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Prognostics and diagnostics/biomarkers

This section considers studies on the use of genomic markers to diagnose, classify, or predict the risk or prognosis of human disease.

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  1. Membranous glomerulonephritis (MGN) is a common kidney disease. Despite many evidences support that many immune and inflammation-related genes could serve as effective biomarkers and treatment targets for MGN ...

    Authors: Chengwei Zhang, Lei Leng, Zhaozheng Li, Yao Zhao and Jundong Jiao

    Citation: BMC Medical Genomics 2020 13:5

    Content type: Research article

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  2. Dysregulation of alternative splicing (AS) is a critical signature of cancer. However, the regulatory mechanisms of cancer-specific AS events, especially the impact of DNA methylation, are poorly understood.

    Authors: Xiaohui Sun, Yiping Tian, Jianming Wang, Zeyuan Sun and Yimin Zhu

    Citation: BMC Medical Genomics 2020 13:4

    Content type: Research article

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  3. MiR-182-5p, a cancer-related microRNA (miRNA), modulates tumorigenesis and patient outcomes in various human malignances. This study interroted the clinicopathological significance and molecular mechanisms of ...

    Authors: Li Gao, Shi-bai Yan, Jie Yang, Jin-liang Kong, Ke Shi, Fu-chao Ma, Lin-zhen Huang, Jie Luo, Shu-ya Yin, Rong-quan He, Xiao-hua Hu and Gang Chen

    Citation: BMC Medical Genomics 2020 13:3

    Content type: Research article

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  4. Rhabdomyosarcoma (RMS), a common soft-tissue malignancy in pediatrics, presents high invasiveness and mortality. However, besides known changes in the PAX3/7-FOXO1 fusion gene in alveolar RMS, the molecular me...

    Authors: Qianru Li, Liang Zhang, Jinfang Jiang, Yangyang Zhang, Xiaomeng Wang, Qiaochu Zhang, Yang Wang, Chunxia Liu and Feng Li

    Citation: BMC Medical Genomics 2019 12:198

    Content type: Research article

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  5. Formalin-fixed, paraffin-embedded (FFPE) tissues for RNA-seq have advantages over fresh frozen tissue including abundance and availability, connection to rich clinical data, and association with patient outcom...

    Authors: Nathan D. Pennock, Sonali Jindal, Wesley Horton, Duanchen Sun, Jayasri Narasimhan, Lucia Carbone, Suzanne S. Fei, Robert Searles, Christina A. Harrington, Julja Burchard, Sheila Weinmann, Pepper Schedin and Zheng Xia

    Citation: BMC Medical Genomics 2019 12:195

    Content type: Research article

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  6. Competitive endogenous RNAs (ceRNAs) have revealed a new mechanism of interaction between RNAs. However, an understanding of the ceRNA regulatory network in Wilms tumour (WT) remains limited.

    Authors: Fucai Tang, Zechao Lu, Jiamin Wang, Zhibiao Li, Weijia Wu, Haifeng Duan and Zhaohui He

    Citation: BMC Medical Genomics 2019 12:194

    Content type: Research article

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  7. Neuroblastoma (NB) is the most common extracranial solid tumor found in children. The frequent gain/loss of many chromosome bands in tumor cells and absence of mutations found at diagnosis suggests that NB is ...

    Authors: Chao Qin, Xiaoyan He, Yanding Zhao, Chun-Yip Tong, Kenneth Y. Zhu, Yongqi Sun and Chao Cheng

    Citation: BMC Medical Genomics 2019 12:192

    Content type: Research article

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  8. Assess process, uptake, validity and resource needs for return of actionable research findings to biobank participants.

    Authors: Tanya Papaz, Eriskay Liston, Laura Zahavich, Dimitri J. Stavropoulos, Rebekah K. Jobling, Raymond H. Kim, Miriam Reuter, Anastasia Miron, Erwin Oechslin, Tapas Mondal, Lynn Bergin, John F. Smythe, Luis Altamirano-Diaz, Jane Lougheed, Roderick Yao, Oyediran Akinrinade…

    Citation: BMC Medical Genomics 2019 12:173

    Content type: Research article

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  9. Previously developed classifications of glioma have provided enormous advantages for the diagnosis and treatment of glioma. Although the role of alternative splicing (AS) in cancer, especially in glioma, has b...

