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Dataset results
374 results for “gene polymorphism”
Data from: Association between COL11A1 (rs1337185) and ADAMTS5 (rs162509) gene polymorphisms and lumbar spine pathologies in Chinese Han population: an observational study
Objectives: A previous study identified a significant association between several single nucleotide polymorphisms (SNPs) and lumbar disc degeneration (LDD) in Indians. To validate the association between these SNPs and specific lumbar spine pathologies, we performed a case-control study in Chinese Han population. Design: An observational study. Setting: University Hospital in Nanning, China. Participants: This study included 428 LDD patients and 400 normal controls. Outcome measures: LDD Patients were classified into 4 subgroups, including disc herniation only (Subgroup 1), discopathies or/and osteochondrosis associated with disc herniation (Subgroup 2), spinal stenosis or/and spondylolisthesis (Subgroup 3), and degenerative scoliosis (Subgroup 4). This study was conducted by examining 2 aspects: environmental factors and SNP genotyping. The environmental factors were evaluated with a questionnaire survey including questions about BMI, smoking habits, the physical demands of their job and exposure to vibrations. Rs1337185, rs5275, rs5277, rs7575934, rs3213718 and rs162509 were genotyped using a PCR-based Invader assay. Results: The physical workload was significantly higher in patients with lumbar spine pathologies than in the normal controls (P=0.035). The genotype and allele frequencies of rs1337185 and rs162509 were significantly different between the LDD patients and the normal controls. In rs1337185, a significant association was found between the C allele (risk allele) and the presence of disc herniation (OR=1.80; 95%CI= 1.21-2.68; P=0.003, adjusted P=0.012), and the presence of spinal stenosis and spondylolisthesis (OR=1.92; 95%CI=1.29-2.89; P= 0.001, adjusted P=0.004). In rs162509, the G allele represented 1.58-fold increased risk to suffer from disc herniation (OR=1.58; 95%CI=1.20-2.09; P=0.001, adjusted P=0.004). Conclusions: The SNPs rs1337185 in COL11A1 and rs162509 in ADAMTS5 are associated with susceptibility to LDD. The C allele of rs1337185 is risky for patients who are affected by lumbar pathologies such as disc herniation, stenosis and spondylolisthesis. The G allele of rs16250 represents a risk factor for the development of disc herniation.
Data from: Polymorphism in the neurofibromin gene, Nf1, is associated with antagonistic selection on wing size and development time in Drosophila melanogaster
In many invertebrates, body size shows genetically based clines, with size increasing in colder climates. Large body size is typically associated with prolonged development times. We consider variation in the CNS-specific gene neurofibromin 1 (Nf1) and its association with body size and development time. We identified two major Nf1 haplotypes in natural populations, Nf1-insertion-A and Nf1-deletion-G. These haplotypes are characterized by a 45-base insertion/deletion (INDEL) in Nf1 intron 2 and an A/G synonymous substitution (locus L17277). Linkage disequilibrium (LD) between the INDEL and adjacent sites is high but appears to be restricted within the Nf1 gene interval. In Australia, the frequency of the Nf1-insertion-A haplotype increases with latitude where wing size is larger, independent of the chromosomal inversion In(3R)Payne. Unexpectedly, the Nf1-insertion-A haplotype is negatively associated with wing size. We found that the Nf1-insertion-A haplotype is enriched in females with shorter development time. This suggests that the Nf1 haplotype cline may be driven by selection for development time rather than size; females from southern (higher latitude) D. melanogaster populations maintain a rapid development time despite being relatively larger, and the higher incidence of Nf1-insertion-A in southern Australia may contribute to this pattern whereas the effects of the Nf1 haplotypes on size may be countered by other loci with antagonistic effects on size and development time. Our results point to the potential complexity involved in identifying selection on genetic variants exhibiting pleiotropic effects when studies are based on spatial patterns or association studies.
Data from: Recurrent gene deletions and the evolution of adaptive cyanogenesis polymorphisms in white clover (Trifolium repens L.)
Understanding the molecular evolution of genes that underlie intraspecific polymorphisms can provide insights into the process of adaptive evolution. For adaptive polymorphisms characterized by gene presence/absence (P/A) variation, underlying loci commonly show signatures of long-term balancing selection, with gene-presence and gene-absence alleles maintained as two divergent lineages. We examined the molecular evolution of two unlinked P/A polymorphisms that underlie a well-documented adaptive polymorphism for cyanogenesis (hydrogen cyanide release with tissue damage) in white clover. Both cyanogenic and acyanogenic plants occur in this species, and the ecological forces that maintain this chemical defense polymorphism have been studied for several decades. Using a sample of 65 plants, we investigated the molecular evolution of sequences flanking the two underlying cyanogenesis genes: Ac/ac (controlling the presence/absence of cyanogenic glucosides), and Li/li (controlling the presence/absence of their hydrolyzing enzyme, linamarase). A combination of genome-walking, PCR assays, DNA sequence analysis, and Southern blotting was used to test whether these adaptive P/A polymorphisms show evidence of long-term balancing selection, or whether gene-absence alleles have evolved repeatedly through independent deletion events. For both loci, we detect no signatures of balancing selection in closest flanking genomic sequences. Instead, we find evidence for variation in the size of the deletions characterizing gene-absence alleles. These observations strongly suggest that both of these polymorphisms have been evolving through recurrent gene deletions over time. We discuss the genetic mechanisms that could account for this surprising pattern and the implications of these findings for mechanisms of rapid adaptive evolution in white clover.
