Noushin Niknafs Kermani

Research output

Research output per year 2013 2013 2015 2016 2017 2018 2019 2020 2022 2023 2024

• 35 Article
• 2 Comment/debate
• 1 Editorial

Research output per year

Research output per year

Search results

• 2024

  Genome-wide repeat landscapes in cancer and cell-free DNA

  Annapragada, A. V., Niknafs, N., White, J. R., Bruhm, D. C., Cherry, C., Medina, J. E., Adleff, V., Hruban, C., Mathios, D., Foda, Z. H., Phallen, J., Scharpf, R. B. & Velculescu, V. E., Mar 13 2024, In: Science translational medicine. 16, 738, eadj9283.

  Research output: Contribution to journal › Article › peer-review

  Open Access
• 2023

  Corrigendum to “HLA class II immunogenic mutation burden predicts response to immune checkpoint blockade”: [Annals of Oncology volume 33 (2022) 728-738, (S0923753422003921), (10.1016/j.annonc.2022.03.013)]

  Shao, X. M., Huang, J., Niknafs, N., Balan, A., Cherry, C., White, J., Velculescu, V. E., Anagnostou, V. & Karchin, R., Jul 2023, In: Annals of Oncology. 34, 7, p. 634 1 p.

  Research output: Contribution to journal › Comment/debate › peer-review

  • Publications 100%
  • Emotions 95%
  • Mutation 67%

• ctDNA response after pembrolizumab in non-small cell lung cancer: phase 2 adaptive trial results

  Anagnostou, V., Ho, C., Nicholas, G., Juergens, R. A., Sacher, A., Fung, A. S., Wheatley-Price, P., Laurie, S. A., Levy, B., Brahmer, J. R., Balan, A., Niknafs, N., Avrutin, E., Zhu, L., Sausen, M., Bradbury, P. A., O’Donnell-Tormey, J., Gaudreau, P. O., Ding, K. & Dancey, J., Oct 2023, In: Nature medicine. 29, 10, p. 2559-2569 11 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Circulating Tumor DNA 100%
  • pembrolizumab 97%
  • Non-Small Cell Lung Carcinoma 62%
  • Clearance 37%
  • Response Evaluation Criteria in Solid Tumors 25%

• Detecting Liver Cancer Using Cell-Free DNA Fragmentomes

  Foda, Z. H., Annapragada, A. V., Boyapati, K., Bruhm, D. C., Vulpescu, N. A., Medina, J. E., Mathios, D., Cristiano, S., Niknafs, N., Luu, H. T., Goggins, M. G., Anders, R. A., Sun, J., Meta, S. H., Thomas, D. L., Kirk, G. D., Adleff, V., Phallen, J., Scharpf, R. B., Kim, A. K., & 1 othersVelculescu, V. E., Mar 1 2023, In: Cancer discovery. 13, 3, p. 616-631 16 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Cell-Free Nucleic Acids 100%
  • Liver Neoplasms 79%
  • DNA Fragmentation 63%
  • Hepatocellular Carcinoma 47%
  • Genome 26%

• Dynamics of Sequence and Structural Cell-Free DNA Landscapes in Small-Cell Lung Cancer

  Sivapalan, L., Iams, W. T., Belcaid, Z., Scott, S. C., Niknafs, N., Balan, A., White, J. R., Kopparapu, P., Cann, C., Landon, B. V., Pereira, G., Velculescu, V. E., Hann, C. L., Lovly, C. M. & Anagnostou, V., Jun 13 2023, In: Clinical cancer research : an official journal of the American Association for Cancer Research. 29, 12, p. 2310-2323 14 p.

