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Genetics, genomics and epigenetics

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. Single nucleotide polymorphisms (SNPs) in DNA repair genes have a potential clinical value in predicting treatment outcomes. In the current study, we examined the association of SNPs in the genes XRCC1-rs25487...

    Authors: Hamideh Salimzadeh, Elinor Bexe Lindskog, Bengt Gustavsson, Yvonne Wettergren and David Ljungman

    Citation: BMC Cancer 2020 20:409

    Content type: Research article

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  2. Recent genome-wide association studies (GWASs) have suggested several susceptibility loci of hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC) by statistical analysis at individual single-nucleoti...

    Authors: Deke Jiang, Jiaen Deng, Changzheng Dong, Xiaopin Ma, Qianyi Xiao, Bin Zhou, Chou Yang, Lin Wei, Carly Conran, S. Lilly Zheng, Irene Oi-lin Ng, Long Yu, Jianfeng Xu, Pak C. Sham, Xiaolong Qi, Jinlin Hou…

    Citation: BMC Cancer 2020 20:403

    Content type: Research article

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  3. Mucinous adenocarcinoma (MAC) is a distinct type of colorectal cancer (CRC) associated with poor response to treatment and poorer prognosis. MAC is diagnosed by WHO definition when the extracellular mucin is m...

    Authors: Xiaodong Li, Katherine Sun, Xiaoyan Liao, Haijuan Gao, Hongfa Zhu and Ruliang Xu

    Citation: BMC Cancer 2020 20:400

    Content type: Research article

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  4. Pathogenic variants that occur in the familial breast cancer genes (BRCA1/2) lead to truncated ineffective proteins in the majority of cases. These variants are mostly represented by small deletions/insertions, n...

    Authors: Nerina C. van der Merwe, Jaco Oosthuizen, Magdalena Theron, George Chong and William D. Foulkes

    Citation: BMC Cancer 2020 20:391

    Content type: Research article

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  5. Osteosarcoma (OS) is the most frequent primary malignancy of bone with a high incidence in adolescence. This study aimed to construct a publicly available, integrated database of human OS, named HOsDb.

    Authors: Yifu Sun, Lishan Wang, Changkuan Li, Rui Gu, Weidong Zang, Wei Song and Peng Xia

    Citation: BMC Cancer 2020 20:390

    Content type: Database

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  6. To assess metastatic breast cancer (MBC) patient psychological factors, perceptions, and comprehension of tumor genomic testing.

    Authors: Elizabeth J. Adams, Sarah Asad, Raquel Reinbolt, Katharine A. Collier, Mahmoud Abdel-Rasoul, Susan Gillespie, James L. Chen, Mathew A. Cherian, Anne M. Noonan, Sagar Sardesai, Jeffrey VanDeusen, Robert Wesolowski, Nicole Williams, Charles L. Shapiro, Erin R. Macrae, Robert Pilarski…

    Citation: BMC Cancer 2020 20:389

    Content type: Research article

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  7. Familial cases of appendiceal mucinous tumours (AMTs) are extremely rare and the underlying genetic aetiology uncertain. We identified potential predisposing germline genetic variants in a father and daughter ...

    Authors: Mei Sim Lung, Catherine A. Mitchell, Maria A. Doyle, Andrew C. Lynch, Kylie L. Gorringe, David D. L. Bowtell, Ian G. Campbell and Alison H. Trainer

    Citation: BMC Cancer 2020 20:369

    Content type: Research article

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  8. Antigen-processing machinery molecules play crucial roles in infectious diseases and cancers. Studies have shown that polymorphisms in endoplasmic reticulum aminopeptidase (ERAP) genes can influence the enzyma...

    Authors: Chuanyin Li, Yaheng Li, Zhiling Yan, Shuying Dai, Shuyuan Liu, Xia Wang, Jun Wang, Xinwen Zhang, Li Shi and Yufeng Yao

    Citation: BMC Cancer 2020 20:341

    Content type: Research article

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  9. Cervical cancer is caused by high-risk Human Papillomavirus (hr-HPV) infection associated with cofactors that has been analyzed as predictors of the remission or persistence of cytological abnormalities remiss...

    Authors: Nayara Nascimento Toledo Silva, Ana Carolina Silva Santos, Verlândia Mendes Nogueira, Cláudia Martins Carneiro and Angélica Alves Lima

    Citation: BMC Cancer 2020 20:323

    Content type: Research article

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  10. RIPK1 (receptor-interacting protein kinase-1) plays a role in cancer development, whereas no clear studies focused on the cervical cancer. The objective of this study was to evaluate the relationship between RIPK...

