 0.30) and a region of replication found in ribophorin I (RPN1) (P-value = 2.63×10(−16), β = −0.23) on chromosome 3. The CCBP2 and RPN1 region is located near GATA binding protein2 gene that has been previously shown to be associated with coronary heart disease. On chromosome 9, we found a novel association in the prostaglandin reductase 1 gene (P-value = 2.29×10(−7), β = 0.16), which is downstream from lysophosphatidic acid receptor 1. This region has previously been shown to be associated with monocyte count. We also replicated monocyte associations of genome-wide significance (P-value = 5.68×10(−17), β = −0.23) at the integrin, alpha 4 gene on chromosome 2. The novel IRF8 results and further replications provide supporting evidence of genetic regions associated with monocyte count.
doi:10.1093/hmg/ddt010
PMCID: PMC3633369  PMID: 23314186
15.  Meta-Analysis of Genome-Wide Scans Provides Evidence for Sex- and Site-Specific Regulation of Bone Mass 
Several genome-wide scans have been performed to detect loci that regulate BMD, but these have yielded inconsistent results, with limited replication of linkage peaks in different studies. In an effort to improve statistical power for detection of these loci, we performed a meta-analysis of genome-wide scans in which spine or hip BMD were studied. Evidence was gained to suggest that several chromosomal loci regulate BMD in a site-specific and sex-specific manner.
Introduction
BMD is a heritable trait and an important predictor of osteoporotic fracture risk. Several genome-wide scans have been performed in an attempt to detect loci that regulate BMD, but there has been limited replication of linkage peaks between studies. In an attempt to resolve these inconsistencies, we conducted a collaborative meta-analysis of genome-wide linkage scans in which femoral neck BMD (FN-BMD) or lumbar spine BMD (LS-BMD) had been studied.
Materials and Methods
Data were accumulated from nine genome-wide scans involving 11,842 subjects. Data were analyzed separately for LS-BMD and FN-BMD and by sex. For each study, genomic bins of 30 cM were defined and ranked according to the maximum LOD score they contained. While various densitometers were used in different studies, the ranking approach that we used means that the results are not confounded by the fact that different measurement devices were used. Significance for high average rank and heterogeneity was obtained through Monte Carlo testing.
Results
For LS-BMD, the quantitative trait locus (QTL) with greatest significance was on chromosome 1p13.3-q23.3 (p = 0.004), but this exhibited high heterogeneity and the effect was specific for women. Other significant LS-BMD QTLs were on chromosomes 12q24.31-qter, 3p25.3-p22.1, 11p12-q13.3, and 1q32-q42.3, including one on 18p11-q12.3 that had not been detected by individual studies. For FN-BMD, the strongest QTL was on chromosome 9q31.1-q33.3 (p = 0.002). Other significant QTLs were identified on chromosomes 17p12-q21.33, 14q13.1-q24.1, 9q21.32-q31.1, and 5q14.3-q23.2. There was no correlation in average ranks of bins between men and women and the loci that regulated BMD in men and women and at different sites were largely distinct.
Conclusions
This large-scale meta-analysis provided evidence for replication of several QTLs identified in previous studies and also identified a QTL on chromosome 18p11-q12.3, which had not been detected by individual studies. However, despite the large sample size, none of the individual loci identified reached genome-wide significance.
