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  1. Article ; Online: Multimodality pictorial review of IgG4-related disease in the abdomen and pelvis.

    Czerniak, Suzanne / Rao, Aditya / Mathur, Mahan

    Abdominal radiology (New York)

    2023  Volume 48, Issue 10, Page(s) 3147–3161

    Abstract: Background: Immunoglobulin G4-related disease (IgG4-RD) is a systemic, immune-mediated disease that can affect multiple organs, including the orbits, salivary glands, thyroid gland, lungs, aorta, pancreas, bile ducts, lymph nodes, and retroperitoneum. ... ...

    Abstract Background: Immunoglobulin G4-related disease (IgG4-RD) is a systemic, immune-mediated disease that can affect multiple organs, including the orbits, salivary glands, thyroid gland, lungs, aorta, pancreas, bile ducts, lymph nodes, and retroperitoneum. While timely diagnosis is particularly important given the efficacy of glucocorticoid treatment for IgG4-RD, accurate recognition can prove a challenge given the overlap between the imaging features of this disease and other entities.
    Purpose: After a review of the epidemiology, pathophysiology, and clinical considerations (including treatment) associated with IgG4-RD, this pictorial review will showcase the variable imaging manifestations of this disease in the abdomen and pelvis. Post-treatment imaging appearance of these entities will be reviewed and mimickers of this disease in the abdomen and pelvis will be presented.
    Conclusion: The presence of mass-like soft tissue with radiographic characteristics of fibrosis affecting multiple organs should raise suspicion for IgG4-RD, although definite diagnosis can only be made with appropriate clinical, serological, and pathologic data.
    MeSH term(s) Humans ; Immunoglobulin G4-Related Disease ; Autoimmune Diseases ; Abdomen/pathology ; Fibrosis ; Pelvis/pathology
    Language English
    Publishing date 2023-07-06
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 2839786-1
    ISSN 2366-0058 ; 2366-004X
    ISSN (online) 2366-0058
    ISSN 2366-004X
    DOI 10.1007/s00261-023-03996-w
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 1262: Show issues Location:
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  2. Article ; Online: Erratum to: a resting state functional magnetic resonance imaging study of concussion in collegiate athletes.

    Czerniak, Suzanne M / Sikoglu, Elif M / Liso Navarro, Ana A / McCafferty, Joseph / Eisenstock, Jordan / Stevenson, J Herbert / King, Jean A / Moore, Constance M

    Brain imaging and behavior

    2015  Volume 9, Issue 3, Page(s) 650

    Language English
    Publishing date 2015-09
    Publishing country United States
    Document type Published Erratum
    ZDB-ID 2377165-3
    ISSN 1931-7565 ; 1931-7557
    ISSN (online) 1931-7565
    ISSN 1931-7557
    DOI 10.1007/s11682-014-9328-6
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  3. Article ; Online: Areas of the brain modulated by single-dose methylphenidate treatment in youth with ADHD during task-based fMRI: a systematic review.

    Czerniak, Suzanne M / Sikoglu, Elif M / King, Jean A / Kennedy, David N / Mick, Eric / Frazier, Jean / Moore, Constance M

    Harvard review of psychiatry

    2013  Volume 21, Issue 3, Page(s) 151–162

    Abstract: Objective: Attention-deficit/hyperactivity disorder (ADHD) is a psychiatric disorder affecting 5% of children. Methylphenidate (MPH) is a common medication for ADHD. Studies examining MPH's effect on pediatric ADHD patients' brain function using ... ...

    Abstract Objective: Attention-deficit/hyperactivity disorder (ADHD) is a psychiatric disorder affecting 5% of children. Methylphenidate (MPH) is a common medication for ADHD. Studies examining MPH's effect on pediatric ADHD patients' brain function using functional magnetic resonance imaging (fMRI) have not been compiled. The goals of this systematic review were to determine (1) which areas of the brain in pediatric ADHD patients are modulated by a single dose of MPH, (2) whether areas modulated by MPH differ by task type performed during fMRI data acquisition, and (3) whether changes in brain activation due to MPH relate to clinical improvements in ADHD-related symptoms.
    Methods: We searched the electronic databases PubMed and PsycINFO (1967-2011) using the following terms: ADHD AND (methylphenidate OR MPH OR ritalin) AND (neuroimaging OR MRI OR fMRI OR BOLD OR event related), and identified 200 abstracts, 9 of which were reviewed based on predefined criteria.
    Results: In ADHD patients the middle and inferior frontal gyri, basal ganglia, and cerebellum were most often affected by MPH. The middle and inferior frontal gyri were frequently affected by MPH during inhibitory control tasks. Correlation between brain regions and clinical improvement was not possible due to the lack of symptom improvement measures within the included studies.
    Conclusions: Throughout nine task-based fMRI studies investigating MPH's effect on the brains of pediatric patients with ADHD, MPH resulted in increased activation within frontal lobes, basal ganglia, and cerebellum. In most cases, this increase "normalized" activation of at least some brain areas to that seen in typically developing children.
    MeSH term(s) Adolescent ; Attention Deficit Disorder with Hyperactivity/drug therapy ; Attention Deficit Disorder with Hyperactivity/physiopathology ; Basal Ganglia/drug effects ; Basal Ganglia/physiopathology ; Brain/drug effects ; Brain/physiopathology ; Central Nervous System Stimulants/pharmacology ; Central Nervous System Stimulants/therapeutic use ; Cerebellum/drug effects ; Cerebellum/physiopathology ; Child ; Female ; Frontal Lobe/drug effects ; Frontal Lobe/physiopathology ; Functional Neuroimaging ; Humans ; Magnetic Resonance Imaging ; Male ; Methylphenidate/pharmacology ; Methylphenidate/therapeutic use
    Chemical Substances Central Nervous System Stimulants ; Methylphenidate (207ZZ9QZ49)
    Language English
    Publishing date 2013-05-09
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review ; Systematic Review
    ZDB-ID 1174775-4
    ISSN 1465-7309 ; 1067-3229
    ISSN (online) 1465-7309
    ISSN 1067-3229
    DOI 10.1097/HRP.0b013e318293749e
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    Zs.A 3888: Show issues Location:
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  4. Article ; Online: Effects of Recent Concussion on Brain Bioenergetics: A Phosphorus-31 Magnetic Resonance Spectroscopy Study.

    Sikoglu, Elif M / Liso Navarro, Ana A / Czerniak, Suzanne M / McCafferty, Joseph / Eisenstock, Jordan / Stevenson, J Herbert / King, Jean A / Moore, Constance M

    Cognitive and behavioral neurology : official journal of the Society for Behavioral and Cognitive Neurology

    2015  Volume 28, Issue 4, Page(s) 181–187

    Abstract: Background: Although clinical evaluations and neurocognitive assessments are commonly used to evaluate the extent of and recovery from concussion, brain bioenergetics could provide a more quantitative marker. The neurometabolic response to a concussion ... ...