  Research output: Contribution to journal › Editorial › peer-review

  Open Access

  • Cell-Free Nucleic Acids 100%
  • Small Cell Lung Carcinoma 88%
  • Circulating Tumor DNA 57%
  • Tumor Burden 47%
  • Aneuploidy 21%

• Persistent mutation burden drives sustained anti-tumor immune responses

  Niknafs, N., Balan, A., Cherry, C., Hummelink, K., Monkhorst, K., Shao, X. M., Belcaid, Z., Marrone, K. A., Murray, J., Smith, K. N., Levy, B., Feliciano, J., Hann, C. L., Lam, V., Pardoll, D. M., Karchin, R., Seiwert, T. Y., Brahmer, J. R., Forde, P. M., Velculescu, V. E., & 1 othersAnagnostou, V., Feb 2023, In: Nature medicine. 29, 2, p. 440-449 10 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Mutation 100%
  • Tumor Burden 64%
  • Immunotherapy 59%
  • Neoplasms 38%
  • Mesothelioma 20%
• 2022

  Estimation of cancer cell fractions and clone trees from multi-region sequencing of tumors

  Zheng, L., Niknafs, N., Wood, L. D., Karchin, R. & Scharpf, R. B., Aug 1 2022, In: Bioinformatics. 38, 15, p. 3677-3683 7 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Pictogram 100%
  • Clone 60%
  • Sequencing 59%
  • Tumor 52%
  • Cancer 50%

• HLA class II immunogenic mutation burden predicts response to immune checkpoint blockade

  Shao, X. M., Huang, J., Niknafs, N., Balan, A., Cherry, C., White, J., Velculescu, V. E., Anagnostou, V. & Karchin, R., Jul 2022, In: Annals of Oncology. 33, 7, p. 728-738 11 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • HLA Antigens 100%
  • Mutation 54%
  • Non-Small Cell Lung Carcinoma 24%
  • Melanoma 23%
  • Computer Neural Networks 9%

• Peripheral blood immune cell dynamics reflect antitumor immune responses and predict clinical response to immunotherapy

  Hwang, M., Canzoniero, J. V., Rosner, S., Zhang, G., White, J. R., Belcaid, Z., Cherry, C., Balan, A., Pereira, G., Curry, A., Niknafs, N., Zhang, J., Smith, K. N., Sivapalan, L., Chaft, J. E., Reuss, J. E., Marrone, K., Murray, J. C., Li, Q. K., Lam, V., & 7 othersLevy, B. P., Hann, C., Velculescu, V. E., Brahmer, J. R., Forde, P. M., Seiwert, T. & Anagnostou, V., Jun 10 2022, In: Journal for immunotherapy of cancer. 10, 6, e004688.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Immunotherapy 100%
  • Blood Cells 93%
  • Neutrophils 88%
  • Lymphocytes 78%
  • Circulating Tumor DNA 36%

• Sex-specific differences in immunogenomic features of response to immune checkpoint blockade

  Scott, S. C., Shao, X. M., Niknafs, N., Balan, A., Pereira, G., Marrone, K. A., Lam, V. K., Murray, J. C., Feliciano, J. L., Levy, B. P., Ettinger, D. S., Hann, C. L., Brahmer, J. R., Forde, P. M., Karchin, R., Naidoo, J. & Anagnostou, V., Aug 3 2022, In: Frontiers in Oncology. 12, 945798.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Sex Characteristics 100%
  • Missense Mutation 73%
  • Exome 42%
  • Neoplasms 34%
  • Non-Small Cell Lung Carcinoma 31%
• 2021

  Detection and characterization of lung cancer using cell-free DNA fragmentomes

  Mathios, D., Johansen, J. S., Cristiano, S., Medina, J. E., Phallen, J., Larsen, K. R., Bruhm, D. C., Niknafs, N., Ferreira, L., Adleff, V., Chiao, J. Y., Leal, A., Noe, M., White, J. R., Arun, A. S., Hruban, C., Annapragada, A. V., Jensen, S. Ø., Ørntoft, M. B. W., Madsen, A. H., & 18 othersCarvalho, B., de Wit, M., Carey, J., Dracopoli, N. C., Maddala, T., Fang, K. C., Hartman, A. R., Forde, P. M., Anagnostou, V., Brahmer, J. R., Fijneman, R. J. A., Nielsen, H. J., Meijer, G. A., Andersen, C. L., Mellemgaard, A., Bojesen, S. E., Scharpf, R. B. & Velculescu, V. E., Dec 1 2021, In: Nature communications. 12, 1, 5060.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Cell-Free Nucleic Acids 100%
  • lungs 86%
  • cancer 74%
  • deoxyribonucleic acid 71%
  • Fragmentation 65%