doi:10.1359/jbmr.060806
PMCID: PMC4016811  PMID: 17228994
osteoporosis; BMD; linkage; meta-analysis; genome search; genome scan
16.  Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture 
Berndt, Sonja I. | Gustafsson, Stefan | Mägi, Reedik | Ganna, Andrea | Wheeler, Eleanor | Feitosa, Mary F. | Justice, Anne E. | Monda, Keri L. | Croteau-Chonka, Damien C. | Day, Felix R. | Esko, Tõnu | Fall, Tove | Ferreira, Teresa | Gentilini, Davide | Jackson, Anne U. | Luan, Jian’an | Randall, Joshua C. | Vedantam, Sailaja | Willer, Cristen J. | Winkler, Thomas W. | Wood, Andrew R. | Workalemahu, Tsegaselassie | Hu, Yi-Juan | Lee, Sang Hong | Liang, Liming | Lin, Dan-Yu | Min, Josine L. | Neale, Benjamin M. | Thorleifsson, Gudmar | Yang, Jian | Albrecht, Eva | Amin, Najaf | Bragg-Gresham, Jennifer L. | Cadby, Gemma | den Heijer, Martin | Eklund, Niina | Fischer, Krista | Goel, Anuj | Hottenga, Jouke-Jan | Huffman, Jennifer E. | Jarick, Ivonne | Johansson, Åsa | Johnson, Toby | Kanoni, Stavroula | Kleber, Marcus E. | König, Inke R. | Kristiansson, Kati | Kutalik, Zoltán | Lamina, Claudia | Lecoeur, Cecile | Li, Guo | Mangino, Massimo | McArdle, Wendy L. | Medina-Gomez, Carolina | Müller-Nurasyid, Martina | Ngwa, Julius S. | Nolte, Ilja M. | Paternoster, Lavinia | Pechlivanis, Sonali | Perola, Markus | Peters, Marjolein J. | Preuss, Michael | Rose, Lynda M. | Shi, Jianxin | Shungin, Dmitry | Smith, Albert Vernon | Strawbridge, Rona J. | Surakka, Ida | Teumer, Alexander | Trip, Mieke D. | Tyrer, Jonathan | Van Vliet-Ostaptchouk, Jana V. | Vandenput, Liesbeth | Waite, Lindsay L. | Zhao, Jing Hua | Absher, Devin | Asselbergs, Folkert W. | Atalay, Mustafa | Attwood, Antony P. | Balmforth, Anthony J. | Basart, Hanneke | Beilby, John | Bonnycastle, Lori L. | Brambilla, Paolo | Bruinenberg, Marcel | Campbell, Harry | Chasman, Daniel I. | Chines, Peter S. | Collins, Francis S. | Connell, John M. | Cookson, William | de Faire, Ulf | de Vegt, Femmie | Dei, Mariano | Dimitriou, Maria | Edkins, Sarah | Estrada, Karol | Evans, David M. | Farrall, Martin | Ferrario, Marco M. | Ferrières, Jean | Franke, Lude | Frau, Francesca | Gejman, Pablo V. | Grallert, Harald | Grönberg, Henrik | Gudnason, Vilmundur | Hall, Alistair S. | Hall, Per | Hartikainen, Anna-Liisa | Hayward, Caroline | Heard-Costa, Nancy L. | Heath, Andrew C. | Hebebrand, Johannes | Homuth, Georg | Hu, Frank B. | Hunt, Sarah E. | Hyppönen, Elina | Iribarren, Carlos | Jacobs, Kevin B. | Jansson, John-Olov | Jula, Antti | Kähönen, Mika | Kathiresan, Sekar | Kee, Frank | Khaw, Kay-Tee | Kivimaki, Mika | Koenig, Wolfgang | Kraja, Aldi T. | Kumari, Meena | Kuulasmaa, Kari | Kuusisto, Johanna | Laitinen, Jaana H. | Lakka, Timo A. | Langenberg, Claudia | Launer, Lenore J. | Lind, Lars | Lindström, Jaana | Liu, Jianjun | Liuzzi, Antonio | Lokki, Marja-Liisa | Lorentzon, Mattias | Madden, Pamela A. | Magnusson, Patrik K. | Manunta, Paolo | Marek, Diana | März, Winfried | Mateo Leach, Irene | McKnight, Barbara | Medland, Sarah E. | Mihailov, Evelin | Milani, Lili | Montgomery, Grant W. | Mooser, Vincent | Mühleisen, Thomas W. | Munroe, Patricia B. | Musk, Arthur W. | Narisu, Narisu | Navis, Gerjan | Nicholson, George | Nohr, Ellen A. | Ong, Ken