    Abstract Background: Although clinical evaluations and neurocognitive assessments are commonly used to evaluate the extent of and recovery from concussion, brain bioenergetics could provide a more quantitative marker. The neurometabolic response to a concussion is thought to increase neuronal energy consumption and thus the demand for nucleoside triphosphate (NTP).
    Objective: We investigated the possible disruption in high-energy metabolism within the prefrontal cortex of college athletes who had either had a concussion within the past 6 months (n=14) or had never had a concussion (n=13). We hypothesized that concussed athletes would have imbalanced brain bioenergetics resulting from increased NTP consumption, and these biochemical changes would correspond to impaired cognitive abilities.
    Methods: We used phosphorus-31 magnetic resonance spectroscopy to quantify high-energy phosphates. We performed the neuroimaging in conjunction with neurocognitive assessments targeting prefrontal cortex-mediated tasks.
    Results: Our results revealed significantly lower γ-NTP levels in the athletes after concussion. Although the concussed and non-concussed participants performed similarly in neurocognitive assessments, lower levels of γ-NTP were associated with worse scores on neurocognitive tasks.
    Conclusions: Our results support the concept of increased energy demand in the prefrontal cortex of a concussed brain, and we found that while neurocognitive assessments appear normal, brain energetics may be abnormal. A longitudinal study could help establish brain NTP levels as a biomarker to aid in diagnosis and to assess recovery in concussed patients.
    MeSH term(s) Adolescent ; Adult ; Athletic Injuries/metabolism ; Brain Concussion/metabolism ; Brain Concussion/physiopathology ; Energy Metabolism/physiology ; Female ; Humans ; Longitudinal Studies ; Magnetic Resonance Spectroscopy/methods ; Male ; Nucleosides/metabolism ; Phosphates/metabolism ; Phosphorus Isotopes ; Prefrontal Cortex/metabolism ; Universities ; Young Adult
    Chemical Substances Nucleosides ; Phosphates ; Phosphorus Isotopes
    Language English
    Publishing date 2015-12
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2108112-8
    ISSN 1543-3641 ; 1543-3633
    ISSN (online) 1543-3641
    ISSN 1543-3633
    DOI 10.1097/WNN.0000000000000076
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    Zs.A 2439: Show issues Location:
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  5. Article ; Online: Vitamin D3 Supplemental Treatment for Mania in Youth with Bipolar Spectrum Disorders.

    Sikoglu, Elif M / Navarro, Ana A Liso / Starr, Debra / Dvir, Yael / Nwosu, Benjamin Udoka / Czerniak, Suzanne M / Rogan, Ryan C / Castro, Martha C / Edden, Richard A E / Frazier, Jean A / Moore, Constance M

    Journal of child and adolescent psychopharmacology

    2015  Volume 25, Issue 5, Page(s) 415–424

    Abstract: Objective: We aimed to determine the effect of an open-label 8 week Vitamin D3 supplementation on manic symptoms, anterior cingulate cortex (ACC) glutamate, and γ-aminobutyric acid (GABA) in youth exhibiting symptoms of mania; that is, patients with ... ...

    Abstract Objective: We aimed to determine the effect of an open-label 8 week Vitamin D3 supplementation on manic symptoms, anterior cingulate cortex (ACC) glutamate, and γ-aminobutyric acid (GABA) in youth exhibiting symptoms of mania; that is, patients with bipolar spectrum disorders (BSD). We hypothesized that an 8 week Vitamin D3 supplementation would improve symptoms of mania, decrease ACC glutamate, and increase ACC GABA in BSD patients. Single time point metabolite levels were also evaluated in typically developing children (TD).
    Methods: The BSD group included patients not only diagnosed with BD but also those exhibiting bipolar symptomology, including BD not otherwise specified (BD-NOS) and subthreshold mood ratings (Young Mania Rating Scale [YMRS] ≥8 and Clinical Global Impressions - Severity [CGI-S] ≥3). Inclusion criteria were: male or female participants, 6-17 years old. Sixteen youth with BSD exhibiting manic symptoms and 19 TD were included. BSD patients were asked to a take daily dose (2000 IU) of Vitamin D3 (for 8 weeks) as a supplement. Neuroimaging data were acquired in both groups at baseline, and also for the BSD group at the end of 8 week Vitamin D3 supplementation.
    Results: Baseline ACC GABA/creatine (Cr) was lower in BSD than in TD (F[1,31]=8.91, p=0.007). Following an 8 week Vitamin D3 supplementation, in BSD patients, there was a significant decrease in YMRS scores (t=-3.66, p=0.002, df=15) and Children's Depression Rating Scale (CDRS) scores (t=-2.93, p=0.01, df=15); and a significant increase in ACC GABA (t=3.18, p=0.007, df=14).
    Conclusions: Following an 8 week open label trial with Vitamin D3, BSD patients exhibited improvement in their mood symptoms in conjunction with their brain neurochemistry.
    MeSH term(s) Adolescent ; Affect/drug effects ; Bipolar Disorder/drug therapy ; Child ; Cholecalciferol/therapeutic use ; Dietary Supplements ; Female ; Glutamic Acid/metabolism ; Gyrus Cinguli/drug effects ; Gyrus Cinguli/metabolism ; Humans ; Male ; Psychiatric Status Rating Scales ; Treatment Outcome ; gamma-Aminobutyric Acid/metabolism
    Chemical Substances Cholecalciferol (1C6V77QF41) ; Glutamic Acid (3KX376GY7L) ; gamma-Aminobutyric Acid (56-12-2)
    Language English
    Publishing date 2015-06-17
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 1055410-5
    ISSN 1557-8992 ; 1044-5463
    ISSN (online) 1557-8992
    ISSN 1044-5463
    DOI 10.1089/cap.2014.0110
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 3091: Show issues Location:
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  6. Article: Fluctuations in total antioxidant capacity, catalase activity and hydrogen peroxide levels of follicular fluid during bovine folliculogenesis.

    Gupta, Sajal / Choi, Audrey / Yu, Hope Y / Czerniak, Suzanne M / Holick, Emily A / Paolella, Louis J / Agarwal, Ashok / Combelles, Catherine M H

    Reproduction, fertility, and development

    2011  Volume 23, Issue 5, Page(s) 673–680

    Abstract: Follicular fluid is an important environment for oocyte development, yet current knowledge regarding its in vivo oxidant and antioxidant levels remains limited. Examining follicular fluid oxidants and antioxidants will improve understanding of their ... ...

    Abstract Follicular fluid is an important environment for oocyte development, yet current knowledge regarding its in vivo oxidant and antioxidant levels remains limited. Examining follicular fluid oxidants and antioxidants will improve understanding of their changes in vivo and contribute to optimisation of in vitro maturation conditions. The aim of the present study was to consider selected markers, namely catalase (CAT) enzyme activity, total antioxidant capacity (TAC) and hydrogen peroxide (H(2)O(2)) in follicular fluid samples (n = 503) originating from bovine antral follicles. The dynamic changes in two relevant antioxidant measures and one reactive oxygen species (ROS) were measured through stages of bovine follicular development and the oestrous cycle. CAT activity and H(2)O(2) levels decreased significantly as follicle size increased, whereas TAC increased significantly as follicle size increased. Lower TAC and higher H(2)O(2) in small follicles suggest increased ROS in the initial stages of folliculogenesis. Because CAT levels are highest in the follicular fluid of small follicles in the setting of an overall low TAC, CAT may represent a dominant antioxidant defence in the initial stages of folliculogenesis. Future studies must focus on other reactive oxygen species and their various scavenger types during antral folliculogenesis.
    MeSH term(s) Animals ; Antioxidants/metabolism ; Catalase/metabolism ; Cattle ; Estrous Cycle/metabolism ; Female ; Follicular Fluid/enzymology ; Hydrogen Peroxide/metabolism ; Ovarian Follicle/enzymology
    Chemical Substances Antioxidants ; Hydrogen Peroxide (BBX060AN9V) ; Catalase (EC 1.11.1.6)
    Language English
    Publishing date 2011-06-02
    Publishing country Australia
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 1019913-5
    ISSN 1448-5990 ; 1031-3613
    ISSN (online) 1448-5990
    ISSN 1031-3613
    DOI 10.1071/RD10270
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    Zs.A 2756: Show issues Location:
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  7. Article ; Online: A resting state functional magnetic resonance imaging study of concussion in collegiate athletes.

