Clinical Use of Liquid-Based Comprehensive Genomic Profiling in Gastrointestinal Stromal Tumors

Authors: Mechahougui, Hiba ^a, Hildebrand, Lindsey ^b, Haberberger, James ^c, Sivakumar, Smruthy ^c, Saiji, Essia ^a, Tukachinsky, Hanna ^c, Madison, Russell ^c, Killian, Jonathan K. ^c, Huang, Richard S.P. ^c, Elvin, Julia A. ^c, Marks, Eric ^b, Heinrich, Michael C. ^{d, e}, Koessler, Thibaud ^a, Lin, Douglas I. ^{c, ∗}

Source: In Laboratory Investigation May 2025 105(5)

Putting comprehensive genomic profiling of ctDNA to work: 10 proposed use cases

Authors: Desai, Aakash, Pasquina, Lincoln W., Nulsen, Candice, Keller-Evans, Rachel B., Mata, Douglas A., Tukachinsky, Hanna, Oxnard, Geoffrey R.

Source: In The Journal of Liquid Biopsy June 2024 4

Real-World comprehensive genomic profiling data for diagnostic clarity in pulmonary Large-Cell neuroendocrine carcinoma

Authors: Burns, Laura, Tukachinsky, Hanna, Raskina, Kira, Huang, Richard S.P., Schrock, Alexa B., Sands, Jacob, Kulke, Matthew H., Oxnard, Geoffrey R., Tapan, Umit

Source: In Lung Cancer February 2024 188

Validity and utility of blood tumor mutational burden (bTMB) is dependent on circulating tumor DNA (ctDNA) shed: SCRUM-Japan MONSTAR-SCREEN

Authors: Mishima, Saori, Nakamura, Yoshiaki, Tukachinsky, Hanna, Taniguchi, Hiroya, Kadowaki, Shigenori, Kato, Ken, Oki, Eiji, Satoh, Taroh, Aoki, Daisuke, Yamazaki, Kentaro, Esaki, Taito, Ueno, Makoto, Nishina, Tomohiro, Sunakawa, Yu, Denda, Tadamichi, Bando, Hideaki, Kuramoto, Naomi, Horasawa, Satoshi, Abutani, Hikaru, Lee, Jessica K., Madison, Russell W., Oxnard, Geoffrey R., Yoshino, Takayuki

Source: In The Journal of Liquid Biopsy September 2023 1

Activating IGF1R hotspot non-frameshift insertions define a novel, potentially targetable molecular subtype of adenoid cystic carcinoma

Authors: Margolis, Matthew, Janovitz, Tyler, Laird, Jason, Mata, Douglas A., Montesion, Meagan, Lee, Jessica K., Madison, Russell W., Schrock, Alexa B., Tukachinsky, Hanna, Allen, Justin M., Erlich, Rachel, Hiemenz, Matthew C., Huang, Richard S.P., Elvin, Julia, Vergilio, Jo-Anne, Lin, Douglas I., Ross, Jeffrey, Oxnard, Geoffrey, Decker, Brennan

Source: In Modern Pathology November 2022 35(11):1618-1623

Predictive Genomic Biomarkers of Hormonal Therapy Versus Chemotherapy Benefit in Metastatic Castration-resistant Prostate Cancer

Authors: Graf, Ryon P., Fisher, Virginia, Mateo, Joaquin, Gjoerup, Ole V., Madison, Russell W., Raskina, Kira, Tukachinsky, Hanna, Creeden, James, Cunningham, Rachel, Huang, Richard S.P., Mata, Douglas A., Ross, Jeffrey S., Oxnard, Geoffrey R., Venstrom, Jeffrey M., Zurita, Amado J.

Source: European urology. 81(1):37-47

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100154225862.0x000001&indx=1&recIds=ETOCvdc_100154225862.0x000001

Clinical and pathological features associated with circulating tumor DNA content in real‐world patients with metastatic prostate cancer

Authors: Antonarakis, Emmanuel S., Tierno, Marni, Fisher, Virginia, Tukachinsky, Hanna, Alexander, Sonja, Hamdani, Omar, Hiemenz, Matthew C., Huang, Richard S.P., Oxnard, Geoffrey R., Graf, Ryon P.

Source: Prostate. 82(7):867-875

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100151136063.0x000001&indx=1&recIds=ETOCvdc_100151136063.0x000001

Equal-depth sequencing of white blood cells (WBC) and plasma from prostate cancer (PCa) liquid biopsies (LBx) and association with clonal hematopoiesis (CH) confounders in clinically relevant genes.

