Selected Publications Citing the MSIsensor


1.Mutational Landscape of Metastatic Cancer Revealed from Prospective Clinical Sequencing of 10,000 Patients

Zehir, A.#, Benayed, R#., Shah, R.H., Syed, A., Middha, S., Kim, H.R., Srinivasan, P., Gao, J., Chakravarty, D., Devlin, S.M., Hellmann, M.D., Barron, D.A., Schram, A.M., Hameed, M., Dogan, S., Ross, D.S., Hechtman, J.F., DeLair, D.F., Yao, J., Mandelker, D.L., Cheng, D.T., Chandramohan, R., Mohanty, A.S., Ptashkin, R.N., Jayakumaran, G., Prasad, M., Syed, M.H., Rema, A.B., Liu, Z.Y., Nafa, K., Borsu, L., Sadowska, J., Casanova, J., Bacares, R., Kiecka, I.J., Razumova, A., Son, J.B., Stewart, L., Baldi, T., Mullaney, K.A., Al-Ahmadie, H., Vakiani, E., Abeshouse, A.A., Penson, A.V., Jonsson, P., Camacho, N., Chang, M.T., Won, H.H., Gross, B.E., Kundra, R., Heins, Z.J., Chen, H.-W., Phillips, S., Zhang, H., Wang, J., Ochoa, A., Wills, J., Eubank, M., Thomas, S.B., Gardos, S.M., Reales, D.N., Galle, J., Durany, R., Cambria, R., Abida, W., Cercek, A., Feldman, D.R., Gounder, M.M., Hakimi, A.A., Harding, J.J., Iyer, G., Janjigian, Y.Y., Jordan, E.J., Kelly, C.M., Lowery, M.A., Morris, L.G.T., Omuro, A.M., Raj, N., Razavi, P., Shoushtari, A.N., Shukla, N., Soumerai, T.E., Varghese, A.M., Yaeger, R., Coleman, J., Bochner, B., Riely, G.J., Saltz, L.B., Scher, H.I., Sabbatini, P.J., Robson, M.E., Klimstra, D.S., Taylor, B.S., Baselga, J., Schultz, N., Hyman, D.M., Arcila, M.E., Solit, D.B., Ladanyi, M. & Berger, M.F.*
Memorial Sloan Kettering Cancer Center, Illumina, Baylor College of Medicine.
Nature Medicine (2017). doi:10.1038/nm.4333

2. A hot L1 retrotransposon evades somatic repression and initiates human colorectal cancer

C. Scott, E.#, Gardner, E.#, Masood, A., Chuang, N., M. Vertino, P. & Devine, S.*
University of Maryland School of Medicine, Emory University School of Medicine, Emory University.
Genome Research (2016). doi: 10.1101/gr.201814.115

3. A molecular portrait of microsatellite instability across multiple cancers

Cortes-Ciriano, I.#, Lee, S.#, Park, W.-Y., Kim, T.-M.* & Park, P.J.*
Harvard Medical School, Ludwig Center at Harvard, Samsung Medical Center, The Catholic University of Korea.
Nature Communications (2017).doi: 10.1038/ncomms15180

4. Differential clonal evolution in oesophageal cancers in response to neo-adjuvant chemotherapy

Findlay, J.M.#, Castro-Giner, F.#, Makino, S.#, Rayner, E.#, Kartsonaki, C., Cross, W., Kovac, M., Ulahannan, D., Palles, C., Gillies, R.S., MacGregor, T.P., Church, D., Maynard, N.D., Buffa, F., Cazier, J.-B., Graham, T.A., Wang, L.-M., Sharma, R.A., Middleton, M. & Tomlinson, I.*
University of Oxford, Churchill Hospital, Oxford Institute for Radiation Oncology, Queen Mary University of London, University of Birmingham, John Radcliffe Hospital, Oxford NIHR Comprehensive Biomedical Research Centre.
Nature Communications (2016).doi: 10.1038/ncomms11111

5. Systematic Pan-Cancer Analysis Reveals Immune Cell Interactions in the Tumor Microenvironment

Varn, F., Wang, Y., Mullins, D., Fiering, S. & Cheng, C.*
Geisel School of Medicine at Dartmouth, Huazhong University of Science and Technology, Norris Cotton Cancer Center.
Cancer Research (2017). doi: 10.1158/0008-5472.CAN-16-2490

6. Detection of Mismatch Repair Deficiency and Microsatellite Instability in Colorectal Adenocarcinoma by Targeted Next Generation Sequencing

Nowak, J., Yurgelun, M., L. Bruce, J., Rojas-Rudilla, V., L. Hall, D., Shivdasani, P., P. Garcia, E., T. Agoston, A., Srivastava, A., Ogino, S., C. Kuo, F., I. Lindeman, N. & Dong, F.*
Harvard Medical School, the Center for Medical Genetics and Prevention, the Department of Medical Oncology, Harvard T.H. Chan School of Public Health.
The Journal of Molecular Diagnostics (2016).doi: 10.1016/j.jmoldx.2016.07.010

