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Ganglioneuroma on fine needle aspiration cytology: Case series and review of the literature

Fang, Camila; Pizzillo, Isabella; Shi, Yan; Sun, Wei; Brandler, Tamar C
We report two cases of an uncommon benign lesion, retroperitoneal ganglioneuroma, first diagnosed on fine needle aspiration (FNA) cytology. Our first case presented with nausea, constipation, vomiting, and neutropenia after three cycles of chemotherapy for breast cancer treatment, while our second patient presented with seemingly unprovoked abdominal pain and progressive neuropathy. Both underwent computed tomography (CT) scans, in which a soft tissue mass was found in the retroperitoneal space in each patient. An endoscopic ultrasound guided (EUS) FNA was performed on both patients, and as a result, the masses were diagnosed as retroperitoneal ganglioneuromas. As retroperitoneal ganglioneuromas have low incidence of proliferation, invasive surgery was avoided in favor of routine follow-up imaging. Cytologically, both masses showed large, scattered ganglion cells with abundant cytoplasm and large nuclei against a background of wavy spindle cells with elongated nuclei. Histologically, both were positive for S-100. When an EUSFNA is performed and quality material is collected, a diagnosis of retroperitoneal ganglioneuroma may be established, preventing invasive surgery and its accompanying risks in favor of routine follow-up imaging.
PMID: 34985204
ISSN: 1097-0339
CID: 5107122

Metastatic breast carcinoma presenting in the uterine cervix: Lessons learned from liquid-based Pap test

Shi, Yan; Yee-Chang, Melissa; Sun, Wei; Simsir, Aylin
PMID: 33171013
ISSN: 1097-0339
CID: 4665032

Risk of Malignancy of Atypical Urine Cytology; Experience from a Large Academic Institution [Meeting Abstract]

Vargas, A; Snow, J; Sun, W; Xia, R; Shi, Y; Simsir, A; Brandler, T
Introduction: In urine cytology, the atypical category suffers from interobserver variability and a wide range of risk of malignancy (ROM). This leads to confusion and inconsistent clinical management of patients with atypical urine diagnoses. Our study identified the rate of atypical diagnoses at our institution over a five-year period and examined the concurrent or follow-up surgical pathology diagnoses (SD) to understand the clinical significance of atypical urine specimens.
Material(s) and Method(s): A retrospective review of adult urine cytology specimens pre- 7/1/2014-6/30/2016 (TD) and post- 7/1/2017-6/30/2019 (TPS) implementation of the Paris System for Reporting Urinary Cytology was performed, which identified 10,132 total urine specimens. Of these, 2,457 specimens from 1,727 patients were categorized as "atypical." 177 cytology specimens were found to have corresponding urinary tract SD within 90 days. Pre- and post-Paris System (TD and TPS) urine cytology diagnoses were compared.
Result(s): The overall rate of "atypical" diagnoses was 2,457/10,132 (24.3%). 177 of 2,457 atypical specimens (7.2%) had corresponding urinary tract SD, of which the ROM was 37.9% (TD 37.8%, TPS 37.9%, p=0.992). 61 of 177 atypical urines (34.5%) were high grade (HGUC/CIS) on SD (TD 32.9%, TPS 35.8%). 66 of 177 atypical urines (37.3%) were low grade urothelial neoplasms (LGUNs), atypical, or dysplastic on SD (TD 39.0%, TPS 35.8%, p=0.660). 44 of 177 atypical urines (24.9%) were benign on SD (TD 23.2%, TPS 26.3%) (Table 1).
Conclusion(s): While the atypical diagnosis rate of nearly 1 in 4 urines is fairly high, over one-third of atypical results signified a high grade malignancy, and over an additional one-third of atypical urines represented LGUN, atypical, or dysplastic surgical pathology diagnoses. These findings emphasize the need for close follow-up in patients with atypical diagnoses on urine cytology. Our findings did not show a significant difference between pre and post TPS follow up data. [Formula presented]
ISSN: 2213-2945
CID: 4659262

A Comparison of Upper and Lower Urothelial Tract Lesions Before and After Implementation of The Paris System for Reporting Urinary Cytology [Meeting Abstract]

Xia, R; Snow, J; Sun, W; Vargas, A; Shi, Y; Simsir, A; Brandler, T
Introduction: Urothelial carcinomas (UC) of the upper urinary tract (UUT) are rare, and usually show higher grade and poorer prognosis than carcinomas of the bladder. The Paris System (TPS) has been integrated into our standard terminology for interpreting urine cytology. Here we compare TPS diagnoses to the traditional reporting system (TD) in interpreting UC of UUT and lower urinary tract (LUT) in correlation with surgical pathology diagnoses (SD).
Material(s) and Method(s): A search of the cytopathology database on urine specimens from 7/1/2014-6/30/2016 (TD) and 7/1/2017-6/30/2019 (TPS) with corresponding lesions in SD, yielded 14-TD cases and 19-TPS in UUT; and 178-TD and 243-TPS cases in LUT. The cytopathology diagnosis using TD and TPS were compared to their corresponding SD.
Result(s): In UUT, 51.5% (17/33) were UC on SD. High-grade UC (HGUC) was correctly identified in UUT in 100% (5/5) with TD, and 75%(3/4) with TPS. No low-grade (LG) diagnoses were rendered in TD or TPS though there were 8 low-grade urothelial neoplasms (LGUN). LGUN was classified as "atypical" (2/3-TD, 2/5-TPS) or "negative" (1/3-TD, 3/5-TPS). Rates of "atypical" diagnoses of UUT were 28.6% (TPS) and 26.3% (TD), with no HGUC on SD. The risk of LGUN with "atypical" diagnoses decreased using TPS from 75.0% (3/4) to 60.0% (3/5). In LUT, HGUC was correctly diagnosed in 55.0%(44/80) (TD) and 47.4%(46/97) (TPS). 4% of LGUNs were classified as LG (3/60-TPS, 1/40-TD). "Atypical" diagnoses for TD and TPS showed 29.5% (23/78) and 30.0% (27/90) risk of LGUN and 34.6%(27/78) and 37.8%(34/90) risk of HGUC respectively. (Table-1)
Conclusion(s): The TD and TPS systems showed high accuracy in reporting UUT-HGUC. However, urine cytology is not optimal to identify LGUN in both TD and TPS systems. Additionally, our results suggest that urine cytology may be more sensitive in detecting HGUC in UUT versus LUT samples.[Table presented]
ISSN: 2213-2945
CID: 4659282

