Consanguinity avoidance and genotype frequencies in human populations.
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Consanguinity↗
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Individualization of tiger by using microsatellites.
In investigating criminal cases of poaching and smuggling involving tigers (Panthera tigris), the number of tiger individuals involved is critical for determining the penalty. Morphological methodologies do not often work because tiger parts do not possess the distinctive characteristics of the individual. Microsatellite DNAs have been proved a reliable marker for the individualization of animals. Seven microsatellite loci derived from domestic cat (Felis catus) were selected to individualize tigers, namely F41, F42, F146, Fca304, Fca391, Fca441 and Fca453. A reference population containing 37 unrelated tigers were used to investigate alleles, allelic frequencies, genotypes and genotype frequencies of each locus. Consequently, the data was used to assess the validity of the combination of seven loci for tiger individualization. All loci were polymorphic and easy to amplify. Three out of the seven loci were significantly departure from the Hardy-Weinberg Equilibrium (P < 0.05). Cumulative discrimination power (DP) calculated with observed genotype frequencies was 0.99999789. Match probability of an individual in the reference population with a random individual in seven loci ranged from 7.34 x 10(-9) to 2.77 x 10(-5). This suggests that combining the seven microsatellite loci provides desirable power to individualize tigers. The combination of seven loci was applied to a case of tiger bone smuggling. Genotypes of all samples were identical in all seven loci, and the P(M) of the evidence samples in the seven loci hit 5.63 x 10(-7), provided evidence that the bones belong to a single tiger.
Animals↗
Enzyme variability in natural populations of Daphnia magna. IV. Ecological differentiation and frequency changes of genotypes at Audley End.
Genotypic frequencies were analysed for two years in a permanent population of the cladoceran crustacean, Daphnia magna, which was polymorphic for an esterase and for malate dehydrogenase. Large temporal changes in genotypic frequencies occurred at both loci. There was no evidence of a seasonal pattern in the frequency changes. In most samples, genotypes at the two enzyme loci were non-randomly associated; these associations showed temporal changes. On some occasions marked spatial heterogeneity in genotypic frequencies existed within the population. Genotypic differences in parthenogenetic and sexual egg production were observed. In a primarily parthenogenetically reproducing population, non-random associations between genotypes of structural and regulatory loci will be the rule. The allozyme variants themselves may or may not be under selection. The relevance of these observations to ecological studies on Daphnia is considered.
Animals↗
Population data on 6 short tandem repeat loci in a sample of Caucasian-Mestizos from Colombia.
Blood samples from 409-452 unrelated Colombian Caucasian-Mestizo individuals were amplified and typed for six short tandem repeat (STR) markers (HUMF13A01, HUMFES/FPS, HUMVWA, HUMCSF1PO, HUMTPOX, HUMTH01). The allele frequencies, genotype frequencies, heterozygosity, mean paternity exclusion chance, polymorphism information content, discrimination power, assumption of independence within and between loci and Hardy Weinberg equilibrium were determined. The results demonstrate that all markers conform to Hardy-Weinberg equilibrium expectations. In addition, the results demonstrate the assumption of independence within and between the loci analysed. The mean exclusion chance (MEC) was 0.9851 for all six STR loci analysed and the discrimination power (DP) was 0.9999973. Therefore, this Colombian population database can be used in identity testing to estimate the frequency of a multiple PCR-based locus DNA profile in forensic cases as well as in paternity testing.
Black People↗
Correlations between water quality and frequencies of allozyme genotypes in spotfin shiner (Notropis spilopteris) populations.
Genotype frequencies of glucose-6-phosphate isomerase (GPI) allozymes differed significantly among populations of the spotfin shiner Notropis spilopterus from sites with varying water quality. Frequencies of shiners with a GPI-2 BB genotype decreased significantly at sites with reduced water quality. Alternatively, the total frequencies of shiners with a genotype of GPI-2 AA and AB increased at sites with reduced water quality. Individuals with certain allozyme genotypes may be more sensitive to the toxic effects of polluted waters than those with other genotypes. The selection of individuals with sensitive genotypes may reduce genetic diversity in populations and thus increase the susceptibility of these populations to additional novel stresses. Because allele and genotype frequencies of GPI-2 were correlated with water quality, electrophoretic determination of genetic structure in fishes may be a useful tool for monitoring the health of aquatic populations.
Journal Article↗
Allele frequency and genotype distribution of polymorphisms within disease-related genes is influenced by ethnic population sub-structuring in Sudan.
