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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 or genetic disorders as well as the analysis of the structure and function of genes and chromosomes and the role of genetic mutations and cytogenetic changes in human genetic disorders.

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  1. Electronic cigarettes (e-cigs) vaping, cigarette smoke, and waterpipe tobacco smoking are associated with various cardiopulmonary diseases. microRNAs are present in higher concentration in exosomes that play a...

    Authors: Kameshwar P. Singh, Krishna P. Maremanda, Dongmei Li and Irfan Rahman

    Citation: BMC Medical Genomics 2020 13:128

    Content type: Research article

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  2. In order to mitigate the risk of allele dropout (ADO) and ensure the accuracy of preimplantation genetic testing for monogenic disease (PGT-M), it is necessary to construct parental haplotypes. Typically, hapl...

    Authors: Qing Li, Yan Mao, Shaoying Li, Hongzi Du, Wenzhi He, Jianchun He, Lingyin Kong, Jun Zhang, Bo Liang and Jianqiao Liu

    Citation: BMC Medical Genomics 2020 13:117

    Content type: Technical advance

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  3. Congenital insensitivity to pain with anhidrosis (CIPA) is an extremely rare autosomal recessive disorder characterized by insensitivity to pain, inability to sweat and intellectual disability. CIPA is caused ...

    Authors: Andrés López-Cortés, Ana Karina Zambrano, Patricia Guevara-Ramírez, Byron Albuja Echeverría, Santiago Guerrero, Eliana Cabascango, Andy Pérez-Villa, Isaac Armendáriz-Castillo, Jennyfer M. García-Cárdenas, Verónica Yumiceba, Gabriela Pérez-M, Paola E. Leone and César Paz-y-Miño

    Citation: BMC Medical Genomics 2020 13:113

    Content type: Case report

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  4. Lung cancer has been the leading cause of tumor related death, and 80% ~ 85% of it is non-small cell lung cancer (NSCLC). Even with the rising molecular targeted therapies, for example EGFR, ROS1 and ALK, the ...

    Authors: Rong Wei, Ziyue Wang, Yaping Zhang, Bin Wang, Ningning Shen, Li E, Xin Li, Lifang Shang, Yangwei Shang, Wenpeng Yan, Xiaoqin Zhang, Wenxia Ma and Chen Wang

    Citation: BMC Medical Genomics 2020 13:112

    Content type: Research article

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  5. Fusion transcripts are involved in tumourigenesis and play a crucial role in tumour heterogeneity, tumour evolution and cancer treatment resistance. However, fusion transcripts have not been studied at high sp...

    Authors: Stefanie Friedrich and Erik L. L. Sonnhammer

    Citation: BMC Medical Genomics 2020 13:110

    Content type: Technical advance

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  6. The goal of this study was to determine whether Levey-Jennings charts, which are widely used in clinical laboratories, can be used to create standardized internal quality controls (IQCs) for prenatal molecular...

    Authors: Binghuan Weng, Ya-li Xu, Jun Ying, Hao-kun Yang, Lan Su, Yan-mei Yang and Min Chen

    Citation: BMC Medical Genomics 2020 13:109

    Content type: Research article

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  7. Colon adenocarcinoma (COAD) is one of the most common gastrointestinal cancers globally. Molecular aberrations of tumor suppressors and/or oncogenes are the main contributors to tumorigenesis. However, the exa...

    Authors: Arash Poursheikhani, Mohammad Reza Abbaszadegan, Negin Nokhandani and Mohammad Amin Kerachian

    Citation: BMC Medical Genomics 2020 13:108

    Content type: Research article

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  8. We have evaluated an NGS-based method to detect recurrent gene fusions of diagnostic and prognostic importance in hematological malignancies. Our goal was to achieve a highly specific assay with a simple workf...

    Authors: Marie Engvall, Nicola Cahill, Britt-Inger Jonsson, Martin Höglund, Helene Hallböök and Lucia Cavelier

    Citation: BMC Medical Genomics 2020 13:106

    Content type: Research article

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  9. Liquid-based cytology (LBC) is now a widely used method for cytologic screening and cancer diagnosis. Since the cells are fixed with alcohol-based fixatives, and the specimens are stored in a liquid condition,...

    Authors: Toshiaki Akahane, Ikumi Kitazono, Shintaro Yanazume, Masaki Kamio, Shinichi Togami, Ippei Sakamoto, Sachio Nohara, Seiya Yokoyama, Hiroaki Kobayashi, Tsubasa Hiraki, Shinsuke Suzuki, Shinichi Ueno and Akihide Tanimoto

    Citation: BMC Medical Genomics 2020 13:101

    Content type: Research article

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  10. Non-invasive prenatal testing (NIPT) has been established as a routine prenatal screening to assess the risk of common foetal aneuploidy disorder (trisomy 21, 18, and 13). NIPT has high sensitivity and high sp...

