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BMC Medical Genomics

Marwan M Refaat, Sylvana Hassanieh, Jad A Ballout, Patrick Zakka, Mostafa Hotait, Athar Khalil, Fadi Bitar, Mariam Arabi, Samir Arnaout, Hadi Skouri, Antoine Abchee, Bernard Abi-Saleh, Maurice Khoury, Andreas Massouras, Georges Nemer
BACKGROUND: Cardiomyopathies affect more than 0.5% of the general population. They are associated with high risk of sudden cardiac death, which can result from either heart failure or electrical abnormalities. Although different mechanisms underlie the various types of cardiomyopathies, a principal pathology is common to all and is usually at the level of the cardiac muscle. With a relatively high incidence rate in most countries, and a subsequent major health burden on both the families and governments, cardiomyopathies are gaining more attention by researchers and pharmaceutical companies as well as health government bodies...
February 14, 2019: BMC Medical Genomics
Miguel Nava, Pranabananda Dutta, Nathan R Zemke, Robin Farias-Eisner, Jaydutt V Vadgama, Yanyuan Wu
BACKGROUND: 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 heterodimerizes with other HER family members, such as HER2 (human epidermal growth factor receptor-2). Previously, we showed that the EGFR is upregulated in trastuzumab resistant HER2 positive (HER2+) breast cancer cells. This study is aimed to determine the downstream effects on transcription following EGFR upregulation in HER2+ breast cancer cells...
February 8, 2019: BMC Medical Genomics
Felicity Newell, Kalpana Patel, Michael Gartside, Lutz Krause, Sandra Brosda, Lauren G Aoude, Kelly A Loffler, Vanessa F Bonazzi, Ann-Marie Patch, Stephen H Kazakoff, Oliver Holmes, Qinying Xu, Scott Wood, Conrad Leonard, Guy Lampe, Reginald V Lord, David C Whiteman, John V Pearson, Katia Nones, Nicola Waddell, Andrew P Barbour
BACKGROUND: Oesophageal adenocarcinoma (EAC) incidence is increasing and has a poor survival rate. Barrett's oesophagus (BE) is a precursor condition that is associated with EAC and often occurs in conjunction with chronic gastro-oesophageal reflux, however many individuals diagnosed with BE never progress to cancer. An understanding of the genomic features of BE and EAC may help with the early identification of at-risk individuals. METHODS: In this study, we assessed the genomic features of 16 BE samples using whole-genome sequencing...
February 4, 2019: BMC Medical Genomics
Marta Olszewska, Ewa Wiland, Nataliya Huleyuk, Monika Fraczek, Alina T Midro, Danuta Zastavna, Maciej Kurpisz
BACKGROUND: Non-random chromosome positioning has been observed in the nuclei of several different tissue types, including human spermatozoa. The nuclear arrangement of chromosomes can be altered in men with decreased semen parameters or increased DNA fragmentation and in males with chromosomal numerical or structural aberrations. An aim of this study was to determine whether and how the positioning of nine chromosome centromeres was (re)arranged in the spermatozoa of fathers and sons - carriers of the same reciprocal chromosome translocation (RCT)...
February 1, 2019: BMC Medical Genomics
Degui Zhi, Zhongming Zhao, Fuhai Li, Zhijin Wu, Xiaoming Liu, Kai Wang
During June 10-12, 2018, the International Conference on Intelligent Biology and Medicine (ICIBM 2018) was held in Los Angeles, California, USA. The conference included 11 scientific sessions, four tutorials, one poster session, four keynote talks and four eminent scholar talks that covered a wide range of topics ranging from 3D genome structure analysis and visualization, next generation sequencing analysis, computational drug discovery, medical informatics, cancer genomics to systems biology. While medical genomics has always been a main theme in ICIBM, this year we for the first time organized the BMC Medical Genomics Supplement for ICIBM...
January 31, 2019: BMC Medical Genomics
Seonggyun Han, Jason E Miller, Seyoun Byun, Dokyoon Kim, Shannon L Risacher, Andrew J Saykin, Younghee Lee, Kwangsik Nho
BACKGROUND: At least 90% of human genes are alternatively spliced. Alternative splicing has an important function regulating gene expression and miss-splicing can contribute to risk for human diseases, including Alzheimer's disease (AD). METHODS: We developed a splicing decision model as a molecular mechanism to identify functional exon skipping events and genetic variation affecting alternative splicing on a genome-wide scale by integrating genomics, transcriptomics, and neuroimaging data in a systems biology approach...
