Eliezer Van Allen, MD

ESMO Recommendations on clinical reporting of genomic test results for solid cancers. Ann Oncol. 2024 Jul 09. View in: Pubmed

Mechanisms of resistance to oncogenic KRAS inhibition in pancreatic cancer. Cancer Discov. 2024 Jul 08. View in: Pubmed

Epigenomic signatures of sarcomatoid differentiation to guide the treatment of renal cell carcinoma. Cell Rep. 2024 Jun 25; 43(6):114350. View in: Pubmed

AI and immunology. Immunity. 2024 Jun 11; 57(6):1177-1181. View in: Pubmed

Randomized Phase II Study Evaluating the Addition of Pembrolizumab to Radium-223 in Metastatic Castration-resistant Prostate Cancer. Cancer Immunol Res. 2024 Jun 04; 12(6):704-718. View in: Pubmed

Urine Biopsy as Dynamic Biomarker to Enhance Clinical Staging of Bladder Cancer in Radical Cystectomy Candidates. JCO Precis Oncol. 2024 Jun; 8:e2300362. View in: Pubmed

Somatic structural variants drive distinct modes of oncogenesis in melanoma. J Clin Invest. 2024 May 14; 134(13). View in: Pubmed

Artificial Intelligence in Oncology: Current Landscape, Challenges, and Future Directions. Cancer Discov. 2024 May 01; 14(5):711-726. View in: Pubmed

Rare germline structural variants increase risk for pediatric solid tumors. bioRxiv. 2024 Apr 29. View in: Pubmed

PCO24-175: Immune Cell Dynamics After Radiotherapy for Oligometastatic Prostate Cancer. J Natl Compr Canc Netw. 2024 Apr 05; 22(2.5). View in: Pubmed

Impact of renal cell carcinoma molecular subtypes on immunotherapy and targeted therapy outcomes. Cancer Cell. 2024 May 13; 42(5):732-735. View in: Pubmed

Integrative Analysis of Germline Rare Variants in Clear and Non-clear Cell Renal Cell Carcinoma. Eur Urol Open Sci. 2024 Apr; 62:107-122. View in: Pubmed

Perspectives of Oncologists on the Ethical Implications of Using Artificial Intelligence for Cancer Care. JAMA Netw Open. 2024 Mar 04; 7(3):e244077. View in: Pubmed

Biomarkers of pembrolizumab efficacy in advanced anal squamous cell carcinoma: analysis of a phase II clinical trial and a cohort of long-term responders. J Immunother Cancer. 2024 01 25; 12(1). View in: Pubmed

Historical perspective and future directions: computational science in immuno-oncology. J Immunother Cancer. 2024 01 08; 12(1). View in: Pubmed

Genomic Tumor Correlates of Clinical Outcomes Following Organ-Sparing Chemoradiation Therapy for Bladder Cancer. Clin Cancer Res. 2023 12 15; 29(24):5116-5127. View in: Pubmed

The role of APOBEC3B in lung tumor evolution and targeted cancer therapy resistance. Nat Genet. 2024 Jan; 56(1):60-73. View in: Pubmed

Integration of Genomic Sequencing Drives Therapeutic Targeting of PDGFRA in T-Cell Acute Lymphoblastic Leukemia/Lymphoblastic Lymphoma. Clin Cancer Res. 2023 11 14; 29(22):4613-4626. View in: Pubmed

Intertumoral lineage diversity and immunosuppressive transcriptional programs in well-differentiated gastroenteropancreatic neuroendocrine tumors. Sci Adv. 2023 09 29; 9(39):eadd9668. View in: Pubmed

Spatially aware deep learning reveals tumor heterogeneity patterns that encode distinct kidney cancer states. Cell Rep Med. 2023 09 19; 4(9):101189. View in: Pubmed

Empirical evaluation of language modeling to ascertain cancer outcomes from clinical text reports. BMC Bioinformatics. 2023 Sep 02; 24(1):328. View in: Pubmed

Interplay of Mendelian and polygenic risk factors in Arab breast cancer patients. Genome Med. 2023 09 01; 15(1):65. View in: Pubmed

Reply to: Addressing racial and ethnic disparities in AACR project GENIE. NPJ Precis Oncol. 2023 Aug 31; 7(1):82. View in: Pubmed

Genome-guided discovery of cancer therapeutic targets. Cell Rep. 2023 Aug 29; 42(8):112978. View in: Pubmed

Circulating and Intratumoral Immune Determinants of Response to Atezolizumab plus Bevacizumab in Patients with Variant Histology or Sarcomatoid Renal Cell Carcinoma. Cancer Immunol Res. 2023 08 03; 11(8):1114-1124. View in: Pubmed

Overcoming Barriers to Tumor Genomic Profiling through Direct-to-Patient Outreach. Clin Cancer Res. 2023 07 05; 29(13):2445-2455. View in: Pubmed

Interferon signaling promotes tolerance to chromosomal instability during metastatic evolution in renal cancer. Nat Cancer. 2023 07; 4(7):984-1000. View in: Pubmed

First-line Systemic Treatment Options for Metastatic Castration-Sensitive Prostate Cancer: A Living Systematic Review and Network Meta-analysis. JAMA Oncol. 2023 05 01; 9(5):635-645. View in: Pubmed

Molecular markers of metastatic disease in KRAS-mutant lung adenocarcinoma. Ann Oncol. 2023 07; 34(7):589-604. View in: Pubmed

Current Landscape of Genomic Biomarkers in Clear Cell Renal Cell Carcinoma. Eur Urol. 2023 08; 84(2):166-175. View in: Pubmed

A Phase I Study of Combination Olaparib and Radium-223 in Men with Metastatic Castration-Resistant Prostate Cancer (mCRPC) with Bone Metastases (COMRADE). Mol Cancer Ther. 2023 04 03; 22(4):511-518. View in: Pubmed

