there s nothing more personal than genomics....xiaolong liu, tarek hammour, edi brogi, a. john...

There’s nothing more personal than genomics.

AACR Annual Meeting 2016 Poster and platform presentations powered by Illumina technology.

Discover more genomic insights.Join Illumina for our Spotlight Theater presentation in the Exhibit Hall to hear how our technologies are

empowering researchers in cancer genomics.

Illumina Spotlight TheaterAACR Exhibit Hall, Spotlight Theater A

Tuesday, April 19 3 PM–4 PM Research Advancements Propelled by the Illumina Cancer Genomics PortfolioSpeaker: Jennifer L. Stone, PhD, Illumina, Inc.Join Dr Stone as she reviews recent cancer research advancements that have leveraged Illumina solutions and highlights the expanding Illumina oncology portfolio that aids the discovery, identification, and analysis of genomic information in cancer.

Illumina in the spotlight.Attend our booth presentations on Monday and Tuesday for a closer look at how our collaborations

are catalyzing genomic innovation to achieve unprecedented breakthroughs in cancer research for

key application areas.

Illumina in-booth presentationsLocated at Illumina booth 322

Monday, April 18 10:30 AM12:30 PM 3 PM

Gene Regulation Molecular ProfilingLiquid Biopsy

Tuesday, April 19 10:30 AM12:30 PM

Companion DiagnosticsCancer Immunology

Authors Title Time Abstract Location

Salvatore Piscuoglio, Charlotte KY Ng, Felipe C. Geyer, Carey A. Eberle, Elena Guerini-Rocco, Caterina Marchio, Anne Vincent-Salomon, Jorge S. Reis-Filho, Britta Weigelt

The mutational landscape of mucinous carcinomas of the breast

Sunday, Apr 171 PM–5 PM

91 Section 4

Yoichi Fujii, Yusuke Sato, Shigekatsu Maekawa, Hiromichi Suzuki, Tetsuichi Yoshizato, Kenichi Yoshida, Yuichi Shiraishi, Kenichi Chiba, Hiroko Tanaka, Tohru Nakagawa, Haruki Kume, Hiroaki Nishimatsu, Yoshikazu Hirano, Masashi Sanada, Hideki Makishima, Satoru Miyano, Yukio Homma, Seishi Ogawa

Genomic landscape and clonal expansions of upper urinary tract urothelial carcinoma

Sunday, Apr 171 PM–5 PM

94 Section 4

Sung-Hye Hong, Geon Kook Lee, Sang Hoon Song, Seung Youn Lee, Jin Young Kim, Ji-Youn Han

A novel PTPRK-FILIP1 fusion gene in invasive mucinous adenocarcinoma of lung without known driver mutations

Sunday, Apr 17 1 PM–5 PM

97 Section 4

Gabriel Malouf, Roger Mouawad, Xiaoping Su, Hui Yao, Eva Comperat, Morgan Roupret, Jean-Philippe Spano, David Khayat

Transcriptionnal profiling of upper-tumor urothelial carcinomas


106 Section 4

Lisa Quetel, Robin Tranchant, Clément Meiller, Sandrine Imbeaud, Annie Renier, Françoise Le Pimpec-Barthes, Jessica Zucman-Rossi, Marie-Claude Jaurand, Didier Jean

Genetic alterations in molecular tumor subgroups of malignant pleural mesothelioma


112 Section 4

Netta Mäkinen, Annukka Pasanen, Hanna-Riikka Heinonen, Kati Kämpjärvi, Simona Bramante, Miika Mehine, Jyrki Jalkanen, Oskari Heikinheimo, Jari Sjöberg, Ralf Bützow, Lauri Aaltonen

Estrogen and progesterone receptor expression in different molecular uterine leiomyoma subclasses


120 Section 5

Manjiao Liu, Zhen Liu, Jian Bai, Hong Cai, Yang Ke, Changqing Zeng

Analysis and comparison of somatic copy number alterations in gastric cardia adenocarcinoma and gastric non-cardia adenocarcinoma


121 Section 5

Sarah Chiang, Britta Weigelt, Huei-Chi Wen, Salvatore Piscuoglio, Luciano G. Martelotto, Charlotte KY Ng, Jörg Balss, Gabrielle Baker, Kimberly S. Cole, Andreas von Deimling, Julie M. Batten, Jonathan D. Marotti, Hwei-Choo Soh, Benjamin L. McCalip, Raymond S. Lim, Kalliopi P. Siziopikou, Randi Burke, Song Lu, Xiaolong Liu, Tarek Hammour, Edi Brogi, A. John Iafrate, Jorge S. Reis-Filho, Stuart J. Schnitt

Solid papillary carcinoma with reverse polarization are driven by IDH2 and PI3K pathway mutations


138 Section 5

Albert Dobi, Gyorgy Petrovics, Hua Li, Shyh-Han Tan, Tanja Stümpel, Denise Young, Shilpa Katta, Qiyuan Li, Kai Ying, Bernward Klocke, Lakshmi Ravindranath, Indu Kohaar, Yongmei Chen, Dezso Ribli, Korbinian Grote, Hau Zou, Joseph Cheng, Clifton L. Dalgard, Shimin Zhang, István Csabai, Jacob Kagan, David Takeda, Massimo Loda, Sudhir Srivastava, Matthias Scherf, Martin Seifert, Timo Gaiser, David G. McLeod, Zoltan Szallasi, Reinhard Ebner, Thomas Werner, Isabell A. Sesterhenn, Matthew Freedman, Shiv Srivastava

LSAMP gene deletion is associated with rapid disease progression in prostate cancer of African American men


140 Section 5

Hye Hyeon Eum, Hae-Ock Lee, Woosung Chung, Kyu-Tae Kim, Kyung-Min Lee, Arum Jo, WonShik Han, Woong-Yang Park

Single-cell RNA sequencing presents explicit expression signatures in primary breast cancer


161 Section 6

Kiran Madwani, Helen J. Huang, Dawne N. Shelton, Siqing Fu, Apostolia M. Tsimberidou, Sarina A. Piha-Paul, Aung Naing, David S. Hong, Daniel D. Karp, Debra L. Andrews, Goran Cabrilo, E. Scott Kopetz, Rajyalakshmi Luthra, Bryan K. Kee, Cathy Eng, Van K. Morris, George A. Karlin-Neumann, Funda Meric-Bernstam, Filip Janku

Quantity of KRAS mutations in cell-free DNA is associated with survival of patients with advanced cancers


493 Section 23

Peter Bronsert, Tim Kees, Bruno Zeitouni, Anne-Lise Peille, Manuel Landesfeind, Heinz-Herbert Fiebig, Simon Kuesters, Vincent Vuaroqueaux

Subtyping of pancreatic cancer patient-derived xenograft tumors and implications for anticancer agent testing


639 Section 29

Sara JC Gosline, Pamela Knight, Thomas Yu, Nripesh Prasad, Angela Jones, Shristi Shrestha, Braden Boone, Shawn E. Levy, Andrew J. Link, Allison C. Galassie, Hubert Weinberg, Stephen Friend, Salvatore La Rosa, Justin Guinney, Annette Bakker

