The GWAS-MAP platform for aggregation of results of genome-wide association studies and the GWAS-MAP|homo database of 70 billion genetic associations of human traits
Hundreds of genome-wide association studies (GWAS) of human traits are performed each year. The results of GWAS are often published in the form of summary statistics. Information from summary statistics can be used for multiple purposes – from fundamental research in biology and genetics to the sear...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
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Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders
2020-12-01
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| Series: | Вавиловский журнал генетики и селекции |
| Subjects: | |
| Online Access: | https://vavilov.elpub.ru/jour/article/view/2848 |
| _version_ | 1797214017021804544 |
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| author | T. I. Shashkova D. D. Gorev E. D. Pakhomov A. S. Shadrina S. Zh. Sharapov Y. A. Tsepilov L. C. Karssen Y. S. Aulchenko |
| author_facet | T. I. Shashkova D. D. Gorev E. D. Pakhomov A. S. Shadrina S. Zh. Sharapov Y. A. Tsepilov L. C. Karssen Y. S. Aulchenko |
| author_sort | T. I. Shashkova |
| collection | DOAJ |
| description | Hundreds of genome-wide association studies (GWAS) of human traits are performed each year. The results of GWAS are often published in the form of summary statistics. Information from summary statistics can be used for multiple purposes – from fundamental research in biology and genetics to the search for potential biomarkers and therapeutic targets. While the amount of GWAS summary statistics collected by the scientific community is rapidly increasing, the use of this data is limited by the lack of generally accepted standards. In particular, the researchers who would like to use GWAS summary statistics in their studies have to become aware that the data are scattered across multiple websites, are presented in a variety of formats, and, often, were not quality controlled. Moreover, each available summary statistics analysis tools will ask for data to be presented in their own internal format. To address these issues, we developed GWAS-MAP, a high-throughput platform for aggregating, storing, analyzing, visualizing and providing access to a database of big data that result from region- and genome-wide association studies. The database currently contains information on more than 70 billion associations between genetic variants and human diseases, quantitative traits, and “omics” traits. The GWAS-MAP platform and database can be used for studying the etiology of human diseases, building predictive risk models and finding potential biomarkers and therapeutic interventions. In order to demonstrate a typical application of the platform as an approach for extracting new biological knowledge and establishing mechanistic hypotheses, we analyzed varicose veins, a disease affecting on average every third adult in Russia. The results of analysis confirmed known epidemiologic associations for this disease and led us to propose a hypothesis that increased levels of MICB and CD209 proteins in human plasma may increase susceptibility to varicose veins. |
| first_indexed | 2024-03-07T16:05:12Z |
| format | Article |
| id | doaj.art-855c604c7c5b41379fca2dd71dd0ff89 |
| institution | Directory Open Access Journal |
| issn | 2500-3259 |
| language | English |
| last_indexed | 2024-04-24T11:07:29Z |
| publishDate | 2020-12-01 |
| publisher | Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders |
| record_format | Article |
| series | Вавиловский журнал генетики и селекции |
| spelling | doaj.art-855c604c7c5b41379fca2dd71dd0ff892024-04-11T15:31:03ZengSiberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and BreedersВавиловский журнал генетики и селекции2500-32592020-12-0124887688410.18699/VJ20.6861118The GWAS-MAP platform for aggregation of results of genome-wide association studies and the GWAS-MAP|homo database of 70 billion genetic associations of human traitsT. I. Shashkova0D. D. Gorev1E. D. Pakhomov2A. S. Shadrina3S. Zh. Sharapov4Y. A. Tsepilov5L. C. Karssen6Y. S. Aulchenko7Laboratory of Theoretical and Applied Functional Genomics, Novosibirsk State UniversityLaboratory of Theoretical and Applied Functional Genomics, Novosibirsk State UniversityLaboratory of Theoretical and Applied Functional Genomics, Novosibirsk State University; PolyKnomics BVLaboratory of Theoretical and Applied Functional Genomics, Novosibirsk State UniversityLaboratory of Theoretical and Applied Functional Genomics, Novosibirsk State UniversityLaboratory of Theoretical and Applied Functional Genomics, Novosibirsk State UniversityPolyKnomics BVLaboratory of Theoretical and Applied Functional Genomics, Novosibirsk State UniversityHundreds of genome-wide association studies (GWAS) of human traits are performed each year. The results of GWAS are often published in the form of summary statistics. Information from summary statistics can be used for multiple purposes – from fundamental research in biology and genetics to the search for potential biomarkers and therapeutic targets. While the amount of GWAS summary statistics collected by the scientific community is rapidly increasing, the use of this data is limited by the lack of generally accepted standards. In particular, the researchers who would like to use GWAS summary statistics in their studies have to become aware that the data are scattered across multiple websites, are presented in a variety of formats, and, often, were not quality controlled. Moreover, each available summary statistics analysis tools will ask for data to be presented in their own internal format. To address these issues, we developed GWAS-MAP, a high-throughput platform for aggregating, storing, analyzing, visualizing and providing access to a database of big data that result from region- and genome-wide association studies. The database currently contains information on more than 70 billion associations between genetic variants and human diseases, quantitative traits, and “omics” traits. The GWAS-MAP platform and database can be used for studying the etiology of human diseases, building predictive risk models and finding potential biomarkers and therapeutic interventions. In order to demonstrate a typical application of the platform as an approach for extracting new biological knowledge and establishing mechanistic hypotheses, we analyzed varicose veins, a disease affecting on average every third adult in Russia. The results of analysis confirmed known epidemiologic associations for this disease and led us to propose a hypothesis that increased levels of MICB and CD209 proteins in human plasma may increase susceptibility to varicose veins.https://vavilov.elpub.ru/jour/article/view/2848databasegenome-wide association studiesquantitative geneticsvaricose veinsgwas-map |
| spellingShingle | T. I. Shashkova D. D. Gorev E. D. Pakhomov A. S. Shadrina S. Zh. Sharapov Y. A. Tsepilov L. C. Karssen Y. S. Aulchenko The GWAS-MAP platform for aggregation of results of genome-wide association studies and the GWAS-MAP|homo database of 70 billion genetic associations of human traits Вавиловский журнал генетики и селекции database genome-wide association studies quantitative genetics varicose veins gwas-map |
| title | The GWAS-MAP platform for aggregation of results of genome-wide association studies and the GWAS-MAP|homo database of 70 billion genetic associations of human traits |
| title_full | The GWAS-MAP platform for aggregation of results of genome-wide association studies and the GWAS-MAP|homo database of 70 billion genetic associations of human traits |
| title_fullStr | The GWAS-MAP platform for aggregation of results of genome-wide association studies and the GWAS-MAP|homo database of 70 billion genetic associations of human traits |
| title_full_unstemmed | The GWAS-MAP platform for aggregation of results of genome-wide association studies and the GWAS-MAP|homo database of 70 billion genetic associations of human traits |
| title_short | The GWAS-MAP platform for aggregation of results of genome-wide association studies and the GWAS-MAP|homo database of 70 billion genetic associations of human traits |
| title_sort | gwas map platform for aggregation of results of genome wide association studies and the gwas map homo database of 70 billion genetic associations of human traits |
| topic | database genome-wide association studies quantitative genetics varicose veins gwas-map |
| url | https://vavilov.elpub.ru/jour/article/view/2848 |
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