The compact genome of the plant pathogen Plasmodiophora brassicae is adapted to intracellular interactions with host Brassica...
After filtering (on allele frequency, SNP positions with heterozygous genotypes and indels) 132,429 SNPs remained and were ... The VCF file was filtered to remove positions where the variant allele frequency was 100 %. Additionally, if a single pathotype ... 21]). Pathotypes alleles are coded in green or red for the reference (Pb3) or alternate alleles, respectively. Clustering was ... Pathotype alleles are coded in green or red for the reference (Pb3) or alternate alleles, respectively. Clustering was ...https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-2597-2
Simultaneous Detection of Linkage Disequilibrium and Genetic Differentiation of Subdivided Populations | Genetics
Under H-W equilibrium, probabilities for heterozygous genotypes are obtained by duplicating the product of allele frequencies. ... Let allele frequencies for two loci be pA0, pA1 and pB0, pB1, and let the haplotype frequencies be h00, h01, h10, h11 in a ... are mean allele frequencies over subpopulations, which are estimated from sample allele frequencies. Here, DTOTAL is the ... The mean population allele frequencies of the two loci over subpopulations were assumed as and hence haplotype frequencies were ...http://www.genetics.org/content/167/4/2003
... in the regression models and because heterozygous genotype frequencies rather than minor allele homozygous genotype frequencies ... The rs17353856 C allele frequencies (white bars) and genotype CGG/CGG frequencies (black line) in the complication score groups ... The CGG genotype consists of rs17353856 C allele (major), rs7900814 G allele (major), and rs12572872 G allele (major). The ... Genotype and allele frequencies in case and control subjects were compared with χ2 test or with the Fisher exact test where ...http://diabetes.diabetesjournals.org/content/60/11/3073
CERA Resources | Grinnell College
... determined allele/genotype frequencies, inbreeding coefficients, genetic identity, and genetic diversity (expected ... heterozygosity); populations significantly inbred and significantly less heterozygous than expected; populations were also ... number of alleles, proportion of polymorphic alleles, inbreeding coefficient, and genetic structure; observed and expected ... frequency and density of species in their locations, variety of species, and a map detailing sampling locations] ...http://www.grinnell.edu/academics/areas/biology/cera/resources?group=15936&qt-search_block=0
Body Mass Index and Obesity- and Diabetes-Associated Genotypes and Risk for Pancreatic Cancer | Cancer Epidemiology, Biomarkers...
... the homozygous and heterozygous genotypes containing the variant allele were combined if (i) the frequency of the homozygote ... The homozygous and heterozygous genotypes containing the common allele were combined if the genotype was in recessive ... Because of the low minor allele frequency, the interaction of the GG genotype with BMI or diabetes could not be examined in ... The G allele is associated with a reduced protein activity (40). Most studies have linked the G allele or the GG genotype with ...http://cebp.aacrjournals.org/content/20/5/779
Relation of a Common Methylenetetrahydrofolate Reductase Mutation and Plasma Homocysteine With Intimal Hyperplasia After...
The allele frequency of the T mutation in the 62 patients was 0.48. The distribution of the 3 genotypes was as follows: ... homozygous normal (CC) genotype, 30.7%; heterozygous (CT) genotype, 41.9%; and homozygous mutant (TT) genotype, 27.4%. These ... and heterozygous genotype (CT), we established 2 genotype groups: the mutant homozygote (TT) and the others (non-TT: CC+CT). ... However, the late lumen loss in those with the TT genotype was significantly greater than that in those with non-TT genotypes ...http://circ.ahajournals.org/content/103/16/2048
One-Locus Two-Allele Models With Maternal (Parental) Selection | Genetics
at the former, genotype AA has zero frequency, whereas at the latter, genotype aa has zero frequency. ... These conditions simplify if β = δ = 0, that is, if offspring of heterozygous mothers are inviable. In this case, the genotype ... Note that neither genotype AA can have a mother with genotype aa, nor can genotype aa have a mother with genotype AA. This ... j be the fitness of an individual with genotype i raised by a mother with genotype j. Genotype frequencies are equal in both ...http://www.genetics.org/content/149/2/1147
Allele and genotype frequencies of the two single nucleotide polymorphisms in the VKORC1 gene that are most important for...
