scholarly journals Family-Based Analysis Using a Dense Single-Nucleotide Polymorphism–Based Map Defines Genetic Variation at PSORS1, the Major Psoriasis-Susceptibility Locus

2002 ◽  
Vol 71 (3) ◽  
pp. 554-564 ◽  
Author(s):  
Colin D. Veal ◽  
Francesca Capon ◽  
Michael H. Allen ◽  
Emma K. Heath ◽  
Julie C. Evans ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Genetic Variation ◽  
Susceptibility Locus ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Family Based ◽  
Dense Single Nucleotide Polymorphism

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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