• Durvalumab with platinum-pemetrexed for unresectable pleural mesothelioma: survival, genomic and immunologic analyses from the phase 2 PrE0505 trial

  Forde, P. M., Anagnostou, V., Sun, Z., Dahlberg, S. E., Kindler, H. L., Niknafs, N., Purcell, T., Santana-Davila, R., Dudek, A. Z., Borghaei, H., Lanis, M., Belcaid, Z., Smith, K. N., Balan, A., White, J. R., Cherry, C., Ashok Sivakumar, I. K., Shao, X. M., Chan, H. Y., Singh, D., & 7 othersThapa, S., Illei, P. B., Pardoll, D. M., Karchin, R., Velculescu, V. E., Brahmer, J. R. & Ramalingam, S. S., Nov 2021, In: Nature medicine. 27, 11, p. 1910-1920 11 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Pemetrexed 100%
  • durvalumab 96%
  • Mesothelioma 66%
  • Cisplatin 60%
  • Platinum 58%
• 2020

  Genomic characterization of malignant progression in neoplastic pancreatic cysts

  Noë, M., Niknafs, N., Fischer, C. G., Hackeng, W. M., Beleva Guthrie, V., Hosoda, W., Debeljak, M., Papp, E., Adleff, V., White, J. R., Luchini, C., Pea, A., Scarpa, A., Butturini, G., Zamboni, G., Castelli, P., Hong, S. M., Yachida, S., Hiraoka, N., Gill, A. J., & 18 othersSamra, J. S., Offerhaus, G. J. A., Hoorens, A., Verheij, J., Jansen, C., Adsay, N. V., Jiang, W., Winter, J., Albores-Saavedra, J., Terris, B., Thompson, E. D., Roberts, N. J., Hruban, R. H., Karchin, R., Scharpf, R. B., Brosens, L. A. A., Velculescu, V. E. & Wood, L. D., Dec 1 2020, In: Nature communications. 11, 1, 4085.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • neoplasms 100%
  • cysts 91%
  • Pancreatic Cyst 90%
  • progressions 70%
  • Mutation 52%
  10 Scopus citations

• Integrative Tumor and Immune Cell Multi-omic Analyses Predict Response to Immune Checkpoint Blockade in Melanoma

  Anagnostou, V., Bruhm, D. C., Niknafs, N., White, J. R., Shao, X. M., Sidhom, J. W., Stein, J., Tsai, H. L., Wang, H., Belcaid, Z., Murray, J., Balan, A., Ferreira, L., Ross-Macdonald, P., Wind-Rotolo, M., Baras, A. S., Taube, J., Karchin, R., Scharpf, R. B., Grasso, C., & 4 othersRibas, A., Pardoll, D. M., Topalian, S. L. & Velculescu, V. E., Nov 17 2020, In: Cell Reports Medicine. 1, 8, 100139.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Mutation 100%
  • Melanoma 98%
  • T-Lymphocytes 73%
  • Neoplasms 38%
  • B-Lymphocyte Subsets 37%
  4 Scopus citations

• Multimodal genomic features predict outcome of immune checkpoint blockade in non-small-cell lung cancer

  Anagnostou, V., Niknafs, N., Marrone, K., Bruhm, D. C., White, J. R., Naidoo, J., Hummelink, K., Monkhorst, K., Lalezari, F., Lanis, M., Rosner, S., Reuss, J. E., Smith, K. N., Adleff, V., Rodgers, K., Belcaid, Z., Rhymee, L., Levy, B., Feliciano, J., Hann, C. L., & 15 othersEttinger, D. S., Georgiades, C., Verde, F., Illei, P., Li, Q. K., Baras, A. S., Gabrielson, E., Brock, M. V., Karchin, R., Pardoll, D. M., Baylin, S. B., Brahmer, J. R., Scharpf, R. B., Forde, P. M. & Velculescu, V. E., Jan 1 2020, In: Nature Cancer. 1, 1, p. 99-111 13 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Non-Small Cell Lung Carcinoma 100%
  • Tumor Burden 45%
  • Mutation 44%
  • Immunotherapy 42%
  • Neoplasms 36%
• 2019