Four single nucleotide polymorphisms (SNPs) and a variable number of tandem repeats (VNTR) polymorphism located within disease associated/causing genes were typed in four populations of different tribal and ethnic affiliation from the Sudan. The genotype and allele frequencies were compared with those of other groups from published and unpublished data of world populations. The combined Sudanese sample conformed with Hardy-Weinberg equilibrium (HWE) expectation. However, population sub-structuring according to ethnic/linguistic group indicated at least two SNPs in departure from HWE. Differences in allele frequencies and genotype distribution between groups was also noted in three of the four SNPs. The other loci were distributed homogeneously within the populations studied with genotype frequencies in agreement with HWE expectation. These results highlight the importance of inter-population stratification for polymorphic markers, as well as the potential influence of evolutionary history and ethnic variation of loci, in the general distribution of SNPs and other polymorphisms.
Evolution, Molecular↗
[The frequencies of apolipoprotein E genotypes in health and disease in the Croatian population--an overview of expectations and real results].
The aim of the overview is to show the distribution of common apolipoprotein E (APOE) genotypes in the Croatian population, and to test whether it could serve as a new molecular biomarker in some clinical entities. The study included the following groups: patients with angiographically confirmed coronary artery disease, myocardial infarction, Alzheimer's dementia, vascular dementia, hyperlipidemias, diabetes mellitus, pancreatitis, and healthy subjects. Group comparisons of different clinical entities and control group were performed using Pearson's Chi2-test. There was no difference in APOE genotype frequencies between coronary artery disease neither myocardial infarction and control group. The ApoE genotype frequencies in patients with Alzheimer's disease were significantly different from those in the control group. APOE-4 allele tends to be a risk factor for the development of Alzheimer's disease. The frequencies were only marginally different in vascular dementia. Patients with hypercholesterolemia, those with inherited familial hypercholesterolemia, children with diabetes mellitus, and patients with pancreatitis of different etiology showed distributions of APOE genotypes that differed from the control group. It is concluded that the frequencies of APOE genotypes yielded no statistically significant result to confirm the association between APOE genotypes and any specific disease with the exception of Alzheimer's disease; APO-epsilon4 allell has become one of the important biomarkers in diagnosis of Alzheimer's dementia.
Apolipoproteins E↗
No evidence for involvement of the promoter polymorphism -866 G/A of the UCP2 gene in childhood-onset obesity in humans.
Recently, an association between obesity and the G-allele of the - 866 G/A polymorphism in the promoter region of uncoupling protein-2 gene (UCP2) was reported. Both allele frequencies and genotype distributions for this polymorphism differed between obese individuals and never-obese controls. We attempted to confirm this finding. Genotyping was performed by polymerase chain reaction with subsequent restriction fragment length polymorphism analysis (PCR-RFLP). We analysed transmission disequilibrium of the (wild type) G-allele for 200 extremely obese children and adolescents from 93 concordant sib pair families using the pedigree disequilibrium test. Additionally, using a one-sided asymptotic Pearson's chi 2-test, we tested whether the G-allele occurs more frequently in 277 extremely obese children and adolescents (including the 93 index patients of the concordant sib pairs) than in 188 never-obese controls. The one-sided asymptotic Cochran Armitage trend test was used to determine differences in genotype frequencies between extremely obese and healthy underweight individuals. The PDT analysis revealed no evidence for transmission disequilibrium in obesity. Allele and genotype frequencies did not differ between the extremely obese and never-obese subjects. In conclusion, we cannot confirm the results of ) in our young sample.
Adolescent↗
Association of a C/T single-nucleotide polymorphism in the 5' untranslated region of the CD40 gene with Graves' disease in Japanese.
CONTEXT: Graves' disease (GD) is caused by an interplay of genetic factors and environmental triggers. Recently, a susceptibility locus for GD was mapped to chromosome 20q11 (GD-2). Furthermore, a novel single nucleotide polymorphism (SNP) in the CD40 gene, which is located in 20q11, was found to be associated and linked with GD in Caucasians and in Koreans. OBJECTIVES: To examine a C/T SNP in the 5' untranslated region of the CD40 gene (CD40-E1SNP) for association with autoimmune thyroid diseases (AITDs) in a Japanese dataset. DESIGN, SETTING, AND PATIENTS: Case-control association studies were performed using the CD40-E1SNP. We studied 485 Japanese patients with AITD (301 with GD, 184 with Hashimoto's thyroiditis [HT]) and 177 matched Japanese control subjects in association studies. MAIN OUTCOME: Frequencies of genotypes and alleles of the CD40- E1SNP. RESULTS: The distribution of genotype frequencies differed significantly between patients with GD and controls in a dominant manner (p = 0.039). The CC+CT genotypes of the CD40-E1SNP were associated with the increased risk for GD (p = 0.015, odds ratio [OR] = 1.9). In contrast, no differences in genotype frequencies were observed between HT patients and controls for the CD40-E1SNP. CONCLUSION: These results suggested that the CD40 gene is involved in susceptibility for GD in the Japanese.
