scholarly journals Long non-coding RNA MIR4300HG polymorphisms are associated with postoperative nausea and vomiting: a genome-wide association study

2020 ◽  
Author(s):  
Shigekazu Sugino ◽  
Daisuke Konno ◽  
Yosuke Kawai ◽  
Masao Nagasaki ◽  
Yasuhiro Endo ◽  
...  
Keyword(s):  
Postoperative Nausea ◽  
Genome Wide Association Study ◽  
Postoperative Nausea And Vomiting ◽  
Nausea And Vomiting ◽  
Candidate Snps ◽  
Nucleotide Polymorphisms ◽  
Non Coding Rna ◽  
Genome Wide ◽  
A Genome ◽  
Long Non Coding Rna

Abstract Background: Genetic factors such as single nucleotide polymorphisms (SNPs) play a key role in the development of postoperative nausea and vomiting (PONV). However, previous findings are not widely applicable to different populations because of population-specific genetic variation. We developed a Japanese-specific DNA microarray for high-throughput genotyping. The aim of the current study was to identify SNPs associated with PONV on a genome-wide scale using this microarray in a sample of Japanese surgical patients. Methods: Associations between 659,636 SNPs and the incidence of PONV 24 h after surgery in a limited sample of 24 female patients were assessed using the microarray. After imputation of genotypes at 24,330,529 SNPs, 78 SNPs were found to be associated with the incidence of PONV. We chose 4 of the 78 SNPs to focus on by in silico functional annotation. Finally, we genotyped these 4 candidate SNPs in 255 patients using real-time PCR to verify association with the incidence of PONV. Results: The T > C variant of rs11232965 in the long non-coding RNA MIR4300HG was significantly associated with reduced incidence of PONV among genotypes and between alleles (p = 0.01 and 0.007). Conclusions: We identified a novel SNP (rs11232965) in the long non-coding RNA MIR4300HG that is associated with PONV. The rs11232965-SNP variant (T > C) is protective against the incidence of PONV. Trial registration: This study was registered at the UMIN Clinical Trials Registry (Identifier: UMIN000022903, date of registration: June 27th, 2016, retrospectively registered, https://upload.umin.ac.jp/cgi-open-bin/ctr_e/ctr_view.cgi?recptno=R000026392).

scholarly journals Long non-coding RNA MIR4300HG polymorphisms are associated with postoperative nausea and vomiting: a genome-wide association study

2020 ◽  
Vol 14 (1) ◽  
Author(s):  
Shigekazu Sugino ◽  
Daisuke Konno ◽  
Yosuke Kawai ◽  
Masao Nagasaki ◽  
Yasuhiro Endo ◽  
...  
Keyword(s):  
Postoperative Nausea ◽  
Genome Wide Association Study ◽  
Postoperative Nausea And Vomiting ◽  
Nausea And Vomiting ◽  
Candidate Snps ◽  
Nucleotide Polymorphisms ◽  
Non Coding Rna ◽  
Genome Wide ◽  
A Genome ◽  
Long Non Coding Rna

Abstract Background Genetic factors such as single-nucleotide polymorphisms (SNPs) play a key role in the development of postoperative nausea and vomiting (PONV). However, previous findings are not widely applicable to different populations because of population-specific genetic variation. We developed a Japanese-specific DNA microarray for high-throughput genotyping. The aim of the current study was to identify SNPs associated with PONV on a genome-wide scale using this microarray in a sample of Japanese surgical patients. Methods Associations between 659,636 SNPs and the incidence of PONV 24 h after surgery in a limited sample of 24 female patients were assessed using the microarray. After imputation of genotypes at 24,330,529 SNPs, 78 SNPs were found to be associated with the incidence of PONV. We chose 4 of the 78 SNPs to focus on by in silico functional annotation. Finally, we genotyped these 4 candidate SNPs in 255 patients using real-time PCR to verify association with the incidence of PONV. Results The T > C variant of rs11232965 in the long non-coding RNA MIR4300HG was significantly associated with reduced incidence of PONV among genotypes and between alleles (p = 0.01 and 0.007). Conclusions We identified a novel SNP (rs11232965) in the long non-coding RNA MIR4300HG that is associated with PONV. The rs11232965-SNP variant (T > C) is protective against the incidence of PONV. Trial registration This study was registered at the UMIN Clinical Trials Registry (Identifier: UMIN000022903, date of registration: June 27, 2016, retrospectively registered.

scholarly journals Long non-coding RNA MIR4300HG polymorphisms are associated with postoperative nausea and vomiting: a genome-wide association study

