Cancer Institute of New Jersey (CINJ), Division of Molecular Oncology

Research Output

2020

All-FIT: Allele-frequency-based imputation of tumor purity from high-depth sequencing data

Loh, J. W., Guccione, C., DI Clemente, F., Riedlinger, G., Ganesan, S. & Khiabanian, H., Apr 1 2020, In : Bioinformatics. 36, 7, p. 2173-2180 8 p.

Research output: Contribution to journalArticle

Biomarkers for Response to Immune Checkpoint Blockade

Ganesan, S. & Mehnert, J., Mar 4 2020, In : Annual Review of Cancer Biology. 4, p. 331-351 21 p.

Research output: Contribution to journalReview article

Open Access

Immunohistochemical analysis of adipokine and adipokine receptor expression in the breast tumor microenvironment: Associations of lower leptin receptor expression with estrogen receptor-negative status and triple-negative subtype

Llanos, A. A. M., Lin, Y., Chen, W., Yao, S., Norin, J., Chekmareva, M. A., Omene, C., Cong, L., Omilian, A. R., Khoury, T., Hong, C. C., Ganesan, S., Foran, D. J., Higgins, M., Ambrosone, C. B., Bandera, E. V. & Demissie, K., Feb 11 2020, In : Breast Cancer Research. 22, 1, 18.

Research output: Contribution to journalArticle

Open Access

The Pan-Cancer Landscape of Coamplification of the Tyrosine Kinases KIT, KDR, and PDGFRA

Disel, U., Madison, R., Abhishek, K., Chung, J. H., Trabucco, S. E., Matos, A. O., Frampton, G. M., Albacker, L. A., Reddy, V., Karadurmus, N., Benson, A., Webster, J., Paydas, S., Cabanillas, R., Nangia, C., Ozturk, M. A., Millis, S. Z., Pal, S. K., Wilky, B., Sokol, E. S. & 14 others, Gay, L. M., Soman, S., Ganesan, S., Janeway, K., Stephens, P. J., Zhu, V. W., Ou, S. H. I., Lovly, C. M., Gounder, M., Schrock, A. B., Ross, J. S., Miller, V. A., Klempner, S. J. & Ali, S. M., Jan 1 2020, In : Oncologist. 25, 1, p. e39-e47

Research output: Contribution to journalArticle

Open Access
2019
4 Scopus citations

A Quasi Birth-and-Death model for tumor recurrence

Santana, L. M., Ganesan, S. & Bhanot, G., Nov 7 2019, In : Journal of Theoretical Biology. 480, p. 175-191 17 p.

Research output: Contribution to journalArticle

Association of JAK2 -V617F Mutations Detected by Solid Tumor Sequencing with Coexistent Myeloproliferative Neoplasms

Riedlinger, G., Hadigol, M., Khiabanian, H. & Ganesan, S., Feb 2019, In : JAMA Oncology. 5, 2, p. 265-267 3 p.

Research output: Contribution to journalLetter

4 Scopus citations

Hodgkin lymphoma and cutaneous T-cell lymphoma sharing the PCM1-JAK2 fusion and a common T-cell clone

Riedlinger, G. M., Chojecki, A., Aviv, H., Weissmann, D., Joshi, S., Murphy, S. M., Hirshfield, K. M. & Ganesan, S., Jan 1 2019, In : JCO Precision Oncology. 3

Research output: Contribution to journalArticle

New Biomarker to Guide Cancer Immunotherapy

Ganesan, S., Bhanot, G., Panda, A., Rathmell, W. K. & de Cubas, A., Dec 2019

Research output: Innovation

PALB2 connects BRCA1 and BRCA2 in the G2/M checkpoint response

Simhadri, S., Vincelli, G., Huo, Y., Misenko, S., Foo, T. K., Ahlskog, J., Sørensen, C. S., Oakley, G. G., Ganesan, S., Bunting, S. F. & Xia, B., Mar 7 2019, In : Oncogene. 38, 10, p. 1585-1596 12 p.

Research output: Contribution to journalArticle

4 Scopus citations

Therapeutic targeting of BRCA1 and TP53 mutant breast cancer through mutant p53 reactivation

Na, B., Yu, X., Withers, T., Gilleran, J., Yao, M., Foo, T. K., Chen, C., Moore, D., Lin, Y., Kimball, S. D., Xia, B., Ganesan, S. & Carpizo, D. R., Dec 1 2019, In : npj Breast Cancer. 5, 1, 14.