    Authors: Yaomin Li, Zhonglu Ren, Yuping Peng, Kaishu Li, Xiran Wang, Guanglong Huang, Songtao Qi and Yawei Liu

    Citation: BMC Medical Genomics 2019 12:165

    Content type: Research article

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  10. Progestin is effective to promote endometrial cancer (EC) cells apoptosis, however, continuous progestin administration causes low level of progestin receptor B (PRB), further resulting in progestin resistance...

    Authors: Wenjiao Cao, Wuyuan Gao, Panchan Zheng, Xiao Sun and Lihua Wang

    Citation: BMC Medical Genomics 2019 12:163

    Content type: Research article

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  11. Patients with metastatic colorectal cancer can benefit from anti-EGFR therapy, such as cetuximab and panitumumab. However, colorectal cancers harboring constitutive activating mutations in KRAS, NRAS and BRAF gen...

    Authors: Yuki Nagakubo, Yosuke Hirotsu, Kenji Amemiya, Toshio Oyama, Hitoshi Mochizuki and Masao Omata

    Citation: BMC Medical Genomics 2019 12:162

    Content type: Research article

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  12. Preimplantation genetic testing for monogenic defects (PGT-M) has been available in clinical practice. This study aimed to validate the applicability of targeted capture sequencing in developing personalized P...

    Authors: Haining Luo, Chao Chen, Yun Yang, Yinfeng Zhang, Yuan Yuan, Wanyang Wang, Renhua Wu, Zhiyu Peng, Ying Han, Lu Jiang, Ruqiang Yao, Xiaoying An, Weiwei Zhang, Yanqun Le, Jiale Xiang, Na Yi…

    Citation: BMC Medical Genomics 2019 12:157

    Content type: Research article

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  13. During human pregnancy, placental trophectoderm cells release extracellular vesicles (EVs) into maternal circulation. Trophoblasts also give rise to cell-free DNA (cfDNA) in maternal blood, and has been used f...

    Authors: Weiting Zhang, Sen Lu, Dandan Pu, Haiping Zhang, Lin Yang, Peng Zeng, Fengxia Su, Zhichao Chen, Mei Guo, Ying Gu, Yanmei Luo, Huamei Hu, Yanping Lu, Fang Chen and Ya Gao

    Citation: BMC Medical Genomics 2019 12:151

    Content type: Research article

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  14. Known collectively as breast fibroepithelial lesions (FELs), the common fibroadenomas (FAs) and the rarer phyllodes tumors (PTs) are a heterogenous group of biphasic neoplasms. Owing to limited tissue availabi...

    Authors: Yirong Sim, Gwendolene Xin Pei Ng, Cedric Chuan Young Ng, Vikneswari Rajasegaran, Suet Far Wong, Wei Liu, Peiyong Guan, Sanjanaa Nagarajan, Wai Yee Ng, Aye Aye Thike, Jeffrey Chun Tatt Lim, Nur Diyana Binte Md Nasir, Veronique Kiak Mien Tan, Preetha Madhukumar, Wei Sean Yong, Chow Yin Wong…

    Citation: BMC Medical Genomics 2019 12:142

    Content type: Research article

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  15. Unprecedented durable responses are identified in clinical studies to target the signaling of programmed cell death protein-1 (PD-1) as well as its ligand (PD-L1) in patients with squamous-cell non-small cell ...

    Authors: Cheng Fang, Chu Zhang, Wei-Qing Zhao, Wen-Wei Hu, Jun Wu and Mei Ji

    Citation: BMC Medical Genomics 2019 12:136

    Content type: Case report

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  16. Long noncoding RNAs (lncRNAs) are involved in a wide range of biological processes in tumorigenesis. However, the role of lncRNA expression in the biology, prognosis, and molecular classification of human mult...

    Authors: Minqiu Lu, Ying Hu, Yin Wu, Huixing Zhou, Yuan Jian, Ying Tian and Wenming Chen

    Citation: BMC Medical Genomics 2019 12:135

    Content type: Research article

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  17. Non-coding RNA has been shown to participate in numerous biological and pathological processes and has attracted increasing attention in recent years. Recent studies have demonstrated that long non-coding RNA ...