    Authors: Zulipiyamu Tuoheti, Lili Han, Sulaiya Husaiyin, Xiaoxi Liu, Chunhua Ma and Mayinuer Niyazi

    Citation: BMC Cancer 2020 20:299

    Content type: Research article

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  11. To screen and analyze differentially expressed genes in pancreatic carcinoma tissues taken from Mongolian and Han patients by Affymetrix Genechip. Methods: Pancreatic ductal cell carcinoma tissues were collect...

    Authors: Jiasheng Xu, Kaili Liao, Zhonghua Fu and Zhenfang Xiong

    Citation: BMC Cancer 2020 20:298

    Content type: Research article

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  12. Sensitive and reliable molecular diagnostics is needed to guide therapeutic decisions for cancer patients. Although less material becomes available for testing, genetic markers are rapidly expanding. Simultane...

    Authors: Elisabeth M. P. Steeghs, Leonie I. Kroeze, Bastiaan B. J. Tops, Leon C. van Kempen, Arja ter Elst, Annemiek W. M. Kastner-van Raaij, Sandra J. B. Hendriks-Cornelissen, Mandy J. W. Hermsen, Erik A. M. Jansen, Petra M. Nederlof, Ed Schuuring, Marjolijn J. L. Ligtenberg and Astrid Eijkelenboom

    Citation: BMC Cancer 2020 20:291

    Content type: Technical advance

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  13. Identifying molecular differences between primary and metastatic colorectal cancers—now possible with the aid of omics technologies—can improve our understanding of the biological mechanisms of cancer progress...

    Authors: Stephany Orjuela, Mirco Menigatti, Peter Schraml, Patryk Kambakamba, Mark D. Robinson and Giancarlo Marra

    Citation: BMC Cancer 2020 20:290

    Content type: Research article

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  14. Esophageal squamous cell carcinoma (ESCC) is an aggressive cancer with one of the highest world incidences in the Eastern Cape region of South Africa. Several genome wide studies have been performed on ESCC co...

    Authors: Jacqueline Brown, Andrzej J. Stepien and Pascale Willem

    Citation: BMC Cancer 2020 20:281

    Content type: Research article

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  15. Infiltrating immune and stromal cells are vital components of the bladder cancer (BC) microenvironment, which can significantly affect BC progression and outcome. However, the contribution of each subset of tu...

    Authors: Ye Zhang, De-hua Ou, Dong-wu Zhuang, Ze-feng Zheng and Ming-en Lin

    Citation: BMC Cancer 2020 20:265

    Content type: Research article

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  16. The human pancreatic cancer cell line A818–6 can be grown in vitro either as a highly malignant, undifferentiated monolayer (ML) or as three-dimensional (3D) single layer hollow spheres (HS) simulating a benig...

    Authors: Doaa Tawfik, Angela Zaccagnino, Alexander Bernt, Monika Szczepanowski, Wolfram Klapper, Albrecht Schwab, Holger Kalthoff and Anna Trauzold

    Citation: BMC Cancer 2020 20:264

    Content type: Research article

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  17. Invasive urothelial carcinoma (iUC) is highly similar between dogs and humans in terms of pathologic presentation, molecular subtypes, response to treatment and age at onset. Thus, the dog is an established an...

    Authors: Heidi G. Parker, Deepika Dhawan, Alex C. Harris, Jose A. Ramos-Vara, Brian W. Davis, Deborah W. Knapp and Elaine A. Ostrander

    Citation: BMC Cancer 2020 20:251

    Content type: Research article

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  18. Despite conflicting results, considerable evidence suggests the association between single nucleotide polymorphisms in MTHFR, XRCC1 and OGG1 genes and, risk of developing breast cancer. Here a case-control study ...

    Authors: Matteo Floris, Daria Sanna, Paolo Castiglia, Carlo Putzu, Valeria Sanna, Antonio Pazzola, Maria Rosaria De Miglio, Francesca Sanges, Giovanna Pira, Antonio Azara, Emanuele Lampis, Antonello Serra, Ciriaco Carru, Maristella Steri, Flavia Costanza, Marco Bisail…

    Citation: BMC Cancer 2020 20:234

    Content type: Research article

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  19. Oral squamous cell carcinoma (OSCC) is an aggressive human malignancy. Because of late diagnosis and recurrence of OSCC, the treatment of patients with OSCC is often ineffective. Thus, finding novel biomarkers...

