The DOI matches its Crossref record; 67 of the 67 references it cites were found in a registry or an index.
Rare variant discovery by deep whole-genome sequencing of 1,070 Japanese individuals
Open accessAbstract
The Tohoku Medical Megabank Organization reports the whole-genome sequences of 1,070 healthy Japanese individuals and construction of a Japanese population reference panel (1KJPN). Here we identify through this high-coverage sequencing (32.4 × on average), 21.2 million, including 12 million novel, single-nucleotide variants (SNVs) at an estimated false discovery rate of <1.0%. This detailed analysis detected signatures for purifying selection on regulatory elements as well as coding regions. We also catalogue structural variants, including 3.4 million insertions and deletions, and 25,923 genic copy-number variants. The 1KJPN was effective for imputing genotypes of the Japanese population genome wide. These data demonstrate the value of high-coverage sequencing for constructing population-specific variant panels, which covers 99.0% SNVs of minor allele frequency ≥0.1%, and its value for identifying causal rare variants of complex human disease phenotypes in genetic association studies.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Fast and accurate short read alignment with Burrows-Wheeler transform
Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607
Initial sequencing and analysis of the human genome
International Human Genome Sequencing Consortium, Whitehead Institute for Biomedical Research, C. F. G. R., Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., Devon, K., Dewar, K., et al. (2001) · Nature · doi:10.1038/35057062 · Cited by 24,216
An integrated encyclopedia of DNA elements in the human genome
The ENCODE Project Consortium (2012) · Nature · doi:10.1038/nature11247 · Cited by 18,072
A framework for variation discovery and genotyping using next-generation DNA sequencing data
DePristo, M. A., Banks, E., Poplin, R., Garimella, K. V., Maguire, J. R., Hartl, C., Philippakis, A. A., del Angel, G., Rivas, M. A., Hanna, M., et al. (2011) · Nature Genetics · doi:10.1038/ng.806 · Cited by 11,456
Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls
The Wellcome Trust Case Control Consortium, Management Committee, Burton, P. R., Clayton, D. G., Cardon, L. R., Craddock, N., Deloukas, P., Duncanson, A., Kwiatkowski, D. P., McCarthy, M. I., et al. (2007) · Nature · doi:10.1038/nature05911 · Cited by 9,442
Finding the missing heritability of complex diseases
Manolio, T. A., Collins, F. S., Cox, N. J., Goldstein, D. B., Hindorff, L. A., Hunter, D. J., McCarthy, M. I., Ramos, E. M., Cardon, L. R., Chakravarti, A., et al. (2009) · Nature · doi:10.1038/nature08494 · Cited by 8,336
An integrated map of genetic variation from 1,092 human genomes
The 1000 Genomes Project Consortium (2012) · Nature · doi:10.1038/nature11632 · Cited by 7,711
A general framework for estimating the relative pathogenicity of human genetic variants
Kircher, M., Witten, D. M., Jain, P., O'Roak, B. J., Cooper, G. M., & Shendure, J. (2014) · Nature Genetics · doi:10.1038/ng.2892 · Cited by 6,183
A haplotype map of the human genome
The International HapMap Consortium (2005) · Nature · doi:10.1038/nature04226 · Cited by 5,858
The ENCODE Project Consortium (2007) · Nature · doi:10.1038/nature05874 · Cited by 5,223
Cited by
Direct determination of diploid genome sequences
Weisenfeld, N. I., Kumar, V., Shah, P., Church, D. M., & Jaffe, D. B. (2017) · Genome Research · doi:10.1101/gr.214874.116 · Cited by 803
Structural variation in the sequencing era
Ho, S. S., Urban, A. E., & Mills, R. E. (2020) · Nature Reviews Genetics · doi:10.1038/s41576-019-0180-9 · Cited by 615
The MHC locus and genetic susceptibility to autoimmune and infectious diseases
Matzaraki, V., Kumar, V., Wijmenga, C., & Zhernakova, A. (2017) · Genome biology · doi:10.1186/s13059-017-1207-1 · Cited by 566
Comprehensive evaluation of structural variation detection algorithms for whole genome sequencing
Kosugi, S., Momozawa, Y., Liu, X., Terao, C., Kubo, M., & Kamatani, Y. (2019) · Genome Biology · doi:10.1186/s13059-019-1720-5 · Cited by 508
The Tohoku Medical Megabank Project: Design and Mission
Kuriyama, S., Yaegashi, N., Nagami, F., Arai, T., Kawaguchi, Y., Osumi, N., Sakaida, M., Suzuki, Y., Nakayama, K., Hashizume, H., et al. (2016) · Journal of Epidemiology · doi:10.2188/jea.je20150268 · Cited by 359
Self-citation
Metadata
- Authors
- Nagasaki, M., Yasuda, J., Katsuoka, F., Nariai, N., Kojima, K., Kawai, Y., Yamaguchi-Kabata, Y., Yokozawa, J., Danjoh, I., Saito, S., Sato, Y., Mimori, T., Tsuda, K., Saito, R., Pan, X., Nishikawa, S., Ito, S., Kuroki, Y., Tanabe, O., Fuse, N., Kuriyama, S., Kiyomoto, H., Hozawa, A., Minegishi, N., Douglas Engel, J., Kinoshita, K., Kure, S., Yaegashi, N., ToMMo Japanese Reference Panel Project, Tsuboi, A., Nagami, F., Kawame, H., Tomita, H., Tsuji, I., Nakaya, J., Sugawara, J., Suzuki, K., Kikuya, M., Abe, M., Nakaya, N., Osumi, N., Yamashita, R., Ogishima, S., Takai, T., Tominaga, T., Taki, Y., Suzuki, Y., & Yamamoto, M.
- Venue
- Nature Communications
- Published
- 2015-08-21
- Volume
- 6
- Issue
- 1
- Pages
- 8018-8018
- ISSN
- 2041-1723 (ISSN-L)
- OpenAlex
- W1175815497
- Cited by
- 400
- References
- 67
- FWCI
- 23.64
- Type
- journal article
- Language
- en
- Open access
- gold
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: Rare variant discovery by deep whole-genome sequencing of 1,070 Japanese individuals. https://app.cochat.ai/papers/10.1038/ncomms9018
- The paper
- Nagasaki, M., Yasuda, J., Katsuoka, F., Nariai, N., Kojima, K., Kawai, Y., Yamaguchi-Kabata, Y., Yokozawa, J., Danjoh, I., Saito, S., Sato, Y., Mimori, T., Tsuda, K., Saito, R., Pan, X., Nishikawa, S., Ito, S., Kuroki, Y., Tanabe, O., . . . Yamamoto, M. (2015). Rare variant discovery by deep whole-genome sequencing of 1,070 Japanese individuals. Nature Communications. https://doi.org/10.1038/ncomms9018
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