    Czerniak, Suzanne M / Sikoglu, Elif M / Liso Navarro, Ana A / McCafferty, Joseph / Eisenstock, Jordan / Stevenson, J Herbert / King, Jean A / Moore, Constance M

    Brain imaging and behavior

    2014  Volume 9, Issue 2, Page(s) 323–332

    Abstract: Sports-related concussions are currently diagnosed through multi-domain assessment by a medical professional and may utilize neurocognitive testing as an aid. However, these tests have only been able to detect differences in the days to week post- ... ...

    Abstract Sports-related concussions are currently diagnosed through multi-domain assessment by a medical professional and may utilize neurocognitive testing as an aid. However, these tests have only been able to detect differences in the days to week post-concussion. Here, we investigate a measure of brain function, namely resting state functional connectivity, which may detect residual brain differences in the weeks to months after concussion. Twenty-one student athletes (9 concussed within 6 months of enrollment; 12 non-concussed; between ages 18 and 22 years) were recruited for this study. All participants completed the Wisconsin Card Sorting Task and the Color-Word Interference Test. Neuroimaging data, specifically resting state functional Magnetic Resonance Imaging data, were acquired to examine resting state functional connectivity. Two sample t-tests were used to compare the neurocognitive scores and resting state functional connectivity patterns among concussed and non-concussed participants. Correlations between neurocognitive scores and resting state functional connectivity measures were also determined across all subjects. There were no significant differences in neurocognitive performance between concussed and non-concussed groups. Concussed subjects had significantly increased connections between areas of the brain that underlie executive function. Across all subjects, better neurocognitive performance corresponded to stronger brain connectivity. Even at rest, brains of concussed athletes may have to 'work harder' than their healthy peers to achieve similar neurocognitive results. Resting state brain connectivity may be able to detect prolonged brain differences in concussed athletes in a more quantitative manner than neurocognitive test scores.
    MeSH term(s) Adolescent ; Athletes ; Athletic Injuries/physiopathology ; Brain/physiopathology ; Brain Concussion/physiopathology ; Brain Mapping ; Female ; Humans ; Interview, Psychological ; Magnetic Resonance Imaging ; Male ; Neuropsychological Tests ; Rest ; Young Adult
    Language English
    Publishing date 2014-08-12
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2377165-3
    ISSN 1931-7565 ; 1931-7557
    ISSN (online) 1931-7565
    ISSN 1931-7557
    DOI 10.1007/s11682-014-9312-1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma.

    Linehan, W Marston / Spellman, Paul T / Ricketts, Christopher J / Creighton, Chad J / Fei, Suzanne S / Davis, Caleb / Wheeler, David A / Murray, Bradley A / Schmidt, Laura / Vocke, Cathy D / Peto, Myron / Al Mamun, Abu Amar M / Shinbrot, Eve / Sethi, Anurag / Brooks, Samira / Rathmell, W Kimryn / Brooks, Angela N / Hoadley, Katherine A / Robertson, A Gordon /
    Brooks, Denise / Bowlby, Reanne / Sadeghi, Sara / Shen, Hui / Weisenberger, Daniel J / Bootwalla, Moiz / Baylin, Stephen B / Laird, Peter W / Cherniack, Andrew D / Saksena, Gordon / Haake, Scott / Li, Jun / Liang, Han / Lu, Yiling / Mills, Gordon B / Akbani, Rehan / Leiserson, Mark D M / Raphael, Benjamin J / Anur, Pavana / Bottaro, Donald / Albiges, Laurence / Barnabas, Nandita / Choueiri, Toni K / Czerniak, Bogdan / Godwin, Andrew K / Hakimi, A Ari / Ho, Thai H / Hsieh, James / Ittmann, Michael / Kim, William Y / Krishnan, Bhavani / Merino, Maria J / Mills Shaw, Kenna R / Reuter, Victor E / Reznik, Ed / Shelley, Carl S / Shuch, Brian / Signoretti, Sabina / Srinivasan, Ramaprasad / Tamboli, Pheroze / Thomas, George / Tickoo, Satish / Burnett, Kenneth / Crain, Daniel / Gardner, Johanna / Lau, Kevin / Mallery, David / Morris, Scott / Paulauskis, Joseph D / Penny, Robert J / Shelton, Candace / Shelton, W Troy / Sherman, Mark / Thompson, Eric / Yena, Peggy / Avedon, Melissa T / Bowen, Jay / Gastier-Foster, Julie M / Gerken, Mark / Leraas, Kristen M / Lichtenberg, Tara M / Ramirez, Nilsa C / Santos, Tracie / Wise, Lisa / Zmuda, Erik / Demchok, John A / Felau, Ina / Hutter, Carolyn M / Sheth, Margi / Sofia, Heidi J / Tarnuzzer, Roy / Wang, Zhining / Yang, Liming / Zenklusen, Jean C / Zhang, Jiashan / Ayala, Brenda / Baboud, Julien / Chudamani, Sudha / Liu, Jia / Lolla, Laxmi / Naresh, Rashi / Pihl, Todd / Sun, Qiang / Wan, Yunhu / Wu, Ye / Ally, Adrian / Balasundaram, Miruna / Balu, Saianand / Beroukhim, Rameen / Bodenheimer, Tom / Buhay, Christian / Butterfield, Yaron S N / Carlsen, Rebecca / Carter, Scott L / Chao, Hsu / Chuah, Eric / Clarke, Amanda / Covington, Kyle R / Dahdouli, Mahmoud / Dewal, Ninad / Dhalla, Noreen / Doddapaneni, Harsha V / Drummond, Jennifer A / Gabriel, Stacey B / Gibbs, Richard A / Guin, Ranabir / Hale, Walker / Hawes, Alicia / Hayes, D Neil / Holt, Robert A / Hoyle, Alan P / Jefferys, Stuart R / Jones, Steven J M / Jones, Corbin D / Kalra, Divya / Kovar, Christie / Lewis, Lora / Li, Jie / Ma, Yussanne / Marra, Marco A / Mayo, Michael / Meng, Shaowu / Meyerson, Matthew / Mieczkowski, Piotr A / Moore, Richard A / Morton, Donna / Mose, Lisle E / Mungall, Andrew J / Muzny, Donna / Parker, Joel S / Perou, Charles M / Roach, Jeffrey / Schein, Jacqueline E / Schumacher, Steven E / Shi, Yan / Simons, Janae V / Sipahimalani, Payal / Skelly, Tara / Soloway, Matthew G / Sougnez, Carrie / Tam, Angela / Tan, Donghui / Thiessen, Nina / Veluvolu, Umadevi / Wang, Min / Wilkerson, Matthew D / Wong, Tina / Wu, Junyuan / Xi, Liu / Zhou, Jane / Bedford, Jason / Chen, Fengju / Fu, Yao / Gerstein, Mark / Haussler, David / Kasaian, Katayoon / Lai, Phillip / Ling, Shiyun / Radenbaugh, Amie / Van Den Berg, David / Weinstein, John N / Zhu, Jingchun / Albert, Monique / Alexopoulou, Iakovina / Andersen, Jeremiah J / Auman, J Todd / Bartlett, John / Bastacky, Sheldon / Bergsten, Julie / Blute, Michael L / Boice, Lori / Bollag, Roni J / Boyd, Jeff / Castle, Erik / Chen, Ying-Bei / Cheville, John C / Curley, Erin / Davies, Benjamin / DeVolk, April / Dhir, Rajiv / Dike, Laura / Eckman, John / Engel, Jay / Harr, Jodi / Hrebinko, Ronald / Huang, Mei / Huelsenbeck-Dill, Lori / Iacocca, Mary / Jacobs, Bruce / Lobis, Michael / Maranchie, Jodi K / McMeekin, Scott / Myers, Jerome / Nelson, Joel / Parfitt, Jeremy / Parwani, Anil / Petrelli, Nicholas / Rabeno, Brenda / Roy, Somak / Salner, Andrew L / Slaton, Joel / Stanton, Melissa / Thompson, R Houston / Thorne, Leigh / Tucker, Kelinda / Weinberger, Paul M / Winemiller, Cynthia / Zach, Leigh Anne / Zuna, Rosemary