  Characterization of genetic subclonal evolution in pancreatic cancer mouse models

  Niknafs, N., Zhong, Y., Moral, J. A., Zhang, L., Shao, M. X., Lo, A., Makohon-Moore, A., Iacobuzio-Donahue, C. A. & Karchin, R., Dec 1 2019, In: Nature communications. 10, 1, 5435.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Molecular Evolution 100%
  • mice 81%
  • tumors 74%
  • Pancreatic Neoplasms 73%
  • cancer 72%

• Dynamics of tumor and immune responses during immune checkpoint blockade in non–small cell lung cancer

  Anagnostou, V., Forde, P. M., White, J. R., Niknafs, N., Hruban, C., Naidoo, J., Marrone, K., Ashok Sivakumar, I. K., Bruhm, D. C., Rosner, S., Phallen, J., Leal, A., Adleff, V., Smith, K. N., Cottrell, T. R., Rhymee, L., Palsgrove, D. N., Hann, C. L., Levy, B., Feliciano, J., & 16 othersGeorgiades, C., Verde, F., Illei, P., Li, Q. K., Gabrielson, E., Brock, M. V., Isbell, J. M., Sauter, J. L., Taube, J., Scharpf, R. B., Karchin, R., Pardoll, D. M., Chaft, J. E., Hellmann, M. D., Brahmer, J. R. & Velculescu, V. E., 2019, In: Cancer Research. 79, 6, p. 1214-1225 12 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Circulating Tumor DNA 100%
  • Non-Small Cell Lung Carcinoma 72%
  • Neoplasms 26%
  • T-Lymphocytes 14%
  • Confidence Intervals 13%
  61 Scopus citations

• Genome-wide cell-free DNA fragmentation in patients with cancer

  Cristiano, S., Leal, A., Phallen, J., Fiksel, J., Adleff, V., Bruhm, D. C., Jensen, S. Ø., Medina, J. E., Hruban, C., White, J. R., Palsgrove, D. N., Niknafs, N., Anagnostou, V., Forde, P., Naidoo, J., Marrone, K., Brahmer, J., Woodward, B. D., Husain, H., van Rooijen, K. L., & 16 othersØrntoft, M. B. W., Madsen, A. H., van de Velde, C. J. H., Verheij, M., Cats, A., Punt, C. J. A., Vink, G. R., van Grieken, N. C. T., Koopman, M., Fijneman, R. J. A., Johansen, J. S., Nielsen, H. J., Meijer, G. A., Andersen, C. L., Scharpf, R. B. & Velculescu, V. E., Jun 20 2019, In: Nature. 570, 7761, p. 385-389 5 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Cell-Free Nucleic Acids 100%
  • DNA Fragmentation 84%
  • Genome 53%
  • Neoplasms 25%
  • Bile Duct Neoplasms 22%
  171 Scopus citations

• Intraductal Papillary Mucinous Neoplasms Arise From Multiple Independent Clones, Each With Distinct Mutations

  Fischer, C. G., Beleva Guthrie, V., Braxton, A. M., Zheng, L., Wang, P., Song, Q., Griffin, J. F., Chianchiano, P. E., Hosoda, W., Niknafs, N., Springer, S., Dal Molin, M., Masica, D., Scharpf, R. B., Thompson, E. D., He, J., Wolfgang, C. L., Hruban, R. H., Roberts, N. J., Lennon, A. M., & 3 othersJiao, Y., Karchin, R. & Wood, L. D., Oct 2019, In: Gastroenterology. 157, 4, p. 1123-1137.e22

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Clone Cells 100%
  • Mutation 70%
  • Neoplasms 40%
  • Carcinogenesis 35%
  • Pancreatic Neoplasms 32%
  24 Scopus citations
• 2018

  A machine learning approach for somatic mutation discovery

  Wood, D. E., White, J. R., Georgiadis, A., Van Emburgh, B., Parpart-Li, S., Mitchell, J., Anagnostou, V., Niknafs, N., Karchin, R., Papp, E., McCord, C., LoVerso, P., Riley, D., Diaz, L. A., Jones, S., Sausen, M., Velculescu, V. E. & Angiuoli, S. V., Sep 5 2018, In: Science translational medicine. 10, 457, aar7939.