Risk of Malignancy in Thyroid Nodules of Thyroid Bethesda Categories III and IV with Negative ThyroSeq Findings [Meeting Abstract]

Xia, R; Sun, W; Liu, C; Shi, Y; Levine, P; Simsir, A; Cangiarella, J; Brandler, T
Introduction: Due to the diagnostic dilemma with indeterminate thyroid Bethesda categories III and IV (atypia of undetermined significance, AUS and Suspicious for follicular neoplasm, SFN), many laboratories utilize molecular testing to aid in risk stratification of these nodules. In this study, we evaluated the risk of malignancy (ROM) in AUS and SFN thyroid nodules with subsequent negative molecular (ThyroSeq) test results.
Material(s) and Method(s): This study was designed to evaluate the negative molecular thyroid fine needle aspiration (FNA) cases at a tertiary medical center in the metropolitan area. 109 cases of AUS and SFN thyroid FNAs over 3 years with surgical pathology follow up were included in the study.
Result(s): Of 109 AUS and SFN cases, 4 cases showed insufficient material for ThyroSeq testing (3.7%), 76 cases showed a molecular alteration (69.7%), and 29 cases were negative for an alteration on ThyroSeq (26.6%). Among the cases with negative ThyroSeq results, 26 cases were benign on surgical pathology (89.7%) (7/26 were follicular adenomas), and 3/29 cases were malignant on histopathology (papillary thyroid carcinoma) (ROM=10.3%, Table 1). AUS and SFN cases with molecular alterations showed a significantly higher ROM (ROM= 60.5%) compared to cases testing negative for molecular alterations (p<0.01, z = -4.61).
Conclusion(s): Our study found that indeterminate thyroid nodules that tested negative for a molecular alteration displayed an ROM of 10.3%. This ROM is comparable to the lower limit of ROM of FNA alone (without additional molecular testing data) in the AUS and SFN categories (10-30%), but is significantly lower than the ROM of indeterminate thyroid cases with known molecular mutations. Therefore, clinical follow-up is recommended for thyroid FNA indeterminate nodules, even those testing negative for a molecular alteration, due to the maintained, albeit lower, ROM. [Formula presented]
ISSN: 2213-2945
CID: 4659292

Adult rhabdomyoma presenting as thyroid nodule on fine-needle aspiration in patient with Birt-Hogg-Dubé syndrome: Case report and literature review

Black, Margaret; Wei, Xiao-Jun; Sun, Wei; Simms, Anthony; Negron, Raquel; Hagiwara, Mari; Chidakel, Aaron R; Hodak, Steven; Persky, Mark S; Shi, Yan
Extracardiac rhabdomyoma is an uncommon benign striated muscle tumor with a predilection for the head and neck region. However, it is extremely rare for extracardiac rhabdomyoma to present as a thyroid nodule. We report a case of rhabdomyoma diagnosed by thyroid fine-needle aspiration (FNA) in a patient with Birt-Hogg-Dubé (BHD) syndrome. A 60-year-old man with BHD syndrome presented for recurrent pneumothorax. Chest CT incidentally identified a thyroid nodule. Subsequent sonography confirmed a 4.44 × 2.28 × 2.82 cm solid, hypoechoic nodule with smooth margins in the right upper pole. Ultrasound-guided FNA revealed many clusters and scattered isolated large polygonal cells with abundant granular cytoplasm and small peripherally located nuclei. Vague striations in the cytoplasm were focally identified. No follicular cells or colloid was present. Immunocytochemistry on one direct smear slide demonstrated diffuse positivity for desmin, supporting muscular differentiation. Subsequent surgery identified an adult rhabdomyoma originating from the inferior constrictor muscle of the neck and anteriorly displacing the thyroid. Because the mass was intimately associated with the thyroid gland, it was initially mistaken for a thyroid nodule on ultrasound. Diagnosis of rhabdomyoma on FNA is challenging, especially when rhabdomyoma mimics a thyroid nodule on imaging. The differential diagnosis includes Hurthle cell neoplasm, granular cell tumor, colloid nodule, and normal striated skeletal muscle. Adequate radiologic data and familiarity with the cytologic features of rhabdomyoma are critical for an accurate diagnosis.
PMID: 32187885
ISSN: 1097-0339
CID: 4352812

A correlative analysis of the paris system (tps) for reporting urine cytology: Results from a large academic institution [Meeting Abstract]

