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Functional and structural genomics

Section edited by Kun Huang

This section considers studies of change in the expression and regulation of genes and genomes conducted at a genomic scale in relation to health and disease states.

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  1. Copy number variants (CNVs) have been reported to be associated with diseases, traits, and evolution. However, it is hard to determine which gene should have priority as a target for further functional experim...

    Authors: Maria Yamasaki, Takashi Makino, Seik-Soon Khor, Hiromi Toyoda, Taku Miyagawa, Xiaoxi Liu, Hitoshi Kuwabara, Yukiko Kano, Takafumi Shimada, Toshiro Sugiyama, Hisami Nishida, Nagisa Sugaya, Mamoru Tochigi, Takeshi Otowa, Yuji Okazaki, Hisanobu Kaiya…

    Citation: BMC Medical Genomics 2020 13:55

    Content type: Research article

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  2. Autism is a complex disease involving both environmental and genetic factors. Recent efforts have implicated the correlation of genomic imprinting and brain development in autism, however the pathogenesis of a...

    Authors: Jian Li, Xue Lin, Mingya Wang, Yunyun Hu, Kaiyu Xue, Shuanglin Gu, Li Lv, Saijun Huang and Wei Xie

    Citation: BMC Medical Genomics 2020 13:54

    Content type: Research article

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  3. The human papillomaviruses (HPV) are a group of viruses that, depending on the strain, can cause cancer or the formation of benign growths known as warts. Scarce information exists with regard to the genetic n...

    Authors: Laith N. AL-Eitan, Amneh H. Tarkhan, Mansour A. Alghamdi, Firas A. Al-Qarqaz and Hadeel S. Al-Kofahi

    Citation: BMC Medical Genomics 2020 13:35

    Content type: Research article

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  4. Application of whole genome sequencing (WGS) enables identification of non-coding variants that play a phenotype-modifying role and are undetectable by exome sequencing. Recently, non-coding regulatory single ...

    Authors: Justyna A. Karolak, Tomasz Gambin, Engela M. Honey, Tomas Slavik, Edwina Popek and Paweł Stankiewicz

    Citation: BMC Medical Genomics 2020 13:34

    Content type: Case report

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  5. Few somatic mutations have been linked to breast cancer metastasis, whereas transcriptomic differences among primary tumors correlate with incidence of metastasis, especially to the lungs and brain. However, t...

    Authors: Wesley L. Cai, Celeste B. Greer, Jocelyn F. Chen, Anna Arnal-Estapé, Jian Cao, Qin Yan and Don X. Nguyen

    Citation: BMC Medical Genomics 2020 13:33

    Content type: Research article

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  6. Chromosome deletions of the long arm of chromosome 4 in 4q syndrome are characterized by mild facial and digital dysmorphism, developmental delay, growth retardation, and skeletal and cardiac anomalies, which ...

    Authors: Maolan Wu, Xiangrong Zheng, Xia Wang, Guoyuan Zhang and Jian Kuang

    Citation: BMC Medical Genomics 2020 13:31

    Content type: Case report

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  7. Kidney transplantation is the most effective treatment for end-stage renal disease. Allograft rejections severely affect survivals of allograft kidneys and recipients.

    Authors: Mei Meng, Weitao Zhang, Qunye Tang, Baixue Yu, Tingting Li, Ruiming Rong, Tongyu Zhu, Ming Xu and Yi Shi

    Citation: BMC Medical Genomics 2020 13:24

    Content type: Research article

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  8. The survival of INA-6 human multiple myeloma cells is strictly dependent upon the Interleukin-6-activated transcription factor STAT3. Although transcriptional analyses have revealed many genes regulated by STA...

    Authors: Stefanie Binder, Ivonne Zipfel, Maik Friedrich, Diana Riedel, Stefanie Ende, Christoph Kämpf, Karolin Wiedemann, Tilo Buschmann, Sven-Holger Puppel, Kristin Reiche, Peter F. Stadler and Friedemann Horn

    Citation: BMC Medical Genomics 2020 13:22

    Content type: Research article

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  9. Coeliac disease (CD) is a autoimmune disease characterised by mucosal inflammation in the small intestine in response to dietary gluten. Genetic factors play a key role with CD individuals carrying either the ...

    Authors: Nerissa L. Hearn, Christine L. Chiu and Joanne M. Lind

    Citation: BMC Medical Genomics 2020 13:16

    Content type: Research article

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  10. Rhodesiense sleeping sickness is caused by infection with T. b rhodesiense parasites resulting in an acute disease that is fatal if not treated in time. The aim of this study was to understand the global impact o...