The molecular landscape of dermal neurofibromatosis


772 Section 34

˝

Solid tumor profiling


Lindsay C. Stetson, Camila Ferreira de Souza, Tathiane Maistro Malta, Thais Sarraf Sabedot, Quinn Ostrom, Peter Liao, Daniela Pretti da Cunha Tirapelli, Luciano Neder, Carlos Gilberto Carlotti, Jr, Rehan Akbani, Sofie Salama, Laila Poisson, Daniel Brat

Multi-omic profiling of gliomas reveals distinct DNA methylation changes at tumor recurrence


780 Section 34

Susan E. Steck, Anna Woloszynska-Read, Samuel Antwi, Hongmei Zhang, Lenore Arab, Elizabeth T.H. Fontham, James Mohler, L. Joseph Su, Feifei Xiao, Gary Smith, Donald Trump, Candace Johnson, Jeannette Bensen

SNPs in vitamin D-related genes are associated with prostate cancer aggressiveness in the North Carolina-Louisiana Prostate Cancer Project (PCaP)


806 Section 36

Edward A. Ruiz-Narvaez, Kathryn L. Lunetta, Chi-Chen Hong, Stephen A. Haddad, Song Yao, Ting-Yuan D. Cheng, Jeannette T. Bensen, Elisa V. Bandera, Christopher A. Haiman, Andrew F. Olshan, Christine B. Ambrosone, Lynn Rosenberg, Julie R. Palmer

Gene-based analysis of the IGF signaling pathway and risk of breast cancer in African American women: The AMBER consortium


814 Section 36

Maria Nattestad, Karen Ng, Sara Goodwin, Timour Baslan, Fritz Sedlazeck, James Gurtowski, Elizabeth Hutton, Yogi Sundaravadanam, Tyler Garvin, Marley Alford, Elizabeth Tseng, Philipp Rescheneder, Jason Chin, Timothy Beck, Melissa Kramer, John McPherson, James Hicks, Michael C. Schatz, William R. McCombie

Comprehensive genome and transcriptome structural analysis of a breast cancer cell line using single molecule sequencing

Sunday, Apr 17 5:20 PM–5:35 PM

850 Room 243, Morial Convention

Center

Joshua D. Campbell, Catalina Perdomo, Sarah Mazzilli, Yaron Geshalter, Samjot S. Dhillon, Gang Liu, Sherry Zhang, Hangqio Lin, Jessica Vick, Christopher Moy, Evan Johnson, Matthew Meyerson, Suso Platero, Marc Lenburg, Mary Reid, Avrum Spira, Jennifer Beane

Genomic characterization of premalignant lung squamous cell carcinoma lesions



Center

Scott M. Langevin, Damaris Kuhnell, Tess L. Parry, Jacek Biesiada, Xiang Zhang, Mario Medvedovic, Susan Kasper

Comprehensive catalog of culture-derived exosomal microRNA cargo from 4 discrete head and neck carcinoma cell lines

Monday, Apr 18 8 AM–12 PM

961 Section 2

Merricka C. Livingstone, Bill D. Roebuck, Natalie M. Johnson, Thomas W. Kensler, John D. Groopman

Temporal trends in microRNAs during subchronic aflatoxin dosing and modulation by the chemopreventive oleane triterpenoid, CDDO-Im


1083 Section 6

Shafquat Azim, Sanjeev K. Srivastava, Arun Bhardwaj, Haseeb Zubair, Mohammad Aslam Khan, Seema Singh, Ajay P. Singh

MYB-regulated gene networks and signaling pathways in pancreatic cancer


1519 Section 27

Bryan Thibodeau, Paola Yumpo Cardenas, Samreen Ahmed, Marc Dunn, Matthew Johnson, George Wilson

Next-generation sequencing of brain metastasis in non-small cell lung cancer


1535 Section 28

Alexander Ring, Victoria Forte, Dany Barrak, Tania Porras, Vasu Punj, Steven Carrasco, Min Yu, Debu Tripathy, Julie Lang

Molecular profiling of circulating tumor cells as a surrogate for distant metastasis in stage IV breast cancer


1549 Section 28

Stefan Kirsch, Urs Lahrmann, Miodrag Guzvic, Zbigniew T. Czyz, Giancarlo Feliciello, Bernhard Polzer, Christoph A. Klein

High-resolution parallel analysis of genome and transcriptome of single disseminated prostate cancer cells


1551 Section 28

Laura Vera Ramirez, Sven Bilke, Robert Walker, Paul Meltzer, Tinghu Qiu, Roland Rad, Jeffrey E. Green

Insertional mutagenesis to identify molecular mechanisms of breast cancer dormancy and metastasis


1576 Section 29

Brooke L. Fridley, Junqiang Dai, Rama Raghavan, Chen Wang, Pengcheng Lu, Stacey Winham, Madalene Earp, Kate Lawrenson, Simon A. Gayther, Kimberly R. Kalli, Ellen L. Goode

Transcriptome characterization of high-grade serous and endometrioid epithelial ovarian cancer tumors

Monday, Apr 18 1 PM–5 PM

1833 Section 3


Milos Babic, Peter Shepard, Joanne Yeakley, Ruchir Shah, Deepak Mav, Raymond B. Nagle, Bruce Seligmann

Differential expression and mechanistic pathways of prostate cancer identified from FFPE tissue using surrogate or whole transcriptome TempO-Seq targeted gene expression assays


1840 Section 3

Dario R. Roque, Will R. Jeck, David N. Hayes, Arthur M. Dizon, Leslie Clark, Stuart Pierce, Weiya Z. Wysham, Tara Castellano, Paola A. Gehrig, Victoria Bae-Jump

Multiple PI3K pathway mutations predominate in low-stage endometrial carcinomas


1852 Section 3

Margarita González-Vallinas, Marco Albrecht, Adriana Pitea, Manuel Rodríguez-Paredes, Damian Stichel, Steffen Sass, Julian Gutekunst, Jennifer Schmitt, Thomas Muley, Michael Meister, Arne Warth, Peter Schirmacher, Fabian J. Theis, Nikola S. Müller, Franziska Matthäus, Kai Breuhahn

Identification of a miRNA/mRNA network driving non-small cell lung cancer (NSCLC) dissemination


1945 Section 7

Stephen V. Liu, Edward S. Kim, Rebecca A. Feldman, Zoran Gatalica, Jeffrey Swensen, Hossein Borghaei, Alexander I. Spira, Gerold Bepler, Sandeep Reddy, Afshin Dowlati

Molecular and genomic characterization of SCLC


2266 Section 22

Mathilde B.H. Thomsen, Iver Nordentoft, Philippe Lamy, Soren Hoyer, Soren Vang, Jakob Hedegaard, Michael Borre, Jorgen B. Jensen, Torben F. Orntoft, Lars Dyrskjot

Spatial and temporal clonal evolution during development of metastatic urothelial carcinoma


2379 Section 28

Miki Ohira-Ichikawa Genomic landscape of aggressive tumor subtype in MYCN-non-amplified neuroblastoma


2424 Section 30

Niloufar Javanmardi, Susanne Fransson, Rose-Marie Sjöberg, Anna Djos, Per Kogner, Tommy Martinsson