Impact of an Expanded Definition of Family History on Outcomes of Active Surveillance for Prostate Cancer. J Urol. 2023 06; 209(6):1112-1119. View in: Pubmed

Spatially aware deep learning reveals tumor heterogeneity patterns that encode distinct kidney cancer states. bioRxiv. 2023 Feb 20. View in: Pubmed

Disparities in the Inclusion of Racial and Ethnic Minority Groups and Older Adults in Prostate Cancer Clinical Trials: A Meta-analysis. JAMA Oncol. 2023 02 01; 9(2):180-187. View in: Pubmed

Integrative Analysis of Germline Rare Variants in Clear and Non-Clear Cell Renal Cell Carcinoma. medRxiv. 2023 Jan 19. View in: Pubmed

Racial and ethnic disparities in a real-world precision oncology data registry. NPJ Precis Oncol. 2023 Jan 19; 7(1):7. View in: Pubmed

Germline variants associated with toxicity to immune checkpoint blockade. Nat Med. 2022 12; 28(12):2584-2591. View in: Pubmed

Randomized Trial of Olaparib With or Without Cediranib for Metastatic Castration-Resistant Prostate Cancer: The Results From National Cancer Institute 9984. J Clin Oncol. 2023 02 01; 41(4):871-880. View in: Pubmed

Phase Ib study of pembrolizumab in combination with trastuzumab emtansine for metastatic HER2-positive breast cancer. J Immunother Cancer. 2022 10; 10(10). View in: Pubmed

Patterns of structural variation define prostate cancer across disease states. JCI Insight. 2022 09 08; 7(17). View in: Pubmed

A patient-driven clinicogenomic partnership for metastatic prostate cancer. Cell Genom. 2022 Sep 14; 2(9). View in: Pubmed

Reply to Yuxuan Song, Yiqing Du, and Tao Xu's Letter to the Editor re: Matthew Mossanen, Filipe L.F. Carvalho, Vinayak Muralidhar, et al. Genomic Features of Muscle-invasive Bladder Cancer Arising After Prostate Radiotherapy. Eur Urol 2022;81:466-73. Eur Urol. 2022 11; 82(5):e141-e142. View in: Pubmed

Mutational Footprint of Platinum Chemotherapy in a Secondary Thyroid Cancer. JCO Precis Oncol. 2022 08; 6:e2200183. View in: Pubmed

Addition of Germline Testing to Tumor-Only Sequencing Improves Detection of Pathogenic Germline Variants in Men With Advanced Prostate Cancer. JCO Precis Oncol. 2022 Aug; 6:e2200329. View in: Pubmed

Association of High Tumor Mutation Burden in Non-Small Cell Lung Cancers With Increased Immune Infiltration and Improved Clinical Outcomes of PD-L1 Blockade Across PD-L1 Expression Levels. JAMA Oncol. 2022 08 01; 8(8):1160-1168. View in: Pubmed

A Process Framework for Ethically Deploying Artificial Intelligence in Oncology. J Clin Oncol. 2022 12 01; 40(34):3907-3911. View in: Pubmed

Tissue-resident memory and circulating T cells are early responders to pre-surgical cancer immunotherapy. Cell. 2022 08 04; 185(16):2918-2935.e29. View in: Pubmed

Multidimensional Molecular Profiling of Metastatic Triple-Negative Breast Cancer and Immune Checkpoint Inhibitor Benefit. JCO Precis Oncol. 2022 07; 6:e2100413. View in: Pubmed

Molecular profiling identifies targeted therapy opportunities in pediatric solid cancer. Nat Med. 2022 08; 28(8):1581-1589. View in: Pubmed

Insights into Immune Escape During Tumor Evolution and Response to Immunotherapy Using a Rat Model of Breast Cancer. Cancer Immunol Res. 2022 06 03; 10(6):680-697. View in: Pubmed

CREB5 reprograms FOXA1 nuclear interactions to promote resistance to androgen receptor-targeting therapies. Elife. 2022 05 12; 11. View in: Pubmed

Computed Tomography Texture Analysis for Predicting Clinical Outcomes in Patients With Metastatic Renal Cell Carcinoma Treated With Immune Checkpoint Inhibitors. Oncologist. 2022 05 06; 27(5):389-397. View in: Pubmed

Germline predisposition to pediatric Ewing sarcoma is characterized by inherited pathogenic variants in DNA damage repair genes. Am J Hum Genet. 2022 06 02; 109(6):1026-1037. View in: Pubmed

Autocrine Canonical Wnt Signaling Primes Noncanonical Signaling through ROR1 in Metastatic Castration-Resistant Prostate Cancer. Cancer Res. 2022 04 15; 82(8):1518-1533. View in: Pubmed

Genome-wide analysis of somatic noncoding mutation patterns in cancer. Science. 2022 04 08; 376(6589):eabg5601. View in: Pubmed

Concurrent TP53 Mutations Facilitate Resistance Evolution in EGFR-Mutant Lung Adenocarcinoma. J Thorac Oncol. 2022 06; 17(6):779-792. View in: Pubmed

Linking a Trio of Molecular Features in Clear-Cell Renal Cell Carcinoma. Cancer Immunol Res. 2022 03 01; 10(3):274. View in: Pubmed

Towards a Better Understanding of Antibody-Drug Conjugates in Urothelial Carcinoma. Eur Urol Oncol. 2022 12; 5(6):719-721. View in: Pubmed

Implementation of a prostate cancer-specific targeted sequencing panel for credentialing of patient-derived cell lines and genomic characterization of patient samples. Prostate. 2022 04; 82(5):584-597. View in: Pubmed

Integrative clinical and molecular characterization of translocation renal cell carcinoma. Cell Rep. 2022 01 04; 38(1):110190. View in: Pubmed

