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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 1 of 15

  1. Content type: Study protocol

    Detection of circulating tumor DNA (ctDNA) is a promising method for postoperative surveillance of lung cancer. However, relatively low positive rate in early stage patients restricts its application. Aberrant...

    Authors: Guannan Kang, Kezhong Chen, Fan Yang, Shannon Chuai, Heng Zhao, Kai Zhang, Bingsi Li, Zhihong Zhang and Jun Wang

    Citation: BMC Cancer 2019 19:579

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  2. Content type: Research article

    Triple-negative breast cancer (TNBC) is a type of breast cancer with a high degree of malignancy. Because of the remarkable biological characteristics of high invasion, metastasis and recurrence, TNBC is often...

    Authors: Cheng Wang, Cheng Xu, Ruijie Niu, Guangfu Hu, Zhangyuan Gu and Zhigang Zhuang

    Citation: BMC Cancer 2019 19:577

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  3. Content type: Research article

    Using a pathway-focused approach, we aimed to provide a subgroup-specific basis for finding novel therapeutic strategies and further refinement of the risk stratification in pediatric medulloblastoma.

    Authors: Ae Kyung Park, Ji Yeoun Lee, Heesun Cheong, Vijay Ramaswamy, Sung-Hye Park, Marcel Kool, Ji Hoon Phi, Seung Ah Choi, Florence Cavalli, Michael D. Taylor and Seung-Ki Kim

    Citation: BMC Cancer 2019 19:571

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  4. Content type: Research article

    Published genetic risk scores for breast cancer (BC) so far have been based on a relatively small number of markers and are not necessarily using the full potential of large-scale Genome-Wide Association Studi...

    Authors: Kristi Läll, Maarja Lepamets, Marili Palover, Tõnu Esko, Andres Metspalu, Neeme Tõnisson, Peeter Padrik, Reedik Mägi and Krista Fischer

    Citation: BMC Cancer 2019 19:557

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  5. Content type: Research article

    Liver function is routinely assessed in clinical practice as liver function tests provide sensitive indicators of hepatocellular injury. However, the prognostic value of enzymes that indicate hepatic injury ha...

    Authors: Ting-Xun Lu, Shuang Wu, Dong-Yan Cai, Ting-Ting Hong, Ying Zhang, Hua-Qiang Gao, Hai-Ying Hua and Xiao-Hong Wu

    Citation: BMC Cancer 2019 19:553

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  6. Content type: Research article

    Mutated BRCA1/2 genes are associated with hereditary breast and ovarian cancer (HBOC). So far most of the identified BRCA1/2 pathogenic variants are single nucleotide variants (SNVs) or insertions/deletions (Inde...

    Authors: Wen-Ming Cao, Ya-Bing Zheng, Yun Gao, Xiao-Wen Ding, Yan Sun, Yuan Huang, Cai-Jin Lou, Zhi-Wen Pan, Guang Peng and Xiao-Jia Wang

    Citation: BMC Cancer 2019 19:551

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  7. Content type: Research article

    Breast cancer is a leading cause of cancer-related death in women worldwide. Despite extensive studies in all areas of basic, clinical and applied research, accurate prognosis remains elusive, thus leading to ...

    Authors: Mariana Bustamante Eduardo, Vlad Popovici, Sara Imboden, Stefan Aebi, Nadja Ballabio, Hans Jörg Altermatt, Andreas Günthert and Rolf Jaggi

    Citation: BMC Cancer 2019 19:549

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  8. Content type: Research article

    The understanding of the molecular biology of pediatric neuronal and mixed neuronal-glial brain tumors is still insufficient due to low frequency and heterogeneity of those lesions which comprise several subty...

    Authors: Magdalena Zakrzewska, Renata Gruszka, Konrad Stawiski, Wojciech Fendler, Joanna Kordacka, Wiesława Grajkowska, Paweł Daszkiewicz, Paweł P. Liberski and Krzysztof Zakrzewski

    Citation: BMC Cancer 2019 19:544

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  9. Content type: Research article

    Hereditary cancer predisposition syndromes are responsible for approximately 5–10% of all diagnosed cancer cases. In the past, single-gene analysis of specific high risk genes was used for the determination of...

