Single nucleotide polymorphisms in ghrelin gene and the resulting genetic variants at ghrelin locus in different strains of indigenous Tswana chickens

2012 ◽  
Vol 11 (46) ◽  
Author(s):  
Patrick M. Kgwatalala,
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Genetic Variants ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Ghrelin Gene ◽  
Different Strains

scholarly journals Candidate gene scan for Single Nucleotide Polymorphisms involved in the determination of normal variability in human craniofacial morphology

2016 ◽  
Author(s):  
Mark Barash ◽  
Philipp E. Bayer ◽  
Angela van Daal
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Candidate Gene ◽  
Genetic Variants ◽  
Massively Parallel Sequencing ◽  
Craniofacial Morphology ◽  
Candidate Gene Approach ◽  
Nucleotide Polymorphisms ◽  
Genetic Associations ◽  
Single Nucleotide ◽  
Genome Wide

AbstractDespite intensive research on genetics of the craniofacial morphology using animal models and human craniofacial syndromes, the genetic variation that underpins normal human facial appearance is still largely elusive. Recent development of novel digital methods for capturing the complexity of craniofacial morphology in conjunction with high-throughput genotyping methods, show great promise for unravelling the genetic basis of such a complex trait.As a part of our efforts on detecting genomic variants affecting normal craniofacial appearance, we have implemented a candidate gene approach by selecting 1,201 single nucleotide polymorphisms (SNPs) and 4,732 tag SNPs in over 170 candidate genes and intergenic regions. We used 3-dimentional (3D) facial scans and direct cranial measurements of 587 volunteers to calculate 104 craniofacial phenotypes. Following genotyping by massively parallel sequencing, genetic associations between 2,332 genetic markers and 104 craniofacial phenotypes were tested.An application of a Bonferroni–corrected genome–wide significance threshold produced significant associations between five craniofacial traits and six SNPs. Specifically, associations of nasal width with rs8035124 (15q26.1), cephalic index with rs16830498 (2q23.3), nasal index with rs37369 (5q13.2), transverse nasal prominence angle with rs59037879 (10p11.23) and rs10512572 (17q24.3), and principal component explaining 73.3% of all the craniofacial phenotypes, with rs37369 (5p13.2) and rs390345 (14q31.3) were observed.Due to over-conservative nature of the Bonferroni correction, we also report all the associations that reached the traditional genome-wide p-value threshold (<5.00E-08) as suggestive. Based on the genome-wide threshold, 8 craniofacial phenotypes demonstrated significant associations with 34 intergenic and extragenic SNPs. The majority of associations are novel, except PAX3 and COL11A1 genes, which were previously reported to affect normal craniofacial variation.This study identified the largest number of genetic variants associated with normal variation of craniofacial morphology to date by using a candidate gene approach, including confirmation of the two previously reported genes. These results enhance our understanding of the genetics that determines normal variation in craniofacial morphology and will be of particular value in medical and forensic fields.Author SummaryThere is a remarkable variety of human facial appearances, almost exclusively the result of genetic differences, as exemplified by the striking resemblance of identical twins. However, the genes and specific genetic variants that affect the size and shape of the cranium and the soft facial tissue features are largely unknown. Numerous studies on animal models and human craniofacial disorders have identified a large number of genes, which may regulate normal craniofacial embryonic development.In this study we implemented a targeted candidate gene approach to select more than 1,200 polymorphisms in over 170 genes that are likely to be involved in craniofacial development and morphology. These markers were genotyped in 587 DNA samples using massively parallel sequencing and analysed for association with 104 traits generated from 3-dimensional facial images and direct craniofacial measurements. Genetic associations (p-values<5.00E-08) were observed between 8 craniofacial traits and 34 single nucleotide polymorphisms (SNPs), including two previously described genes and 26 novel candidate genes and intergenic regions. This comprehensive candidate gene study has uncovered the largest number of novel genetic variants affecting normal facial appearance to date. These results will appreciably extend our understanding of the normal and abnormal embryonic development and impact our ability to predict the appearance of an individual from a DNA sample in forensic criminal investigations and missing person cases.