    Authors: Ratakorn Srisuttee, Areeya Arayataweegool, Patnarin Mahattanasakul, Napadon Tangjaturonrasme, Virachai Kerekhanjanarong, Somboon Keelawat, Apiwat Mutirangura and Nakarin Kitkumthorn

    Citation: BMC Cancer 2020 20:218

    Content type: Research article

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  20. Poly (ADP-ribose) polymerase (PARP) inhibitors are approved for the treatment of breast cancer susceptibility genes 1 and 2 (BRCA1/2) mutant ovarian and breast cancers, and are now being evaluated in metastatic c...

    Authors: Andrew D. Simmons, Minh Nguyen and Elias Pintus

    Citation: BMC Cancer 2020 20:215

    Content type: Case report

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  21. The incidence of breast cancer among young women (aged ≤40 years) has increased in North America and Europe. Fewer than 10% of cases among young women are attributable to inherited BRCA1 or BRCA2 mutations, sugge...

    Authors: Nicole E. Mealey, Dylan E. O’Sullivan, Joy Pader, Yibing Ruan, Edwin Wang, May Lynn Quan and Darren R. Brenner

    Citation: BMC Cancer 2020 20:212

    Content type: Research article

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  22. Acute lymphoblastic leukemia (ALL), the most common childhood malignancy, is characterized by recurring structural chromosomal alterations and genetic alterations, whose detection is critical in diagnosis, ris...

    Authors: Honghong Zhang, Hongsheng Wang, Xiaowen Qian, Shuai Gao, Jieqi Xia, Junwen Liu, Yanqin Cheng, Jie Man and Xiaowen Zhai

    Citation: BMC Cancer 2020 20:211

    Content type: Research article

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  23. Classical MPNs including ET and PMF have a chronic course and potential for leukaemic transformation. Timely diagnosis is obligatory to ensure appropriate management and positive outcomes. The aim of this stud...

    Authors: Uzma Zaidi, Gul Sufaida, Munazza Rashid, Bushra Kaleem, Sidra Maqsood, Samina Naz Mukry, Rifat Zubair Ahmed Khan, Saima Munzir, Munira Borhany and Tahir Sultan Shamsi

    Citation: BMC Cancer 2020 20:205

    Content type: Research article

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  24. Poly (ADP-ribose) polymerase inhibitors targeting BRCA1/2 mutations are available for treating patients with high-grade serous ovarian cancer. These treatments may be more appropriately directed to patients who m...

    Authors: Kyung Jin Eoh, Hye Min Kim, Jung-Yun Lee, Sunghoon Kim, Sang Wun Kim, Young Tae Kim and Eun Ji Nam

    Citation: BMC Cancer 2020 20:204

    Content type: Research article

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  25. The fine-needle aspiration (FNA) biopsy was broadly applied to clinical diagnostics evaluation for thyroid carcinomas nodule, while companioning with higher uncertainty rate (15~30%) to identify malignancy for...

    Authors: Dandan Wu, Shudong Hu, Yongzhong Hou, Yingying He and Shubai Liu

    Citation: BMC Cancer 2020 20:199

    Content type: Research article

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  26. BRCA1/2 germline mutation related cancers are candidates for new immune therapeutic interventions. This study was a hypothesis generating exploration of genomic data collected at diagnosis for 19 patients. The...

    Authors: Ewa Przybytkowski, Thomas Davis, Abdelrahman Hosny, Julia Eismann, Ursula A. Matulonis, Gerburg M. Wulf and Sheida Nabavi

    Citation: BMC Cancer 2020 20:197

    Content type: Research article

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  27. Donor acute lymphoblastic leukemia with recipient intact is a rare condition. We report a case of donor developing acute lymphoblastic leukemia 8 yrs after donating both bone marrow and peripheral blood hemato...

    Authors: Di Zhou, Ting Xie, Suning Chen, Yipeng Ling, Yueyi Xu, Bing Chen, Jian Ouyang and Yonggong Yang

    Citation: BMC Cancer 2020 20:195

    Content type: Case report

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  28. Altered glycosylation associated with hepatocellular carcinoma (HCC) is well documented. However, few reports have investigated the association between dedifferentiation and glycosylation. Therefore, the aim o...

    Authors: Hiroomi Takayama, Masayuki Ohta, Yukio Iwashita, Hiroki Uchida, Yuki Shitomi, Kazuhiro Yada and Masafumi Inomata

    Citation: BMC Cancer 2020 20:192

    Content type: Research article

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  29. This case represents the first report of malignant primary cardiac tumour in a patient with Lynch Syndrome associated with MSH2 pathogenic variant.