Authors: Antonarakis, Emmanuel S., Marshall, Catherine Handy, Brown, Derek W, Decker, Brennan James, Fine, Alexander D., Xu, Chang, Johnson, Kimberly, Sun, Daokun, McDevitt, Michael, Hughes, Jason D., Madison, Russell, Graf, Ryon P, Pasquina, Lincoln W, Schrock, Alexa Betzig, Gasco, Amaya, Tukachinsky, Hanna

Source: Journal of Clinical Oncology; 2/20/2025 Supplement 5, Vol. 43, p221-221, 288p

Evaluation of a variant origin prediction (VOP) algorithm to distinguish clonal hematopoiesis (CH) variants from tumor-derived variants and to predict metastatic castrate resistant prostate cancer (mCRPC) clinical responses.

Authors: Sun, Daokun, He, Shai, Brown, Derek W, Tukachinsky, Hanna, Hughes, Jason D., Polisecki, Eliana, Madison, Russell, Pasquina, Lincoln W, Fine, Alexander D., Decker, Brennan J., Fabrizio, David, He, Jie, Shah, Kalpit, Assaf, Zoe June, Powles, Thomas, Sweeney, Christopher, Albacker, Lee A., White, Jared, Dennis, Lucas, Xu, Chang

Source: Journal of Clinical Oncology; 2/20/2025 Supplement 5, Vol. 43, p201-201, 288p

The Molecular, Immunologic, and Clinicodemographic Landscape of MYC-Amplified Advanced Prostate Cancer

Authors: Jin, Will H., Zhang, Liangliang, Graf, Ryon, Raskina, Kira, Tukachinsky, Hanna, Huang, Richard S.P., McGregor, Kimberly, Alshalalfa, Mohamed, Hougen, Helen Y., Khan, Anwar, Punnen, Sanoj, Schrock, Alexa B., Venstrom, Jeffrey, Mahal, Brandon A.

Source: In Clinical Genitourinary Cancer February 2024 22(1):e163-e169

Comparative Genomic Analysis of Intrahepatic Cholangiocarcinoma: Biopsy Type, Ancestry, and Testing Patterns

Authors: Israel, Mason A., Danziger, Natalie, McGregor, Kimberly A., Murugesan, Karthikeyan, Gjoerup, Ole, Sokol, Ethan S., Tukachinsky, Hanna, Kurzrock, Razelle, Kato, Shumei, Sicklick, Jason K., Nimeiri, Halla S., Oxnard, Geoffrey R., Ross, Jeffrey S.

Source: Oncologist. 26(9):787-796

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100129260777.0x000001&indx=1&recIds=ETOCvdc_100129260777.0x000001

Contrasting genomic profiles from metastatic sites, primary tumors, and liquid biopsies of advanced prostate cancer

Authors: Necchi, Andrea, Cucchiara, Vito, Grivas, Petros, Bratslavsky, Gennady, Jacob, Joseph, Spiess, Philippe E., Sokol, Ethan S., Killian, Jonathan Keith, Lin, Douglas, Ramkissoon, Shakti, Huang, Richard S. P., Madison, Russell W., Venstrom, Jeffrey M., Schrock, Alexa B., Danziger, Natalie, Decker, Brennan, Gjoerup, Ole, Graf, Ryon P., Oxnard, Geoffrey R., Tukachinsky, Hanna, Ross, Jeffrey S.

Source: Cancer. 127(24):4557-4564

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100157759760.0x000001&indx=1&recIds=ETOCvdc_100157759760.0x000001

Pan-Cancer Interrogation of MUTYH Variants Reveals Biallelic Inactivation and Defective Base Excision Repair Across a Spectrum of Solid Tumors.

Authors: Paller, Channing J.¹ (AUTHOR) cpaller1@jhmi.edu, Tukachinsky, Hanna² (AUTHOR), Maertens, Alexandra³ (AUTHOR), Decker, Brennan² (AUTHOR), Sampson, Julian R.⁴ (AUTHOR), Cheadle, Jeremy P.⁴ (AUTHOR), Antonarakis, Emmanuel S.⁵ (AUTHOR)

Source: JCO Precision Oncology. 12/1/2024, Vol. 8, p1-14. 14p.

