Detecting associated genes for complex traits shared across East Asian and European populations under the framework of composite null hypothesis testing
Abstract Background Detecting trans-ethnic common associated genetic loci can offer important insights into shared genetic components underlying complex diseases/traits across diverse continental populations. However, effective statistical methods for such a goal are currently lacking. Methods By le...
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2022-09-01
|
| Series: | Journal of Translational Medicine |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12967-022-03637-8 |
| _version_ | 1798001534995267584 |
|---|---|
| author | Jiahao Qiao Zhonghe Shao Yuxuan Wu Ping Zeng Ting Wang |
| author_facet | Jiahao Qiao Zhonghe Shao Yuxuan Wu Ping Zeng Ting Wang |
| author_sort | Jiahao Qiao |
| collection | DOAJ |
| description | Abstract Background Detecting trans-ethnic common associated genetic loci can offer important insights into shared genetic components underlying complex diseases/traits across diverse continental populations. However, effective statistical methods for such a goal are currently lacking. Methods By leveraging summary statistics available from global-scale genome-wide association studies, we herein proposed a novel genetic overlap detection method called CONTO (COmposite Null hypothesis test for Trans-ethnic genetic Overlap) from the perspective of high-dimensional composite null hypothesis testing. Unlike previous studies which generally analyzed individual genetic variants, CONTO is a gene-centric method which focuses on a set of genetic variants located within a gene simultaneously and assesses their joint significance with the trait of interest. By borrowing the similar principle of joint significance test (JST), CONTO takes the maximum P value of multiple associations as the significance measurement. Results Compared to JST which is often overly conservative, CONTO is improved in two aspects, including the construction of three-component mixture null distribution and the adjustment of trans-ethnic genetic correlation. Consequently, CONTO corrects the conservativeness of JST with well-calibrated P values and is much more powerful validated by extensive simulation studies. We applied CONTO to discover common associated genes for 31 complex diseases/traits between the East Asian and European populations, and identified many shared trait-associated genes that had otherwise been missed by JST. We further revealed that population-common genes were generally more evolutionarily conserved than population-specific or null ones. Conclusion Overall, CONTO represents a powerful method for detecting common associated genes across diverse ancestral groups; our results provide important implications on the transferability of GWAS discoveries in one population to others. |
| first_indexed | 2024-04-11T11:37:46Z |
| format | Article |
| id | doaj.art-4e498171f84d4b49ba7d3921e0ef9d71 |
| institution | Directory Open Access Journal |
| issn | 1479-5876 |
| language | English |
| last_indexed | 2024-04-11T11:37:46Z |
| publishDate | 2022-09-01 |
| publisher | BMC |
| record_format | Article |
| series | Journal of Translational Medicine |
| spelling | doaj.art-4e498171f84d4b49ba7d3921e0ef9d712022-12-22T04:25:55ZengBMCJournal of Translational Medicine1479-58762022-09-0120111210.1186/s12967-022-03637-8Detecting associated genes for complex traits shared across East Asian and European populations under the framework of composite null hypothesis testingJiahao Qiao0Zhonghe Shao1Yuxuan Wu2Ping Zeng3Ting Wang4Department of Biostatistics, School of Public Health, Xuzhou Medical UniversityDepartment of Biostatistics, School of Public Health, Xuzhou Medical UniversityDepartment of Biostatistics, School of Public Health, Xuzhou Medical UniversityDepartment of Biostatistics, School of Public Health, Xuzhou Medical UniversityDepartment of Biostatistics, School of Public Health, Xuzhou Medical UniversityAbstract Background Detecting trans-ethnic common associated genetic loci can offer important insights into shared genetic components underlying complex diseases/traits across diverse continental populations. However, effective statistical methods for such a goal are currently lacking. Methods By leveraging summary statistics available from global-scale genome-wide association studies, we herein proposed a novel genetic overlap detection method called CONTO (COmposite Null hypothesis test for Trans-ethnic genetic Overlap) from the perspective of high-dimensional composite null hypothesis testing. Unlike previous studies which generally analyzed individual genetic variants, CONTO is a gene-centric method which focuses on a set of genetic variants located within a gene simultaneously and assesses their joint significance with the trait of interest. By borrowing the similar principle of joint significance test (JST), CONTO takes the maximum P value of multiple associations as the significance measurement. Results Compared to JST which is often overly conservative, CONTO is improved in two aspects, including the construction of three-component mixture null distribution and the adjustment of trans-ethnic genetic correlation. Consequently, CONTO corrects the conservativeness of JST with well-calibrated P values and is much more powerful validated by extensive simulation studies. We applied CONTO to discover common associated genes for 31 complex diseases/traits between the East Asian and European populations, and identified many shared trait-associated genes that had otherwise been missed by JST. We further revealed that population-common genes were generally more evolutionarily conserved than population-specific or null ones. Conclusion Overall, CONTO represents a powerful method for detecting common associated genes across diverse ancestral groups; our results provide important implications on the transferability of GWAS discoveries in one population to others.https://doi.org/10.1186/s12967-022-03637-8Trans-ethnic genetic overlapComposite null hypothesis testingSummary statisticsGene-centric association analysisCONTOJoint significance test |
| spellingShingle | Jiahao Qiao Zhonghe Shao Yuxuan Wu Ping Zeng Ting Wang Detecting associated genes for complex traits shared across East Asian and European populations under the framework of composite null hypothesis testing Journal of Translational Medicine Trans-ethnic genetic overlap Composite null hypothesis testing Summary statistics Gene-centric association analysis CONTO Joint significance test |
| title | Detecting associated genes for complex traits shared across East Asian and European populations under the framework of composite null hypothesis testing |
| title_full | Detecting associated genes for complex traits shared across East Asian and European populations under the framework of composite null hypothesis testing |
| title_fullStr | Detecting associated genes for complex traits shared across East Asian and European populations under the framework of composite null hypothesis testing |
| title_full_unstemmed | Detecting associated genes for complex traits shared across East Asian and European populations under the framework of composite null hypothesis testing |
| title_short | Detecting associated genes for complex traits shared across East Asian and European populations under the framework of composite null hypothesis testing |
| title_sort | detecting associated genes for complex traits shared across east asian and european populations under the framework of composite null hypothesis testing |
| topic | Trans-ethnic genetic overlap Composite null hypothesis testing Summary statistics Gene-centric association analysis CONTO Joint significance test |
| url | https://doi.org/10.1186/s12967-022-03637-8 |
| work_keys_str_mv | AT jiahaoqiao detectingassociatedgenesforcomplextraitssharedacrosseastasianandeuropeanpopulationsundertheframeworkofcompositenullhypothesistesting AT zhongheshao detectingassociatedgenesforcomplextraitssharedacrosseastasianandeuropeanpopulationsundertheframeworkofcompositenullhypothesistesting AT yuxuanwu detectingassociatedgenesforcomplextraitssharedacrosseastasianandeuropeanpopulationsundertheframeworkofcompositenullhypothesistesting AT pingzeng detectingassociatedgenesforcomplextraitssharedacrosseastasianandeuropeanpopulationsundertheframeworkofcompositenullhypothesistesting AT tingwang detectingassociatedgenesforcomplextraitssharedacrosseastasianandeuropeanpopulationsundertheframeworkofcompositenullhypothesistesting |