Snow, J; Wang, Q; Sun, W; Shi, Y; Simsir, A; Brandler, T
Background: TPS is a reporting system that includes specific diagnostic categories and cytologic criteria for the accurate diagnosis of high-grade urothelial carcinoma (HGUC). Its success is dependent on its acceptance and widespread use by the cytology and urology communities. Since its development in 2013, institutions have been transitioning to TPS in an effort to standardize terminology and increase the sensitivity of diagnosing HGUC. We present our data comparing TPS diagnoses (PD) to the traditional reporting system (TD) in correlation with the gold standard surgical pathology diagnosis (SD).
Design(s): A search of the pathology database was conducted on urine cytology specimens from adult patients from 7/1/2014-6/30/2016 (TD) and 7/1/2017-6/30/2019 (PD). 454 cytology specimens from 382 patients were found to have corresponding urinary tract SD within 90 days and were included in the study. 192/454 urines were from prior to TPS implementation; 262/454 were from after TPS implementation. TD included: Positive for malignancy/urothelial carcinoma (POS), suspicious for malignancy/urothelial carcinoma (SUS), atypical, low-grade urothelial neoplasia/carcinoma (LG), and negative for malignancy (NEG). TD and PD were compared to their corresponding SD.
Result(s): 34/41 (83%) of HGUC were correctly identified using PD compared to 36/49 (73%) using TD. 15/23 (65%) of SHGUC correlated with HGUC on SD using PD compared with 13/16 (81%) with TD. Rates of "Atypical" diagnoses were decreased from 82/192 (42%) with TD to 95/262 (36%) with PD while the risk of malignancy (ROM) with "Atypical" diagnosis increased using PD from 33% to 36%. LG was identified on cytology in 1/43 (2%) using TD and 3/65 (5%) with PD. In both TD and PD, LG cytologic diagnosis had 100% specificity. 31/65 (48%) of LGUN were correctly categorized as NHGUC using PD while 10/43 (23%) were NEG in TD. (Table 1 and Figure 1) (Table presented)
Conclusion(s): Implementation of TPS in our laboratory led to a higher accuracy in the cytologic diagnosis of HGUC. Additionally, the "Atypical" rate decreased from 42% to 36% while the ROM showed a modest increase. While 12% of HGUCs diagnosed with TPS were found to be benign on SD, 60% of these cases actually had prior and/or subsequent HGUC/CIS on SD indicating that original PD was in fact concordant. LGUN is difficult to diagnose on cytology, and TPS afforded an increase in NHGUC diagnoses in line with the main goal of the PD- diagnosis of HGUC
ISSN: 1530-0285
CID: 4471012

An investigation into low suspicion thyroid imaging reporting and data system (TI-RADS) nodules with fine needle aspiration (FNA) cytology, molecular and surgical pathology findings [Meeting Abstract]

Sun, W; Yee, J; Shi, Y; Szeto, O; Simsir, A; Brandler, T
Background: The American College of Radiology (ACR) 2017 Thyroid Imaging Reporting and Data System (TI-RADS) added a new risk stratification system for classifying thyroid nodules based on sonographic appearance (T1-T5). FNA is generally not recommended for benign or low suspicion nodules. However, other factors such as nodule size and family history may trigger an order for an FNA. Our study aimed to examine the cytologic diagnosis, molecular profiles and surgical follow up in a select group of patients with sonographically benign appearing thyroid nodules.
Design(s): We performed a retrospective review in our pathology database of cases from 1/1/2016-4/1/2018, prior to our institution's adoption of the TI-RADS classification system. Thyroid nodules with in-house ultrasound exam (US), FNA cytology, The Bethesda System (TBS) cytology diagnosis, molecular testing, and surgery were included. The USs from these cases were retrospectively reviewed and assigned TI-RADS scores (TR1-TR5) by a board certified radiologist. There were no TR1 nodules. TR2 (not suspicious) and TR3 (mildly suspicious) nodules were selected for evaluation.
Result(s): From 1/1/2016-4/1/2018, there were a total of 34 patients that fit the selection criteria. Of these, there were 5 TR2 thyroid nodules and 29 TR3 thyroid nodules with corresponding FNA TBS, molecular and surgical diagnoses (table1). (Table presented)
Conclusion(s): Our study shows that sonographically benign appearing/low suspicion thyroid nodules may display molecular alterations; 50% of those proved to be RAS mutations in our study. Approximately 60% of aspirated TR2 nodules and 66% of TR3 nodules were malignant or NIFTP on excision. Despite their lower suspicion index on US, with lower TI-RADS scores, benign appearing nodules on US need to be evaluated in the context of clinical, cytologic and molecular information in order to determine clinical course
ISSN: 1530-0285
CID: 4471062

Application of GATA 3 and TTF-1 in differentiating parathyroid and thyroid nodules on cytology specimens

Shi, Yan; Brandler, Tamar C; Yee-Chang, Melissa; Cangiarella, Joan; Wei, Xiao-Jun; Leung, Allen; Szeto, Oliver; Deng, Fang-Ming; Liu, Cheng Z; Simsir, Aylin; Sun, Wei
BACKGROUND:Differentiating parathyroid from thyroid lesions can be difficult on fine-needle aspiration (FNA) due to overlapping cytomorphologic features. While the traditional parathyroid hormone (PTH) assays can help in the distinction, these tests may be cumbersome, particularly when the lesion is unexpected clinically and a needle wash is not collected at the time of FNA. Therefore, we chose to investigate the application of immunohistochemical staining (IHC) with GATA 3 and thyroid transcription factor-1 (TTF-1) on air-dried cytology smears to distinguish parathyroid and thyroid lesions. METHODS:Air-dried touch preparation (TP) slides were prepared from consecutively selected parathyroid and thyroid specimens. Thirteen FNA cases with the clinical concern for parathyroid lesions were also included in the study. IHC was performed on unstained and ultrafast Papanicolaou (UFP) stained air-dried slides. RESULTS:On TP slides, GATA 3 expression was observed in all cases of parathyroid origin but no immunoreactivity was present in thyroid lesions. TTF-1 expression was observed in all cases of thyroid origin but not in parathyroid lesions. GATA 3 and TTF-1 expression of 13 FNA cases were consistent with the clinical impression or concurrent PTH tests. CONCLUSIONS:IHC with GATA 3 and TTF-1 on air-dried cytology smears is a simple and effective way to differentiate parathyroid vs thyroid lesions on FNA. Air-dried unstained and UFP-stained slides perform equally well with IHC, but UFP-stained slides provide the added benefit of morphologic evaluation and assessment of smear cellularity prior to IHC.
PMID: 31713988
ISSN: 1097-0339
CID: 4185152