Genomic Features of Muscle-invasive Bladder Cancer Arising After Prostate Radiotherapy. Eur Urol. 2022 05; 81(5):466-473. View in: Pubmed

Artificial intelligence-aided clinical annotation of a large multi-cancer genomic dataset. Nat Commun. 2021 12 15; 12(1):7304. View in: Pubmed

Genomic attributes of homology-directed DNA repair deficiency in metastatic prostate cancer. JCI Insight. 2021 12 08; 6(23). View in: Pubmed

Building Tools for Machine Learning and Artificial Intelligence in Cancer Research: Best Practices and a Case Study with the PathML Toolkit for Computational Pathology. Mol Cancer Res. 2022 02; 20(2):202-206. View in: Pubmed

Inherited TP53 Variants and Risk of Prostate Cancer. Eur Urol. 2022 Mar; 81(3):243-250. View in: Pubmed

RAF1 amplification drives a subset of bladder tumors and confers sensitivity to MAPK-directed therapeutics. J Clin Invest. 2021 11 15; 131(22). View in: Pubmed

Tumor Mutations Across Racial Groups in a Real-World Data Registry. JCO Precis Oncol. 2021 11; 5:1654-1658. View in: Pubmed

Racial and Ethnic Disparities Among Participants in Precision Oncology Clinical Studies. JAMA Netw Open. 2021 11 01; 4(11):e2133205. View in: Pubmed

Subtype heterogeneity and epigenetic convergence in neuroendocrine prostate cancer. Nat Commun. 2021 10 01; 12(1):5775. View in: Pubmed

Integrating molecular profiles into clinical frameworks through the Molecular Oncology Almanac to prospectively guide precision oncology. Nat Cancer. 2021 10; 2(10):1102-1112. View in: Pubmed

Biologically informed deep neural network for prostate cancer discovery. Nature. 2021 10; 598(7880):348-352. View in: Pubmed

Molecular correlates of response to eribulin and pembrolizumab in hormone receptor-positive metastatic breast cancer. Nat Commun. 2021 09 21; 12(1):5563. View in: Pubmed

Molecular features of exceptional response to neoadjuvant anti-androgen therapy in high-risk localized prostate cancer. Cell Rep. 2021 09 07; 36(10):109665. View in: Pubmed

Nivolumab in combination with cabozantinib for metastatic triple-negative breast cancer: a phase II and biomarker study. NPJ Breast Cancer. 2021 Aug 25; 7(1):110. View in: Pubmed

Discovery and Features of an Alkylating Signature in Colorectal Cancer. Cancer Discov. 2021 10; 11(10):2446-2455. View in: Pubmed

Transcriptional profiling of primary prostate tumor in metastatic hormone-sensitive prostate cancer and association with clinical outcomes: correlative analysis of the E3805 CHAARTED trial. Ann Oncol. 2021 09; 32(9):1157-1166. View in: Pubmed

Gene Fusions Create Partner and Collateral Dependencies Essential to Cancer Cell Survival. Cancer Res. 2021 08 01; 81(15):3971-3984. View in: Pubmed

Clinical Inflection Point Detection on the Basis of EHR Data to Identify Clinical Trial-Ready Patients With Cancer. JCO Clin Cancer Inform. 2021 06; 5:622-630. View in: Pubmed

Evolution of delayed resistance to immunotherapy in a melanoma responder. Nat Med. 2021 06; 27(6):985-992. View in: Pubmed

Impact of Pathogenic Germline DNA Damage Repair alterations on Response to Intense Neoadjuvant Androgen Deprivation Therapy in High-risk Localized Prostate Cancer. Eur Urol. 2021 09; 80(3):295-303. View in: Pubmed

Phase II Multicenter Study of Enzalutamide in Metastatic Castration-Resistant Prostate Cancer to Identify Mechanisms Driving Resistance. Clin Cancer Res. 2021 07 01; 27(13):3610-3619. View in: Pubmed

Intrinsic Immunogenicity of Small Cell Lung Carcinoma Revealed by Its Cellular Plasticity. Cancer Discov. 2021 08; 11(8):1952-1969. View in: Pubmed

Tumor and immune reprogramming during immunotherapy in advanced renal cell carcinoma. Cancer Cell. 2021 05 10; 39(5):649-661.e5. View in: Pubmed

Transcriptional mediators of treatment resistance in lethal prostate cancer. Nat Med. 2021 03; 27(3):426-433. View in: Pubmed

Dissecting the immunogenomic biology of cancer for biomarker development. Nat Rev Clin Oncol. 2021 03; 18(3):133-134. View in: Pubmed

Systematic auditing is essential to debiasing machine learning in biology. Commun Biol. 2021 02 10; 4(1):183. View in: Pubmed

Integrative molecular characterization of sarcomatoid and rhabdoid renal cell carcinoma. Nat Commun. 2021 02 05; 12(1):808. View in: Pubmed

Evaluating the molecular diagnostic yield of joint genotyping-based approach for detecting rare germline pathogenic and putative loss-of-function variants. Genet Med. 2021 05; 23(5):918-926. View in: Pubmed

Beyond conventional immune-checkpoint inhibition - novel immunotherapies for renal cell carcinoma. Nat Rev Clin Oncol. 2021 04; 18(4):199-214. View in: Pubmed

Integrated Analysis of Germ Cell Tumors. Methods Mol Biol. 2021; 2195:181-187. View in: Pubmed

Predicting immunotherapy response through genomics. Curr Opin Genet Dev. 2021 02; 66:1-9. View in: Pubmed

Clinical Efficacy and Molecular Response Correlates of the WEE1 Inhibitor Adavosertib Combined with Cisplatin in Patients with Metastatic Triple-Negative Breast Cancer. Clin Cancer Res. 2021 02 15; 27(4):983-991. View in: Pubmed