    The New England journal of medicine

    2016  Volume 374, Issue 2, Page(s) 135–145

    Abstract: Background: Papillary renal-cell carcinoma, which accounts for 15 to 20% of renal-cell carcinomas, is a heterogeneous disease that consists of various types of renal cancer, including tumors with indolent, multifocal presentation and solitary tumors ... ...

    Abstract Background: Papillary renal-cell carcinoma, which accounts for 15 to 20% of renal-cell carcinomas, is a heterogeneous disease that consists of various types of renal cancer, including tumors with indolent, multifocal presentation and solitary tumors with an aggressive, highly lethal phenotype. Little is known about the genetic basis of sporadic papillary renal-cell carcinoma, and no effective forms of therapy for advanced disease exist.
    Methods: We performed comprehensive molecular characterization of 161 primary papillary renal-cell carcinomas, using whole-exome sequencing, copy-number analysis, messenger RNA and microRNA sequencing, DNA-methylation analysis, and proteomic analysis.
    Results: Type 1 and type 2 papillary renal-cell carcinomas were shown to be different types of renal cancer characterized by specific genetic alterations, with type 2 further classified into three individual subgroups on the basis of molecular differences associated with patient survival. Type 1 tumors were associated with MET alterations, whereas type 2 tumors were characterized by CDKN2A silencing, SETD2 mutations, TFE3 fusions, and increased expression of the NRF2-antioxidant response element (ARE) pathway. A CpG island methylator phenotype (CIMP) was observed in a distinct subgroup of type 2 papillary renal-cell carcinomas that was characterized by poor survival and mutation of the gene encoding fumarate hydratase (FH).
    Conclusions: Type 1 and type 2 papillary renal-cell carcinomas were shown to be clinically and biologically distinct. Alterations in the MET pathway were associated with type 1, and activation of the NRF2-ARE pathway was associated with type 2; CDKN2A loss and CIMP in type 2 conveyed a poor prognosis. Furthermore, type 2 papillary renal-cell carcinoma consisted of at least three subtypes based on molecular and phenotypic features. (Funded by the National Institutes of Health.).
    MeSH term(s) Carcinoma, Papillary/genetics ; Carcinoma, Papillary/metabolism ; CpG Islands/physiology ; DNA Methylation ; Humans ; Kidney Neoplasms/genetics ; Kidney Neoplasms/metabolism ; MicroRNAs/chemistry ; Mutation ; NF-E2-Related Factor 2/genetics ; NF-E2-Related Factor 2/metabolism ; Phenotype ; Proto-Oncogene Proteins c-met/chemistry ; Proto-Oncogene Proteins c-met/genetics ; Proto-Oncogene Proteins c-met/metabolism ; RNA, Messenger/chemistry ; RNA, Neoplasm/chemistry ; Sequence Analysis, RNA ; Signal Transduction/physiology
    Chemical Substances MicroRNAs ; NF-E2-Related Factor 2 ; NFE2L2 protein, human ; RNA, Messenger ; RNA, Neoplasm ; MET protein, human (EC 2.7.10.1) ; Proto-Oncogene Proteins c-met (EC 2.7.10.1)
    Language English
    Publishing date 2016-01-14
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 207154-x
    ISSN 1533-4406 ; 0028-4793
    ISSN (online) 1533-4406
    ISSN 0028-4793
    DOI 10.1056/NEJMoa1505917
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  9. Article ; Online: Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer

    Hoadley, Katherine A. / Yau, Christina / Hinoue, Toshinori / Wolf, Denise M. / Lazar, Alexander / Drill, Esther / Shen, Ronglai / Taylor, Alison M. / Cherniack, Andrew D. / Thorsson, Vésteinn / Akbani, Rehan / Bowlby, Reanne / Wong, Christopher K. / Wiznerowicz, Maciej / Sanchez-Vega, Francisco / Robertson, A. Gordon / Schneider, Barbara G. / Lawrence, Michael S. / Noushmehr, Houtan /
    Malta, Tathiane M. / Stuart, Joshua M. / Benz, Christopher C. / Laird, Peter W. / Caesar-Johnson, Samantha J. / Demchok, John A. / Felau, Ina / Kasapi, Melpomeni / Ferguson, Martin L. / Hutter, Carolyn M. / Sofia, Heidi J. / Tarnuzzer, Roy / Wang, Zhining / Yang, Liming / Zenklusen, Jean C. / Zhang, Jiashan (Julia) / Chudamani, Sudha / Liu, Jia / Lolla, Laxmi / Naresh, Rashi / Pihl, Todd / Sun, Qiang / Wan, Yunhu / Wu, Ye / Cho, Juok / DeFreitas, Timothy / Frazer, Scott / Gehlenborg, Nils / Getz, Gad / Heiman, David I. / Kim, Jaegil / Lin, Pei / Meier, Samuel A. / Noble, Michael S. / Saksena, Gordon / Voet, Doug / Zhang, Hailei / Bernard, Brady / Chambwe, Nyasha / Dhankani, Varsha / Knijnenburg, Theo / Kramer, Roger / Leinonen, Kalle / Liu, Yuexin / Miller, Michael / Reynolds, Sheila / Shmulevich, Ilya / Thorsson, Vesteinn / Zhang, Wei / Broom, Bradley M. / Hegde, Apurva M. / Ju, Zhenlin / Kanchi, Rupa S. / Korkut, Anil / Li, Jun / Liang, Han / Ling, Shiyun / Liu, Wenbin / Lu, Yiling / Mills, Gordon B. / Ng, Kwok-Shing / Rao, Arvind / Ryan, Michael / Wang, Jing / Weinstein, John N. / Zhang, Jiexin / Abeshouse, Adam / Armenia, Joshua / Chakravarty, Debyani / Chatila, Walid K. / de Bruijn, Ino / Gao, Jianjiong / Gross, Benjamin E. / Heins, Zachary J. / Kundra, Ritika / La, Konnor / Ladanyi, Marc / Luna, Augustin / Nissan, Moriah G. / Ochoa, Angelica / Phillips, Sarah M. / Reznik, Ed / Sander, Chris / Schultz, Nikolaus / Sheridan, Robert / Sumer, S. Onur / Sun, Yichao / Taylor, Barry S. / Wang, Jioajiao / Zhang, Hongxin / Anur, Pavana / Peto, Myron / Spellman, Paul / Benz, Christopher / Hayes, D. Neil / Parker, Joel S. / Wilkerson, Matthew D. / Ally, Adrian / Balasundaram, Miruna / Brooks, Denise / Carlsen, Rebecca / Chuah, Eric / Dhalla, Noreen / Holt, Robert / Jones, Steven J.M. / Kasaian, Katayoon / Lee, Darlene / Ma, Yussanne / Marra, Marco A. / Mayo, Michael / Moore, Richard A. / Mungall, Andrew J. / Mungall, Karen / Sadeghi, Sara / Schein, Jacqueline E. / Sipahimalani, Payal / Tam, Angela / Thiessen, Nina / Tse, Kane / Wong, Tina / Berger, Ashton C. / Beroukhim, Rameen / Cibulskis, Carrie / Gabriel, Stacey B. / Gao, Galen F. / Ha, Gavin / Meyerson, Matthew / Schumacher, Steven E. / Shih, Juliann / Kucherlapati, Melanie H. / Kucherlapati, Raju S. / Baylin, Stephen / Cope, Leslie / Danilova, Ludmila / Bootwalla, Moiz S. / Lai, Phillip H. / Maglinte, Dennis T. / Van Den Berg, David J. / Weisenberger, Daniel J. / Auman, J. Todd / Balu, Saianand / Bodenheimer, Thomas / Fan, Cheng / Hoyle, Alan P. / Jefferys, Stuart R. / Jones, Corbin D. / Meng, Shaowu / Mieczkowski, Piotr A. / Mose, Lisle E. / Perou, Amy H. / Perou, Charles M. / Roach, Jeffrey / Shi, Yan / Simons, Janae V. / Skelly, Tara / Soloway, Matthew G. / Tan, Donghui / Veluvolu, Umadevi / Fan, Huihui / Shen, Hui / Zhou, Wanding / Bellair, Michelle / Chang, Kyle / Covington, Kyle / Creighton, Chad J. / Dinh, Huyen / Doddapaneni, HarshaVardhan / Donehower, Lawrence A. / Drummond, Jennifer / Gibbs, Richard / Glenn, Robert / Hale, Walker / Han, Yi / Hu, Jianhong / Korchina, Viktoriya / Lee, Sandra / Lewis, Lora / Li, Wei / Liu, Xiuping / Morgan, Margaret / Morton, Donna / Muzny, Donna / Santibanez, Jireh / Sheth, Margi / Shinbrot, Eve / Wang, Linghua / Wang, Min / Wheeler, David A. / Xi, Liu / Zhao, Fengmei / Hess, Julian / Appelbaum, Elizabeth L. / Bailey, Matthew / Cordes, Matthew G. / Ding, Li / Fronick, Catrina C. / Fulton, Lucinda A. / Fulton, Robert S. / Kandoth, Cyriac / Mardis, Elaine R. / McLellan, Michael D. / Miller, Christopher A. / Schmidt, Heather K. / Wilson, Richard K. / Crain, Daniel / Curley, Erin / Gardner, Johanna / Lau, Kevin / Mallery, David / Morris, Scott / Paulauskis, Joseph / Penny, Robert / Shelton, Candace / Shelton, Troy / Sherman, Mark / Thompson, Eric / Yena, Peggy / Bowen, Jay / Gastier-Foster, Julie M. / Gerken, Mark / Leraas, Kristen M. / Lichtenberg, Tara M. / Ramirez, Nilsa C. / Wise, Lisa / Zmuda, Erik / Corcoran, Niall / Costello, Tony / Hovens, Christopher / Carvalho, Andre L. / de Carvalho, Ana C. / Fregnani, José H. / Filho, Adhemar Longatto / Reis, Rui M. / Scapulatempo-Neto, Cristovam / Silveira, Henrique C.S. / Vidal, Daniel O. / Burnette, Andrew / Eschbacher, Jennifer / Hermes, Beth / Noss, Ardene / Singh, Rosy / Anderson, Matthew L. / Castro, Patricia D. / Ittmann, Michael / Huntsman, David / Kohl, Bernard / Lệ Xuân / Thorp, Richard / Andry, Chris / Duffy, Elizabeth R. / Lyadov, Vladimir / Paklina, Oxana / Setdikova, Galiya / Shabunin, Alexey / Tavobilov, Mikhail / McPherson, Christopher / Warnick, Ronald / Berkowitz, Ross / Cramer, Daniel / Feltmate, Colleen / Horowitz, Neil / Kibel, Adam / Muto, Michael / Raut, Chandrajit P. / Malykh, Andrei / Barnholtz-Sloan, Jill S. / Barrett, Wendi / Devine, Karen / Fulop, Jordonna / Ostrom, Quinn T. / Shimmel, Kristen / Wolinsky, Yingli / Sloan, Andrew E. / De Rose, Agostino / Giuliante, Felice / Goodman, Marc / Karlan, Beth Y. / Hagedorn, C. H. / Eckman, John / Harr, Jodi / Myers, Jerome / Tucker, Kelinda / Zach, Leigh Anne / Deyarmin, Brenda / Hu, Hai / Kvecher, Leonid / Larson, Caroline / Mural, Richard J. / Somiari, Stella / Vicha, Ales / Zelinka, Tomas / Bennett, Joseph / Iacocca, Mary / Rabeno, Brenda / Swanson, Patricia / Latour, Mathieu / Lacombe, Louis / Têtu, Bernard / Bergeron, Alain / McGraw, Mary / Staugaitis, Susan M. / Chabot, John / Hibshoosh, Hanina / Sepulveda, Antonia / Su, Tao / Wang, Timothy / Potapova, Olga / Voronina, Olga / Desjardins, Laurence / Mariani, Odette / Roman-Roman, Sergio / Sastre, Xavier / Stern, Marc-Henri / Cheng, Feixiong / Signoretti, Sabina / Berchuck, Andrew / Bigner, Darell / Lipp, Eric / Marks, Jeffrey / McCall, Shannon / McLendon, Roger / Secord, Angeles / Sharp, Alexis / Behera, Madhusmita / Brat, Daniel J. / Chen, Amy / Delman, Keith / Force, Seth / Khuri, Fadlo / Magliocca, Kelly / Maithel, Shishir / Olson, Jeffrey J. / Owonikoko, Taofeek / Pickens, Alan / Ramalingam, Suresh / Shin, Dong M. / Sica, Gabriel / Van Meir, Erwin G. / Zhang, Hongzheng / Eijckenboom, Wil / Gillis, Ad / Korpershoek, Esther / Looijenga, Leendert / Oosterhuis, Wolter / Stoop, Hans / van Kessel, Kim E. / Zwarthoff, Ellen C. / Calatozzolo, Chiara / Cuppini, Lucia / Cuzzubbo, Stefania / DiMeco, Francesco / Finocchiaro, Gaetano / Mattei, Luca / Perin, Alessandro / Pollo, Bianca / Chen, Chu / Houck, John / Lohavanichbutr, Pawadee / Hartmann, Arndt / Stoehr, Christine / Stoehr, Robert / Taubert, Helge / Wach, Sven / Wullich, Bernd / Kycler, Witold / Murawa, Dawid / Chung, Ki / Edenfield, W. Jeffrey / Martin, Julie / Baudin, Eric / Bubley, Glenn / Bueno, Raphael / De Rienzo, Assunta / Richards, William G. / Kalkanis, Steven / Mikkelsen, Tom / Scarpace, Lisa / Girard, Nicolas / Aymerich, Marta / Campo, Elias / Giné, Eva / Guillermo, Armando López / Van Bang, Nguyen / Hanh, Phan Thi / Phu, Bui Duc / Tang, Yufang / Colman, Howard / Evason, Kimberley / Dottino, Peter R. / Martignetti, John A. / Gabra, Hani / Juhl, Hartmut / Akeredolu, Teniola / Stepa, Serghei / Hoon, Dave / Ahn, Keunsoo / Kang, Koo Jeong / Beuschlein, Felix / Breggia, Anne / Birrer, Michael / Bell, Debra / Borad, Mitesh / Bryce, Alan H. / Castle, Erik / Chandan, Vishal / Cheville, John / Copland, John A. / Farnell, Michael / Flotte, Thomas / Giama, Nasra / Ho, Thai / Kendrick, Michael / Kocher, Jean-Pierre / Kopp, Karla / Moser, Catherine / Nagorney, David / O’Brien, Daniel / O’Neill, Brian Patrick / Patel, Tushar / Petersen, Gloria / Que, Florencia / Rivera, Michael / Roberts, Lewis / Smallridge, Robert / Smyrk, Thomas / Stanton, Melissa / Thompson, R. Houston / Torbenson, Michael / Yang, Ju Dong / Zhang, Lizhi / Brimo, Fadi / Ajani, Jaffer A. / Gonzalez, Ana Maria Angulo / Behrens, Carmen / Bondaruk, olanta / Broaddus, Russell / Czerniak, Bogdan / Esmaeli, Bita / Fujimoto, Junya / Gershenwald, Jeffrey / Guo, Charles / Logothetis, Christopher / Meric-Bernstam, Funda / Moran, Cesar / Ramondetta, Lois / Rice, David / Sood, Anil / Tamboli, Pheroze / Thompson, Timothy / Troncoso, Patricia / Tsao, Anne / Wistuba, Ignacio / Carter, Candace / Haydu, Lauren / Hersey, Peter / Jakrot, Valerie / Kakavand, Hojabr / Kefford, Richard / Lee, Kenneth / Long, Georgina / Mann, Graham / Quinn, Michael / Saw, Robyn / Scolyer, Richard / Shannon, Kerwin / Spillane, Andrew / Stretch, Jonathan / Synott, Maria / Thompson, John / Wilmott, James / Al-Ahmadie, Hikmat / Chan, Timothy A. / Ghossein, Ronald / Gopalan, Anuradha / Levine, Douglas A. / Reuter, Victor / Singer, Samuel / Singh, Bhuvanesh / Tien, Nguyen Viet / Broudy, Thomas / Mirsaidi, Cyrus / Nair, Praveen / Drwiega, Paul / Miller, Judy / Smith, Jennifer / Zaren, Howard / Park, Joong-Won / Hung, Nguyen Phi / Kebebew, Electron / Linehan, Marston / Metwalli, Adam R. / Pacak, Karel / Pinto, Peter A. / Schiffman, Mark / Schmidt, Laura S. / Vocke, Cathy D. / Wentzensen, Nicolas / Worrell, Robert / Yang, Hannah / Moncrieff, Marc / Goparaju, Chandra / Melamed, Jonathan / Pass, Harvey / Botnariuc, Natalia / Caraman, Irina / Cernat, Mircea / Chemencedji, Inga / Clipca, Adrian / Doruc, Serghei / Gorincioi, Ghenadie / Mura, Sergiu / Pirtac, Maria / Stancul, Irina / Tcaciuc, Diana / Albert, Monique / Alexopoulou, Iakovina / Arnaout, Angel / Bartlett, John / Engel, Jay / Gilbert, Sebastien / Parfitt, Jeremy / Sekhon, Harman / Thomas, George / Rassl, Doris M. / Rintoul, Robert C. / Bifulco, Carlo / Tamakawa, Raina / Urba, Walter / Hayward, Nicholas / Timmers, Henri / Antenucci, Anna / Facciolo, Francesco / Grazi, Gianluca / Marino, Mirella / Merola, Roberta / de Krijger, Ronald / Gimenez-Roqueplo, Anne-Paule / Piché, Alain / Chevalier, Simone / McKercher, Ginette / Birsoy, Kivanc / Barnett, Gene / Brewer, Cathy / Farver, Carol / Naska, Theresa / Pennell, Nathan A. / Raymond, Daniel / Schilero, Cathy / Smolenski, Kathy / Williams, F. / Morrison, Carl / Borgia, Jeffrey A. / Liptay, Michael J. / Pool, Mark / Seder, Christopher W. / Junker, Kerstin / Omberg, Larsson / Dinkin, Mikhail / Manikhas, George / Alvaro, Domenico / Bragazzi, Maria Consiglia / Cardinale, Vincenzo / Carpino, Guido / Gaudio, Eugenio / Chesla, David / Cottingham, Sandra / Dubina, Michael / Moiseenko, Fedor / Dhanasekaran, Renumathy / Becker, Karl Friedrich / Janssen, Klaus-Peter / Slotta-Huspenina, Julia / Abdel-Rahman, Mohamed H. / Aziz, Dina / Bell, Sue / Cebulla, Colleen M. / Davis, Amy / Duell, Rebecca / Elder, J. Bradley / Hilty, Joe / Kumar, Bahavna / Lang, James / Lehman, Norman L. / Mandt, Randy / Nguyen, Phuong / Pilarski, Robert / Rai, Karan / Schoenfield, Lynn / Senecal, Kelly / Wakely, Paul / Hansen, Paul / Lechan, Ronald / Powers, James / Tischler, Arthur / Grizzle, William E. / Sexton, Katherine C. / Kastl, Alison / Henderson, Joel / Porten, Sima / Waldmann, Jens / Fassnacht, Martin / Asa, Sylvia L. / Schadendorf, Dirk / Couce, Marta / Graefen, Markus / Huland, Hartwig / Sauter, Guido / Schlomm, Thorsten / Simon, Ronald / Tennstedt, Pierre / Olabode, Oluwole / Nelson, Mark / Bathe, Oliver / Carroll, Peter R. / Chan, June M. / Disaia, Philip / Glenn, Pat / Kelley, Robin K. / Landen, Charles N. / Phillips, Joanna / Prados, Michael / Simko, Jeffry / Smith-McCune, Karen / VandenBerg, Scott / Roggin, Kevin / Fehrenbach, Ashley / Kendler, Ady / Sifri, Suzanne / Steele, Ruth / Jimeno, Antonio / Carey, Francis / Forgie, Ian / Mannelli, Massimo / Carney, Michael / Hernandez, Brenda / Campos, Benito / Herold-Mende, Christel / Jungk, Christin / Unterberg, A. / Deimling, Andreas von / Bossler, Aaron / Galbraith, Joseph / Jacobus, Laura / Knudson, Michael / Knutson, Tina / Ma, Deqin / Milhem, Mohammed / Sigmund, Rita / Godwin, Andrew K. / Madan, Rashna / Rosenthal, Howard G. / Adebamowo, Clement / Adebamowo, Sally N. / Boussioutas, Alex / Beer, David / Giordano, Thomas / Mes-Masson, Anne-Marie / Saad, Fred / Bocklage, Therese / Landrum, Lisa / Mannel, Robert / Moore, Kathleen / Moxley, Katherine / Postier, Russel / Walker, Joan / Zuna, Rosemary / Feldman, Michael / Valdivieso, Federico / Dhir, Rajiv / Luketich, James / Pinero, Edna M. Mora / Quintero-Aguilo, Mario / Carlotti, Carlos Gilberto / Santos, José Sebastião dos / Kemp, Rafael / Sankarankuty, Ajith / Tirapelli, Daniela / Catto, James / Agnew, Kathy / Swisher, Elizabeth / Creaney, Jenette / Robinson, Bruce / Shelley, Carl Simon / Godwin, Eryn M. / Kendall, Sara / Shipman, Cassaundra / Bradford, Carol / Carey, Thomas / Haddad, Andrea / Moyer, Jeffey / Peterson, Lisa / Prince, Mark / Rozek, Laura / Wolf, Gregory / Bowman, Rayleen / Fong, Kwun M. / Yang, Ian / Korst, Robert / Rathmell, W. Kimryn / Fantacone-Campbell, J. Leigh / Hooke, Jeffrey A. / Kovatich, Albert J. / Shriver, Craig D. / DiPersio, John / Drake, Bettina / Govindan, Ramaswamy / Heath, Sharon / Ley, Timothy / Van Tine, Brian / Westervelt, Peter / Rubin, Mark A. / Lee, Jung Il / Aredes, Natália D. / Mariamidze, Armaz

