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Genetics, genomics and epigenetics

Section edited by Ian Cree

This section considers articles on all aspects of genome-scale analysis, functional genomics, genetic association studies, pharmacogenomics and epigenetics in relation to cancer biology, diagnosis and therapy.

Page 3 of 13

  1. Content type: Research article

    DNA methylation changes occurring in cancer cells are featured with both promoter CpG island hypermethylation and diffuse genomic hypomethylation. Long interspersed element-1 (LINE-1) is repeated in an intersp...

    Authors: Seorin Jeong, Kyoungbun Lee, Xianyu Wen, Younghoon Kim, Nam-Yun Cho, Ja-June Jang and Gyeong Hoon Kang

    Citation: BMC Cancer 2017 17:588

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  2. Content type: Research article

    Most gastrointestinal stromal tumors (GISTs) harbor mutually exclusive gain of function mutations in the receptor tyrosine kinase (RTK) KIT (70–80%) or in the related receptor PDGFRA (~10%). These GISTs genera...

    Authors: Martin G. Belinsky, Kathy Q. Cai, Yan Zhou, Biao Luo, Jianming Pei, Lori Rink and Margaret von Mehren

    Citation: BMC Cancer 2017 17:512

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  3. Content type: Research article

    BRCA1 and BRCA2 mutations explain approximately one-fifth of the inherited susceptibility in high-risk Finnish hereditary breast and ovarian cancer (HBOC) families. EMSY is located in ...

    Authors: Kirsi M. Määttä, Riikka Nurminen, Minna Kankuri-Tammilehto, Anne Kallioniemi, Satu-Leena Laasanen and Johanna Schleutker

    Citation: BMC Cancer 2017 17:496

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  4. Content type: Study protocol

    The ‘common variant, common disease’ model predicts that a significant component of hereditary breast cancer unexplained by pathogenic variants in moderate or high-penetrance genes is due to the cumulative eff...

    Authors: Tatiane Yanes, Bettina Meiser, Mary-Anne Young, Rajneesh Kaur, Gillian Mitchell, Kristine Barlow-Stewart, Tony Roscioli, Jane Halliday and Paul James

    Citation: BMC Cancer 2017 17:491

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  5. Content type: Research article

    The disco-interacting protein 2 homolog C (DIP2C) gene is an uncharacterized gene found mutated in a subset of breast and lung cancers. To understand the role of DIP2C in tumour development we studied the gene in...

    Authors: Chatarina Larsson, Muhammad Akhtar Ali, Tatjana Pandzic, Anders M. Lindroth, Liqun He and Tobias Sjöblom

    Citation: BMC Cancer 2017 17:487

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  6. Content type: Research article

    Epigenetic changes, including DNA methylation, disrupt normal cell function, thus contributing to multiple steps of carcinogenesis. Nasopharyngeal carcinoma (NPC) is endemic in southern China and is highly ass...

    Authors: Weilin Zhao, Yingxi Mo, Shumin Wang, Kaoru Midorikawa, Ning Ma, Yusuke Hiraku, Shinji Oikawa, Guangwu Huang, Zhe Zhang, Mariko Murata and Kazuhiko Takeuchi

    Citation: BMC Cancer 2017 17:489

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  7. Content type: Research article

    DNA repair of alkylation damage is defective in various cancers. This occurs through somatically acquired inactivation of the MGMT gene in various cancer types, including breast cancers. In addition to MGMT, t...

    Authors: Olafur Andri Stefansson, Stefan Hermanowicz, Jasper van der Horst, Holmfridur Hilmarsdottir, Zuzanna Staszczak, Jon Gunnlaugur Jonasson, Laufey Tryggvadottir, Thorkell Gudjonsson and Stefan Sigurdsson

    Citation: BMC Cancer 2017 17:469

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  8. Content type: Research article

    Sequencing analysis of circulating tumor cells (CTCs) enables “liquid biopsy” to guide precision oncology strategies. However, this requires low-template whole genome amplification (WGA) that is prone to error...

