Publications

Genotype imputations based on 1000 Genomes (1KG) Project data have the advantage of imputing many more SNPs than imputations based on HapMap data. It also provides an opportunity to discover associations with relatively rare variants. Recent investigations are increasingly using 1KG data for genotype imputations, but only limited evaluations of the performance of this approach are available. In this paper, we empirically evaluated imputation performance using 1KG data by comparing imputation results to those using the HapMap Phase II data that have been widely used. We used three reference panels: the CEU panel consisting of 120 haplotypes from HapMap II and 1KG data (June 2010 release) and the EUR panel consisting of 566 haplotypes also from 1KG data (August 2010 release). We used Illumina 324,607 autosomal SNPs genotyped in 501 individuals of European ancestry. Our most important finding was that both 1KG reference panels provided much higher imputation yield than the HapMap II panel. There were more than twice as many successfully imputed SNPs as there were using the HapMap II panel (6.7 million vs. 2.5 million). Our second most important finding was that accuracy using both 1KG panels was high and almost identical to accuracy using the HapMap II panel. Furthermore, after removing SNPs with MACH Rsq <0.3, accuracy for both rare and low frequency SNPs was very high and almost identical to accuracy for common SNPs. We found that imputation using the 1KG-EUR panel had advantages in successfully imputing rare, low frequency and common variants. Our findings suggest that 1KG-based imputation can increase the opportunity to discover significant associations for SNPs across the allele frequency spectrum. Because the 1KG Project is still underway, we expect that later versions will provide even better imputation performance.

Obesity is a major health problem that can be influenced by eating behaviors. Evidence suggests that the sensory properties of food influence eating behaviors and lead to overeating and overweight. A previous genome-wide linkage scan for eating behavior traits assessed with the Three-Factor Eating Questionnaire (cognitive dietary restraint, disinhibition and hunger) performed in the Quebec Family Study (QFS) revealed a quantitative trait locus for disinhibition on chromosome 19p13. This region encodes a cluster of seven olfactory receptor (OR) genes, including OR7D4, previously associated with odor perceptions. Direct sequencing of the OR7D4 gene revealed 16 sequence variants. Nine OR7D4 sequence variants with minor allele frequency (MAF)>1% as well as 100 SNPs spanning the cluster of OR genes on 19p13 were tested for association with age- and sex-adjusted eating behaviors as well as adiposity traits in 890 subjects. One OR7D4 sequence variant (rs2878329 G>A) showed evidence of association with reduced levels of adiposity (p=0.03), cognitive dietary restraint (p=0.05) and susceptibility to hunger (p=0.008). None of the OR7D4 SNPs was associated with disinhibition, but a SNP (rs2240927) in another OR gene (OR7E24) showed evidence of association (p=0.03). Another SNP in the OR7G3 gene (rs10414255) was also found to be associated with adiposity and eating behaviors. These results are the first to suggest that variations in human olfactory receptor genes can influence eating behaviors and adiposity. The associations reported in the present study should be interpreted with caution considering the number of tests performed and considered as potential new hypotheses about the effects OR polymorphisms on eating behaviors and obesity that need to be further explored in other populations.

Homozygosity has long been associated with rare, often devastating, Mendelian disorders1, and Darwin was one of the first to recognize that inbreeding reduces evolutionary fitness2. However, the effect of the more distant parental relatedness that is common in modern human populations is less well understood. Genomic data now allow us to investigate the effects of homozygosity on traits of public health importance by observing contiguous homozygous segments (runs of homozygosity), which are inferred to be homozygous along their complete length. Given the low levels of genome-wide homozygosity prevalent in most human populations, information is required on very large numbers of people to provide sufficient power3, 4. Here we use runs of homozygosity to study 16 health-related quantitative traits in 354,224 individuals from 102 cohorts, and find statistically significant associations between summed runs of homozygosity and four complex traits: height, forced expiratory lung volume in one second, general cognitive ability and educational attainment (P < 1 × 10−300, 2.1 × 10−6, 2.5 × 10−10 and 1.8 × 10−10, respectively). In each case, increased homozygosity was associated with decreased trait value, equivalent to the offspring of first cousins being 1.2 cm shorter and having 10 months’ less education. Similar effect sizes were found across four continental groups and populations with different degrees of genome-wide homozygosity, providing evidence that homozygosity, rather than confounding, directly contributes to phenotypic variance. Contrary to earlier reports in substantially smaller samples5, 6, no evidence was seen of an influence of genome-wide homozygosity on blood pressure and low density lipoprotein cholesterol, or ten other cardio-metabolic traits. Since directional dominance is predicted for traits under directional evolutionary selection7, this study provides evidence that increased stature and cognitive function have been positively selected in human evolution, whereas many important risk factors for late-onset complex diseases may not have been.

