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.

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  1. Research article

    A genetic variant in long non-coding RNA MALAT1 associated with survival outcome among patients with advanced lung adenocarcinoma: a survival cohort analysis

    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...

    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

    BMC Cancer 2017 17:167

    Published on: 3 March 2017

  2. Research article

    A novel FOXO1-mediated dedifferentiation blocking role for DKK3 in adrenocortical carcinogenesis

    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...

    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

    BMC Cancer 2017 17:164

    Published on: 1 March 2017

  3. Research article

    Validation of an NGS mutation detection panel for melanoma

    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...

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

    BMC Cancer 2017 17:150

    Published on: 22 February 2017

  4. Research article

    Characterization of BRCA1 and BRCA2 variants in multi-ethnic Asian cohort from a Malaysian case-control study

    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...

    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

    BMC Cancer 2017 17:149

    Published on: 22 February 2017

  5. Research article

    Identification of somatic and germ-line DICER1 mutations in pleuropulmonary blastoma, cystic nephroma and rhabdomyosarcoma tumors within a DICER1 syndrome pedigree

    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...

    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

    BMC Cancer 2017 17:146

    Published on: 21 February 2017

  6. Research article

    Clinical performance evaluation of a sensitive, rapid low-throughput test for KRAS mutation analysis using formalin-fixed, paraffin-embedded tissue samples

    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 ...

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

    BMC Cancer 2017 17:139

    Published on: 16 February 2017

  7. Research article

    Viral E6 is overexpressed via high viral load in invasive cervical cancer with episomal HPV16

    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...

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

    BMC Cancer 2017 17:136

    Published on: 15 February 2017

  8. Case report

    First insight into the somatic mutation burden of neurofibromatosis type 2-associated grade I and grade II meningiomas: a case report comprehensive genomic study of two cranial meningiomas with vastly different clinical presentation

    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...

    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

    BMC Cancer 2017 17:127

    Published on: 13 February 2017

  9. Research article

    microRNA-29c inhibits cell proliferation by targeting NASP in human gastric cancer

    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...

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

    BMC Cancer 2017 17:109

    Published on: 7 February 2017

  10. Research article

    MDM2 promoter polymorphism del1518 (rs3730485) and its impact on endometrial and ovarian cancer risk

    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...

    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

    BMC Cancer 2017 17:97

    Published on: 3 February 2017

  11. Case report

    Stepwise addition of genetic changes correlated with histological change from “well-differentiated” to “sarcomatoid” phenotypes: a 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...

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

    BMC Cancer 2017 17:65

    Published on: 19 January 2017

  12. Research article

    Genetic polymorphisms of SCN9A are associated with oxaliplatin-induced neuropathy

    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% ...

    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

    BMC Cancer 2017 17:63

    Published on: 19 January 2017

  13. Research article

    Genomic pathways modulated by Twist in breast cancer

    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...

    Farhad Vesuna, Yehudit Bergman and Venu Raman

    BMC Cancer 2017 17:52

    Published on: 13 January 2017

  14. Case report

    Use of liquid biopsies to monitor disease progression in a sarcoma patient: a 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 ...

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

    BMC Cancer 2017 17:29

    Published on: 6 January 2017

  15. Case report

    Case report: whole exome sequencing of primary cardiac angiosarcoma highlights potential for targeted therapies

    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...

    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

    BMC Cancer 2017 17:17

    Published on: 5 January 2017

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