  Research output: Contribution to journal › Article › peer-review

  • Machine Learning 100%
  • Mutation 49%
  • Neoplasms 28%
  • Atlases 27%
  • Genome 17%
  25 Scopus citations

• Correction: Whole-genome sequencing of salivary gland adenoid cystic carcinoma (Cancer Prevention Research (2016) 9 (265-274) DOI: 10.1158/1940-6207.CAPR-15-0316)

  Rettig, E. M., Talbot, C. C., Sausen, M., Jones, S., Bishop, J. A., Wood, L. D., Tokheim, C., Niknafs, N., Karchin, R., Fertig, E. J., Wheelan, S. J., Marchionni, L., Considine, M., Ling, S., Fakhry, C., Papadopoulos, N., Kinzler, K. W., Vogelstein, B., Ha, P. K. & Agrawal, N., Apr 2018, In: Cancer Prevention Research. 11, 4, p. 249 1 p.

  Research output: Contribution to journal › Comment/debate › peer-review

  Open Access

  • Conflict of Interest 100%
  • Adenoid Cystic Carcinoma 99%
  • Whole Genome Sequencing 91%
  • Salivary Glands 81%
  • Disclosure 43%

• Ipilimumab plus nivolumab and DNA-repair defects in AR-V7-expressing metastatic prostate cancer

  Boudadi, K., Suzman, D. L., Anagnostou, V., Fu, W., Luber, B., Wang, H., Niknafs, N., White, J. R., Silberstein, J. L., Sullivan, R., Dowling, D., Harb, R., Nirschl, T. R., Veeneman, B. A., Tomlins, S. A., Wang, Y., Jendrisak, A., Graf, R. P., Dittamore, R., Carducci, M. A., & 8 othersEisenberger, M. A., Haffner, M. C., Meeker, A. K., Eshleman, J. R., Luo, J., Velculescu, V. E., Drake, C. G. & Antonarakis, E. S., Jun 19 2018, In: Oncotarget. 9, 47, p. 28561-28571 11 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Ipilimumab 100%
  • Nivolumab 96%
  • DNA Repair 65%
  • Progression-Free Survival 64%
  • Prostatic Neoplasms 56%
  66 Scopus citations

• Pathologic features of response to neoadjuvant anti-PD-1 in resected non-small-cell lung carcinoma: A proposal for quantitative immune-related pathologic response criteria (irPRC)

  Cottrell, T. R., Thompson, E. D., Forde, P. M., Stein, J. E., Duffield, A. S., Anagnostou, V., Rekhtman, N., Anders, R. A., Cuda, J., Illei, P. B., Gabrielson, E., Askin, F. B., Niknafs, N., Smith, K. N., Velez, M. J., Sauter, J. L., Isbell, J. M., Jones, D. R., Battafarano, R. J., Yang, S. C., & 10 othersDanilova, L., Wolchok, J. D., Topalian, S. L., Velculescu, V. E., Pardoll, D. M., Brahmer, J. R., Hellmann, M. D., Chaft, J. E., Cimino-Mathews, A. & Taube, J. M., Aug 2018, In: Annals of Oncology. 29, 8, p. 1853-1860 8 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Residual Neoplasm 100%
  • Non-Small Cell Lung Carcinoma 84%
  • Pathologists 46%
  • Tertiary Lymphoid Structures 39%
  • Nivolumab 32%
  93 Scopus citations
• 2017

  Epigenetic Therapy Ties MYC Depletion to Reversing Immune Evasion and Treating Lung Cancer

  Topper, M. J., Vaz, M., Chiappinelli, K. B., DeStefano Shields, C. E., Niknafs, N., Yen, R. W. C., Wenzel, A., Hicks, J., Ballew, M., Stone, M., Tran, P. T., Zahnow, C. A., Hellmann, M. D., Anagnostou, V., Strissel, P. L., Strick, R., Velculescu, V. E. & Baylin, S. B., Nov 30 2017, In: Cell. 171, 6, p. 1284-1300.e21

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • DNA Methyltransferase Inhibitor 100%
  • Immune Evasion 69%
  • Histone 59%
  • Epigenomics 48%
  • Lung Neoplasms 43%
  153 Scopus citations

