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

Authors: Zheng, Lily, Niknafs, Noushin, Wood, Laura D, Karchin, Rachel, Scharpf, Robert B

Source: Bioinformatics. 38(15):3677-3683

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100161607315.0x000001&indx=1&recIds=ETOCvdc_100161607315.0x000001

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

Authors: Anagnostou, Valsamo, Bruhm, Daniel C., Niknafs, Noushin, White, James R., Shao, Xiaoshan M., Sidhom, John William, Stein, Julie, Tsai, Hua-Ling, Wang, Hao, Belcaid, Zineb, Murray, Joseph, Balan, Archana, Ferreira, Leonardo, Ross-Macdonald, Petra, Wind-Rotolo, Megan, Baras, Alexander S., Taube, Janis, Karchin, Rachel, Scharpf, Robert B., Grasso, Catherine, Ribas, Antoni, Pardoll, Drew M., Topalian, Suzanne L., Velculescu, Victor E.

Source: In Cell Reports Medicine 17 November 2020 1(8)

Tracing the genetic fingerprints of tumour evolution: The pursuit of identifying mutations with differential weights within the overall tumour mutation burden and their role in therapeutic responses with immune checkpoint blockade

Authors: Niknafs, Noushin, Conroy, Michael, Anagnostou, Valsamo

Source: Clinical and translational medicine. 13(6)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100186357285.0x000001&indx=1&recIds=ETOCvdc_100186357285.0x000001

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

Authors: Fischer, Catherine G., Beleva Guthrie, Violeta, Braxton, Alicia M., Zheng, Lily, Wang, Pei, Song, Qianqian, Griffin, James F., Chianchiano, Peter E., Hosoda, Waki, Niknafs, Noushin, Springer, Simeon, Dal Molin, Marco, Masica, David, Scharpf, Robert B., Thompson, Elizabeth D., He, Jin, Wolfgang, Christopher L., Hruban, Ralph H., Roberts, Nicholas J., Lennon, Anne Marie, Jiao, Yuchen, Karchin, Rachel, Wood, Laura D.

Source: In Gastroenterology October 2019 157(4):1123-1137

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

Authors: Anagnostou, Valsamo, Niknafs, Noushin, Marrone, Kristen, Bruhm, Daniel C., White, James R., Naidoo, Jarushka, Hummelink, Karlijn, Monkhorst, Kim, Lalezari, Ferry, Lanis, Mara, Rosner, Samuel, Reuss, Joshua E., Smith, Kellie N., Adleff, Vilmos, Rodgers, Kristen, Belcaid, Zineb, Rhymee, Lamia, Levy, Benjamin, Feliciano, Josephine, Hann, Christine L., Ettinger, David S., Georgiades, Christos, Verde, Franco, Illei, Peter, Li, Qing Kay, Baras, Alexander S., Gabrielson, Edward, Brock, Malcolm V., Karchin, Rachel, Pardoll, Drew M., Baylin, Stephen B., Brahmer, Julie R., Scharpf, Robert B., Forde, Patrick M., Velculescu, Victor E.

Source: Nature cancer. 1(1):99-111

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100126850236.0x000001&indx=1&recIds=ETOCvdc_100126850236.0x000001

Characterization of genetic subclonal evolution in pancreatic cancer mouse models

Authors: Niknafs, Noushin, Zhong, Yi, Moral, John, Zhang, Lance, Shao, Melody, Lo, April, Makohon-Moore, Alvin, Iacobuzio-Donahue, Christine, Karchin, Rachel

Source: Nature communications. 10(1):1-10

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100190908144.0x000001&indx=1&recIds=ETOCvdc_100190908144.0x000001