K. | Oostra, Ben A. | Palmer, Colin N.A. | Palotie, Aarno | Peden, John F. | Pedersen, Nancy | Peters, Annette | Polasek, Ozren | Pouta, Anneli | Pramstaller, Peter P. | Prokopenko, Inga | Pütter, Carolin | Radhakrishnan, Aparna | Raitakari, Olli | Rendon, Augusto | Rivadeneira, Fernando | Rudan, Igor | Saaristo, Timo E. | Sambrook, Jennifer G. | Sanders, Alan R. | Sanna, Serena | Saramies, Jouko | Schipf, Sabine | Schreiber, Stefan | Schunkert, Heribert | Shin, So-Youn | Signorini, Stefano | Sinisalo, Juha | Skrobek, Boris | Soranzo, Nicole | Stančáková, Alena | Stark, Klaus | Stephens, Jonathan C. | Stirrups, Kathleen | Stolk, Ronald P. | Stumvoll, Michael | Swift, Amy J. | Theodoraki, Eirini V. | Thorand, Barbara | Tregouet, David-Alexandre | Tremoli, Elena | Van der Klauw, Melanie M. | van Meurs, Joyce B.J. | Vermeulen, Sita H. | Viikari, Jorma | Virtamo, Jarmo | Vitart, Veronique | Waeber, Gérard | Wang, Zhaoming | Widén, Elisabeth | Wild, Sarah H. | Willemsen, Gonneke | Winkelmann, Bernhard R. | Witteman, Jacqueline C.M. | Wolffenbuttel, Bruce H.R. | Wong, Andrew | Wright, Alan F. | Zillikens, M. Carola | Amouyel, Philippe | Boehm, Bernhard O. | Boerwinkle, Eric | Boomsma, Dorret I. | Caulfield, Mark J. | Chanock, Stephen J. | Cupples, L. Adrienne | Cusi, Daniele | Dedoussis, George V. | Erdmann, Jeanette | Eriksson, Johan G. | Franks, Paul W. | Froguel, Philippe | Gieger, Christian | Gyllensten, Ulf | Hamsten, Anders | Harris, Tamara B. | Hengstenberg, Christian | Hicks, Andrew A. | Hingorani, Aroon | Hinney, Anke | Hofman, Albert | Hovingh, Kees G. | Hveem, Kristian | Illig, Thomas | Jarvelin, Marjo-Riitta | Jöckel, Karl-Heinz | Keinanen-Kiukaanniemi, Sirkka M. | Kiemeney, Lambertus A. | Kuh, Diana | Laakso, Markku | Lehtimäki, Terho | Levinson, Douglas F. | Martin, Nicholas G. | Metspalu, Andres | Morris, Andrew D. | Nieminen, Markku S. | Njølstad, Inger | Ohlsson, Claes | Oldehinkel, Albertine J. | Ouwehand, Willem H. | Palmer, Lyle J. | Penninx, Brenda | Power, Chris | Province, Michael A. | Psaty, Bruce M. | Qi, Lu | Rauramaa, Rainer | Ridker, Paul M. | Ripatti, Samuli | Salomaa, Veikko | Samani, Nilesh J. | Snieder, Harold | Sørensen, Thorkild I.A. | Spector, Timothy D. | Stefansson, Kari | Tönjes, Anke | Tuomilehto, Jaakko | Uitterlinden, André G. | Uusitupa, Matti | van der Harst, Pim | Vollenweider, Peter | Wallaschofski, Henri | Wareham, Nicholas J. | Watkins, Hugh | Wichmann, H.-Erich | Wilson, James F. | Abecasis, Goncalo R. | Assimes, Themistocles L. | Barroso, Inês | Boehnke, Michael | Borecki, Ingrid B. | Deloukas, Panos | Fox, Caroline S. | Frayling, Timothy | Groop, Leif C. | Haritunian, Talin | Heid, Iris M. | Hunter, David | Kaplan, Robert C. | Karpe, Fredrik | Moffatt, Miriam | Mohlke, Karen L. | O’Connell, Jeffrey R. | Pawitan, Yudi | Schadt, Eric E. | Schlessinger, David | Steinthorsdottir, Valgerdur | Strachan, David P. | Thorsteinsdottir, Unnur | van Duijn, Cornelia M. | Visscher, Peter M. | Di Blasio, Anna Maria | Hirschhorn, Joel N. | Lindgren, Cecilia M. | Morris, Andrew P. | Meyre, David | Scherag, André | McCarthy, Mark I. | Speliotes, Elizabeth K. | North, Kari E. | Loos, Ruth J.F. | Ingelsson, Erik
Nature genetics  2013;45(5):501-512.