    Authors: Shonan Sho, Colin M. Court, Paul Winograd, Sangjun Lee, Shuang Hou, Thomas G. Graeber, Hsian-Rong Tseng and James S. Tomlinson

    Citation: BMC Cancer 2017 17:457

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  9. Content type: Research article

    Epithelial to mesenchymal transition (EMT) is the process by which stationary epithelial cells transdifferentiate to mesenchymal cells with increased motility. EMT is integral in early stages of development an...

    Authors: Princy Parsana, Sarah R. Amend, James Hernandez, Kenneth J. Pienta and Alexis Battle

    Citation: BMC Cancer 2017 17:447

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  10. Content type: Research article

    Identification of BRCA mutations in breast cancer (BC) patients influences treatment and survival and may be of importance for their relatives. Testing is often restricted to women fulfilling high-risk criteria. ...

    Authors: Eli Marie Grindedal, Cecilie Heramb, Inga Karsrud, Sarah Louise Ariansen, Lovise Mæhle, Dag Erik Undlien, Jan Norum and Ellen Schlichting

    Citation: BMC Cancer 2017 17:438

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  11. Content type: Research article

    Esophageal carcinoma is the third most common gastrointestinal malignancy worldwide and is largely unresponsive to therapy. African-Americans have an increased risk for esophageal squamous cell carcinoma (ESCC...

    Authors: Hayriye Verda Erkizan, Kory Johnson, Svetlana Ghimbovschi, Deepa Karkera, Gregory Trachiotis, Houtan Adib, Eric P. Hoffman and Robert G. Wadleigh

    Citation: BMC Cancer 2017 17:426

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  12. Content type: Research article

    Malignant mesothelioma (MM) is an aggressive cancer of the pleural and peritoneal cavities caused by exposure to asbestos. Asbestos-induced mesotheliomas in wild-type mice have been used extensively as a precl...

    Authors: Sophie Sneddon, Ann-Marie Patch, Ian M. Dick, Stephen Kazakoff, John V. Pearson, Nicola Waddell, Richard J. N. Allcock, Robert A. Holt, Bruce W. S. Robinson and Jenette Creaney

    Citation: BMC Cancer 2017 17:396

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  13. Content type: Research article

    CUL4A has been known for its oncogenic properties in various human cancers. However, its role in intrahepatic cholangiocarcinoma (iCCA) has not been explored.

    Authors: Gong -Kai Huang, Ting-Ting Liu, Shao-Wen Weng, Huey-Ling You, Yu-Ching Wei, Chang-Han Chen, Hock-Liew Eng and Wan-Ting Huang

    Citation: BMC Cancer 2017 17:395

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  14. Content type: Research article

    The detection of somatic mutations in primary tumors is critical for the understanding of cancer evolution and targeting therapy. Multiple technologies have been developed to enable the detection of such mutat...

    Authors: Agus Darwanto, Anne-Mette Hein, Sascha Strauss, Yi Kong, Andrew Sheridan, Dan Richards, Eric Lader, Monika Ngowe, Timothy Pelletier, Danielle Adams, Austin Ricker, Nishit Patel, Andreas Kühne, Simon Hughes, Dan Shiffman, Dirk Zimmermann…

    Citation: BMC Cancer 2017 17:358

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  15. Content type: Research article

    Genetic factors may influence an individual’s sensitivity to ionising radiation and therefore modify his/her risk of developing papillary thyroid carcinoma (PTC). Previously, we reported that common single nuc...

    Authors: Christine Lonjou, Francesca Damiola, Monika Moissonnier, Geoffroy Durand, Irina Malakhova, Vladimir Masyakin, Florence Le Calvez-Kelm, Elisabeth Cardis, Graham Byrnes, Ausrele Kesminiene and Fabienne Lesueur

    Citation: BMC Cancer 2017 17:328

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  16. Content type: Research article

    Neoadjuvant chemotherapy is a key component of breast cancer treatment regimens and pathologic complete response to this therapy varies among patients. This is presumably due to differences in the molecular me...