This review of the exercise genomics literature encompasses the highest-quality articles published in 2015 across seven broad topics: physical activity behavior, muscular strength and power, cardiorespiratory fitness and endurance performance, body weight and adiposity, insulin and glucose metabolism, lipid and lipoprotein metabolism, and hemodynamic traits. One study used a quantitative trait locus for wheel running in mice to identify single nucleotide polymorphisms (SNPs) in humans associated with physical activity levels. Two studies examined the association of candidate gene ACTN3 R577X genotype on muscular performance. Several studies examined gene-physical activity interactions on cardiometabolic traits. One study showed that physical inactivity exacerbated the body mass index (BMI)-increasing effect of an FTO SNP but only in individuals of European ancestry, whereas another showed that high-density lipoprotein cholesterol (HDL-C) SNPs from genome-wide association studies exerted a smaller effect in active individuals. Increased levels of moderate-to-vigorous-intensity physical activity were associated with higher Matsuda insulin sensitivity index in PPARG Ala12 carriers but not Pro12 homozygotes. One study combined genome-wide and transcriptome-wide profiling to identify genes and SNPs associated with the response of triglycerides (TG) to exercise training. The genome-wide association study results showed that four SNPs accounted for all of the heritability of △TG, whereas the baseline expression of 11 genes predicted 27% of △TG. A composite SNP score based on the top eight SNPs derived from the genomic and transcriptomic analyses was the strongest predictor of ΔTG, explaining 14% of the variance. The review concludes with a discussion of a conceptual framework defining some of the critical conditions for exercise genomics studies and highlights the importance of the recently launched National Institutes of Health Common Fund program titled "Molecular Transducers of Physical Activity in Humans."

Macronutrient intake, the proportion of calories consumed from carbohydrate, fat, and protein, is an important risk factor for metabolic diseases with significant familial aggregation. Previous studies have identified two genetic loci for macronutrient intake, but incomplete coverage of genetic variation and modest sample sizes have hindered the discovery of additional loci. Here, we expanded the genetic landscape of macronutrient intake, identifying 12 suggestively significant loci (P < 1 × 10−6) associated with intake of any macronutrient in 91,114 European ancestry participants. Four loci replicated and reached genome-wide significance in a combined meta-analysis including 123,659 European descent participants, unraveling two novel loci; a common variant in RARB locus for carbohydrate intake and a rare variant in DRAM1 locus for protein intake, and corroborating earlier FGF21 and FTO findings. In additional analysis of 144,770 participants from the UK Biobank, all identified associations from the two-stage analysis were confirmed except for DRAM1. Identified loci might have implications in brain and adipose tissue biology and have clinical impact in obesity-related phenotypes. Our findings provide new insight into biological functions related to macronutrient intake.

RICE, TREVA, JP DESPRÉS, LOUIS PÉRUSSE, JACQUES GAGNON, ARTHUR S LEON, JAMES S SKINNER, JACK H WILMORE, DC RAO, CLAUDE BOUCHARD. Segregation analysis of abdominal visceral fat: The HERITAGE Family Study. A major gene hypothesis for abdominal visceral fat (AVF) level, both before and after adjustment for total body fat mass, was investigated in 86 white families who participated in the HERITAGE Family Study. In this study, sedentary families were tested for a battery of measures (baseline), endurance exercise trained for 20 weeks, and then remeasured again. The baseline measures reported here are unique in that the variance due to a potentially important environmental factor (activity level) was limited. AVF area was assessed at L4 to L5 by the use of computerized tomography scan, and total body fat mass was assessed with underwater weighing. For fat mass, a putative locus accounted for 64% of the variance, but there was no evidence of a multifactorial component (i.e., no polygenic and/or common familial environmental effects). For AVF area, both a major gene effect accounting for 54% of the variance and a multifactorial component accounting for 17% of the variance were significant. However, after AVF area was adjusted for the effects of total level of body fat, the support for a major gene was reduced. In particular, there was a major effect for fat mass‐adjusted AVF area, but it was not transmitted from parents to offspring (i.e., the three transmission probabilities were equal). The importance of this study is twofold. First, these results confirm a previous study that suggested that there is a putative major locus for AVF and for total body fat mass. Second, the findings from the HERITAGE Family Study suggest that the factors underlying AVF area in sedentary families may be similar to those in the population at large, which includes both sedentary and active families. Whether the gene(s) responsible for the high levels of AVF area is the same as that which influences total body fat content remains to be further investigated.