Research output: Contribution to journalArticle

Open Access
2018

BRAF in lung cancers: Analysis of patient cases reveals recurrent BRAF mutations, fusions, kinase duplications, and concurrent alterations

Sheikine, Y., Pavlick, D., Klempner, S. J., Trabucco, S. E., Chung, J. H., Rosenzweig, M., Wang, K., Velcheti, V., Frampton, G. M., Peled, N., Murray, M., Chae, Y. K., Albacker, L. A., Gay, L., Husain, H., Suh, J. H., Millis, S. Z., Reddy, V. P., Elvin, J. A., Hartmaier, R. J. & 9 others, Dowlati, A., Stephens, P., Ross, J. S., Bivona, T. G., Miller, V. A., Ganesan, S., Schrock, A. B., Ou, S. H. I. & Ali, S. M., Jan 1 2018, In : JCO Precision Oncology. 2

Research output: Contribution to journalArticle

Comprehensive genomic profiling AIDS in treatment of a metastatic endometrial cancer

Dhami, J., Hirshfield, K. M., Ganesan, S., Hellmann, M., Rojas, V., Amorosa, J. K., Riedlinger, G. M., Zhong, H., Ali, S. M., Pavlick, D., Elvin, J. A. & Rodriguez-Rodriguez, L., Apr 2018, In : Cold Spring Harbor Molecular Case Studies. 4, 2, a002089.

Research output: Contribution to journalArticle

Detection of clonal hematopoiesis of indeterminate potential in clinical sequencing of solid tumor specimens

Severson, E. A., Riedlinger, G. M., Connelly, C. F., Vergilio, J. A., Goldfinger, M., Ramkissoon, S., Frampton, G. M., Ross, J. S., Fratella-Calabrese, A., Gay, L., Ali, S., Miller, V., Elvin, J., Hadigol, M., Hirshfield, K. M., Rodriguez-Rodriguez, L., Ganesan, S. & Khiabanian, H., May 31 2018, In : Blood. 131, 22, p. 2501-2505 5 p.

Research output: Contribution to journalLetter

16 Scopus citations

Endogenous retroviral signatures predict immunotherapy response in clear cell renal cell carcinoma

Smith, C. C., Beckermann, K. E., Bortone, D. S., Cubas, A. A., Bixby, L. M., Lee, S. J., Panda, A., Ganesan, S., Bhanot, G., Wallen, E. M., Milowsky, M. I., Kim, W. Y., Rathmell, K., Swanstrom, R., Parker, J. S., Serody, J. S., Selitsky, S. R. & Vincent, B. G., Nov 1 2018, In : Journal of Clinical Investigation. 128, 11, p. 4804-4820 17 p.

Research output: Contribution to journalArticle

24 Scopus citations

Endogenous retrovirus expression is associated with response to immune checkpoint blockade in clear cell renal cell carcinoma

Panda, A., de Cubas, A. A., Stein, M., Riedlinger, G., Kra, J., Mayer, T., Smith, C. C., Vincent, B. G., Serody, J. S., Beckermann, K. E., Ganesan, S., Bhanot, G. & Rathmell, W. K., Aug 23 2018, In : JCI Insight. 3, 16

Research output: Contribution to journalArticle

16 Scopus citations

Evidence of intertissue differences in the DNA damage response and the pro-oncogenic role of NF-kB in mice with disengaged BRCA1–PALB2 interaction

Mahdi, A. H., Huo, Y., Tan, Y., Simhadri, S., Vincelli, G., Gao, J., Ganesan, S. & Xia, B., Jul 15 2018, In : Cancer Research. 78, 14, p. 3969-3981 13 p.

Research output: Contribution to journalArticle

2 Scopus citations

High-throughput adaptive sampling for whole-slide histopathology image analysis (HASHI) via convolutional neural networks: Application to invasive breast cancer detection

Cruz-Roa, A., Gilmore, H., Basavanhally, A., Feldman, M., Ganesan, S., Shih, N., Tomaszewski, J., Madabhushi, A. & González, F., May 2018, In : PloS one. 13, 5, e0196828.

Research output: Contribution to journalArticle

18 Scopus citations

Immune activation and benefit from avelumab in EBV-positive gastric cancer

Panda, A., Mehnert, J., Hirshfield, K., Riedlinger, G., Damare, S., Saunders, T., Kane, M., Sokol, L., Stein, M., Poplin, E., Rodriguez-Rodriguez, L., Silk, A., Aisner, J., Chan, N., Malhotra, J., Frankel, M., Kaufman, H. L., Ali, S., Ross, J. S., White, E. P. & 2 others, Bhanot, G. & Ganesan, S., Mar 1 2018, In : Journal of the National Cancer Institute. 110, 3, p. 316-320 5 p.

