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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 14

  1. Content type: Research article

    The heterogeneous behavior of patients with melanoma makes prognostication challenging. To address this, a gene expression profile (GEP) test to predict metastatic risk was previously developed. This study eva...

    Authors: Jonathan S. Zager, Brian R. Gastman, Sancy Leachman, Rene C. Gonzalez, Martin D. Fleming, Laura K. Ferris, Jonhan Ho, Alexander R. Miller, Robert W. Cook, Kyle R. Covington, Kristen Meldi-Plasseraud, Brooke Middlebrook, Lewis H. Kaminester, Anthony Greisinger, Sarah I. Estrada, David M. Pariser…

    Citation: BMC Cancer 2018 18:130

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  2. Content type: Research article

    MicroRNAs (miRNAs or miRs) are small molecules known to be involved in post-transcriptional gene expression. Many of them have been shown to influence risk for various diseases. Recent studies suggest that low...

    Authors: Aleksandra Butrym, Piotr Łacina, Kazimierz Kuliczkowski, Katarzyna Bogunia-Kubik and Grzegorz Mazur

    Citation: BMC Cancer 2018 18:107

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  3. Content type: Research article

    A unified analysis of DNA sequences from hundreds of tumors concluded that the driver mutations primarily occur in the earliest stages of cancer formation, with relatively few driver mutation events detected i...

    Authors: Karen Gomez, Sayaka Miura, Louise A. Huuki, Brianna S. Spell, Jeffrey P. Townsend and Sudhir Kumar

    Citation: BMC Cancer 2018 18:85

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  4. Content type: Research article

    Sessile serrated adenomas with BRAF mutation progress rapidly to cancer following the development of dysplasia (SSAD). Approximately 75% of SSADs methylate the mismatch repair gene MLH1, develop mismatch repair d...

    Authors: Lochlan J. Fennell, Saara Jamieson, Diane McKeone, Tracie Corish, Megan Rohdmann, Tori Furner, Mark Bettington, Cheng Liu, Futoshi Kawamata, Catherine Bond, Jolieke Van De Pols, Barbara Leggett and Vicki Whitehall

    Citation: BMC Cancer 2018 18:35

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  5. Content type: Research article

    Aberrant overexpression of PIWI/piRNA pathway proteins is shown for many types of tumors. Interestingly, these proteins are downregulated in testicular germ cell tumors (TGCTs) compared to normal testis tissue...

    Authors: Ildar V. Gainetdinov, Yulia V. Skvortsova, Sofia A. Kondratieva, Alexey Klimov, Alexey A. Tryakin and Tatyana L. Azhikina

    Citation: BMC Cancer 2018 18:20

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  6. Content type: Research article

    Prostate Cancer (PCa) is the second most prevalent cancer among U.S. males. In recent decades many men with low risk PCa have been over diagnosed and over treated. Given significant co-morbidities associated w...

    Authors: Katerina Pestova, Adam J. Koch, Charles P. Quesenberry, Jun Shan, Ying Zhang, Amethyst D. Leimpeter, Beth Blondin, Svetlana Sitailo, Lela Buckingham, Jing Du, Huixin Fei and Stephen K. Van Den Eeden

    Citation: BMC Cancer 2018 18:2

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  7. Content type: Research article

    Associations between polymorphisms of UDP-glucuronosyltransferases (UGTs) or efflux transporters (e.g., P-glycoprotein and MRP2) and different types of cancer have been described, whereas the role of influx tr...

    Authors: Sabrina Falkowski, Jean-Baptiste Woillard, Deborah Postil, Nicole Tubiana-Mathieu, Eric Terrebonne, Antoine Pariente, Denis Smith, Rosine Guimbaud, Claire Thalamas, Koukeb Rouguieg-Malki, Pierre Marquet and Nicolas Picard

    Citation: BMC Cancer 2017 17:901

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  8. Content type: Study protocol

    A wide range of studies has investigated the diagnostic proficiency of extracellular microRNAs (miRNAs) in hepatocellular cancer (HCC). HCC is expected to increase in Sub-Saharan Africa (SSA), due to endemic l...

    Authors: K. Sartorius, B. Sartorius, A. Kramvis, E. Singh, A. Turchinovich, B. Burwinkel, T. Madiba and C. A. Winkler

    Citation: BMC Cancer 2017 17:894

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  9. Content type: Research article

    EphA2 is a crucial oncogene in gastric cancer (GC) development and metastasis, this study aims to identify microRNAs that target it and serve as key regulators of gastric carcinogenesis.

