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Rare variants of large effect in BRCA2 and CHEK2 affect risk of lung cancer
Open accessAbstract
We conducted imputation to the 1000 Genomes Project of four genome-wide association studies of lung cancer in populations of European ancestry (11,348 cases and 15,861 controls) and genotyped an additional 10,246 cases and 38,295 controls for follow-up. We identified large-effect genome-wide associations for squamous lung cancer with the rare variants BRCA2 p.Lys3326X (rs11571833, odds ratio (OR) = 2.47, P = 4.74 × 10−20) and CHEK2 p.Ile157Thr (rs17879961, OR = 0.38, P = 1.27 × 10−13). We also showed an association between common variation at 3q28 (TP63, rs13314271, OR = 1.13, P = 7.22 × 10−10) and lung adenocarcinoma that had been previously reported only in Asians. These findings provide further evidence for inherited genetic susceptibility to lung cancer and its biological basis. Additionally, our analysis demonstrates that imputation can identify rare disease-causing variants with substantive effects on cancer risk from preexisting genome-wide association study data.
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Metadata
- Authors
- Wang, Y., McKay, J. D., Rafnar, T., Wang, Z., Timofeeva, M. N., Broderick, P., Zong, X., Laplana, M., Wei, Y., Han, Y., Lloyd, A., Delahaye-Sourdeix, M., Chubb, D., Gaborieau, V., Wheeler, W., Chatterjee, N., Thorleifsson, G., Sulem, P., Liu, G., Kaaks, R., Henrion, M., Kinnersley, B., Vallée, M., Le Calvez-Kelm, F., Stevens, V. L., Gapstur, S. M., Chen, W. V., Zaridze, D., Szeszenia-Dabrowska, N., Lissowska, J., Rudnai, P., Fabianova, E., Mates, D., Bencko, V., Foretova, L., Janout, V., Krokan, H. E., Gabrielsen, M. E., Skorpen, F., Vatten, L., Njølstad, I., Chen, C., Goodman, G., Benhamou, S., Vooder, T., Välk, K., Nelis, M., Metspalu, A., Lener, M., Lubiński, J., Johansson, M., Vineis, P., Agudo, A., Clavel-Chapelon, F., Bueno-de-Mesquita, H. B., Trichopoulos, D., Khaw, K.-T., Johansson, M., Weiderpass, E., Tjønneland, A., Riboli, E., Lathrop, M., Scelo, G., Albanes, D., Caporaso, N. E., Ye, Y., Gu, J., Wu, X., Spitz, M. R., Dienemann, H., Rosenberger, A., Su, L., Matakidou, A., Eisen, T., Stefansson, K., Risch, A., Chanock, S. J., Christiani, D. C., Hung, R. J., Brennan, P., Landi, M. T., Houlston, R. S., & Amos, C. I.
- Venue
- Nature Genetics
- Published
- 2014-06-01
- Volume
- 46
- Issue
- 7
- Pages
- 736-741
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- OpenAlex
- W2072881647
- Cited by
- 454
- References
- 71
- FWCI
- 21.60
- Type
- journal article
- Language
- en
- Open access
- green
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 ›
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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.