    Authors: Jiangquan Liao, Jie Wang, Yongmei Liu, Jun Li and Lian Duan

    Citation: BMC Medical Genomics 2019 12:124

    Content type: Research article

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  18. Incidental and secondary findings (IFs and SFs) are subject to ongoing discussion as potential consequences of clinical exome sequencing (ES). International policy documents vary on the reporting of these find...

    Authors: Marlies Saelaert, Heidi Mertes, Tania Moerenhout, Elfride De Baere and Ignaas Devisch

    Citation: BMC Medical Genomics 2019 12:123

    Content type: Research article

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  19. Immunoglobulin A nephropathy (IgAN) is the most common primary glomerulonephritis worldwide. Recent evidence suggests that genetic factors are related to the pathogenesis of IgAN. We conducted a genome-wide as...

    Authors: Kyung Hwan Jeong, Jin Sug Kim, Yu Ho Lee, Yang Gyun Kim, Ju-Young Moon, Su Kang Kim, Sun Woo Kang, Tae Hee Kim, Sang Ho Lee and Yeong Hoon Kim

    Citation: BMC Medical Genomics 2019 12:122

    Content type: Research article

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  20. Chromosomal microarray analysis has been shown to be a valuable and cost effective assay for elucidating copy number variants (CNVs) in children with intellectual disability and developmental delay (ID/DD).

    Authors: Marketa Wayhelova, Jan Smetana, Vladimira Vallova, Eva Hladilkova, Hana Filkova, Marta Hanakova, Marcela Vilemova, Petra Nikolova, Barbora Gromesova, Renata Gaillyova and Petr Kuglik

    Citation: BMC Medical Genomics 2019 12:111

    Content type: Research article

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  21. Copy Number variation (CNVs) in genes related to drug absorption, distribution, metabolism and excretion (ADME) are relevant in the interindividual variability of drug response. Studies of the CNVs in ADME gen...

    Authors: Brian Ramírez, María José Niño-Orrego, Daniel Cárdenas, Kevin Enrique Ariza, Karol Quintero, Nora Constanza Contreras Bravo, Caroll Tamayo-Agudelo, María Alejandra González, Paul Laissue and Dora Janeth Fonseca Mendoza

    Citation: BMC Medical Genomics 2019 12:110

    Content type: Research article

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  22. Nicolaides-Baraitser syndrome (NCBRS) is a neurodevelopmental disorder caused by pathogenic sequence variants in SMARCA2 which encodes the catalytic component of the chromatin remodeling BAF complex. Pathogenic v...

    Authors: Eric Chater-Diehl, Resham Ejaz, Cheryl Cytrynbaum, Michelle T. Siu, Andrei Turinsky, Sanaa Choufani, Sarah J. Goodman, Omar Abdul-Rahman, Melanie Bedford, Naghmeh Dorrani, Kendra Engleman, Josue Flores-Daboub, David Genevieve, Roberto Mendoza-Londono, Wendy Meschino, Laurence Perrin…

    Citation: BMC Medical Genomics 2019 12:105

    Content type: Research article

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  23. Different pathogenic germline mutations in the RET oncogene are identified in MEN 2, a hereditary syndrome characterized by medullary thyroid carcinoma (MTC) and other endocrine tumors. Although genetic predispos...

    Authors: Larissa V. Bim, Fábio C. P. Navarro, Flávia O. F. Valente, José V. Lima-Junior, Rosana Delcelo, Magnus R. Dias-da-Silva, Rui M. B. Maciel, Pedro A. F. Galante and Janete M. Cerutti

    Citation: BMC Medical Genomics 2019 12:104

    Content type: Research article

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  24. Cleft palate (CP) is the second most common congenital birth defect; however, the relationship between CP-associated genes and epigenetic regulation remains largely unknown. In this study, we investigated the ...

    Authors: Akiko Suzuki, Aimin Li, Mona Gajera, Nada Abdallah, Musi Zhang, Zhongming Zhao and Junichi Iwata

    Citation: BMC Medical Genomics 2019 12:93

    Content type: Research article

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  25. Acute myeloid leukemia (AML) is a disease with marked molecular heterogeneity and a high early death rate. Our aim was to investigate an integrated Gene expression, Mirna and miRNA-mRNA Interactions (GMI) sign...