Approaches exploiting extremes of the trait distribution may reveal novel loci for common traits, but it is unknown whether such loci are generalizable to the general population. In a genome-wide search for loci associated with upper vs. lower 5th percentiles of body mass index, height and waist-hip ratio, as well as clinical classes of obesity including up to 263,407 European individuals, we identified four new loci (IGFBP4, H6PD, RSRC1, PPP2R2A) influencing height detected in the tails and seven new loci (HNF4G, RPTOR, GNAT2, MRPS33P4, ADCY9, HS6ST3, ZZZ3) for clinical classes of obesity. Further, we show that there is large overlap in terms of genetic structure and distribution of variants between traits based on extremes and the general population and little etiologic heterogeneity between obesity subgroups.
doi:10.1038/ng.2606
PMCID: PMC3973018  PMID: 23563607
17.  Repeat Bone Mineral Density Screening and Prediction of Hip and Major Osteoporotic Fracture 
IMPORTANCE
Screening for osteoporosis with bone mineral density (BMD) is recommended for older adults. It is unclear whether repeating a BMD screening test improves fracture risk assessment.
OBJECTIVES
To determine whether changes in BMD after 4 years provide additional information on fracture risk beyond baseline BMD and to quantify the change in fracture risk classification after a second BMD measure.
DESIGN, SETTING, AND PARTICIPANTS
Population-based cohort study involving 310 men and 492 women from the Framingham Osteoporosis Study with 2 measures of femoral neck BMD taken from 1987 through 1999.
MAIN OUTCOMES AND MEASURES
Risk of hip or major osteoporotic fracture through 2009 or 12 years following the second BMD measure.
RESULTS
Mean age was 74.8 years. The mean (SD) BMD change was −0.6% per year (1.8%). Throughout a median follow-up of 9.6 years, 76 participants experienced an incident hip fracture and 113 participants experienced a major osteoporotic fracture. Annual percent BMD change per SD decrease was associated with risk of hip fracture (hazard ratio [HR], 1.43 [95% CI, 1.16 to 1.78]) and major osteoporotic fracture (HR, 1.21 [95% CI, 1.01 to 1.45]) after adjusting for baseline BMD. At 10 years’ follow-up, 1 SD decrease in annual percent BMD change compared with the mean BMD change was associated with 3.9 excess hip fractures per 100 persons. In receiver operating characteristic (ROC) curve analyses, the addition of BMD change to a model with baseline BMD did not meaningfully improve performance. The area under the curve (AUC) was 0.71 (95% CI, 0.65 to 0.78) for the baseline BMD model compared with 0.68 (95% CI, 0.62 to 0.75) for the BMD percent change model. Moreover, the addition of BMD change to a model with baseline BMD did not meaningfully improve performance (AUC, 0.72 [95% CI, 0.66 to 0.79]). Using the net reclassification index, a second BMD measure increased the proportion of participants reclassified as high risk of hip fracture by 3.9% (95% CI, −2.2% to 9.9%), whereas it decreased the proportion classified as low risk by −2.2% (95% CI, −4.5% to 0.1%).