2020 ◽  
Author(s):  
Shigekazu Sugino ◽  
Daisuke Konno ◽  
Yosuke Kawai ◽  
Masao Nagasaki ◽  
Yasuhiro Endo ◽  
...  
Keyword(s):  
Postoperative Nausea ◽  
Genome Wide Association Study ◽  
Postoperative Nausea And Vomiting ◽  
Nausea And Vomiting ◽  
Candidate Snps ◽  
Nucleotide Polymorphisms ◽  
Non Coding Rna ◽  
Genome Wide ◽  
A Genome ◽  
Long Non Coding Rna

Abstract Background: Genetic factors such as single nucleotide polymorphisms (SNPs) play a key role in the development of postoperative nausea and vomiting (PONV). However, previous findings are not widely applicable to different populations because of population-specific genetic variation. We developed a Japanese-specific DNA microarray for high-throughput genotyping. The aim of the current study is to identify causal SNPs associated with PONV on a genome-wide scale using this microarray in a sample of Japanese surgical patients. associations between 659,636 SNPs and the incidence of PONV 24 h after surgery in a limited sample of 24 female patients using the microarray. After imputation of genotypes at 24,330,529 SNPs, 78 SNPs were found to be associated with the incidence of PONV. We chose 4 of the 78 SNPs to focus on by in silico functional annotation. Finally, we genotyped these 4 candidate SNPs in 255 patients using real-time PCR to verify association with the incidence of PONV. Results: The T > C variant of rs11232965 in the long non-coding RNA MIR4300HG was significantly associated with reduced incidence of PONV among genotypes and between alleles (p = 0.01 and 0.007). Conclusions: We identified a novel causal SNP (rs11232965) in the long non-coding RNA MIR4300HG that is associated with PONV. The rs11232965-SNP variant (T > C) is protective against the incidence of PONV. Trial registration: This study was registered at the UMIN Clinical Trials Registry (Identifier: UMIN000022903, date of registration: June 27th, 2016, retrospectively registered, https://upload.umin.ac.jp/cgi-open-bin/ctr_e/ctr_view.cgi?recptno=R000026392).

scholarly journals Long non-coding RNA MIR4300HG polymorphisms are associated with postoperative nausea and vomiting: a genome-wide association study

2020 ◽  
Author(s):  
Shigekazu Sugino ◽  
Daisuke Konno ◽  
Yosuke Kawai ◽  
Masao Nagasaki ◽  
Yasuhiro Endo ◽  
...  
Keyword(s):  
Postoperative Nausea ◽  
Genome Wide Association Study ◽  
Postoperative Nausea And Vomiting ◽  
Nausea And Vomiting ◽  
Candidate Snps ◽  
Nucleotide Polymorphisms ◽  
Non Coding Rna ◽  
Genome Wide ◽  
A Genome ◽  
Long Non Coding Rna

Abstract Background: Genetic factors such as single nucleotide polymorphisms (SNPs) play a key role in the development of postoperative nausea and vomiting (PONV). However, previous findings are not widely applicable to different populations because of population-specific genetic variation. We developed a Japanese-specific DNA microarray for high-throughput genotyping. The aim of the current study was to identify SNPs associated with PONV on a genome-wide scale using this microarray in a sample of Japanese surgical patients. Methods: Associations between 659,636 SNPs and the incidence of PONV 24 h after surgery in a limited sample of 24 female patients were assessed using the microarray. After imputation of genotypes at 24,330,529 SNPs, 78 SNPs were found to be associated with the incidence of PONV. We chose 4 of the 78 SNPs to focus on by in silico functional annotation. Finally, we genotyped these 4 candidate SNPs in 255 patients using real-time PCR to verify association with the incidence of PONV. Results: The T > C variant of rs11232965 in the long non-coding RNA MIR4300HG was significantly associated with reduced incidence of PONV among genotypes and between alleles (p = 0.01 and 0.007). Conclusions: We identified a novel SNP (rs11232965) in the long non-coding RNA MIR4300HG that is associated with PONV. The rs11232965-SNP variant (T > C) is protective against the incidence of PONV. Trial registration: This study was registered at the UMIN Clinical Trials Registry (Identifier: UMIN000022903, date of registration: June 27th, 2016, retrospectively registered, https://upload.umin.ac.jp/cgi-open-bin/ctr_e/ctr_view.cgi?recptno=R000026392).

scholarly journals Long non-coding RNA MIR4300HG polymorphisms are associated with postoperative nausea and vomiting: a genome-wide association study