Allele and genotype frequencies of the two single nucleotide polymorphisms in the VKORC1 gene that are most important for ... while the frequency of the heterozygous genotype, GA, is 0.496. The frequency of the G allele is 0.504 and of the A allele is ... The alleles frequencies for this SNP were 0.660 for the G allele and 0.340 for the A allele. Genotypes and allele frequencies ... genotype (0.393). Allele frequencies are shown in Figure 3B: the frequency of the G allele is 0.660 and of the A allele is ...http://hamdanjournal.org/journal/index.php?journal=HAMDAN&page=article&op=view&path%5B%5D=463&path%5B%5D=937
... heterozygous, and homozygous variant) when the allele frequencies allowed or into two groups (major allele homozygous and minor ... The minimum detectable odds ratio (OR) was calculated for each sequence variant based on its genotype frequency, our study ... Therefore, for some genes, we added selected SNPs from dbSNP, 14 which either (a) had a high frequency of the rare allele (to ... Unfortunately, because of the nature of the method of genotyping where all the SNPs are analyzed on one chip, genotyping that ...http://cancerres.aacrjournals.org/content/66/22/11062
A Paradox of Evolution
... only causing problems when matched with another heterozygous genotype as a homozygous allele. Furthermore, natural levels of ... Deleterious heterozygous traits are maintained at low frequencies because if heterozygous, they are not expressed, and can be ... Thus, if the frequency of such a disease is only one in ten thousand, to reduce the deleterious allele just tenfold would take ... Even fatal diseases caused by recessive alleles, such as sickle-cell anemia in its homozygous form, are not eliminated from the ...http://www.adherents.com/misc/paradoxEvolution.html
A Markov Chain Monte Carlo Approach for Joint Inference of Population Structure and Inbreeding Rates From Multilocus Genotype...
5)where pA is the allele frequency of A in its assigned subpopulation. If individual i is heterozygous at locus l (suppose the ... 2000), denote marker allele frequencies by , and such that pklj is the allele frequency of the jth allele type at the lth locus ... xil. , F, zil., p.l.) is the genotype frequency of individual i at locus l. If the two alleles for this genotype are from ... If the two alleles for this genotype are from different subpopulations (i.e., zil1 ≠ zil2), we assume the genotype frequency is ...http://www.genetics.org/content/176/3/1635
Andrew Fire | Stanford Medicine Profiles
At heterozygous loci, remarkably different rearrangement frequencies were seen for the various IGHV alleles, and these ... frequencies were consistent between individuals. The specific alleles that make up an individual's Ig genotype may therefore be ... new large data sets should allow the rearrangement frequency of different genes and alleles to be seen with clarity. We ... It is likely that in some manner the frequency of an initiation of transcription at nine of these sites is affected by one or ...https://med.stanford.edu/profiles/andrew-fire
... genotype frequencies were 30% for C/C homozygous (Ala/Ala), 30% for C/T heterozygous (Ala/Val), and 40% for T/T homozygous (Val ... allele for MTHFR or LOH in the MTHFR region. Similarly, the presence of the Val allele was associated with a more profound ... The frequency of the Val/Val genotype for MTHFR is ∼10% in the general population ( 36). The higher than expected prevalence ( ... Primary GBMs with significant hypomethylation tended to be heterozygous or homozygous for the low-functioning Val allele of the ...http://cancerres.aacrjournals.org/content/66/17/8469
Genetic variation in MEFV and human longevity
Although the frequency of M694V proinflammatory genotype and allele in centenarians was lower this was not statistically ... The heterozygous genotype was also significantly overexpressed in AMI patients and underexpressed in centenarians compared with ... Conversely, the wild-type pyrin genotype may predispose to a greater chance to live longer under some conditions.. Indentifier ... After adjustment for AMI risk factors, the results predicted M694V genotype was an independent risk factor to develop AMI. ...http://genomics.senescence.info/longevity/gene.php?id=MEFV
Genetic and Immunologic Biomarkers in Type 1 Diabetes
... separately for each genotype, as well as for total allelic frequency (i.e., heterozygous and homozygous minor allele combined ... rs2069762 Allele Frequencies Count Freq G 200 0.3367 T 394 0.6633 PAGE 67. 67 Figure 31 IL 2 production measured by ELISA in ... The allele frequencies observed in our population for the rs2069762 were not out of line with prior expectations [ 152 ] While ... 37 used to test the differences in genotype and allele (respectively) distribution between patients and control subjects. ...http://ufdc.ufl.edu/UFE0045760/00001
Prospective Evaluation of the Risk Conferred by Factor V Leiden and Thermolabile Methylenetetrahydrofolate Reductase...