    Authors: Pasquale Paolisso, Giulia Saturi, Alberto Foà, Maristella Saponara, Margherita Nannini, Maria Abbondanza Pantaleo, Ornella Leone, Daniela Turchetti, Daniele Calistri, Carlo Savini, Davide Pacini, Carmine Pizzi and Nazzareno Galiè

    Citation: BMC Cancer 2020 20:191

    Content type: Case report

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  30. CYP2A6 is an enzyme involved in oxidation of a number of environmental chemicals, including nicotine, pro-carcinogenic nitrosamines and polycyclic aromatic hydrocarbons (PAHs). The whole gene deletion of CYP2A...

    Authors: Maidina Abudushataer, Noriko Sato, Makiko Mieno, Motoji Sawabe, Masaaki Muramatsu and Tomio Arai

    Citation: BMC Cancer 2020 20:186

    Content type: Research article

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  31. Hepatocellular carcinoma (HCC) is the second most common cause of cancer-related death in the world. N6-methyladenosine (m6A) RNA methylation is dynamically regulated by m6A RNA methylation modulators (“writer,” ...

    Authors: Nanfang Qu, Sanyu Qin, Xuemei Zhang, Xiaotong Bo, Zhengchun Liu, Chao Tan, Guiqiong Wen and Haixing Jiang

    Citation: BMC Cancer 2020 20:165

    Content type: Research article

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  32. The loss of a single copy of adenomatous polyposis coli (Apc) in leucine-rich repeats and immunoglobulin-like domains 1 (Lrig1)-expressing colonic progenitor cells induces rapid growth of adenomas in mice with hi...

    Authors: Jessica L. Preston and Nicholas Stiffler

    Citation: BMC Cancer 2020 20:126

    Content type: Research article

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  33. Colorectal cancer (CRC) is the second leading cancer killer in the US today and patients with metastatic disease have only a 14% 5-year survival. One of the most impactful recent advances in cancer therapy, im...

    Authors: Yuanyuan Shen, Yue Guan, Justin J. Hummel, Chi-Ren Shyu and Jonathan B. Mitchem

    Citation: BMC Cancer 2020 20:124

    Content type: Research article

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  34. Cancer subtyping has mainly relied on pathological and molecular means. Massively parallel sequencing-enabled subtyping requires genomic markers to be developed based on global features rather than individual ...

    Authors: Zhenggang Wu, Xi Long, Shui Ying Tsang, Taobo Hu, Jian-Feng Yang, Wai Kin Mat, Hongyang Wang and Hong Xue

    Citation: BMC Cancer 2020 20:84

    Content type: Research article

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  35. Breast cancer (BC) is known to be the most common malignancy in females whereas colorectal cancer (CRC) incidence also higher in both genders in Sri Lanka. TP53 is an important tumour suppressor gene and its soma...

    Authors: Vahinipriya Manoharan, Eric Hamilton Karunanayake, Kamani Hemamala Tennekoon, Sumadee De Silva, Ahamed Ilyas Ahamed Imthikab, Kanishka De Silva, Preethika Angunawela, Sameera Vishwakula and John Lunec

    Citation: BMC Cancer 2020 20:72

    Content type: Research article

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  36. Osteosarcoma is a primary malignant tumor originating from mesenchymal tissue, with a poor distant metastasis prognosis. The molecular mechanisms of osteosarcoma metastasis are extremely complicated.

    Authors: Mi Li, Xin Jin, Hao Li, Gang Wu, Shanshan Wang, Caihong Yang and Sisi Deng

    Citation: BMC Cancer 2020 20:65

    Content type: Research article

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  37. Glioblastoma (GBM) is a highly malignant brain neoplasm with poor survival. Despite its aggressive nature, metastatic spread of GBM is identified only rarely. While the molecular alterations associated with GB...

    Authors: Melissa Umphlett, Stephanie Shea, Jessica Tome-Garcia, Yizhou Zhang, Adilia Hormigo, Mary Fowkes, Nadejda M. Tsankova and Raymund L. Yong

    Citation: BMC Cancer 2020 20:47

    Content type: Case report

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  38. The occurrence of a mediastinal germ cell tumor (GCT) and hematological malignancy in the same patient is very rare. Due to its rarity, there have been only two reports of the concurrent cases undergoing detai...