    Authors: Kenneth M. K. Mark, Frederick S. Varn, Matthew H. Ung, Feng Qian and Chao Cheng

    Citation: BMC Cancer 2017 17:306

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  17. Content type: Research article

    Current diagnostic tools for prostate cancer lack specificity and sensitivity for detecting very early lesions. DNA methylation is a stable genomic modification that is detectable in peripheral patient fluids ...

    Authors: Marie K. Kirby, Ryne C. Ramaker, Brian S. Roberts, Brittany N. Lasseigne, David S. Gunther, Todd C. Burwell, Nicholas S. Davis, Zulfiqar G. Gulzar, Devin M. Absher, Sara J. Cooper, James D. Brooks and Richard M. Myers

    Citation: BMC Cancer 2017 17:273

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  18. Content type: Research article

    Breast carcinogenesis is a multistep process involving genetic and epigenetic changes. Tumor tissues are frequently characterized by gene-specific hypermethylation and global DNA hypomethylation. Aberrant DNA ...

    Authors: Melanie Spitzwieser, Elisabeth Entfellner, Bettina Werner, Walter Pulverer, Georg Pfeiler, Stefan Hacker and Margit Cichna-Markl

    Citation: BMC Cancer 2017 17:260

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  19. Content type: Research article

    H3K27me3 histone marks shape the inhibition of gene transcription. In prostate cancer, the deregulation of H3K27me3 marks might play a role in prostate tumor progression.

    Authors: Marjolaine Ngollo, Andre Lebert, Marine Daures, Gaelle Judes, Khaldoun Rifai, Lucas Dubois, Jean-Louis Kemeny, Frederique Penault-Llorca, Yves-Jean Bignon, Laurent Guy and Dominique Bernard-Gallon

    Citation: BMC Cancer 2017 17:261

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  20. Content type: Research article

    Mucin 1 (MUC1) contributes to the growth and metastasis of various cancers, including lung cancer, and MUC1 gene length polymorphisms are associated with susceptibility to lung cancer and its prognosis. In contra...

    Authors: Yasushi Horimasu, Nobuhisa Ishikawa, Sonosuke Tanaka, Chihiro Hirano, Hiroshi Iwamoto, Shinichiro Ohshimo, Kazunori Fujitaka, Hironobu Hamada, Noboru Hattori and Nobuoki Kohno

    Citation: BMC Cancer 2017 17:263

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  21. Content type: Research article

    Triple negative breast cancer (TNBC) is a heterogeneous disease that lacks unifying molecular alterations that can guide therapy decisions. We previously identified distinct molecular subtypes of TNBC (TNBCtyp...

    Authors: Bojana Jovanović, Quanhu Sheng, Robert S. Seitz, Kasey D. Lawrence, Stephan W. Morris, Lance R. Thomas, David R. Hout, Brock L. Schweitzer, Yan Guo, Jennifer A. Pietenpol and Brian D. Lehmann

    Citation: BMC Cancer 2017 17:241

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  22. Content type: Research article

    The defects in DNA repair genes are potentially linked to development and response to therapy in medulloblastoma. Therefore the purpose of this study was to establish the spectrum and frequency of germline varian...

    Authors: Joanna Trubicka, Tomasz Żemojtel, Jochen Hecht, Katarzyna Falana, Dorota Piekutowska- Abramczuk, Rafał Płoski, Marta Perek-Polnik, Monika Drogosiewicz, Wiesława Grajkowska, Elżbieta Ciara, Elżbieta Moszczyńska, Bożenna Dembowska-Bagińska, Danuta Perek, Krystyna H. Chrzanowska, Małgorzata Krajewska-Walasek and Maria Łastowska

    Citation: BMC Cancer 2017 17:239

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  23. Content type: Research article

    Distinct characteristic features categorize Merkel cell carcinoma (MCC) into two subgroups according to the Merkel cell polyomavirus infection. Many mutational studies on MCC have been carried out in recent ye...