Neuroblastoma: Telomere elongation is responsible for aggressive behavior


2430 Section 30

Wenyue Sun, Bishwanath Chatterjee, John F. Shern, Yonghong Wang, Holly S. Stevenson, Daniel C. Edelman, Paul S. Meltzer, Javed Khan, Frederic G. Barr

DNA methylation characterization of fusion-positive and fusion-negative rhabdomyosarcoma primary tumors and cell lines


2434 Section 30

Santosh Yadav, Muralidharan Anbalagan, Melody Baddoo, Erik Flemington, Krzysztof Moroz, Kathleen Hering-Smith, Nick Makridakis

Landscape of somatic mutations in DNA repair genes in prostate cancer

Tuesday, Apr 19 8 AM–12 PM

2753 Section 3

Akpeli V. Nordor, Sophie Richon, Thierry Fournier, Dominique Bellet, Virginie Dangles-Marie, Martin J. Aryee

Common DNA methylation patterns in cancer and placental cells involved in migration and invasion, immune escape, and angiogenesis induction


2762 Section 4

Min-Ae Song, Theodore M. Brasky, Catalin Marian, Daniel Y. Weng, Cenny Taslim, Adana A. Llanos, Ramona G. Dumitrescu, Zhenhua Liu, Joel B. Mason, Bhaskar V. Kallakury, Jo L. Freudenheim, Peter G. Shields

One-carbon metabolism genetic variant and genome-wide DNA methylation in breast tissues from healthy women


2777 Section 4

Muhammad G. Kibriya, Mohammed Kamal, Mustafizur Rahman, Shantanu Roy, Maruf Raza, Rupash Paul, Habibul Ahsan, Zahidul Haq, Farzana Jasmine

Interaction of microsatellite instability (MSI) and tumor for differential DNA methylation in colorectal carcinoma


2778 Section 4

Costanza Paoletti, Andi K. Cani, Kimberly Aung, Elizabeth P. Darga, Emily M. Cannell, Daniel H. Hovelson, Maryam Yazdani, Allen R. Blevins, Nahomi Tokudome, Paul J. Baratta, Jose M. Larios, Dafydd G. Thomas, Martha E. Brown, Christina Gersch, Anne F. Schott, Daniel Robinson, Arul M. Chinnaiyan, Farideh Bischoff, Daniel F. Hayes, James M. Rae, Scott A. Tomlins

Genetic profiling of circulating tumor cells (CTC) in metastatic breast cancer (MBC) patients


3151 Section 22

Qiuyin Cai, Jirong Long, Hua Xie, Xiaofei Wang, Jie Wu, Regina Courtney, Xiao Ou Shu, Wei Zheng, William J. Blot

Association of oral microbiome with lung cancer risk: results from the Southern Community Cohort Study


3455 Section 36


Krysta M. Coyle, Patrick Murphy, Dejan Vidovic, Cheryl A. Dean, Margaret L. Thomas, Derek Clements, Mohammad Sultan, Ahmad Vaghar-Kashani, Carman Giacomantonio, Lucy Helyer, Ian Weaver, Shashi Gujar, Patrick WK Lee, Paola Marcato

ALDH1A3-inducible RARRES1 is a tumor suppressor in triple-negative breast cancer and is methylated in claudin-low breast cancers

Tuesday, Apr 19 1 PM–5 PM

3661 Section 8

Junya Fujimoto, Sayuri Nunomura, Wenhua Lang, Yihua Liu, Jinsong Wei, Joshua Ochieng, Yasminka Jakubek, Edwin Ostrin, Jason Petersen, Gareth Davies, Nadine Darwiche, Erik Ehli, Jerry Fowler, Paul Scheet, Humam Kadara

Development of KRAS-mutant lung adenocarcinoma in tobacco carcinogen-exposed mice with knockout of the airway lineage-specific G-protein-coupled receptor GPRC5A


4056 Section 28

Sebastian Schölch, Lahiri K. Nanduri, Daniel Kühn, Jürgen Weitz, Moritz Koch, Nuh N. Rahbari

Establishment and initial characterization of human hepatocellular carcinoma organoid culture


4263 Section 35

Charlotte R. Feddersen, Adam J. Dupuy Discovery and characterization of 2 novel drivers of hepatocellular carcinoma

Tuesday, Apr 19 4:20 PM–4:35 PM


Center

Miharu Kobayashi, Laura Cohelo, Dominic Guanzon, Katherin Scholz-Romero, Melissa Brown, Richard Kline, Li Li, Gregory Rice, Carlos Salomon

Exosomes isolated from ovarian cancer cells transfer oncogenic features to the target cells promoting epithelial to mesenchymal transition



Center

Kevin C. Johnson, E. Andres Houseman, Jessica E. King, Camilo E. Fadul, Brock C. Christensen

Tandem profiling of 5-methyl and 5-hydroxymethylcytosine in glioblastoma identifies tumor-specific distribution of 5-hydroxymethylcytosine and associations with patient survival

Wednesday, Apr 20 8 AM–12 PM

4431 Section 3

Aditya Sharma, Elaine Notis, Christine Mella, Steven J. Kuerbitz

Genome-wide CpG island methylation profiling analysis identifies an epigenetically dysregulated necroptosis mediator in osteosarcoma


4433 Section 3

Lissette Delgado-Cruzata, Hui-Chen Wu, Jin Shen, Tiffany Thomas, Abby B. Siegel, Yu-Jing Zhang, Abhishek Goyal, Christine C. Hsu, Helen E. Remotti, Regina M. Santella

Relationship between DNA methylation of TET genes and levels of 5-methylcytosine and 5-hydroxymethylcytosine in hepatocellular carcinoma


4439 Section 3

Mary E. Sehl, Patricia A. Ganz, Steve Horvath DNA methylation age is accelerated in breast tissue of healthy women donors


4444 Section 3

Yuan-Wan Sun, Karam El-Bayoumy, Yuka Imamura Kawasawa, Anna Salzberg, Cesar Aliaga, Krishnegowda Gowdahalli, Shantu Amin, Kun-Ming Chen

Genome-wide analysis of DNA methylation induced by environmental carcinogen dibenzo[def,p]chrysene in ovarian tissues of mice


4454 Section 3

Sofie van Huffel, Robert C. Day, Jisha Antony, Judith Marsman, Julia A. Horsfield, Anita K. Dunbier

4C-seq analysis of a breast cancer susceptibility locus on 6q25.1


4518 Section 6

Swati Garg, Mahadeo A. Sukhai, Maksym Misyura, Mariam Thomas, Tong Zhang, Lillian L. Siu, Philippe L. Bedard, Tracy L. Stockley, Suzanne Kamel-Reid

Impact of TP53 status and functional classification on molecular profiles in breast cancer subtypes


4765 Section 18


Kasmintan A. Schrader, Carolyn Chu’ng, Eric Zhao, Hui-li Wong, Yaoqing Shen, Martin Jones, Tom Thomson, Howard Lim, Sean Young, Carol Cremin, Robert Holt, Peter Eirew, Joanna Karasinska, Jacquie Schein, Yongjun Zhao, Andy Mungall, Richard Moore, Yussanne Ma, Alexandra Fok, Robyn Roscoe, Stephen Yip, Gillian Mitchell, Aly Karsan, Steven Jones, David Schaeffer, Janessa Laskin, Marco Marra, Daniel Renouf