Pan-cancer analysis of whole genomes

Campbell, Peter J; Getz, Gad; Korbel, Jan O; Stuart, Joshua M; Jennings, Jennifer L; Stein, Lincoln D; Perry, Marc D; Nahal-Bose, Hardeep K; Ouellette, B F Francis; Li, Constance H; Rheinbay, Esther; Nielsen, G Petur; Sgroi, Dennis C; Wu, Chin-Lee; Faquin, William C; Deshpande, Vikram; Boutros, Paul C; Lazar, Alexander J; Hoadley, Katherine A; Louis, David N; Dursi, L Jonathan; Yung, Christina K; Bailey, Matthew H; Saksena, Gordon; Raine, Keiran M; Buchhalter, Ivo; Kleinheinz, Kortine; Schlesner, Matthias; Zhang, Junjun; Wang, Wenyi; Wheeler, David A; Ding, Li; Simpson, Jared T; O'Connor, Brian D; Yakneen, Sergei; Ellrott, Kyle; Miyoshi, Naoki; Butler, Adam P; Royo, Romina; Shorser, Solomon I; Vazquez, Miguel; Rausch, Tobias; Tiao, Grace; Waszak, Sebastian M; Rodriguez-Martin, Bernardo; Shringarpure, Suyash; Wu, Dai-Ying; Demidov, German M; Delaneau, Olivier; Hayashi, Shuto; Imoto, Seiya; Habermann, Nina; Segre, Ayellet V; Garrison, Erik; Cafferkey, Andy; Alvarez, Eva G; Heredia-Genestar, José María; Muyas, Francesc; Drechsel, Oliver; Bruzos, Alicia L; Temes, Javier; Zamora, Jorge; Baez-Ortega, Adrian; Kim, Hyung-Lae; Mashl, R Jay; Ye, Kai; DiBiase, Anthony; Huang, Kuan-Lin; Letunic, Ivica; McLellan, Michael D; Newhouse, Steven J; Shmaya, Tal; Kumar, Sushant; Wedge, David C; Wright, Mark H; Yellapantula, Venkata D; Gerstein, Mark; Khurana, Ekta; Marques-Bonet, Tomas; Navarro, Arcadi; Bustamante, Carlos D; Siebert, Reiner; Nakagawa, Hidewaki; Easton, Douglas F; Ossowski, Stephan; Tubio, Jose M C; De La Vega, Francisco M; Estivill, Xavier; Yuen, Denis; Mihaiescu, George L; Omberg, Larsson; Ferretti, Vincent; Sabarinathan, Radhakrishnan; Pich, Oriol; Gonzalez-Perez, Abel; Taylor-Weiner, Amaro; Fittall, Matthew W; Demeulemeester, Jonas; Tarabichi, Maxime; Roberts, Nicola D; Van Loo, Peter; Cortés-Ciriano, Isidro; Urban, Lara; Park, Peter; Zhu, Bin; Pitkänen, Esa; Li, Yilong; Saini, Natalie; Klimczak, Leszek J; Weischenfeldt, Joachim; Sidiropoulos, Nikos; Alexandrov, Ludmil B; Rabionet, Raquel; Escaramis, Georgia; Bosio, Mattia; Holik, Aliaksei Z; Susak, Hana; Prasad, Aparna; Erkek, Serap; Calabrese, Claudia; Raeder, Benjamin; Harrington, Eoghan; Mayes, Simon; Turner, Daniel; Juul, Sissel; Roberts, Steven A; Song, Lei; Koster, Roelof; Mirabello, Lisa; Hua, Xing; Tanskanen, Tomas J; Tojo, Marta; Chen, Jieming; Aaltonen, Lauri A; Rätsch, Gunnar; Schwarz, Roland F; Butte, Atul J; Brazma, Alvis; Chanock, Stephen J; Chatterjee, Nilanjan; Stegle, Oliver; Harismendy, Olivier; Bova, G Steven; Gordenin, Dmitry A; Haan, David; Sieverling, Lina; Feuerbach, Lars; Chalmers, Don; Joly, Yann; Knoppers, Bartha; Molnár-Gábor, Fruzsina; Phillips, Mark; Thorogood, Adrian; Townend, David; Goldman, Mary; Fonseca, Nuno A; Xiang, Qian; Craft, Brian; Piñeiro-Yáñez, Elena; Muñoz, Alfonso; Petryszak, Robert; Füllgrabe, Anja; Al-Shahrour, Fatima; Keays, Maria; Haussler, David; Weinstein, John; Huber, Wolfgang; Valencia, Alfonso; Papatheodorou, Irene; Zhu, Jingchun; Fan, Yu; Torrents, David; Bieg, Matthias; Chen, Ken; Chong, Zechen; Cibulskis, Kristian; Eils, Roland; Fulton, Robert S; Gelpi, Josep L; Gonzalez, Santiago; Gut, Ivo G; Hach, Faraz; Heinold, Michael; Hu, Taobo; Huang, Vincent; Hutter, Barbara; Jäger, Natalie; Jung, Jongsun; Kumar, Yogesh; Lalansingh, Christopher; Leshchiner, Ignaty; Livitz, Dimitri; Ma, Eric Z; Maruvka, Yosef E; Milovanovic, Ana; Nielsen, Morten Muhlig; Paramasivam, Nagarajan; Pedersen, Jakob Skou; Puiggròs, Montserrat; Sahinalp, S Cenk; Sarrafi, Iman; Stewart, Chip; Stobbe, Miranda D; Wala, Jeremiah A; Wang, Jiayin; Wendl, Michael; Werner, Johannes; Wu, Zhenggang; Xue, Hong; Yamaguchi, Takafumi