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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

    While cure rates for childhood acute lymphoblastic leukemia (cALL) now exceed 80%, over 60% of survivors will face treatment-related long-term sequelae, including cardiometabolic complications such as obesity,...

    Authors: Jade England, Simon Drouin, Patrick Beaulieu, Pascal St-Onge, Maja Krajinovic, Caroline Laverdière, Emile Levy, Valérie Marcil and Daniel Sinnett

    Citation: BMC Cancer 2017 17:751

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  2. Content type: Research article

    Understanding the underlying molecular mechanisms involved in the formation of cutaneous malignant melanoma is critical for improved diagnosis and treatment. Keratinocytic nuclear receptor Retinoid X Receptor ...

    Authors: Sharmeen Chagani, Rong Wang, Evan L. Carpenter, Christiane V. Löhr, Gitali Ganguli-Indra and Arup K. Indra

    Citation: BMC Cancer 2017 17:736

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  3. Content type: Research article

    Circulating cell-free miRNAs have emerged as promising minimally-invasive biomarkers for early detection, prognosis and monitoring of cancer. They can exist in the bloodstream incorporated into extracellular v...

    Authors: Edgars Endzeliņš, Andreas Berger, Vita Melne, Cristina Bajo-Santos, Kristīne Soboļevska, Artūrs Ābols, Marta Rodriguez, Daiga Šantare, Anastasija Rudņickiha, Vilnis Lietuvietis, Alicia Llorente and Aija Linē

    Citation: BMC Cancer 2017 17:730

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  4. Content type: Research article

    The aim of this study was to identify miRNAs specifically dysregulated in BRAF-mutated colorectal cancer, which could lead to a better understanding of the molecular mechanisms underlying oncogenesis of this mali...

    Authors: Hidekazu Takahashi, Masanobu Takahashi, Shinobu Ohnuma, Michiaki Unno, Yuki Yoshino, Kota Ouchi, Shin Takahashi, Yasuhide Yamada, Hideki Shimodaira and Chikashi Ishioka

    Citation: BMC Cancer 2017 17:723

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  5. Content type: Research article

    Cancer stem cells (CSCs) are considered to be the major factor in tumor initiation, progression, metastasis, recurrence and chemoresistance. Maintaining the stemness and promoting differentiation of these cell...

    Authors: Xiaofeng Yu, Lin Mi, Jie Dong and Jian Zou

    Citation: BMC Cancer 2017 17:716

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  6. Content type: Case report

    Multiple Myeloma is a cancer of plasma cells associated with significantly reduced survival. Long term survivorship from myeloma is very rare and despite advances in its treatment the disease is generally cons...

    Authors: Vallari Shah, Kevin D. Boyd, Richard S. Houlston and Martin F. Kaiser

    Citation: BMC Cancer 2017 17:718

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  7. Content type: Research article

    microRNAs are small non-protein-coding RNA molecules that regulate gene expression, and have a potential epigenetic role in disease progression and survival of colorectal cancer. In terms of tumor-normal expre...

    Authors: John R. Stevens, Jennifer S. Herrick, Roger K. Wolff and Martha L. Slattery

    Citation: BMC Cancer 2017 17:707

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  8. Content type: Research article

    Integrator complex subunit 6 (INTS6) was found to play a tumour suppressing role in certain types of solid tumours. In this study, we wanted to determine the expression level of INTS6 in hepatocellular carcino...

    Authors: Ka Yin Lui, Hui Zhao, Chunhui Qiu, Chuo Li, Zhigang Zhang, Haoran Peng, Rongdang Fu, Hu-an Chen and Min-qiang Lu

    Citation: BMC Cancer 2017 17:644

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  9. Content type: Research article

    Male breast cancer (MBC) represents a poorly characterised group of tumours, the management of which is largely based on practices established for female breast cancer. However, recent studies demonstrate biol...