Genomic analysis of pancreatic ductal adenocarcinoma in a patient with MUTYH-associated polyposis


5226 Section 34

Gary J. Latham, Julie Krosting, Michael Dodge, Robert Zeigler, Liangjing Chen, Jason Plyler, Shobha Gokul, Junya Fujimoto, Vassiliki Papadimitrakopoulou, Ignacio Wistuba, Richard Blidner, Brian Haynes

A unified and streamlined targeted sequencing system for the quantification of DNA mutations and RNA expression markers in lung cancer


1389 Section 21

Gloria Juan, Katherine Paweletz, Abraham Anderson, Erick Gamelin, Gregory Friberg, Robert Loberg, Florian Vogl

Detection of Aurora kinase A (AURKA) focal amplification in plasma samples of patients with recurrent ovarian cancer


439 Section 21

Maria J. Worsham, Kang Mei Chen, Indrani Datta, Josena K. Stephen, Dhananjay Chitale, George Divine

Differentially methylation between ER-negative and ER-positive breast cancer identifies master regulators to expose potential epigenetic drivers of aggressive disease


4484 Section 4

Joanne Xiu, Ryan Bender, Brian Abbott, Zoran Gatalica, Sandeep Reddy, Mohamed Salem, Shelly Seward

Mutations on the homologous recombination pathway in 13 cancer types


2750 Section 3

Hassan Ashktorab, Hamed Azimi, Mike Nickerson, Sara Bass, Joseph Boland, Meredith Yeager, Sudhir Varma, Mohamed Daremipouran, Zaki Sherif, Shima Ghavimi, Babak Shokrani, Edward Lee, Adeyinka Laiyemo, Hassan Brim

Targeted sequencing revealed distinctive and pathogenic mutations in African Americans with colorectal cancer


4488 Section 5

Vincent Faugeroux, Céline Lefebvre, Emma Pailler, Valérie Pierron, Fanny Billiot, Charles Marcaillou, Philippe Vielh, Semih Dogan, Philippe Rameau, Maud Ngocamus, Jean Charles Soria, Karim Fizazi, Yohann Loriot, Sylvia Julien, Françoise Farace

Whole-exome sequencing of single circulating tumor cells according to epithelial-mesenchymal marker expression in metastatic prostate cancer


4953 Section 25

Ken Suzawa, Shuta Tomida, Takahiro Matsubara, Kadoaki Ohashi, Yuho Maki, Hiromasa Yamamoto, Mizuki Morita, Junichi Soh, Hiroaki Asano, Kazunori Tsukuda, Katuyuki Kiura, Shinichiro Miyoshi, Shinichi Toyooka

Detection of EGFR mutations in circulating cell-free DNA of non-small cell lung cancer patients by next-generation sequencing


2249 Section 22

Claudio Forcato, Julie Lalibertè, Chiara Bolognesi, Ivana Cataldo, Genny Buson, Chiara Mangano, Cinzia Cantù, Francesca Fontana, Paola Tononi, Gianni Medoro, Tim Harkins, Rita T. Lawlor, Aldo Scarpa, Nicolò Manaresi

Digital sorting rescues low-cellularity tumor FFPE samples for genome-wide copy number profiling


3617 Section 6

Yi Fang Lee, Mark Consugar, Kimberly Helzer, Mei Hui Tan, Lori Emrick, Ali Asgar Bhagat

Highly accurate genetic profiling of circulating tumor cells using a label-free inertial microfluidic approach coupled with droplet PCR-based next-generation sequencing


3953 Section 23

Bob T. Li, Filip Janku, Pasi A. Janne, Gordon B. Mills, Kiran Madwani, Ryan S. Alden, Cloud P. Paweletz, Marc Ladanyi, Alex Aravanis, Byoungsok Jung, Sante Gnerre, Amy J. Sehnert, David B. Solit, Gregory J. Riely, Geoffrey R. Oxnard

Ultra-deep next generation sequencing (NGS) of plasma cell-free DNA (cfDNA) from patients with advanced lung cancers: results from the Actionable Genome Consortium



Center


Patrice Penfornis, Joseph D. Fernandes, Radhika R. Pochampally

Polycomb protein SUZ12 is regulated by a novel miRNA like RNA (miR-G655A) present in extracellular vesicles secreted by mesenchymal stem/tromal cells


947 Section 2

Robert Iliev, Petra Faltejskova-Vychytilova, Zuzana Ozanova, Silvia Rybecka, Jaroslav Juracek, Jitka Mlcochova, Lenka Radova, Michal Stanik, Jan Dolezel, Michal Fedorko, Dalibor Pacik, Ondrej Slaby

miRNA and piRNA expression profiles in renal cell carcinoma tissue detected by next-generation sequencing


1953 Section 7

Julianna Tdr Parks, Luo Byron, Brian Crain, Snedecor June, Zhao Chen, Tingting Du, Gabriel L. Sica, Taofee K. Owonikoko, Stewart G. Neill, Scott Newman, Debra F. Saxe, Jennifer S. LoCoco, Han-Yu Chuang, Charles Lin, Kathryn M. Stephens, Michael R. Rossi, Matthew C. Friedenberg

An evaluation of NGS to identify gene fusions using RNA from FFPE solid tumor samples


3607 Section 6

Konstantinos Mavrommatis, Lauren Intagliata, Garth McGrath, Daniel Civello, Maureen Cronin

Establishing a robust NGS laboratory workflow and analysis pipeline for FFPE specimen RNA-Seq to support biopharmaceutical translational research


3626 Section 6


Giorgia Simonetti, Antonella Padella, Marco Manfrini, ítalo Faria do Valle, Cristina Papayannidis, Carmen Baldazzi, Maria Chiara Fontana, Viviana Guadagnuolo, Anna Ferrari, Elisa Zago, Marianna Garonzi, Simona Bernardi, Annalisa Astolfi, Maria Chiara Abbenante, Giovanni Marconi, Elisa Zuffa, Eugenia Franchini, Ilaria Iacobucci, Michele Cavo, Emanuela Ottaviani, Nicoletta Testoni, Alberto Ferrarini, Massimo Delledonne, Torsten Haferlach, Daniel Remondini, Giovanni Martinelli

A cell cycle-related genomic and transcriptomic signature distinguish aneuploid and euploid acute myeloid leukemia


90 Section 4

Scott R. Daigle, Samuel Angiuoli, Sian Jones, Scott Ribich, Heike Keilhack, Mark Sausen, Peter T. Ho, Stephen J. Blakemore

Development and application of a 62-gene panel for assessment of somatic sequence and structural variants in tumor DNA derived from non-Hodgkin lymphoma patients treated in a phase 1 clinical trial with the EZH2 inhibitor tazemetostat


137 Section 5

Aldo M. Roccaro, Yawara Kawano, Antonio Sacco, Jihye Park, Michele Moschetta, Yuji Mishima, Elizabeth Morgan, Ruben Carrasco, Irene Ghobrial