Integrated molecular drivers coordinate biological and clinical states in melanoma. Nat Genet. 2020 12; 52(12):1373-1383. View in: Pubmed

Re: Russell E.N. Becker, Alexa R. Meyer, Aaron Brant, et al. Clinical Restaging and Tumor Sequencing are Inaccurate Indicators of Response to Neoadjuvant Chemotherapy for Muscle-invasive Bladder Cancer. Eur Urol. In press. https://doi.org/10.1016/j.eururo.2020.07.016. Eur Urol. 2021 02; 79(2):e56-e57. View in: Pubmed

Identification of a Synthetic Lethal Relationship between Nucleotide Excision Repair Deficiency and Irofulven Sensitivity in Urothelial Cancer. Clin Cancer Res. 2021 04 01; 27(7):2011-2022. View in: Pubmed

Accelerating precision medicine in metastatic prostate cancer. Nat Cancer. 2020 11; 1(11):1041-1053. View in: Pubmed

Detection of Pathogenic Variants With Germline Genetic Testing Using Deep Learning vs Standard Methods in Patients With Prostate Cancer and Melanoma. JAMA. 2020 11 17; 324(19):1957-1969. View in: Pubmed

Germ Cell Tumor Molecular Heterogeneity Revealed Through Analysis of Primary and Metastasis Pairs. JCO Precis Oncol. 2020; 4. View in: Pubmed

Functional Precision Medicine Identifies New Therapeutic Candidates for Medulloblastoma. Cancer Res. 2020 12 01; 80(23):5393-5407. View in: Pubmed

Effect of Eribulin With or Without Pembrolizumab on Progression-Free Survival for Patients With Hormone Receptor-Positive, ERBB2-Negative Metastatic Breast Cancer: A Randomized Clinical Trial. JAMA Oncol. 2020 10 01; 6(10):1598-1605. View in: Pubmed

Genomic Predictors of Good Outcome, Recurrence, or Progression in High-Grade T1 Non-Muscle-Invasive Bladder Cancer. Cancer Res. 2020 10 15; 80(20):4476-4486. View in: Pubmed

A phase 2 trial of buparlisib in patients with platinum-resistant metastatic urothelial carcinoma. Cancer. 2020 10 15; 126(20):4532-4544. View in: Pubmed

Targeting the innate immunoreceptor RIG-I overcomes melanoma-intrinsic resistance to T cell immunotherapy. J Clin Invest. 2020 08 03; 130(8):4266-4281. View in: Pubmed

Natural Language Processing to Ascertain Cancer Outcomes From Medical Oncologist Notes. JCO Clin Cancer Inform. 2020 08; 4:680-690. View in: Pubmed

CoMut: visualizing integrated molecular information with comutation plots. Bioinformatics. 2020 08 01; 36(15):4348-4349. View in: Pubmed

Author Correction: Integrative molecular and clinical modeling of clinical outcomes to PD1 blockade in patients with metastatic melanoma. Nat Med. 2020 Jul; 26(7):1147. View in: Pubmed

FiTAc-seq: fixed-tissue ChIP-seq for H3K27ac profiling and super-enhancer analysis of FFPE tissues. Nat Protoc. 2020 08; 15(8):2503-2518. View in: Pubmed

Clonal hematopoiesis is associated with adverse outcomes in multiple myeloma patients undergoing transplant. Nat Commun. 2020 06 12; 11(1):2996. View in: Pubmed

Cancer Moonshot Immuno-Oncology Translational Network (IOTN): accelerating the clinical translation of basic discoveries for improving immunotherapy and immunoprevention of cancer. J Immunother Cancer. 2020 06; 8(1). View in: Pubmed

Interplay of somatic alterations and immune infiltration modulates response to PD-1 blockade in advanced clear cell renal cell carcinoma. Nat Med. 2020 06; 26(6):909-918. View in: Pubmed

Genomic Profiling of Smoldering Multiple Myeloma Identifies Patients at a High Risk of Disease Progression. J Clin Oncol. 2020 07 20; 38(21):2380-2389. View in: Pubmed

Characterizing diversity in the tumor-immune microenvironment of distinct subclasses of gastroesophageal adenocarcinomas. Ann Oncol. 2020 08; 31(8):1011-1020. View in: Pubmed

Inactivation of Fbxw7 Impairs dsRNA Sensing and Confers Resistance to PD-1 Blockade. Cancer Discov. 2020 09; 10(9):1296-1311. View in: Pubmed

Single-cell RNA sequencing reveals compromised immune microenvironment in precursor stages of multiple myeloma. Nat Cancer. 2020 05; 1(5):493-506. View in: Pubmed

Mammalian SWI/SNF Complex Genomic Alterations and Immune Checkpoint Blockade in Solid Tumors. Cancer Immunol Res. 2020 08; 8(8):1075-1084. View in: Pubmed

Engaging Patients in Precision Oncology: Development and Usability of a Web-Based Patient-Facing Genomic Sequencing Report. JCO Precis Oncol. 2020; 4. View in: Pubmed

Germline Features Associated with Immune Infiltration in Solid Tumors. Cell Rep. 2020 03 03; 30(9):2900-2908.e4. View in: Pubmed

ATM Loss Confers Greater Sensitivity to ATR Inhibition Than PARP Inhibition in Prostate Cancer. Cancer Res. 2020 06 01; 80(11):2094-2100. View in: Pubmed

Tumor Mutational Burden and PTEN Alterations as Molecular Correlates of Response to PD-1/L1 Blockade in Metastatic Triple-Negative Breast Cancer. Clin Cancer Res. 2020 06 01; 26(11):2565-2572. View in: Pubmed

Identification of cancer driver genes based on nucleotide context. Nat Genet. 2020 02; 52(2):208-218. View in: Pubmed

The role of site-specific therapy for cancers of unknown of primary: A meta-analysis. Eur J Cancer. 2020 03; 127:118-122. View in: Pubmed