    Elsevier Inc. Cell. 2018 Apr. 05, v. 173, no. 2 p.291-304.e6

    2018  

    Abstract: We conducted comprehensive integrative molecular analyses of the complete set of tumors in The Cancer Genome Atlas (TCGA), consisting of approximately 10,000 specimens and representing 33 types of cancer. We performed molecular clustering using data on ... ...

    Institution The Cancer Genome Atlas Network
    Abstract We conducted comprehensive integrative molecular analyses of the complete set of tumors in The Cancer Genome Atlas (TCGA), consisting of approximately 10,000 specimens and representing 33 types of cancer. We performed molecular clustering using data on chromosome-arm-level aneuploidy, DNA hypermethylation, mRNA, and miRNA expression levels and reverse-phase protein arrays, of which all, except for aneuploidy, revealed clustering primarily organized by histology, tissue type, or anatomic origin. The influence of cell type was evident in DNA-methylation-based clustering, even after excluding sites with known preexisting tissue-type-specific methylation. Integrative clustering further emphasized the dominant role of cell-of-origin patterns. Molecular similarities among histologically or anatomically related cancer types provide a basis for focused pan-cancer analyses, such as pan-gastrointestinal, pan-gynecological, pan-kidney, and pan-squamous cancers, and those related by stemness features, which in turn may inform strategies for future therapeutic development.
    Keywords DNA hypermethylation ; aneuploidy ; genome ; histology ; microRNA ; therapeutics ; cancer ; TCGA ; transcriptome ; proteome ; methylome ; subtypes ; tissues ; organs ; cell-of-origin
    Language English
    Dates of publication 2018-0405
    Size p. 291-304.e6.
    Publishing place Elsevier Inc.
    Document type Article ; Online
    Note NAL-AP-2-clean ; Resource is Open Access
    ZDB-ID 187009-9
    ISSN 1097-4172 ; 0092-8674
    ISSN (online) 1097-4172
    ISSN 0092-8674
    DOI 10.1016/j.cell.2018.03.022
    Database NAL-Catalogue (AGRICOLA)

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  10. Article ; Online: An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