Article data of The Impact of MDR-1 Gene Polymorphism (rs1128503) on Response to Imatinib and nilotinib Treatment in A Sample of Iraqi Chronic Myeloid Leukemia-Chronic Phase Patients
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Article data of The Impact of MDR-1 Gene Polymorphism (rs1128503) on Response to Imatinib and nilotinib Treatment in A Sample of Iraqi Chronic Myeloid Leukemia-Chronic Phase Patients
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Comprehensive analysis of type 2 diabetes-associated gene polymorphisms in a cohort of 99 anonymized metastatic colorectal cancer patients, including their frequency.
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Data from: Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting
Imprinted gene expression occurs during seed development in plants and is associated with differential DNA methylation of parental alleles, particularly at proximal transposable elements (TEs). Imprinting variability could contribute to observed parent-of-origin effects on seed development. We investigated intraspecific variation in imprinting, coupled with analysis of DNA methylation and small RNAs, among three Arabidopsis strains with diverse seed phenotypes. The majority of imprinted genes were parentally biased in the same manner among all strains. However, we identified several examples of allele-specific imprinting correlated with intraspecific epigenetic variation at a TE. We successfully predicted imprinting in additional strains based on methylation variability. We conclude that there is standing variation in imprinting even in recently diverged genotypes due to intraspecific epiallelic variation. Our data demonstrate that epiallelic variation and genomic imprinting intersect to produce novel gene expression patterns in seeds.
Vitamin D receptor gene polymorphism of Chinese patients with Systemic Lupus Erythematosus
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Association of Vitamin D receptor gene polymorphism with susceptibility and prognosis of Systemic Lupus Erythematosus in Chinese patients
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Folate metabolism genes' polymorphism among ethnic Kazakh women with preeclampsia in Kazakhstan
<p>Research raw dataset</p>
Frequency of polymorphisms in the IKZF1 and CDKN2A/2B genes and descriptive analysis in pediatric patients with acute lymphoblastic leukemia: a multicenter hospital-based prevalence study in Rio de Janeiro
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Mimicry genes reduce pre-adult survival rate in Papilio polytes: A possible new mechanism for maintaining female-limited polymorphism in Batesian mimicry
<p>Batesian mimicry, in which harmless organisms resemble unpalatable or harmful species, is a well-studied adaptation for predation avoidance. The females of some Batesian mimic species comprise mimetic and non-mimetic individuals. Mimetic females of such polymorphic species clearly have a selective advantage due to decreased predation pressure, but the selective forces that maintain non-mimetic females in a population remain unclear. In the swallowtail butterfly, <em>Papilio polytes</em>, female polymorphism is controlled by the <em>H</em> (non-mimetic) and <em>h</em> (mimetic) alleles at a single autosomal locus. Here, we examined if the dominant <em>H</em> allele has a deleterious effect on the pre-adult survival rate (egg-to-adult emergence rate). We repeated an assortative mating-like treatment—i.e. breeding of males and females whose mothers had the same phenotype (mimetic or non-mimetic)—for three consecutive generations, while avoiding inbreeding. Results showed that pre-adult survival rate decreased over generations only in lines derived from mothers with the mimetic phenotype (hereafter, mimetic-assorted lines). This lowered survival was due to an increased mortality at the final instar larval stage and the pupal stages. Interestingly, the pre-adult mortality in the mimetic-assorted lines seemed to be associated with a male-biased sex ratio at adult emergence. These results suggest that the dominant <em>H</em> allele displays a mildly deleterious effect that is expressed more strongly in females and homozygous individuals than in heterozygous individuals. We propose that this cost of mimicry in larval and pupal stages contributes to the maintenance of female-limited polymorphism in <em>P. polytes</em>.</p>
Figure 2 from: Alvarado AT, Muñoz AM, Bartra MS, Valderrama-Wong M, González D, Quiñones LA, Varela N, Bendezú MR, García JA, Loja-Herrera B (2021) Frequency of CYP1A1*2A polymorphisms and deletion of the GSMT1 gene in a Peruvian mestizo population. Pharmacia 68(4): 747-754. https://doi.org/10.3897/pharmacia.68.e71621
Figure 2 Genotypic analysis of CYP1A1*2A and GSTM1 (-) (2% agarose gel). Std represents the 100 bp molecular weight marker. The 340 bp amplicon represents the undigested CYP1A1 gene fragment. The 200 bp and 140 bp fragments correspond to the fragments cut with the enzyme Mspl. The 273 bp amplicon corresponds to the presence of GSTM1.
MTHFR gene polymorphism
<p>Data set</p>
MMP8 gene polymorphisms in colorectal cancer susceptibility
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The Impact of SCN9A Gene Polymorphism on Individual Pain Perception in the General Population
ClinicalTrials.gov study NCT01507493. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Relationship Between Polymorphisms of TRPV1 and KCC2 Gene in Children With Febrile Seizures
ClinicalTrials.gov study NCT04368936. IPD Sharing: YES. Countries: 0. Publications: 6.
Assessment of the Different Etiological and Susceptibility Markers in Patients With Pancreatitis: Investigating IG4, Cytomegalovirus, Coxsackie- Virus, Genetic Polymorphism of Vitamin D Receptor Gene
ClinicalTrials.gov study NCT03830073. IPD Sharing: Not stated. Countries: 0. Publications: 4.
Association of Brain Derived Neurotrophic Factor (BDNF) rs6265 Gene Polymorphism With Susceptibility to Epilepsy
ClinicalTrials.gov study NCT05096871. IPD Sharing: Not stated. Countries: 0. Publications: 4.
Oxidative Stress Gene Polymorphism and Ovarian Reserve Functione
ClinicalTrials.gov study NCT03682341. IPD Sharing: NO. Countries: 0. Publications: 1.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.