A novel Synthetic phenotype association study approach reveals the landscape of association for genomic variants and phenotypes
Identifikátory výsledku
Kód výsledku v IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61989592%3A15310%2F22%3A73616565" target="_blank" >RIV/61989592:15310/22:73616565 - isvavai.cz</a>
Výsledek na webu
<a href="https://www.sciencedirect.com/science/article/pii/S2090123222000996" target="_blank" >https://www.sciencedirect.com/science/article/pii/S2090123222000996</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1016/j.jare.2022.04.004" target="_blank" >10.1016/j.jare.2022.04.004</a>
Alternativní jazyky
Jazyk výsledku
angličtina
Název v původním jazyce
A novel Synthetic phenotype association study approach reveals the landscape of association for genomic variants and phenotypes
Popis výsledku v původním jazyce
Introduction: Genome-Wide Association Studies (GWAS) identify tagging variants in the genome that are statistically associated with the phenotype because of their linkage disequilibrium (LD) relationship with the causative mutation (CM). When both low-density genotyped accession panels with phenotypes and resequenced data accession panels are available, tagging variants can assist with post-GWAS challenges in CM discovery.Objectives: Our objective was to identify additional GWAS evaluation criteria to assess correspondence between genomic variants and phenotypes, as well as enable deeper analysis of the localized landscape of association. Methods: We used genomic variant positions as Synthetic phenotypes in GWAS that we named "Synthetic phenotype association study" (SPAS). The extreme case of SPAS is what we call an "Inverse GWAS" where we used CM positions of cloned soybean genes. We developed and validated the Accuracy concept as a measure of the correspondence between variant positions and phenotypes.Results: The SPAS approach demonstrated that the genotype status of an associated variant used as a Synthetic phenotype enabled us to explore the relationships between tagging variants and CMs, and fur-ther, that utilizing CMs as Synthetic phenotypes in Inverse GWAS illuminated the landscape of associa-tion. We implemented the Accuracy calculation for a curated accession panel to an online Accuracy calculation tool (AccuTool) as a resource for gene identification in soybean. We demonstrated our con-cepts on three examples of soybean cloned genes. As a result of our findings, we devised an enhanced "GWAS to Genes" analysis (Synthetic phenotype to CM strategy, SP2CM). Using SP2CM, we identified a CM for a novel gene.Conclusion: The SP2CM strategy utilizing Synthetic phenotypes and the Accuracy calculation of corre-spondence provides crucial information to assist researchers in CM discovery. The impact of this work is a more effective evaluation of landscapes of GWAS associations.
Název v anglickém jazyce
A novel Synthetic phenotype association study approach reveals the landscape of association for genomic variants and phenotypes
Popis výsledku anglicky
Introduction: Genome-Wide Association Studies (GWAS) identify tagging variants in the genome that are statistically associated with the phenotype because of their linkage disequilibrium (LD) relationship with the causative mutation (CM). When both low-density genotyped accession panels with phenotypes and resequenced data accession panels are available, tagging variants can assist with post-GWAS challenges in CM discovery.Objectives: Our objective was to identify additional GWAS evaluation criteria to assess correspondence between genomic variants and phenotypes, as well as enable deeper analysis of the localized landscape of association. Methods: We used genomic variant positions as Synthetic phenotypes in GWAS that we named "Synthetic phenotype association study" (SPAS). The extreme case of SPAS is what we call an "Inverse GWAS" where we used CM positions of cloned soybean genes. We developed and validated the Accuracy concept as a measure of the correspondence between variant positions and phenotypes.Results: The SPAS approach demonstrated that the genotype status of an associated variant used as a Synthetic phenotype enabled us to explore the relationships between tagging variants and CMs, and fur-ther, that utilizing CMs as Synthetic phenotypes in Inverse GWAS illuminated the landscape of associa-tion. We implemented the Accuracy calculation for a curated accession panel to an online Accuracy calculation tool (AccuTool) as a resource for gene identification in soybean. We demonstrated our con-cepts on three examples of soybean cloned genes. As a result of our findings, we devised an enhanced "GWAS to Genes" analysis (Synthetic phenotype to CM strategy, SP2CM). Using SP2CM, we identified a CM for a novel gene.Conclusion: The SP2CM strategy utilizing Synthetic phenotypes and the Accuracy calculation of corre-spondence provides crucial information to assist researchers in CM discovery. The impact of this work is a more effective evaluation of landscapes of GWAS associations.
Klasifikace
Druh
J<sub>imp</sub> - Článek v periodiku v databázi Web of Science
CEP obor
—
OECD FORD obor
10611 - Plant sciences, botany
Návaznosti výsledku
Projekt
—
Návaznosti
S - Specificky vyzkum na vysokych skolach
Ostatní
Rok uplatnění
2022
Kód důvěrnosti údajů
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Údaje specifické pro druh výsledku
Název periodika
Journal of Advanced Research
ISSN
2090-1232
e-ISSN
2090-1224
Svazek periodika
42
Číslo periodika v rámci svazku
DEC
Stát vydavatele periodika
EG - Egyptská arabská republika
Počet stran výsledku
17
Strana od-do
117-133
Kód UT WoS článku
000906715800001
EID výsledku v databázi Scopus
2-s2.0-85128629104