... allele frequency 1.36%), all being heterozygous for the mutation. This value was lower than expected from previous studies in ... Genotype Frequencies of FV Leiden Among Both the Thrombotic Group and the Recurrent Fetal Loss Group Compared With the Normal ... The allele frequencies of the 2 polymorphisms in the 3 study groups are shown in Table 1⇓. The allelic frequency of FV Leiden ... allele frequency of 7.6%, P=0.0115). In contrast, the carrier frequency for thermolabile MTHFR was no higher, and there was no ...http://atvb.ahajournals.org/content/20/1/266.long
Allele frequency - Wikipedia
... and one heterozygous genotype (AB). If we sample 10 individuals from the population, and we observe the genotype frequencies ... For 3 alleles see Allele § Allele and genotype frequencies) Allele frequency can always be calculated from genotype frequency, ... are the frequencies of the three genotypes at a locus with two alleles, then the frequency p of the A-allele and the frequency ... The allele frequency is distinct from the genotype frequency, although they are related, and allele frequencies can be ...https://en.wikipedia.org/wiki/Allele_frequency
... were homozygous for the wild-type allele. The genotype frequency was in the Hardy-Weinberg equilibrium. The genotype frequency ... Because only one subject was found to be homozygous for the Arg972 IRS-1 variant, she was combined with the heterozygous group ... were homozygous for the wild-type allele. The genotype frequency of the Arg972 IRS-1 variant was 8.7% among diabetic patients ... The genotype frequency of the Ala variant was 12.3% among diabetic patients well controlled with oral therapy and 17.6% among ...http://care.diabetesjournals.org/content/27/6/1394
Tau gene and Parkinson's disease: a case-control study and meta-analysis | Journal of Neurology, Neurosurgery & Psychiatry
Overall, the genotype frequency for individuals homozygous for the H1 allele in the control population was 57.9% (95% CI, 52.5 ... to 63.5%); for heterozygous individuals (H1H2) it was 36.9% (32.1% to 41.9%), and homozygous individuals for the H2 allele it ... For the case-control study, tau haplotype and genotype frequencies were calculated using the standard Pearson χ2 test. To test ... Furthermore, as the population frequency of the "at risk" tau-H1H1 genotype in this meta-analysis was 58% in the control ...http://jnnp.bmj.com/content/75/7/962
The origin and evolution of fragrance in rice (Oryza sativa L.) | Proceedings of the National Academy of Sciences
... and found that it was absent from all wild genotypes, except for a single accession that was heterozygous for the allele (Table ... Frequency of the badh2.1 Allele in Diverse Rice Germplasm.. We examined the occurrence of the badh2.1 allele in 280 accessions ... with the fragrant allele detected at the highest frequency in Group V and at the lowest frequency in temperate japonica and aus ... given the high frequency of the allele in Group V and vanishingly low frequency in temperate japonica. In our collection of 280 ...http://www.pnas.org/content/106/34/14444.full
JPM | Free Full-Text | Genetically Guided Statin Therapy on Statin Perceptions, Adherence, and Cholesterol Lowering: A Pilot...
Primary care patients (n = 58) who were nonadherent to statins and their providers received SLCO1B1*5 genotyping and guided ... The effects of SLCO1B1*5 genotype guided statin therapy (GGST) are unknown. ... The frequency of the C allele in Caucasians was not different than that reported in the literature (14% versus 15%, p = 0.94). ... Genotypes were successfully determined in the remaining 58 GGST subjects; we identified 11 heterozygous carriers and one ...http://www.mdpi.com/2075-4426/4/2/147/htm
Repeated Replication and a Prospective Meta-Analysis of the Association Between Chromosome 9p21.3 and Coronary Artery Disease |...
Heterozygous and homozygous odds ratios (ORs) for the risk allele and corresponding 95% confidence intervals (CIs) were ... Here, we used reported genotype frequencies for the marker with highest linkage disequilibrium (LD; r2=0.87 for rs238206 [used ... 0.9 by another SNP already genotyped or slated for fine-map genotyping. SNPs were genotyped by Sequenom assay in 1137 WTCCC CAD ... Genotyping. In the GerMIFS II, the UK MI study, AtheroGene, the MONICA/KORA study, PopGen, and PRIME samples, genotyping was ...http://circ.ahajournals.org/content/117/13/1675
CHRNA5 | Cancer Genetics Web
However, genotype frequencies were significantly different between cases and controls (P < 0.05), while allele frequencies were ... Compared to homozygous genotypes (TT or AA), the risk of lung cancer in those with the heterozygous genotype (TA) was ... Each SNP in analyzed groups was assessed by allele frequency, genotype distribution and haplotype analysis.. KEY FINDINGS: The ... The frequencies of AA, AG, and GG genotypes were 10.5, 47.3, and 42.2%, respectively. The polymorphism of CHRNA5 did not have a ...http://www.cancerindex.org/geneweb/CHRNA5.htm
Autosomal Recessive Atrial Dilated Cardiomyopathy With Standstill Evolution Associated With Mutation of Natriuretic Peptide...
... minor allele frequency=0.0154%; all genotypes: TT=0; TC=2; CC=6501 at the Exome Variant Server, NHLBI ESP, Seattle, WA) ( ... The heterozygous mutation has been found in 2 of 13 006 alleles (NPPA NM_006172.3, T=2; C=13004; GLN, ARG, 150/152; ... Genotype frequencies of all the SNPs analyzed resulted in Hardy-Weinberg equilibrium among controls. Genotype frequencies of ... For each SNP, a χ2 test was done to assess whether the observed genotype frequencies were in Hardy-Weinberg equilibrium among ...http://circgenetics.ahajournals.org/content/6/1/27
the t-allele frequency differed and the t/t genotype was more prevalent at the private maternity hospital. the hemoglobin (hb) ... the t-allele frequency in the total sample was 0.23, and the prevalence rates of heterozygous and homozygous carriers were 36.2 ... showing a relatively high frequency of variant hbs and the t allele. these data could provide an important basis for further ... the tested frequencies were 3 to 6 khz at the intensity of 70 dbna for f1 and f2. results: the obtained results showed a ...http://www.oalib.com/search?kw=%20Newborns&searchField=keyword
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