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

Authors: Cristiano, Stephen, Leal, Alessandro, Phallen, Jillian, Fiksel, Jacob, Adleff, Vilmos, Bruhm, Daniel, Jensen, Sarah, Medina, Jamie, Hruban, Carolyn, White, James, Palsgrove, Doreen, Niknafs, Noushin, Anagnostou, Valsamo, Forde, Patrick, Naidoo, Jarushka, Marrone, Kristen, Brahmer, Julie, Woodward, Brian, Husain, Hatim, Rooijen, Karlijn, Ørntoft, Mai-Britt, Madsen, Anders, Velde, Cornelis, Verheij, Marcel, Cats, Annemieke, Punt, Cornelis, Vink, Geraldine, Grieken, Nicole, Koopman, Miriam, Fijneman, Remond, Johansen, Julia, Nielsen, Hans, Meijer, Gerrit, Andersen, Claus, Scharpf, Robert, Velculescu, Victor

Source: Nature. 570(7761):385-389

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100181211215.0x000001&indx=1&recIds=ETOCvdc_100181211215.0x000001

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

Authors: Topper, Michael J., Vaz, Michelle, Chiappinelli, Katherine B., DeStefano Shields, Christina E., Niknafs, Noushin, Yen, Ray-Whay Chiu, Wenzel, Alyssa, Hicks, Jessica, Ballew, Matthew, Stone, Meredith, Tran, Phuoc T., Zahnow, Cynthia A., Hellmann, Matthew D., Anagnostou, Valsamo, Strissel, Pamela L., Strick, Reiner, Velculescu, Victor E., Baylin, Stephen B.

Source: In Cell 30 November 2017 171(6):1284-1300

3D genomic mapping reveals multifocality of human pancreatic precancers.

Authors: Braxton, Alicia M., Kiemen, Ashley L., Grahn, Mia P., Forjaz, André, Parksong, Jeeun, Mahesh Babu, Jaanvi, Lai, Jiaying, Zheng, Lily, Niknafs, Noushin, Jiang, Liping, Cheng, Haixia, Song, Qianqian, Reichel, Rebecca, Graham, Sarah, Damanakis, Alexander I., Fischer, Catherine G., Mou, Stephanie, Metz, Cameron, Granger, Julie, Liu, Xiao-Ding

Source: Nature; May2024, Vol. 629 Issue 8012, p679-687, 9p

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

Authors: Annapragada, Akshaya V., Niknafs, Noushin, White, James R., Bruhm, Daniel C., Cherry, Christopher, Medina, Jamie E., Adleff, Vilmos, Hruban, Carolyn, Mathios, Dimitrios, Foda, Zachariah H., Phallen, Jillian, Scharpf, Robert B., Velculescu, Victor E.

Source: Science Translational Medicine; 3/13/2024, Vol. 16 Issue 738, p1-18, 18p

Subject Terms: CELL-free DNA, CIRCULATING tumor DNA, MACHINE learning, WHOLE genome sequencing, FRAGMENTED landscapes, EARLY diagnosis, PROSTATE cancer, THYROID cancer

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

Authors: Springer, Simeon, Wang, Yuxuan, Dal Molin, Marco, Masica, David L., Jiao, Yuchen, Kinde, Isaac, Blackford, Amanda, Raman, Siva P., Wolfgang, Christopher L., Tomita, Tyler, Niknafs, Noushin, Douville, Christopher, Ptak, Janine, Dobbyn, Lisa, Allen, Peter J., Klimstra, David S., Schattner, Mark A., Schmidt, C. Max, Yip-Schneider, Michele, Cummings, Oscar W., Brand, Randall E., Zeh, Herbert J., Singhi, Aatur D., Scarpa, Aldo, Salvia, Roberto, Malleo, Giuseppe, Zamboni, Giuseppe, Falconi, Massimo, Jang, Jin-Young, Kim, Sun-Whe, Kwon, Wooil, Hong, Seung-Mo, Song, Ki-Byung, Kim, Song Cheol, Swan, Niall, Murphy, Jean, Geoghegan, Justin, Brugge, William, Fernandez-Del Castillo, Carlos, Mino-Kenudson, Mari, Schulick, Richard, Edil, Barish H., Adsay, Volkan, Paulino, Jorge, van Hooft, Jeanin, Yachida, Shinichi, Nara, Satoshi, Hiraoka, Nobuyoshi, Yamao, Kenji, Hijioka, Susuma, van der Merwe, Schalk, Goggins, Michael, Canto, Marcia Irene, Ahuja, Nita, Hirose, Kenzo, Makary, Martin, Weiss, Matthew J., Cameron, John, Pittman, Meredith, Eshleman, James R., Diaz, Luis A., Jr., Papadopoulos, Nickolas, Kinzler, Kenneth W., Karchin, Rachel, Hruban, Ralph H., Vogelstein, Bert, Lennon, Anne Marie