N; Yellapantula, Venkata; Davis-Dusenbery, Brandi N; Grossman, Robert L; Kim, Youngwook; Heinold, Michael C; Hinton, Jonathan; Jones, David R; Menzies, Andrew; Stebbings, Lucy; Hess, Julian M; Rosenberg, Mara; Dunford, Andrew J; Gupta, Manaswi; Imielinski, Marcin; Meyerson, Matthew; Beroukhim, Rameen; Reimand, Jüri; Dhingra, Priyanka; Favero, Francesco; Dentro, Stefan; Wintersinger, Jeff; Rudneva, Vasilisa; Park, Ji Wan; Hong, Eun Pyo; Heo, Seong Gu; Kahles, André; Lehmann, Kjong-Van; Soulette, Cameron M; Shiraishi, Yuichi; Liu, Fenglin; He, Yao; Demircioğlu, Deniz; Davidson, Natalie R; Greger, Liliana; Li, Siliang; Liu, Dongbing; Stark, Stefan G; Zhang, Fan; Amin, Samirkumar B; Bailey, Peter; Chateigner, Aurélien; Frenkel-Morgenstern, Milana; Hou, Yong; Huska, Matthew R; Kilpinen, Helena; Lamaze, Fabien C; Li, Chang; Li, Xiaobo; Li, Xinyue; Liu, Xingmin; Marin, Maximillian G; Markowski, Julia; Nandi, Tannistha; Ojesina, Akinyemi I; Pan-Hammarström, Qiang; Park, Peter J; Pedamallu, Chandra Sekhar; Su, Hong; Tan, Patrick; Teh, Bin Tean; Wang, Jian; Xiong, Heng; Ye, Chen; Yung, Christina; Zhang, Xiuqing; Zheng, Liangtao; Zhu, Shida; Awadalla, Philip; Creighton, Chad J; Wu, Kui; Yang, Huanming; Göke, Jonathan; Zhang, Zemin; Brooks, Angela N; Fittall, Matthew W; Martincorena, Iñigo; Rubio-Perez, Carlota; Juul, Malene; Schumacher, Steven; Shapira, Ofer; Tamborero, David; Mularoni, Loris; Hornshøj, Henrik; Deu-Pons, Jordi; Muiños, Ferran; Bertl, Johanna; Guo, Qianyun; Gonzalez-Perez, Abel; Xiang, Qian; Bazant, Wojciech; Barrera, Elisabet; Al-Sedairy, Sultan T; Aretz, Axel; Bell, Cindy; Betancourt, Miguel; Buchholz, Christiane; Calvo, Fabien; Chomienne, Christine; Dunn, Michael; Edmonds, Stuart; Green, Eric; Gupta, Shailja; Hutter, Carolyn M; Jegalian, Karine; Jones, Nic; Lu, Youyong; Nakagama, Hitoshi; Nettekoven, Gerd; Planko, Laura; Scott, David; Shibata, Tatsuhiro; Shimizu, Kiyo; Stratton, Michael R; Yugawa, Takashi; Tortora, Giampaolo; VijayRaghavan, K; Zenklusen, Jean C; Townend, David; Knoppers, Bartha M; Aminou, Brice; Bartolome, Javier; Boroevich, Keith A; Boyce, Rich; Buchanan, Alex; Byrne, Niall J; Chen, Zhaohong; Cho, Sunghoon; Choi, Wan; Clapham, Peter; Dow, Michelle T; Dursi, Lewis Jonathan; Eils, Juergen; Farcas, Claudiu; Fayzullaev, Nodirjon; Flicek, Paul; Heath, Allison P; Hofmann, Oliver; Hong, Jongwhi H; Hudson, Thomas J; Hübschmann, Daniel; Ivkovic, Sinisa; Jeon, Seung-Hyup; Jiao, Wei; Kabbe, Rolf; Kahles, Andre; Kerssemakers, Jules N A; Kim, Hyunghwan; Kim, Jihoon; Koscher, Michael; Koures, Antonios; Kovacevic, Milena; Lawerenz, Chris; Liu, Jia; Mijalkovic, Sanja; Mijalkovic-Lazic, Ana Mijalkovic; Miyano, Satoru; Nastic, Mia; Nicholson, Jonathan; Ocana, David; Ohi, Kazuhiro; Ohno-Machado, Lucila; Pihl, Todd D; Prinz, Manuel; Radovic, Petar; Short, Charles; Sofia, Heidi J; Spring, Jonathan; Struck, Adam J; Tijanic, Nebojsa; Vicente, David; Wang, Zhining; Williams, Ashley; Woo, Youngchoon; Wright, Adam J; Yang, Liming; Hamilton, Mark P; Johnson, Todd A; Kahraman, Abdullah; Kellis, Manolis; Polak, Paz; Sallari, Richard; Sinnott-Armstrong, Nasa; von Mering, Christian; Beltran, Sergi; Gerhard, Daniela S; Gut, Marta; Trotta, Jean-Rémi; Whalley, Justin P; Niu, Beifang; Espiritu, Shadrielle M G; Gao, Shengjie; Huang, Yi; Lalansingh, Christopher M; Teague, Jon W; Wendl, Michael C; Abascal, Federico; Bader, Gary D; Bandopadhayay, Pratiti; Barenboim, Jonathan; Brunak, Søren; Carlevaro-Fita, Joana; Chakravarty, Dimple; Chan, Calvin Wing Yiu; Choi, Jung Kyoon; Diamanti, Klev; Fink, J Lynn; Frigola, Joan; Gambacorti-Passerini, Carlo; Garsed, Dale W; Haradhvala, Nicholas J; Harmanci, Arif O; Helmy, Mohamed; Herrmann, Carl; Hobolth, Asger; Hodzic, Ermin; Hong, Chen; Isaev, Keren; Izarzugaza, Jose