The NBDC-DDBJ imputation server facilitates the use of controlled access reference panel datasets in Japan
Abstract Accurate genotype imputation requires large-scale reference panel datasets. When conducting genotype imputation on the Japanese population, researchers can use such datasets under collaborative studies or controlled access conditions in public databases. We developed the NBDC-DDBJ imputatio...
| Main Authors: | , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Nature Publishing Group
2022-12-01
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| Series: | Human Genome Variation |
| Online Access: | https://doi.org/10.1038/s41439-022-00225-6 |
| _version_ | 1797977562696122368 |
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| author | Tsuyoshi Hachiya Manabu Ishii Yosuke Kawai Seik-Soon Khor Minae Kawashima Licht Toyo-Oka Nobutaka Mitsuhashi Asami Fukuda Yuichi Kodama Takatomo Fujisawa Katsushi Tokunaga Toshihisa Takagi |
| author_facet | Tsuyoshi Hachiya Manabu Ishii Yosuke Kawai Seik-Soon Khor Minae Kawashima Licht Toyo-Oka Nobutaka Mitsuhashi Asami Fukuda Yuichi Kodama Takatomo Fujisawa Katsushi Tokunaga Toshihisa Takagi |
| author_sort | Tsuyoshi Hachiya |
| collection | DOAJ |
| description | Abstract Accurate genotype imputation requires large-scale reference panel datasets. When conducting genotype imputation on the Japanese population, researchers can use such datasets under collaborative studies or controlled access conditions in public databases. We developed the NBDC-DDBJ imputation server, which securely provides users with a web user interface to execute genotype imputation on the server. Our benchmarking analysis showed that the accuracy of genotype imputation was improved by leveraging controlled access datasets to increase the number of haplotypes available for analysis compared to using publicly available reference panels such as the 1000 Genomes Project. The NBDC-DDBJ imputation server facilitates the use of controlled access datasets for accurate genotype imputation. |
| first_indexed | 2024-04-11T05:08:56Z |
| format | Article |
| id | doaj.art-c177f320f20348a09f39f5165e6e345f |
| institution | Directory Open Access Journal |
| issn | 2054-345X |
| language | English |
| last_indexed | 2024-04-11T05:08:56Z |
| publishDate | 2022-12-01 |
| publisher | Nature Publishing Group |
| record_format | Article |
| series | Human Genome Variation |
| spelling | doaj.art-c177f320f20348a09f39f5165e6e345f2022-12-25T12:09:43ZengNature Publishing GroupHuman Genome Variation2054-345X2022-12-01911510.1038/s41439-022-00225-6The NBDC-DDBJ imputation server facilitates the use of controlled access reference panel datasets in JapanTsuyoshi Hachiya0Manabu Ishii1Yosuke Kawai2Seik-Soon Khor3Minae Kawashima4Licht Toyo-Oka5Nobutaka Mitsuhashi6Asami Fukuda7Yuichi Kodama8Takatomo Fujisawa9Katsushi Tokunaga10Toshihisa Takagi11Genome Analytics Japan Inc.Genome Analytics Japan Inc.Genome Medical Science Project, National Center for Global Health and MedicineGenome Medical Science Project, National Center for Global Health and MedicineDepartment of NBDC Program, Japan Science and Technology AgencyDepartment of NBDC Program, Japan Science and Technology AgencyDepartment of NBDC Program, Japan Science and Technology AgencyBioinformation and DDBJ Center, National Institute of GeneticsBioinformation and DDBJ Center, National Institute of GeneticsBioinformation and DDBJ Center, National Institute of GeneticsGenome Medical Science Project, National Center for Global Health and MedicineDepartment of NBDC Program, Japan Science and Technology AgencyAbstract Accurate genotype imputation requires large-scale reference panel datasets. When conducting genotype imputation on the Japanese population, researchers can use such datasets under collaborative studies or controlled access conditions in public databases. We developed the NBDC-DDBJ imputation server, which securely provides users with a web user interface to execute genotype imputation on the server. Our benchmarking analysis showed that the accuracy of genotype imputation was improved by leveraging controlled access datasets to increase the number of haplotypes available for analysis compared to using publicly available reference panels such as the 1000 Genomes Project. The NBDC-DDBJ imputation server facilitates the use of controlled access datasets for accurate genotype imputation.https://doi.org/10.1038/s41439-022-00225-6 |
| spellingShingle | Tsuyoshi Hachiya Manabu Ishii Yosuke Kawai Seik-Soon Khor Minae Kawashima Licht Toyo-Oka Nobutaka Mitsuhashi Asami Fukuda Yuichi Kodama Takatomo Fujisawa Katsushi Tokunaga Toshihisa Takagi The NBDC-DDBJ imputation server facilitates the use of controlled access reference panel datasets in Japan Human Genome Variation |
| title | The NBDC-DDBJ imputation server facilitates the use of controlled access reference panel datasets in Japan |
| title_full | The NBDC-DDBJ imputation server facilitates the use of controlled access reference panel datasets in Japan |
| title_fullStr | The NBDC-DDBJ imputation server facilitates the use of controlled access reference panel datasets in Japan |
| title_full_unstemmed | The NBDC-DDBJ imputation server facilitates the use of controlled access reference panel datasets in Japan |
| title_short | The NBDC-DDBJ imputation server facilitates the use of controlled access reference panel datasets in Japan |
| title_sort | nbdc ddbj imputation server facilitates the use of controlled access reference panel datasets in japan |
| url | https://doi.org/10.1038/s41439-022-00225-6 |
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