Research output: Contribution to journalArticle

32 Scopus citations

Inference of germline mutational status and evaluation of loss of heterozygosity in high-depth, tumor-only sequencing data

Khiabanian, H., Hirshfield, K. M., Goldfinger, M., Bird, S., Stein, M., Aisner, J., Toppmeyer, D., Wong, S., Chan, N., Dhar, K., Gheeya, J., Vig, H., Hadigol, M., Pavlick, D., Ansari, S., Ali, S., Xia, B., Rodriguez-Rodriguez, L. & Ganesan, S., Jan 1 2018, In : JCO Precision Oncology. 2

Research output: Contribution to journalArticle

Multiple primary malignancies in patients with anal squamous cell carcinoma

Li, D., Yegya-Raman, N., Kim, S., Ganesan, S., Sayan, M., August, D., Spencer, K., Hathout, L., Maloney-Patel, N., Malhotra, U., Yue, N. J. & Jabbour, S. K., Oct 1 2018, In : Journal of Gastrointestinal Oncology. 9, 5, p. 853-857 5 p.

Research output: Contribution to journalArticle

Nuclear shape and orientation features from H&E images predict survival in early-stage estrogen receptor-positive breast cancers

Lu, C., Romo-Bucheli, D., Wang, X., Janowczyk, A., Ganesan, S., Gilmore, H., Rimm, D. & Madabhushi, A., Nov 1 2018, In : Laboratory Investigation. 98, 11, p. 1438-1448 11 p.

Research output: Contribution to journalArticle

14 Scopus citations

Quantitative nuclear histomorphometry predicts oncotype DX risk categories for early stage ER+ breast cancer

Whitney, J., Corredor, G., Janowczyk, A., Ganesan, S., Doyle, S., Tomaszewski, J., Feldman, M., Gilmore, H. & Madabhushi, A., May 30 2018, In : BMC cancer. 18, 1, 610.

Research output: Contribution to journalArticle

7 Scopus citations

RET rearrangements are actionable alterations in breast cancer

Paratala, B. S., Chung, J. H., Williams, C. B., Yilmazel, B., Petrosky, W., Williams, K., Schrock, A. B., Gay, L. M., Lee, E., Dolfi, S. C., Pham, K., Lin, S., Yao, M., Kulkarni, A., DiClemente, F., Liu, C., Rodriguez-Rodriguez, L., Ganesan, S., Ross, J. S., Ali, S. M. & 2 others, Leyland-Jones, B. & Hirshfield, K. M., Dec 1 2018, In : Nature communications. 9, 1, 4821.

Research output: Contribution to journalArticle

10 Scopus citations
2017

Accurate and reproducible invasive breast cancer detection in whole-slide images: A Deep Learning approach for quantifying tumor extent

Cruz-Roa, A., Gilmore, H., Basavanhally, A., Feldman, M., Ganesan, S., Shih, N. N. C., Tomaszewski, J., González, F. A. & Madabhushi, A., Apr 18 2017, In : Scientific reports. 7, 46450.

Research output: Contribution to journalArticle

109 Scopus citations

BRAF fusion as a novel mechanism of acquired resistance to vemurafenib in BRAFV600E mutant melanoma

Kulkarni, A., Al-Hraishawi, H., Simhadri, S., Hirshfield, K. M., Chen, S., Pine, S., Jeyamohan, C., Sokol, L., Ali, S., Teo, M. L., White, E., Rodriguez-Rodriguez, L., Mehnert, J. M. & Ganesan, S., Sep 15 2017, In : Clinical Cancer Research. 23, 18, p. 5631-5638 8 p.

Research output: Contribution to journalArticle

23 Scopus citations

Comprehensive genomic profiling of malignant phyllodes tumors of the breast

Nozad, S., Sheehan, C. E., Gay, L. M., Elvin, J. A., Vergilio, J. A., Suh, J., Ramkissoon, S., Schrock, A. B., Hirshfield, K., Ali, N., Ganesan, S., Ali, S. M., Miller, V. A., Stephens, P. J., Ross, J. S. & Chung, J. H., Apr 1 2017, In : Breast Cancer Research and Treatment. 162, 3, p. 597-602 6 p.

Research output: Contribution to journalArticle

13 Scopus citations

Functional and mutational landscapes of BRCA1 for homology-directed repair and therapy resistance

Anantha, R. W., Simhadri, S., Foo, T. K., Miao, S., Liu, J., Shen, Z., Ganesan, S. & Xia, B., Apr 11 2017, In : eLife. 6, e21350.