    Authors: Tuukka Veija, Virve Koljonen, Tom Bohling, Mia Kero, Sakari Knuutila and Virinder Kaur Sarhadi

    Citation: BMC Cancer 2017 17:236

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  24. Content type: Research article

    Aberrant DNA methylation profiles are a characteristic of all known cancer types, epitomized by the CpG island methylator phenotype (CIMP) in colorectal cancer (CRC). Hypermethylation has been observed at CpG ...

    Authors: Tyler McInnes, Donghui Zou, Dasari S. Rao, Francesca M. Munro, Vicky L. Phillips, John L. McCall, Michael A. Black, Anthony E. Reeve and Parry J. Guilford

    Citation: BMC Cancer 2017 17:228

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  25. Content type: Research article

    Tumour stem cells are considered important to promote disease progression, recurrence and treatment resistance following chemotherapy in colon cancer. However, genomic analyses of colorectal cancer have mainly...

    Authors: Diana Cervantes-Madrid, Yvonne Wettergren, Peter Falk, Kent Lundholm and Annika G. Asting

    Citation: BMC Cancer 2017 17:219

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  26. Content type: Research article

    Recently studies have demonstrated that the long non-coding RNA (lncRNA) metastasis associated lung adenocarcinoma transcript 1 (MALAT1) may participate in the development and progression of lung cancer. In th...

    Authors: Jian-Zhong Wang, Jing-Jun Xiang, Li-Ge Wu, Yan-Sen Bai, Zhuo-Wang Chen, Xiang-Qian Yin, Qing Wang, Wen-Hao Guo, Ying Peng, Huan Guo and Ping Xu

    Citation: BMC Cancer 2017 17:167

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  27. Content type: Research article

    Dysregulated WNT signaling dominates adrenocortical malignancies. This study investigates whether silencing of the WNT negative regulator DKK3 (Dickkopf-related protein 3), an implicated adrenocortical differe...

    Authors: Joyce Y. Cheng, Taylor C. Brown, Timothy D. Murtha, Adam Stenman, C. Christofer Juhlin, Catharina Larsson, James M. Healy, Manju L. Prasad, Wolfram T. Knoefel, Andreas Krieg, Ute I. Scholl, Reju Korah and Tobias Carling

    Citation: BMC Cancer 2017 17:164

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  28. Content type: Research article

    Genetic testing for BRCA1 and BRCA2 has led to the accurate identification of individuals at higher risk of cancer and the development of new therapies. Approximately 10-20% of the genetic testing for BRCA1 and B...

    Authors: Kah Nyin Lai, Weang Kee Ho, In Nee Kang, Peter Choon Eng Kang, Sze Yee Phuah, Shivaani Mariapun, Cheng-Har Yip, Nur Aishah Mohd Taib and Soo-Hwang Teo

    Citation: BMC Cancer 2017 17:149

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  29. Content type: Research article

    Knowledge of the genotype of melanoma is important to guide patient management. Identification of mutations in BRAF and c-KIT lead directly to targeted treatment, but it is also helpful to know if there are dr...

    Authors: Anne Reiman, Hugh Kikuchi, Daniela Scocchia, Peter Smith, Yee Wah Tsang, David Snead and Ian A Cree

    Citation: BMC Cancer 2017 17:150

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  30. Content type: Research article

    DICER1 syndrome is a pediatric cancer predisposition condition causing a variety of tumor types in children and young adults. In this report we studied a family with two relatives presenting a variety of neopl...

    Authors: Lorena Fernández-Martínez, José Antonio Villegas, Íñigo Santamaría, Ana S. Pitiot, Marta G. Alvarado, Soledad Fernández, Héctor Torres, Ángeles Paredes, Pilar Blay and Milagros Balbín

    Citation: BMC Cancer 2017 17:146

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  31. Content type: Research article

    Testing for KRAS mutations in metastatic colorectal cancer (mCRC) on formalin-fixed, paraffin embedded (FFPE) tumor tissue has become standard of care. Different molecular methods exist to determine hotspot KRAS ...

