Identifying positional candidate genes on chromosome 10 that are involved in APP processing

2021 ◽  
Author(s):  
Preeti Khandelwal
Keyword(s):  
Candidate Genes ◽  
Chromosome 10 ◽  
Positional Candidate ◽  
App Processing

The role of gene polymorphisms in the pathogenesis of chronic obstructive pulmonary disease

Biologia ◽  
2008 ◽  
Vol 63 (1) ◽  
Author(s):  
Eva Slabá ◽  
Pavol Joppa ◽  
Ján Šalagovič ◽  
Ružena Tkáčová
Keyword(s):  
Chronic Obstructive Pulmonary Disease ◽  
Inflammatory Response ◽  
Candidate Genes ◽  
Pulmonary Disease ◽  
Gene Polymorphisms ◽  
Association Studies ◽  
Chronic Obstructive ◽  
Obstructive Pulmonary Disease ◽  
Positional Candidate ◽  
Linkage Analyses

AbstractChronic obstructive pulmonary disease (COPD) is a major cause of morbidity and mortality worldwide. Irreversible airflow limitation, both progressive and associated with an inflammatory response of the lungs to noxious particles or gases, is a hallmark of the disease. Cigarette smoking is the most important environmental risk factor for COPD, nevertheless, only approximately 20–30% of smokers develop symptomatic disease. Epidemiological studies, case-control studies in relatives of patients with COPD, and twin studies suggest that COPD is a genetically complex disease with environmental factors and many involved genes interacting together. Two major strategies have been employed to identify the genes and the polymorphisms that likely contribute to the development of complex diseases: association studies and linkage analyses. Biologically plausible pathogenetic mechanisms are prerequisites to focus the search for genes of known function in association studies. Protease-antiprotease imbalance, generation of oxidative stress, and chronic inflammation are recognized as the principal mechanisms leading to irreversible airflow obstruction and parenchymal destruction in the lung. Therefore, genes which have been implicated in the pathogenesis of COPD are involved in antiproteolysis, antioxidant barrier and metabolism of xenobiotic substances, inflammatory response to cigarette smoke, airway hyperresponsiveness, and pulmonary vascular remodelling. Significant associations with COPD-related phenotypes have been reported for polymorphisms in genes coding for matrix metalloproteinases, microsomal epoxide hydrolase, glutathione-S-transferases, heme oxygenase, tumor necrosis factor, interleukines 1, 8, and 13, vitamin D-binding protein and β-2-adrenergic receptor (ADRB2), whereas adequately powered replication studies failed to confirm most of the previously observed associations. Genome-wide linkage analyses provide us with a novel tool to identify the general locations of COPD susceptibility genes, and should be followed by association analyses of positional candidate genes from COPD pathophysiology, positional candidate genes selected from gene expression studies, or dense single nucleotide polymorphism panels across regions of linkage. Haplotype analyses of genes with multiple polymorphic sites in linkage disequilibrium, such as the ADRB2 gene, provide another promising field that has yet to be explored in patients with COPD. In the present article we review the current knowledge about gene polymorphisms that have been recently linked to the risk of developing COPD and/or may account for variations in the disease course.

scholarly journals Refinement of the locus for hereditary congenital facial palsy on chromosome 3q21 in two unrelated families and screening of positional candidate genes

2006 ◽  
Vol 14 (12) ◽  
pp. 1306-1312 ◽  
Author(s):  
Caroline B Michielse ◽  
Meena Bhat ◽  
Angela Brady ◽  
Hussain Jafrid ◽  
José A J M van den Hurk ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Facial Palsy ◽  
Positional Candidate

Meta-analysis of grain iron and zinc associated QTLs identified hotspot chromosomal regions and positional candidate genes for breeding biofortified rice

Plant Science ◽  
2019 ◽  
Vol 288 ◽  
pp. 110214 ◽  
Author(s):  
Qasim Raza ◽  
Awais Riaz ◽  
Muhammad Sabar ◽  
Rana Muhammad Atif ◽  
Khurram Bashir
Keyword(s):  
Candidate Genes ◽  
Meta Analysis ◽  
Positional Candidate ◽  
Iron And Zinc

scholarly journals Genome-wide association study to identify genomic regions and positional candidate genes associated with male fertility in beef cattle

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
H. Sweett ◽  
P. A. S. Fonseca ◽  
A. Suárez-Vega ◽  
A. Livernois ◽  
F. Miglior ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Candidate Genes ◽  
Male Fertility ◽  
Production Efficiency ◽  
Genome Wide Association Study ◽  
Gene Annotation ◽  
Enrichment Analysis ◽  
Single Step ◽  
Positional Candidate ◽  
Functional Candidate Gene

