scholarly journals Editorial Room for the candidate gene approach in the genome-wide association era: an example from GSTP1 gene polymorphism

2012 ◽  
Vol 4 ◽  
pp. 606-607
Author(s):  
Wojciech Mlynarski
Keyword(s):  
Gene Polymorphism ◽  
Candidate Gene ◽  
Genome Wide Association ◽  
Candidate Gene Approach ◽  
Genome Wide ◽  
Gstp1 Gene

scholarly journals The Genetics of Seborrheic Dermatitis: A Candidate Gene Approach and Pilot Genome-Wide Association Study

2018 ◽  
Vol 138 (4) ◽  
pp. 991-993 ◽  
Author(s):  
Martijn G.H. Sanders ◽  
Luba M. Pardo ◽  
André G. Uitterlinden ◽  
Adrian M. Smith ◽  
Rebecca S. Ginger ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Gene ◽  
Genome Wide Association Study ◽  
Seborrheic Dermatitis ◽  
Genome Wide Association ◽  
Candidate Gene Approach ◽  
Genome Wide

scholarly journals Genome-Wide Association Studies Identify 15 Genetic Markers Associated with Marmite Taste Preference

2017 ◽  
Author(s):  
Thomas R. Roos ◽  
Nikolay A. Kulemin ◽  
Ildus I. Ahmetov ◽  
Avi Lasarow ◽  
Keith Grimaldi
Keyword(s):  
Candidate Gene ◽  
Genetic Markers ◽  
Bitter Taste ◽  
Taste Preference ◽  
Genome Wide Association ◽  
Candidate Gene Approach ◽  
Genome Wide ◽  
Human Trait ◽  
Genome Wide Significance ◽  
Complex Human Trait

AbstractMarmite is a popular food eaten around the world, to which individuals have commonly considered themselves either “lovers” or “haters”. We aimed to determine whether this food preference has a genetic basis.Weperformed a genome-wide association study (GWAS) for Marmite taste preference using genotype and questionnaire data froma cohort of 261 healthy adults. We found 1 single nucleotide polymorphism (SNP) associated with Marmite taste preferencethat reached genome-wide significance (p<5x10-8) in our GWAS analyses. We found another 4 SNPsassociated with Marmite taste preference that reached genome-wide significance (p<5x10-8) in at leastoneGWAS and/or for at least one phenotype analysed. Moreover, we identified 10 additional SNPs potentially associated with Marmite taste preference through candidate gene analysis. Our results indicate that there is a genetic basis to Marmite taste preference and we have identified 15 genetic markers for this trait. Overall, we conclude that Marmite tastepreference is a complex human trait influenced by multiple genetic markers, as well as the environment.Summary of Main ResultsMarmite taste preference is a complex human trait with many factors influencing whether an individual loves or hates Marmite.The relative contribution of genetics versus environment (ie. heritability) for Marmite taste preference is unknown.The genetic contribution to Marmite taste preference involves multiple genetic markers each contributing a small amount (ie. the trait is polygenic). There is not one single Marmite gene with a large contribution like in thecase of the TAS2R38gene and bitter taste perception.We have found a total of 15 SNPs associated with Marmite taste preference: 5 SNPs by a genetic-association screen atgenome-wide significance, and 10 SNPs by a candidate gene approach at nominal significance.We did not find an association between the TAS2R38bitter taste receptor gene and Marmite taste preference.It is important to independently replicate the findings of this study in order to validate these genetic markers and get a more accurate idea of their true effect on Marmite taste preference.

scholarly journals Genetic Determinants of Ototoxicity During and After Childhood Cancer Treatment: Protocol for the PanCareLIFE Study (Preprint)

2018 ◽  
Author(s):  
Eva Clemens ◽  
Annelot JM Meijer ◽  
Linda Broer ◽  
Thorsten Langer ◽  
Anne-Lotte LF van der Kooi ◽  
...  
Keyword(s):  
Cancer Treatment ◽  
Childhood Cancer ◽  
Candidate Gene ◽  
Genetic Susceptibility ◽  
Cancer Patients ◽  
Hearing Impairment ◽  
Genome Wide Association ◽  
Candidate Gene Approach ◽  
Cranial Radiotherapy ◽  
Genome Wide

