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
cnvlib package - CNVkit 0.9.5 documentation
with heterozygous genotype, or allele frequency between the specified thresholds.. Return type:. VariantArray. ... To create the b-allele frequencies column, alterate allele frequencies from the VCF are aligned to the .cnr file bins. Bins ... tumor_boost (bool) - Normalize tumor-sample allele frequencies to the matched normal sample's allele frequencies. ... Set zygosity (genotype) according to allele frequencies.. Creates or replaces 'zygosity' column if 'alt_freq' column is present ...http://cnvkit.readthedocs.io/en/latest/cnvlib.html
... 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
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
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
Non-homogeneous combination of two porous genomes induces complex body shape trajectories in cyprinid hybrids | Frontiers in...
... maximum-likelihood hybrid estimate of the h index for heterozygous genotypes is thus sensitive to parental allele frequencies [ ... Estimates of the frequency of null alleles for each population and marker. With k visible alleles per locus (frequencies ,0.01 ... As indicated by Nolte et al., an underdominance signal may be an artefact due to a high frequency of null alleles in ... However, in our study the high frequency of null alleles can be an artefact only at the Lid8 locus (See Additional file 2). ...https://frontiersinzoology.biomedcentral.com/articles/10.1186/1742-9994-10-22
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
Genetic Testing - The Key to Truly Personalized Medicine - Integrative Medicine for Mental Health
This mutation has mutant allele frequency of 39% for the heterozygous genotype and a 17% frequency for the homozygous mutant. ... One set of probes is complementary to the wild-type allele and another set is complementary to the variant allele. These probes ... genotype (what is the change in nucleotide), phenotype (whether the patient is heterozygous or homozygous [one of two mutated ... The DNA is then genotyped by determining the signal intensity ratio of the dyes bonded to the wild-type probe and the mutant ...http://www.immh.org/article-source/2016/6/29/genetic-testing-the-key-to-truly-personalized-medicine
An omnibus permutation test on ensembles of two-locus analyses can detect pure epistasis and genetic heterogeneity in genome...
Aa, Bb, Cc and Dd denote heterozygous genotypes. aa, bb, cc and dd denote homozygous variant genotypes. All allele frequencies ... Aa and Bb denote heterozygous genotypes. aa and bb denote homozygous variant genotypes. All allele frequencies are equal (p A ... Aa, Bb and Cc denote heterozygous genotypes. aa, bb and cc denote homozygous variant genotypes. All allele frequencies are ... A population of genotype strings is initialised according to the allele frequency of each SNP in the population-based ...https://springerplus.springeropen.com/articles/10.1186/2193-1801-2-230
Order of alleles. I have a question from class where we have to write out the genotype of the triply heterozygous mother (given ... can you calculate the allele frequencies? Can you calculate the genotype frequencies? Show your calculations. ... Consider the following two genotypes: AABB , aabb where A and B are dominant and a and b are recessive: 1) What is the genotype ... If the frequency of the dominant phenotypes (AA + Aa) is 0.8 and the population is in Hardy-Weinberg equilibrium, ...https://brainmass.com/biology/genetics/pg6
... 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 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
Kompetitive Allele Specific PCR (KASP™) genotyping of 48 polymorphisms at different caprine loci in French Alpine and Saanen...
Using a novel and fast genotyping method called Kompetitive Allele Specific PCR (KASP™), we carried out a pilot study on 48 ... Geno- type. Genotype frequencies. Milk yield (kg). Milk fat (%). Milk protein (%). Milk lactose (%). Genotype frequencies. Milk ... The results of the current study showed that the homozygous genotypes were more frequent than heterozygous in most cases. All ... The different genotype frequencies are shown in Table 2. The results of our study outlined that homozygous genotypes were more ...https://peerj.com/articles/4416/
SOD1 Gene +35A/C (exon3/intron3) Polymorphism in Type 2 Diabetes Mellitus among South Indian Population
Occurrence of different genotypes and normal (A) and mutant (C) allele frequencies were determined. The frequency of the three ... heterozygous genotype A/C (3%), and homozygous mutant C/C (2%). The mutant (C) allele and the mutant genotypes (AC/CC) were ... The A allele frequency was found to be 1.0 for diabetic patients and 0.91 for controls. The C allele frequency was completely ... As the mutant genotype and allele frequency were completely absent in type 2 diabetic patients among South Indian population, ...https://www.hindawi.com/journals/gri/2016/3787268/
... 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
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
... 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
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
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
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