scholarly journals FANCA Polymorphism Is Associated with the Rate of Proliferation in Uterine Leiomyoma in Korea

2020 ◽  
Vol 10 (4) ◽  
pp. 228
Author(s):  
Eunyoung Ha ◽  
Seungmee Lee ◽  
So Min Lee ◽  
Jeeyeon Jung ◽  
Hyewon Chung ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Missense Mutation ◽  
Uterine Leiomyoma ◽  
Direct Sequencing ◽  
Uterine Leiomyomas ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Slow Group ◽  
Fresh Frozen ◽  
Fast Group

Uterine leiomyomas are the most common benign gynecologic tumors. This study was aimed to identify single nucleotide polymorphism of Fanconi anemia complementation group A (FANCA), associated with the rate of proliferation in uterine leiomyomas. In vitro study of patient-derived primary-cultured leiomyoma cells and direct sequencing of fresh frozen leiomyoma from each subject was conducted. Leiomyomas obtained from 44 patients who had underwent surgery were both primary-cultured and freshly frozen. Primary-cultured leiomyoma cells were divided into, according to the rate of proliferation, fast and slow groups. Single nucleotide polymorphism (SNP) of FANCA were determined from fresh frozen tissues of each patient using direct sequencing. Direct sequencing revealed a yet unidentified role of FANCA, a caretaker in the DNA damage-response pathway, as a possible biomarker molecule for the prediction of uterine leiomyoma proliferation. We identified that rs2239359 polymorphism, which causes a missense mutation in FANCA, is associated with the rate of proliferation in uterine leiomyomas. The frequency of C allele in the fast group was 35.29% while that in slow group was 11.11% (odds ratio (OR) 4.036 (1.176–13.855), p = 0.0266). We also found that the TC + CC genotype was more frequently observed in the fast group compared with that in the slow group (OR 6.44 (1.90–31.96), p = 0.0227). Taken together, the results in the current study suggested that a FANCA missense mutation may play an important regulatory role in the proliferation of uterine leiomyoma and thus may serve as a prognostic marker.

scholarly journals Leptin gene polymorphism of Ongole Grade cattle based on single nucleotide polymorphism

2018 ◽  
Vol 43 (4) ◽  
pp. 309
Author(s):  
N. Hilmia ◽  
D. Rahmat ◽  
D. Dudi
Keyword(s):  
Amino Acids ◽  
Single Nucleotide Polymorphism ◽  
Gene Polymorphism ◽  
Direct Sequencing ◽  
Snp Analysis ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Exon 2 ◽  
Specific Allele ◽  
Polymerase Chain

Point mutation on exon 2 of leptin gene, which changes amino acid encoding from Arginine to Cysteine, may alters the physiological function of the leptin hormone. This study aimed to identify leptin gene polymorphism of Ongole Grade (OG) cattle based on Single Nucleotide Polymorphism (SNP). The DNA sample was taken from 48 head of OG cattle at Balai Pengembangan Perbibitan Ternak Sapi Potong(BPPT SP) Cijeungjing West Java, which was isolated from white blood cell using the high salt method. Amplification of DNA was done by Polymerase Chain Reaction (PCR), followed by direct sequencing to obtain nucleotide sequence. The SNP analysis was carried out from alignment of sequencing result using Bioedit and MEGA 5.2 program. The results indicated in exon 2 leptin gene of OG cattle there was one synonymous SNPs that did not changeamino acids Serine encoding on g.1025T >C/S17S, while two non synonymous SNPaltered amino acids encoding, those were g.1047C> T /R25C and g.1048G>A/R25H. Those mutations changed amino acids encoding from Arginine to Cysteine and Arginine to Histidine respectively.In OG cattle, the frequency of A allele (44.8%) was higher than C allele (33.3%) and T allele (21.9%). Six genotypes were also identified, i.e. AA (41.7%), CC (20.8%), CT (20.8%), CA(4.2%), TT (10.4%) and TA (2.1 %). Heterozigosity of OG cattle based on leptin gene was 0.65 that was a high category. The A allele was a specific allele on Indonesian local cattle.

scholarly journals Single Nucleotide Polymorphism that Accompanies a Missense Mutation (Gln488His) Impedes the Dimerization of Hsp90

2009 ◽  
Vol 28 (1) ◽  
pp. 24-28 ◽  
Author(s):  
Takeshi Kobayakawa ◽  
Shin-ichi Yamada ◽  
Akio Mizuno ◽  
Yuko Ohara-Nemoto ◽  
Tomomi T. Baba ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Missense Mutation ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide

scholarly journals Polymorphism of Prolactin Gene and Its Association with Egg Production Trait in Four Commercial Chicken Lines