• Evolution of neoantigen landscape during immune checkpoint blockade in non-small cell lung cancer

  Anagnostou, V., Smith, K. N., Forde, P. M., Niknafs, N., Bhattacharya, R., White, J., Zhang, T., Adleff, V., Phallen, J., Wali, N., Hruban, C., Guthrie, V. B., Rodgers, K., Naidoo, J., Kang, H., Sharfman, W., Georgiades, C., Verde, F., Illei, P., Li, Q. K., & 9 othersGabrielson, E., Brock, M. V., Zahnow, C. A., Baylin, S. B., Scharpf, R. B., Brahmer, J. R., Karchin, R., Pardoll, D. M. & Velculescu, V. E., Mar 2017, In: Cancer discovery. 7, 3, p. 264-276 13 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Non-Small Cell Lung Carcinoma 100%
  • Neoplasms 36%
  • T-Lymphocytes 34%
  • Mutation 31%
  • T-Cell Antigen Receptor 18%
  391 Scopus citations

• High grade serous ovarian carcinomas originate in the fallopian tube

  Labidi-Galy, S. I., Papp, E., Hallberg, D., Niknafs, N., Adleff, V., Noe, M., Bhattacharya, R., Novak, M., Jones, S., Phallen, J., Hruban, C. A., Hirsch, M. S., Lin, D. I., Schwartz, L., Maire, C. L., Tille, J. C., Bowden, M., Ayhan, A., Wood, L. D., Scharpf, R. B., & 6 othersKurman, R., Wang, T. L., Shih, I. M., Karchin, R., Drapkin, R. & Velculescu, V. E., Dec 1 2017, In: Nature communications. 8, 1, 1093.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Fallopian Tubes 100%
  • grade 80%
  • cancer 77%
  • Carcinoma in Situ 75%
  • Ovarian Neoplasms 60%
  215 Scopus citations

• Matching phenotypes to whole genomes: Lessons learned from four iterations of the personal genome project community challenges

  Cai, B., Li, B., Kiga, N., Thusberg, J., Bergquist, T., Chen, Y. C., Niknafs, N., Carter, H., Tokheim, C., Beleva-Guthrie, V., Douville, C., Bhattacharya, R., Yeo, H. T. G., Fan, J., Sengupta, S., Kim, D., Cline, M., Turner, T., Diekhans, M., Zaucha, J., & 20 othersPal, L. R., Cao, C., Yu, C. H., Yin, Y., Carraro, M., Giollo, M., Ferrari, C., Leonardi, E., Tosatto, S. C. E., Bobe, J., Ball, M., Hoskins, R. A., Repo, S., Church, G., Brenner, S. E., Moult, J., Gough, J., Stanke, M., Karchin, R. & Mooney, S. D., Sep 2017, In: Human mutation. 38, 9, p. 1266-1276 11 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Genome 100%
  • Phenotype 88%
  • Eye Color 28%
  • Whole Genome Sequencing 21%
  • High-Throughput Nucleotide Sequencing 17%
  5 Scopus citations
• 2016

  Exome-scale discovery of hotspot mutation regions in human cancer using 3D protein structure

  Tokheim, C., Bhattacharya, R., Niknafs, N., Gygax, D. M., Kim, R., Ryan, M., Masica, D. L. & Karchin, R., Jul 1 2016, In: Cancer Research. 76, 13, p. 3719-3731 13 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Exome 100%
  • Missense Mutation 64%
  • Mutation 46%
  • Proteins 30%
  • Neoplasms 26%

• Whole genome sequencing defines the genetic heterogeneity of familial pancreatic cancer