Dual conditional loss of BLIMP-1 and p53 in B cells drives B cell lymphomagenesis


679 Section 30

Sophia E. Maharry, Christopher J. Walker, Sandya Liyanarachchi, Sujay Mehta, James S. Blachly, Denis C. Guttridge, Clara D. Bloomfield, Albert de la Chapelle, Ann-Kathrin Eisfeld

Dissection of the major hematopoietic quantitative trait locus in chromosome 6q23.3 identifies miR-3662 as a player in hematopoiesis and AML


1117 Section 7

Andrew D. Kelly, Heike Kroeger, Jumpei Yamazaki, Rodolphe Taby, Frank Neumann, Sijia Yu, Justin T. Lee, Rong He, Shoudan Liang, Yue Lu, Matteo Cesaroni, Sherry A. Pierce, Steven M. Kornblau, Carlos E. Bueso-Ramos, Farhad Ravandi, Hagop M. Kantarjain, Jaroslav Jelinek, Jean-Pierre J. Issa

A CpG island methylator phenotype in acute myeloid leukemia independent of IDH mutations and associated with a favorable outcome


2779 Section 4

Hematological cancer profiling


Nataly Cruz-Rodriguez, Sandra M. Quijano, Leonardo J. Enciso, Alba L. Combita, Jovanny Zabaleta

Gene expression signature predicts induction treatment response and clinical outcome in adult Colombian patients with acute lymphoblastic leukemia


3121 Section 21

Jeonghwan Youk, Sunghoon Cho, Daeyoon Kim, Youngil Koh, Inho Kim, Murim Choi, Sung-Soo Yoon

CDK11B, PTPRN2, and WDPCP were frequently duplicated genes in refractory/relapsed normal karyotype AML patients: identifying structural variations using whole genome sequencing


5225 Section 34

Tarantelli Chiara, Eugenio Gaudio, Ivo Kwee, Alberto Arribas, Andrea Rinaldi, Elena Bernasconi, Luciano Cascione, Petra Hillmann, Anastasios Stathis, Laura Carrassa, Massimo Broggini, Georg Stussi, Doriano Fabbro, Emanuele Zucca, Vladimir Cmiljanovic, Francesco Bertoni

The dual PI3K/MTOR inhibitor PQR309 is active in mature B cell lymphoma cell lines bearing resistance to the PI3K-delta inhibitor idelalisib and specific gene expression features


380 Section 19

Predictive and diagnostic biomarkers


Monica M. Reinholz, Debrah M. Thompson, Ihab Botros, Matt Rounseville, Patrick C. Roche

NGS-based measurement of gene expression of 2560 oncology-related biomarkers in formalin-fixed, paraffin-embedded (FFPE) tissues


1383 Section 21

Kerry Deutsch, Fang Yin Lo, Claire Olson, Sharon Austin, Kellie Howard, Amanda Leonti, Lindsey Maassel, Christopher Subia, Tuuli Saloranta, Nicole Christopherson, Kathryn Shiji, Shradha Patil, Stuart Schwartz, Peter Papenhausen, Steven Anderson, Anup Madan

Bioinformatic analysis of RNA-Seq data to search for novel diagnostic/prognostic biomarkers of pancreatic ductal adenocarcinoma


104 Section 4

Omar J. Sosa, Vinícius F. Paixão, João C. Setubal, Eduardo M. Reis

Bioinformatic analysis of RNA-Seq data to search for novel diagnostic/prognostic biomarkers of pancreatic ductal adenocarcinoma


105 Section 4

Amrita Datta, Hogyoung Kim, Allison Feibus, Melody Badoo, Adedoyin Johnson, Ahmed Moustafa, Jonathan Silberstein, Krishnarao Moparty, Raju Thomas, Asim B. Abdel-Mageed

Urine cfDNA SNPs as early biomarkers of prostate cancer


424 Section 21

Christa Haldrup, Anne-Sofie Lynnerup, Tine M. Storebjerg, Søren Vang, Peter Wild, Tapio Visakorpi, Christian Arsov, Wolfgang A. Schulz, Johan Lindberg, Henrik Grönberg, Lars Egevad, Michael Borre, Torben F. Ørntoft, Søren Høyer, Karina D. Sørensen

Large-scale evaluation of SLC18A2 in prostate cancer reveals diagnostic and prognostic biomarker potential at 3 molecular levels


451 Section 21

Malgorzata A. Komor, Annemieke C. Hiemstra, Thang V. Pham, Sander R. Piersma, Robert P. Sebra, Bo W. Han, Meredith Ashby, Beatriz Carvalho, Gerrit A. Meijer, Connie R. Jimenez, Remond JA Fijneman

Proteogenomic analysis of alternative splicing: the search for novel biomarkers for colorectal cancer



Center

John F. Palma, Yu Chuan Tai, Wei-min Liu, Steve Anderson, Anup Madan, John W. Longshore, Arundhati Rao

RT-PCR and NGS comparison: detection of known EGFR mutations in non-small cell lung cancer clinical samples with routine laboratory testing


1394 Section 21


Perry Maxwell, Jurgen Del Favero, Marc-Aurel Fuchs, Josep Tabernero, Tim Maughan, Mark Middleton, Richard Addams, Christian Rolfo, Brian Hennessey, Pierre Laurent-Puig, Alberto Bardelli, Thierry Andre, Vlad Popovici, Patrick Johnstone, Richard Wilson, Mark Lawler, Sandra Van Schaeybroeck, Manuel Salto Tellez

Validation of a MEK/MET-specific NGS panel for early-phase trial interrogation


1396 Section 21

Cecchin Erika, Eva Dreussi, Sara Gagno, Chiara Zanusso, Marcella Montico, Claudio Belluco, Antonino De Paoli, Salvatore Pucciarelli, Luca Quartuccio, Salvatore De Vita, Vincenzo Canzonieri, Angela Buonadonna, Maria Luisa Friso, Sara Lonardi, Giuseppe Toffoli

IL-17F-rs9463772 independently predicts long-term outcome in locally advanced rectal cancer


1420 Section 22

Niroshan Nadarajah, Manja Meggendorfer, Wolfgang Kern, Claudia Haferlach, Torsten Haferlach

Significance assessment of mutations in 944 MDS patients using publicly available variant databases and mutation impact prediction software


1514 Section 27

Lindsay M. Morton, Joshua N. Sampson, Gregory T. Armstrong, Ting-Huei Chen, Melissa Hudson, Eric Karlins, Casey L. Dagnall, Shenchao Li, Carmen L. Wilson, Kumar Srivastava, Wei Liu, Guolian Kang, Kevin Oeffinger, Tara O. Henderson, Chaya S. Moskowitz, Todd M. Gibson, Diana M. Merino, Jeannette R. Wong, Sue Hammond, Joseph P. Neglia, Lucie M. Turcotte, Jeremy Miller, Laura Bowen, William A. Wheeler, Wendy M. Leisenring, John A. Whitton, Laurie Burdette, Belynda D. Hicks, Mitchell J. Machiela, Aurelie Vogt, Zhaoming Wang, Meredith Yeager, Geoffrey Neale, Matthew Lear, Louise C. Strong, Yutaka Yasui, Marilyn Stovall, Rita E. Weathers, Susan A. Smith, Rebecca Howell, Stella M. Davies, Gretchen A. Radloff, Amy Berrington de González, Peter D. Inskip, Preetha Rajaraman, Joseph F. Fraumeni, Jr., Smita Bhatia, Stephen J. Chanock, Margaret A. Tucker, Leslie L. Robison

