scholarly journals Germline mutation analysis of Tpit in Poodle dogs with ACTH-dependent hyperadrenocorticism

2012 ◽  
Vol 64 (4) ◽  
pp. 853-859
Author(s):  
V. De Marco ◽  
L.R. Carvalho ◽  
A.E.C. Billerbeck ◽  
B.B. Mendonça
Keyword(s):  
Genomic Dna ◽  
Terminal Differentiation ◽  
Germline Mutations ◽  
Coding Region ◽  
Nucleotide Polymorphism ◽  
Control Groups ◽  
Single Nucleotide ◽  
Automatic Sequence ◽  
High Incidence ◽  
And Control

There is a high incidence of pituitary-dependent hyperadrenocorticism (PDH) in Poodle dogs, with family members being affected by the disease, suggesting a genetic involvement. Tpit is an obligate transcription factor for the expression of pro-opiomelanocortingene and for corticotroph terminal differentiation. The aim of the present study was to screen the Tpit gene for germline mutations in Poodles with PDH. Fifty Poodle dogs (33 female, 8.71±2.8 years) with PDH and 50 healthy Poodle dogs (32 females, 9.4241 2.8 years) were studied. Genomic DNA was isolated from peripheral blood, amplified by PCR and submitted to automatic sequence. No mutation in the coding region of Tpit was found, whereas the new single nucleotide polymorphism p.S343G, in heterozygous state, was found in the same frequency in both PDH and control groups. We concluded that Tpit gain-of-function mutations are not involved in the etiology of PDH in Poodle dogs.

scholarly journals Genotyping analysis of the Pax9 Gene in patients with maxillary canine impaction

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 254 ◽  
Author(s):  
Evy Eida Vitria ◽  
Iwan Tofani ◽  
Lindawati Kusdhany ◽  
Endang Winiati Bachtiar
Keyword(s):  
Inclusion Criteria ◽  
Nucleotide Polymorphism ◽  
Chromosome 14 ◽  
Control Groups ◽  
Maxillary Canine ◽  
Single Nucleotide ◽  
Ncbi Dbsnp ◽  
Polymerase Chain ◽  
And Control ◽  
The Relationship

Background: Paired-box gene 9 (PAX9) mutation is potentially associated with impaction in some patient populations. Here, we analyzed the relationship between PAX9 polymorphism and the occurrence of maxillary canine impaction. Methods: Patients with and without maxillary canine impaction were selected based on specific inclusion criteria, and samples of genomic DNA were obtained from a buccal mucosa swab. DNA was amplified by polymerase chain reaction and sequenced for further bioinformatics analysis to identify single nucleotide polymorphism (SNP) genotypes. Genotype and allele counting was performed in both case and control groups prior to conducting statistical analysis. Results: Four SNPs were identified in patients with maxillary canine impaction, with relative confidence determined based on chromatogram-peak assessment. All SNPs were located in exon 3 of PAX9 and in the region sequenced by the primer pair −197Fex3 and +28Rex3. Three of the SNPs (rs375436662, rs12881240, and rs4904210) were reported previously and are annotated in NCBI (dbSNP version 150), whereas another SNP mapped to chromosome 14 has not been reported. Patients with a CC genotype at SNP 3 [odds ratio (OR): 2.61 vs. TT; 1.28 vs. CT] and a CC genotype at SNP 4 [OR: 0.71 vs. GG; 0.79 vs. CG] were more likely to have maxillary canine impaction. Conclusions: These results demonstrated that the presence of SNPs 3 and 4 is associated with increased likelihood of suffering from maxillary canine impaction.

scholarly journals Advanced Oxidation Protein Products and the CLOCK 3111T/C Single Nucleotide Polymorphism in Menopausal Women with Insomnia