Research output: Contribution to journalArticle

22 Scopus citations

Hybrid capture-based genomic profiling of circulating tumor DNA from patients with estrogen receptor-positive metastatic breast cancer

Chung, J. H., Pavlick, D., Hartmaier, R., Schrock, A. B., Young, L., Forcier, B., Ye, P., Levin, M. K., Goldberg, M., Burris, H., Gay, L. M., Hoffman, A. D., Stephens, P. J., Frampton, G. M., Lipson, D. M., Nguyen, D. M., Ganesan, S., Park, B. H., Vahdat, L. T., Leyland-Jones, B. & 6 others, Mughal, T. I., Pusztai, L., O'Shaughnessy, J., Miller, V. A., Ross, J. S. & Ali, S. M., Jan 1 2017, In : Annals of Oncology. 28, 11, p. 2866-2873 8 p.

Research output: Contribution to journalArticle

35 Scopus citations

Identifying a clinically applicable mutational burden threshold as a potential biomarker of response to immune checkpoint therapy in solid tumors

Panda, A., Betigeri, A., Subramanian, K., Ross, J. S., Pavlick, D. C., Ali, S., Markowski, P., Silk, A., Kaufman, H. L., Lattime, E., Mehnert, J. M., Sullivan, R., Lovly, C. M., Sosman, J., Johnson, D. B., Bhanot, G. & Ganesan, S., Jan 1 2017, In : JCO Precision Oncology. 2017, 1, p. 1-13 13 p.

Research output: Contribution to journalArticle

Looking beyond drivers and passengers in cancer genome sequencing data

De, S. & Ganesan, S., May 2017, In : Annals of Oncology. 28, 5, p. 938-945 8 p.

Research output: Contribution to journalReview article

9 Scopus citations

Nuclear topology modulates the mutational landscapes of cancer genomes

Smith, K. S., Liu, L. L., Ganesan, S., Michor, F. & De, S., Nov 1 2017, In : Nature Structural and Molecular Biology. 24, 11, p. 1000-1006 7 p.

Research output: Contribution to journalArticle

13 Scopus citations

Patient-derived xenograft models of non-small cell lung cancer and their potential utility in personalized medicine

Morgan, K. M., Riedlinger, G. M., Rosenfeld, J., Ganesan, S. & Pine, S. R., Jan 19 2017, In : Frontiers in Oncology. 7, JAN, 2.

Research output: Contribution to journalArticle

18 Scopus citations

Protein-lysine methyltransferases G9a and GLP1 promote responses to DNA damage

Ginjala, V., Rodriguez-Colon, L., Ganguly, B., Gangidi, P., Gallina, P., Al-Hraishawi, H., Kulkarni, A., Tang, J., Gheeya, J., Simhadri, S., Yao, M., Xia, B. & Ganesan, S., Dec 1 2017, In : Scientific reports. 7, 1, 16613.

Research output: Contribution to journalArticle

4 Scopus citations

Regulation of spindle integrity and mitotic fidelity by BCCIP

Huhn, S. C., Liu, J., Ye, C., Lu, H., Jiang, X., Feng, X., Ganesan, S., White, E. & Shen, Z., Apr 10 2017, (Accepted/In press) In : Oncogene.

Research output: Contribution to journalArticle

5 Scopus citations

Riluzole exerts distinct antitumor effects from a metabotropic glutamate receptor 1-specific inhibitor on breast cancer cells

Dolfi, S. C., Medina, D. J., Kareddula, A., Paratala, B., Rose, A., Dhami, J., Chen, S., Ganesan, S., Mackay, G., Vazquez, A. & Hirshfield, K. M., Jan 1 2017, In : Oncotarget. 8, 27, p. 44639-44653 15 p.

Research output: Contribution to journalArticle

3 Scopus citations

Roadmap to a comprehensive clinical data warehouse for precision medicine applications in oncology

Foran, D. J., Chen, W., Chu, H., Sadimin, E., Loh, D., Riedlinger, G., Goodell, L. A., Ganesan, S., Hirshfield, K., Rodriguez, L. & Dipaola, R. S., Mar 2 2017, In : Cancer Informatics. 16, 1176935117694349.

Research output: Contribution to journalArticle

7 Scopus citations

Roles of BCCIP deficiency in mammary tumorigenesis

Droz-Rosario, R., Lu, H., Liu, J., Liu, N. A., Ganesan, S., Xia, B., Haffty, B. & Shen, Z., Oct 18 2017, In : Breast Cancer Research. 19, 1

Research output: Contribution to journalArticle

1 Scopus citations

Surveillance nanotechnology for multi-organ cancer metastases

Kantamneni, H., Zevon, M., Donzanti, M. J., Zhao, X., Sheng, Y., Barkund, S. R., McCabe, L. H., Banach-Petrosky, W., Higgins, L. M., Ganesan, S., Riman, R., Roth, C., Tan, M. C., Pierce, M., Ganapathy, V. & Moghe, P., Dec 1 2017, In : Nature biomedical engineering. 1, 12, p. 993-1003 11 p.