5' Untranslated Regions↗
Angiotensin-converting enzyme genotypes and risk for myocardial infarction in women.
OBJECTIVES: We tested for an association between the angiotensin-converting enzyme (ACE) DD polymorphic genotype and myocardial infarction (MI) in a sample group composed exclusively of women. BACKGROUND: The human ACE gene occurs with either an insertion (I allele) or a deletion (D allele) of a 287-base pair (bp) Alu element. Part of the variance in serum ACE levels may be accounted for by this polymorphism. Also, the DD genotype has been associated with an increased risk of MI in predominantly male populations. However, the risk in women is poorly defined. METHODS: Genomic DNA was extracted from buffy coat blood using a phenol/chloroform method. Angiotensin-converting enzyme alleles were identified using primers to bracket the insertion region in intron 16. Amplification using polymerase chain reaction allowed identification of a 490-bp (I allele) or a 190-bp (D allele) product, or both. RESULTS: Allelic and genotypic frequencies in control subjects were similar to those reported in mostly male populations, and frequencies of genotypes were in the Hardy-Weinberg equilibrium. In contrast, the distribution of genotypes in patients with MI diverged from the equilibrium. Specifically, DD genotypic frequency was increased in women with (n = 141) versus without (n = 338) a previous MI (39% vs. 29%, odds ratio [OR] 1.54, 95% confidence interval 1.02 to 2.32, p < 0.04). Risk was particularly increased in women <60 years old (OR 2.04, p < 0.05). In contrast, the DD genotype did not predict angiographic coronary artery disease. CONCLUSIONS: Consistent with findings in male-dominated populations, a modest association of the ACE DD genotype with MI was found in women. The basis for this association requires further study.
Aged↗
[Genetics of the HL-A system. Haplotype and genotype gene frequencies observed in 113 families].
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Adult↗
Normal frequencies of the C677T genotypes on the methylenetetrahydrofolate reductase (MTHFR) gene among lymphoproliferative disorders but not in multiple myeloma.
The folate availability seems to be critical for the DNA integrity since it is required for the transfer of methyl groups in the biosynthesis of thymidilate. Although the excessive incorporation of uracils to the DNA can be efficiently removed, this mechanism of reparation produces many double-strand breaks from two opposing nicks. Several chromosomal abnormalities (mainly translocations and deletions perhaps not well understood) are involved in the origin of lymphoproliferative disorders. The TT homozygosity at nucleotide 677 in the gene of methylene tetrahydrofolatereductase (MTHFR), a key enzyme in folate metabolism, was recently linked to a significant protection against colon carcinoma and acute lymphoblastic leukaemia in adults. We analysed the genotype frequencies of C677T-MTHFR in a group of 143 patients with lymphoproliferative disorders (REAL classification) and 200 controls. Overally, the frequencies of the polymorphic allele were similar (35.3% and 32.0% respectively)(P=0.6). We did not find differences between patients and controls except for myeloma/plasmacytoma group (n=26) which showed a CC genotype less than expected (19% vs 46%) (p=0.01) with a frequency ratio of 0.28 (0.10-0.77). Even among the IgG myeloma cases only one patient showed a common genotype (CC) (1/15, 7%) (P=0.003). If these preliminary data are validated with prospective studies, the 677C allele of MTHFR gene could be confirmed as an effective multiple myeloma protective factor (specially for the IgG cases).
Adult↗
ACE gene polymorphism in children with nephrotic syndrome in the Indonesian population.