    Authors: Julius Mulindwa, Enock Matovu, John Enyaru and Christine Clayton

    Citation: BMC Medical Genomics 2020 13:14

    Content type: Research article

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  11. Multiple acyl-CoA dehydrogenase deficiency (MADD), previously called glutaric aciduria type II, is a rare congenital metabolic disorder of fatty acids and amino acids oxidation, with recessive autosomal transm...

    Authors: Robin Chautard, Cécile Laroche-Raynaud, Anne-Sophie Lia, Pauline Chazelas, Paco Derouault, Franck Sturtz, Yasser Baaj, Alice Veauville-Merllié, Cécile Acquaviva, Frédéric Favreau and Pierre-Antoine Faye

    Citation: BMC Medical Genomics 2020 13:12

    Content type: Case report

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  12. Psoriasis is a chronic inflammatory skin disease, for which genome-wide association studies (GWAS) have identified many genetic variants as risk markers. However, the details of underlying molecular mechanisms...

    Authors: Naoto Kubota and Mikita Suyama

    Citation: BMC Medical Genomics 2020 13:8

    Content type: Research article

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  13. Prostate cancer (PCa) has the highest incidence rates of cancers in men in western countries. Unlike several other types of cancer, PCa has few genetic drivers, which has led researchers to look for additional...

    Authors: Ieva Rauluseviciute, Finn Drabløs and Morten Beck Rye

    Citation: BMC Medical Genomics 2020 13:6

    Content type: Research article

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  14. 12q14 microdeletion syndrome is characterized by low birth weight and failure to thrive, proportionate short stature and developmental delay. The opposite syndrome (microduplication) has not yet been character...

    Authors: Sofia Dória, Daniela Alves, Maria João Pinho, Joel Pinto and Miguel Leão

    Citation: BMC Medical Genomics 2020 13:2

    Content type: Case report

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  15. Systemic sclerosis (SSc), a multi-organ disorder, is characterized by vascular abnormalities, dysregulation of the immune system, and fibrosis. The mechanisms underlying tissue pathology in SSc have not been e...

    Authors: Elham Karimizadeh, Ali Sharifi-Zarchi, Hassan Nikaein, Seyedehsaba Salehi, Bahar Salamatian, Naser Elmi, Farhad Gharibdoost and Mahdi Mahmoudi

    Citation: BMC Medical Genomics 2019 12:199

    Content type: Research article

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  16. Trisomy 8 mosaicism has a wide phenotypic variability, ranging from mild dysmorphic features to severe malformations. This report concluded a female pregnant woman with trisomy 8 mosaicism, and carefully cytog...

    Authors: Shaohua Sun, Fang Zhan, Jiusheng Jiang, Xuerui Zhang, Lei Yan, Weiyi Cai, Hailiang Liu and Donghua Cao

    Citation: BMC Medical Genomics 2019 12:197

    Content type: Case report

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  17. Psoriasis is a chronic inflammatory skin disease characterized by hyperproliferation and abnormal differentiation of keratinocytes. It is one of the most prevalent chronic inflammatory skin conditions in adult...

    Authors: Liviu-Ionut Moldovan, Thomas Birkballe Hansen, Morten Trillingsgaard Venø, Trine Line Hauge Okholm, Thomas Levin Andersen, Henrik Hager, Lars Iversen, Jørgen Kjems, Claus Johansen and Lasse Sommer Kristensen

    Citation: BMC Medical Genomics 2019 12:174

    Content type: Research article

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  18. Since 1969, 49 cases have been presented on ring chromosome 4. All of these cases have been characterized for the loss of genetic material. The genes located in these chromosomal regions are related to the phe...

    Authors: César Paz-y-Miño, Ana Proaño, Stella D. Verdezoto, Juan Luis García, Jesús María Hernández-Rivas and Paola E. Leone

    Citation: BMC Medical Genomics 2019 12:167

    Content type: Case report

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  19. Hepatocellular carcinoma (HCC) is the major type of primary liver cancer. Intrahepatic metastasis, such as portal vein tumor thrombosis (PVTT), strongly indicates poor prognosis of HCC. But now, there are limi...

    Authors: Dongfang Wang, Yanjing Zhu, Jing Tang, Qiuyu Lian, Guijuan Luo, Wen Wen, Michael Q. Zhang, Hongyang Wang, Lei Chen and Jin Gu

    Citation: BMC Medical Genomics 2019 12:164

    Content type: Research article

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  20. Genetics play an important role in intracranial aneurysm (IA) pathophysiology. Genome-wide association studies have identified several single nucleotide polymorphisms (SNPs) that are linked to IA but how they ...