    Authors: Siddhartha Deb, Kylie L. Gorringe, Jia-Min B. Pang, David J. Byrne, Elena A. Takano, kConFab Investigators, Alexander Dobrovic and Stephen B. Fox

    Citation: BMC Cancer 2017 17:641

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  10. Content type: Research article

    A fusion gene is a hybrid gene consisting of parts from two previously independent genes. Chromosomal rearrangements leading to gene breakage are frequent in high-grade serous ovarian carcinomas and have been ...

    Authors: Marianne Lislerud Smebye, Antonio Agostini, Bjarne Johannessen, Jim Thorsen, Ben Davidson, Claes Göran Tropé, Sverre Heim, Rolf Inge Skotheim and Francesca Micci

    Citation: BMC Cancer 2017 17:642

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  11. Content type: Research article

    Acute myeloid leukemia (AML) is an aggressive malignancy only cured by intensive therapy. However, many elderly and unfit patients cannot receive such treatment due to an unacceptable risk of treatment-related...

    Authors: Håkon Reikvam, Randi Hovland, Rakel Brendsdal Forthun, Sigrid Erdal, Bjørn Tore Gjertsen, Hanne Fredly and Øystein Bruserud

    Citation: BMC Cancer 2017 17:630

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  12. Content type: Research article

    Genetic counselling and testing for Lynch syndrome (LS) have recently been introduced in several Latin America countries. We aimed to characterize the clinical, molecular and mismatch repair (MMR) variants spe...

    Authors: Benedito Mauro Rossi, Edenir Inêz Palmero, Francisco López-Kostner, Carlos Sarroca, Carlos Alberto Vaccaro, Florencia Spirandelli, Patricia Ashton-Prolla, Yenni Rodriguez, Henrique de Campos Reis Galvão, Rui Manuel Reis, André Escremim de Paula, Luis Gustavo Capochin Romagnolo, Karin Alvarez, Adriana Della Valle, Florencia Neffa, Pablo German Kalfayan…

    Citation: BMC Cancer 2017 17:623

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  13. Content type: Research article

    Prostate cancer is a major contributor to mortality worldwide, and significant efforts are being undertaken to decipher specific cellular and molecular pathways underlying the disease. Chronic stress is known ...

    Authors: Ivan E. Flores, Jorge A. Sierra-Fonseca, Olinamyr Davalos, Luis A. Saenz, Maria M. Castellanos, Jaidee K. Zavala and Kristin L. Gosselink

    Citation: BMC Cancer 2017 17:621

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  14. Content type: Research article

    Several susceptibility genes have been established for female breast cancer, of which mutations in BRCA1 and especially in BRCA2 are also known risk factors for male breast cancer (MBC). The role of other breast ...

    Authors: Sanna Hallamies, Liisa M. Pelttari, Paula Poikonen-Saksela, Antti Jekunen, Arja Jukkola-Vuorinen, Päivi Auvinen, Carl Blomqvist, Kristiina Aittomäki, Johanna Mattson and Heli Nevanlinna

    Citation: BMC Cancer 2017 17:620

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  15. Content type: Research article

    Describe a single-center real-world experience with comprehensive genomic profiling (CGP) to identify genotype directed therapy (GDT) options for patients with malignancies refractory to standard treatment opt...

    Authors: Talal Hilal, Mary Nakazawa, Jacob Hodskins, John L. Villano, Aju Mathew, Guarav Goel, Lars Wagner, Susanne M. Arnold, Philip DeSimone, Lowell B. Anthony and Peter J. Hosein

    Citation: BMC Cancer 2017 17:602

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  16. 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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  17. 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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  18. 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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  19. 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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  20. 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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  21. 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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  22. 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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  23. 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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  24. 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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  25. 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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  26. 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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  27. 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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  28. 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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  29. 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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  31. 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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  32. 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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  33. 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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  34. 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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  35. 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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  36. 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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  38. 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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  39. 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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  40. 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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  41. 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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  42. 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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  43. 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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  44. 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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  46. 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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  47. 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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  48. 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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  49. 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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  50. 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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