2018 ◽  
Vol 68 (3) ◽  
pp. 391 ◽  
Author(s):  
MOHAMED M.M. OSMAN ◽  
SHAABAN A. HEMEDA ◽  
ABEER A.I. HASSANIN ◽  
WALAA A. HUSSEINY
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Egg Production ◽  
Direct Sequencing ◽  
Nucleotide Polymorphism ◽  
Wing Vein ◽  
Single Nucleotide ◽  
Exon 2 ◽  
Avian Reproduction ◽  
Commercial Chicken ◽  
Prolactin Gene

Broodiness is a behavioral trait observed in most common breeds of domestic fowl and due to its fundamental role in avian reproduction, it has been of great interest to poultry scientists, breeders and producers of hatching eggs. Prolactin gene (PRL) is generally accepted as crucial to the onset and maintenance of broodiness in birds and thus plays a crucial role in egg production. Therefore, the present study aimed to screen the Single Nucleotides Polymorphisms (SNPs) of prolactin gene in four commercial chicken lines namely Hubbard F15, Lohmann, Cobb500, and Avian48 using PCR and direct sequencing. A total number of forty chickens (ten females from each of the four commercial chicken lines) were used. Blood samples were collected aseptically from brachial (wing) vein of the chickens for genomic DNA extraction. PCR reaction was done using five pairs of primers, one sense (F) and one antisense (R) primer for each of the five exons of prolactin gene. Finally, DNA sequencing and Single Nucleotide Polymorphisms (SNPs) analysis was done using Laser gene Megalign program. The results showed three SNPs in Hubbard F15 chicken line; one synonymous SNP at the position 3838 bp (ACC/ACT-transition) in exon 2 while in exon 5, two SNPs were detected; one non-synonymous single nucleotide polymorphism at the position 7921bp (CCT/TCT-transition) which results in amino acid changes at codon positions 169 (P/S), and one synonymous single nucleotide polymorphism at the position 8187 bp T/ C. The study concluded that this SNP in PRL gene could be used as the potential molecular markers for egg production traits in chicken.

scholarly journals Differential DNA Methylation between Fetus and Mother as a Strategy for Detecting Fetal DNA in Maternal Plasma

2002 ◽  
Vol 48 (1) ◽  
pp. 35-41 ◽  
Author(s):  
Leo LM Poon ◽  
Tse N Leung ◽  
Tze K Lau ◽  
Katherine CK Chow ◽  
YM Dennis Lo
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Direct Sequencing ◽  
Methylation Status ◽  
Maternal Plasma ◽  
Primer Extension ◽  
Nucleotide Polymorphism ◽  
Primer Extension Assay ◽  
Single Nucleotide ◽  
Epigenetic Markers ◽  
Fetal Dna

Abstract Background: Fetal DNA has been detected in maternal plasma by the use of genetic differences between mother and fetus. We explore the possibility of using epigenetic markers for the specific detection of fetal DNA in maternal plasma. Methods: A differentially methylated region in the human IGF2-H19 locus and a single-nucleotide polymorphism in this region were chosen for the study. The methylation status in this region is maintained in such a way that the paternal allele is methylated and the maternal allele is unmethylated. The single-nucleotide polymorphism was typed by direct sequencing of PCR products. The methylation status of this region was ascertained by bisulfite conversion and methylation-specific PCR. Differentially methylated fetal alleles were detected in maternal plasma by direct sequencing and a primer-extension assay. Results: Women in the second (n = 21; 17–21 weeks) and third (n = 18; 37–42 weeks) trimesters of pregnancy were recruited. Among these 39 volunteers, the 16 who were heterozygous for the single-nucleotide polymorphism were chosen for further analysis. In 11 of these 16 cases, paternally inherited methylated fetal alleles were different from the methylated alleles of the respective mothers. Using direct sequencing, we detected paternally inherited methylated fetal DNA in 6 of 11 (55%) cases. In 8 of the 16 heterozygous cases, the fetuses possessed an unmethylated maternally inherited allele that was different from the unmethylated allele of the mother. Using a primer-extension assay, we detected fetal-derived maternally inherited alleles in maternal plasma of four of eight (50%) cases. Conclusions: These results represent the first use of fetal epigenetic markers in noninvasive prenatal analysis. These data may also have implications for the investigation of other types of chimerism.

scholarly journals Alternative genotyping method for the single nucleotide polymorphism A2959G (AF159246) of the bovine CAST gene

2008 ◽  
Vol 43 (5) ◽  
pp. 657-659 ◽  
Author(s):  
Rogério Abdallah Curi ◽  
Luis Artur Loyola Chardulo ◽  
Antônio Carlos Silveira ◽  
Henrique Nunes de Oliveira
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Bos Taurus ◽  
Direct Sequencing ◽  
Bos Indicus ◽  
Basic Structure ◽  
Meat Tenderness ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Pcr Rflp ◽  
Cast Gene

The objective of this work was to genotype the single nucleotide polymorphism (SNP) A2959G (AF159246) of bovine CAST gene by PCR-RFLP technique, and to report its use for the first time. For this, 147 Bos indicus and Bos taurus x Bos indicus animals were genotyped. The accuracy of the method was confirmed through the direct sequencing of PCR products of nine individuals. The lowest frequency of the meat tenderness favorable allele (A) in Bos indicus was confirmed. The use of PCR-RFLP for the genotyping of the bovine CAST gene SNP was shown to be robust and inexpensive, which will greatly facilitate its analysis by laboratories with basic structure.