  Roberts, N. J., Norris, A. L., Petersen, G. M., Bondy, M. L., Brand, R., Gallinger, S., Kurtz, R. C., Olson, S. H., Rustgi, A. K., Schwartz, A. G., Stoffel, E., Syngal, S., Zogopoulos, G., Ali, S. Z., Axilbund, J., Chaffee, K. G., Chen, Y. C., Cote, M. L., Childs, E., Douville, C., & 25 othersGoes, F. S., Herman, J., Iacobuzio-Donahue, C., Kramer, M., Makohon-Moore, A., McCombie, R. W., McMahon, K. W., Niknafs, N., Parla, J., Pirooznia, M., Potash, J. B., Rhim, A. D., Smith, A. L., Wang, Y., Wolfgang, C., Wood, L. D., Zandi, P. P., Goggins, M., Karchin, R., Eshleman, J. R., Papadopoulos, N., Kinzler, K. W., Vogelstein, B., Hruban, R. H. & Klein, A. P., Feb 2016, In: Cancer discovery. 6, 2, p. 166-175 10 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Genetic Heterogeneity 100%
  • Whole Genome Sequencing 98%
  • Pancreatic Neoplasms 80%
  • Genome 19%
  • Exome 11%
  161 Scopus citations

• Whole-genome sequencing of salivary gland adenoid cystic carcinoma

  Rettig, E. M., Talbot, C. C., Sausen, M., Jones, S., Bishop, J. A., Wood, L. D., Tokheim, C., Niknafs, N., Karchin, R., Fertig, E. J., Wheelan, S. J., Marchionni, L., Considine, M., Fakhry, C., Papadopoulos, N., Kinzler, K. W., Vogelstein, B., Ha, P. K. & Agrawal, N., Apr 2016, In: Cancer Prevention Research. 9, 4, p. 265-274 10 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Adenoid Cystic Carcinoma 100%
  • Whole Genome Sequencing 91%
  • Salivary Glands 81%
  • Neoplasms 25%
  • Genes 13%
  44 Scopus citations
• 2015

  A Combination of Molecular Markers and Clinical Features Improve the Classification of Pancreatic Cysts

  Springer, S., Wang, Y., Dal Molin, M., Masica, D. L., Jiao, Y., Kinde, I., Blackford, A., Raman, S. P., Wolfgang, C. L., Tomita, T., Niknafs, N., Douville, C., Ptak, J., Dobbyn, L., Allen, P. J., Klimstra, D. S., Schattner, M. A., Schmidt, C. M., Yip-Schneider, M., Cummings, O. W., & 47 othersBrand, R. E., Zeh, H. J., Singhi, A. D., Scarpa, A., Salvia, R., Malleo, G., Zamboni, G., Falconi, M., Jang, J. Y., Kim, S. W., Kwon, W., Hong, S. M., Song, K. B., Kim, S. C., Swan, N., Murphy, J., Geoghegan, J., Brugge, W., Fernandez-Del Castillo, C., Mino-Kenudson, M., Schulick, R., Edil, B. H., Adsay, V., Paulino, J., Van Hooft, J., Yachida, S., Nara, S., Hiraoka, N., Yamao, K., Hijioka, S., Van Der Merwe, S., Goggins, M., Canto, M. I., Ahuja, N., Hirose, K., Makary, M., Weiss, M. J., Cameron, J., Pittman, M., Eshleman, J. R., Diaz, L. A., Papadopoulos, N., Kinzler, K. W., Karchin, R., Hruban, R. H., Vogelstein, B. & Lennon, A. M., Nov 2015, In: Gastroenterology. 149, 6, p. 1501-1510 10 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Pancreatic Cyst 100%
  • Biomarkers 44%
  • Cysts 35%
  • Pancreatic Neoplasms 26%
  • Cyst Fluid 18%
  227 Scopus citations

• SubClonal Hierarchy Inference from Somatic Mutations: Automatic Reconstruction of Cancer Evolutionary Trees from Multi-region Next Generation Sequencing

  Niknafs, N., Beleva-Guthrie, V., Naiman, D. Q. & Karchin, R., 2015, In: PLoS computational biology. 11, 10, e1004416.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Evolutionary Tree 100%
  • somatic mutation 92%
  • Sequencing 82%
  • Tumor 73%
  • tumor 72%