BACKGROUND: The angiotensin converting enzyme (ACE) gene carries insertion (I) and deletion (D) polymorphism within its intron 16. The presence of D-allele in the ACE gene has been reported as a probable genetic risk factor for idiopathic nephrotic syndrome (INS), especially the subtype of focal segmental glomerulosclerosis (FSGS). The D-allele may be related to poor responsiveness to steroid therapy. To clarify the relationship between the D-allele and INS, we studied the prevalence of the D-allele in the Javanese-Indonesian patients. Additionally, we also analyzed relationship between each genotype and steroid sensitivity among the MCNS patients. METHODS: Eighty-five Javanese-Indonesian patients under 15 years of age with INS were enrolled in this study: 16 patients with FSGS and 69 patients with minimal change nephrotic syndrome (MCNS). As controls, 68 healthy adult Javanese-Indonesians with no history of kidney disease volunteered to participate in this study. Genotypes based on the polymorphisms (I/D) were determined by using a PCR method. As for the steroid responsiveness, the information of 14 out of 16 FSGS patient (87.5%) and 69 out of 69 MCNS patients (100%) was available. RESULTS: The genotype frequencies in the FSGS patients were II 37% (6/16), ID 44% (7/16) and DD 19% (3/16), and the D-allele frequency was 41% (13/32). The genotype frequencies in the MCNS patients were II 56% (39/69), ID 38% (26/69) and DD 6% (4/69), and the D-allele frequency was 25% (34/138). The genotype frequencies in the controls were II 60% (41/68), ID 31% (21/68), and DD 9% (6/68), and the D-allele frequency was 26% (33/136). None of the FSGS patients were sensitive to steroid, while almost all MCNS patients (66/69) were sensitive to steroid. The genotype frequencies among steroid-sensitive MCNS patients were consistent with those of the controls, suggesting that there was no relationship between each genotype and steroid sensitivity. CONCLUSIONS: In the Javanese-Indonesian population, none of the comparisons showed any significant differences in the genotypic distribution and allelic frequencies among the three groups, FSGS, MCNS and controls, although D-allele tended to exist more frequently in FSGS patients than in the MCNS patients and controls. In addition, the D-allele frequency was not related to steroid sensitivity in the MCNS patients.
Adolescent↗
Polymorphisms of the human homologue of the Drosophila white gene are associated with mood and panic disorders.
The Drosophila white gene is a member of the ATP-binding cassette (ABC) transporter superfamily and is involved in the cellular uptake of tryptophan. Its human homologue gene (hW) has been mapped to chromosome 21q22.3. Tryptophan is the precursor for the neurotransmitter serotonin, which has been implicated in the regulation of mood and anxiety. The locus 21q22.3 has also been reported to be associated with mood disorders. The 3'-untranslated region (3'-UTR) in the hW gene has been shown to contain a polymorphic poly(T) region. We have identified a new polymorphism G2457A in the 3'-UTR in the present study. We examined the relationship between these polymorphisms and mood and panic disorders, and a significant association between the poly(T) polymorphisms and mood disorders was detected (P=0.039 (allele frequency)). Associations were found between the polymorphisms and mood (poly(T) polymorphism: P=0.047 (allele frequency), G2457A: P=0.040 (allele frequency), P=0.044 (genotype frequency)) and panic disorders (G2457A: P=0.026 (allele frequency), P=0.011 (genotype frequency)) in males, but not in females. These findings suggest that the hW gene may be an important gene in the control of mood and anxiety as well as one of the genetic factors related to mood disorders and panic disorder in males. The statistical significance of the association remains relatively low and larger materials facilitating further dissection of the clinical phenotype will be needed to confirm and independently validate this finding and to evaluate its significance.
3' Untranslated Regions↗
[Single nucleotide polymorphism analysis of the chicken Myostatin gene in different chicken lines].
Myostatin is a new member of the TGF-beta superfamily. It is specifically expressed in skeletal muscle cells and functions as a negative regulator of skeletal muscle growth. This study was aimed to identify the single nucleotide polymorphisms (SNPs) of Myostatin gene in various breeds including Beijing Youji, Baierji, Shiqiza, Dwarf Yellow Chickens, Mini Yellow Chickens, Huiyang Huxuji, Recessive White Chickens, AA and Hyline Layer. The 17 pairs of primers for Myostatin gene were designed based on the chicken genomic sequence. The total 5 SNPs were identified in the chicken Myostatin gene by PCR-SSCP of which 3 were in the 5'-regulatory region and 2 were in the 3'-regulatory region of the Myostatin gene in different chicken lines. The sequence data showed that one of the three SNPs localized in the 5'-regulatory region was due to 3 single point mutations (G304A, A322G, C334T, respectively), other two were single point mutation of G167A and T177C, respectively. The other two SNPs in the 3'-regulatory region of the Myostatin gene are A to T (7263) and A to G (6935). Population genetic analysis indicated that genotype frequencies of the Myostatin locus (P60/P61) in Beijing youji were quite different from those of other tested chicken lines. Frequency of the BB genotype was very high (0.70) while the AA genotype was only 0.033 in 5'-regulatory region (P60/P61) in Beijing youji population. The genotype frequencies (P93/P94) were significantly different among the lines (P < 0.01): frequencies of the EE genotype in Beijing Youji were lower than those in the other lines, while frequencies of the EE genotype in Baierji and Hyline Layer were higher than the rest. Frequency of allele C (P80/P81) in 9 breeds was higher than that of allele D. Frequency of genotype MM (P76/P77) was low, and that of MN was high in 7 breeds.