    Authors: Christine Weyn, Sofie Van Raemdonck, Robina Dendooven, Vincent Maes, Karen Zwaenepoel, Suzan Lambin and Patrick Pauwels

    Citation: BMC Cancer 2017 17:139

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  32. Content type: Research article

    The integration of HR-HPV genome into host DNA is regarded as a key step for the development of cervical cancer. However, HR-HPV genome indeed exists as episome except for integrant. It may be alternative mech...

    Authors: Die Hong, Jia Liu, Ying Hu, Xiaonan Lu, Baohua Li, Yang Li, Dongxiao Hu, Weiguo Lu, Xing Xie and Xiaodong Cheng

    Citation: BMC Cancer 2017 17:136

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  33. Content type: Case report

    Neurofibromatosis type 2 (NF2) is a rare autosomal dominant nervous system tumor predisposition disorder caused by constitutive inactivation of one of the two copies of NF2. Meningiomas affect about one half of N...

    Authors: Ramita Dewan, Alexander Pemov, Amalia S. Dutra, Evgenia D. Pak, Nancy A. Edwards, Abhik Ray-Chaudhury, Nancy F. Hansen, Settara C. Chandrasekharappa, James C. Mullikin, Ashok R. Asthagiri, John D. Heiss, Douglas R. Stewart and Anand V. Germanwala

    Citation: BMC Cancer 2017 17:127

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  34. Content type: Research article

    Gastric cancer is one of the most common malignancies worldwide. Recent studies have shown that microRNAs play crucial roles in regulating cellular proliferation process in gastric cancer. MicroRNA-29c (miR-29...

    Authors: Beiqin Yu, Xuehua Chen, Jianfang Li, Qinlong Gu, Zhenggang Zhu, Chen Li, Liping Su and Bingya Liu

    Citation: BMC Cancer 2017 17:109

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  35. Content type: Research article

    The del1518 (rs3730485) polymorphism is an in/del variant in the MDM2 promoter P1. The variant is in complete linkage disequilibrium with MDM2 SNP309 (rs2279744) and has previously been found associated with an i...

    Authors: Liv B. Gansmo, Merete Bjørnslett, Mari Kyllesø Halle, Helga B. Salvesen, Pål Romundstad, Kristian Hveem, Lars Vatten, Anne Dørum, Per E. Lønning and Stian Knappskog

    Citation: BMC Cancer 2017 17:97

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  36. Content type: Research article

    The insulin-like growth factor (IGF) system plays an important role in the development and progression of cancer. However, little is known about the expression of the IGF system components and their clinicopat...

    Authors: Xinwei Feng, Jianhua Lin, Shan Xing, Wanli Liu and Ge Zhang

    Citation: BMC Cancer 2017 17:90

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  37. Content type: Research article

    Oxaliplatin is a chemotherapy agent active against digestive tumors. Peripheral neuropathy is one of the most important dose-limiting toxicity of this drug. It occurs in around 60–80% of the patients, and 15% ...

    Authors: María Sereno, Gerardo Gutiérrez-Gutiérrez, Juan Moreno Rubio, María Apellániz-Ruiz, Lara Sánchez-Barroso, Enrique Casado, Sandra Falagan, Miriam López-Gómez, María Merino, César Gómez-Raposo, Nuria Rodriguez-Salas, Francisco Zambrana Tébar and Cristina Rodríguez-Antona

    Citation: BMC Cancer 2017 17:63

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  38. Content type: Case report

    Sarcomatoid cancer is defined by the World Health Organization as a category of non-small cell lung cancers with sarcoma or sarcoma-like differentiation. They are characterized by poor prognosis and resistance...