7. Microsatellite instability in prostate cancer by PCR or next-generation sequencing

Hempelmann, J., Lockwood, C., Konnick, E., Schweizer, M., Antonarakis, E., L. Lotan, T., Montgomery, B., S. Nelson, P., Klemfuss, N., J. Salipante, S. & C. Pritchard, C.*
University of Washington, Johns Hopkins University School of Medicine, VA Puget Sound Health Care System, Fred Hutchinson Cancer Research Center.
Journal for ImmunoTherapy of Cancer (2018). doi: https://doi.org/10.1186/s40425-018-0341-y

8.Carbon dating cancer: defining the chronology of metastatic progression in colorectal cancer

Lote, H.#, Spiteri, I.#, Ermini, L.#, Vatsiou, A., Roy, A., McDonald, A., Maka, N., Balsitis, M., Bose, N., Simbolo, M., Mafficini, A., Lampis, A., Hahne, J., Trevisani, F., Eltahir, Z., Mentrasti, G., Findlay, C., Kalkman, E.A.J., Punta, M.* & Valeri, N.*
The Institute of Cancer Research, The Royal Marsden NHS Trust, The Institute of Cancer Research, Crosshouse Hospital, Beatson West of Scotland Cancer Centre, Southern General Hospital, Crosshouse Hospital, ARC-NET Research Centre University of Verona, University of California San Francisco, Department of Psychology, Arizona State University, The Institute of Cancer Research, University of Padua.
Annals of Oncology (2017).doi: 10.1093/annonc/mdx074

9.The value of cell-free DNA for molecular pathology

Stewart, C., Kothari, P., Mouliere, F., Mair, R., Somnay, S., Benayed, R., Zehir, A., Weigelt, B., Dawson, S.-J., E Arcila, M., F Berger, M. & Wy Tsui, D.*
Memorial Sloan Kettering Cancer Center, University of Cambridge, Cancer Research UK Cambridge Institute, Memorial Sloan Kettering Cancer Center, Peter MacCallum Cancer Centre, University of Melbourne.
The Journal of Pathology (2018). doi: 10.1002/path.5048

10. Is There a Role for Programmed Death Ligand-1 Testing and Immunotherapy in Colorectal Cancer With Microsatellite Instability? Part I, Colorectal Cancer: Microsatellite Instability, Testing, and Clinical Implications

Marginean, C.* & Melosky, B.
University of Ottawa, University of British Columbia.
Archives of Pathology & Laboratory Medicine (2017).doi: 10.5858/arpa.2017-0040-RA

11.Precision oncology: Charting a path forward to broader deployment of genomic profiling

M. Schram, A., F. Berger, M. & Hyman, D.*
Memorial Sloan Kettering Cancer Center, Weill Cornell Medical College.
PLOS Medicine (2017). doi: 10.1371/journal.pmed.1002242

12.Recurrent, truncating SOX9 mutations are associated with SOX9 overexpression, KRAS mutation, and TP53 wild type status in colorectal carcinoma

M Javier, B., Yaeger, R., Wang, L., Sánchez-Vega, F., Zehir, A., Middha, S., Sadowska, J., Vakiani, E., Shia, J., Klimstra, D., Ladanyi, M., A Iacobuzio-Donahue, C. & F Hechtman, J.*
Memorial Sloan Kettering Cancer Center.
Oncotarget (2016). doi: 10.18632/oncotarget.9682

13.Identification of Targetable Kinase Alterations in Patients with Colorectal Carcinoma That are Preferentially Associated with Wild-Type RAS/RAF

F Hechtman, J.*, Zehir, A., D Yaeger, R., Wang, L., Middha, S., Zheng, T., Hyman, D., Solit, D., E Arcila, M., Borsu, L., Shia, J., Vakiani, E., Saltz, L. & Ladanyi, M.
Memorial Sloan Kettering Cancer Center.
Molecular Cancer Research (2015). doi: 10.1158/1541-7786.MCR-15-0392-T

14. MSIseq: Software for Assessing Microsatellite Instability from Catalogs of Somatic Mutations

Ni Huang, M., McPherson, J.R., Cutcutache, I., Teh, B.T., Tan, P. & Rozen, S.G.*
Duke-NUS Graduate Medical School, National Cancer Centre Singapore, National University of Singapore, Genome Institute of Singapore.
Scientific Reports (2015). doi: 10.1038/srep13321

15.Performance evaluation for rapid detection of pan-cancer microsatellite instability with MANTIS

Kautto, E., Bonneville, R., Miya, J., Yu, L., A. Krook, M., W. Reeser, J. & Roychowdhury, S.*
The Ohio State University.
Oncotarget (2015).doi: 10.18632/oncotarget.13918

To Cite MSIsensor2


MSIsensor: microsatellite instability detection using paired tumor-normal sequence data
Niu B., Ye K., Zhang Q., Lu C., Xie M., McLellan M.D., Wendl M.C., Ding L.
Bioinformatics 30, 1015-1016 (2013).doi:10.1101/115717