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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. Content type: Research article

    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

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  2. Content type: Research article

    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

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  3. Content type: Research article

    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

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  4. Content type: Research article

    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

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  5. Content type: Research article

    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

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  6. Content type: Research article

    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

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  7. Content type: Technical advance

    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

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  8. Content type: Technical advance

    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

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  9. Content type: Research article

    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

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  10. Content type: Research article

    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

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  11. Content type: Research article

    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

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  12. Content type: Research article

    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

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  13. Content type: Research article

    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

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  14. Content type: Research article

    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

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  15. Content type: Technical advance

    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

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  16. Content type: Research article

    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

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  17. Content type: Research article

    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

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  18. Content type: Research article

    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

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  19. Content type: Case report

    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

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  20. Content type: Research article

    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

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  21. Content type: Database

    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

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  22. Content type: Research article

    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

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  23. Content type: Case report

    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

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  24. Content type: Database

    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

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  25. Content type: Case report

    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

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  26. Content type: Research article

    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

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  27. Content type: Research article

    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

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  28. Content type: Research article

    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

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  29. Content type: Case report

    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

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  30. Content type: Research article

    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

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  31. Content type: Research article

    Giant cell arteritis (GCA) is the most common form of vasculitis affecting elderly people. It is one of the few true ophthalmic emergencies but symptoms and signs are variable thereby making it a challenging d...

    Authors: Elisabeth De Smit, Samuel W. Lukowski, Lisa Anderson, Anne Senabouth, Kaisar Dauyey, Sharon Song, Bruce Wyse, Lawrie Wheeler, Christine Y. Chen, Khoa Cao, Amy Wong Ten Yuen, Neil Shuey, Linda Clarke, Isabel Lopez Sanchez, Sandy S. C. Hung, Alice Pébay…

    Citation: BMC Medical Genomics 2018 11:61

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  32. Content type: Case report

    The proto-oncogene KRAS performs an essential function in normal tissue signaling, and the mutation of KRAS gene is a key step in the development of many cancers. Somatic KRAS mutations are often detected in p...

    Authors: Ruen Yao, Tingting Yu, Yufei Xu, Guoqiang Li, Lei Yin, Yunfang Zhou, Jian Wang and Zhilong Yan

    Citation: BMC Medical Genomics 2018 11:60

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  33. Content type: Research article

    Elevated blood pressure is an important risk factor for cardiovascular disease and is also an important factor in global mortality. Military pilots are at high risk of cardiovascular disease because they under...

    Authors: Xing-Cheng Zhao, Shao-Hua Yang, Yi-Quan Yan, Xin Zhang, Lin Zhang, Bo Jiao, Shuai Jiang and Zhi-Bin Yu

    Citation: BMC Medical Genomics 2018 11:59

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  34. Content type: Research article

    Sensorineural hearing loss (SNHL) is the most common sensory impairment. Comprehensive next-generation sequencing (NGS) has become the standard for the etiological diagnosis of early-onset SNHL. However, accur...

    Authors: Rubén Cabanillas, Marta Diñeiro, Guadalupe A. Cifuentes, David Castillo, Patricia C. Pruneda, Rebeca Álvarez, Noelia Sánchez-Durán, Raquel Capín, Ana Plasencia, Mónica Viejo-Díaz, Noelia García-González, Inés Hernando, José L. Llorente, Alfredo Repáraz-Andrade, Cristina Torreira-Banzas, Jordi Rosell…

    Citation: BMC Medical Genomics 2018 11:58

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  35. Content type: Research article

    Generalized pustular psoriasis (GPP) is a rare, episodic, potentially life-threatening inflammatory disease. However, the pathogenesis of GPP, and universally accepted therapies for treating it, remain undefined.

    Authors: Lingyan Wang, Xiaoling Yu, Chao Wu, Teng Zhu, Wenming Wang, Xiaofeng Zheng and Hongzhong Jin

    Citation: BMC Medical Genomics 2018 11:52

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  36. Content type: Research article

    In children with sensory processing dysfunction (SPD), who do not meet criteria for autism spectrum disorder (ASD) or intellectual disability, the contribution of de novo pathogenic mutation in neurodevelopmen...

    Authors: Elysa Jill Marco, Anne Brandes Aitken, Vishnu Prakas Nair, Gilberto da Gente, Molly Rae Gerdes, Leyla Bologlu, Sean Thomas and Elliott H. Sherr

    Citation: BMC Medical Genomics 2018 11:50

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  37. Content type: Research article

    There is a paucity of knowledge concerning erythrocytes in the aetiology of Multiple Sclerosis (MS) despite their potential to contribute to disease through impaired antioxidant capacity and altered haemorheol...

    Authors: Kira Groen, Vicki E. Maltby, Rodney A. Lea, Katherine A. Sanders, J. Lynn Fink, Rodney J. Scott, Lotti Tajouri and Jeannette Lechner-Scott

    Citation: BMC Medical Genomics 2018 11:48

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  38. Content type: Research article

    Current medical practice includes the application of genomic sequencing (GS) in clinical and research settings. Despite expanded use of this technology, the process of disclosure of genomic results to patients...