January 31, 2019: BMC Medical Genomics
Fang Shi, Yao Yao, Yannan Bin, Chun-Hou Zheng, Junfeng Xia
BACKGROUND: Although synonymous single nucleotide variants (sSNVs) do not alter the protein sequences, they have been shown to play an important role in human disease. Distinguishing pathogenic sSNVs from neutral ones is challenging because pathogenic sSNVs tend to have low prevalence. Although many methods have been developed for predicting the functional impact of single nucleotide variants, only a few have been specifically designed for identifying pathogenic sSNVs. RESULTS: In this work, we describe a computational model, IDSV (Identification of Deleterious Synonymous Variants), which uses random forest (RF) to detect deleterious sSNVs in human genomes...
January 31, 2019: BMC Medical Genomics
William Z D Zeng, Benjamin S Glicksberg, Yangyan Li, Bin Chen
BACKGROUND: Normal tissue samples are often employed as a control for understanding disease mechanisms, however, collecting matched normal tissues from patients is difficult in many instances. In cancer research, for example, the open cancer resources such as TCGA and TARGET do not provide matched tissue samples for every cancer or cancer subtype. The recent GTEx project has profiled samples from healthy individuals, providing an excellent resource for this field, yet the feasibility of using GTEx samples as the reference remains unanswered...
January 31, 2019: BMC Medical Genomics
Aimin Li, Guimin Qin, Akiko Suzuki, Mona Gajera, Junichi Iwata, Peilin Jia, Zhongming Zhao
BACKGROUND: Cleft lip (CL) is one of the most common congenital birth defects with complex etiology. While genome-wide association studies (GWAS) have made significant advances in our understanding of mutations and their related genes with potential involvement in the etiology of CL, it remains unknown how these genes are functionally regulated and interact with each other in lip development. Currently, identifying the disease-causing genes in human CL is urgently needed. So far, the causative CL genes have been largely undiscovered, making it challenging to design experiments to validate the functional influence of the mutations identified from large genomic studies such as CL GWAS...
January 31, 2019: BMC Medical Genomics
Alice Djotsa Nono, Ken Chen, Xiaoming Liu
BACKGROUND: Identifying cancer driver genes (CDG) is a crucial step in cancer genomic toward the advancement of precision medicine. However, driver gene discovery is a very challenging task because we are not only dealing with huge amount of data; but we are also faced with the complexity of the disease including the heterogeneity of background somatic mutation rate in each cancer patient. It is generally accepted that CDG harbor variants conferring growth advantage in the malignant cell and they are positively selected, which are critical to cancer development; whereas, non-driver genes harbor random mutations with no functional consequence on cancer...
January 31, 2019: BMC Medical Genomics
Xueyan Zhao, Xin Geng, Vinodh Srinivasasainagendra, Ninad Chaudhary, Suzanne Judd, Virginia Wadley, Orlando M Gutiérrez, Henry Wang, Ethan M Lange, Leslie A Lange, Daniel Woo, Frederick W Unverzagt, Monika Safford, Mary Cushman, Nita Limdi, Rakale Quarells, Donna K Arnett, Marguerite R Irvin, Degui Zhi
BACKGROUND: Cardiovascular disease, diabetes, and kidney disease are among the leading causes of death and disability worldwide. However, knowledge of genetic determinants of those diseases in African Americans remains limited. RESULTS: In our study, associations between 4956 GWAS catalog reported SNPs and 67 traits were examined among 7726 African Americans from the REasons for Geographic and Racial Differences in Stroke (REGARDS) study, which is focused on identifying factors that increase stroke risk...
January 31, 2019: BMC Medical Genomics
Mahmoud M Mostafa, Christopher F Rider, Suharsh Shah, Suzanne L Traves, Paul M K Gordon, Anna Miller-Larsson, Richard Leigh, Robert Newton
BACKGROUND: Glucocorticoids act on the glucocorticoid receptor (GR; NR3C1) to resolve inflammation and, as inhaled corticosteroids (ICS), are the cornerstone of treatment for asthma. However, reduced efficacy in severe disease or exacerbations indicates a need to improve ICS actions. METHODS: Glucocorticoid-driven transcriptomes were compared using PrimeView microarrays between primary human bronchial epithelial (HBE) cells and the model cell lines, pulmonary type II A549 and bronchial epithelial BEAS-2B cells...
January 31, 2019: BMC Medical Genomics
Yang Chen, Rong Xu
BACKGROUND: Diet plays an important role in Alzheimer's disease (AD) initiation, progression and outcomes. Previous studies have shown individual food-derived substances may have neuroprotective or neurotoxic effects. However, few works systematically investigate the role of food and food-derived metabolites on the development and progression of AD. METHODS: In this study, we systematically investigated 7569 metabolites and identified AD-associated food metabolites using a novel network-based approach...
