Mary Ann and J. Milburn Smith Child Health Research Program, Children's Memorial Hospital, Children's Memorial Research Center, Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
Human Genetics (Impact Factor: 4.82). 08/2011; 131(3):341-51. DOI: 10.1007/s00439-011-1079-5
There is increasing evidence suggesting that higher intakes of fish or n-3 polyunsaturated fatty acids supplements may decrease the risk of preterm delivery (PTD). We hypothesized that genetic variants of the enzymes critical to fatty acids biosynthesis and metabolism may be associated with PTD. We genotyped 231 potentially functional single nucleotide polymorphisms (SNPs) and tagSNPs in 9 genes (FADS1, FADS2, PTGS1, PTGS2, ALOX5, ALOX5AP, PTGES, PTGES2, and PTGES3) among 1,110 black mothers, including 542 mothers who delivered preterm (<37 weeks gestation) and 568 mothers who delivered full-term babies (≥37 weeks gestation) at Boston Medical Center. After excluding SNPs that are in complete linkage disequilibrium or have lower minor allele frequency (<1%) or call rate (<90%), we examined the association of 206 SNPs with PTD using multiple logistic regression models. We also imputed 190 HapMap SNPs via program MACH and examined their associations with PTD. Finally, we explored gene-level and pathway-level associations with PTD using the adaptive rank truncated product (ARTP) methods. A total of 21 SNPs were associated with PTD (p value ranging from 0.003 to 0.05), including 3 imputed SNPs. Gene-level ARTP statistics indicated that the gene PTGES2 was significantly associated with PTD with a gene-based p value equal to 0.01. No pathway-based association was found. In this large and comprehensive candidate gene study, we found a modest association of genes in fatty acid metabolism pathway with PTD. Further investigation of these gene polymorphisms jointly with fatty acid measures and other genetic factors would help better understand the pathogenesis of PTD.
"insight into the genetic architecture of complex traits (Liu et al. 2012; Wang et al. 2007; Yu et al. 2009). In other words, the association study within a biological pathway combining evidence from multiple genetic variants with a relatively small effect may potentially evaluate the pathway level contribution to the complex trait. "
[Show abstract][Hide abstract] ABSTRACT: There is increasing evidence suggesting that fatty acids biosynthesis and metabolism are regulated by peroxisome proliferator-activated receptors (PPARs), mostly through the PPAR signaling pathway at the transcriptomic level. We hypothesized that the genetic variants of the enzymes in the PPAR signaling pathway may be associated with the traits of porcine meat quality (PMQ). We mined 77 potentially functional single nucleotide polymorphisms in the PPAR signaling pathway of the pig. There were 13 TagSNPs in 13 different genes mapped within the reported pig quantitative trait loci (QTLs) regions related to PMQ based on the Pig QTL database. Based on the association study with ten measured PMQ traits in both the pathway level and the SNP level, we tested eight significantly associated traits with additive effect in the PPAR signaling pathway and explored only one significant TagSNP in gene RXRB, which is directly associated with the trait of skin weight. Moreover, several interactions of TagSNPs were also significantly related to some of PMQ traits. In this large and comprehensive candidate gene set study, we found a modest association of genes and SNPs in the PPAR signaling pathway with PMQ. Further investigation of these gene polymorphisms jointly with fatty acid measures and other genetic factors would help us better understand the regulation mechanisms of PMQ.
"Several lines of evidence support a genetic basis of PTB including its familial aggregation, population differences in its prevalence and genetic association studies of PTB with variants in candidate genes (Hao et al., 2004; Ward et al., 2005; Gibson et al., 2007; Chaudhari et al., 2008; Menon, 2008; Dolan, 2010; Menon et al., 2010; Liu et al., 2012; Myking et al., 2011; Karjalainen et al., 2012). In addition, the association of mitochondrial genome variation with preterm delivery has been explored, but finding no support in favor of mitochondrial genetic contribution to preterm delivery risk (Alleman et al., 2012). "
[Show abstract][Hide abstract] ABSTRACT: Preterm birth (PTB) is a complex trait, but little is known regarding its major genetic determinants. The objective of this study is to localize genes that influence susceptibility to PTB in Mexican Americans (MAs), a minority population in the United States (US), using predominantly microfilmed birth certificate-based data obtained from the San Antonio Family Birth Weight Study. Only 1,302 singleton births from 288 families with information on PTB and significant covariates were considered for genetic analysis. PTB is defined as a childbirth that occurs at <37 completed weeks of gestation, and the prevalence of PTB in this sample was 6.4%. An approximately 10 cM genetic map was used to conduct a genome-wide linkage analysis using the program SOLAR. The heritability of PTB was high (h(2)±SE: 0.75±0.20) and significant (P=4.5 x 10(-5)), after adjusting for the significant effects of birth weight and birth order. We found significant evidence for linkage of PTB (LOD=3.6; nominal P=2.3 x 10(-5); empirical P=1.0 x 10(-5)) on chromosome 18q between markers D18S1364 and D18S541. Several other chromosomal regions (2q, 9p, 16q, and 20q) were also potentially linked with PTB. A strong positional candidate gene in the 18q linked region is SERPINB2 or PAI-2, a member of the plasminogen activator system that is associated with various reproductive processes. In conclusion, to our knowledge, perhaps for the first time in MAs or US populations, we have localized a major susceptibility locus for PTB on chromosome 18q21.33-q23.
Molecular Human Reproduction 05/2013; 19(10). DOI:10.1093/molehr/gat036 · 3.75 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Propanoate metabolism and fatty acid metabolism are crucial metabolic pathways in vivo that have been studied extensively and have shown a significant influence on the growth and diseases of animals. In order to identify the essential genes significantly associated with porcine growth traits at the pathway level, we selected 14 candidate genes with 58 SNPs, including 24 tag SNPs and 34 predicted SNPs, in the two essential pathways to test using the SNaPshot mini-sequencing method. Association analysis was performed using both static and dynamic phenotypic records. The results showed that four SNPs, respectively in SUCLA2, SUCLG2, ACADS, and ALDH1B1, were significantly associated with growth in pigs. In addition, an exciting finding was that the change of transcription factor binding site that resulted from alteration of the bases in SUCLG2 brought out a transcription factor binding site for POU1F1a, which is the product of a notable marker gene for growth of animals.
Chinese Science Bulletin 07/2012; 57(21). DOI:10.1007/s11434-012-5328-3 · 1.58 Impact Factor
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