scholarly journals Association between single-nucleotide polymorphisms within candidate genes and fertility in Landrace and Duroc pigs

2019 ◽  
Vol 61 (1) ◽  
Author(s):  
Nina Hårdnes Tremoen ◽  
Maren Van Son ◽  
Ina Andersen-Ranberg ◽  
Eli Grindflek ◽  
Frøydis Deinboll Myromslien ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Candidate Genes ◽  
Genetic Variants ◽  
Genetic Variance ◽  
Female Fertility ◽  
Breeding Value ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Cox 2 ◽  
Snp Panels

AbstractFinding effective predictors of traits related to boar fertility is essential for increasing the efficiency of artificial insemination systems in pig breeding. The objective of this study was to find associations between single-nucleotide polymorphisms (SNPs) within candidate genes and fertility in the breeds Landrace and Duroc. Animals with breeding values for total number of piglets born, were re-sequenced for exonic regions of 14 candidate genes related to male and female fertility using samples from 16 Landrace boars and 16 Duroc boars (four with high and four with low breeding value of total number of piglets born for each breed for male fertility, and the same for female fertility) to detect genetic variants. Genotyping for the detected SNPs was done in 619 Landrace boars and 513 Duroc boars. Two SNPs in BMPR1 and one SNP in COX-2 were found significantly associated with the total number of piglets born in Landrace. In Duroc, two SNPs in PLCz, one SNP in VWF and one SNP in ZP3 were found significantly associated with total number of piglets born. These SNPs explained between 0.27% and 1.18% of the genetic variance. These effects are too low for being used directly for selection purposes but can be of interest in SNP-panels used for genomic selection.

Single nucleotide polymorphisms in the open reading frame of the stearoyl-CoA desaturase gene and resulting genetic variants in Canadian Holstein and Jersey cows

DNA Sequence ◽  
2007 ◽  
Vol 18 (5) ◽  
pp. 357-362 ◽  
Author(s):  
Patrick M. Kgwatalala ◽  
Patrick M. Kgwatalala ◽  
Eveline M. Ibeagha-Awemu ◽  
Patrick M. Kgwatalala ◽  
Eveline M. Ibeagha-Awemu ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Genetic Variants ◽  
Open Reading Frame ◽  
Nucleotide Polymorphisms ◽  
Desaturase Gene ◽  
Single Nucleotide ◽  
Reading Frame ◽  
Stearoyl Coa Desaturase ◽  
Jersey Cows

scholarly journals Single Nucleotide Polymorphisms in SAR1A Codon Regions Associated with Hydroxyurea Response in Sickle Cell Disease and Potentially Influenced in Mirnas Binding

Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 987-987
Author(s):  
Chutima Kumkhaek ◽  
Christine Kim ◽  
James G. Taylor ◽  
Jianqiong Zhu ◽  
Wulin Aerbajinai ◽  
...  
Keyword(s):  
Sickle Cell Disease ◽  
Single Nucleotide Polymorphisms ◽  
Sickle Cell ◽  
Genetic Variants ◽  
Clinical Heterogeneity ◽  
Nucleotide Polymorphisms ◽  
Cell Disease ◽  
Single Nucleotide ◽  
Coding Regions ◽  
Hbf Induction