M G; Johnson, Rory; Juul, Randi Istrup; Kim, Jaegil; Kim, Jong K; Jan Komorowski; Lanzós, Andrés; Larsson, Erik; Lee, Donghoon; Li, Shantao; Li, Xiaotong; Lin, Ziao; Liu, Eric Minwei; Lochovsky, Lucas; Lou, Shaoke; Madsen, Tobias; Marchal, Kathleen; Martinez-Fundichely, Alexander; McGillivray, Patrick D; Meyerson, William; Paczkowska, Marta; Park, Keunchil; Park, Kiejung; Pons, Tirso; Pulido-Tamayo, Sergio; Reyes-Salazar, Iker; Reyna, Matthew A; Rubin, Mark A; Salichos, Leonidas; Sander, Chris; Schumacher, Steven E; Shackleton, Mark; Shen, Ciyue; Shrestha, Raunak; Shuai, Shimin; Tsunoda, Tatsuhiko; Umer, Husen M; Uusküla-Reimand, Liis; Verbeke, Lieven P C; Wadelius, Claes; Wadi, Lina; Warrell, Jonathan; Wu, Guanming; Yu, Jun; Zhang, Jing; Zhang, Xuanping; Zhang, Yan; Zhao, Zhongming; Zou, Lihua; Lawrence, Michael S; Raphael, Benjamin J; Bailey, Peter J; Craft, David; Goldman, Mary J; Aburatani, Hiroyuki; Binder, Hans; Dinh, Huy Q; Heath, Simon C; Hoffmann, Steve; Imbusch, Charles David; Kretzmer, Helene; Laird, Peter W; Martin-Subero, Jose I; Nagae, Genta; Shen, Hui; Wang, Qi; Weichenhan, Dieter; Zhou, Wanding; Berman, Benjamin P; Brors, Benedikt; Plass, Christoph; Akdemir, Kadir C; Bowtell, David D L; Burns, Kathleen H; Busanovich, John; Chan, Kin; Dueso-Barroso, Ana; Edwards, Paul A; Etemadmoghadam, Dariush; Haber, James E; Jones, David T W; Ju, Young Seok; Kazanov, Marat D; Koh, Youngil; Kumar, Kiran; Lee, Eunjung Alice; Lee, Jake June-Koo; Lynch, Andy G; Macintyre, Geoff; Markowetz, Florian; Navarro, Fabio C P; Pearson, John V; Rippe, Karsten; Scully, Ralph; Villasante, Izar; Waddell, Nicola; Yang, Lixing; Yao, Xiaotong; Yoon, Sung-Soo; Zhang, Cheng-Zhong; Bergstrom, Erik N; Boot, Arnoud; Covington, Kyle; Fujimoto, Akihiro; Huang, Mi Ni; Islam, S M Ashiqul; McPherson, John R; Morganella, Sandro; Mustonen, Ville; Ng, Alvin Wei Tian; Prokopec, Stephenie D; Vázquez-García, Ignacio; Wu, Yang; Yousif, Fouad; Yu, Willie; Rozen, Steven G; Rudneva, Vasilisa A; Shringarpure, Suyash S; Turner, Daniel J; Xia, Tian; Atwal, Gurnit; Chang, David K; Cooke, Susanna L; Faltas, Bishoy M; Haider, Syed; Kaiser, Vera B; Karlić, Rosa; Kato, Mamoru; Kübler, Kirsten; Margolin, Adam; Martin, Sancha; Nik-Zainal, Serena; P'ng, Christine; Semple, Colin A; Smith, Jaclyn; Sun, Ren X; Thai, Kevin; Wright, Derek W; Yuan, Ke; Biankin, Andrew V; Garraway, Levi; Grimmond, Sean M; Adams, David J; Anur, Pavana; Cao, Shaolong; Christie, Elizabeth L; Cmero, Marek; Cun, Yupeng; Dawson, Kevin J; Dentro, Stefan C; Deshwar, Amit G; Donmez, Nilgun; Drews, Ruben M; Gerstung, Moritz; Ha, Gavin; Haase, Kerstin; Jerman, Lara; Ji, Yuan; Jolly, Clemency; 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Mileshkin, Linda; Miller, David K; Arnau, Gisela Mir; Mitchell, Chris; Newell, Felicity; Nones, Katia; Patch, Ann-Marie; Quinn, Michael C; Taylor, Darrin F; Thorne, Heather; Traficante, Nadia; Vedururu, Ravikiran; Waddell, Nick M; Waring, Paul M; Wood, Scott; Xu, Qinying; deFazio, Anna; Anderson, Matthew J; Antonello, Davide; Barbour, Andrew P; Bassi, Claudio; Bersani, Samantha; Cataldo, Ivana; Chantrill, Lorraine A; Chiew, Yoke-Eng; Chou, Angela; Cingarlini, Sara; Cloonan, Nicole; Corbo, Vincenzo; Davi, Maria Vittoria; Duthie, Fraser R; Gill, Anthony J; Graham, Janet S; Harliwong, Ivon; Jamieson, Nigel B; Johns, Amber L; Kench, James G; Landoni, Luca; Lawlor, Rita T; Mafficini, Andrea; Merrett, Neil D; Miotto, Marco; Musgrove, Elizabeth A; Nagrial, Adnan M; Oien, Karin A; Pajic, Marina; Pinese, Mark; Robertson, Alan J; Rooman, Ilse; Rusev, Borislav C; Samra, Jaswinder S; Scardoni, Maria; Scarlett, Christopher J; Scarpa, Aldo; Sereni, Elisabetta; Sikora, Katarzyna