Genome-wide association study identifies 2 susceptibility loci that modify radiation-related risk for breast cancer after childhood cancer: a report from the Childhood Cancer Survivor Study and St. Jude Lifetime Cohort

Monday, Apr 18 3:20 PM–3:35 PM


Center

Arup Ratan Chakraborty, Erica Hlavin Bell, Simon Kriste, Vanessa Drendel, Joseph McElRoy, Martin Werner, Anca Grosu, Arnab Chakravarti

Novel putative diagnostic methylation biomarkers for prostate cancer identified by whole-genome DNA methylation profiling


2781 Section 4

Francesca Bianchi, Loris De Cecco, Tiziana Triulzi, Sandra Romero-Cordoba, Michele Sommariva, Chiara Storti, Piera Aiello, Elda Tagliabue, Andrea Balsari, Lucia Sfondrini

AIRE is expressed and associated with good prognosis in breast cancer


3924 Section 22

Keiko Shinjo, Keisuke Katsushima, Genta Nagae, Hiroyuki Aburatani, Kenji Yamao, Yutaka Kondo

Development of DNA methylation biomarkers for pancreatic cancer diagnosis


4448 Section 3

Semra Demokan, Sevde Comert, Cansu Ozkoklesen, Murat Ulusan, Gulsum Ak, Canan Alatli, Nejat Dalay

Discovery of novel epigenetic biomarkers in premalignant/malignant oral cavity lesions by methylation arrays


4458 Section 4

Yinan Zheng, Brian T. Joyce, Elena Colicino, Lei Liu, Wei Zhang, Qi Dai, Martha J. Shrubsole, Warren A. Kibbe, Tao Gao, Zhou Zhang, Nadereh Jafari, Joel Schwartz, Andrea A. Baccarelli, Lifang Hou

Blood epigenetic age may predict cancer incidence and mortality


4480 Section 4

Woochang Lee, Heejoon Jo, Xiaoying Yin, David A. Eberhard, Nirali M. Patel, Michele C. Hayward, Ashley H. Salazar, Joel S. Parker, William Y. Kim, Henry S. Earp III, Norman E. Sharpless, David N. Hayes

Integration of targeted RNA sequencing to targeted DNA sequencing for the characterization of clinically relevant variants in a population of thousands of patients treated on clinical trial


4499 Section 5

Konstantinos Leventakos, Aaron S. Mansfield, Stephen J. Murphy, Sarah H. Johnson, Sarah E. Kerr, Marie Christine Aubry, George Vasmatzis, Julian R. Molina

A prognostic model for pulmonary carcinoid tumors based on large chromosomal alterations


4513 Section 5


Dennis Poel, Maarten Neerincx, Daoud L.S. Sie, Nicole C.T. van Grieken, R. Shankaraiah, F. S.W. van der Wolf, J.H.T.M. van Waesberghe, J.D. Burggraaf, Paul P. Eijk, Bauke Ylstra, Cees Verhoef, Mark A. van de Wiel, Henk M.W. Verheul, Tineke E. Buffart

miR expression profiles can predict response to systemic treatment in patients with advanced colorectal cancer


4928 Section 24

Nancy A. Uhrhammer, Nagi El Saghir, Yannick Bidet, Manon Delahaye-Sourdeix, Flora Ponelle, Marie Ollier, Sandrine Viala, Firas Kreidieh, Nathalie Khoueiry-Zgheib, Yves-Jean Bignon

Next-generation sequencing of a panel of genes contributing to breast cancer risk


5224 Section 34

Andre Marziali Pro-Seq: a novel method to improve sequencing accuracy for liquid biopsy of ctDNA from healthy individuals and cancer patients


3141 Section 22

Takeo Fujii, Cecile Rose T. Vibat, Daniel D. Karp, Sarina A. Piha-Paul, Vivek Subbiah, Apostolia M. Tsimberidou, Siquing Fu, David S. Hong, Helen J. Huang, Kiran Madwani, Debra L. Andrews, Saege Hancock, Aung Naing, Rajyalakshmi Luthra, Bryan K. Kee, Scott Kopetz, Mark G. Erlander, Vlada Melnikova, Funda Meric-Bernstam, Filip Janku

Circulating tumor DNA assay performance for detection and monitoring of KRAS mutations in urine from patients with advanced cancers


3146 Section 22

Jordi Remon, Jean Charles Soria, David Planchard, Cecile Jovelet, Chloe Pannet, Ludovic Lacroix, Annas Gazzah, Andrew Lawson, Sarah Smalley, Kenth Howarth, David Gale, Emma Green, Vincent Plagnol, Nitzan Rosenfeld, Ken Oulassen, Nathalie Chaput, Benjamin Besse

Liquid biopsies for molecular profiling of mutations in non-small cell lung cancer patients lacking tissue samples


3192 Section 23

Pedro Mendez, Jun-Hee Yoon, Sharon Lee, James Kim, Jenny Dang, Thomas Kim, David Jablons, Il Jin Kim

A new innovative and robust targeted deep sequencing system: 36 hours turnaround time from patient samples to the final mutation report


3609 Section 6

Lynne Apone, Pingfang Liu, Vaish Panchapakesa, Deyra Rodriguez, Karen Duggan, Krishnan Keerthana, Nicole Nichols, Yanxia Bei, Julie Menin, Brad Langhorst, Christine Sumner, Christine Chater, Joanna Bybee, Laurie Mazzola, Danielle Rivizzigno, Fiona Stewart, Eileen Dimalanta, Theodore Davis

Enhancing clinical utility of NGS with reduced bias, low DNA input, library construction


3620 Section 6

Chia-Ling Hsieh, Clare Zlatkov, Byron Luo, Chen Zhao, Kathryn Stephens, Han-Yu Chuang, Lisa Kelly, Katherine Chang, Rachel Liang, Jianli Cao, Scott Lang, Ashley Adams, Naseem Ajili, Laurel Ball, Glorianna Caves, Danny Chou, Katie Clark, Brian Crain, Anthony Daulo, Sarah Dumm, Ridwana Ekram, Yonmee Han, Anne Jager, Suzanne Johansen, Li Teng, Jenn Lococo, Jaime McLean, Juli Parks, Jason Rostron, Jennifer Sayne, Jennifer Silhavy, June Snedecor, Mckenzi Toh, Stephanie Tong, Elizabeth Upsall, Paulina Walichiewicz, Xiao Chen, Amanda Young, Ali Kuraishy, Karen Gutekunst, Matt Friedenberg, Charles Lin

Development of a comprehensive and highly sensitive next-generation sequencing assay for detection of copy number variations