    Liu, Jianfang / Lichtenberg, Tara / Hoadley, Katherine A. / Poisson, Laila M. / Lazar, Alexander / Cherniack, Andrew D. / Kovatich, Albert J. / Benz, Christopher C. / Levine, Douglas A. / Lee, Adrian V. / Omberg, Larsson / Wolf, Denise M. / Shriver, Craig D. / Thorsson, Vesteinn / Hu, Hai / Caesar-Johnson, Samantha J. / Demchok, John A. / Felau, Ina / Kasapi, Melpomeni /
    Ferguson, Martin L. / Hutter, Carolyn M. / Sofia, Heidi J. / Tarnuzzer, Roy / Wang, Zhining / Yang, Liming / Zenklusen, Jean C. / Zhang, Jiashan (Julia) / Chudamani, Sudha / Liu, Jia / Lolla, Laxmi / Naresh, Rashi / Pihl, Todd / Sun, Qiang / Wan, Yunhu / Wu, Ye / Cho, Juok / DeFreitas, Timothy / Frazer, Scott / Gehlenborg, Nils / Getz, Gad / Heiman, David I. / Kim, Jaegil / Lawrence, Michael S. / Lin, Pei / Meier, Samuel A. / Noble, Michael S. / Saksena, Gordon / Voet, Doug / Zhang, Hailei / Bernard, Brady / Chambwe, Nyasha / Dhankani, Varsha / Knijnenburg, Theo / Kramer, Roger / Leinonen, Kalle / Liu, Yuexin / Miller, Michael / Reynolds, Sheila / Shmulevich, Ilya / Zhang, Wei / Akbani, Rehan / Broom, Bradley M. / Hegde, Apurva M. / Ju, Zhenlin / Kanchi, Rupa S. / Korkut, Anil / Li, Jun / Liang, Han / Ling, Shiyun / Liu, Wenbin / Lu, Yiling / Mills, Gordon B. / Ng, Kwok-Shing / Rao, Arvind / Ryan, Michael / Wang, Jing / Weinstein, John N. / Zhang, Jiexin / Abeshouse, Adam / Armenia, Joshua / Chakravarty, Debyani / Chatila, Walid K. / de Bruijn, Ino / Gao, Jianjiong / Gross, Benjamin E. / Heins, Zachary J. / Kundra, Ritika / La, Konnor / Ladanyi, Marc / Luna, Augustin / Nissan, Moriah G. / Ochoa, Angelica / Phillips, Sarah M. / Reznik, Ed / Sanchez-Vega, Francisco / Sander, Chris / Schultz, Nikolaus / Sheridan, Robert / Sumer, S. Onur / Sun, Yichao / Taylor, Barry S. / Wang, Jioajiao / Zhang, Hongxin / Anur, Pavana / Peto, Myron / Spellman, Paul / Benz, Christopher / Stuart, Joshua M. / Wong, Christopher K. / Yau, Christina / Hayes, D. Neil / Parker, Joel S. / Wilkerson, Matthew D. / Ally, Adrian / Balasundaram, Miruna / Bowlby, Reanne / Brooks, Denise / Carlsen, Rebecca / Chuah, Eric / Dhalla, Noreen / Holt, Robert / Jones, Steven J.M. / Kasaian, Katayoon / Lee, Darlene / Ma, Yussanne / Marra, Marco A. / Mayo, Michael / Moore, Richard A. / Mungall, Andrew J. / Mungall, Karen / Robertson, A. Gordon / Sadeghi, Sara / Schein, Jacqueline E. / Sipahimalani, Payal / Tam, Angela / Thiessen, Nina / Tse, Kane / Wong, Tina / Berger, Ashton C. / Beroukhim, Rameen / Cibulskis, Carrie / Gabriel, Stacey B. / Gao, Galen F. / Ha, Gavin / Meyerson, Matthew / Schumacher, Steven E. / Shih, Juliann / Kucherlapati, Melanie H. / Kucherlapati, Raju S. / Baylin, Stephen / Cope, Leslie / Danilova, Ludmila / Bootwalla, Moiz S. / Lai, Phillip H. / Maglinte, Dennis T. / Van Den Berg, David J. / Weisenberger, Daniel J. / Auman, J. Todd / Balu, Saianand / Bodenheimer, Thomas / Fan, Cheng / Hoyle, Alan P. / Jefferys, Stuart R. / Jones, Corbin D. / Meng, Shaowu / Mieczkowski, Piotr A. / Mose, Lisle E. / Perou, Amy H. / Perou, Charles M. / Roach, Jeffrey / Shi, Yan / Simons, Janae V. / Skelly, Tara / Soloway, Matthew G. / Tan, Donghui / Veluvolu, Umadevi / Fan, Huihui / Hinoue, Toshinori / Laird, Peter W. / Shen, Hui / Zhou, Wanding / Bellair, Michelle / Chang, Kyle / Covington, Kyle / Creighton, Chad J. / Dinh, Huyen / Doddapaneni, HarshaVardhan / Donehower, Lawrence A. / Drummond, Jennifer / Gibbs, Richard / Glenn, Robert / Hale, Walker / Han, Yi / Hu, Jianhong / Korchina, Viktoriya / Lee, Sandra / Lewis, Lora / Li, Wei / Liu, Xiuping / Morgan, Margaret / Morton, Donna / Muzny, Donna / Santibanez, Jireh / Sheth, Margi / Shinbro, Eve / Wang, Linghua / Wang, Min / Wheeler, David A. / Xi, Liu / Zhao, Fengmei / Hess, Julian / Appelbaum, Elizabeth L. / Bailey, Matthew / Cordes, Matthew G. / Ding, Li / Fronick, Catrina C. / Fulton, Lucinda A. / Fulton, Robert S. / Kandoth, Cyriac / Mardis, Elaine R. / McLellan, Michael D. / Miller, Christopher A. / Schmidt, Heather K. / Wilson, Richard K. / Crain, Daniel / Curley, Erin / Gardner, Johanna / Lau, Kevin / Mallery, David / Morris, Scott / Paulauskis, Joseph / Penny, Robert / Shelton, Candace / Shelton, Troy / Sherman, Mark / Thompson, Eric / Yena, Peggy / Bowen, Jay / Gastier-Foster, Julie M. / Gerken, Mark / Leraas, Kristen M. / Lichtenberg, Tara M. / Ramirez, Nilsa C. / Wise, Lisa / Zmuda, Erik / Corcoran, Niall / Costello, Tony / Hovens, Christopher / Carvalho, Andre L. / de Carvalho, Ana C. / Fregnani, José H. / Filho, Adhemar Longatto / Reis, Rui M. / Scapulatempo-Neto, Cristovam / Silveira, Henrique C.S. / Vidal, Daniel O. / Burnette, Andrew / Eschbacher, Jennifer / Hermes, Beth / Noss, Ardene / Singh, Rosy / Anderson, Matthew L. / Castro, Patricia D. / Ittmann, Michael / Huntsman, David / Kohl, Bernard / Lệ Xuân / Thorp, Richard / Andry, Chris / Duffy, Elizabeth R. / Lyadov, Vladimir / Paklina, Oxana / Setdikova, Galiya / Shabunin, Alexey / Tavobilov, Mikhail / McPherson, Christopher / Warnick, Ronald / Berkowitz, Ross / Cramer, Daniel / Feltmate, Colleen / Horowitz, Neil / Kibel, Adam / Muto, Michael / Raut, Chandrajit P. / Malykh, Andrei / Barnholtz-Sloan, Jill S. / Barrett, Wendi / Devine, Karen / Fulop, Jordonna / Ostrom, Quinn T. / Shimmel, Kristen / Wolinsky, Yingli / Sloan, Andrew E. / De Rose, Agostino / Giuliante, Felice / Goodman, Marc / Karlan, Beth Y. / Hagedorn, C. H. / Eckman, John / Harr, Jodi / Myers, Jerome / Tucker, Kelinda / Zach, Leigh Anne / Deyarmin, Brenda / Kvecher, Leonid / Larson, Caroline / Mural, Richard J. / Somiari, Stella / Vicha, Ales / Zelinka, Tomas / Bennett, Joseph / Iacocca, Mary / Rabeno, Brenda / Swanson, Patricia / Latour, Mathieu / Lacombe, Louis / Têtu, Bernard / Bergeron, Alain / McGraw, Mary / Staugaitis, Susan M. / Chabot, John / Hibshoosh, Hanina / Sepulveda, Antonia / Su, Tao / Wang, Timothy / Potapova, Olga / Voronina, Olga / Desjardins, Laurence / Mariani, Odette / Roman-Roman, Sergio / Sastre, Xavier / Stern, Marc-Henri / Cheng, Feixiong / Signoretti, Sabina / Berchuck, Andrew / Bigner, Darell / Lipp, Eric / Marks, Jeffrey / McCall, Shannon / McLendon, Roger / Secord, Angeles / Sharp, Alexis / Behera, Madhusmita / Brat, Daniel J. / Chen, Amy / Delman, Keith / Force, Seth / Khuri, Fadlo / Magliocca, Kelly / Maithel, Shishir / Olson, Jeffrey J. / Owonikoko, Taofeek / Pickens, Alan / Ramalingam, Suresh / Shin, Dong M. / Sica, Gabriel / Van Meir, Erwin G. / Zhang, Hongzheng / Eijckenboom, Wil / Gillis, Ad / Korpershoek, Esther / Looijenga, Leendert / Oosterhuis, Wolter / Stoop, Hans / van Kessel, Kim E. / Zwarthoff, Ellen C. / Calatozzolo, Chiara / Cuppini, Lucia / Cuzzubbo, Stefania / DiMeco, Francesco / Finocchiaro, Gaetano / Mattei, Luca / Perin, Alessandro / Pollo, Bianca / Chen, Chu / Houck, John / Lohavanichbutr, Pawadee / Hartmann, Arndt / Stoehr, Christine / Stoehr, Robert / Taubert, Helge / Wach, Sven / Wullich, Bernd / Kycler, Witold / Murawa, Dawid / Wiznerowicz, Maciej / Chung, Ki / Edenfield, W. 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Kimryn / Fantacone-Campbell, J. Leigh / Hooke, Jeffrey A. / DiPersio, John / Drake, Bettina / Govindan, Ramaswamy / Heath, Sharon / Ley, Timothy / Van Tine, Brian / Westervelt, Peter / Rubin, Mark A. / Lee, Jung Il / Aredes, Natália D. / Mariamidze, Armaz

    Elsevier Inc. Cell. 2018 Apr. 05, v. 173, no. 2 p.400-416.e11

    2018  

    Abstract: For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features ... ...

    Institution The Cancer Genome Atlas Research Network
    Abstract For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale.
    Keywords data collection ; genome ; genomics ; humans ; The Cancer Genome Atlas ; TCGA ; clinical data resource ; translational research ; follow-up time ; overall survival ; disease-specific survival ; disease-free interval ; progression-free interval ; Cox proportional hazards regression model
    Language English
    Dates of publication 2018-0405
    Size p. 400-416.e11.
    Publishing place Elsevier Inc.
    Document type Article ; Online
    Note NAL-AP-2-clean ; Resource is Open Access
    ZDB-ID 187009-9
    ISSN 1097-4172 ; 0092-8674
    ISSN (online) 1097-4172
    ISSN 0092-8674
    DOI 10.1016/j.cell.2018.02.052
    Database NAL-Catalogue (AGRICOLA)

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