A model combining clinical and genomic factors to predict response to PD-1/PD-L1 blockade in advanced urothelial carcinoma. Br J Cancer. 2020 02; 122(4):555-563. View in: Pubmed

Prevalence of pathogenic germline cancer risk variants in high-risk urothelial carcinoma. Genet Med. 2020 04; 22(4):709-718. View in: Pubmed

Integrative molecular and clinical modeling of clinical outcomes to PD1 blockade in patients with metastatic melanoma. Nat Med. 2019 12; 25(12):1916-1927. View in: Pubmed

CREB5 Promotes Resistance to Androgen-Receptor Antagonists and Androgen Deprivation in Prostate Cancer. Cell Rep. 2019 11 19; 29(8):2355-2370.e6. View in: Pubmed

Results of a Multicenter Phase II Study of Atezolizumab and Bevacizumab for Patients With Metastatic Renal Cell Carcinoma With Variant Histology and/or Sarcomatoid Features. J Clin Oncol. 2020 01 01; 38(1):63-70. View in: Pubmed

Harmonization of Tumor Mutational Burden Quantification and Association With Response to Immune Checkpoint Blockade in Non-Small-Cell Lung Cancer. JCO Precis Oncol. 2019; 3. View in: Pubmed

Scaling computational genomics to millions of individuals with GPUs. Genome Biol. 2019 11 01; 20(1):228. View in: Pubmed

Clinical Validation of PBRM1 Alterations as a Marker of Immune Checkpoint Inhibitor Response in Renal Cell Carcinoma. JAMA Oncol. 2019 Nov 01; 5(11):1631-1633. View in: Pubmed

Assessment of Deep Natural Language Processing in Ascertaining Oncologic Outcomes From Radiology Reports. JAMA Oncol. 2019 Oct 01; 5(10):1421-1429. View in: Pubmed

Metabolomic adaptations and correlates of survival to immune checkpoint blockade. Nat Commun. 2019 09 25; 10(1):4346. View in: Pubmed

Finding the edge of the seat. Nat Med. 2019 09; 25(9):1328. View in: Pubmed

Publisher Correction: The long tail of oncogenic drivers in prostate cancer. Nat Genet. 2019 Jul; 51(7):1194. View in: Pubmed

Integrative Molecular Characterization of Resistance to Neoadjuvant Chemoradiation in Rectal Cancer. Clin Cancer Res. 2019 09 15; 25(18):5561-5571. View in: Pubmed

Intrinsic Resistance to Immune Checkpoint Blockade in a Mismatch Repair-Deficient Colorectal Cancer. Cancer Immunol Res. 2019 08; 7(8):1230-1236. View in: Pubmed

Genomic Evolutionary Patterns of Leiomyosarcoma and Liposarcoma. Clin Cancer Res. 2019 08 15; 25(16):5135-5142. View in: Pubmed

Mechanisms of Resistance to Immune Checkpoint Blockade: Why Does Checkpoint Inhibitor Immunotherapy Not Work for All Patients? Am Soc Clin Oncol Educ Book. 2019 Jan; 39:147-164. View in: Pubmed

Genomic correlates of clinical outcome in advanced prostate cancer. Proc Natl Acad Sci U S A. 2019 06 04; 116(23):11428-11436. View in: Pubmed

Correction: Detection of circulating tumour DNA is associated with inferior outcomes in Ewing sarcoma and osteosarcoma: a report from the Children's Oncology Group. Br J Cancer. 2019 Apr; 120(8):869. View in: Pubmed

Association of Inherited Pathogenic Variants in Checkpoint Kinase 2 (CHEK2) With Susceptibility to Testicular Germ Cell Tumors. JAMA Oncol. 2019 Apr 01; 5(4):514-522. View in: Pubmed

Genomic correlates of response to immune checkpoint blockade. Nat Med. 2019 03; 25(3):389-402. View in: Pubmed

Mutational Analysis of 472 Urothelial Carcinoma Across Grades and Anatomic Sites. Clin Cancer Res. 2019 04 15; 25(8):2458-2470. View in: Pubmed

Compound Genomic Alterations of TP53, PTEN, and RB1 Tumor Suppressors in Localized and Metastatic Prostate Cancer. Eur Urol. 2019 07; 76(1):89-97. View in: Pubmed

Genomics of response to immune checkpoint therapies for cancer: implications for precision medicine. Genome Med. 2018 11 29; 10(1):93. View in: Pubmed

Immunogenomic analyses associate immunological alterations with mismatch repair defects in prostate cancer. J Clin Invest. 2018 11 01; 128(11):5185. View in: Pubmed

A Cancer Cell Program Promotes T Cell Exclusion and Resistance to Checkpoint Blockade. Cell. 2018 11 01; 175(4):984-997.e24. View in: Pubmed

Everolimus and pazopanib (E/P) benefit genomically selected patients with metastatic urothelial carcinoma. Br J Cancer. 2018 09; 119(6):707-712. View in: Pubmed

Immunogenomic analyses associate immunological alterations with mismatch repair defects in prostate cancer. J Clin Invest. 2018 10 01; 128(10):4441-4453. View in: Pubmed

A framework to rank genomic alterations as targets for cancer precision medicine: the ESMO Scale for Clinical Actionability of molecular Targets (ESCAT). Ann Oncol. 2018 09 01; 29(9):1895-1902. View in: Pubmed

Genomic correlates of response to immune checkpoint blockade in microsatellite-stable solid tumors. Nat Genet. 2018 09; 50(9):1271-1281. View in: Pubmed

Detection of circulating tumour DNA is associated with inferior outcomes in Ewing sarcoma and osteosarcoma: a report from the Children's Oncology Group. Br J Cancer. 2018 08; 119(5):615-621. View in: Pubmed