    Authors: Georgios N. Tsaousis, Eirini Papadopoulou, Angela Apessos, Konstantinos Agiannitopoulos, Georgia Pepe, Stavroula Kampouri, Nikolaos Diamantopoulos, Theofanis Floros, Rodoniki Iosifidou, Ourania Katopodi, Anna Koumarianou, Christos Markopoulos, Konstantinos Papazisis, Vasileios Venizelos, Ioannis Xanthakis, Grigorios Xepapadakis…

    Citation: BMC Cancer 2019 19:535

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  10. Content type: Research article

    C-C chemokine receptor 5 (CCR5) has attracted wide concern for its critical role in the progression of human immunodeficiency virus type 1 (HIV-1) infection. Several studies have demonstrated that CCR5 affects...

    Authors: Shuyuan Liu, Jun Chen, Zhiling Yan, Shuying Dai, Chuanyin Li, Yufeng Yao and Li Shi

    Citation: BMC Cancer 2019 19:525

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  11. Content type: Research article

    Patients with lymph node metastasis-negative (pN0) invasive breast cancer have favorable outcomes following initial treatment. However, false negatives which occur during routine histologic examination of lymp...

    Authors: Ryoko Kikuchi-Koike, Kazunori Nagasaka, Hitoshi Tsuda, Yasuyuki Ishii, Masaru Sakamoto, Yoshihiro Kikuchi, Shiho Fukui, Yuko Miyagawa, Haruko Hiraike, Takayuki Kobayashi, Takayuki Kinoshita, Yae Kanai, Tatsuhiro Shibata, Issei Imoto, Johji Inazawa, Osamu Matsubara…

    Citation: BMC Cancer 2019 19:521

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  12. Content type: Research article

    Chronic Lymphocytic Leukemia (CLL) is the most frequent lymphoproliferative disorder in western countries and is characterized by a remarkable clinical heterogeneity. During the last decade, multiple genomic s...

    Authors: Adrián Mosquera Orgueira, Beatriz Antelo Rodríguez, Natalia Alonso Vence, José Ángel Díaz Arias, Nicolás Díaz Varela, Manuel Mateo Pérez Encinas, Catarina Allegue Toscano, Elena María Goiricelaya Seco, Ángel Carracedo Álvarez and José Luis Bello López

    Citation: BMC Cancer 2019 19:515

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  13. Content type: Research article

    Deletion of the CDKN2A locus is centrally involved in the development of several malignancies. In malignant pleural mesothelioma (MPM), it is one of the most frequently reported genomic alteration. MPM is strongl...

    Authors: Eeva Kettunen, Sauli Savukoski, Kaisa Salmenkivi, Tom Böhling, Esa Vanhala, Eeva Kuosma, Sisko Anttila and Henrik Wolff

    Citation: BMC Cancer 2019 19:507

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  14. Content type: Study protocol

    Breast cancer ranks first in women, and is the second cause of death in this gender. In addition to genetics, the environment contributes to the development of the disease, although the factors involved are no...

    Authors: Julio Plaza-Díaz, Ana I. Álvarez-Mercado, Carmen M Ruiz-Marín, Iris Reina-Pérez, Alejandro J. Pérez-Alonso, María Belén Sánchez-Andujar, Pablo Torné, Tania Gallart-Aragón, María Teresa Sánchez-Barrón, Saturnino Reyes Lartategui, Federico García, Natalia Chueca, Ana Moreno-Delgado, Katia Torres-Martínez, María José Sáez-Lara, Cándido Robles-Sánchez…

    Citation: BMC Cancer 2019 19:495

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  15. Content type: Research article

    Telomere genetics has recently been emerged as an important field in molecular oncology. Various genome-wide association studies in different population groups have revealed that polymorphisms in Telomere main...

    Authors: Gh. Rasool Bhat, Amrita Bhat, Sonali Verma, Itty Sethi, Ruchi Shah, Varun Sharma, Khursheed A. Dar, Deepak Abrol, Subiya Kaneez, Sandeep Kaul, Ramesh Ganju and Rakesh Kumar

    Citation: BMC Cancer 2019 19:493

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  16. Content type: Research article

    The relationship between polymorphisms in vascular endothelial growth factor (VEGF) and gastric cancer is still inconclusive. We investigated whether there is an association between VEGF genetic polymorphisms ...

    Authors: Yeon-Ji Kim, Woo Chul/ Chung, Kyong-Hwa Jun and Hyung-Min Chin

    Citation: BMC Cancer 2019 19:483

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  17. Content type: Research article

    Recent studies have extensively investigated the role of miRNAs in colorectal cancer (CRC), and several associations have been reported. In addition, single nucleotide polymorphisms (SNPs) in promoter regions ...