Therapeutic induction of fetal hemoglobin (HbF) is one of the most promising approaches to ameliorate the severity of hemoglobinopathies such as β-thalassemia and sickle cell disease (SCD). Among HbF induction agents, hydroxyurea (HU) was approved by FDA to use for the treatment of SCD. However, there is variability in HU response among SCD patients. Individual genetic variants are mostly influenced in differences in pharmacological responsiveness to drug. We previously reported that the small guanosine triphosphate (GTP)-binding protein, secretion-associated and RAS-related (SAR1A) protein was a specific HU-inducible gene. The single nucleotide polymorphisms (SNPs) in SAR1A promoter also contributed to inter-individual differences in regulation of HbF expression and SCD patient responses to HU. Additionally, microRNAs (miRNAs) have been identified as potential key genes that regulate HbF induction and related with the clinical heterogeneity of SCD. Here, we demonstrate that SNPs within SAR1A coding regions are associated with differences in individual responses to HU therapy and potentially influenced in miRNAs binding. In order to determine SNPs in SAR1A coding regions, we sequenced all 8 exons of SAR1A gene in 32 SCD patients. Three (rs56090714, rs3812693, rs56381518)and twenty-four (rs78341510, rs114346554, rs72807054, rs1370644731, rs1491135303, rs1412150420, rs1423653432, rs1480964347, rs1479076497, rs1180306451, rs1482823291, rs1275470720, rs201493587, rs1470556171, rs2394643, rs80028936, rs7919647, rs115340990, rs15801, rs1046747, rs79535872, rs7653, rs1280408553, and rs10586) variants were identified in codon 1 and 8, respectively. Interestingly, codon 2 was found a novel mutation at position 119, C&gt;A. No mutation was detected in codon 3, 4, 5, 6 and 7. Among these SNPs, rs7919647 at codon 8 was highest frequency (96.9%) in SCD patients. Next, we analyzed the association of SNPs and clinical and laboratory profiles using multiple regression. The rs56381518, rs1479076497, rs1180306451, rs1482823291, rs2394643 and rs115340990 showed significant association with total Hb levels after HU treatment in SCD patients. Only rs1180306451 was associated with absolute HbF levels (P= 0.0161). While no SNPs were observed significant association with HbF, F-cell or F-reticulocyte levels. In addition, the potential miRNAs binding to SNPs at 3'UTR regions were determined by using MicroSNiPer. We found miRNAs that may bind to SNPs as shown in Table 1. miR-625-5p, miR-5003-3p, miR-1236-5p, miR4271, miR-345-3p, miR4725-3p, miR-378a-3p, miR-548q and miR-135a-3p were previously identified only in mild-SCD patients. Furthermore, it has been reported that miR-1200 and miR-19b-1-5p were differentially expressed in high HbF levels condition. Our findings highlight the importance of genetic variants in SAR1A codon region that may predict the hydroxyurea response in SCD patients and miRNAs role in clinical heterogeneity of SCD. Disclosures No relevant conflicts of interest to declare.

scholarly journals Single Nucleotide Polymorphisms in Close Proximity to the Fibroblast Growth Factor 21 (FGF21) Gene Found to Be Associated with Sugar Intake in a Swedish Population

Nutrients ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 3954
Author(s):  
Suzanne Janzi ◽  
Esther González-Padilla ◽  
Kevin Najafi ◽  
Stina Ramne ◽  
Emma Ahlqvist ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Genetic Variants ◽  
Sweet Taste ◽  
Total Sugar ◽  
Fibroblast Growth Factor 21 ◽  
Nucleotide Polymorphisms ◽  
Fto Gene ◽  
Swedish Population ◽  
Single Nucleotide ◽  
Sugar Intake

Hereditary mechanisms are partially responsible for individual differences in sensitivity to and the preference for sweet taste. The primary aim of this study was to examine the associations between 10 genetic variants and the intake of total sugar, added sugar, and sugars with sweet taste (i.e., monosaccharides and sucrose) in a middle-aged Swedish population. Two single nucleotide polymorphisms (SNPs) within the Fibroblast grow factor 21 (FGF21) gene, seven top hits from a genome-wide association study (GWAS) on total sugar intake, and one SNP within the fat mass and obesity associated (FTO) gene (the only SNP reaching GWAS significance in a previous study), were explored in relation to various forms of sugar intake in 22,794 individuals from the Malmö Diet and Cancer Study, a population-based cohort for which data were collected between 1991–1996. Significant associations (p = 6.82 × 10−7 − 1.53 × 10−3) were observed between three SNPs (rs838145, rs838133, and rs8103840) in close relation to the FGF21 gene with high Linkage Disequilibrium, and all the studied sugar intakes. For the rs11642841 within the FTO gene, associations were found exclusively among participants with a body mass index ≥ 25 (p < 5 × 10−3). None of the remaining SNPs studied were associated with sugar intake in our cohort. A further GWAS should be conducted to identify novel genetic variants associated with the intake of sugar.

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