    Authors: Mingguang Shi and Guofu Xu

    Citation: BMC Medical Genomics 2019 12:90

    Content type: Research article

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  26. Targeted next-generation sequencing (NGS) enables rapid identification of common and rare genetic variation. The detection of variants contributing to therapeutic drug response or adverse effects is essential ...

    Authors: Markus Gulilat, Tyler Lamb, Wendy A. Teft, Jian Wang, Jacqueline S. Dron, John F. Robinson, Rommel G. Tirona, Robert A. Hegele, Richard B. Kim and Ute I. Schwarz

    Citation: BMC Medical Genomics 2019 12:81

    Content type: Technical advance

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  27. Presently, a 50-gene expression model (PAM50) serves as a breast cancer (BC) subtype classifier that is insufficient to distinguish, within each single PAM50-classified subtype, patient subpopulations having d...

    Authors: J. Astor Ankney, Ling Xie, John A. Wrobel, Li Wang and Xian Chen

    Citation: BMC Medical Genomics 2019 12:78

    Content type: Technical advance

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  29. Obesity has been associated with gene methylation regulation. Recent studies have shown that epigenetic signature plays a role in metabolic homeostasis after Roux-en Y gastric bypass (RYGB). To conduct a genom...

    Authors: C. F. Nicoletti, M. A. S. Pinhel, A. Diaz-Lagares, F. F. Casanueva, A. Jácome, V. C. Pinhanelli, B. A. P. de Oliveira, A. B. Crujeiras and C. B. Nonino

    Citation: BMC Medical Genomics 2019 12:72

    Content type: Research article

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  30. The etiology of cleft lip with or without cleft palate (CL/P), a common congenital birth defect, is complex and involves the contribution of genetic and environmental factors. Although many candidate genes hav...

    Authors: Mona Gajera, Neha Desai, Akiko Suzuki, Aimin Li, Musi Zhang, Goo Jun, Peilin Jia, Zhongming Zhao and Junichi Iwata

    Citation: BMC Medical Genomics 2019 12:70

    Content type: Research article

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  31. Pancreatic and biliary tract cancer (PC and BTC, respectively) are difficult to diagnose because of their clinical characteristics; however, recent studies suggest that serum microRNAs (miRNAs) might be the ke...

    Authors: Kwondo Kim, DongAhn Yoo, Hee Seung Lee, Kyong Joo Lee, Soo Been Park, Chanyang Kim, Jung Hyun Jo, Dawoon E. Jung and Si Young Song

    Citation: BMC Medical Genomics 2019 12:62

    Content type: Research article

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  32. To explore long-non-coding RNA (lncRNA), microRNA (miRNA) and messenger RNA (mRNA) expression profiles and their biological functions in the urine samples in calcium oxalate (CaOx) patients.

    Authors: Xiongfa Liang, Yongchang Lai, Weizhou Wu, Dong Chen, Fangling Zhong, Jian Huang, Tao Zeng, Xiaolu Duan, Yapeng Huang, Shike Zhang, Shujue Li and Wenqi Wu

    Citation: BMC Medical Genomics 2019 12:57

    Content type: Research article

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  33. The onset of acute Graft-versus-Host Disease (aGvHD) has been correlated with the gut microbiota (GM) composition, but experimental observations are still few, mainly involving cohorts of adult patients. In th...

    Authors: Elena Biagi, Daniele Zama, Simone Rampelli, Silvia Turroni, Patrizia Brigidi, Clarissa Consolandi, Marco Severgnini, Eleonora Picotti, Pietro Gasperini, Pietro Merli, Nunzia Decembrino, Marco Zecca, Simone Cesaro, Maura Faraci, Arcangelo Prete, Franco Locatelli…

    Citation: BMC Medical Genomics 2019 12:49

    Content type: Research article

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  34. The Human Epidermal Growth Factor Receptor (EGFR/HER1) can be activated by several ligands including Transforming Growth Factor alpha (TGF-α) and Epidermal Growth Factor (EGF). Following ligand binding, EGFR h...

    Authors: Miguel Nava, Pranabananda Dutta, Nathan R. Zemke, Robin Farias-Eisner, Jaydutt V. Vadgama and Yanyuan Wu

    Citation: BMC Medical Genomics 2019 12:32

    Content type: Research article

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  35. Exosomes are a subset of extracellular vesicles 30–200 nm in diameter secreted from cells, which contain functional mRNAs and microRNAs. Cerebrospinal fluid (CSF) is the primary source for liquid biopsy to exa...