Source: In Gastroenterology November 2015 149(6):1501-1510

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

Authors: Cai, Binghuang, Li, Biao, Kiga, Nikki, Thusberg, Janita, Bergquist, Timothy, Chen, Yun‐Ching, Niknafs, Noushin, Carter, Hannah, Tokheim, Collin, Beleva‐Guthrie, Violeta, Douville, Christopher, Bhattacharya, Rohit, Yeo, Hui Ting Grace, Fan, Jean, Sengupta, Sohini, Kim, Dewey, Cline, Melissa, Turner, Tychele, Diekhans, Mark, Zaucha, Jan, Pal, Lipika R., Cao, Chen, Yu, Chen‐Hsin, Yin, Yizhou, Carraro, Marco, Giollo, Manuel, Ferrari, Carlo, Leonardi, Emanuela, Tosatto, Silvio C.E., Bobe, Jason, Ball, Madeleine, Hoskins, Roger A., Repo, Susanna, Church, George, Brenner, Steven E., Moult, John, Gough, Julian, Stanke, Mario, Karchin, Rachel, Mooney, Sean D.

Source: Human mutation. 38(9):1266-1276

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100089398594.0x000001&indx=1&recIds=ETOCvdc_100089398594.0x000001

Genomic characterization of malignant progression in neoplastic pancreatic cysts

Authors: Noë, Michaël, Niknafs, Noushin, Fischer, Catherine G., Hackeng, Wenzel M., Beleva Guthrie, Violeta, Hosoda, Waki, Debeljak, Marija, Papp, Eniko, Adleff, Vilmos, White, James R., Luchini, Claudio, Pea, Antonio, Scarpa, Aldo, Butturini, Giovanni, Zamboni, Giuseppe, Castelli, Paola, Hong, Seung-Mo, Yachida, Shinichi, Hiraoka, Nobuyoshi, Gill, Anthony J., Samra, Jaswinder S., Offerhaus, G. Johan A., Hoorens, Anne, Verheij, Joanne, Jansen, Casper, Adsay, N. Volkan, Jiang, Wei, Winter, Jordan, Albores-Saavedra, Jorge, Terris, Benoit, Thompson, Elizabeth D., Roberts, Nicholas J., Hruban, Ralph H., Karchin, Rachel, Scharpf, Robert B., Brosens, Lodewijk A. A., Velculescu, Victor E., Wood, Laura D.

Source: Nature communications. 11(1)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100176334964.0x000001&indx=1&recIds=ETOCvdc_100176334964.0x000001

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

Authors: Anagnostou, Valsamo, Ho, Cheryl, Nicholas, Garth, Juergens, Rosalyn Anne, Sacher, Adrian, Fung, Andrea S., Wheatley-Price, Paul, Laurie, Scott A., Levy, Benjamin, Brahmer, Julie R., Balan, Archana, Niknafs, Noushin, Avrutin, Egor, Zhu, Liting, Sausen, Mark, Bradbury, Penelope A., O’Donnell-Tormey, Jill, Gaudreau, Pierre Olivier, Ding, Keyue, Dancey, Janet