    Authors: Kerry E. Poppenberg, Kaiyu Jiang, Michael K. Tso, Kenneth V. Snyder, Adnan H. Siddiqui, John Kolega, James N. Jarvis, Hui Meng and Vincent M. Tutino

    Citation: BMC Medical Genomics 2019 12:149

    Content type: Research article

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  21. Bleomycin, etoposide and cisplatin (BEP) are three chemotherapeutic agents widely used individually or in combination with each other or other chemotherapeutic agents in the treatment of various cancers. These...

    Authors: Prabin Upadhyaya, Alessandra Di Serafino, Luca Sorino, Patrizia Ballerini, Marco Marchisio, Laura Pierdomenico, Liborio Stuppia and Ivana Antonucci

    Citation: BMC Medical Genomics 2019 12:146

    Content type: Research article

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  22. Wild-type (wt) polyglutamine (polyQ) regions are implicated in stabilization of protein-protein interactions (PPI). Pathological polyQ expansion, such as that in human Ataxin-1 (ATXN1), that causes spinocerebe...

    Authors: Sara Rocha, Jorge Vieira, Noé Vázquez, Hugo López-Fernández, Florentino Fdez-Riverola, Miguel Reboiro-Jato, André D. Sousa and Cristina P. Vieira

    Citation: BMC Medical Genomics 2019 12:145

    Content type: Research article

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  23. Healthcare providers increasingly use information about pathogenic variants in cancer predisposition genes, including sequence variants and large rearrangements (LRs), in medical management decisions. While se...

    Authors: Debora Mancini-DiNardo, Thaddeus Judkins, John Kidd, Ryan Bernhisel, Courtney Daniels, Krystal Brown, Kirsten Meek, Jonathan Craft, Jayson Holladay, Brian Morris and Benjamin B. Roa

    Citation: BMC Medical Genomics 2019 12:138

    Content type: Research article

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  24. The mechanisms underlying neurodegeneration in the striatum of Huntingon’s Disease (HD) brain are currently unknown. While the striatum is massively degenerated in symptomatic individuals, which makes cellular...

    Authors: Filisia Agus, Diego Crespo, Richard H. Myers and Adam Labadorf

    Citation: BMC Medical Genomics 2019 12:137

    Content type: Research Article

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  25. Diabetic retinopathy (DR) is the leading cause of blindness in the working age population. Transthyretin (TTR) showed a significantly decreased concentration in DR patients and exerted a visual protective effe...

    Authors: Jun Shao, Yunbin Zhang, Guangming Fan, Yu Xin and Yong Yao

    Citation: BMC Medical Genomics 2019 12:134

    Content type: Research article

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  26. Genome-wide association studies (GWASs) have identified single-nucleotide polymorphisms (SNPs) that may be genetic factors underlying Alzheimer’s disease (AD). However, how these AD-associated SNPs (AD SNPs) c...

    Authors: Masataka Kikuchi, Norikazu Hara, Mai Hasegawa, Akinori Miyashita, Ryozo Kuwano, Takeshi Ikeuchi and Akihiro Nakaya

    Citation: BMC Medical Genomics 2019 12:128

    Content type: Research article

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  27. Burkholderia mallei (Bm) is a facultative intracellular bacterial pathogen causing highly-fatal glanders in solipeds and humans. The ability of Bm to thrive intracellularly is thought to be related to exploitatio...

    Authors: Sophie A. Aschenbroich, Eric R. Lafontaine, Maria Cecilia Lopez, Henry V. Baker and Robert J. Hogan

    Citation: BMC Medical Genomics 2019 12:127

    Content type: Research article

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  28. Identifying molecular biomarkers characteristic of ischemic stroke has the potential to aid in distinguishing stroke cases from stroke mimicking symptoms, as well as advancing the understanding of the physiolo...

    Authors: Konstantinos Theofilatos, Aigli Korfiati, Seferina Mavroudi, Matthew C. Cowperthwaite and Max Shpak

    Citation: BMC Medical Genomics 2019 12:118

    Content type: Research article

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  29. Balanced structural variants are mostly described in disease with gene disruption or subtle rearrangement at breakpoints.