• The genomic landscape of response to EGFR blockade in colorectal cancer

  Bertotti, A., Papp, E., Jones, S., Adleff, V., Anagnostou, V., Lupo, B., Sausen, M., Phallen, J., Hruban, C. A., Tokheim, C., Niknafs, N., Nesselbush, M., Lytle, K., Sassi, F., Cottino, F., Migliardi, G., Zanella, E. R., Ribero, D., Russolillo, N., Mellano, A., & 15 othersMuratore, A., Paraluppi, G., Salizzoni, M., Marsoni, S., Kragh, M., Lantto, J., Cassingena, A., Li, Q. K., Karchin, R., Scharpf, R., Sartore-Bianchi, A., Siena, S., Diaz, L. A., Trusolino, L. & Velculescu, V. E., Oct 8 2015, In: Nature. 526, 7572, p. 263-267 5 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • ErbB Receptors 100%
  • Colorectal Neoplasms 83%
  • Neoplasms 24%
  • Transplants 17%
  • Therapeutics 17%
  251 Scopus citations
• 2014

  A Probabilistic Model to Predict Clinical Phenotypic Traits from Genome Sequencing

  Chen, Y. C., Douville, C., Wang, C., Niknafs, N., Yeo, G., Beleva-Guthrie, V., Carter, H., Stenson, P. D., Cooper, D. N., Li, B., Mooney, S. & Karchin, R., Sep 1 2014, In: PLoS computational biology. 10, 9

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • probabilistic models 100%
  • Sequencing 79%
  • Probabilistic Model 75%
  • Statistical Models 74%
  • Genome 73%
  7 Scopus citations
• 2013

  CRAVAT: Cancer-related analysis of variants toolkit

  Douville, C., Carter, H., Kim, R., Niknafs, N., Diekhans, M., Stenson, P. D., Cooper, D. N., Ryan, M. & Karchin, R., Mar 2013, In: Bioinformatics. 29, 5, p. 647-648 2 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Cancer 100%
  • Genes 92%
  • Mutation 82%
  • Sequencing 77%
  • Gene 63%
  80 Scopus citations

• Exome sequencing identifies frequent inactivating mutations in BAP1, ARID1A and PBRM1 in intrahepatic cholangiocarcinomas

  Jiao, Y., Pawlik, T. M., Anders, R. A., Selaru, F. M., Streppel, M. M., Lucas, D. J., Niknafs, N., Guthrie, V. B., Maitra, A., Argani, P., Offerhaus, G. J. A., Roa, J. C., Roberts, L. R., Gores, G. J., Popescu, I., Alexandrescu, S. T., Dima, S., Fassan, M., Simbolo, M., Mafficini, A., & 16 othersCapelli, P., Lawlor, R. T., Ruzzenente, A., Guglielmi, A., Tortora, G., De Braud, F., Scarpa, A., Jarnagin, W., Klimstra, D., Karchin, R., Velculescu, V. E., Hruban, R. H., Vogelstein, B., Kinzler, K. W., Papadopoulos, N. & Wood, L. D., Dec 2013, In: Nature genetics. 45, 12, p. 1470-1473 4 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Exome 100%
  • Cholangiocarcinoma 96%
  • Chromatin Assembly and Disassembly 48%
  • Mutation 46%
  • Genes 33%
  397 Scopus citations

• MuPIT interactive: Webserver for mapping variant positions to annotated, interactive 3D structures

  Niknafs, N., Kim, D., Kim, R., Diekhans, M., Ryan, M., Stenson, P. D., Cooper, D. N. & Karchin, R., Nov 2013, In: Human genetics. 132, 11, p. 1235-1243 9 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Nucleotides 100%
  • Mutation 69%
  • Exome 21%
  • Proteins 19%
  • Atlases 19%

• Mutational signature of aristolochic acid exposure as revealed by whole-exome sequencing

  Hoang, M. L., Chen, C. H., Sidorenko, V. S., He, J., Dickman, K. G., Yun, B. H., Moriya, M., Niknafs, N., Douville, C., Karchin, R., Turesky, R. J., Pu, Y. S., Vogelstein, B., Papadopoulos, N., Grollman, A. P., Kinzler, K. W. & Rosenquist, T. A., Aug 7 2013, In: Science translational medicine. 5, 197, 197ra102.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • aristolochic acid I 100%
  • Whole Exome Sequencing 75%
  • Mutation 15%
  • 2'-deoxyadenosine 13%
  • Neoplasms 11%
  164 Scopus citations