CONCLUSIONS AND RELEVANCE
In untreated men and women of mean age 75 years, a second BMD measure after 4 years did not meaningfully improve the prediction of hip or major osteoporotic fracture. Repeating a BMD measure within 4 years to improve fracture risk stratification may not be necessary in adults this age untreated for osteoporosis.
doi:10.1001/jama.2013.277817
PMCID: PMC3903386  PMID: 24065012
18.  Meta-Analysis Investigating Associations Between Healthy Diet and Fasting Glucose and Insulin Levels and Modification by Loci Associated With Glucose Homeostasis in Data From 15 Cohorts 
American Journal of Epidemiology  2012;177(2):103-115.
Whether loci that influence fasting glucose (FG) and fasting insulin (FI) levels, as identified by genome-wide association studies, modify associations of diet with FG or FI is unknown. We utilized data from 15 US and European cohort studies comprising 51,289 persons without diabetes to test whether genotype and diet interact to influence FG or FI concentration. We constructed a diet score using study-specific quartile rankings for intakes of whole grains, fish, fruits, vegetables, and nuts/seeds (favorable) and red/processed meats, sweets, sugared beverages, and fried potatoes (unfavorable). We used linear regression within studies, followed by inverse-variance-weighted meta-analysis, to quantify 1) associations of diet score with FG and FI levels and 2) interactions of diet score with 16 FG-associated loci and 2 FI-associated loci. Diet score (per unit increase) was inversely associated with FG (β = −0.004 mmol/L, 95% confidence interval: −0.005, −0.003) and FI (β = −0.008 ln-pmol/L, 95% confidence interval: −0.009, −0.007) levels after adjustment for demographic factors, lifestyle, and body mass index. Genotype variation at the studied loci did not modify these associations. Healthier diets were associated with lower FG and FI concentrations regardless of genotype at previously replicated FG- and FI-associated loci. Studies focusing on genomic regions that do not yield highly statistically significant associations from main-effect genome-wide association studies may be more fruitful in identifying diet-gene interactions.
doi:10.1093/aje/kws297
PMCID: PMC3707424  PMID: 23255780
diabetes; dietary pattern; gene-environment interaction; glucose; insulin
19.  Genetic susceptibility loci for subtypes of breast cancer in an African American population 
Background
Most genome-wide association scans (GWAS) have been carried out in European ancestry populations; no risk variants for breast cancer have been identified solely from African ancestry GWAS data. Few GWAS hits have replicated in African ancestry populations.
Methods
In a nested case-control study of breast cancer in the Black Women’s Health Study (1,199 cases/1,948 controls), we evaluated index SNPs in 21 loci from GWAS of European or Asian ancestry populations, overall, in subtypes defined by estrogen (ER) and progesterone (PR) receptor status (ER+/PR+, n=336; ER−/PR−, n=229), and in triple-negative breast cancer (TNBC, N=81). To evaluate the contribution of genetic factors to population differences in breast cancer subtype, we also examined global percent African ancestry.
Results
Index SNPs in five loci were replicated, including three associated with ER−/PR− breast cancer (TERT rs10069690 in 5p15.33, rs704010 in 10q22.3, and rs8170 in 19p13.11): per allele odds ratios were 1.29 (95% confidence interval (CI) 1.04–1.59), p=0.02, 1.52 (95% CI 1.12–2.08), p=0.01, and 1.30 (95% CI 1.01–1.68), p=0.04, respectively. Stronger associations were observed for TNBC. Furthermore, cases in the highest quintile of percent African ancestry were three times more likely to have TNBC than ER+/PR+ cancer.
Conclusions
These findings provide the first confirmation of the TNBC SNP rs8170 in an African ancestry population, and independent confirmation of the TERT ER− SNP. Further, the risk of developing ER− breast cancer, particularly TNBC, increased with increasing proportion of global African ancestry.