AbstractFertility plays a key role in the success of calf production, but there is evidence that reproductive efficiency in beef cattle has decreased during the past half-century worldwide. Therefore, identifying animals with superior fertility could significantly impact cow-calf production efficiency. The objective of this research was to identify candidate regions affecting bull fertility in beef cattle and positional candidate genes annotated within these regions. A GWAS using a weighted single-step genomic BLUP approach was performed on 265 crossbred beef bulls to identify markers associated with scrotal circumference (SC) and sperm motility (SM). Eight windows containing 32 positional candidate genes and five windows containing 28 positional candidate genes explained more than 1% of the genetic variance for SC and SM, respectively. These windows were selected to perform gene annotation, QTL enrichment, and functional analyses. Functional candidate gene prioritization analysis revealed 14 prioritized candidate genes for SC of which MAP3K1 and VIP were previously found to play roles in male fertility. A different set of 14 prioritized genes were identified for SM and five were previously identified as regulators of male fertility (SOD2, TCP1, PACRG, SPEF2, PRLR). Significant enrichment results were identified for fertility and body conformation QTLs within the candidate windows. Gene ontology enrichment analysis including biological processes, molecular functions, and cellular components revealed significant GO terms associated with male fertility. The identification of these regions contributes to a better understanding of fertility associated traits and facilitates the discovery of positional candidate genes for future investigation of causal mutations and their implications.

scholarly journals Transcriptome profiles of hypothalamus and adrenal gland linked to haplotype related to coping behavior in pigs

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Kevin Gley ◽  
Eduard Murani ◽  
Nares Trakooljul ◽  
Manuela Zebunke ◽  
Birger Puppe ◽  
...  
Keyword(s):  
Adrenal Gland ◽  
Candidate Genes ◽  
Hpa Axis ◽  
Genome Wide Association Study ◽  
Coping Behavior ◽  
Positional Candidate ◽  
Genome Wide ◽  
Ngf Signaling ◽  
And Coping ◽  
Haplotype Information

Abstract The hypothalamic-pituitary-adrenal (HPA) axis is an important component of neuroendocrine stress regulation and coping behavior. Transcriptome profiles of the hypothalamus and adrenal gland were assessed to identify molecular pathways and candidate genes for coping behavior in pigs. Ten each of high- (HR) and low- (LR) reactive pigs (n = 20) were selected for expression profiling based haplotype information of a prominent QTL-region on SSC12 discovered in our previous genome-wide association study (GWAS) on coping behavior. Comparing the HR and LR pigs showed 692 differentially expressed genes (DEGs) in the adrenal gland and 853 DEGs in the hypothalamus, respectively. Interestingly, 47% (17 out of 36) of DEGs found in both tissues were located in GWAS regions identified on SSC12, indicating that there are significant functional positional candidate genes for coping behaviour. Pathway analysis assigned DEGs to glucocorticoid receptor signaling in the adrenal gland. Furthermore, oxidative phosphorylation, mitochondrial dysfunction, and NGF signaling as well as cholecystokinin/Gastrin-mediated were identified in the hypothalamus. We narrowed the list of candidate genes in GWAS regions by analyzing their DEGs in the HPA axis. The top identified transcripts, including ATP1B2, AURKB, MPDU1 and NDEL1 provide evidence for molecular correlates of coping behavior in GWAS regions.

Integration of expression profiles and genetic mapping data to identify candidate genes in intracranial aneurysm

2007 ◽  
Vol 32 (1) ◽  
pp. 45-57 ◽  
Author(s):  
Shantel Weinsheimer ◽  
Guy M. Lenk ◽  
Monique van der Voet ◽  
Susan Land ◽  
Antti Ronkainen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Intracranial Aneurysm ◽  
Genetic Mapping ◽  
Candidate Genes ◽  
Expression Profiles ◽  
Adherens Junction ◽  
Gene Expression Profiles ◽  
Mapping Data ◽  
Positional Candidate ◽  
Genetic Mapping Data

Intracranial aneurysm (IA) is a complex genetic disease for which, to date, 10 loci have been identified by linkage. Identification of the risk-conferring genes in the loci has proven difficult, since the regions often contain several hundreds of genes. An approach to prioritize positional candidate genes for further studies is to use gene expression data from diseased and nondiseased tissue. Genes that are not expressed, either in diseased or nondiseased tissue, are ranked as unlikely to contribute to the disease. We demonstrate an approach for integrating expression and genetic mapping data to identify likely pathways involved in the pathogenesis of a disease. We used expression profiles for IAs and nonaneurysmal intracranial arteries (IVs) together with the 10 reported linkage intervals for IA. Expressed genes were analyzed for membership in Kyoto Encyclopedia of Genes and Genomes (KEGG) biological pathways. The 10 IA loci harbor 1,858 candidate genes, of which 1,561 (84%) were represented on the microarrays. We identified 810 positional candidate genes for IA that were expressed in IVs or IAs. Pathway information was available for 294 of these genes and involved 32 KEGG biological function pathways represented on at least 2 loci. A likelihood-based score was calculated to rank pathways for involvement in the pathogenesis of IA. Adherens junction, MAPK, and Notch signaling pathways ranked high. Integration of gene expression profiles with genetic mapping data for IA provides an approach to identify candidate genes that are more likely to function in the pathology of IA.

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