BACKGROUND Survival rates after childhood cancer now reach nearly 80% in developed countries. However, treatments that lead to survival and cure can cause serious adverse effects with lifelong negative impacts on survivor quality of life. Hearing impairment is a common adverse effect in children treated with cisplatin-based chemotherapy or cranial radiotherapy. Ototoxicity can extend from high-tone hearing impairment to involvement of speech frequencies. Hearing impairment can impede speech and language and neurocognitive development. Although treatment-related risk factors for hearing loss following childhood cancer treatment have been identified, the individual variability in toxicity of adverse effects after similar treatment between childhood cancer patients suggests a role for genetic susceptibility. Currently, 12 candidate gene approach studies have been performed to identify polymorphisms predisposing to platinum-induced ototoxicity in children being treated for cancer. However, results were inconsistent and most studies were underpowered and/or lacked replication. OBJECTIVE We describe the design of the PanCareLIFE consortium’s work packages that address the genetic susceptibility of platinum-induced ototoxicity. METHODS As a part of the PanCareLIFE study within the framework of the PanCare consortium, we addressed genetic susceptibility of treatment-induced ototoxicity during and after childhood cancer treatment in a large European cohort by a candidate gene approach and a genome-wide association screening. RESULTS This study included 1124 survivors treated with cisplatin, carboplatin, or cranial radiotherapy for childhood cancer, resulting in the largest clinical European cohort assembled for this late effect to date. Within this large cohort we defined a group of 598 cisplatin-treated childhood cancer patients not confounded by cranial radiotherapy. The PanCareLIFE initiative provided, for the first time, a unique opportunity to confirm already identified determinants for hearing impairment during childhood cancer using a candidate gene approach and set up the first international genome-wide association study of cisplatin-induced direct ototoxicity in childhood cancer patients to identify novel allelic variants. Results will be validated in an independent replication cohort. Patient recruitment started in January 2015 and final inclusion was October 2017. We are currently performing the analyses and the first results are expected by the end of 2019 or the beginning of 2020.  CONCLUSIONS Genetic factors identified as part of this pan-European project, PanCareLIFE, may contribute to future risk prediction models that can be incorporated in future clinical trials of platinum-based therapies for cancer and may help with the development of prevention strategies. INTERNATIONAL REGISTERED REPOR DERR1-10.2196/11868

scholarly journals Genome-Wide Association Study (GWAS) to Identify Salt-Tolerance QTLs Carrying Novel Candidate Genes in Rice During Early Vegetative Stage

Rice ◽  
2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Leila Nayyeripasand ◽  
Ghasem Ali Garoosi ◽  
Asadollah Ahmadikhah
Keyword(s):  
Association Study ◽  
Candidate Gene ◽  
Candidate Genes ◽  
Salinity Tolerance ◽  
Genome Wide Association Study ◽  
Dry Weight ◽  
Genome Wide Association ◽  
Vegetative Stage ◽  
Genome Wide ◽  
Genomic Regions

Abstract Background Rice is considered as a salt-sensitive plant, particularly at early vegetative stage, and its production is suffered from salinity due to expansion of salt affected land in areas under cultivation. Hence, significant increase of rice productivity on salinized lands is really necessary. Today genome-wide association study (GWAS) is a method of choice for fine mapping of QTLs involved in plant responses to abiotic stresses including salinity stress at early vegetative stage. In this study using > 33,000 SNP markers we identified rice genomic regions associated to early stage salinity tolerance. Eight salinity-related traits including shoot length (SL), root length (RL), root dry weight (RDW), root fresh weight (RFW), shoot fresh weight (SFW), shoot dry weight (SDW), relative water content (RWC) and TW, and 4 derived traits including SL-R, RL-R, RDW-R and RFW-R in a diverse panel of rice were evaluated under salinity (100 mM NaCl) and normal conditions in growth chamber. Genome-wide association study (GWAS) was applied based on MLM(+Q + K) model. Results Under stress conditions 151 trait-marker associations were identified that were scattered on 10 chromosomes of rice that arranged in 29 genomic regions. A genomic region on chromosome 1 (11.26 Mbp) was identified which co-located with a known QTL region SalTol1 for salinity tolerance at vegetative stage. A candidate gene (Os01g0304100) was identified in this region which encodes a cation chloride cotransporter. Furthermore, on this chromosome two other candidate genes, Os01g0624700 (24.95 Mbp) and Os01g0812000 (34.51 Mbp), were identified that encode a WRKY transcription factor (WRKY 12) and a transcriptional activator of gibberellin-dependent alpha-amylase expression (GAMyb), respectively. Also, a narrow interval on the same chromosome (40.79–42.98 Mbp) carries 12 candidate genes, some of them were not so far reported for salinity tolerance at seedling stage. Two of more interesting genes are Os01g0966000 and Os01g0963000, encoding a plasma membrane (PM) H+-ATPase and a peroxidase BP1 protein. A candidate gene was identified on chromosome 2 (Os02g0730300 at 30.4 Mbp) encoding a high affinity K+ transporter (HAK). On chromosome 6 a DnaJ-encoding gene and pseudouridine synthase gene were identified. Two novel genes on chromosome 8 including the ABI/VP1 transcription factor and retinoblastoma-related protein (RBR), and 3 novel genes on chromosome 11 including a Lox, F-box and Na+/H+ antiporter, were also identified. Conclusion Known or novel candidate genes in this research were identified that can be used for improvement of salinity tolerance in molecular breeding programmes of rice. Further study and identification of effective genes on salinity tolerance by the use of candidate gene-association analysis can help to precisely uncover the mechanisms of salinity tolerance at molecular level. A time dependent relationship between salt tolerance and expression level of candidate genes could be recognized.

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