Impact
The findings demonstrate the importance of genetic factors in the disproportionately high occurrence of TNBC in African American women.
doi:10.1158/1055-9965.EPI-12-0769
PMCID: PMC3538887  PMID: 23136140
breast carcinoma; triple-negative; genetic susceptibility; GWAS replication; African-American; SNPs
20.  Relations of Long-Term and Contemporary Lipid Levels and Lipid Genetic Risk Scores with Coronary Artery Calcium in the Framingham Heart Study 
Objectives
This study evaluated the association of timing of lipid levels and lipid genetic risk score (GRS) with subclinical atherosclerosis.
Background
Atherosclerosis is a slowly progressive disorder influenced by suboptimal lipid levels. Long-term versus contemporary lipid levels may more strongly impact the development of coronary artery calcium (CAC).
Methods
Framingham Heart Study (FHS) Offspring Cohort participants (n=1156, 44%M, 63±9 years) underwent serial fasting lipids [low-density lipoprotein (LDL-C), high-density lipoprotein, and triglycerides], Exam 1 (1971–1975) – Exam 7 (1998–2001). FHS Third Generation Cohort participants (n=1954, 55%M, 45±6 years) had fasting lipid profiles assessed, 2002–2005. Computed tomography (2002–2005) measured CAC. Lipid GRSs were computed from significantly associated single nucleotide polymorphisms. The association between early, long-term average, and contemporary lipids, and lipid GRS, with elevated CAC was assessed using logistic regression.
Results
In FHS Offspring, Exam 1 and long-term average versus Exam 7 lipid measurements, including untreated lipid levels, were strongly associated with elevated CAC. In the FHS Third Generation, contemporary lipids were associated with CAC. The LDL-C GRS was associated with CAC (age/sex-adjusted OR 1.14, 95%CI 1.00–1.29, p=0.04). However, addition of the GRS to the lipid models did not result in a significant increase in the OR or C-statistic for any lipid measure.
Conclusions
Early and long-term average lipid levels, as compared with contemporary measures, are more strongly associated with elevated CAC. Lipid GRS was associated with lipid levels but did not predict elevated CAC. Adult early and long-term average lipid levels provide important information when assessing subclinical atherosclerosis and cardiovascular risk.
doi:10.1016/j.jacc.2012.09.007
PMCID: PMC3702262  PMID: 23141485
Lipids; Genetic risk score; Coronary artery calcium
21.  Procollagen type III N-terminal peptide (P3NP) and lean mass: a cross-sectional study 
Background
Procollagen type III N-terminal peptide (P3NP) is released during collagen synthesis in muscle. Increased circulating P3NP is a marker not only of muscle growth, but also of muscle repair and fibrosis. Thus, P3NP may be a potential biomarker for sarcopenia.
Objective
To determine the association between plasma P3NP and lean mass and strength
Design, Setting, and Participants
A cross-sectional study of men and women from the Framingham Offspring Study. Participants included a convenience sample of 687 members with a measure of plasma P3NP and lean mass, and 806 members with P3NP and quadriceps strength assessment.
Measurements
Linear regression was used to estimate the association between total and appendicular lean mass and plasma P3NP, and quadriceps strength and P3NP
Results
Mean age was 58 years. Median plasma P3NP was similar in men (3.4 mg/L), premenopausal women (3.1 mg/L), and postmenopausal women (3.0 mg/L). In adjusted models, higher P3NP was associated with a modest decrease in total and appendicular lean mass in postmenopausal women [β= −0.13 unit P3NP/kg total lean mass; p=0.003]. A similar trend was found among premenopausal women, although results were not statistically significant [β=−0.10 unit P3NP/kg total lean mass; p=0.41]. No association between P3NP and lean mass was observed in men. P3NP was not associated with strength in men or women.
Conclusion
Our results suggest that plasma P3NP might be a useful biomarker of muscle mass in postmenopausal women if longitudinal studies demonstrate that it has adequate sensitivity and specificity to predict muscle loss.
PMCID: PMC3828748  PMID: 24244927
procollagen type III N-telopeptide; P3NP; lean mass
22.  Identification of Novel Candidate Genes for Alzheimer Disease by Autozygosity Mapping Using Genome Wide SNP Data From an Israeli-Arab Community 
Journal of Alzheimer's disease : JAD  2011;23(2):10.3233/JAD-2010-100714.
