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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

    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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  2. 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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  3. 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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  4. 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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  5. 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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  6. 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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  7. 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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  8. 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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  9. 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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  10. 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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  11. 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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  12. 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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  13. 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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  14. 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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  15. 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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  16. 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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  17. 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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  18. 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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  19. 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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  20. 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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  21. Content type: Research article

    Biliary Atresia (BA) is rare and genetically complex, and the pathogenesis is elusive. The disease course is variable and can represent heterogeneity, which hinders effective disease management. Deciphering th...

    Authors: Guo Cheng, Patrick Ho-Yu Chung, Edwin Kin-Wai Chan, Man-Ting So, Pak-Chung Sham, Stacey S. Cherny, Paul Kwong-Hang Tam and Maria-Mercè Garcia-Barceló

    Citation: BMC Medical Genomics 2017 10:22

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  22. Content type: Research article

    Duchenne muscular dystrophy (DMD) is caused by mutations in the DMD gene, which codes for the dystrophin protein. While progress has been made in defining the molecular basis and pathogenesis of DMD, major gaps r...

    Authors: Larry W. Markham, Candice L. Brinkmeyer-Langford, Jonathan H. Soslow, Manisha Gupte, Douglas B. Sawyer, Joe N. Kornegay and Cristi L. Galindo

    Citation: BMC Medical Genomics 2017 10:21

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  23. Content type: Research Article

    Basal-like constitutes an important molecular subtype of breast cancer characterised by an aggressive behaviour and a limited therapy response. The outcome of patients within this subtype is, however, divergen...

    Authors: Heloisa H. Milioli, Inna Tishchenko, Carlos Riveros, Regina Berretta and Pablo Moscato

    Citation: BMC Medical Genomics 2017 10:19

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  24. Content type: Research article

    The importance of accurate and affordable mutation calling in fixed pathology samples is becoming increasingly important as we move into the era of personalised medicine. The Affymetrix OncoScan® Array platfor...

    Authors: Henry M. Wood, Joseph M. Foster, Morag Taylor, Emma Tinkler-Hundal, Fiona S. Togneri, Paula Wojtowicz, Assa Oumie, Karen G. Spink, Fiona Brew and Philip Quirke

    Citation: BMC Medical Genomics 2017 10:17

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  25. Content type: Research article

    The PALB2 gene encodes a protein that plays a crucial role in maintaining genomic integrity. Germline inactivating mutations in PALB2 are associated with an increased risk of breast and ovarian cancer. The preval...

    Authors: Anna Kluska, Aneta Balabas, Magdalena Piatkowska, Katarzyna Czarny, Katarzyna Paczkowska, Dorota Nowakowska, Michal Mikula and Jerzy Ostrowski

    Citation: BMC Medical Genomics 2017 10:14

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  26. Content type: Research article

    The use of genome-wide (whole genome or exome) sequencing for population-based newborn screening presents an opportunity to detect and treat or prevent many more serious early-onset health conditions than is p...

    Authors: Jan M. Friedman, Martina C. Cornel, Aaron J. Goldenberg, Karla J. Lister, Karine Sénécal and Danya F. Vears

    Citation: BMC Medical Genomics 2017 10:9

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  27. Content type: Research article

    Familial breast cancer (BC) represents 5 to 10% of all BC cases. Mutations in two high susceptibility BRCA1 and BRCA2 genes explain 16–40% of familial BC, while other high, moderate and low susceptibility genes e...

    Authors: Nadine Jalkh, Eliane Chouery, Zahraa Haidar, Christina Khater, David Atallah, Hamad Ali, Makia J. Marafie, Mohamed R. Al-Mulla, Fahd Al-Mulla and Andre Megarbane

    Citation: BMC Medical Genomics 2017 10:8

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  28. Content type: Case report

    Microcephaly has become a major public health problem in Brazil. The total number of newborns with microcephaly was reported to be >4000 in June 2016. Studies suggest that Zika Virus is a major cause of new mi...

    Authors: Diogo Antonio Tschoeke, Louisi Souza de Oliveira, Luciana Leomil, Amilcar Tanuri and Fabiano Lopes Thompson

    Citation: BMC Medical Genomics 2017 10:5

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  29. Content type: Debate

    It is becoming increasingly difficult to keep information about genetic ancestry separate from information about health, and consumers of genetic ancestry tests are becoming more aware of the potential health ...