January 31, 2019: BMC Medical Genomics
Fan Zhang, Linda Ding, Li Cui, Robert Barber, Bin Deng
BACKGROUND: While changes in mRNA expression during tumorigenesis have been used widely as molecular biomarkers for the diagnosis of a number of cancers, the approach has limitations. For example, traditional methods do not consider the regulatory and positional relationship between mRNA and lncRNA. The latter has been largely shown to possess tumor suppressive or oncogenic properties. The combined analysis of mRNA and lncRNA is likely to facilitate the identification of biomarkers with higher confidence...
January 31, 2019: BMC Medical Genomics
Shicai Fan, Jianxiong Tang, Qi Tian, Chunguo Wu
BACKGROUND: Lots of researches have been conducted in the selection of gene signatures that could distinguish the cancer patients from the normal. However, it is still an open question on how to extract the robust gene features. METHODS: In this work, a gene signature selection strategy for TCGA data was proposed by integrating the gene expression data, the methylation data and the prior knowledge about cancer biomarkers. Different from the traditional integration method, the expanded 450 K methylation data were applied instead of the original 450 K array data, and the reported biomarkers were weighted in the feature selection...
January 31, 2019: BMC Medical Genomics
Yuchao Xia, Yun Liu, Minghua Deng, Ruibin Xi
BACKGROUND: Since tumor often has a high level of intra-tumor heterogeneity, multiple tumor samples from the same patient at different locations or different time points are often sequenced to study tumor intra-heterogeneity or tumor evolution. In virus-related tumors such as human papillomavirus- and Hepatitis B Virus-related tumors, virus genome integrations can be critical driving events. It is thus important to investigate the integration sites of the virus genomes. Currently, a few algorithms for detecting virus integration sites based on high-throughput sequencing have been developed, but their insufficient performance in their sensitivity, specificity and computational complexity hinders their applications in multiple related tumor sequencing...
January 31, 2019: BMC Medical Genomics
Lijun Cheng, Pankita H Pandya, Enze Liu, Pooja Chandra, Limei Wang, Mary E Murray, Jacquelyn Carter, Michael Ferguson, Mohammad Reza Saadatzadeh, Khadijeh Bijangi-Visheshsaraei, Mark Marshall, Lang Li, Karen E Pollok, Jamie L Renbarger
BACKGROUND: While most pediatric sarcomas respond to front-line therapy, some bone sarcomas do not show radiographic response like soft-tissue sarcomas (rhabdomyosarccomas) but do show 90% necrosis. Though, new therapies are urgently needed to improve survival and quality of life in pediatric patients with sarcomas. Complex chromosomal aberrations such as amplifications and deletions of DNA sequences are frequently observed in pediatric sarcomas. Evaluation of copy number variations (CNVs) associated with pediatric sarcoma patients at the time of diagnosis or following therapy offers an opportunity to assess dysregulated molecular targets and signaling pathways that may drive sarcoma development, progression, or relapse...
January 31, 2019: BMC Medical Genomics
Yu-Chiao Chiu, Hung-I Harry Chen, Tinghe Zhang, Songyao Zhang, Aparna Gorthi, Li-Ju Wang, Yufei Huang, Yidong Chen
BACKGROUND: The study of high-throughput genomic profiles from a pharmacogenomics viewpoint has provided unprecedented insights into the oncogenic features modulating drug response. A recent study screened for the response of a thousand human cancer cell lines to a wide collection of anti-cancer drugs and illuminated the link between cellular genotypes and vulnerability. However, due to essential differences between cell lines and tumors, to date the translation into predicting drug response in tumors remains challenging...
January 31, 2019: BMC Medical Genomics
Yixuan Wang, Xuanping Zhang, Shuai Ding, Yu Geng, Jianye Liu, Zhongmeng Zhao, Rong Zhang, Xiao Xiao, Jiayin Wang
BACKGROUND: Haplotype phasing is an important step in many bioinformatics workflows. In cancer genomics, it is suggested that reconstructing the clonal haplotypes of a tumor sample could facilitate a comprehensive understanding of its clonal architecture and further provide valuable reference in clinical diagnosis and treatment. However, the sequencing data is an admixture of reads sampled from different clonal haplotypes, which complicates the computational problem by exponentially increasing the solution-space and leads the existing algorithms to an unacceptable time-/space- complexity...
January 31, 2019: BMC Medical Genomics
Mark Menor, Yong Zhu, Yu Wang, Jicai Zhang, Bin Jiang, Youping Deng
BACKGROUND: Prognostic signatures are vital to precision medicine. However, development of somatic mutation prognostic signatures for cancers remains a challenge. In this study we developed a novel method for discovering somatic mutation based prognostic signatures. RESULTS: Somatic mutation and clinical data for lung adenocarcinoma (LUAD) and colorectal adenocarcinoma (COAD) from The Cancer Genome Atlas (TCGA) were randomly divided into training (n = 328 for LUAD and 286 for COAD) and validation (n = 167 for LUAD and 141 for COAD) datasets...
January 31, 2019: BMC Medical Genomics
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