3624 Section 6

Travis A. Clark, Mark Kennedy, Jie He, Geneva Young, Mandy Zhao, Mike Coyne, Virginia Breese, Lauren Young, Shan Zhong, Mark Bailey, Bernard Fendler, Erica Schleifman, Eric Peters, Phil J. Stephens, Geoff A. Otto, Doron Lipson

Rigorous validation of a clinical circulating tumor DNA assay for cancer molecular profiling


3965 Section 23

Adam H. Greer, Glenn Mills, Hong Yin Amplicon-based NGS detects targeted variants in paired tissue and ctDNA samples


3967 Section 23

Michael Fremed, Sajida Piperdi, Wendong Zhang, Shahina Maqbool, Brent Calder, Raquel Castellanos, Jonathan Gill, Michael Roth, Bang Hoang, David Geller, Richard Gorlick, Daniel Weiser

Circulating tumor DNA as “liquid biopsy” in pediatric osteosarcoma


3133A Section 21

Kohichiroh Yasui, Akira Tomie, Naoto Iwai, Tomoko Kitaichi, Osamu Dohi, Yasuyuki Gen, Yoshito Itoh

Epigenetic silencing of miR-199a-3p is associated with increased cell survival, enhanced cell motility, and sensitivity to tivantinib through regulation of c-Met expression in hepatocellular carcinoma


963 Section 2


Salvatore Piscuoglio, Charlotte KY Ng, Y. Hannah Wen, Arto Mannermaa, Paolo Peterlongo, Carlo Tondini, Marketa Janatova, Teo Soo Hwang, Pei-Sze Ng, Lai-Meng Looi, William Foulkes, Georgia Chenevix-Trench, Britta Weigelt, Melissa C. Southey, Marc Tischkowitz, Jorge S. Reis-Filho

Mutational landscape of breast cancers from PALB2 germline mutation carriers


134 Section 5

Anthony M. Musolf, Claire L. Simpson, Mariza de Andrade, Diptasri Mandal, Colette Gaba, Ping Yang, Ming You, Elena Y. Kupert, Marshall W. Anderson, Ann G. Schwartz, Susan M. Pinney, Christopher I. Amos, Joan E. Bailey-Wilson

Chromatin remodeling gene ARID1B is linked to familial lung cancer


2542 Section 35

Christopher Ricketts, J. Keith Killian, Cathy D. Vocke, Carole Sourbier, Youfeng Yang, Maria J. Merino, Paul S. Meltzer, W. Marston Linehan

A renal CpG island methylator phenotype (R-CIMP) in kidney tumors associated with germline mutations of FH and SDHB

Monday, Apr 18 4:20 PM–4:35 PM


Center

Brandon L. Pierce, Muhammad Kibriya, Farzana Jasmine, Joseph Graziano, Habibul Ahsan

Arsenic exposure and mosaic loss of the Y chromosome among Bangladeshi men


4303 Section 36

Joaquin Mateo, Suzanne Carreira, Helen Mossop, Pasquale Rescigno, Michael Kolinsky, Elena Castro, Ada Balasopoulou, Jo Hunt, Desamparados Roda, Claudia Bertan, Jane Goodall, Susana Miranda, Penny Flohr, Nuria Porta, Zsofia Kote-Jarai, David Olmos, Christopher J. Lord, Emma Hall, Ros Eeles, Johann S. de Bono

DNA repair genes aberrations in germline DNA in metastatic castration-resistant prostate cancer patients



Center

Germline testing

Therapeutic response profiling


Sheida Nabavi, Ashish Juvekar, Nicholas Wang, Lewis C. Cantley, Gerburg M. Wulf.

Analysis of resistance to the combination of a PI3K and PARP inhibitor using a genomic sequencing approach


159 Section 6

Juliette Sauveur, Abdelkamel Chettab, Eva Matera, Aurore Cleret, Ariel Savina, Charles Dumontet

Mechanisms of resistance to trastuzumab emtansine in gastric cancer


309 Section 16

Belen Hernandez, Kathryn Cronise, James C. Costello, Rodney Page, Susan Lana, Kenneth L. Jones, Dawn L. Duval

Canine transitional cell carcinoma of the bladder expresses activated BRAF, but is not sensitive to vemurafenib


617 Section 28

Francesca Mascia, Kaytee L. Pokrzywinski, V. Ashutosh Rao microRNA regulation of Nrf2 and the antioxidant response in breast cancer cells following redox therapy


1090 Section 6

Emilia Komulainen, Alice Shia, Jasmin Bansal, Francessa Cavicchioli, Karen O’Leary, John Foster, Peter Schmid

Inhibition of heat shock protein 27 (HSP27) expression by apatorsen as a therapeutic strategy in breast cancer


3759 Section 16

Sharareh Siamakpour-Reihani, Wei Chen, David Corcoran, Chen-Ting Lee, Ying Zhou, Mark W. Dewhirst, Jen-Tsan A. Chi, Janet K. Horton

Radiation response genome-wide analysis using paired pre- and post-radiation FFPE human breast tumor samples


1647 Section 32

Wing-Yee Lo, Corinna Mohr, Friederike Steudel, Marjanka Schmidt, Douglas Easton, Reiner Hoppe, Werner Schroth, Peter Ruth, Robert Lukowski, Hiltrud Brauch, in collaboration with the Breast Cancer Association Consortium

The role of genetic variation in calcium-activated potassium channels in breast cancer patients treated with tamoxifen


2030 Section 14


Prashanth Prabakaran, Kwangok P. Nickel, David T. Yang, Lauryn R. Werner, Justine Y. Bruce, Aaron M. Wieland, Timothy M. McCulloch, Gregory K. Hartig, Paul M. Harari, Adam D. Swick, Randall J. Kimple

Patient-derived adenoid cystic carcinoma xenografts to study molecular target modulation of tumor radiosensitivity


3044 Section 18

Michaela L. Granados, Laurie G. Hudson, Li Luo, Sabrina L. Samudio-Ruiz

DNA methylation analysis in cisplatin-resistant ovarian cancer cells and recurrent ovarian cancer patient samples


4437 Section 3

Jai N. Patel, Chen Jiang, Kouros Owzar, Daniel L. Hertz, Flora A. Mulkey, William K. Kelly, Susan Halabi, Yoichi Furukawa, Cameron Lassiter, Susan G. Dorsey, Paula N. Friedman, Eric J. Small, Michael A. Carducci, John F. Mahoney, Michael J. Kelley, Yusuke Nakamura, Michiaki Kubo, Mark J. Ratain, Michael J. Morris, Howard L. McLeod

A discovery study to identify clinical and genetic risk factors for bevacizumab-related gastrointestinal hemorrhage in metastatic castration-resistant prostate cancer (mCRPC) patients treated on CALGB 90401


2037 Section 14

Qianghu Wang, Ravesanker Ezhilarasan, Eskil Eskilsson, Joy Gumin, Jie Yang, Mona Jaffari, Ming Tang, Kenneth D. Aldape, Frederick F. Lang, Roel G.W. Verhaak, Erik P. Sulman

A glioblastoma methylation assay (GaMA) developed from genomic analysis of glioma spheroid cultures predicts response toradiation therapy in patients with glioblastoma