    Authors: Andrew Smart, Deborah A. Bolnick and Richard Tutton

    Citation: BMC Medical Genomics 2017 10:3

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  30. Content type: Technical advance

    The KRAS gene is mutated in about 40 % of colorectal cancer (CRC) cases, which has been clinically validated as a predictive mutational marker of intrinsic resistance to anti-EGFR inhibitor (EGFRi) therapy. Since...

    Authors: Bernard Omolo, Mingli Yang, Fang Yin Lo, Michael J. Schell, Sharon Austin, Kellie Howard, Anup Madan and Timothy J. Yeatman

    Citation: BMC Medical Genomics 2016 9:65

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  31. Content type: Correspondence

    The increasing use of next generation DNA sequencing in clinical medicine is exposing the need for more genetics education in physician training. We piloted an initiative to determine the feasibility of incorp...

    Authors: Glenn S. Gerhard, Qunyan Jin, Barbara V. Paynton and Steven N. Popoff

    Citation: BMC Medical Genomics 2016 9:62

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  32. Content type: Research article

    Histopathological assessment has a low potential to predict clinical outcome in patients with the same stage of colorectal cancer. More specific and sensitive biomarkers to determine patients’ survival are nee...

    Authors: Nurul Ainin Abdul Aziz, Norfilza M. Mokhtar, Roslan Harun, Md Manir Hossain Mollah, Isa Mohamed Rose, Ismail Sagap, Azmi Mohd Tamil, Wan Zurinah Wan Ngah and Rahman Jamal

    Citation: BMC Medical Genomics 2016 9:58

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  34. Content type: Research article

    The difficulties in using formalin-fixed and paraffin-embedded (FFPE) tumour specimens for molecular marker studies have hampered progress in translational cancer research. The cDNA-mediated, annealing, select...

    Authors: Mahesh Iddawela, Oscar M. Rueda, Marcus Klarqvist, Stefan Graf, Helena M. Earl and Carlos Caldas

    Citation: BMC Medical Genomics 2016 9:54

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  35. Content type: Research article

    The diagnosis of acute appendicitis can be surprisingly difficult without computed tomography, which carries significant radiation exposure. Circulating blood cells may carry informative changes in their RNA e...

    Authors: Lakhmir S. Chawla, Ian Toma, Danielle Davison, Khashayar Vaziri, Juliet Lee, Raymond Lucas, Michael G. Seneff, Aoibhinn Nyhan and Timothy A. McCaffrey

    Citation: BMC Medical Genomics 2016 9:40

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  36. Content type: Research Article

    At the molecular level breast cancer comprises a heterogeneous set of subtypes associated with clear differences in gene expression and clinical outcomes. Single sample predictors (SSPs) are built via a two-st...

    Authors: Herman MJ. Sontrop, Marcel JT. Reinders and Perry D. Moerland

    Citation: BMC Medical Genomics 2016 9:26

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    The Erratum to this article has been published in BMC Medical Genomics 2016 9:39

  37. Content type: Research article

    Noninvasive prenatal testing (NIPT) to detect fetal aneuploidy using next-generation sequencing on ion semiconductor platforms has become common. There are several sequencers that can generate sufficient DNA r...

    Authors: Sunshin Kim, HeeJung Jung, Sung Hee Han, SeungJae Lee, JeongSub Kwon, Min Gyun Kim, Hyungsik Chu, Hongliang Chen, Kyudong Han, Hwanjong Kwak, Sunghoon Park, Hee Jae Joo, Byung Chul Kim and Jong Bhak

    Citation: BMC Medical Genomics 2016 9:22

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  38. Content type: Research article

    Essential hypertension is a significant risk factor for cardiovascular diseases. Emerging research suggests a role of DNA methylation in blood pressure physiology. We aimed to investigate epigenetic associatio...

    Authors: Adrian E. Boström, Jessica Mwinyi, Sarah Voisin, Wenting Wu, Bernd Schultes, Kang Zhang and Helgi B. Schiöth

    Citation: BMC Medical Genomics 2016 9:20

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  39. Content type: Research article

    Liver cancer, of which hepatocellular carcinoma (HCC) is by far the most common type, is the second most deadly cancer (746,000 deaths in 2012). Currently, the only curative treatment for HCC is surgery to rem...

    Authors: Qing Yan Xie, Anthony Almudevar, Christa L. Whitney-Miller, Christopher T. Barry and Matthew N. McCall

    Citation: BMC Medical Genomics 2016 9:18

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  40. Content type: Research article

    Faced with an increasing number of choices for biologic therapies, rheumatologists have a critical need for better tools to inform rheumatoid arthritis (RA) disease management. The ability to identify patients...