Analysis in silico of the single nucleotide polymorphism G–152A in the promoter of the angiotensinogen gene of Indonesian patients with essential hypertension

2018 ◽  
Vol 12 (1) ◽  
pp. 15-25
Author(s):  
Akhiyan Hadi Susanto ◽  
Widodo ◽  
Mohammad Saifur Rohman ◽  
Didik Huswo Utomo ◽  
Mifetika Lukitasari
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Essential Hypertension ◽  
In Silico ◽  
Direct Sequencing ◽  
Hypoxia Inducible Factor ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Hypoxia Inducible Factor 1 ◽  
Angiotensinogen Gene ◽  
Docking Approach

Abstract Background Single nucleotide polymorphism (SNP) G–152A (rs11568020) in the promoter of the angiotensinogen gene (AGT) may modulate its transcription. Translation of mRNA to angiotensinogen induces hypertension during hypoxia. The G allele at position –152 is located within the hypoxia-response element (HRE) transcription factor-binding site for the hypoxia-inducible factor 1 (HIF-1) heterodimer. However, the function of the –152 site in HIF-1 binding is not fully elucidated. Objectives To determine the frequency of SNP G–152A in Indonesian patients with hypertension and the function of this SNP. Methods We determined the frequency of the SNP in 100 patients by direct sequencing, and the influence of SNP G–152A on predicted binding of HIF-1 to the HRE using a docking approach in silico. Results The AGT promoter in our patients had genetic variants –152G and –152A (19:1). Predicted binding indicated that HIF-1 directly contacts the major groove of the G allele, but not the A allele. Scoring according to weighted sum High Ambiguity Driven biomolecular DOCKing showed that the score for the A allele–HIF-1 complex (–47.1 ± 6.9 kcal/mol) was higher than that for the G allele–HIF-1 complex (–94.6 ± 14.1 kcal/mol), indicating more favorable binding of HIF-1 to the G allele. Conclusions SNP G–152A reduces the favorability of binding of HIF-1 to the HRE. The occurrence of this SNP in the AGT promoter of Indonesian patients with essential hypertension suggests that the G allele is a genetic susceptibility factor in hypertension regulated by HIF-1.

scholarly journals Cancer Protection Elicited by a Single Nucleotide Polymorphism Close to the Adrenomedullin Gene

2013 ◽  
Vol 98 (4) ◽  
pp. E807-E810 ◽  
Author(s):  
Sonia Martínez-Herrero ◽  
Alfredo Martínez
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Allele Frequency ◽  
Minor Allele Frequency ◽  
Direct Sequencing ◽  
Minor Allele ◽  
Cardiac Insufficiency ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Healthy Donors ◽  
A Minor

Context: The risk of developing cancer is regulated by genetic variants, including polymorphisms. Characterizing such variants may help in developing protocols for personalized medicine. Objective: Adrenomedullin is a regulatory peptide involved in cancer promotion and progression. Carriers of a single nucleotide polymorphism (SNP) in the proximity of the adrenomedullin gene have lower levels of circulating peptide. The aim of the present work was to investigate whether carriers of this SNP (rs4910118) are protected against cancer. Design: This was a retrospective study. DNA samples were obtained from the Carlos III DNA National Bank (University of Salamanca, Salamanca, Spain). Setting: Samples represent a variety of donors and patients from Spain. Patients or Other Participants: DNA from patients with breast cancer (n = 238), patients with lung cancer (n = 348), patients with cardiac insufficiency (n = 474), and healthy donors of advanced age (n = 500) was used. Interventions: All samples were genotyped using double-mismatch PCR, and confirmation was achieved by direct sequencing. Main Outcome Measures: The minor allele frequency was calculated in all groups. The Pearson χ2 was used to compare SNP frequencies. Results: Of 1560 samples, 14 had the minor allele, with a minor allele frequency in healthy donors of 0.90%. Patients with cancer had a statistically significantly lower frequency than healthy donors (odds ratio = 0.216, 95% confidence interval = 0.048–0.967, P = .028). Conclusions: Carriers of the minor allele have a 4.6-fold lower risk of developing cancer than homozygotes for the major allele. Knowledge of the rs4910118 genotype may be useful for stratifying patients in clinical trials and for designing prevention strategies.

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