Research output: Contribution to journalArticle

13 Scopus citations

The DNA repair function of CUX1 contributes to radioresistance

Ramdzan, Z. M., Ginjala, V., Pinder, J. B., Chung, D., Donovan, C. M., Kaur, S., Leduy, L., Dellaire, G., Ganesan, S. & Nepveu, A., Jan 1 2017, In : Oncotarget. 8, 12, p. 19021-19038 18 p.

Research output: Contribution to journalArticle

5 Scopus citations

Widespread alternative exon usage in clinically distinct subtypes of Invasive Ductal Carcinoma

Bjørklund, S. S., Panda, A., Kumar, S., Seiler, M., Robinson, D., Gheeya, J., Yao, M., Alnæs, G. I. G., Toppmeyer, D., Riis, M., Naume, B., Børresen-Dale, A. L., Kristensen, V. N., Ganesan, S. & Bhanot, G., Dec 1 2017, In : Scientific reports. 7, 1, 5568.

Research output: Contribution to journalArticle

9 Scopus citations
2016

A novel role of chromodomain protein CBX8 in DNA damage response

Oza, J., Ganguly, B., Kulkarni, A., Ginjala, V., Yao, M. & Ganesan, S., Oct 28 2016, In : Journal of Biological Chemistry. 291, 44, p. 22881-22893 13 p.

Research output: Contribution to journalArticle

5 Scopus citations
30 Scopus citations

Clinical actionability of comprehensive genomic profiling for management of rare or refractory cancers

Hirshfield, K., Tolkunov, D., Zhong, H., Ali, S. M., Stein, M., Murphy, S., Vig, H., Vazquez, A., Glod, J., Moss, R. A., Belyi, V., Chan, C., Chen, S., Goodell, L., Foran, D., Yelensky, R., Palma, N. A., Sun, J. X., Miller, V. A., Stephens, P. J. & 10 others, Ross, J. S., Kaufman, H., Poplin, E., Mehnert, J., Tan, A. R., Bertino, J., Aisner, J., DiPaola, R. S., Rodriguez-Rodriguez, L. & Ganesan, S., Nov 2016, In : Oncologist. 21, 11, p. 1315-1325 11 p.

Research output: Contribution to journalArticle

33 Scopus citations

Comprehensive genomic profiling identifies a subset of Crizotinib- responsive ALK-rearranged non-small cell lung cancer not detected by fluorescence in situ hybridization

Ali, S. M., Hensing, T., Schrock, A. B., Allen, J., Sanford, E., Gowen, K., Kulkarni, A., He, J., Suh, J. H., Lipson, D., Elvin, J. A., Yelensky, R., Chalmers, Z., Chmielecki, J., Peled, N., Klempner, S. J., Firozvi, K., Frampton, G. M., Molina, J. R., Amenon, S. & 14 others, Brahmer, J. R., MacMahon, H., Nowak, J., Ignatius Ou, S. H., Zauderer, M., Ladanyi, M., Zakowski, M., Fischbach, N., Ross, J. S., Stephens, P. J., Miller, V. A., Wakelee, H., Ganesan, S. & Salgia, R., Jun 2016, In : Oncologist. 21, 6, p. 762-770 9 p.

Research output: Contribution to journalArticle

65 Scopus citations

Immune activation and response to pembrolizumab in POLE-mutant endometrial cancer

Mehnert, J. M., Panda, A., Zhong, H., Hirshfield, K., Damare, S., Lane, K., Sokol, L., Stein, M. N., Rodriguez-Rodriquez, L., Kaufman, H. L., Ali, S., Ross, J. S., Pavlick, D. C., Bhanot, G., White, E. P., DiPaola, R. S., Lovell, A., Cheng, J. & Ganesan, S., Jun 1 2016, In : Journal of Clinical Investigation. 126, 6, p. 2334-2340 7 p.

Research output: Contribution to journalArticle

140 Scopus citations
45 Scopus citations

Next-generation sequencing based testing for breast cancer

Ganesan, S. & Hirshfield, K. M., Jan 1 2016, Molecular Pathology of Breast Cancer. Springer International Publishing, p. 299-328 30 p.

Research output: Chapter in Book/Report/Conference proceedingChapter