scholarly journals Impact of Amerind ancestry and FADS genetic variation on omega-3 deficiency and cardiometabolic traits in Hispanic populations

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Chaojie Yang ◽  
Brian Hallmark ◽  
Jin Choul Chai ◽  
Timothy D. O’Connor ◽  
Lindsay M. Reynolds ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Genetic Ancestry ◽  
Hispanic American ◽  
Omega 3 ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Interindividual Differences ◽  
Hispanic Populations ◽  
Low Levels ◽  
Long Chain

AbstractLong chain polyunsaturated fatty acids (LC-PUFAs) have critical signaling roles that regulate dyslipidemia and inflammation. Genetic variation in the FADS gene cluster accounts for a large portion of interindividual differences in circulating and tissue levels of LC-PUFAs, with the genotypes most strongly predictive of low LC-PUFA levels at strikingly higher frequencies in Amerind ancestry populations. In this study, we examined relationships between genetic ancestry and FADS variation in 1102 Hispanic American participants from the Multi-Ethnic Study of Atherosclerosis. We demonstrate strong negative associations between Amerind genetic ancestry and LC-PUFA levels. The FADS rs174537 single nucleotide polymorphism (SNP) accounted for much of the AI ancestry effect on LC-PUFAs, especially for low levels of n-3 LC-PUFAs. Rs174537 was also strongly associated with several metabolic, inflammatory and anthropomorphic traits including circulating triglycerides (TGs) and E-selectin in MESA Hispanics. Our study demonstrates that Amerind ancestry provides a useful and readily available tool to identify individuals most likely to have FADS-related n-3 LC-PUFA deficiencies and associated cardiovascular risk.

scholarly journals Amerind ancestry predicts the impact of FADS genetic variation on omega-3 PUFA deficiency, cardiometabolic and inflammatory risk in Hispanic populations

2021 ◽  
Author(s):  
Chaojie Yang ◽  
Brian Hallmark ◽  
Jin Choul Chai ◽  
Timothy D O'Connor ◽  
Lindsay M Reynolds ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Plasma Phospholipid ◽  
Genetic Ancestry ◽  
Health Study ◽  
Omega 3 ◽  
Anthropometric Measures ◽  
Single Nucleotide ◽  
Hispanic Community ◽  
Hispanic Populations ◽  
The Impact

Hispanic populations have higher rates of obesity, elevated triglycerides, and a greater prevalence of diabetes. Long chain polyunsaturated fatty acids (LC-PUFAs) and LC-PUFA metabolites have critical signaling roles that regulate dyslipidemia and inflammation. Genetic variation in the FADS cluster accounts for a large part of the interindividual differences in circulating and tissue levels of LC-PUFAs, with the genotypes most strongly predictive of low LC-PUFA levels at strikingly higher frequencies in Amerind (AI) ancestry populations. In this study, we examined relationships between genetic ancestry and FADS variation, plasma phospholipid levels of LC-PUFAs, anthropometric measures, and circulating metabolic and inflammatory biomarkers in 1,102 Hispanic American participants, representing six distinct ancestry populations from the Multi-Ethnic Study of Atherosclerosis. We demonstrate strong negative associations between AI genetic ancestry and LC-PUFA levels. The FADS rs174537 single nucleotide polymorphism (SNP) accounted for much of the AI ancestry effect on LC-PUFAs, especially for low levels of n-3 LC-PUFAs. Rs174537 was also strongly associated with several metabolic, inflammatory and anthropomorphic traits including circulating triglycerides (TGs) and E-selectin in MESA Hispanics. We further replicated the association with circulating TGs in two additional Hispanic cohorts: the Hispanic Community Health Study/Study of Latinos and the Arizona Insulin Resistance Registry. Our study demonstrates that Amerind ancestry provides a useful and readily available tool to identify individuals most likely to have FADS-related n-3 LC-PUFA deficiencies and associated cardiovascular risk.

Discovery and trait association of single nucleotide polymorphisms from gene regions of influence on meat tenderness and long-chain omega-3 fatty acid content in Australian lamb

2012 ◽  
Vol 52 (7) ◽  
pp. 591 ◽  
Author(s):  
M. I. Knight ◽  
H. D. Daetwyler ◽  
B. J. Hayes ◽  
M. J. Hayden ◽  
A. J. Ball ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Fatty Acid ◽  
Shear Force ◽  
Fatty Acid Content ◽  
Meat Tenderness ◽  
Nucleotide Polymorphisms ◽  
Omega 3 ◽  
Single Nucleotide ◽  
Omega 3 Fatty Acid ◽  
Long Chain