Intron retention is a source of neoepitopes in cancer. Nat Biotechnol. 2018 12; 36(11):1056-1058. View in: Pubmed

Comprehensive Characterization of Cancer Driver Genes and Mutations. Cell. 2018 08 09; 174(4):1034-1035. View in: Pubmed

ERCC2 Helicase Domain Mutations Confer Nucleotide Excision Repair Deficiency and Drive Cisplatin Sensitivity in Muscle-Invasive Bladder Cancer. Clin Cancer Res. 2019 02 01; 25(3):977-988. View in: Pubmed

Detection of Somatic Structural Variants Enables Quantification and Characterization of Circulating Tumor DNA in Children With Solid Tumors. JCO Precis Oncol. 2018; 2018. View in: Pubmed

LSD1 Ablation Stimulates Anti-tumor Immunity and Enables Checkpoint Blockade. Cell. 2018 07 26; 174(3):549-563.e19. View in: Pubmed

Neoadjuvant-Intensive Androgen Deprivation Therapy Selects for Prostate Tumor Foci with Diverse Subclonal Oncogenic Alterations. Cancer Res. 2018 08 15; 78(16):4716-4730. View in: Pubmed

Early loss of mitochondrial complex I and rewiring of glutathione metabolism in renal oncocytoma. Proc Natl Acad Sci U S A. 2018 07 03; 115(27):E6283-E6290. View in: Pubmed

Structural Alterations Driving Castration-Resistant Prostate Cancer Revealed by Linked-Read Genome Sequencing. Cell. 2018 07 12; 174(2):433-447.e19. View in: Pubmed

Enrichment of FGFR3-TACC3 Fusions in Patients With Bladder Cancer Who Are Young, Asian, or Have Never Smoked. JCO Precis Oncol. 2018; 2. View in: Pubmed

The Clinical Activity of PD-1/PD-L1 Inhibitors in Metastatic Non-Clear Cell Renal Cell Carcinoma. Cancer Immunol Res. 2018 07; 6(7):758-765. View in: Pubmed

Interactive or static reports to guide clinical interpretation of cancer genomics. J Am Med Inform Assoc. 2018 05 01; 25(5):458-464. View in: Pubmed

Whole-exome sequencing of cell-free DNA and circulating tumor cells in multiple myeloma. Nat Commun. 2018 04 27; 9(1):1691. View in: Pubmed

Cancer-Germline Antigen Expression Discriminates Clinical Outcome to CTLA-4 Blockade. Cell. 2018 04 19; 173(3):624-633.e8. View in: Pubmed

Integrated genomic characterization of oral carcinomas in post-hematopoietic stem cell transplantation survivors. Oral Oncol. 2018 06; 81:1-9. View in: Pubmed

Oncogenic Signaling Pathways in The Cancer Genome Atlas. Cell. 2018 04 05; 173(2):321-337.e10. View in: Pubmed

Comprehensive Characterization of Cancer Driver Genes and Mutations. Cell. 2018 04 05; 173(2):371-385.e18. View in: Pubmed

The long tail of oncogenic drivers in prostate cancer. Nat Genet. 2018 05; 50(5):645-651. View in: Pubmed

Phase I Trial of a Tablet Formulation of Pilaralisib, a Pan-Class I PI3K Inhibitor, in Patients with Advanced Solid Tumors. Oncologist. 2018 04; 23(4):401-e38. View in: Pubmed

Inherited DNA-Repair Defects in Colorectal Cancer. Am J Hum Genet. 2018 03 01; 102(3):401-414. View in: Pubmed

Convergent Therapeutic Strategies to Overcome the Heterogeneity of Acquired Resistance in BRAFV600E Colorectal Cancer. Cancer Discov. 2018 04; 8(4):417-427. View in: Pubmed

Change in Neutrophil-to-lymphocyte ratio (NLR) in response to immune checkpoint blockade for metastatic renal cell carcinoma. J Immunother Cancer. 2018 01 22; 6(1):5. View in: Pubmed

Genomic correlates of response to immune checkpoint therapies in clear cell renal cell carcinoma. Science. 2018 Feb 16; 359(6377):801-806. View in: Pubmed

Mutational patterns in chemotherapy resistant muscle-invasive bladder cancer. Nat Commun. 2017 12 19; 8(1):2193. View in: Pubmed

Genomic Resistance Patterns to Second-Generation Androgen Blockade in Paired Tumor Biopsies of Metastatic Castration-Resistant Prostate Cancer. JCO Precis Oncol. 2017; 1. View in: Pubmed

Tumor Evolution: A Problem of Histocompatibility. Cell. 2017 11 30; 171(6):1252-1253. View in: Pubmed

Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors. Nat Commun. 2017 11 06; 8(1):1324. View in: Pubmed

Ex Vivo Profiling of PD-1 Blockade Using Organotypic Tumor Spheroids. Cancer Discov. 2018 02; 8(2):196-215. View in: Pubmed

The Potential and Challenges of Expanded Germline Testing in Clinical Oncology. JAMA. 2017 09 05; 318(9):801-803. View in: Pubmed

Decomposing Oncogenic Transcriptional Signatures to Generate Maps of Divergent Cellular States. Cell Syst. 2017 08 23; 5(2):105-118.e9. View in: Pubmed

Genomic profiling of ER+ breast cancers after short-term estrogen suppression reveals alterations associated with endocrine resistance. Sci Transl Med. 2017 Aug 09; 9(402). View in: Pubmed

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The Mutational Landscape of Circulating Tumor Cells in Multiple Myeloma. Cell Rep. 2017 04 04; 19(1):218-224. View in: Pubmed

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Loss of PTEN Is Associated with Resistance to Anti-PD-1 Checkpoint Blockade Therapy in Metastatic Uterine Leiomyosarcoma. Immunity. 2017 02 21; 46(2):197-204. View in: Pubmed