Uncoupling Protein 3 (UCP3) is a mitochondrial protein expressed in skeletal muscle. Both VO2max and mechanical efficiency have been negatively correlated with mRNA levels of UCP3. PURPOSE We examined the hypothesis of an association between a C-T polymorphism in the 5' regulatory region (−55bp) of the UCP3 gene and elite endurance athlete (EEA) status. METHODS Subjects were 183 Caucasian male EEA with measured VO2max ≥ 75 mL O2/Kg/min and 121 age and ethnicity matched sedentary controls (CON; VO2max ≤ 49 mL O2/Kg/min). The polymorphism was detected by allele refractory mutation system polymerase chain reaction (ARMS-PCR) and agarose gel electrophoresis. RESULTS There were no significant differences in allelic (EEA; C=72%, T=28% vs. CON; C=74%, T=26%) or genotypic (EEA; CC=55%, CT=33%, TT=12% vs. CON; CC=54%, CT=40%, TT=6%) frequencies between groups. CONCLUSION The present findings do not support the hypothesis that the −55bp C-T polymorphism of the UCP3 gene is a marker of elite endurance athlete status. Supported by CRC-RCMI UPR-MSC Grant #1P20RR11126, RCMI Basic Sciences #G12RR03051 and FIDI, UPR-Cayey

Interindividual differences in muscle mass are due to environmental factors but also for a large part due to genetic determination. Earlier studies provide heritability estimates > 75%. Identifying a gene for muscle mass might also be a causative gene for maximal musclular strength due to the moderate to high correlation between these two traits. Results from animal studies show that myostatin (GDF-8) is an important regulator of muscle development. The high degree of myostatin sequence conservation in non-human species led to this study to see whether GDF-8 is also responsible for a part of the interindividual differences in muscle mass in humans. PURPOSE: To test whether myostatin is associated with muscle mass in a human case-control study. METHODS: An extended set of anthropometrical measurements was taken from 50 male power athletes (29.8 ± 8.8 years) and 57 control subjects (22.4 ± 3.7 years), not selected for muscularity. Muscle mass was determined by circumference measures corrected by skinfolds. Using mathematical formulas muscle mass of am and leg was calculated. Four recently described polymorphic sites in the myostatin gene were genotyped: Ala 55, Lys 193, Glut 164 and Pro 198. RESULTS: There appeared to be no evidence for allele frequency differences in the four studied polymorphisms in the myostatin gene between the two groups, indicating that variation in muscle hypertrophy is not associated with variation at the myostatin locus. Also myostatin sequence variation within groups was sparse. Only two individuals, one in the control and one in the power athlete group, were heterozygous for K153R. Their extremity muscle mass indicators as well as somatotype components did not indicate a specific extreme phenotypic profile in both K153R heterozygotes. CONCLUSION: The lack of a significant relationship between myostatin genotypes and overall muscle mass might suggest that muscularity is not significantly influenced by genetic variation at the myostatin locus.

This study examined the associations between elite endurance athlete (EEA) status and three mitochondrial DNA (mtDNA) restriction fragment length polymorphisms (RFLPs) in the subunit 5 of the NADH dehydrogenase (MTND5) locus and one in the D-loop region. A group of 125 Caucasian male EEA well endowed with the phenotypic expression of ˙VO2max (78.9 ± 3.8 mL·kg-1·min-1, mean ± SD) and 65 sedentary controls (SCON: ˙VO2max = 39.8 ± 8.2 mL·kg-1·min-1) participated in the study.˙VO2max was determined during an incremental exercise test on a cycle ergometer or a motor-driven treadmill. mtDNA was extracted from white blood cells or lymphoblastoid cell lines and specific regions were amplified by the polymerase chain reaction. The Pearson Chi-square statistic test and Fisher exact test revealed no significant association (P > 0.05) between any of the three mtDNA RFLPs and EEA status. The MTND5-BamHI RFLP at bp 13,470 (morph 3) was found in 12.8% of the EEA and 12.3% of the SCON (χ2 = 0.009, P = 0.92). The prevalence of the MTND5-NciI RFLP at bp 13,364 (morph 2) was 12.9% and 14% for the EEA and SCON, respectively (χ2 = 0.043, P = 0.83). The D-loop-KpnI RFLP at bp 16,133 (morph 1) was found in 5.8% of the EEA and in 1.6% of the SCON (Fisher exact test = 1.80, P = 0.18). The MTND5-HincII RFLP at bp 12,406 (morph 1) was not present in this study sample. These results indicate no evidence for a difference in the frequency of two polymorphic restriction sites in the subunit 5 of the NADH dehydrogenase gene of mtDNA and one in the D-loop region between elite endurance athletes and sedentary controls.