    Authors: Taichiro Goto, Yosuke Hirotsu, Hitoshi Mochizuki, Takahiro Nakagomi, Toshio Oyama, Kenji Amemiya and Masao Omata

    Citation: BMC Cancer 2017 17:65

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  39. Content type: Research article

    The basic helix-loop-helix transcription factor TWIST1 (Twist) is involved in embryonic cell lineage determination and mesodermal differentiation. There is evidence to indicate that Twist expression plays a ro...

    Authors: Farhad Vesuna, Yehudit Bergman and Venu Raman

    Citation: BMC Cancer 2017 17:52

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  40. Content type: Case report

    Many patients experience local recurrence or metastases after receiving potentially curative treatment, and early detection of these events is important for disease control. Recent technological advances make ...

    Authors: Heidi M. Namløs, Olga Zaikova, Bodil Bjerkehagen, Daniel Vodák, Eivind Hovig, Ola Myklebost, Kjetil Boye and Leonardo A. Meza-Zepeda

    Citation: BMC Cancer 2017 17:29

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  41. Content type: Case report

    Primary cardiac angiosarcomas are rare, but they are the most aggressive type of primary cardiac neoplasms. When patients do present, it is with advanced pulmonary and/or cardiac symptoms. Therefore, many time...

    Authors: Leah Zhrebker, Irene Cherni, Lara M. Gross, Margaret M. Hinshelwood, Merrick Reese, Jessica Aldrich, Joseph M. Guileyardo, William C. Roberts, David Craig, Daniel D. Von Hoff, Robert G. Mennel and John D. Carpten

    Citation: BMC Cancer 2017 17:17

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  42. Content type: Research article

    Human chromosomes are capped and stabilized by telomeres. Telomere length regulates a ‘cellular mitotic clock’ that defines the number of cell divisions and hence, cellular life span. This study aimed to synth...

    Authors: Cho Naing, Kyan Aung, Pei Kuan Lai and Joon Wah Mak

    Citation: BMC Cancer 2017 17:24

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  43. Content type: Research article

    Approximately 8–15% epithelial ovarian cancer patients are BRCA1 or BRCA2 germline mutation carriers. Brazilian inhabitants may have peculiar genetic characteristics associated with ethnic diversity, and studies ...

    Authors: Simone Maistro, Natalia Teixeira, Giselly Encinas, Maria Lucia Hirata Katayama, Vivian Dionisio Tavares Niewiadonski, Larissa Garcia Cabral, Roberto Marques Ribeiro, Nelson Gaburo Junior, Ana Carolina Ribeiro Chaves de Gouvêa, Dirce Maria Carraro, Ester Cerdeira Sabino, Maria del Pilar Estevez Diz, Roger Chammas, Geertruida Hendrika de Bock and Maria Aparecida Azevedo Koike Folgueira

    Citation: BMC Cancer 2016 16:934

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  44. Content type: Research article

    Detection and localization of genomic alterations and breakpoints are crucial in cancer research. The purpose of this study was to investigate, in a methodological and biological perspective, different female,...

    Authors: Fatemeh Kaveh, Lars O. Baumbusch, Daniel Nebdal, Anne-Lise Børresen-Dale, Ole Christian Lingjærde, Hege Edvardsen, Vessela N. Kristensen and Hiroko K. Solvang

    Citation: BMC Cancer 2016 16:913

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    The Correction to this article has been published in BMC Cancer 2018 18:80

  45. Content type: Research article

    Rhabdomyosarcoma (RMS), which can be classified as embryonal RMS (ERMS) and alveolar RMS (ARMS), represents the most frequent soft tissue sarcoma in the pediatric population; the latter shows greater aggressiv...

    Authors: L. Tombolan, E. Poli, P. Martini, A. Zin, C. Millino, B. Pacchioni, B. Celegato, G. Bisogno, C. Romualdi, A. Rosolen and G. Lanfranchi

    Citation: BMC Cancer 2016 16:886

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