1646 Section 32

Jeffrey P. Bond, Elizabeth VanSickle, Thomas S. Dexhemier, Richard R. Neubig, Giselle L. Sholler

Neuroblastoma drug response profiles are associated with gene expression profiles


68 Section 3

Takashi Kobunai, Kenta Tsunekuni, Kazuaki Matsuoka, Hiroshi Tsukihara, Teiji Takechi

Mutational and copy number profiling of cancer-related genes in 26 human tumor xenografts and their correlations with antitumor drug sensitivities


5175 Section 33

Glen J. Weiss, Julia Beck, Donald P. Braun, Kirsten Bornemann-Kolatzki, Heather Barilla, Rhiannon Cubello, Ashish Sangal, Robert P. Whitehead, Madappa Kundranda, Vivek Khemka, Howard B. Urnovitz, Ekkehard Schutz

Changes in tumor cell-free DNA copy number instability (CNI) predict therapeutic response in metastatic cancers


3138 Section 22


Humam Kadara, Murim Choi, Jiexin Zhang, Edwin Parra Cuentas, Jaime Rodriguez Canales, Stephen Gaffney, Zi-Ming Zhao, Carmen Behrens, Junya Fujimoto, Chi-Wan Chow, Neda Kalhor, Cesar Moran, David Rimm, Stephen G. Swisher, Don L. Gibbons, John V. Heymach, Edward Kaftan, Jeffrey Townsend, Thomas J. Lynch, Joseph Schlessinger, J. Jack Lee, Richard Lifton, Ignacio I. Wistuba, Roy S. Herbst

Whole-exome sequencing and immune profiling of early-stage lung adenocarcinoma


89 Section 4

Woosung Chung, Hye Hyeon Eum, Kyu-Tae Kim, Kyung-Min Lee, Arum Jo, WonShik Han, Hae-Ock Lee, Woong-Yang Park

Identification of the carcinoma and immune cells in the breast cancer by single-cell RNA sequencing


160 Section 6

Edwin R. Parra, Pan Tong, Humam Kadara, Vassiliki Papadimitrakopoulou, Julie Izzo, Jaime Rodriguez-Canales, Carmen Behrens, John D. Minna, Jing Wang, Ignacio I. Wistuba, John V. Heymach, Ferdinandos Skoulidis

Impact of APOBEC mutagenesis on the immune microenvironment of lung adenocarcinoma (LUAC)


532 Section 25

Etienne Mahe, David Mulder, Mark Dowar, Mahadeo Sukhai, Linh Nguyen, Pamela Ohashi, Jan Delabie, Tracy L. Stockley, Trevor Pugh, Suzanne Kamel-Reid

Improving T cell receptor clonotyping of T cell lymphomas using hybrid Capture and next-generation sequencing



Center

Tanuka Biswas, Rebecca Fritzemeier, Adam Mark, Tobias Meißner, Brandon M. Young, Mark D. Pegram

Antibody-dependent cell-mediated cytotoxicity (ADCC) tolerance to monoclonal antibody therapeutics in human breast and colon cancer cell lines


2123 Section 17

Markus Daniel Lacher, Charles L. Wiseman, Joseph Wagner Molecular profile of a GM-CSF overexpressing breast cancer whole-cell vaccine with systemic antitumor activity


2369 Section 27

Dustin Bauknight, Andrew Buckner, Lindsey Brinton, Timothy Bullock, Kimberly Kelly

T cell-targeted peptides for monitoring immune response in melanoma


4147 Section 31

Anton Valouev, David Jaffe, Neil Weisenfeld, Heather Ordonez, Adrian Fehr, Patrick Marks, Michael Schnall-Levin, Tarjei Mikkelsen

Complete phased sequencing of HLA genes using linked reads


3613 Section 6

Immuno-oncology profiling


Eric Lader, Melanie Hussong, Matthew Fosbrink Development of a quantitative targeted RNA-Seq methodology for use in differential gene expression analysis


1845 Section 3

Vasily N. Aushev, Davide Degli Esposti, Eunjee Lee, Hector Vargas, Zdenko Herceg, Jun Zhu, Jia Chen

miR-500a is involved in breast cancer-related gene expression pathways and associated with patients survival


1896 Section 5

Manuel Landesfeind, Bruno Zeitouni, Anne-Lise Peille, Vincent Vuaroqueaux

Combining whole-exome and RNA-Seq data improves the quality of PDX mutation profiles


2701 Section 1

Carolyn J. Vivian, Amanda E. Brinker, Gerald C. Gooden, Christophe Legendre, Samuel Turpin, Devin C. Koestler, Bodour Salhia, Danny R. Welch

Mitochondrial genomic backgrounds affect nuclear DNA methylation and gene expression


2784 Section 4

Hong Yin, Adam H. Greer, Glenn Mills Target RNA sequencing analysis of hypoxia-induced expression of stem cell genes in primary cultures of prostate cancer cells


2800 Section 5

Kaytee L. Pokrzywinski, Francesca Mascia, V. Ashutosh Rao Therapeutic targeting of the mitochondria: An evaluation of the transcriptional link between the antioxidant response and autophagy


2917 Section 9

Sophia Kyriazopoulou-Panagiotopoulou, Patrick Marks, Haynes Heaton, Heather Ordonez, Kristina Giorda, Cassandra Jabara, Billy Lau, John M. Bell, Michael Schnall-Levin, Hanlee P. Ji

Linked reads enable detailed, phased resolution of structural variation in the cancer genome


3602 Section 6

Sukhinder K. Sandhu, Cassie Schumacher, Laurie Kurihara, Tim Harkins, Vladimir Makarov

Targeted exome and panel analysis from low-input and FFPE DNA using hybridization capture for cancer genome studies


3637 Section 7

Maura A. McGrail, Staci L. Solin, Jeffrey A. Haltom, Laura E. Schultz, Jeffrey J. Essner, Heather R. Shive

Expression profiling of zebrafish rb1 neuroectodermal-like brain tumors: a new model of CNS PNETs


4179 Section 32

Dominique Scherer, Isabelle Miran, Chafika Mazouni, Benjamin Sarfati, Marine Bernard, Julien Adam, Emilie Louvet, Francoise Drusch, Philippe Vielh, Khalid Alhazmi, Cornelia M. Ulrich, Suzette Delaloge, Jean Feunteun

Gene expression profiles in adipose tissue of cancer-bearing breasts differ from that of tumor-free breasts


4286 Section 36

Claire Olson, Fang Yin Lo, Kerry Deutsch, Sharon Austin, Kellie Howard, Amanda Leonti, Lindsey Maassel, Christopher Subia, Tuuli Saloranta, Nicole Christopherson, Kathryn Shiji, Shradha Patil, Steven Anderson, Anup Madan

Synergistic effects of promoter-associated DNA methylation and genetic alterations to better understand oncogenic gene expression profiles


4436 Section 3

Khamael Kadhim Al-Taee, Martin R. Berger, Hassan Adwan Reisolated metastatic pancreatic cancer cells show distinct modulation of gene expression during liver colonization


1548 Section 28

Gene expression profiling

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