2020 ◽  
Vol 10 (4) ◽  
pp. 352-356
Author(s):  
Natalya V. Semenova Natalya V. Semenova ◽  
Irina Madaeva ◽  
Anastasiya Brichagina ◽  
Olga Nikitina ◽  
Sergey Kolesnikov ◽  
...  
Keyword(s):  
Pittsburgh Sleep Quality Index ◽  
Advanced Oxidation ◽  
Severity Index ◽  
Nucleotide Polymorphism ◽  
Control Groups ◽  
Advanced Oxidation Protein Products ◽  
Single Nucleotide ◽  
Menopausal Women ◽  
And Control ◽  
Insomnia Severity

Background: The aim of this study was to assess the dependence of advanced oxidation protein products (AOPPs) levels on the genotype of the CLOCK 3111T/C SNP in Caucasian menopausal women with and without insomnia. Methods and Results: The study involved 105 Caucasian menopausal women volunteers aged between 45 and 60 years. The Pittsburgh Sleep Quality Index, PSQI, Insomnia Severity Index (ISI), and Epworth Sleepiness Scale (ESS) were employed. The study of the CLOCK 3111T/C SNP (rs1801260) was performed by PCR. The blood level of advanced oxidation protein products (AOPPs) was detected by IEMA. Based on the results of a clinical-anamnestic examination, the women were divided into two groups: the main (with insomnia) and the control (without insomnia). Given the small number of women carrying the CC genotype of the CLOCK 3111T/C SNP, the СС carriers and TC carriers were combined into one group as the carriers of the minor 3111C allele. There were no statistically significant differences in the AOPP levels between carriers of different genotypes (TT genotype and TC+CC genotypes) in controls and patients. A comparative analysis of AOPP levels in the women of the main and control groups showed higher AOPP levels in women with insomnia carrying the TT genotype than in the control of the same genotype (P=0.013). Conclusion: Insomnia in menopausal women is associated with increased protein oxidation only in carriers of the TT genotype of the CLOCK 3111T/C SNP.

High Microsatellite and SNP Genotyping Success Rates Established in a Large Number of Genomic DNA Samples Extracted From Mouth Swabs and Genotypes

2006 ◽  
Vol 9 (4) ◽  
pp. 501-506 ◽  
Author(s):  
Josine L. Min ◽  
Nico Lakenberg ◽  
Margreet Bakker-Verweij ◽  
Eka Suchiman ◽  
Dorret I. Boomsma ◽  
...  
Keyword(s):  
Success Rate ◽  
Genomic Dna ◽  
Snp Genotyping ◽  
High Yield ◽  
Success Rates ◽  
Nucleotide Polymorphism ◽  
High Quality ◽  
Single Nucleotide ◽  
Dna Yield ◽  
Yield And Quality

AbstractIn this article, we present the genomic DNA yield and the microsatellite and single nucleotide polymorphism (SNP) genotyping success rates of genomic DNA extracted from a large number of mouth swab samples. In total, the median yield and quality was determined in 714 individuals and the success rates in 378,480 genotypings of 915 individuals. The median yield of genomic DNA per mouth swab was 4.1 μg (range 0.1–42.2 μg) and was not reduced when mouth swabs were stored for at least 21 months prior to extraction. A maximum of 20 mouth swabs is collected per participant. Mouth swab samples showed in, respectively, 89% for 390 microsatellites and 99% for 24 SNPs a genotyping success rate higher than 75%. A very low success rate of genotyping (0%–10%) was obtained for 3.2% of the 915 mouth swab samples using microsatellite markers. Only 0.005% of the mouth swab samples showed a geno-typing success rate lower than 75% (range 58%–71%) using SNPs. Our results show that mouth swabs can be easily collected, stored by our conditions for months prior to DNA extraction and result in high yield and high-quality DNA appropriate for genotyping with high success rate including whole genome searches using microsatellites or SNPs.

