A novel Synthetic phenotype association study approach reveals the landscape of association for genomic variants and phenotypes

Result code in 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>

Result on the web

<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>

Result language

angličtina

Original language name

A novel Synthetic phenotype association study approach reveals the landscape of association for genomic variants and phenotypes

Original language description

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.

Czech name

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Czech description

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Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

—

OECD FORD branch

10611 - Plant sciences, botany

Project

—

Continuities

S - Specificky vyzkum na vysokych skolach

Publication year

2022

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

Journal of Advanced Research

ISSN

2090-1232

e-ISSN

2090-1224

Volume of the periodical

42

Issue of the periodical within the volume

DEC

Country of publishing house

EG - EGYPT

Number of pages

17

Pages from-to

117-133

UT code for WoS article

000906715800001

EID of the result in the Scopus database

2-s2.0-85128629104