Browsing by Author "Szallasi, Zoltan"
Now showing items 1-15 of 15
-
Biasogram: Visualization of Confounding Technical Bias in Gene Expression Data
Krzystanek, Marcin; Szallasi, Zoltan; Eklund, Aron C. (Public Library of Science, 2013)Gene expression profiles of clinical cohorts can be used to identify genes that are correlated with a clinical variable of interest such as patient outcome or response to a particular drug. However, expression measurements ... -
A Breast Cancer Meta-Analysis of Two Expression Measures of Chromosomal Instability Reveals a Relationship with Younger Age at Diagnosis and High Risk Histopathological Variables
Endesfelder, David; McGranahan, Nicholas; Birkbak, Nicolai Juul; Szallasi, Zoltan; Kschischo, Maik; Graham, Trevor A.; Swanton, Charles (Impact Journals LLC, 2011)Breast cancer in younger patients often presents with adverse histopathological features, including increased frequency of estrogen receptor negative and lymph node positive disease status. Chromosomal instability (CIN) ... -
The CIN4 Chromosomal Instability qPCR Classifier Defines Tumor Aneuploidy and Stratifies Outcome in Grade 2 Breast Cancer
Szász, Attila Marcell; Eklund, Aron C.; Sztupinszki, Zsófia; Rowan, Andrew; Tőkés, Anna-Mária; Székely, Borbála; Kiss, András; Szendrői, Miklós; Győrffy, Balázs; Swanton, Charles; Kulka, Janina; Li, Qiyuan; Szallasi, Zoltan (Public Library of Science, 2013)Purpose Quantifying chromosomal instability (CIN) has both prognostic and predictive clinical utility in breast cancer. In order to establish a robust and clinically applicable gene expression-based measure of CIN, we ... -
Complete Genes May Pass from Food to Human Blood
Spisák, Sándor; Solymosi, Norbert; Ittzés, Péter; Bodor, András; Kondor, Dániel; Vattay, Gábor; Barták, Barbara K.; Sipos, Ferenc; Galamb, Orsolya; Tulassay, Zsolt; Szállási, Zoltán; Rasmussen, Simon; Sicheritz-Ponten, Thomas; Brunak, Søren; Molnár, Béla; Csabai, István (Public Library of Science, 2013)Our bloodstream is considered to be an environment well separated from the outside world and the digestive tract. According to the standard paradigm large macromolecules consumed with food cannot pass directly to the ... -
A comprehensive survey of the mutagenic impact of common cancer cytotoxics
Szikriszt, Bernadett; Póti, Ádám; Pipek, Orsolya; Krzystanek, Marcin; Kanu, Nnennaya; Molnár, János; Ribli, Dezső; Szeltner, Zoltán; Tusnády, Gábor E.; Csabai, István; Szallasi, Zoltan; Swanton, Charles; Szüts, Dávid (BioMed Central, 2016)Background: Genomic mutations caused by cytotoxic agents used in cancer chemotherapy may cause secondary malignancies as well as contribute to the evolution of treatment-resistant tumour cells. The stable diploid genome ... -
The Genome of the Chicken DT40 Bursal Lymphoma Cell Line
Molnár, János; Póti, Ádám; Pipek, Orsolya; Krzystanek, Marcin; Kanu, Nnennaya; Swanton, Charles; Tusnády, Gábor E.; Szallasi, Zoltan; Csabai, István; Szüts, Dávid (Genetics Society of America, 2014)The chicken DT40 cell line is a widely used model system in the study of multiple cellular processes due to the efficiency of homologous gene targeting. The cell line was derived from a bursal lymphoma induced by avian ... -
In silico prediction of tumor antigens derived from functional missense mutations of the cancer gene census
Khalili, Jahan S.; Hanson, Russell W.; Szallasi, Zoltan (Landes Bioscience, 2012)Antigen-specific immune responses against peptides derived from missense gene mutations have been identified in multiple cancers. The application of personalized peptide vaccines based on the tumor mutation repertoire of ... -
Jetset: Selecting the Optimal Microarray Probe Set to Represent a Gene
Li, Qiyuan; Birkbak, Nicolai Juul; Gyorffy, Balazs; Szallasi, Zoltan; Eklund, Aron C (BioMed Central, 2011)Background: Interpretation of gene expression microarrays requires a mapping from probe set to gene. On many Affymetrix gene expression microarrays, a given gene may be detected by multiple probe sets, which may deliver ... -