Source: Nature Medicine; October 2023, Vol. 29 Issue: 10 p2559-2569, 11p

10. HLA class II Immunogenic Mutation Burden predicts response to immune checkpoint blockade

Authors: Shao, Xiaoshan, Huang, Justin, Niknafs, Noushin, Balan, Archana, Cherry, Christopher, White, James, Velculescu, Victor, Anagnostou, Valsamo, Karchin, Rachel

Source: Cancer genetics. 268(S1):4-4

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100176329109.0x000001&indx=1&recIds=ETOCvdc_100176329109.0x000001

Persistent mutation burden drives sustained anti-tumor immune responses

Authors: Niknafs, Noushin, Balan, Archana, Cherry, Christopher, Hummelink, Karlijn, Monkhorst, Kim, Shao, Xiaoshan M., Belcaid, Zineb, Marrone, Kristen A., Murray, Joseph, Smith, Kellie N., Levy, Benjamin, Feliciano, Josephine, Hann, Christine L., Lam, Vincent, Pardoll, Drew M., Karchin, Rachel, Seiwert, Tanguy Y., Brahmer, Julie R., Forde, Patrick M., Velculescu, Victor E., Anagnostou, Valsamo

Source: Nature Medicine; February 2023, Vol. 29 Issue: 2 p440-449, 10p

Early detection of lung cancer using cfDNA fragmentation.

Authors: Mathios, Dimitrios, Johansen, Jakob Sidenius, Cristiano, Stephen, Medina, Jamie, Phallen, Jillian, Richter Larsen, Klaus, Bruhm, Daniel, Niknafs, Noushin, Nielsen, Hans J., Meijer, Gerrit A., Andersen, Claus Lindbjerg, Bojesen, Stig Egil, Scharpf, Robert, Velculescu, Victor E.

Source: Journal of clinical oncology. 39(15 suppl):8519-8519

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100173217733.0x000001&indx=1&recIds=ETOCvdc_100173217733.0x000001

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

Authors: Scott, Susan C., Shao, Xiaoshan M., Niknafs, Noushin, Balan, Archana, Pereira, Gavin, Marrone, Kristen A., Lam, Vincent K., Murray, Joseph C., Feliciano, Josephine L., Levy, Benjamin P., Ettinger, David S., Hann, Christine L., Brahmer, Julie R., Forde, Patrick M., Karchin, Rachel, Naidoo, Jarushka, Anagnostou, Valsamo

Source: Frontiers in Oncology; 8/3/2022, Vol. 12, p1-12, 12p

Subject Terms: IMMUNE checkpoint proteins, NON-small-cell lung carcinoma, SEXUAL dimorphism, IMMUNE response, IMMUNE checkpoint inhibitors

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

Authors: Niknafs, Noushin¹, Beleva-Guthrie, Violeta¹, Naiman, Daniel Q.², Karchin, Rachel^1,3 karchin@jhu.edu

Source: PLoS Computational Biology. 10/5/2015, Vol. 11 Issue 10, p1-26. 26p. 4 Diagrams, 2 Charts, 2 Graphs.

Subject Terms: *SOMATIC mutation, *GENETIC mutation, *CANCER relapse, *NUCLEOTIDE sequence, *PHYSIOLOGY

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

Authors: Mathios, Dimitrios, Johansen, Jakob Sidenius, Cristiano, Stephen, Medina, Jamie E., Phallen, Jillian, Larsen, Klaus R., Bruhm, Daniel C., Niknafs, Noushin, Ferreira, Leonardo, Adleff, Vilmos, Chiao, Jia Yuee, Leal, Alessandro, Noe, Michael, White, James R., Arun, Adith S., Hruban, Carolyn, Annapragada, Akshaya V., Jensen, Sarah Østrup, Ørntoft, Mai-Britt Worm, Madsen, Anders Husted

Source: Nature Communications; 8/20/2021, Vol. 12 Issue 1, p1-14, 14p

Subject Terms: LUNG cancer, CELL-free DNA, SMALL cell lung cancer, NON-small-cell lung carcinoma, COMPUTED tomography, CIRCULATING tumor DNA