Evidence map›Paper›PMID 36539398›Full record

ArticleHuman genome variation2022

The NBDC-DDBJ imputation server facilitates the use of controlled access reference panel datasets in Japan.

Tsuyoshi Hachiya, Manabu Ishii, Yosuke Kawai, Seik-Soon Khor, Minae Kawashima, Licht Toyo-Oka, Nobutaka Mitsuhashi, Asami Fukuda, Yuichi Kodama, Takatomo Fujisawa and 2 more

Abstract read
In one paragraph

Article in Human genome variation, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed.

  1. Review
  2. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

12 authors.

Tsuyoshi HachiyaGenome Analytics Japan Inc., Tokyo, Japan.ORCID http://orcid.org/0000-0002-5274-3266
Manabu IshiiGenome Analytics Japan Inc., Tokyo, Japan.
Yosuke KawaiGenome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan.ORCID http://orcid.org/0000-0003-0666-1224
Seik-Soon KhorGenome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan.ORCID http://orcid.org/0000-0002-6809-4731
Minae KawashimaDepartment of NBDC Program, Japan Science and Technology Agency, Tokyo, Japan. kawashima@biosciencedbc.jp.
Licht Toyo-OkaDepartment of NBDC Program, Japan Science and Technology Agency, Tokyo, Japan.
Nobutaka MitsuhashiDepartment of NBDC Program, Japan Science and Technology Agency, Tokyo, Japan.
Asami FukudaBioinformation and DDBJ Center, National Institute of Genetics, Shizuoka, Japan.
Yuichi KodamaBioinformation and DDBJ Center, National Institute of Genetics, Shizuoka, Japan.
Takatomo FujisawaBioinformation and DDBJ Center, National Institute of Genetics, Shizuoka, Japan.
Katsushi TokunagaGenome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan.
Toshihisa TakagiDepartment of NBDC Program, Japan Science and Technology Agency, Tokyo, Japan.

Funding

Japan Agency for Medical Research and Development (AMED) JP19km0405501
6 · The paper itself

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.

Identifiers

PMID36539398
PMCPMC9768127

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.