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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 &quot;Synthetic phenotype association study&quot; (SPAS). The extreme case of SPAS is what we call an &quot;Inverse GWAS&quot; 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 &quot;GWAS to Genes&quot; 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 &quot;Synthetic phenotype association study&quot; (SPAS). The extreme case of SPAS is what we call an &quot;Inverse GWAS&quot; 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 &quot;GWAS to Genes&quot; 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