    Authors: Jin Huang, Yijing He, Howard L. Mcleod, Yanchun Xie, Desheng Xiao, Huabin Hu, Pan Chen, Liangfang Shen, Shan Zeng, Xianli Yin, Jie Ge, Li Li, Lanhua Tang, Jian Ma and Zihua Chen

    Citation: BMC Cancer 2017 17:886

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  10. Content type: Research article

    Histones undergo extensive post-translational modifications and this epigenetic regulation plays an important role in modulating transcriptional programs capable of driving cancer progression. Acetylation of h...

    Authors: Shivashankar Damodaran, Nathan Damaschke, Joseph Gawdzik, Bing Yang, Cedric Shi, Glenn O. Allen, Wei Huang, John Denu and David Jarrard

    Citation: BMC Cancer 2017 17:874

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  11. Content type: Research article

    Hepatocellular carcinoma (HCC) is the leading cause of cancer mortality. Chemical and virus induction are two major risk factors, however, the potential molecular mechanisms of their differences remain elusive...

    Authors: Qin Tang, Qi Wang, Qiong Zhang, Sheng-Yan Lin, Yanhong Zhu, Xiangliang Yang and An-Yuan Guo

    Citation: BMC Cancer 2017 17:862

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  12. Content type: Research article

    The significance of PLK1 (polo-like kinase 1) has become increasingly essential as both a biomarker and a target for cancer treatment. Here, we aimed to determine the downstream genes of PLK1 and their effects...

    Authors: Zhe Zhang, Guojun Zhang, Zhipeng Gao, Shiguang Li, Zeliang Li, Jianbin Bi, Xiankui Liu, Zhenhua Li and Chuize Kong

    Citation: BMC Cancer 2017 17:861

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  13. Content type: Case report

    Colorectal carcinoma (CRC) is one of the most common causes of cancer-related deaths. The mean age of patients with CRC ranges from 49 to 60 years. Pediatric CRC is unusual, which often escapes early diagnosis...

    Authors: Yung-Sung Yeh, Yu-Tang Chang, Cheng-Jen Ma, Ching-Wen Huang, Hsiang-Lin Tsai, Yi-Ting Chen and Jaw-Yuan Wang

    Citation: BMC Cancer 2017 17:849

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  14. Content type: Research article

    A systematic review was conducted to assess the diagnostic test accuracy of polymerase chain reaction (PCR)-based microsatellite instability (MSI) testing for identifying Lynch syndrome in patients with colore...

    Authors: Helen Coelho, Tracey Jones-Hughes, Tristan Snowsill, Simon Briscoe, Nicola Huxley, Ian M. Frayling and Chris Hyde

    Citation: BMC Cancer 2017 17:836

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  16. Content type: Research article

    MicroRNAs (miRNAs) exhibit essential regulatory functions related to cell growth, apoptosis, development and differentiation. Dysregulated expression of miRNAs is associated with a wide variety of human diseas...

    Authors: Guanyu Wang, Fulu Dong, Zhiyao Xu, Sherven Sharma, Xiaotong Hu, Dafang Chen, Lumin Zhang, Jinping Zhang and Qinghua Dong

    Citation: BMC Cancer 2017 17:805

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  17. Content type: Research article

    Female breast cancer is frequently diagnosed at a later stage and the leading cause of cancer deaths world-wide. Levels of cell-free circulating microRNAs (miRNAs) can potentially be used as biomarkers to meas...

    Authors: Amal Qattan, Haya Intabli, Wafa Alkhayal, Chafica Eltabache, Taher Tweigieri and Suad Bin Amer

    Citation: BMC Cancer 2017 17:799

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  18. Content type: Research article

    Colorectal cancer is a heterogeneous group of malignancies with complex molecular subtypes. While colon cancer has been widely investigated, studies on rectal cancer are very limited. Here, we performed multi-...

    Authors: Mingshan Liu, Yang Liu, Jiabo Di, Zhe Su, Hong Yang, Beihai Jiang, Zaozao Wang, Meng Zhuang, Fan Bai and Xiangqian Su

    Citation: BMC Cancer 2017 17:787

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  19. Content type: Research article

    Gastric cancer (GC) is one of the most frequently diagnosed digestive tract cancers and carries a high risk of mortality. Acetaldehyde (AA), a carcinogenic intermediate of ethanol metabolism contributes to the...

    Authors: Sudakshina Ghosh, Biswabandhu Bankura, Soumee Ghosh, Makhan Lal Saha, Arup Kumar Pattanayak, Souvik Ghatak, Manalee Guha, Senthil Kumar Nachimuthu, Chinmoy Kumar Panda, Suvendu Maji, Subrata Chakraborty, Biswanath Maity and Madhusudan Das

    Citation: BMC Cancer 2017 17:782

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  20. Content type: Research article

    ESR1 mutations have attracted attention as a potentially important marker and treatment target in endocrine therapy-resistant breast cancer patients. The E380Q mutation, which is one o...