    Authors: Ty M. Thomson, Reynald M. Lescarbeau, David A. Drubin, Daphna Laifenfeld, David de Graaf, David A. Fryburg, Bruce Littman, Renée Deehan and Aaron Van Hooser

    Citation: BMC Medical Genomics 2015 8:26

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  41. Content type: Research article

    Targeted PCR-based genetic testing for BRCA1 and BRCA2 can be performed at a lower cost than full gene testing; however, it may overlook mutations responsible for familial breast and/or ovarian cancers. In the pr...

    Authors: Anna Kluska, Aneta Balabas, Agnieszka Paziewska, Maria Kulecka, Dorota Nowakowska, Michal Mikula and Jerzy Ostrowski

    Citation: BMC Medical Genomics 2015 8:19

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  42. Content type: Research article

    The gene expression profile of cytologically-normal bronchial airway epithelial cells has previously been shown to be altered in patients with lung cancer. Although bronchoscopy is often used for the diagnosis...

    Authors: Duncan H Whitney, Michael R Elashoff, Kate Porta-Smith, Adam C Gower, Anil Vachani, J Scott Ferguson, Gerard A Silvestri, Jerome S Brody, Marc E Lenburg and Avrum Spira

    Citation: BMC Medical Genomics 2015 8:18

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  45. Content type: Technical advance

    Adoption of new technology in both basic research and clinical settings requires rigorous validation of analytical performance. The OncoScan® FFPE Assay is a multiplexing tool that offers genome-wide copy numb...

    Authors: Joseph M Foster, Assa Oumie, Fiona S Togneri, Fabiana Ramos Vasques, Debra Hau, Morag Taylor, Emma Tinkler-Hundal, Katie Southward, Paul Medlow, Keith McGreeghan-Crosby, Iris Halfpenny, Dominic J McMullan, Phil Quirke, Katherine E Keating, Mike Griffiths, Karen G Spink…

    Citation: BMC Medical Genomics 2015 8:5

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  46. Content type: Research article

    Early detection and treatment of non-invasive neoplasms can effectively reduce the incidence of advanced gastric carcinoma (GC), but only when the lineage is continuous between non-invasive and advanced tumour...

    Authors: Diem Thi-Ngoc Vo, Takahisa Nakayama, Hiroto Yamamoto, Ken-ichi Mukaisho, Takanori Hattori and Hiroyuki Sugihara

    Citation: BMC Medical Genomics 2015 8:6

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  47. Content type: Research article

    Exacerbations of chronic obstructive pulmonary disease (COPD), characterized by acute deterioration in symptoms, may be due to bacterial or viral infections, environmental exposures, or unknown factors. Exacer...

    Authors: Jarrett D Morrow, Weiliang Qiu, Divya Chhabra, Stephen I Rennard, Paula Belloni, Anton Belousov, Sreekumar G Pillai and Craig P Hersh

    Citation: BMC Medical Genomics 2015 8:1

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  48. Content type: Research article

    Molecular karyotyping is now the first-tier genetic test for patients affected with unexplained intellectual disability (ID) and/or multiple congenital anomalies (MCA), since it identifies a pathogenic copy nu...

    Authors: Guylaine D’Amours, Mathieu Langlois, Géraldine Mathonnet, Raouf Fetni, Sonia Nizard, Myriam Srour, Frédérique Tihy, Michael S Phillips, Jacques L Michaud and Emmanuelle Lemyre

    Citation: BMC Medical Genomics 2014 7:70

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  49. Content type: Research article

    Neoadjuvant chemoradiotherapy (nCRT) followed by radical surgery is the preferred treatment strategy for locally advanced rectal cancer. However, complete tumor regression is observed in a significant proporti...

    Authors: Camila Miranda Lopes-Ramos, Angelita Habr-Gama, Bruna de Souza Quevedo, Natália Mariana Felício, Fabiana Bettoni, Fernanda Christtanini Koyama, Paula Fontes Asprino, Pedro Alexandre Galante, Joaquim Gama-Rodrigues, Anamaria Aranha Camargo, Rodrigo Oliva Perez and Raphael Bessa Parmigiani

    Citation: BMC Medical Genomics 2014 7:68

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  50. Content type: Research article

    In developing countries, many cases with rare neurological diseases remain undiagnosed due to limited diagnostic experience. We encountered a case in China where two siblings both began to develop idiopathic p...

    Authors: Lingling Shi, Bingxiao Li, Yonglan Huang, Xueying Ling, Tianyun Liu, Gholson J Lyon, Anding Xu and Kai Wang

    Citation: BMC Medical Genomics 2014 7:66

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