| Literature DB >> 23094032 |
Koenraad Frans Cuypers1, Ruth J F Loos, Kirsti Kvaløy, Bettina Kulle, Pål Romundstad, Turid Lingaas Holmen.
Abstract
INTRODUCTION: Obesity-susceptibility loci have been related to adiposity traits in adults and may affect body fat estimates in adolescence. There are indications that different sets of obesity-susceptibility loci influence level of and change in obesity-related traits from adolescence to adulthood.Entities:
Mesh:
Year: 2012 PMID: 23094032 PMCID: PMC3477114 DOI: 10.1371/journal.pone.0046912
Source DB: PubMed Journal: PLoS One ISSN: 1932-6203 Impact factor: 3.240
Genotype information and quality control statistics for the 9 obesity-susceptibility variants included in the study.
| SNP | Chrom. | Position | Nearest gene | Effect allele | Effect allele | Other allele | References | Call rate | Genotype freq | HWE | |||
| frequency | Risk allele homozygous | Heterozygous | Other allele homo | p-value | |||||||||
| % | % | % | % | ||||||||||
| rs2815752 | 1 | 72585028 | NEGR1 | A | 59.2 | G | 1,6 | 99.7 | 34.5 | 49.3 | 16.2 | 0.525 | |
| rs6548238 | 2 | 624905 | TMEM18 | C | 83.7 | T | 1,6 | 99.4 | 69.9 | 27.5 | 2.6 | 0.669 | |
| rs10938397 | 4 | 44877284 | GNPDA2 | G | 38.8 | A | 1,6 | 99.4 | 15.2 | 47.3 | 37.6 | 0.765 | |
| rs987237 | 6 | 50911009 | TFAP2B | G | 17.7 | A | 9 | 98.4 | 3.3 | 28.8 | 67.9 | 0.745 | |
| rs10838738 | 11 | 47619625 | MTCH2 | G | 36.3 | A | 1,6 | 99.6 | 13.9 | 44.7 | 41.4 | 0.221 | |
| rs4074134 | 11 | 27603861 | BDNF | G | 81.5 | A | 7,8 | 99.7 | 66.4 | 30.2 | 3.4 | 0.752 | |
| rs1121980 | 16 | 52366748 | In FTO | A | 44.4 | G | 1,3 | 99.7 | 18.9 | 51.0 | 30.1 | 0.139 | |
| rs17782313 | 18 | 56002077 | MC4R | C | 26.9 | T | 4 | 98.4 | 6.7 | 40.4 | 52.9 | 0.203 | |
| rs11084753 | 19 | 39013977 | KCTD15 | G | 69.5 | A | 1,6 | 99.2 | 47.6 | 43.7 | 8.7 | 0.181 | |
Article reference: 1) Loos et al., 2009; 2) Hinney et al., 2007; 3) Loos et al., 2008; 4) Willer et al., 2009; 5) Zhao et al., 2009; 6) Thorleifson et al., 2009;
HWE: Hardy-Weinberg equilibrium; Call-rate: rate of successful genotyping. All variants passed initial quality-control criteria with a call-rate ≥95% and genotype distribution were in Hardy-Weinberg equilibrium (P>0.05). The genotype distribution and effect allele frequencies varied from 17.7% for rs987237 to 83.7% for rs654238), which were in consistency with previous reports.
Associations of the individual obesity-susceptibility SNPs and the GPS1 with adiposity-related traits2 in adolescence of Young-HUNT13.
| Z-scores BMI | Z-scores WC | |||||||||
| SNP | Chrom | Nearest gene | B | CI (95%) | P-value | Literature | B | CI (95%) | P-value | Literature |
| rs2815752 | 1 | NEGR1 | −.019 | −.091, .052 | .596 | 0.01 | −.010 | −.082, .061 | .780 | 0.062 |
| rs6548238 | 2 | TMEM18 | .074 | −.020, .168 | .124 | 0.10 | .071 | −.023, .165 | .137 | 0.068 |
| rs10938397 | 4 | GNPDA2 | −.004 | −.075, .067 | .920 | 0.06 | .019 | −.051, 090 | .591 | 0.041 |
| rs987237 | 6 | TFAP2B | .040 | −.050, .130 | .387 | 0.069 | −.004 | −.094, .086 | .935 | 0.056 |
| rs4074134 | 11 | BDNF | .026 | −.063, .114 | .571 | 0.03 | .021 | −.068, .110 | .642 | 0.034 |
| rs10838738 | 11 | MTCH2 | −.021 | −.092, .050 | .569 | 0.03 | −.030 | −.100, .041 | .411 | 0.001 |
| rs1121980 | 16 | inFTO | .057 | −.013, .128 | .110 | 0.06 | .070 | .000, .140 | .052 | 0.004 |
| rs17782313 | 18 | MC4R | .177 | .098, .256 | .0001 | 0.07 | .155 | .076, .235 | .0001 | −0.006 |
| rs11084753 | 19 | KCTD15 | .107 | .030, .183 | .006 | 0.05 | .053 | −.023, .130 | .172 | 0.009 |
| GPS | .046 | .020, .073 | .001 | 0.044 | .038 | .012, .064 | .005 | 0.025 | ||
The genetic predisposition score (GPS) is the sum of effect alleles from each of the nine individual SNPs.
Age and sex specific z-scores of BMI and waist circumference in adolescence.
Number of participants: for individual SNPs = 1643 and for GPS = 1634 (those missing more than 3 SNPs excluded).