    Authors: Eun-Gyo Kim, Jung Oh Kim, Han Sung Park, Chang Soo Ryu, Jisu Oh, Hak Hoon Jun, Jong Woo Kim and Nam Keun Kim

    Citation: BMC Cancer 2019 19:480

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  18. Content type: Research article

    Gene variants are dependable and sensitive biomarkers for target-specific therapies in breast cancer (BC). However, detection of mutations within tissues has many limitations. Plasma circulating free DNA (cfDN...

    Authors: Xin Yang, Kuo Zhang, Caiji Zhang, Rongxue Peng and Chengming Sun

    Citation: BMC Cancer 2019 19:465

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  19. Content type: Research article

    Helicobacter pylori infection is recognized as the main risk factor for gastric cancer (GC), the fifth most common neoplasia worldwide. H. pylori interacts with the immune system, disrupting the cytokine network ...

    Authors: Cecilia Martínez-Campos, Kirvis Torres-Poveda, Margarita Camorlinga-Ponce, Lourdes Flores-Luna, Carmen Maldonado-Bernal, Vicente Madrid-Marina and Javier Torres

    Citation: BMC Cancer 2019 19:453

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  20. Content type: Research article

    Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal malignancies and is not a clinically homogeneous disease, but subsets of patients with distinct prognosis and response to therapy can be identi...

    Authors: Maria Cristina Curia, Fabiana Fantini, Rossano Lattanzio, Francesca Tavano, Francesco Di Mola, Mauro Piantelli, Pasquale Battista, Pierluigi Di Sebastiano and Alessandro Cama

    Citation: BMC Cancer 2019 19:452

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  21. Content type: Research article

    TIMP-2 gene plays an important role in the development of breast cancer. The present study was conducted to evaluate whether TIMP-2 gene polymorphisms are associated with breast cancer risk in a Han Chinese cohor...

    Authors: Kai Wang, Guanying Wang, Shangke Huang, Anqi Luo, Xin Jing, Gang Li, Yi Zhou and Xinhan Zhao

    Citation: BMC Cancer 2019 19:446

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  22. Content type: Research article

    The progress of treatments of childhood acute lymphoblastic leukemia (ALL) has made it possible to reach a survival rate superior to 80%. However, the treatments lead to several long-term adverse effects, incl...

    Authors: Maxime Caru, Kateryna Petrykey, Simon Drouin, Patrick Beaulieu, Pascal St-Onge, Valérie Lemay, Laurence Bertout, Caroline Laverdiere, Gregor Andelfinger, Maja Krajinovic, Daniel Sinnett and Daniel Curnier

    Citation: BMC Cancer 2019 19:443

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  23. Content type: Research article

    Several subunits of the SWI/SNF chromatin remodeling complex are implicated in both cancer and neurodevelopmental disorders (NDD). Though there is no clinical evidence for an increased tumor risk in individual...

    Authors: Bernt Popp, Abbas Agaimy, Cornelia Kraus, Karl X. Knaup, Arif B. Ekici, Steffen Uebe, André Reis, Michael Wiesener and Christiane Zweier

    Citation: BMC Cancer 2019 19:435

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  24. Content type: Research article

    Wilms’ tumor is also called nephroblastoma and is the most common pediatric renal cancer. Several genetic and epigenetic factors have been found to account for the development of Wilms’ tumor. MiRNAs play impo...

    Authors: Zhuo Liu, Feng He, Shengrong OuYang, Yuanyuan Li, Feifei Ma, Huibo Chang, Dingding Cao and Jianxin Wu

    Citation: BMC Cancer 2019 19:405

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  25. Content type: Technical advance

    With the introduction of Olaparib treatment for BRCA-deficient recurrent ovarian cancer, testing for somatic and/or germline mutations in BRCA1/2 genes in tumor tissues became essential for treatment decisions. I...

    Authors: Falk Zakrzewski, Laura Gieldon, Andreas Rump, Michael Seifert, Konrad Grützmann, Alexander Krüger, Sina Loos, Silke Zeugner, Karl Hackmann, Joseph Porrmann, Johannes Wagner, Karin Kast, Pauline Wimberger, Gustavo Baretton, Evelin Schröck, Daniela Aust…

    Citation: BMC Cancer 2019 19:396

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  26. Content type: Research article

    The impact of Tet oncogene family member 2 (TET2) mutations on the prognosis of acute myeloid leukemia (AML) is still controversial. A meta analysis is needed in order to assess the prognostic significance of TET...