    Authors: Kentaro Otake, Hidenori Kamiguchi and Yoshihiko Hirozane

    Citation: BMC Medical Genomics 2019 12:7

    Content type: Technical advance

    Published on:

  36. We assessed the stability of BAFF, interferon, plasma cell and LDG neutrophil gene expression signatures over time, and whether changes in expression coincided with changes in SLE disease activity.

    Authors: Michelle Petri, Wei Fu, Ann Ranger, Norm Allaire, Patrick Cullen, Laurence S. Magder and Yuji Zhang

    Citation: BMC Medical Genomics 2019 12:4

    Content type: Research article

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  37. There is a clear need for assays that can predict the risk of metastatic prostate cancer following curative procedures. Importantly these assays must be analytically robust in order to provide quality data for...

    Authors: Paul Wallace Medlow, Christopher James Steele, Andrena Marie McCavigan, Wesley Reardon, Christopher Michael Brown, Shauna May Lambe, Felipe Augusto Andre Ishiy, Steven Michael Walker, Gemma Elizabeth Logan, Olaide Yaqeen Raji, Viktor Berge, Betina Katz, Elaine Williamson Kay, Katherine Sheehan, Ronald William Watson, Denis Paul Harkin…

    Citation: BMC Medical Genomics 2018 11:125

    Content type: Research article

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  38. The etiology of more than half of all patients with X-linked intellectual disability remains elusive, despite array-based comparative genomic hybridization, whole exome or genome sequencing. Since short read m...

    Authors: Alena Zablotskaya, Hilde Van Esch, Kevin J. Verstrepen, Guy Froyen and Joris R. Vermeesch

    Citation: BMC Medical Genomics 2018 11:123

    Content type: Research article

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  39. Chromosome translocations are a hallmark of B-cell precursor acute lymphoblastic leukemia (BCP-ALL). Additional genomic aberrations are also crucial in both BCP-ALL leukemogenesis and treatment management. Her...

    Authors: Thayana Conceição Barbosa, Bruno Almeida Lopes, Caroline Barbieri Blunck, Marcela Braga Mansur, Adriana Vanessa Santini Deyl, Mariana Emerenciano and Maria S. Pombo-de-Oliveira

    Citation: BMC Medical Genomics 2018 11:122

    Content type: Case report

    Published on:

  40. Glioblastoma multiforme, the most prevalent and aggressive brain tumour, has a poor prognosis. The molecular mechanisms underlying gliomagenesis remain poorly understood. Therefore, molecular research, includi...

    Authors: Pengfei Xu, Jian Yang, Junhui Liu, Xue Yang, Jianming Liao, Fanen Yuan, Yang Xu, Baohui Liu and Qianxue Chen

    Citation: BMC Medical Genomics 2018 11:96

    Content type: Research article

    Published on:

  41. Nucleotide Excision Repair (NER) is a major pathway of mammalian DNA repair that is associated with drug resistance and has not been well characterized in acute lymphoblastic leukemia (ALL). The objective of t...

    Authors: Omar M. Ibrahim, Homood M. As Sobeai, Stephen G. Grant and Jean J. Latimer

    Citation: BMC Medical Genomics 2018 11:95

    Content type: Database

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  42. Whole-exome sequencing (WES) has become an invaluable tool for genetic diagnosis in paediatrics. However, it has not been widely adopted in the prenatal setting. This study evaluated the use of WES in prenatal...

    Authors: Gordon K C Leung, Christopher C Y Mak, Jasmine L F Fung, Wilfred H S Wong, Mandy H Y Tsang, Mullin H C Yu, Steven L C Pei, K S Yeung, Gary T K Mok, C P Lee, Amelia P W Hui, Mary H Y Tang, Kelvin Y K Chan, Anthony P Y Liu, Wanling Yang, P C Sham…

    Citation: BMC Medical Genomics 2018 11:93

    Content type: Research article

    Published on:

  43. Verheij syndrome is a rare microdeletion syndrome of chromosome 8q24.3 that harbors PUF60, SCRIB, and NRBP2 genes. Subsequently, loss of function mutations in PUF60 have been found in children with clinical featu...