The linear regression models were adjusted for pubertal maturity regarding BMI and additionally also for height regarding WC, assuming an additive effect. Pregnant participants were excluded.
Chrom: chromosome.
Comparable effect sizes in the literature:
den Hoed et al. [21];
Zhao et al.
Willer et al. [17].
Figure 1Distribution of the genetic predisposition score (GPS) and the cumulative effects of risk alleles from the nine variants on BMI z-scores and Waist circumference z-scores.
The genetic predisposition score (GPS, n: 1 634 adolescents) was constructed by summing the effect alleles of each SNP ( = BMI-increasing alleles defined in the original genome-wide association studies). (rs4074134 near BDNF, rs17782313 near MC4R, rs987237 near TFAP2B, rs1121980 in FTO, rs2815752 near NEGR1, rs6548238 near TMEM18, rs10838738 in MTCH2, rs10938397 near GNPDA2, rs11084753 near KCTD15).
Associations of the individual obesity-susceptibility SNPs and the GPS1 with adiposity-related traits2 in young adulthood (HUNT3)3.
| Z-scores BMI | Z-scores WC | ||||||||||
| SNP | Chrom | Nearest gene | B | CI (95%) | P-value | Literature | B | CI (95%) | P-value | Literature | |
| rs2815752 | 1 | NEGR1 | −.028 | −.098, .042 | .436 | 0.024 | −.007 | −.077, .063 | .845 | 0.022 | |
| rs6548238 | 2 | TMEM18 | .018 | −.075, .125 | .699 | 0.070 | .017 | −.076, .109 | .726 | 0.050 | |
| rs10938397 | 4 | GNPDA2 | −.001 | −.071, .069 | .976 | 0.045 | −.013 | −.083, .057 | .719 | 0.039 | |
| rs987237 | 6 | TFAP2B | .022 | −.067, .111 | .624 | − | −.035 | −.124, .054 | .439 | 0.035 | |
| rs4074134 | 11 | BDNF | .054 | −.034, .142 | .226 | 0.055 | .072 | −.016, .159 | .109 | 0.049 | |
| rs10838738 | 11 | MTCH2 | .048 | −.022, .117 | .182 | 0.021 | .062 | −.007, .131 | .080 | 0.011 | |
| rs1121980 | 16 | In FTO | .086 | .017, .156 | .015 | 0.086 | .071 | .002, .140 | .045 | 0.080 | |
| rs17782313 | 18 | MC4R | .103 | .025, .181 | .010 | 0.047 | .069 | −.009, .147 | .082 | 0.042 | |
| rs11084753 | 19 | KCTD15 | .062 | −.014, .138 | .110 | 0.016 | .047 | −.028, .123 | .220 | 0.024 | |
| GPS | .041 | .015, .067 | .002 | 0.039 | .033 | .008, .059 | .011 | 0.033 | |||
The genetic predisposition score (GPS) is the sum of effect alleles from each of the nine individual SNPs.
Sex specific z-scores of BMI and waist circumference in young adulthood.
Number of participants: for individual SNPs = 1643 and for GPS = 1634 (those missing more than 3 SNPs excluded).
The linear regression models were adjusted for age regarding BMI and additionally also for height regarding WC, assuming an additive effect.
Pregnant participants were excluded.
Chrom: chromosome.
Comparable effect sizes in the literature:
Li et al. [35];
Lindgren et al. [19].
Associations of the individual obesity susceptibility SNPs and the GPS1 with change in adiposity-related traits2 from adolescence into adulthood3.
| Delta BMI | Delta WC | |||||||
| SNP | Chrom. | Nearest gene | Diff.DeltaZ | CI (95%) | P-value | Diff.DeltaZ | CI (95%) | P-value |
| rs2815752 | 1 | NEGR1 | −.009 | −.064, .045 | .734 | .001 | −.066, .067 | .986 |
| rs6548238 | 2 | TMEM18 | −.047 | −.119, .025 | .201 | −.051 | −.139, .036 | .250 |
| rs10938397 | 4 | GNPDA2 | −.011 | −.066, .043 | .685 | −.041 | −.107, .025 | .224 |
| rs987237 | 6 | TFAP2B | −.018 | −.087, .051 | .604 | −.028 | −.112, .057 | .521 |
| rs4074134 | 11 | BDNF | .025 | −.043, .093 | .406 | .038 | −.044, .121 | .363 |
| rs10838738 | 11 | MTCH2 | .064 | .010, .118 | .020 | .085 | .019, .151 | .011 |
| rs1121980 | 16 | In FTO | .026 | −.028, .080 | .343 | −.000 | −.066, .066 | .996 |
| rs17782313 | 18 | MC4R | −.048 | −.108, .013 | .125 | −.064 | −.138, .010 | .090 |
| rs11084753 | 19 | KCTD15 | −.038 | −.097, .020 | .201 | −.005 | −.077, .067 | .891 |
| GPS | −.003 | −.023, .017 | .762 | −.004 | −.029, .020 | .726 | ||
The genetic predisposition score (GPS) is the sum of effect alleles from each of the nine individual SNPs.
Delta BMI and delta WC are differences between sex-specific z-scores in young adulthood and age-and-sex-specific z-scores in adolescence of BMI and WC respectively.
Number of participants: for individual SNPs = 1643 and for GPS = 1634 (those missing more than 3 SNPs excluded).
The linear regression models were adjusted for pubertal development and age-difference between adolescence and adulthood regarding change BMI and additionally also for height regarding change WC, assuming an additive effect. Pregnant participants were excluded.
Chrom: chromosome.