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Assigning clinical meaning to somatic and germ-line whole-exome sequencing data in a prospective cancer precision medicine study. Genet Med. 2017 07; 19(7):787-795. View in: Pubmed

The fuzzy world of precision medicine: deliberations of a precision medicine tumor board. Per Med. 2017 Jan; 14(1):37-50. View in: Pubmed

Somatic Mutations and Neoepitope Homology in Melanomas Treated with CTLA-4 Blockade. Cancer Immunol Res. 2017 01; 5(1):84-91. View in: Pubmed

Genomic evolution and chemoresistance in germ-cell tumours. Nature. 2016 11 30; 540(7631):114-118. View in: Pubmed

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Genomic Evolution after Chemoradiotherapy in Anal Squamous Cell Carcinoma. Clin Cancer Res. 2017 Jun 15; 23(12):3214-3222. View in: Pubmed

Somatic cancer variant curation and harmonization through consensus minimum variant level data. Genome Med. 2016 11 04; 8(1):117. View in: Pubmed

Delivering on the promise of precision cancer medicine. Genome Med. 2016 10 25; 8(1):110. View in: Pubmed

Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma. Cell Rep. 2016 10 18; 17(4):1206. View in: Pubmed

Genomic Heterogeneity and Exceptional Response to Dual Pathway Inhibition in Anaplastic Thyroid Cancer. Clin Cancer Res. 2017 May 01; 23(9):2367-2373. View in: Pubmed

Genomic Approaches to Understanding Response and Resistance to Immunotherapy. Clin Cancer Res. 2016 Dec 01; 22(23):5642-5650. View in: Pubmed

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A comparative assessment of clinical whole exome and transcriptome profiling across sequencing centers: implications for precision cancer medicine. Oncotarget. 2016 Aug 16; 7(33):52888-52899. View in: Pubmed

Clinical Validation of Chemotherapy Response Biomarker ERCC2 in Muscle-Invasive Urothelial Bladder Carcinoma. JAMA Oncol. 2016 Aug 01; 2(8):1094-6. View in: Pubmed

The impact of tumor profiling approaches and genomic data strategies for cancer precision medicine. Genome Med. 2016 07 26; 8(1):79. View in: Pubmed

Inherited DNA-Repair Gene Mutations in Men with Metastatic Prostate Cancer. N Engl J Med. 2016 Aug 04; 375(5):443-53. View in: Pubmed

Whole-Exome Sequencing in Two Extreme Phenotypes of Response to VEGF-Targeted Therapies in Patients With Metastatic Clear Cell Renal Cell Carcinoma. J Natl Compr Canc Netw. 2016 07; 14(7):820-4. View in: Pubmed

Genomic determinants of cancer immunotherapy. Curr Opin Immunol. 2016 08; 41:32-38. View in: Pubmed

A phase 1 study of buparlisib and bevacizumab in patients with metastatic renal cell carcinoma progressing on vascular endothelial growth factor-targeted therapies. Cancer. 2016 Aug 01; 122(15):2389-98. View in: Pubmed

Precision medicine for advanced prostate cancer. Curr Opin Urol. 2016 May; 26(3):231-9. View in: Pubmed

Summary and Recommendations from the National Cancer Institute's Clinical Trials Planning Meeting on Novel Therapeutics for Non-Muscle Invasive Bladder Cancer. Bladder Cancer. 2016 Apr 27; 2(2):165-202. View in: Pubmed

Somatic ERCC2 mutations are associated with a distinct genomic signature in urothelial tumors. Nat Genet. 2016 06; 48(6):600-606. View in: Pubmed

Characterizing genomic alterations in cancer by complementary functional associations. Nat Biotechnol. 2016 05; 34(5):539-46. View in: Pubmed

Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma. Cell Rep. 2016 Apr 26; 15(4):857-865. View in: Pubmed

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq. Science. 2016 Apr 08; 352(6282):189-96. View in: Pubmed

Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade. Science. 2016 Mar 25; 351(6280):1463-9. View in: Pubmed

Exome sequencing reveals recurrent germ line variants in patients with familial Waldenström macroglobulinemia. Blood. 2016 05 26; 127(21):2598-606. View in: Pubmed

Oncologists' and cancer patients' views on whole-exome sequencing and incidental findings: results from the CanSeq study. Genet Med. 2016 10; 18(10):1011-9. View in: Pubmed

Divergent clonal evolution of castration-resistant neuroendocrine prostate cancer. Nat Med. 2016 Mar; 22(3):298-305. View in: Pubmed

Mutations in TSC1, TSC2, and MTOR Are Associated with Response to Rapalogs in Patients with Metastatic Renal Cell Carcinoma. Clin Cancer Res. 2016 05 15; 22(10):2445-2452. View in: Pubmed

Genetic Effect of Chemotherapy Exposure in Children of Testicular Cancer Survivors. Clin Cancer Res. 2016 05 01; 22(9):2183-9. View in: Pubmed

Genomic Characterization of Brain Metastases Reveals Branched Evolution and Potential Therapeutic Targets. Cancer Discov. 2015 Nov; 5(11):1164-1177. View in: Pubmed

Genomic correlates of response to CTLA-4 blockade in metastatic melanoma. Science. 2015 Oct 09; 350(6257):207-211. View in: Pubmed

Next-generation sequencing to guide cancer therapy. Genome Med. 2015; 7(1):80. View in: Pubmed

Integrative Clinical Genomics of Advanced Prostate Cancer. Cell. 2015 Jul 16; 162(2):454. View in: Pubmed

Characterization of Clinical Cases of Collecting Duct Carcinoma of the Kidney Assessed by Comprehensive Genomic Profiling. Eur Urol. 2016 09; 70(3):516-21. View in: Pubmed

CSER and eMERGE: current and potential state of the display of genetic information in the electronic health record. J Am Med Inform Assoc. 2015 Nov; 22(6):1231-42. View in: Pubmed