    Authors: Qiong Xu, Chun-yang Li, Yi Wang, Hui-ping Li, Bing-bing Wu, Yong-hui Jiang and Xiu Xu

    Citation: BMC Medical Genomics 2018 11:92

    Content type: Case report

    Published on:

  44. Bladder cancer has numerous genomic features that are potentially actionable by targeted agents. Nevertheless, both pre-clinical and clinical research using molecular targeted agents have been very limited in ...

    Authors: Adnan Ahmad Ansari, Inkeun Park, Inki Kim, Sojung Park, Sung-Min Ahn and Jae-lyun Lee

    Citation: BMC Medical Genomics 2018 11:88

    Content type: Database

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  45. Mutations occurring in the orthodenticle homeobox 2 gene (OTX2) are responsible for a rare genetic syndrome, characterized mainly by microphthalmia/anophthalmia associated with extra-ocular defects such as brain ...

    Authors: Anna Pichiecchio, Giovanni Vitale, Camilla Caporali, Cecilia Parazzini, Donatella Milani, Maria Paola Recalcati, Laura D’Amico, Sabrina Signorini, Umberto Balottin and Stefano Bastianello

    Citation: BMC Medical Genomics 2018 11:87

    Content type: Case report

    Published on:

  46. The transition from ductal carcinoma in situ (DCIS) to invasive breast carcinoma (IBC) is an important step during breast carcinogenesis. Understanding its molecular changes may help to identify high-risk DCIS...

    Authors: Silke Schultz, Harald Bartsch, Karl Sotlar, Karina Petat-Dutter, Michael Bonin, Steffen Kahlert, Nadia Harbeck, Ulrich Vogel, Harald Seeger, Tanja Fehm and Hans J. Neubauer

    Citation: BMC Medical Genomics 2018 11:80

    Content type: Research article

    Published on:

  47. Lymph node metastasis is one of the most important prognostic factors in head and neck squamous cell carcinomas (HNSCCs) and critical for delineating their treatment. However, clinical and histological criteri...

    Authors: Alessandra Vidotto, Giovana M. Polachini, Marina de Paula-Silva, Sonia M. Oliani, Tiago Henrique, Rossana V. M. López, Patrícia M. Cury, Fabio D. Nunes, José F. Góis-Filho, Marcos B. de Carvalho, Andréia M. Leopoldino and Eloiza H. Tajara

    Citation: BMC Medical Genomics 2018 11:73

    Content type: Research article

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  48. Moyamoya disease (MMD) is characterized by progressive stenosis of intracranial arteries in the circle of Willis with unknown etiology even after the identification of a Moyamoya susceptible gene, RNF213. Rece...

    Authors: Haruto Uchino, Masaki Ito, Ken Kazumata, Yuka Hama, Shuji Hamauchi, Shunsuke Terasaka, Hidenao Sasaki and Kiyohiro Houkin

    Citation: BMC Medical Genomics 2018 11:72

    Content type: Research article

    Published on:

  49. Balanced reciprocal chromosomal translocations (RCTs) are the ones of the most common structural aberrations in the population, with an incidence of 1:625. RCT carriers usually do not demonstrate changes in ph...

    Authors: Magdalena Pasińska, Ewelina Łazarczyk, Katarzyna Jułga, Magdalena Bartnik-Głaska, Beata Nowakowska and Olga Haus

    Citation: BMC Medical Genomics 2018 11:69

    Content type: Case report

    Published on:

  50. Matched tumor-normal sequencing, applied in precision cancer medicine, can identify unidentified germline Medically Actionable Variants (gMAVS) in cancer predisposition genes. We report patient preferences for...

    Authors: Neda Stjepanovic, Tracy L. Stockley, Philippe L. Bedard, Jeanna M. McCuaig, Melyssa Aronson, Spring Holter, Kara Semotiuk, Natasha B. Leighl, Raymond Jang, Monika K. Krzyzanowska, Amit M. Oza, Abha Gupta, Christine Elser, Lailah Ahmed, Lisa Wang, Suzanne Kamel-Reid…

    Citation: BMC Medical Genomics 2018 11:65

    Content type: Research article

    Published on:

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