    Authors: Kevin Yauy, Anouck Schneider, Bee Ling Ng, Jean-Baptiste Gaillard, Satish Sati, Christine Coubes, Constance Wells, Magali Tournaire, Thomas Guignard, Pauline Bouret, David Geneviève, Jacques Puechberty, Franck Pellestor and Vincent Gatinois

    Citation: BMC Medical Genomics 2019 12:116

    Content type: Case report

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  30. Population studies suggest that genetic factors play an important role in refractive error development; however, the precise role of genetic background and the composition of the signaling pathways underlying ...

    Authors: Tatiana V. Tkatchenko, Rupal L. Shah, Takayuki Nagasaki and Andrei V. Tkatchenko

    Citation: BMC Medical Genomics 2019 12:113

    Content type: Research article

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  31. Synthetic lethal interactions (SLIs) that occur between gene pairs are exploited for cancer therapeutics. Studies in the model eukaryote yeast have identified ~ 550,000 negative genetic interactions that have ...

    Authors: Morgan W. B. Kirzinger, Frederick S. Vizeacoumar, Bjorn Haave, Cristina Gonzalez-Lopez, Keith Bonham, Anthony Kusalik and Franco J. Vizeacoumar

    Citation: BMC Medical Genomics 2019 12:112

    Content type: Research article

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  32. A normally developed placenta is integral to a successful pregnancy. Preeclampsia (PE) and intrauterine growth restriction (IUGR) are two common pregnancy related complications that maybe a result of abnormal ...

    Authors: Zain Awamleh, Gregory B. Gloor and Victor K. M. Han

    Citation: BMC Medical Genomics 2019 12:91

    Content type: Research article

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  33. Gastric emptying is impaired in patients with gastroparesis whereas it is either unchanged or accelerated in obese individuals. The goal of the current study was to identify changes in gene expression in the s...

    Authors: B. Paul Herring, Meng Chen, Plamen Mihaylov, April M. Hoggatt, Anita Gupta, Attila Nakeeb, Jennifer N. Choi and John M. Wo

    Citation: BMC Medical Genomics 2019 12:89

    Content type: Research article

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  34. Large granular lymphocyte (LGL) leukemia is an uncommon cancer characterized by sustained clonal proliferation of LGL cells. Antibodies reactive to retroviruses have been documented in the serum of patients wi...

    Authors: Weiling Li, Lei Yang, Robert S. Harris, Lin Lin, Thomas L. Olson, Cait E. Hamele, David J. Feith, Thomas P. Loughran Jr and Mary Poss

    Citation: BMC Medical Genomics 2019 12:88

    Content type: Research article

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  35. The vast majority of cases with Beckwith-Wiedemann syndrome (BWS) are caused by a molecular defect in the imprinted chromosome region 11p15.5. The underlying mechanisms include epimutations, uniparental disomy...

    Authors: Caroline Lekszas, Indrajit Nanda, Barbara Vona, Julia Böck, Farah Ashrafzadeh, Nahid Donyadideh, Farnoosh Ebrahimzadeh, Najmeh Ahangari, Reza Maroofian, Ehsan Ghayoor Karimiani and Thomas Haaf

    Citation: BMC Medical Genomics 2019 12:83

    Content type: Case report

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  36. Clinical data identified an association between the use of HMG-CoA reductase inhibitors (statins) and incident diabetes in patients with underlying diabetes risk factors such as obesity, hypertension and dysli...

    Authors: Daniel Margerie, Philippe Lefebvre, Violeta Raverdy, Uwe Schwahn, Hartmut Ruetten, Philip Larsen, Alain Duhamel, Julien Labreuche, Dorothée Thuillier, Bruno Derudas, Céline Gheeraert, Hélène Dehondt, Quentin Dhalluin, Jérémy Alexandre, Robert Caiazzo, Pamela Nesslany…

    Citation: BMC Medical Genomics 2019 12:80

    Content type: Research article

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  37. Intra-tumor heterogeneity stems from genetic, epigenetic, functional, and environmental differences among tumor cells. A major source of genetic heterogeneity comes from DNA sequence differences and/or whole c...

    Authors: Yanding Zhao, Robert Carter, Sivaraman Natarajan, Frederick S. Varn, Duane A. Compton, Charles Gawad, Chao Cheng and Kristina M. Godek

    Citation: BMC Medical Genomics 2019 12:79

    Content type: Research article

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  38. The co-occurrence of multiple de novo copy number variations (CNVs) is a rare phenomenon in the human genome. Recently, an “organismal CNV mutator phenotype” has been reported to result in transient genomic in...