    Authors: Takashi Takeshita, Yutaka Yamamoto, Mutsuko Yamamoto-Ibusuki, Aiko Sueta, Mai Tomiguchi, Keiichi Murakami, Yoko Omoto and Hirotaka Iwase

    Citation: BMC Cancer 2017 17:786

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  21. Content type: Research article

    Expression of caveolin-1 (Cav-1) is frequently altered in many human cancers and both tumor suppression and promotion functions of Cav-1 have been suggested based on its expression status. However, it remains ...

    Authors: Byung-Kyu Ryu, Min-Goo Lee, Nam-Hoon Kim, Kil Yeon Lee, Shin-Ju Oh, Jung-Rock Moon, Hyo Jong Kim and Sung-Gil Chi

    Citation: BMC Cancer 2017 17:766

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  22. Content type: Research article

    Among the sex hormones, oestrogen may play a role in colorectal cancer, particularly in conjunction with oestrogen receptor-β (ERβ). The expression of ERβ isoform variants and their correlations with familial ...

    Authors: Paulo Roberto Stevanato Filho, Samuel Aguiar Júnior, Maria Dirlei Begnami, Hellen Kuasne, Ranyell Matheus Spencer, Wilson Toshihiko Nakagawa, Tiago Santoro Bezerra, Bruna Catin Kupper, Renata Maymi Takahashi, Mateus Barros Filho, Silvia Regina Rogatto and Ademar Lopes

    Citation: BMC Cancer 2017 17:754

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  23. Content type: Research article

    Neuroendocrine prostate cancer (NEPC) may be rising in prevalence as patients with advanced prostate cancer potentially develop resistance to contemporary anti-androgen treatment through a neuroendocrine pheno...

    Authors: Harrison K. Tsai, Jonathan Lehrer, Mohammed Alshalalfa, Nicholas Erho, Elai Davicioni and Tamara L. Lotan

    Citation: BMC Cancer 2017 17:759

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  24. Content type: Research article

    Burkitt lymphoma (BL) is characterized by overexpression of the c-myc oncogene, which in the vast majority of cases is a consequence of an IGH/MYC translocation. While myc is the seminal event, BL is a complex am...

    Authors: Cliff I. Oduor, Yasin Kaymaz, Kiprotich Chelimo, Juliana A. Otieno, John Michael Ong’echa, Ann M. Moormann and Jeffrey A. Bailey

    Citation: BMC Cancer 2017 17:761

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  25. Content type: Research article

    To better predict the likelihood of response to chemotherapy, we have conducted a study comparing the gene expression patterns of primary tumours with their corresponding response to systemic chemotherapy in t...

    Authors: Cemile Dilara Savci-Heijink, Hans Halfwerk, Jan Koster and Marc Joan Van de Vijver

    Citation: BMC Cancer 2017 17:755

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  26. Content type: Research article

    The association of genes XRCC1, TP53 and MDM2 with breast cancer (BC) has never been tested in Kyrgyz population. We, therefore, aimed to identify an association of alleles and genotypes of polymorphic markers Ar...

    Authors: Jainagul Isakova, Elnura Talaibekova, Nazira Aldasheva, Denis Vinnikov and Almaz Aldashev

    Citation: BMC Cancer 2017 17:758

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  27. 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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  28. Content type: Research article

    Melanoma is the most lethal type of skin cancer. Since chemoresistance is a significant barrier, identification of regulators affecting chemosensitivity is necessary in order to create new forms of interventio...

    Authors: Priscila Daniele Ramos Cirilo, Luciana Nogueira de Sousa Andrade, Bruna Renata Silva Corrêa, Mei Qiao, Tatiane Katsue Furuya, Roger Chammas and Luiz Otavio Ferraz Penalva

    Citation: BMC Cancer 2017 17:750

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  29. Content type: Research article

    Non-coding RNAs play an important role in human carcinogenesis. YRNAs (Ro-associated Y), a novel class of non-coding RNAs, have been identified as biomarker in various malignancies, but remain to be studied in...

    Authors: Yuri Tolkach, Anna Franziska Stahl, Eva-Maria Niehoff, Chenming Zhao, Glen Kristiansen, Stefan Cajetan Müller and Jörg Ellinger

    Citation: BMC Cancer 2017 17:749

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  30. 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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  31. 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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  32. 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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  33. 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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  34. 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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  35. 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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  36. 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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  37. 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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  38. 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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  39. 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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  40. 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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  41. 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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  42. 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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  43. 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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  44. 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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  45. 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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  46. 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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  47. 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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  48. 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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  49. 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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  50. 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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