Scientific Contributions

The Translational Genomics Lab (TGL) has supported more than 40 clinical trials, extracted nucleic acid from more than 20,000 samples, prepared more than 20,000 next generation libraries, sequenced more than 17,000 libraries, and performed more than 13,000 NanoString assays. Below are some selected publications and clinical trials that have utilized our services.

Selected Publications

• Fibroblast growth factor receptor 3 alterations and response to immune checkpoint inhibition in metastatic urothelial cancer: a real world experience. Rose TL, Heir WH, Mayhew GM, Shibata Y, Eulitt P, Uronis JM, Zhou M, Nielsen M, Smith AB, Woods M, Hayward MC, Salazar AH, Milowsky MI, Wobker SE, McGinty K, Millburn MV, Eisner JR, Kim WY. British Journal of Cancer. 2022.
• Rapid idiosyncratic mechanisms of clinical resistance to KRAS G12C inhibition. Tsai YS, Woodcock MG, Azam SH, Thorne LB, Kanchi KL, Parker JS, Vincent BG, Pecot CV. The Journal of Clinical Investigation. 2022.
• Comprehensive Viral Genotyping Reveals Prognostic Viral Phylogenetic Groups in HPV16-Associated Squamous Cell Carcinoma of the Oropharynx. Schrank TP, Landess L, Stepp WH, Rehmani H, Weir WH, Lenze N, Lal A, Wu D, Kothari A, Hackman TG, Sheth S, Patel S, Jefferys SR, Issaeva N, Yarbrough WG. Molecular Cancer Research. 2022.
• Transcriptome-targeted analysis of human peripheral blood-derived macrophages when cultured on biomaterial meshes. Mora-Navarro C, Ozpinar EW, Sze D, Martin DP, Freytes DO. Biomedical Materials. 2021.
• A multi-omic single-cell landscape of human gynecologic malignancies. Regner MJ, Wisniewska K, Garcia-Recio S, Thennavan A, Mendez-Giraldez R, Malladi VS, Hawkins G, Parker JS, Perou CM, Bae-Jump VL, Franco HL. Molecular Cell. 2021.
• Single-Cell RNA Sequencing Reveals Endothelial Cell Transcriptome Heterogeneity Under Homeostatic Laminar Flow. Liu Z, Ruter DL, Quigley K, Tanke NT, Jiang Y, Bautch VL. Arteriosclerosis, Thrombosis, and Vascular Biology. 2021.
• Functional coordination of non-myocytes plays a key role in adult zebrafish heart regeneration. Ma H, Liu Z, Yang Y, Feng D, Dong Y, Garbutt TA, Hu Z, Wang L, Luan C, Cooper CD, Li Y, Welch JD, Qian L, Liu J. EMBO Reports. 2021.
• An approach for normalization and quality control for NanoString RNA expression data. Bhattacharya A, Hamilton AM, Furberg H, Pietzak E, Purdue MP, Troester MA, Hoadley KA, Love MI. Briefings in Bioinformatics. 2021.
• CRTC1/MAML2 directs a PGC-1α-IGF-1 circuit that confers vulnerability to PPARγ inhibition. Musicant AM, Parag-Sharma K, Gong W, Sengupta M, Chatterjee A, Henry EC, Tsai YH, Hayward MC, Sheth S, Betancourt R, Hackman TG, Padilla RJ, Parker JS, Giudice J, Flaveny CA, Hayes DN, Amelio AL. Cell Reports. 2021.
• FGFR4 regulates tumor subtype differentiation in luminal breast cancer and metastatic disease. Garcia-Recio S, Thennavan A, East MP, Parker JS, Cejalvo JM, Garay JP, Hollern DP, He X, Mott KR, Galván P, Fan C, Selitsky SR, Coffey AR, Marron D, Brasó-Maristany F, Burgués O, Albanell J, Rojo F, Lluch A, Martinez de Dueñas E, Rosen JM, Johnson GL, Carey LA, Prat A, Perou CM. The Journal of Clinical Investigation. 2020.
• Bimodal age distribution at diagnosis in breast cancer persists across molecular and genomic classifications. Allott EH, Shan Y, Chen M, Sun X, Garcia-Recio S, Kirk EL, Olshan AF, Geradts J, Earp HS, Carey LA, Perou CM, Pfeiffer RM, Anderson WF, Troester MA. Breast Cancer Research and Treatment. 2020.
• TP53 protein levels, RNA-based pathway assessment, and race among invasive breast cancer cases. Williams LA, Butler EN, Sun X, Allott EH, Cohen SM, Fuller AM, Hoadley KA, Perou CM, Geradts J, Olshan AF, Troester MA. npj Breast Cancer. 2018.
• A Phase I Trial of the PI3K Inhibitor Buparlisib Combined With Capecitabine in Patients With Metastatic Breast Cancer. McRee AJ, Marcom PK, Moore DT, Zamboni WC, Kornblum ZA, Hu Z, Phipps R,  Anders CK, Reeder-Hayes K, Carey LA, Weck KE, Perou CM,  Dees EC. Clinical Breast Cancer. 2018.
• Racial Differences in PAM50 Subtypes in the Carolina Breast Cancer Study. Troester MA, Sun X, Allott EH, Geradts J, Cohen SM, Tse CK, Kirk EL, Thorne LB, Mathews M, Li Y, Hu Z, Robinson WR, Hoadley KA, Olopade OI, Reeder-Hayes KE, Earp HS, Olshan AF, Carey LA, Perou CM. Journal of the National Cancer Institute. 2018.
• Combined Targeted DNA Sequencing in Non-Small Cell Lung Cancer (NSCLC) Using UNCseq and NGScopy, and RNA Sequencing Using UNCqeR for the Detection of Genetic Aberrations in NSCLC. Zhao X, Wang A, Walter V, Patel NM, Eberhard DA, Hayward MC, Salazar AH, Jo H, Soloway MG, Wilkerson MD, Parker JS, Yin X, Zhang G, Siegel MB, Rosson GB, Earp HS, Sharpless NE, Gulley ML, Weck KE, Hayes DN, Moschos SJ. PLOS One. 2015.