Alzheimer disease (AD) is highly prevalent in Wadi Ara, despite the low frequency of APOE ε4 in this genetically isolated Arab community in northern Israel. We hypothesized that the reduced genetic variability in combination with increased homozygosity would facilitate identification of genetic variants that contribute to the high rate of AD in this community. AD cases (N=124) and controls (N=142) from Wadi Ara were genotyped for a a genome-wide set of more than 300,000 single nucleotides polymorphisms (SNPs) which were used to calculate measures of population stratification and inbreeding, and to identify regions of autozygosity. Although a high degree of relatedness was evident in both cases and controls, controls were significantly more related and contained more autozygous regions than cases (P = 0.004). Eight autozygous regions on seven different chromosomes were more frequent in controls than cases, and 105 SNPs in these regions, primarily on chromosomes 6 and 9, were nominally associated with AD. Associations with SNPs in NOTCH4 and AGPAT1 (both on chromosome 6) were confirmed in a meta analysis of four genome-wide association study (GWAS) datasets. Analysis of the full Wadi Ara GWAS dataset revealed 99 SNP associations with AD at P ≤ 10−5, however none of these were confirmed in the replication GWAS datasets. The unique population structure of Wadi Ara enhanced efforts to identify genetic variants that might partially explain the high prevalence of AD in the region. Several of these variants show modest evidence for association in other Caucasian populations.
doi:10.3233/JAD-2010-100714
PMCID: PMC3819807  PMID: 21098978
Alzheimer Disease; Genome-Wide Association Study; Population Groups; Meta-Analysis
24.  Small Dense Low Density Lipoprotein Cholesterol and Coronary Heart Disease: Results from the Framingham Offspring Study 
Clinical chemistry  2010;56(6):967-976.
Objective
A direct assay for small dense low density lipoprotein cholesterol (sdLDL-C) has been developed. Our goal was to establish normal ranges for this assay as well as to measure values in patients with established coronary heart disease (CHD) versus control subjects.
Methods
Direct LDL-C and sdLDL-C analyses were carried out on samples from 3,188 male and female participants of the Framingham Offspring Study, which included 173 male and 74 female CHD cases.
Results
Male gender and female postmenopausal status were both associated with significantly (p<0.0001) higher sdLDL-C values. Use of cholesterol-lowering medications was significantly (p<0.0001) higher in CHD cases than in controls (46.8% versus 11.4% in men, and 35.1% versus 8.8% in women). Direct LDL-C levels were significantly lower in male CHD patients than in male controls (3.22 versus 3.51 mmol/L, p<0.0001), but their mean sdLDL-C levels were similar to those in controls (0.83 versus 0.84 mmol/L, p=0.609). Female CHD patients had similar LDL-C values to female controls (3.53 versus 3.46 mmol/L, p=0.543), but had significantly higher sdLDL-C values (0.83 versus 0.68 mmol/L, p=0.0015). Both male and female cases also had significantly (p<0.01) higher percentages of LDL-C as sdLDLC than controls.
Conclusions
Despite four fold greater cholesterol lowering therapy use, CHD patients had mean LDL-C values well above the LDL-C goal of < 2.6 mmol/L or 100 mg/dl, and male CHD cases had similar sdLDL C values and female CHD cases had significantly higher values than controls. These findings may explain some of the high residual risk of future CHD events in CHD patients.