    Authors: Atsushi Hattori, Kohji Okamura, Yumiko Terada, Rika Tanaka, Yuko Katoh-Fukui, Yoichi Matsubara, Keiko Matsubara, Masayo Kagami, Reiko Horikawa and Maki Fukami

    Citation: BMC Medical Genomics 2019 12:77

    Content type: Research article

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  39. Mexico is among the countries showing the highest heterogeneity of CFTR variants. However, no de novo variants have previously been reported in Mexican patients with cystic fibrosis (CF).

    Authors: Angélica Martínez-Hernández, Julieta Larrosa, Francisco Barajas-Olmos, Humberto García-Ortíz, Elvia C. Mendoza-Caamal, Cecilia Contreras-Cubas, Elaheh Mirzaeicheshmeh, José Luis Lezana and Lorena Orozco

    Citation: BMC Medical Genomics 2019 12:68

    Content type: Case report

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  40. Chemoresistance is a primary clinical challenge for the management of small cell lung cancer. Additionally, transcriptional regulation by super enhancer (SE) has an important role in tumor evolution. The funct...

    Authors: Jiarong Bao, Man Li, Shumei Liang, Yunchu Yang, Jingfang Wu, Qingqing Zou, Shun Fang, Size Chen and Linlang Guo

    Citation: BMC Medical Genomics 2019 12:67

    Content type: Research article

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  41. In cystic fibrosis (CF), impaired immune cell responses, driven by the dysfunctional CF transmembrane conductance regulator (CFTR) gene, may determine the disease severity but clinical heterogeneity remains a maj...

    Authors: Justin E. Ideozu, Vittobai Rangaraj, Hiam Abdala-Valencia, Xi Zhang, Manoj Kandpal, Marc A. Sala, Ramana V. Davuluri and Hara Levy

    Citation: BMC Medical Genomics 2019 12:66

    Content type: Research article

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  42. Transcriptome wide changes have been assessed extensively during the progression of neurodegenerative diseases. Alternative polyadenylation (APA) occurs in over 70% of human protein coding genes and it has rec...

    Authors: Radhika Patel, Cillian Brophy, Mark Hickling, Jonathan Neve and André Furger

    Citation: BMC Medical Genomics 2019 12:60

    Content type: Research article

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  43. Endometrial cancer (EMCA) is the fifth most common cancer among women in the world. Identification of potentially pathogenic germline variants from individuals with EMCA will help characterize genetic features...

    Authors: Jason E. Miller, Raghu P. Metpally, Thomas N. Person, Sarathbabu Krishnamurthy, Venkata Ramesh Dasari, Manu Shivakumar, Daniel R. Lavage, Adam M. Cook, David J. Carey, Marylyn D. Ritchie, Dokyoon Kim and Radhika Gogoi

    Citation: BMC Medical Genomics 2019 12:59

    Content type: Research article

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    The Correction to this article has been published in BMC Medical Genomics 2019 12:65

  44. Human Endogenous Retroviruses type K HML-2 (HK2) are integrated into 117 or more areas of human chromosomal arms while two newly discovered HK2 proviruses, K111 and K222, spread extensively in pericentromeric ...

    Authors: Mark H. Kaplan, Mark Kaminski, Judith M. Estes, Scott D. Gitlin, Joseph Zahn, James T. Elder, Trilokraj Tejasvi, Elizabeth Gensterblum, Amr H. Sawalha, Joseph Patrick McGowan, Michael H. Dosik, Haner Direskeneli, Guher Saruhan Direskeneli, Sally N. Adebamowo, Clement A. Adebamowo, Mohammad Sajadi…

    Citation: BMC Medical Genomics 2019 12:58

    Content type: Research article

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  45. Prompted by the revolution in high-throughput sequencing and its potential impact for treating cancer patients, we initiated a clinical research study to compare the ability of different sequencing assays and ...

    Authors: Mayu O. Frank, Takahiko Koyama, Kahn Rhrissorrakrai, Nicolas Robine, Filippo Utro, Anne-Katrin Emde, Bo-Juen Chen, Kanika Arora, Minita Shah, Heather Geiger, Vanessa Felice, Esra Dikoglu, Sadia Rahman, Alice Fang, Vladimir Vacic, Ewa A. Bergmann…

    Citation: BMC Medical Genomics 2019 12:56

    Content type: Research article

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    The Correction to this article has been published in BMC Medical Genomics 2019 12:114

  46. Preterm birth (PTB), defined as infant delivery before 37 weeks of completed gestation, results from the interaction of both genetic and environmental components and constitutes a complex multifactorial syndro...

    Authors: Silvana Pereyra, Claudio Sosa, Bernardo Bertoni and Rossana Sapiro

    Citation: BMC Medical Genomics 2019 12:53

    Content type: Research article

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