    Authors: Julia Wynn, Katie Lewis, Laura M. Amendola, Barbara A. Bernhardt, Sawona Biswas, Manasi Joshi, Carmit McMullen and Sarah Scollon

    Citation: BMC Medical Genomics 2018 11:45

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  39. Content type: Case report

    Birt-Hogg-Dubé syndrome (BHD) is an autosomal dominant disorder caused by germline mutations in the folliculin gene (FLCN). Nearly 150 pathogenic mutations have been identified in FLCN. The most frequent pattern ...

    Authors: Mitsuko Furuya, Hironori Kobayashi, Masaya Baba, Takaaki Ito, Reiko Tanaka and Yukio Nakatani

    Citation: BMC Medical Genomics 2018 11:42

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  40. Content type: Research article

    Mouse homozygous mutants in Wnt/planar cell polarity (PCP) pathway genes have been shown to cause neural tube defects (NTDs) through the disruption of normal morphogenetic processes critical to neural tube clo...

    Authors: Zhongzhong Chen, Yunping Lei, Xuanye Cao, Yufang Zheng, Fang Wang, Yihua Bao, Rui Peng, Richard H. Finnell, Ting Zhang and Hongyan Wang

    Citation: BMC Medical Genomics 2018 11:38

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  41. Content type: Case report

    Lipid storage myopathy (LSM) is a diverse group of lipid metabolic disorders with great variations in the clinical phenotype and age of onset. Classical multiple acyl-CoA dehydrogenase deficiency (MADD) is kno...

    Authors: Liuh Ling Goh, Yingshan Lee, Ee Shien Tan, James Soon Chuan Lim, Chia Wei Lim and Rinkoo Dalan

    Citation: BMC Medical Genomics 2018 11:37

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  42. Content type: Research article

    Ritodrine is a commonly used tocolytic to prevent preterm labour. However, it can cause unexpected serious adverse reactions, such as pulmonary oedema, pulmonary congestion, and tachycardia. It is unknown whet...

    Authors: Heewon Seo, Eun Jin Kwon, Young-Ah You, Yoomi Park, Byung Joo Min, Kyunghun Yoo, Han-Sung Hwang, Ju Han Kim and Young Ju Kim

    Citation: BMC Medical Genomics 2018 11:4

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  43. Content type: Research article

    Cardiovascular disease and its sequelae are major causes of global mortality, and better methods are needed to identify patients at risk for future cardiovascular events. Gene expression analysis can inform on...

    Authors: James A. Wingrove, Karen Fitch, Brian Rhees, Steven Rosenberg and Deepak Voora

    Citation: BMC Medical Genomics 2018 11:1

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  44. Content type: Research article

    Sessile serrated adenomas/polyps are distinguished from hyperplastic colonic polyps subjectively by their endoscopic appearance and histological morphology. However, hyperplastic and sessile serrated polyps ca...

    Authors: Yasir Rahmatallah, Magomed Khaidakov, Keith K. Lai, Hannah E. Goyne, Laura W. Lamps, Curt H. Hagedorn and Galina Glazko

    Citation: BMC Medical Genomics 2017 10:81

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  45. Content type: Research article

    Inhibition of the PD-L1/PD-1 immune checkpoint axis represents one of the most promising approaches of immunotherapy for various cancer types. However, immune checkpoint inhibition is successful only in subpop...

    Authors: Jan Budczies, Carsten Denkert, Balázs Győrffy, Peter Schirmacher and Albrecht Stenzinger

    Citation: BMC Medical Genomics 2017 10:74

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  46. Content type: Research article

    PD is a progressive neurodegenerative disorder commonly treated by levodopa. The findings from genetic studies on adverse effects (ADRs) and levodopa efficacy are mostly inconclusive. Here, we aim to identify ...

    Authors: Debleena Guin, Manish Kumar Mishra, Puneet Talwar, Chitra Rawat, Suman S. Kushwaha, Shrikant Kukreti and Ritushree Kukreti

    Citation: BMC Medical Genomics 2017 10:56

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  47. Content type: Technical advance

    Formalin fixed paraffin embedded (FFPE) tumor samples are a major source of DNA from patients in cancer research. However, FFPE is a challenging material to work with due to macromolecular fragmentation and nu...

    Authors: Jackie L. Ludgate, James Wright, Peter A. Stockwell, Ian M. Morison, Michael R. Eccles and Aniruddha Chatterjee

    Citation: BMC Medical Genomics 2017 10:54

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  48. Content type: Case report

    Intratumor heterogeneity (ITH) poses an urgent challenge for cancer precision medicine because it can cause drug resistance against cancer target therapy and immunotherapy. The search for trunk mutations that ...

    Authors: Zhan Zhou, Shanshan Wu, Jun Lai, Yuan Shi, Chixiao Qiu, Zhe Chen, Yufeng Wang, Xun Gu, Jie Zhou and Shuqing Chen

    Citation: BMC Medical Genomics 2017 10:49

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  49. Content type: Technical advance

    The growing number of Next Generation Sequencing (NGS) tests is transforming the routine clinical diagnosis of hereditary cancers. Identifying whether a cancer is the result of an underlying disease-causing mu...

    Authors: Donavan T. Cheng, Meera Prasad, Yvonne Chekaluk, Ryma Benayed, Justyna Sadowska, Ahmet Zehir, Aijazuddin Syed, Yan Elsa Wang, Joshua Somar, Yirong Li, Zarina Yelskaya, Donna Wong, Mark E. Robson, Kenneth Offit, Michael F. Berger, Khedoudja Nafa…

    Citation: BMC Medical Genomics 2017 10:33

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