2020 ◽  
Author(s):  
Shigekazu Sugino ◽  
Daisuke Konno ◽  
Yosuke Kawai ◽  
Masao Nagasaki ◽  
Yasuhiro Endo ◽  
...  
Keyword(s):  
Postoperative Nausea ◽  
Genome Wide Association Study ◽  
Postoperative Nausea And Vomiting ◽  
Nausea And Vomiting ◽  
Surgical Patients ◽  
Candidate Snps ◽  
Non Coding Rna ◽  
Genome Wide ◽  
A Genome ◽  
Long Non Coding Rna

Abstract Background: Genetic factors such as single nucleotide polymorphisms (SNPs) play a key role in the development of postoperative nausea and vomiting (PONV). However, previous findings are not widely applicable to different populations because of population-specific genetic variation. We developed a Japanese-specific DNA microarray for high-throughput genotyping. The aim of the current study is to identify causal SNPs associated with PONV on a genome-wide scale using this microarray in a sample of Japanese surgical patients. Methods: Genomic DNA was obtained from 256 surgical patients. We first determined associations between 659,636 SNPs and the incidence of PONV 24hrs after surgery in a limited sample of 24 female patients using the microarray. After imputation of genotypes at 24,330,529 SNPs, 78 SNPs were found to be associated with the incidence of PONV. We chose 4 of the 78 SNPs to focus on by in silico functional annotation. Finally, we genotyped these 4 candidate SNPs in 255 patients using real-time PCR to verify association with the incidence of PONV. Results: The T > C variant of rs11232965 in the long non-coding RNA MIR4300HG was significantly associated with reduced incidence of PONV among genotypes and between alleles (p = 0.01 and 0.007). Conclusions: We identified a novel causal SNP (rs11232965) in the long non-coding RNA MIR4300HG that is associated with PONV. The rs11232965-SNP variant (T > C) is protective against the incidence of PONV. Trial registration: This study was registered at the UMIN Clinical Trials Registry (Identifier: UMIN000022903, date of registration: June 27th, 2016, retrospectively registered, https://upload.umin.ac.jp/cgi-open-bin/ctr_e/ctr_view.cgi?recptno=R000026392).

scholarly journals Genome-wide Association Study Using Pooled DNA to Identify Candidate Markers Mediating Susceptibility to Postoperative Nausea and Vomiting

2011 ◽  
Vol 115 (1) ◽  
pp. 54-64 ◽  
Author(s):  
Piotr K. Janicki ◽  
Ryan Vealey ◽  
Jiabin Liu ◽  
Jeremiah Escajeda ◽  
Marek Postula ◽  
...  
Keyword(s):  
Association Study ◽  
Allele Frequency ◽  
Postoperative Nausea ◽  
Genome Wide Association Study ◽  
Postoperative Nausea And Vomiting ◽  
Nausea And Vomiting ◽  
Genome Wide Association ◽  
Individual Genotyping ◽  
Genome Wide ◽  
Pooled Dna

Background A family history has been established as a risk factor for postoperative nausea and vomiting (PONV), but the identities of susceptibility genes remain unknown. The goal of this study was to identify the genetic loci that may contribute to PONV susceptibility in an adult population. Methods The authors performed a genome-wide association study involving pooling of DNA obtained from 122 patients with severe PONV and 129 matched controls. Each pool was hybridized to a single nucleotide polymorphism (SNP) microarray, and probe intensity was used to predict allele frequency. Differences in allele frequency between SNP in the PONV and control groups were ranked after accounting for the pooling error. The highest ranking SNPs were selected for individual genotyping in the subjects from whom the DNA pool was comprised and in the new verification cohort consisting of 208 subjects (104 PONV patients and 104 controls). Results The authors identified 41 SNP targets showing substantial difference in allelic frequency between pools. These markers were first genotyped in the individual DNA samples from which the pools were comprised. The authors observed evidence for an association between PONV and 19 different loci in the genome. In the separate verification cohort, the association with PONV was observed for four SNPs. This association remained significant after correcting for multiple testing (P < 0.0023) for one SNP (rs2165870), which is located upstream of the promoter for the muscarinic acetylcholine receptor 3 subtype (CHRM3) gene. Conclusions The authors performed the genome-wide association study for PONV using pooled DNA samples. Through individual genotyping, they confirmed association of at least one SNP that is predictive of PONV susceptibility.

scholarly journals SNPs and GVHD prediction: where to next?