    Authors: Hui-Hui Xu, Mei-Zhen Dai, Kai Wang, Yang Zhang, Fei-Yan Pan and Wei-Wu Shi

    Citation: BMC Medical Genomics 2020 13:96

    Content type: Case report

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  11. Left-sided heart failure (HF) is documented as a key prognostic factor in HF. However, the relative molecular mechanisms underlying left-sided HF is unknown. The purpose of this study is to unearth significant...

    Authors: Jiamin Zhou, Wei Zhang, Chunying Wei, Zhiliang Zhang, Dasong Yi, Xiaoping Peng, Jingtian Peng, Ran Yin, Zeqi Zheng, Hongmei Qi, Yunfeng Wei and Tong Wen

    Citation: BMC Medical Genomics 2020 13:93

    Content type: Research article

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  12. Medulloblastoma (MB) is one of the most common malignant cancers in children. MB is primarily classified into four subgroups based on molecular and clinical characteristics as (1) WNT (2) Sonic-hedgehog (SHH) ...

    Authors: Varun Kesherwani, Mamta Shukla, Don W. Coulter, J. Graham Sharp, Shantaram S. Joshi and Nagendra K. Chaturvedi

    Citation: BMC Medical Genomics 2020 13:87

    Content type: Research article

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  13. A growing evidence suggests that long non-coding RNAs (lncRNAs) can function as a microRNA (miRNA) sponge in various diseases including oral cancer. However, the pathophysiological function of lncRNAs remains ...

    Authors: Junhao Yin, Xiaoli Zeng, Zexin Ai, Miao Yu, Yang’ou Wu and Shengjiao Li

    Citation: BMC Medical Genomics 2020 13:84

    Content type: Research article

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  14. Intellectual disability (ID) is a heterogeneous neurodevelopmental disorder with a complex genetic underpinning in its etiology. Chromosome microarray (CMA) is recommended as the first-tier diagnostic test for...

    Authors: Jun Wang, Yan Wang, Liwen Wang, Wang Yang Chen and Min Sheng

    Citation: BMC Medical Genomics 2020 13:70

    Content type: Research article

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  15. Chromothripsis is an event of genomic instability leading to complex chromosomal alterations in cancer. Frequent long-range chromatin interactions between transcription factors (TFs) and targets may promote ex...

    Authors: Chun-Lin Lin, Xi Tan, Meizhen Chen, Meena Kusi, Chia-Nung Hung, Chih-Wei Chou, Ya-Ting Hsu, Chiou-Miin Wang, Nameer Kirma, Chun-Liang Chen, Ching-Hung Lin, Kate I. Lathrop, Richard Elledge, Virginia G. Kaklamani, Kohzoh Mitsuya and Tim H.-M. Huang

    Citation: BMC Medical Genomics 2020 13:69

    Content type: Research article

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  16. The causes for thousands of individually rare recessive diseases have been discovered since the adoption of next generation sequencing (NGS). Following the molecular diagnosis in older children in a family, pa...

    Authors: Mahmoud Y. Issa, Zinayida Chechlacz, Valentina Stanley, Renee D. George, Jennifer McEvoy-Venneri, Denice Belandres, Hasnaa M. Elbendary, Khaled R. Gaber, Ahmed Nabil, Mohamed S. Abdel-Hamid, Maha S. Zaki and Joseph G. Gleeson

    Citation: BMC Medical Genomics 2020 13:68

    Content type: Research article

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  17. Despite the emergence of cell-free DNA (cfDNA) as a clinical biomarker in cancer, the tissue origins of cfDNA in healthy individuals have to date been inferred only by indirect and relative measurement methods...

    Authors: Danny Laurent, Fiona Semple, Philip J. Starkey Lewis, Elaine Rose, Holly A. Black, Jennifer Coe, Stuart J. Forbes, Mark J. Arends, James W. Dear and Timothy J. Aitman

    Citation: BMC Medical Genomics 2020 13:60

    Content type: Research article

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  18. The use of high-throughput analytical techniques has enabled the description of acute lymphoblastic leukaemia (ALL) subtypes. The TCF3-HLF translocation is a very rare rearrangement in ALL that is associated with...

    Authors: Monika Lejman, Monika Włodarczyk, Joanna Zawitkowska and Jerzy R. Kowalczyk

    Citation: BMC Medical Genomics 2020 13:58

    Content type: Case report

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  19. As the sixth most common cancer worldwide, head and neck squamous cell carcinoma (HNSCC) develops visceral metastases during the advanced stage of the disease and exhibits a low five-year survival rate. The im...

    Authors: Zhaoming Zhong, Min Hong, Xiao Chen, Yan Xi, Yuanyuan Xu, Deyu Kong, Jun Deng, Yun Li, Rui Hu, Chuanzheng Sun and Jin Liang

    Citation: BMC Medical Genomics 2020 13:57

    Content type: Research article

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  20. The established role miRNA-mRNA regulation of gene expression has in oncogenesis highlights the importance of integrating miRNA with downstream mRNA targets. These findings call for investigations aimed at ide...

