The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.
MSIsensor: microsatellite instability detection using paired tumor-normal sequence data
Open accessAbstract
Motivation: Microsatellite instability (MSI) is an important indicator of larger genome instability and has been linked to many genetic diseases, including Lynch syndrome. MSI status is also an independent prognostic factor for favorable survival in multiple cancer types, such as colorectal and endometrial. It also informs the choice of chemotherapeutic agents. However, the current PCR–electrophoresis-based detection procedure is laborious and time-consuming, often requiring visual inspection to categorize samples. We developed MSIsensor, a C++ program for automatically detecting somatic microsatellite changes. It computes length distributions of microsatellites per site in paired tumor and normal sequence data, subsequently using these to statistically compare observed distributions in both samples. Comprehensive testing indicates MSIsensor is an efficient and effective tool for deriving MSI status from standard tumor-normal paired sequence data. Availability and implementation: https://github.com/ding-lab/msisensor Contact: kye@genome.wustl.edu or lding@genome.wustl.edu Supplementary information: Supplementary data are available at Bioinformatics online.
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Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing
Benjamini, Y., & Hochberg, Y. (1995) · Journal of the Royal Statistical Society Series B: Statistical Methodology · doi:10.1111/j.2517-6161.1995.tb02031.x · Cited by 109,482
Cited by
Zehir, A., Benayed, R., Shah, R. H., Syed, A., Middha, S., Kim, H. R., Srinivasan, P., Gao, J., Chakravarty, D., Devlin, S. M., et al. (2017) · Nature Medicine · doi:10.1038/nm.4333 · Cited by 3,380
Comprehensive Characterization of Cancer Driver Genes and Mutations
Bailey, M. H., Tokheim, C., Porta-Pardo, E., Sengupta, S., Bertrand, D., Weerasinghe, A., Colaprico, A., Wendl, M. C., Kim, J., Reardon, B., et al. (2018) · Cell · doi:10.1016/j.cell.2018.02.060 · Cited by 2,256
Self-citationImmunotherapy in colorectal cancer: Rationale, challenges and potential
Ganesh, K., Stadler, Z. K., Cercek, A., Mendelsohn, R. B., Shia, J., Segal, N. H., & Diaz, L. A. (2019) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-019-0126-x · Cited by 1,954
Classification and characterization of microsatellite instability across 18 cancer types
Hause, R. J., Pritchard, C. C., Shendure, J., & Salipante, S. J. (2016) · Nature Medicine · doi:10.1038/nm.4191 · Cited by 991
Molecular subtypes of pancreatic cancer
Collisson, E. A., Bailey, P., Chang, D. K., & Biankin, A. V. (2019) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-019-0109-y · Cited by 892
Metadata
- Authors
- Niu, B., Ye, K., Zhang, Q., Lu, C., Xie, M., McLellan, M. D., Wendl, M. C., & Ding, L.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2013-12-25
- Volume
- 30
- Issue
- 7
- Pages
- 1015-1016
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2117564738
- Cited by
- 832
- References
- 1
- FWCI
- 3.56
- Type
- journal article
- Language
- en
- Open access
- bronze
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- Niu, B., Ye, K., Zhang, Q., Lu, C., Xie, M., McLellan, M. D., Wendl, M. C., & Ding, L. (2014). MSIsensor: microsatellite instability detection using paired tumor-normal sequence data. Bioinformatics. https://doi.org/10.1093/bioinformatics/btt755
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