doi:10.1373/clinchem.2009.137489
PMCID: PMC3791882  PMID: 20431054
small dense LDL-cholesterol; coronary heart disease; risk factor; Framingham Offspring Study; obesity
25.  Assessment of Gene-by-Sex Interaction Effect on Bone Mineral Density 
Liu, Ching-Ti | Estrada, Karol | Yerges-Armstrong, Laura M. | Amin, Najaf | Evangelou, Evangelos | Li, Guo | Minster, Ryan L. | Carless, Melanie A. | Kammerer, Candace M. | Oei, Ling | Zhou, Yanhua | Alonso, Nerea | Dailiana, Zoe | Eriksson, Joel | García-Giralt, Natalia | Giroux, Sylvie | Husted, Lise Bjerre | Khusainova, Rita I. | Koromila, Theodora | Kung, Annie WaiChee | Lewis, Joshua R. | Masi, Laura | Mencej-Bedrac, Simona | Nogues, Xavier | Patel, Millan S. | Prezelj, Janez | Richards, J Brent | Sham, Pak Chung | Spector, Timothy | Vandenput, Liesbeth | Xiao, Su-Mei | Zheng, Hou-Feng | Zhu, Kun | Balcells, Susana | Brandi, Maria Luisa | Frost, Morten | Goltzman, David | González-Macías, Jesús | Karlsson, Magnus | Khusnutdinova, Elza K. | Kollia, Panagoula | Langdahl, Bente Lomholt | Ljunggren, Östen | Lorentzon, Mattias | Marc, Janja | Mellström, Dan | Ohlsson, Claes | Olmos, José M. | Ralston, Stuart H. | Riancho, José A. | Rousseau, François | Urreizti, Roser | Van Hul, Wim | Zarrabeitia, María T. | Castano-Betancourt, Martha | Demissie, Serkalem | Grundberg, Elin | Herrera, Lizbeth | Kwan, Tony | Medina-Gómez, Carolina | Pastinen, Tomi | Sigurdsson, Gunnar | Thorleifsson, Gudmar | vanMeurs, Joyce B.J. | Blangero, John | Hofman, Albert | Liu, Yongmei | Mitchell, Braxton D. | O’Connell, Jeffrey R. | Oostra, Ben A. | Rotter, Jerome I | Stefansson, Kari | Streeten, Elizabeth A. | Styrkarsdottir, Unnur | Thorsteinsdottir, Unnur | Tylavsky, Frances A. | Uitterlinden, Andre | Cauley, Jane A. | Harris, Tamara B. | Ioannidis, John P.A. | Psaty, Bruce M. | Robbins, John A | Zillikens, M. Carola | vanDuijn, Cornelia M. | Prince, Richard L. | Karasik, David | Rivadeneira, Fernando | Kiel, Douglas P. | Cupples, L. Adrienne | Hsu, Yi-Hsiang
Background
Sexual dimorphism in various bone phenotypes, including bone mineral density (BMD), is widely observed; however the extent to which genes explain these sex differences is unclear. To identify variants with different effects by sex, we examined gene-by-sex autosomal interactions genome-wide, and performed eQTL analysis and bioinformatics network analysis.
Methods
We conducted an autosomal genome-wide meta-analysis of gene-by-sex interaction on lumbar spine (LS-) and femoral neck (FN-) BMD, in 25,353 individuals from eight cohorts. In a second stage, we followed up the 12 top SNPs (P<1×10−5) in an additional set of 24,763 individuals. Gene-by-sex interaction and sex-specific effects were examined in these 12 SNPs.
Results
We detected one novel genome-wide significant interaction associated with LS-BMD at the Chr3p26.1-p25.1 locus, near the GRM7 gene (male effect = 0.02 & p-value = 3.0×10−5; female effect = −0.007 & p-value=3.3×10−2) and eleven suggestive loci associated with either FN- or LS-BMD in discovery cohorts. However, there was no evidence for genome-wide significant (P<5×10−8) gene-by-sex interaction in the joint analysis of discovery and replication cohorts.
Conclusion
Despite the large collaborative effort, no genome-wide significant evidence for gene-by-sex interaction was found influencing BMD variation in this screen of autosomal markers. If they exist, gene-by-sex interactions for BMD probably have weak effects, accounting for less than 0.08% of the variation in these traits per implicated SNP.
doi:10.1002/jbmr.1679
PMCID: PMC3447125  PMID: 22692763
gene-by-sex; interaction; BMD; association; aging

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