    Authors: Ruiqi Wang, Xiaoning Gao and Li Yu

    Citation: BMC Cancer 2019 19:389

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  27. Content type: Research article

    Gene expression profiling provides key information for prognosis of breast cancer to establish treatment strategy. However, the genetic assessment should be available before induction of treatment to be useful...

    Authors: Jeeyeon Lee, Eun Hye Lee, Ho Yong Park, Wan Wook Kim, Ryu Kyung Lee, Yee Soo Chae, Soo Jung Lee, Jee-Eun Kim, Byeong-il Kang, Jee Young Park, Ji-Young Park and Jin Hyang Jung

    Citation: BMC Cancer 2019 19:388

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  28. Content type: Research article

    Intratumoral epidermal growth factor receptor (EGFR) mutational heterogeneity is yet controversial in non-small cell lung cancer (NSCLC) patients. Single-cell analysis provides the genetic profile of single cance...

    Authors: Longhua Guo, Zhihong Chen, Chongrui Xu, Xuchao Zhang, Honghong Yan, Jian Su, Jinji Yang, Zhi Xie, Weibang Guo, Feng Li, Yilong Wu and Qing Zhou

    Citation: BMC Cancer 2019 19:369

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  29. Content type: Research article

    Osteosarcoma is the most common malignant bone tumor in children. Survival remains poor among histologically poor responders, and there is a need to identify them at diagnosis to avoid delivering ineffective t...

    Authors: Krithika Bhuvaneshwar, Michael Harris, Yuriy Gusev, Subha Madhavan, Ramaswamy Iyer, Thierry Vilboux, John Deeken, Elizabeth Yang and Sadhna Shankar

    Citation: BMC Cancer 2019 19:357

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  30. Content type: Research article

    High risk human papillomaviruses (HPV) plays important roles in the development of cervical cancer, a number of other anogenital cancer and they are increasingly found in oropharyngeal squamous cell carcinoma ...

    Authors: Ge Gao, Jintu Wang, Jan L. Kasperbauer, Nicole M. Tombers, Fei Teng, Honglan Gou, Yonggang Zhao, Zhenhong Bao and David I. Smith

    Citation: BMC Cancer 2019 19:352

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  31. Content type: Research article

    Visceral organ metastasis is associated with poor survival outcomes in terms of metastasis free- and overall survival in breast carcinomas. Identification of a gene expression profile in tumours that selects a...

    Authors: C. D. Savci-Heijink, H. Halfwerk, J. Koster, H. M. Horlings and M. J. van de Vijver

    Citation: BMC Cancer 2019 19:333

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  32. Content type: Research article

    Non-muscular invasive bladder cancer (NMIBC) has a high risk of recurrence. As androgen receptor (AR) reportedly affects bladder cancer, we assessed the correlation between NMIBC recurrence and tumor AR expressio...

    Authors: Masato Yasui, Takashi Kawahara, Koji Izumi, Masahiro Yao, Yukari Ishiguro, Hitoshi Ishiguro, Hiroji Uemura and Yasuhide Miyoshi

    Citation: BMC Cancer 2019 19:331

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  33. Content type: Research article

    In the majority of familial breast cancer (BC) families, the etiology of the disease remains unresolved. To identify missing BC heritability resulting from relatively rare variants (minor allele frequency ≤ 1%...

    Authors: Rajendra Bahadur Shahi, Sylvia De Brakeleer, Ben Caljon, Ingrid Pauwels, Maryse Bonduelle, Sofie Joris, Christel Fontaine, Marian Vanhoeij, Sonia Van Dooren, Erik Teugels and Jacques De Grève

    Citation: BMC Cancer 2019 19:313

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  34. Content type: Research article

    Feline injection-site sarcoma (FISS), an aggressive iatrogenic subcutaneous malignancy, is challenging to manage clinically and little is known about the molecular basis of its pathogenesis. Tumor transcriptom...

    Authors: Qi Wei, Stephen A. Ramsey, Maureen K. Larson, Noah E. Berlow, Donasian Ochola, Christopher Shiprack, Amita Kashyap, Bernard Séguin, Charles Keller and Christiane V. Löhr

    Citation: BMC Cancer 2019 19:311

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  35. Content type: Research article

    High-grade serous ovarian cancer is a detrimental disease. Treatment options in patients with a recurrent disease are dependent on BRCA1/2 mutation status since only patients with known BRCA mutation are eligible...

    Authors: Andreja Gornjec, Srdjan Novakovic, Vida Stegel, Marko Hocevar, Ziva Pohar Marinsek, Barbara Gazic, Mateja Krajc and Erik Skof

    Citation: BMC Cancer 2019 19:296

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  36. Content type: Research article

    Lung adenocarcinoma is the most common type of lung cancers. Whole-genome sequencing studies disclosed the genomic landscape of lung adenocarcinomas. however, it remains unclear if the genetic alternations cou...