Animals↗
[ACE gene I/D-polymorphism and hereditary predisposition to myocardial infarction].
The authors compare distribution of genotype frequencies and alleles of I/D of ACE gene polymorphism in patients with various forms of ischemic heart disease (IHD): with acute myocardial infarction (MI), stable effort angina (functional class II-III); in patients with postinfarction cardiosclerosis (PICS). A relationship was found between I/D polymorphism and acute MI. Frequency of DD genotype in MI patients was 0.57, in controls--0.21, p < 0.0001, RR = 4.9. The DD genotype may serve a marker of hereditary predisposition to MI. Genotype DD frequency in the group with acute MI was higher than that with PICS. In acute MI frequency of allele D was 0.76, in PICS--0.51, p < 0.0005. It is suggested that low frequency of genotype DD in the PICS group results from higher lethality of patients with DD genotype in the nearest rehabilitation period. Patients with repeated MI have a significantly higher frequency of genotype DD and complications after MI. Thus, there is a relationship between insertion-deletion polymorphism of ACE gene and myocardial infarction. Deletion DD genotype raises the risk to develop MI and probability of life-threatening complications and repeated MI.
Bacterial Outer Membrane Proteins↗
Association of genetic polymorphism in GH gene with milk production traits in Beijing Holstein cows.
Associations were analysed between polymorphisms of the growth hormone gene (GH-MspI) (localized in intron 3) and milk production traits of Beijing Holstein cows (a total of 543 cows). Polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP) method was used for identification of various genotypes. Frequencies of genotypes were 0.77, 0.21 and 0.02 for A/A, A/B and B/B, respectively. The frequency of the GH A allele is 0.875. The results of the least squares means show that in all three lactations, the GH A/A cows yielded more milk (P less than 0.01 for lactation I and P less than 0.05 for lactations II and III), whereas A/B cows showed higher milk fat content than A/A individuals (P less than 0.05 for lactations I and II, and P less than 0.01 for lactation III). The A/A cows yielded more fat than A/B individuals (P less than 0.01 only in lactation I). The A/A cows yielded more milk protein than A/B individuals (P less than 0.01 for lactations I, II, and III). The A/A cows produced milk of higher protein content than of A/B individuals (P less than 0.05 only in lactation II).
Animals↗
Stromal cell-derived factor-1 (SDF-1) gene and susceptibility of Iranian patients with lung cancer.
Stromal cell derived factor-1 (SDF-1), a CXC chemokine that play important roles in tumor growth, angiogenesis and metastasis of tumor cells, has a polymorphism at position 801 of its 3'-untranslated region, known as SDF1-3'A. This polymorphism has been investigated in HIV-1 infection and the susceptibility to breast cancer. In this investigation 72 lung cancer patients and 262 cases of normal healthy control were investigated for the genotype frequency of SDF-1 gene. Genotype frequency was carried out by PCR-RFLP method. Of 72 cancer patients 9 (12.5%) cases were emerged with AA genotype, 38 (52.8%) patients with AG and 25 (34.7%) with GG genotype. Comparison of these data with genotype frequency of SDF-1 gene of 262 normal healthy controls indicates a significant difference among patient and control groups (P=0.008). Results also showed that the frequency of AA and AG genotypes was higher among patients, while the frequency of GG genotype was lower compared to the controls. By considering the importance of SDF-1 in several physiological processes and also its significant biological behavior in cancer metastasis and on the basis of the results of this study we conclude that AA and AG genotypes of SDF-1 may be considered as factors increasing the susceptibility of Iranian patients to lung cancer.
3' Untranslated Regions↗