    Authors: Rency S. Varghese, Yuan Zhou, Megan Barefoot, Yifan Chen, Cristina Di Poto, Abdalla Kara Balla, Everett Oliver, Zaki A. Sherif, Deepak Kumar, Alexander H. Kroemer, Mahlet G. Tadesse and Habtom W. Ressom

    Citation: BMC Medical Genomics 2020 13:56

    Content type: Research article

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  21. Sepsis represents a complex disease with dysregulated inflammatory response and high mortality rate. Long noncoding RNAs (lncRNAs) have been reported to play regulatory roles in a variety of biological process...

    Authors: Zhenjiang Bai, Yiping Li, Yanhong Li, Jian Pan, Jian Wang and Fang Fang

    Citation: BMC Medical Genomics 2020 13:36

    Content type: Research article

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  22. Pediatric leukemias have a diverse genomic landscape associated with complex structural variants, including gene fusions, insertions and deletions, and single nucleotide variants. Routine karyotype and fluores...

    Authors: Erin L. Crowgey, Nitin Mahajan, Wing Hing Wong, Anilkumar Gopalakrishnapillai, Sonali P. Barwe, E. Anders Kolb and Todd E. Druley

    Citation: BMC Medical Genomics 2020 13:32

    Content type: Research article

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  23. Influenza infections produce a spectrum of disease severity, ranging from a mild respiratory illness to respiratory failure and death. The host-response pathways associated with the progression to severe influ...

    Authors: Yoann Zerbib, Emily K. Jenkins, Maryam Shojaei, Adrienne F. A. Meyers, John Ho, T. Blake Ball, Yoav Keynan, Amarnath Pisipati, Aseem Kumar, Anand Kumar, Marek Nalos, Benjamin M. Tang, Klaus Schughart and Anthony McLean

    Citation: BMC Medical Genomics 2020 13:28

    Content type: Research article

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  24. The amniotic fluid (AF) cell-free transcriptome is modulated by physiologic and pathologic processes during pregnancy. AF gene expression changes with advancing gestation reflect fetal development and organ ma...

    Authors: Adi L. Tarca, Roberto Romero, Roger Pique-Regi, Percy Pacora, Bogdan Done, Marian Kacerovsky, Gaurav Bhatti, Sunil Jaiman, Sonia S. Hassan, Chaur-Dong Hsu and Nardhy Gomez-Lopez

    Citation: BMC Medical Genomics 2020 13:25

    Content type: Research article

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  25. In 2013, our laboratory designed a targeted sequencing panel, “LipidSeq”, to study the genetic determinants of dyslipidemia and metabolic disorders. Over the last 6 years, we have analyzed 3262 patient samples...

    Authors: Jacqueline S. Dron, Jian Wang, Adam D. McIntyre, Michael A. Iacocca, John F. Robinson, Matthew R. Ban, Henian Cao and Robert A. Hegele

    Citation: BMC Medical Genomics 2020 13:23

    Content type: Research article

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  26. The most common histological subtypes of esophageal cancer are squamous cell carcinoma (ESCC) and adenocarcinoma (EAC). It has been demonstrated that non-marginal differences in gene expression and somatic alt...

    Authors: Suyan Tian, Chi Wang, Jing Zhang and Dan Yu

    Citation: BMC Medical Genomics 2020 13:18

    Content type: Research article

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  27. Whole-genome sequencing (WGS) is becoming an increasingly important tool for detecting genomic variation. Blood derived DNA is the current standard for WGS for research or clinical purposes but may not always ...

    Authors: Roderick A. Yao, Oyediran Akinrinade, Marie Chaix and Seema Mital

    Citation: BMC Medical Genomics 2020 13:11

    Content type: Research article

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  28. Inhibitors of apoptosis proteins (IAPs) are a family of antiapoptotic proteins modulating cell cycle, signal transduction and apoptosis. Dysregulated IAPs have been reported to contribute to tumor progression ...

    Authors: Jianfeng Liang, Wanni Zhao, Pan Tong, Ping Li, Yuanli Zhao, Hua Li and Jun Liang

    Citation: BMC Medical Genomics 2020 13:7

    Content type: Research article

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  29. 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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  30. 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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  31. 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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  32. 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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  33. 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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  34. 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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  35. 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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  36. 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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  37. 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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  38. 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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  39. 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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  40. 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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  41. 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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  42. 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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  43. 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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  44. 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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  45. 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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  46. 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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  47. 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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  48. 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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  49. 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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  50. 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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2019 Journal Metrics

Announcement

As a result of the significant disruption that is being caused by the COVID-19 pandemic we are very aware that many researchers will have difficulty in meeting the timelines associated with our peer review process during normal times.  Please do let us know if you need additional time. Our systems will continue to remind you of the original timelines but we intend to be highly flexible at this time.