MECP2 Is a Frequently Amplified Oncogene with a Novel Epigenetic Mechanism That Mimics the Role of Activated RAS in Malignancy
Neupane, Manish; Clark, Allison Paige; Landini, S.; Birkbak, N; Eklund, A. C.; Lim, E.; Culhane, Aedin; Barry, William T.; Schumacher, Sandra Kay; Beroukhim, Rameen; Szallasi, Zoltan; Vidal, Marc; Hill, David E.; Silver, Daniel P. (American Association for Cancer Research (AACR), 2015)An unbiased genome-scale screen for unmutated genes that drive cancer growth when overexpressed identified MECP2 as a novel oncogene. MECP2 resides in a region of the Xchromosome that is significantly amplified across 18% ... -
Opposite prognostic roles of HIF1α and HIF2α expressions in bone metastatic clear cell renal cell cancer
Szendrői, Attila; Szász, A. Marcell; Kardos, Magdolna; Tőkés, Anna-Mária; Idan, Roni; Szűcs, Miklós; Kulka, Janina; Nyirády, Péter; Szendrői, Miklós; Szállási, Zoltán; Győrffy, Balázs; Tímár, József (Impact Journals LLC, 2016)BACKGROUND Prognostic markers of bone metastatic clear cell renal cell cancer (ccRCC) are poorly established. We tested prognostic value of HIF1α/HIF2α and their selected target genes in primary tumors and corresponding ... -
Pan-cancer analysis of genomic scar signatures associated with homologous recombination deficiency suggests novel indications for existing cancer drugs
Marquard, Andrea M; Eklund, Aron C; Joshi, Tejal; Krzystanek, Marcin; Favero, Francesco; Wang, Zhigang C; Richardson, Andrea L; Silver, Daniel P; Szallasi, Zoltan; Birkbak, Nicolai J (BioMed Central, 2015)Background: Ovarian and triple-negative breast cancers with BRCA1 or BRCA2 loss are highly sensitive to treatment with PARP inhibitors and platinum-based cytotoxic agents and show an accumulation of genomic scars in the ... -
A robust prognostic gene expression signature for early stage lung adenocarcinoma
Krzystanek, Marcin; Moldvay, Judit; Szüts, David; Szallasi, Zoltan; Eklund, Aron Charles (BioMed Central, 2016)Background: Stage I lung adenocarcinoma is usually not treated with adjuvant chemotherapy; however, around half of these patients do not survive 5 years. Therefore, a reliable prognostic biomarker for early stage patients ... -
Thrombocytosis portends adverse prognostic significance in patients with stage II colorectal carcinoma
Guo, Tianhua; Krzystanek, Marcin; Szallasi, Zoltan; Szallasi, Arpad (F1000Research, 2014)Thrombocytosis portends adverse prognostic significance in many types of cancers including ovarian and lung carcinoma. In this study, we determined the prevalence and prognostic significance of thrombocytosis (defined as ... -
Tumor Mutation Burden Forecasts Outcome in Ovarian Cancer with BRCA1 or BRCA2 Mutations
Birkbak, Nicolai Juul; Kochupurakkal, Bose; Izarzugaza, Jose M. G.; Eklund, Aron C.; Li, Yang; Liu, Joyce; Szallasi, Zoltan; Matulonis, Ursula A.; Richardson, Andrea L.; Iglehart, J. Dirk; Wang, Zhigang C. (Public Library of Science, 2013)Background: Increased number of single nucleotide substitutions is seen in breast and ovarian cancer genomes carrying disease-associated mutations in BRCA1 or BRCA2. The significance of these genome-wide mutations is ... -
TumorTracer: a method to identify the tissue of origin from the somatic mutations of a tumor specimen
Marquard, Andrea Marion; Birkbak, Nicolai Juul; Thomas, Cecilia Engel; Favero, Francesco; Krzystanek, Marcin; Lefebvre, Celine; Ferté, Charles; Jamal-Hanjani, Mariam; Wilson, Gareth A.; Shafi, Seema; Swanton, Charles; André, Fabrice; Szallasi, Zoltan; Eklund, Aron Charles (BioMed Central, 2015)Background: A substantial proportion of cancer cases present with a metastatic tumor and require further testing to determine the primary site; many of these are never fully diagnosed and remain cancer of unknown primary ...