Single nucleotide polymorphisms of CBF4 locus region of Arabidopsis thaliana correspond to drought tolerance

2004 ◽  
Vol 1 (3) ◽  
pp. 181-190 ◽  
Author(s):  
Hao Gang-Ping ◽  
Wu Zhong-Yi ◽  
Chen Mao-Sheng ◽  
Cao Ming-Qing ◽  
Dominique Brunel ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Drought Tolerance ◽  
World Wide ◽  
Nucleotide Variation ◽  
Nucleotide Polymorphisms ◽  
Water Deficiency ◽  
Coding Region ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Adaptation To Drought

AbstractThe levels of drought tolerance and nucleotide polymorphism at the CBF4 locus were examined in a world-wide sample of 17 core accessions of Arabidopsis thaliana. The results showed that different accessions exhibited considerable differences in adaptation to drought stress. Compared with Columbia accession, the frequency of nucleotide polymorphism at the CBF4 locus of 25av, 203av and 244av accessions, including single nucleotide polymorphism (SNP) and insertion/deletion (Indel), was high, on average 1 SNP per 35.8 bp and 1 Indel per 143 bp. No significance in all regions of Tajima's D test indicated that the neutral mutation hypothesis could explain the nucleotide polymorphism in this CBF4 gene region. The higher polymorphism was the result of purification selection. Nucleotide polymorphism in the non-coding region was three times higher than in the coding region. This might indicate a recent relaxation of selection pressures on the non-coding region of CBF4 gene. In the coding region of CBF4, SNP frequency was 1 SNP per 96.4 bp and one non-synonymous mutation was detected from 25av, 203av and 244av accessions: the amino acid variation gly↔val at position 205, caused by the nucleotide variation G↔T at position 1034 (corresponding to the nucleotide at position 19 696 of GenBank accession no. AB015478 as 1). Furthermore, four differential SNPs were discovered in haplotype 6 constituted by 203av, one of them located in the 3′ non-coding region (A↔C at position 1106) and the others in the 5′ non-coding region (A↔G, A↔C and G↔A at positions 27, 129 and 171, respectively). The drought tolerance assay indicated that accession 203av was the best at tolerating water deficiency. We propose that haplotype 6 is consistent with its drought tolerance.

scholarly journals ADHD and DIRAS Single Nucleotide Polymorphism as an Indicator of Prolonged Concussion Recovery

CommonHealth ◽  
2021 ◽  
Vol 2 (3) ◽  
pp. 94-101
Author(s):  
Taziah Kenney ◽  
Jane McDevitt
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Rare Allele ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Adhd Diagnosis ◽  
Hyperactivity Disorder ◽  
Recovery Times ◽  
Prolonged Recovery ◽  
Concussion Recovery ◽  
And Control

The purpose of this study was to determine the association between the presence of a single nucleotide polymorphism (SNP; rs1412005) within DIRAS2 (i.e., a gene associated with attention-deficit/hyperactivity disorder (ADHD) and prolonged recovery following a sport-related concussion. A case-control study design was implemented, where cases and controls were selected from a cohort of 117 deidentified concussed athletes. Eleven samples from this patient cohort self-reported ADHD diagnosis and were age and sex-matched to 22 participants with no self-reported ADHD diagnoses. The average recovery times were 21.50 + 13.96 days and 15.66 + 8.50 days for the case and control groups, respectively. The authors found that only 13.6% of the individuals without an ADHD diagnosis recovered in > 30 days (p = 0.044). Also, the authors found that 72.7% of the carriers of the T allele (i.e., minor allele) recovered in greater than 30 days (p = 0.213).  Researchers concluded that individuals with ADHD had a higher risk of prolonged concussion recovery lasting greater than 30 days. Also, carrying the rare allele was associated with prolonged recovery, which suggests this SNP could be a potential genetic marker for both prolonged concussion recovery and the presence of ADHD.

scholarly journals THE PROGNOSTIC SIGNIFICANCE OF TET2 SINGLE NUCLEOTIDE POLYMORPHISM IN EGYPTIAN CHRONIC MYELOID LEUKEMIA

2020 ◽  
Vol 12 (1) ◽  
pp. e2020004
Author(s):  
Enas A Dammag ◽  
Nahla A.M. Hamed ◽  
Nabil A El Halawani ◽  
Heba S Kassem ◽  
Mona W Ayad
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Chronic Myeloid Leukemia ◽  
Myeloid Leukemia ◽  
Statistical Significance ◽  
Control Group ◽  
Spleen Size ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Prognostic Criteria ◽  
And Control