O; Simbolo, Michele; Taschuk, Morgan L; Toon, Christopher W; Vicentini, Caterina; Wu, Jianmin; Zeps, Nikolajs; Behren, Andreas; Burke, Hazel; Cebon, Jonathan; Dagg, Rebecca A; De Paoli-Iseppi, Ricardo; Dutton-Regester, Ken; Field, Matthew A; Fitzgerald, Anna; Hersey, Peter; Jakrot, Valerie; Johansson, Peter A; Kakavand, Hojabr; Kefford, Richard F; Lau, Loretta M S; Long, Georgina V; Pickett, Hilda A; Pritchard, Antonia L; Pupo, Gulietta M; Saw, Robyn P M; Schramm, Sarah-Jane; Shang, Catherine A; Shang, Ping; Spillane, Andrew J; Stretch, Jonathan R; Tembe, Varsha; Thompson, John F; Vilain, Ricardo E; Wilmott, James S; Yang, Jean Y; Hayward, Nicholas K; Mann, Graham J; Scolyer, Richard A; Bartlett, John; Bavi, Prashant; Chadwick, Dianne E; Chan-Seng-Yue, Michelle; Cleary, Sean; Connor, Ashton A; Czajka, Karolina; Denroche, Robert E; Dhani, Neesha C; Eagles, Jenna; Gallinger, Steven; Grant, Robert C; Hedley, David; Hollingsworth, Michael A; Jang, Gun Ho; Johns, Jeremy; Kalimuthu, Sangeetha; Liang, Sheng-Ben; Lungu, Ilinca; Luo, Xuemei; Mbabaali, Faridah; McPherson, Treasa A; Miller, Jessica K; Moore, Malcolm J; Notta, Faiyaz; Pasternack, Danielle; Petersen, Gloria M; Roehrl, Michael H A; Sam, Michelle; Selander, Iris; Serra, Stefano; Shahabi, Sagedeh; Thayer, Sarah P; Timms, Lee E; Wilson, Gavin W; Wilson, Julie M; Wouters, Bradly G; McPherson, John D; Beck, Timothy A; Bhandari, Vinayak; Collins, Colin C; Fleshner, Neil E; Fox, Natalie S; Fraser, Michael; Heisler, Lawrence E; Lalonde, Emilie; Livingstone, Julie; Meng, Alice; Sabelnykova, Veronica Y; Shiah, Yu-Jia; Van der Kwast, Theodorus; Bristow, Robert G; Ding, Shuai; Fan, Daiming; Li, Lin; Nie, Yongzhan; Xiao, Xiao; Xing, Rui; Yang, Shanlin; Yu, Yingyan; Zhou, Yong; Banks, Rosamonde E; Bourque, Guillaume; Brennan, Paul; Letourneau, Louis; Riazalhosseini, Yasser; Scelo, Ghislaine; Vasudev, Naveen; Viksna, Juris; Lathrop, Mark; Tost, Jörg; Ahn, Sung-Min; Aparicio, Samuel; Arnould, Laurent; Aure, M R; Bhosle, Shriram G; Birney, Ewan; Borg, Ake; Boyault, Sandrine; Brinkman, Arie B; Brock, Jane E; Broeks, Annegien; Børresen-Dale, Anne-Lise; Caldas, Carlos; Chin, Suet-Feung; Davies, Helen; Desmedt, Christine; Dirix, Luc; Dronov, Serge; Ehinger, Anna; Eyfjord, Jorunn E; Fatima, Aquila; Foekens, John A; Futreal, P Andrew; Garred, Øystein; Giri, Dilip D; Glodzik, Dominik; Grabau, Dorthe; Hilmarsdottir, Holmfridur; Hooijer, Gerrit K; Jacquemier, Jocelyne; Jang, Se Jin; Jonasson, Jon G; Jonkers, Jos; Kim, Hyung-Yong; King, Tari A; Knappskog, Stian; Kong, Gu; Krishnamurthy, Savitri; Lakhani, Sunil R; Langerød, Anita; Larsimont, Denis; Lee, Hee Jin; Lee, Jeong-Yeon; Lee, Ming Ta Michael; Lingjærde, Ole Christian; MacGrogan, Gaetan; Martens, John W M; O'Meara, Sarah; Pauporté, Iris; Pinder, Sarah; Pivot, Xavier; Provenzano, Elena; Purdie, Colin A; Ramakrishna, Manasa; Ramakrishnan, Kamna; Reis-Filho, Jorge; Richardson, Andrea L; Ringnér, Markus; Rodriguez, Javier Bartolomé; Rodríguez-González, F Germán; Romieu, Gilles; Salgado, Roberto; Sauer, Torill; Shepherd, Rebecca; Sieuwerts, Anieta M; Simpson, Peter T; Smid, Marcel; Sotiriou, Christos; Span, Paul N; Stefánsson, Ólafur Andri; Stenhouse, Alasdair; Stunnenberg, Henk G; Sweep, Fred; Tan, Benita Kiat Tee; Thomas, Gilles; Thompson, Alastair M; Tommasi, Stefania; Treilleux, Isabelle; Tutt, Andrew; Ueno, Naoto T; Van Laere, Steven; Van den Eynden, Gert G; Vermeulen, Peter; Viari, Alain; Vincent-Salomon, Anne; Wong, Bernice H; Yates, Lucy; Zou, Xueqing; van Deurzen, Carolien H M; van de Vijver, Marc J; Van't Veer, Laura; Ammerpohl, Ole; Aukema, Sietse; Bergmann, Anke K; Bernhart, Stephan H; Borkhardt, Arndt; Borst, Christoph; Burkhardt, Birgit; Claviez, Alexander; Goebler, Maria