Blood ◽  
2012 ◽  
Vol 119 (22) ◽  
pp. 5066-5068 ◽  
Author(s):  
Anne M. Dickinson
Keyword(s):  
Genome Wide Association Study ◽  
Snp Array ◽  
Candidate Snps ◽  
Cell Transplant ◽  
Nucleotide Polymorphisms ◽  
Hematopoietic Stem ◽  
Novel Approach ◽  
Genome Wide ◽  
Impute Data ◽  
A Genome

The article by Chien at al in this issue of Blood uses a novel approach to assess the role of single nucleotide polymorphisms (SNPs) in acute graft-versus-host disease (GVHD). Using a genome-wide association study (GWAS) employing an Affymetrix GeneChip Genome-Wide Human 500 000 SNP array, they screened 1298 allogeneic hematopoietic stem cell transplant donors and recipients and tested whether the results from 40 previously reported candidate SNPs could be replicated. They also used a novel approach to impute data using IMPUTE software (http://nathgen.stats-ox.ac.uk/impute/impute.html) where the genotyping data were not available.1

scholarly journals Genetic variants associated with motion sickness point to roles for inner ear development, neurological processes, and glucose homeostasis

2014 ◽  
Author(s):  
Bethann S Hromatka ◽  
Joyce Y Tung ◽  
Amy K Kiefer ◽  
Chuong B Do ◽  
David A Hinds ◽  
...  
Keyword(s):  
Nervous System ◽  
Motion Sickness ◽  
Glucose Homeostasis ◽  
Genetic Factors ◽  
Genome Wide Association Study ◽  
Nausea And Vomiting ◽  
Nucleotide Polymorphisms ◽  
Cranial Development ◽  
Genome Wide ◽  
A Genome

Roughly one in three individuals is highly susceptible to motion sickness and yet the underlying causes of this condition are not well understood. Despite high heritability, no associated genetic factors have been discovered to date. Here, we conducted the first genome-wide association study on motion sickness in 80,494 individuals from the 23andMe database who were surveyed about car sickness. Thirty-five single-nucleotide polymorphisms (SNPs) were associated with motion sickness at a genome-wide-significant level (p< 5e-8). Many of these SNPs are near genes involved in balance, and eye, ear, and cranial development (e.g., PVRL3, TSHZ1, MUTED, HOXB3, HOXD3). Other SNPs may affect motion sickness through nearby genes with roles in the nervous system, glucose homeostasis, or hypoxia. We show that several of these SNPs display sex-specific effects, with as much as three times stronger effects in women. We searched for comorbid phenotypes with motion sickness, confirming associations with known comorbidities including migraines, postoperative nausea and vomiting (PONV), vertigo, and morning sickness, and observing new associations with altitude sickness and many gastrointestinal conditions. We also show that two of these related phenotypes (PONV and migraines) share underlying genetic factors with motion sickness. These results point to the importance of the nervous system in motion sickness and suggest a role for glucose levels in motion-induced nausea and vomiting, a finding that may provide insight into other nausea-related phenotypes such as PONV. They also highlight personal characteristics (e.g., being a poor sleeper) that correlate with motion sickness, findings that could help identify risk factors or treatments.

scholarly journals Genome-Wide Association Study (GWAS) for Examining the Genomics Controlling Prickle Production in Red Raspberry (Rubus idaeus L.)

Agronomy ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 27
Author(s):  
Archana Khadgi ◽  
Courtney A. Weber
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Genomic Region ◽  
Rubus Idaeus ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Red Raspberry ◽  
Genome Wide ◽  
A Genome ◽  
Genotype By Sequencing

Red raspberry (Rubus idaeus L.) is an expanding high-value berry crop worldwide. The presence of prickles, outgrowths of epidermal tissues lacking vasculature, on the canes, petioles, and undersides of leaves complicates both field management and harvest. The utilization of cultivars with fewer prickles or prickle-free canes simplifies production. A previously generated population segregating for prickles utilizing the s locus between the prickle-free cultivar Joan J (ss) and the prickled cultivar Caroline (Ss) was analyzed to identify the genomic region associated with prickle development in red raspberry. Genotype by sequencing (GBS) was combined with a genome-wide association study (GWAS) using fixed and random model circulating probability unification (FarmCPU) to analyze 8474 single nucleotide polymorphisms (SNPs) and identify significant markers associated with the prickle-free trait. A total of four SNPs were identified on chromosome 4 that were associated with the phenotype and were located near or in annotated genes. This study demonstrates how association genetics can be used to decipher the genetic control of important horticultural traits in Rubus, and provides valuable information about the genomic region and potential genes underlying the prickle-free trait.

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