Selected Clinical Trials Supported

• NCT03819569 (LCCC1834): GRADE-SRM: Genomic Risk Assessment and Decisional Evaluation for Small Renal Masses (GRADE-SRM)
• NCT03802604: Combination of Talimogene Laherparepvec With Atezolizumab in Early Breast Cancer (PROMETEO)
• NCT03769415 (LCCC1829): Harnessing Analysis RNA Expression and Molecular Subtype to Optimize Novel TherapY MBCA (HARMONY)
• NCT03442569 (LCCC1632): PhII Trial Panitumumab, Nivolumab, Ipilimumab in Kras/Nras/BRAF Wild-type MSS Refractory mCRC
• NCT03248427: Neadjuvant Multi-agent Chemotherapy or Letrozole Plus Ribociclib in Luminal B/HER2-negative Breast Cancer. (CORALLEEN)
• NCT03244384: Testing MK-3475 (Pembrolizumab) After Surgery for Localized Muscle-Invasive Bladder Cancer and Locally Advanced Urothelial Cancer (AMBASSADOR)
• NCT02768792 (LCCC1522): High Dose Cytarabine Followed by Pembrolizumab in Relapsed/Refractory AML
• NCT02768701 (LCCC1525): Study Of Single-dose Cyclophosphamide +Pembrolizumab In Patients With Metastatic Triple Negative Breast Cancer
• NCT02767362 (LCCC1514): A Pre-Op Window Study Evaluating Anti-Proliferative Effects of Atorvastatin on the Endometrium
• NCT02758132: Denosumab Plus Enzalutamide, Abiraterone and Prednisone Compared to Denosumab Plus Enzalutamide Alone for Men With Castrate Resistant Prostate Cancer (CRPC) With Bone Metastases
• NCT02690558 (LCCC1520): Phase 2 Study of Pembrolizumab in Combination With Gemcitabine and Cisplatin as Neoadjuvant Therapy
• NCT02338310: Trial of Perioperative Endocrine Therapy – Individualising Care (POETIC)
• NCT02328313 (LCCC1410): Impact of Physical Activity on Biomarker of Aging and Body Composition Among Breast Cancer Survivors Age 65 and Older
• NCT02167932 (LCCC1334): The Impact of a Physical Activity Program on Biomarkers of Aging During Chemotherapy for Breast Cancer
• NCT02138617 (LCCC1217): Genotype-Directed Study Of Irinotecan Dosing In FOLFIRI + Bevacizumab Treated Metastatic Colorectal Cancer
• NCT02102165: Aiming to Understand the Molecular Aberrations in Metastatic Breast Cancer. (AURORA)
• NCT02065687: Paclitaxel and Carboplatin With or Without Metformin Hydrochloride in Treating Patients With Stage III, IV, or Recurrent Endometrial Cancer
• NCT02028507: Phase III Palbociclib With Endocrine Therapy vs. Capecitabine in HR+/HER2- MBC With Resistance to Aromatase Inhibitors (PEARL)
• NCT02019758: Budesonide Versus Fluticasone for Treatment of Eosinophilic Esophagitis
• NCT01953588: Fulvestrant and/or Anastrozole in Treating Postmenopausal Patients With Stage II-III Breast Cancer Undergoing Surgery
• NCT01949337: Enzalutamide With or Without Abiraterone and Prednisone in Treating Patients With Castration-Resistant Metastatic Prostate Cancer
• NCT01937117: Pertuzumab and Trastuzumab as Neoadjuvant Treatment in Patients With HER2-Positive Breast Cancer
• NCT01457196 (LCCC1108): Development of a Tumor Molecular Analyses Program and Its Use to Support Treatment Decisions
• NCT01426880: Addition of Carboplatin to Neoadjuvant Therapy for Triple-negative and HER2-positive Early Breast Cancer (GeparSixto)
• NCT01377363: Evaluation of Degree of Conversion of HER2 Receptor Between Primary Breast Cancer and Metastasis
• NCT01111058: Everolimus Versus Placebo in Head and Neck Cancer.
• NCT01099358: Study in Advanced Solid Tumors
• NCT01084083: Induction Chemotherapy Followed By Cetuximab and Radiation in HPV-Associated Resectable Stage III/IV Oropharynx Cancer
• NCT00785291: Paclitaxel, Nab-paclitaxel, or Ixabepilone With or Without Bevacizumab in Treating Patients With Stage IIIC or Stage IV Breast Cancer.
• NCT00280761 (LCCC0216): Biomarkers in Patients With Rectal Cancer Undergoing Chemotherapy and Radiation Therapy