Subject Terms: *ISLANDS of Langerhans tumors, *EXCISION repair, *GENETIC variation, *ADRENAL glands, *ADRENAL tumors, CANCER susceptibility, CENTRAL nervous system tumors

Correction: Comprehensive genomic profiling of ESR1, PIK3CA, AKT1, and PTEN in HR(+)HER2(−) metastatic breast cancer: prevalence along treatment course and predictive value for endocrine therapy resistance in real-world practice.

Authors: Bhave, Manali A., Quintanilha, Julia C. F., Tukachinsky, Hanna, Li, Gerald, Scott, Takara, Ross, Jeffrey S., Pasquina, Lincoln, Huang, Richard S. P., McArthur, Heather, Levy, Mia A., Graf, Ryon P., Kalinsky, Kevin

Source: Breast Cancer Research & Treatment; Oct2024, Vol. 207 Issue 3, p611-614, 4p

Comprehensive genomic profiling of ESR1, PIK3CA, AKT1, and PTEN in HR(+)HER2(−) metastatic breast cancer: prevalence along treatment course and predictive value for endocrine therapy resistance in real-world practice.

Authors: Bhave, Manali A., Quintanilha, Julia C. F., Tukachinsky, Hanna, Li, Gerald, Scott, Takara, Ross, Jeffrey S., Pasquina, Lincoln, Huang, Richard S. P., McArthur, Heather, Levy, Mia A., Graf, Ryon P., Kalinsky, Kevin

Source: Breast Cancer Research & Treatment; Oct2024, Vol. 207 Issue 3, p599-609, 11p

Mechanism of inhibition of the tumor suppressor Patched by Sonic Hedgehog

Authors: Tukachinsky, Hanna, Petrov, Kostadin, Watanabe, Miyako, Salic, Adrian

Source: Proceedings of the National Academy of Sciences of the United States of America, 2016 Oct 01. 113(40), E5866-E5875.

Access URL: https://www.jstor.org/stable/26471966

Prognostic value of circulating tumor DNA fraction (TF) for patients with metastatic renal cell carcinoma (mRCC).

Authors: Zurita, Amado J., Danziger, Natalie, Scott, Takara, Gjoerup, Ole, Zhong, Lei, Tukachinsky, Hanna, Ross, Jeffrey S., Graf, Ryon

Source: Journal of Clinical Oncology; 2024 Supplement 4, Vol. 42, p455-455, 140p

Real-world effectiveness of PARP inhibitors (PARPi) in metastatic castration-resistant prostate cancer (mCRPC) by genomic homologous recombination repair (HRR) alterations and homologous recombination deficiency signature (HRDsig).

Authors: Triner, Daniel, Graf, Ryon, Gjoerup, Ole, Tukachinsky, Hanna, Ross, Jeffrey S., Cheng, Heather H., Pritchard, Colin C., Zurita, Amado J., Mateo, Joaquin, Cieslik, Marcin, Morgan, Todd Matthew

Source: Journal of Clinical Oncology; 2024 Supplement 4, Vol. 42, p186-186, 235p

Novel potential mechanisms of acquired resistance to anti-EGFR monoclonal antibody (mAb) therapy detected in liquid biopsies (LBx) from patients (pts) with advanced colorectal cancer (CRC).

Authors: Parseghian, Christine Megerdichian, Lee, Jessica Kim, Quintanilha, Julia, Schrock, Alexa B., Graf, Ryon, Pasquina, Lincoln, Sivakumar, Smruthy, Oxnard, Geoffrey R., Tukachinsky, Hanna, Klempner, Samuel J., Kopetz, Scott

Source: Journal of Clinical Oncology; 2024 Supplement 3, Vol. 42, p199-199, 235p

POLE variant phenotypic classification to enable identification of patients with colorectal cancer (CRC) who may benefit from immune checkpoint inhibition (ICI).

Authors: Keller, Rachel Beth, Fleischmann, Zoe, Sivakumar, Smruthy, Sharaf, Radwa, Janovitz, Tyler, Schrock, Alexa B., Tukachinsky, Hanna, Zhong, Lei, Mata, Douglas A., Lopez, Lyle, Sokol, Ethan, Frampton, Garrett M., Lin, Douglas I., Oxnard, Geoffrey R., Williams, Erik A., Elvin, Julia A., Decker, Brennan J.

Source: Journal of Clinical Oncology; 2024 Supplement 3, Vol. 42, p194-194, 235p