Whole genome association studies in humans have shown a strong relationship between omega-3 levels in plasma and single nucleotide polymorphisms (SNP) located close to genes whose protein products are involved in the biosynthesis of long-chain omega-3 fatty acids. In sheep and other livestock species, the calpain/calpastatin system is the principal influence on natural variation in meat tenderness between animals. Using targeted next generation sequencing, we sequenced the fatty acid desaturase locus (FADS1/2/3), ELOVL2 and SLC26A10 and the calpain/calpastatin (CAPN1/2/3 and CAST) gene loci of 35 industry sires from the Australian flock. A total of 753 SNP were identified and 182 of these SNP were selected for incorporation onto a research SNP panel that represented the genetic variation across the nine genes. A total of 1252 animals were genotyped from the Australian Sheep CRC Information Nucleus Flock for these SNP and the genomic association was calculated for omega-3 fatty acid content and objective meat tenderness in lamb. Six SNP within CAST and CAPN2 showed association with shear force at Day 5 post-mortem at a significance level of P ≤ 0.01. When these were fitted simultaneously in a mixed-model analysis with fixed effects and covariates, three SNP remained significant. These SNP each had an unfavourable effect on shear force of between 1.1 and 1.8 N, with a combined effect of 4.1 N. The frequency of the favourable alleles in the progeny measured indicates that these SNP hold good potential for improving the management of meat tenderness across Merino, Border Leicester and Terminal sire types. No SNP within the FADS1/2/3, ELOVL2 and SLC26A10 gene regions were associated with lamb muscle omega-3 levels. This indicates that genetic variation in the long-chain omega-3 biosynthesis pathway genes analysed here may not be important for omega-3 content in lamb within the Information Nucleus Flock population.

scholarly journals Single Nucleotide Polymorphism in SMAD7 and CHI3L1 and Colorectal Cancer Risk

2018 ◽  
Vol 2018 ◽  
pp. 1-23 ◽  
Author(s):  
Amal Ahmed Abd El-Fattah ◽  
Nermin Abdel Hamid Sadik ◽  
Olfat Gamil Shaker ◽  
Amal Mohamed Kamal
Keyword(s):  
Colorectal Cancer ◽  
Genetic Variation ◽  
Sequence Variation ◽  
Regulatory Protein ◽  
Nucleotide Polymorphisms ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
The Third ◽  
Common Cancer ◽  
Cancer Initiation

Colorectal cancer (CRC) is one of the leading cancers throughout the world. It represents the third most common cancer and the fourth in mortality. Most of CRC are sporadic, arise with no known high-penetrant genetic variation and with no previous family history. The etiology of sporadic CRC is considered to be multifactorial and arises from the interaction of genetic variants of low-penetrant genes and environmental risk factors. The most common well-studied genetic variation is single nucleotide polymorphisms (SNPs). SNP arises as a point mutation. If the frequency of the sequence variation reaches 1% or more in the population, it is referred to as polymorphism, but if it is lower than 1%, the allele is typically considered as a mutation. Lots of SNPs have been associated with CRC development and progression, for example, genes of TGF-β1 and CHI3L1 pathways. TGF-β1 is a pleiotropic cytokine with a dual role in cancer development and progression. TGF-β1 mediates its actions through canonical and noncanonical pathways. The most important negative regulatory protein for TGF-β1 activity is termed SMAD7. The production of TGF-βcan be controlled by another protein called YKL-40. YKL-40 is a glycoprotein with an important role in cancer initiation and metastasis. YKL-40 is encoded by the CHI3L1 gene. The aim of the present review is to give a brief introduction of CRC, SNP, and examples of some SNPs that have been documented to be associated with CRC. We also discuss two important signaling pathways TGF-β1 and CHI3L1 that influence the incidence and progression of CRC.

scholarly journals The distinctive geographic patterns of common pigmentation variants at the OCA2 gene

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Kenneth K. Kidd ◽  
Andrew J. Pakstis ◽  
Michael P. Donnelly ◽  
Ozlem Bulbul ◽  
Lotfi Cherni ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Oculocutaneous Albinism ◽  
Selection Effects ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Eye Color ◽  
Geographic Patterns ◽  
Population Genetic Variation ◽  
Oca2 Gene

Abstract Oculocutaneous Albinism type 2 (OCA2) is a gene of great interest because of genetic variation affecting normal pigmentation variation in humans. The diverse geographic patterns for variant frequencies at OCA2 have been evident but have not been systematically investigated, especially outside of Europe. Here we examine population genetic variation in and near the OCA2 gene from a worldwide perspective. The very different patterns of genetic variation found across world regions suggest strong selection effects may have been at work over time. For example, analyses involving the variants that affect pigmentation of the iris argue that the derived allele of the rs1800407 single nucleotide polymorphism, which produces a hypomorphic protein, may have contributed to the previously demonstrated positive selection in Europe for the enhancer variant responsible for light eye color. More study is needed on the relationships of the genetic variation at OCA2 to variation in pigmentation in areas beyond Europe.

scholarly journals Genetic variation and identification of single nucleotide polymorphism of insulin-like growth factor- 1 gene in Tilapia guineensis

2020 ◽  
Vol 21 (11) ◽  
Author(s):  
Esther Ukenye ◽  
IWALEWA MEGBOWON ◽  
OLALEKAN OGUNTADE ◽  
TOPE OKETOKI ◽  
OLUWAFEMI AMUSA ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphism ◽  
Genetic Variation ◽  
Growth Factor ◽  
Coastal Waters ◽  
Growth Traits ◽  
Selection Marker ◽  
Insulin Like Growth Factor ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide

Abstract. Ukenye E, Megbowon I, Oguntade O, Oketoki T, Amusa O, Usman A, Sokenu B, Adeleke R, Joseph B, Omatah C. 2020. Genetic variation and identification of single nucleotide polymorphism of insulin-like growth factor- 1 gene in Tilapia guineensis Biodiversitas 21: 5317-5321. Tilapia guineensis is an important cichlid species of West African coastal waters with good nutritional, economic, and aquaculture relevance. The knowledge of the genetic basis of variation in growth traits in Tilapia fish is of great importance to support genetic improvement in the context of aquaculture. In this study, regions of the Tilapia guineensis IGF-1 gene were sequenced, aligned and compared across populations to identify single nucleotide polymorphism and genetic diversity among four populations of T. guineensis in South-west Nigerian coastal waters. A total of thirty-four SNPs were identified across the studied populations and were detected in the forward reaction with twenty-two transversions and twelve transitions. Badagry population showed the highest genetic diversity with the highest molecular diversity indices; number of polymorphic sites, pairwise differences, number of segregating sites and nucleotide diversity while the least diverse population was Pepe. Analysis of molecular variance (AMOVA) revealed that genetic variation was mostly within populations. This finding provides more information regarding variation in insulin growth factor I of T. guineensis and will encourage association study for production traits that will inform useful selection marker for breeding program.

Single Nucleotide Polymorphism (SNP) Analysis of JAK2 and Relevant Cytokine Receptor Genes in Myeloproliferative Disorders.

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 661-661
Author(s):  
Animesh Pardanani ◽  
Brooke Fridley ◽  
Terra Lasho ◽  
Sara Achenbach ◽  
D. Gary Gilliland ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Genetic Variation ◽  
Odds Ratio ◽  
Myeloproliferative Disorders ◽  
Cytokine Receptor ◽  
Jak2v617f Mutation ◽  
P Value ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
P Values

Abstract Background: Constitutive activation of the JAK-STAT signaling pathway through acquisition of the JAK2V617F mutation plays a key role in the pathogenesis of related myeloproliferative disorders (MPD) including polycythemia vera (PV), agnogenic myeloid metaplasia (AMM), and essential thrombocythemia (ET). Hypothesis: Genetic variation in JAK2 and/or the cytokine receptor genes for erythropoietin (EPOR), thrombopoietin (MPL), and granulocyte colony stimulating factor (GCSFR), influences the expression of a specific disease phenotype (PV, AMM, or ET). Methods: We studied 179 Caucasian MPD patients (PV=84, AMM=58, ET=37) for genetic variation in 4 candidate genes (i.e. JAK2, EPOR, MPL, GCSFR) through single nucleotide polymorphism (SNP) and haplotype analyses. A total of 32 LD (linkage disequilibrium) tag-SNPs with a minimum allele frequency of at least 5% were selected from the HapMap CEU database (JAK2=13, EPOR=4, MPL=5, GCSFR=10). Genotyping was performed using archived DNA from enriched neutrophils. Results: Seventy six (94%), 26 (45%), and 14 (38%) patients with PV, AMM, and ET, respectively, carried the JAK2V617F mutation. Significant differences in allele frequencies was observed at 6 SNP loci (rs10758669, rs3808850, rs7849191, rs7046736, rs10815148, and rs12342421, p-values < 0.0005), all within the JAK2 gene, in comparing our overall study population with the founder Caucasian population in the HapMap database. In the additive genotype-phenotype association analysis adjusted for gender and age at diagnosis, 3 SNP loci in JAK2 (rs7046736, rs10815148, and rs12342421) were found to be significantly, but reciprocally associated with PV (p-values < 0.00006, odds ratio=0.37, 2.82, and 2.39, respectively) and ET (p-values < 0.002, odds ratio=2.50, 0.36, and 0.41, respectively), but not AMM, in terms of the minor allele being ’protective’. These three SNPs were all in high LD, with the ’r2’ measures of LD between 0.59 and 0.71. Furthermore, 2 additional JAK2 SNP loci (rs10758669, p-value = 0.0024 and rs10974947, p-value = 0.0046) were significantly associated with PV (odds ratio=1.88 and 0.47, respectively), but not ET or AMM. Similarly, presence of the minor allele at a single SNP locus in EPOR (rs318699, p-value = 0.0012) was significantly associated with PV only (odds ratio=2.16). For the phenotype-genotype intragene haplotype analyses, the EPOR intragene haplotypes GAAA and GGAA were significantly associated with PV (simulated global p-value = 0.058, simulated individual p-values 0.0013 and 0.0068, haplotype frequency of 35% and 56%, respectively). In addition to EPOR, 6 intragene haplotypes within JAK2 where significantly associated with PV (simulated global p-value < 0.0001, individual simulated p-values < 0.03). Conclusion: The current study demonstrates a genotype-phenotype association that involves JAK2 and EPOR in the setting of PV, but not that of AMM. Some JAK2 SNPs were found to be associated with both PV and ET but in opposite direction. Therefore, genetic variation among MPDs might contribute to phenotypic diversity in the presence of specific mutations.

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