Phase II study of tivantinib (ARQ 197) in patients with metastatic triple-negative breast cancer. Invest New Drugs. 2015 Oct; 33(5):1108-14. View in: Pubmed

Phase 2 trial of sunitinib and gemcitabine in patients with sarcomatoid and/or poor-risk metastatic renal cell carcinoma. Cancer. 2015 Oct 01; 121(19):3435-43. View in: Pubmed

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Long-term Benefit of PD-L1 Blockade in Lung Cancer Associated with JAK3 Activation. Cancer Immunol Res. 2015 Aug; 3(8):855-63. View in: Pubmed

Integrative clinical genomics of advanced prostate cancer. Cell. 2015 May 21; 161(5):1215-1228. View in: Pubmed

Genomic Correlate of Exceptional Erlotinib Response in Head and Neck Squamous Cell Carcinoma. JAMA Oncol. 2015 May; 1(2):238-44. View in: Pubmed

PLZF, a tumor suppressor genetically lost in metastatic castration-resistant prostate cancer, is a mediator of resistance to androgen deprivation therapy. Cancer Res. 2015 May 15; 75(10):1944-8. View in: Pubmed

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A functional landscape of resistance to ALK inhibition in lung cancer. Cancer Cell. 2015 Mar 09; 27(3):397-408. View in: Pubmed

Clinical Acquired Resistance to RAF Inhibitor Combinations in BRAF-Mutant Colorectal Cancer through MAPK Pathway Alterations. Cancer Discov. 2015 Apr; 5(4):358-67. View in: Pubmed

Complementary genomic approaches highlight the PI3K/mTOR pathway as a common vulnerability in osteosarcoma. Proc Natl Acad Sci U S A. 2014 Dec 23; 111(51):E5564-73. View in: Pubmed

Kinome-wide functional screen identifies role of PLK1 in hormone-independent, ER-positive breast cancer. Cancer Res. 2015 Jan 15; 75(2):405-14. View in: Pubmed

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Response and acquired resistance to everolimus in anaplastic thyroid cancer. N Engl J Med. 2014 Oct 09; 371(15):1426-33. View in: Pubmed

Somatic ERCC2 mutations correlate with cisplatin sensitivity in muscle-invasive urothelial carcinoma. Cancer Discov. 2014 Oct; 4(10):1140-53. View in: Pubmed

Assessing the clinical utility of cancer genomic and proteomic data across tumor types. Nat Biotechnol. 2014 Jul; 32(7):644-52. View in: Pubmed

Whole-exome sequencing and clinical interpretation of formalin-fixed, paraffin-embedded tumor samples to guide precision cancer medicine. Nat Med. 2014 Jun; 20(6):682-8. View in: Pubmed

Whole-exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer. Nat Biotechnol. 2014 May; 32(5):479-84. View in: Pubmed

Activating mTOR mutations in a patient with an extraordinary response on a phase I trial of everolimus and pazopanib. Cancer Discov. 2014 May; 4(5):546-53. View in: Pubmed

Successful whole-exome sequencing from a prostate cancer bone metastasis biopsy. Prostate Cancer Prostatic Dis. 2014 Mar; 17(1):23-7. View in: Pubmed

The genetic landscape of clinical resistance to RAF inhibition in metastatic melanoma. Cancer Discov. 2014 Jan; 4(1):94-109. View in: Pubmed

MAP kinase pathway alterations in BRAF-mutant melanoma patients with acquired resistance to combined RAF/MEK inhibition. Cancer Discov. 2014 Jan; 4(1):61-8. View in: Pubmed

A phase II trial of AS1411 (a novel nucleolin-targeted DNA aptamer) in metastatic renal cell carcinoma. Invest New Drugs. 2014 Feb; 32(1):178-87. View in: Pubmed

Processes and preliminary outputs for identification of actionable genes as incidental findings in genomic sequence data in the Clinical Sequencing Exploratory Research Consortium. Genet Med. 2013 Nov; 15(11):860-7. View in: Pubmed

A survey of informatics approaches to whole-exome and whole-genome clinical reporting in the electronic health record. Genet Med. 2013 Oct; 15(10):824-32. View in: Pubmed

Punctuated evolution of prostate cancer genomes. Cell. 2013 Apr 25; 153(3):666-77. View in: Pubmed

Clinical analysis and interpretation of cancer genome data. J Clin Oncol. 2013 May 20; 31(15):1825-33. View in: Pubmed

A genome-scale RNA interference screen implicates NF1 loss in resistance to RAF inhibition. Cancer Discov. 2013 Mar; 3(3):350-62. View in: Pubmed

Moving toward personalized medicine in castration-resistant prostate cancer. Urol Clin North Am. 2012 Nov; 39(4):483-90. View in: Pubmed

Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer. Nat Genet. 2012 May 20; 44(6):685-9. View in: Pubmed

A Common Language for Transformative Healthcare Networking. New England Journal of Medicine. 2012. View in: Pubmed

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The paradox of positive thinking. J Clin Oncol. 2011 Jul 01; 29(19):2730-1. View in: Pubmed

Off-label use of rituximab in a multipayer insurance system. J Oncol Pract. 2011 Mar; 7(2):76-9. View in: Pubmed

One day later. Continuing psychological stress after a cardiac intensive care rotation. J Gen Intern Med. 2010 Aug; 25(8):882-3. View in: Pubmed

A role in transition. Ann Intern Med. 2009 Sep 15; 151(6):427-8. View in: Pubmed

Comments on the recent clinical guidance statement on HIV screening. Ann Intern Med. 2009 Aug 18; 151(4):286; author reply 287. View in: Pubmed

Novel secondary hormonal therapy in advanced prostate cancer: an update. Curr Opin Urol. 2009 May; 19(3):315-21. View in: Pubmed