Elisabeth; Haake, Andrea; Haas, Siegfried; Hansmann, Martin; Hoell, Jessica I; Hummel, Michael; Karsch, Dennis; Klapper, Wolfram; Kneba, Michael; Kreuz, Markus; Kube, Dieter; Küppers, Ralf; Lenze, Dido; Loeffler, Markus; López, Cristina; Mantovani-Löffler, Luisa; Möller, Peter; Ott, German; Radlwimmer, Bernhard; Richter, Julia; Rohde, Marius; Rosenstiel, Philip C; Rosenwald, Andreas; Schilhabel, Markus B; Schreiber, Stefan; Stadler, Peter F; Staib, Peter; Stilgenbauer, Stephan; Sungalee, Stephanie; Szczepanowski, Monika; Toprak, Umut H; Trümper, Lorenz H P; Wagener, Rabea; Zenz, Thorsten; Hovestadt, Volker; von Kalle, Christof; Kool, Marcel; Korshunov, Andrey; Landgraf, Pablo; Lehrach, Hans; Northcott, Paul A; Pfister, Stefan M; Reifenberger, Guido; Warnatz, Hans-Jörg; Wolf, Stephan; Yaspo, Marie-Laure; Assenov, Yassen; Gerhauser, Clarissa; Minner, Sarah; Schlomm, Thorsten; Simon, Ronald; Sauter, Guido; Sültmann, Holger; Biswas, Nidhan K; Maitra, Arindam; Majumder, Partha P; Sarin, Rajiv; Barbi, Stefano; Bonizzato, Giada; Cantù, Cinzia; Dei Tos, Angelo P; Fassan, Matteo; Grimaldi, Sonia; Luchini, Claudio; Malleo, Giuseppe; Marchegiani, Giovanni; Milella, Michele; Paiella, Salvatore; Pea, Antonio; Pederzoli, Paolo; Ruzzenente, Andrea; Salvia, Roberto; Sperandio, Nicola; Arai, Yasuhito; Hama, Natsuko; Hiraoka, Nobuyoshi; Hosoda, Fumie; Nakamura, Hiromi; Ojima, Hidenori; Okusaka, Takuji; Totoki, Yasushi; Urushidate, Tomoko; Fukayama, Masashi; Ishikawa, Shumpei; Katai, Hitoshi; Katoh, Hiroto; Komura, Daisuke; Rokutan, Hirofumi; Saito-Adachi, Mihoko; Suzuki, Akihiro; Taniguchi, Hirokazu; Tatsuno, Kenji; Ushiku, Tetsuo; Yachida, Shinichi; Yamamoto, Shogo; Aikata, Hiroshi; Arihiro, Koji; Ariizumi, Shun-Ichi; Chayama, Kazuaki; Furuta, Mayuko; Gotoh, Kunihito; Hayami, Shinya; Hirano, Satoshi; Kawakami, Yoshiiku; Maejima, Kazuhiro; Nakamura, Toru; Nakano, Kaoru; Ohdan, Hideki; Sasaki-Oku, Aya; Tanaka, Hiroko; Ueno, Masaki; Yamamoto, Masakazu; Yamaue, Hiroki; Choo, Su Pin; Cutcutache, Ioana; Khuntikeo, Narong; Ong, Choon Kiat; Pairojkul, Chawalit; Popescu, Irinel; Ahn, Keun Soo; Aymerich, Marta; Lopez-Guillermo, Armando; López-Otín, Carlos; Puente, Xose S; Campo, Elias; Amary, Fernanda; Baumhoer, Daniel; Behjati, Sam; Bjerkehagen, Bodil; Futreal, P A; Myklebost, Ola; Pillay, Nischalan; Tarpey, Patrick; Tirabosco, Roberto; Zaikova, Olga; Flanagan, Adrienne M; Boultwood, Jacqueline; Bowen, David T; Cazzola, Mario; Green, Anthony R; Hellstrom-Lindberg, Eva; Malcovati, Luca; Nangalia, Jyoti; Papaemmanuil, Elli; Vyas, Paresh; Ang, Yeng; Barr, Hugh; Beardsmore, Duncan; Eldridge, Matthew; Gossage, James; Grehan, Nicola; Hanna, George B; Hayes, Stephen J; Hupp, Ted R; Khoo, David; Lagergren, Jesper; Lovat, Laurence B; MacRae, Shona; O'Donovan, Maria; O'Neill, J Robert; Parsons, Simon L; Preston, Shaun R; Puig, Sonia; Roques, Tom; Sanders, Grant; Sothi, Sharmila; Tavaré, Simon; Tucker, Olga; Turkington, Richard; Underwood, Timothy J; Welch, Ian; Fitzgerald, Rebecca C; Berney, Daniel M; De Bono, Johann S; Cahill, Declan; Camacho, Niedzica; Dennis, Nening M; Dudderidge, Tim; Edwards, Sandra E; Fisher, Cyril; Foster, Christopher S; Ghori, Mohammed; Gill, Pelvender; Gnanapragasam, Vincent J; Gundem, Gunes; Hamdy, Freddie C; Hawkins, Steve; Hazell, Steven; Howat, William; Isaacs, William B; Karaszi, Katalin; 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Zhang, Hongxin; Zhang, Jiashan
Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1-3. Here we report the integrative analysis of 2,658Â whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5Â driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10-18.
PMID: 32025007
ISSN: 1476-4687
CID: 5018742