Background: Chronic myeloid leukemia (CML) is a myeloproliferative neoplasm. The pathogenesis of CML is based on the oncoprotein termed BCR‐ABL1. TET2 initiates DNA demethylation and is frequently mutated in hematological malignancies including CML.(1) The relation between TET2 acquisition and CML transformation and/or imitinab resistance is needed to be investigated. (2) Aim: To evaluate Ten Eleven Translocation 2 gene (TET2) single nucleotide polymorphism (SNP) (rs2454206, rs34402524, rs61744960) in chronic myeloid leukemia (CML) in relation to the disease prognostic criteria. Materials & Method: The study included 84 subjects; 54 CML in chronic phase and 30 healthy subjects as control group matched for age and sex. Routine investigations including CBC, bone marrow aspiration, biochemical investigations and molecular study were performed in CML patients to identify the disease stage. DNA extraction and SNP assay for TET2 gene polymorphism was done using (Thermo-Fisher predesigned SNP, USA) PCR prism 7500. Results: The mean age was 45.98±15.7 yrs in CML patients and   39.3±6.587 yrs in control group (p>0.05). TET2 SNP rs 34402524 was either heterozygous and homozygous in CML (48%,and 46.2%) but was mainly homozygous among control (80%) group (p=0.012). TET2 SNP rs 2454206 cases within CML (65.4%) and control (63.3%) group had wild patterns (p=0.046). TET2 SNP rs 61744960 showed a homozygous pattern among all groups (CML and control) showing no statistical significance (p=0.528). TET2 SNP in CML cases did not alter the prognostic criteria as no statistical significance was noted (p>0.05) yet, it was significantly related to spleen size in rs 34402524 where homozygous group had huger sizes and higher BCR-ABL1 levels 6 months after starting TKIs (p<0.05). Conclusions/Recommendation: TET2 SNP is a common in Egyptian chronic myeloid leukemia. TET2 SNP rs 3442524 was associated with huger spleen size and higher BCR-ABL1 levels after 6 months of starting TKIs suggesting disease progression.

Analysis of porcine OSBPL5 gene allelic expression in skeletal muscle and association of a single-nucleotide polymorphism in the coding region with production traits

2019 ◽  
Vol 99 (4) ◽  
pp. 914-920
Author(s):  
Meng Wang ◽  
Deli Wei ◽  
Guiling Cao ◽  
Guiyu Zhu ◽  
Yunliang Jiang
Keyword(s):  
Skeletal Muscle ◽  
Single Nucleotide Polymorphism ◽  
Growth Regulation ◽  
Average Daily Gain ◽  
Allelic Expression ◽  
Production Traits ◽  
Coding Region ◽  
Nucleotide Polymorphism ◽  
Specific Expression ◽  
Single Nucleotide

Genes that exhibit allelic expression imbalance and imprinted genes play important roles in the survival of the embryo and postnatal growth regulation. In this study, the porcine oxysterol-binding protein-related 5 (OSBPL5) gene was examined, and the 2140G>A mutation (rs318687202) was found in its coding region by a comparison of Laiwu and Landrace pigs. By allele-specific expression analysis based on a specific single-nucleotide polymorphism (SNP), the imprinting status of OSBPL5 gene in skeletal muscle from both neonate and adult pigs was determined. The results showed that the OSBPL5 was paternally imprinted in skeletal muscle from adults but biallelically expressed with predominantly maternal imprinting in neonates. The distribution of the 2140G>A SNP in four pig populations was analyzed, which showed that GG genotype was dominant in Duroc and Dapulian populations, whereas the AG genotype was dominant in Junmu-1 and Laiwu populations. Pigs with the GG genotype had significantly larger litters and greater cannon bone circumferences but a lower average daily gain than pigs with the AA genotype. In conclusion, we determined the difference in the allelic expression of OSBPL5 between adult and neonate pigs and identified an SNP in its coding region that is associated with production traits.

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