    Authors: Jiaxian Yu, Yueming Hu, Yafei Xu, Jue Wang, Jiajie Kuang, Wei Zhang, Jianlin Shao, Dianjing Guo and Yejun Wang

    Citation: BMC Cancer 2019 19:263

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  37. Content type: Research article

    To systematically assess the prevalence of BRCA1 and BRCA2 gene mutations in women with Hereditary Breast and/or Ovarian Cancer (HBOC) in Arab countries and to describe the variability in the BRCA gene mutatio...

    Authors: Khadiga Abdulrashid, Nour AlHussaini, Wifag Ahmed and Lukman Thalib

    Citation: BMC Cancer 2019 19:256

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  38. Content type: Research article

    Prostate cancer (PCa) is the most common diagnosed malignancy and the second leading cause of cancer-related deaths among men in the United States. High-throughput genotyping has enabled discovery of germline ...

    Authors: Tarun Karthik Kumar Mamidi, Jiande Wu and Chindo Hicks

    Citation: BMC Cancer 2019 19:229

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  39. Content type: Research article

    Gastric cancer (GC) is one of the most commonly occuring gastrointestinal tumor types, and early diagnosis and operation have a notable effect on the prognosis of patients. Although certain markers, including ...

    Authors: Jiaxin Liu, Zhao Liu, Xiaozhi Zhang, Tuotuo Gong and Demao Yao

    Citation: BMC Cancer 2019 19:227

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  40. Content type: Research article

    Non-small cell lung cancer (NSCLC) as the most frequent type of lung cancer is associated with extensive mortality. Researchers have studied the suitability of several molecules as biomarkers for early detecti...

    Authors: Farbod Esfandi, Mohammad Taheri, Mir Davood Omrani, Mohammad Behgam Shadmehr, Shahram Arsang-Jang, Roshanak Shams and Soudeh Ghafouri-Fard

    Citation: BMC Cancer 2019 19:222

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  41. Content type: Research article

    Breast cancer is a highly heterogeneous disease resulting in diverse clinical behaviours and therapeutic responses. DNA methylation is a major epigenetic alteration that is commonly perturbed in cancers. The a...

    Authors: Bernardo P. de Almeida, Joana Dias Apolónio, Alexandra Binnie and Pedro Castelo-Branco

    Citation: BMC Cancer 2019 19:219

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  42. Content type: Research article

    Although surgical resection provides a cure for patients with intrahepatic cholangiocarcinoma (ICC), the risk of mortality and recurrence remains high. Several biomarkers are reported to be associated with the...

    Authors: Chao Bi, Mei Liu, Weiqi Rong, Fan Wu, Yang Zhang, Shengtao Lin, Yunhe Liu, Jianxiong Wu and Liming Wang

    Citation: BMC Cancer 2019 19:213

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  43. Content type: Research article

    Cancer immunotherapy with immune checkpoint blockade (CKB) is now standard of care for multiple cancers. The clinical response to CKB is associated with T cell immunity targeting cancer-induced mutations that ...

    Authors: Pooja Narang, Meixuan Chen, Amit A. Sharma, Karen S. Anderson and Melissa A. Wilson

    Citation: BMC Cancer 2019 19:200

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  44. Content type: Research article

    IDH1/2 mutated glioma has been associated with a germline risk variant, the rs55705857 G allele. The Utah Population Database (UPDB), a computerized genealogy of people in Utah, is a unique resource to evaluate c...

    Authors: Sarah Hummel, Wendy Kohlmann, Thomas M. Kollmeyer, Robert Jenkins, Joshua Sonnen, Cheryl A. Palmer, Howard Colman, Diana Abbott, Lisa Cannon-Albright and Adam L. Cohen

    Citation: BMC Cancer 2019 19:190

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  45. Content type: Research article

    Colorectal cancer (CRC) is one of the most common cancers worldwide, and genetic variations exert distinct roles in its pathogenesis. Single nucleotide polymorphisms (SNPs) in interleukin 1 alpha (IL1A) were repo...

    Authors: Hong Ji, Le Lu, Jingjing Huang, Yang Liu, Binchao Zhang, Hui Tang, Dangze Sun, Yafei Zhang, Hao Shang, Yiming Li and Hongwei Lu

    Citation: BMC Cancer 2019 19:181

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