    Authors: Keiichi Akizuki, Masaaki Sekine, Yasunori Kogure, Takuro Kameda, Kotaro Shide, Junji Koya, Ayako Kamiunten, Yoko Kubuki, Yuki Tahira, Tomonori Hidaka, Takumi Kiwaki, Hiroyuki Tanaka, Yuichiro Sato, Hiroaki Kataoka, Keisuke Kataoka and Kazuya Shimoda

    Citation: BMC Cancer 2020 20:5

    Content type: Research article

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  39. The principle of loss of iodine uptake and increased glucose metabolism according to dedifferentiation of thyroid cancer is clinically assessed by imaging. Though these biological properties are widely applied...

    Authors: Hoon Young Suh, Hongyoon Choi, Jin Chul Paeng, Gi Jeong Cheon, June-Key Chung and Keon Wook Kang

    Citation: BMC Cancer 2019 19:1260

    Content type: Research article

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  40. SPINK4 is known as a gastrointestinal peptide in the gastrointestinal tract and is abundantly expressed in human goblet cells. The clinical significance of SPINK4 in colorectal cancer (CRC) is largely unknown.

    Authors: Xiaojie Wang, Qian Yu, Waleed M. Ghareeb, Yiyi Zhang, Xingrong Lu, Ying Huang, Shenghui Huang, Yanwu Sun, Jiayi Lin, Jin Liu and Pan Chi

    Citation: BMC Cancer 2019 19:1258

    Content type: Research article

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  41. Breast cancer risk, development, and treatment are influenced by genetic variation in certain genes, namely those involved in cell proliferation, tumor suppression, and drug metabolism. In turn, the relevance ...

    Authors: Laith N. AL-Eitan, Doaa M. Rababa’h, Mansour A. Alghamdi and Rame H. Khasawneh

    Citation: BMC Cancer 2019 19:1257

    Content type: Research article

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  42. As biomarkers, DNA methylation is used to detect colorectal cancer (CRC) and make assessment of CRC prognosis. The published findings showed the association between the methylation of SFRP1, SFRP2, and WIF1, loca...

    Authors: Xinyan Liu, Jinming Fu, Haoran Bi, Anqi Ge, Tingting Xia, Yupeng Liu, Hongru Sun, Dapeng Li and Yashuang Zhao

    Citation: BMC Cancer 2019 19:1212

    Content type: Research article

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  43. The prognoses of head and neck squamous cell carcinoma (HNSCC) and esophageal squamous cell carcinoma (ESCC) are poor, especially when both tumors occur at the same time. We examined the clonal relatedness of ...

    Authors: Somkiat Sunpaweravong, Sacarin Bunbanjerdsuk, Tanjitti Pongrujikorn, Chaiwat Naktang, Patrapim Sunpaweravong, Anupong Nitiruangjaras, Tanadech Dechaphankul and Natini Jinawath

    Citation: BMC Cancer 2019 19:1174

    Content type: Research article

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  44. Genetic testing for BRCA1/2 genes is widely used as a strategy to reduce incidence and morbidity of hereditary breast and ovarian cancer (HBOC). The purpose of this study is to analyse the demographic and molecul...

    Authors: Ainara Ruiz de Sabando, Edurne Urrutia Lafuente, Fermín García-Amigot, Angel Alonso Sánchez, Lourdes Morales Garofalo, Sira Moreno, Eva Ardanaz and Maria A. Ramos-Arroyo

    Citation: BMC Cancer 2019 19:1145

    Content type: Research article

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    The Correction to this article has been published in BMC Cancer 2019 19:1227

  45. The significance of very early chimerism assessment before day + 28, which is considered the moment of engraftment, is still unclear. In this retrospective study, we evaluated the clinical impact of very early...

    Authors: Monika Lejman, Agnieszka Zaucha-Prażmo, Joanna Zawitkowska, Aleksandra Mroczkowska, Dominik Grabowski, Jerzy R. Kowalczyk and Katarzyna Drabko

    Citation: BMC Cancer 2019 19:1141

    Content type: Research article

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  46. Hepatocellular carcinoma (HCC) is the sixth-most common malignancy worldwide. Multiple previous studies have assessed the relationship between TM6SF2 gene polymorphism and the risk of developing HCC, with disc...

    Authors: Shan Tang, Jing Zhang, Ting-Ting Mei, Hai-Qing Guo, Xin-Huan Wei, Wen-Yan Zhang, Ya-Li Liu, Shan Liang, Zuo-Peng Fan, Li-Xia Ma, Wei Lin, Yi-Rong Liu, Li-Xia Qiu and Hai-Bin Yu

    Citation: BMC Cancer 2019 19:1128

    Content type: Research article

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