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    824 results match your criteria BMC Medical Genomics [Journal]

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    Application of Neural Networks for classification of Patau, Edwards, Down, Turner and Klinefelter Syndrome based on first trimester maternal serum screening data, ultrasonographic findings and patient demographics.
    BMC Med Genomics 2018 Feb 13;11(1):19. Epub 2018 Feb 13.
    Department of Genetics and Bioengineering, International Burch University, Francuske revolucije bb, Ilidza, 71210, Sarajevo, Bosnia and Herzegovina.
    Background: The usage of Artificial Neural Networks (ANNs) for genome-enabled classifications and establishing genome-phenotype correlations have been investigated more extensively over the past few years. The reason for this is that ANNs are good approximates of complex functions, so classification can be performed without the need for explicitly defined input-output model. This engineering tool can be applied for optimization of existing methods for disease/syndrome classification. Read More

    Adopting clinical genomics: a systematic review of genomic literacy among physicians in cancer care.
    BMC Med Genomics 2018 Feb 13;11(1):18. Epub 2018 Feb 13.
    Simon Fraser University, K8666, Shrum Science Building, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada.
    Background: This article investigates the genomic knowledge of oncology care physicians in the adoption of clinical genomics. We apply Rogers' knowledge framework from his diffusion of innovation theory to identify three types of knowledge in the process of translation and adoption: awareness, how-to, and principles knowledge. The objectives of this systematic review are to: (1) examine the level of knowledge among physicians in clinical cancer genomics, and (2) identify potential interventions or strategies for development of genomic education for oncology practice. Read More

    Unearthing new genomic markers of drug response by improved measurement of discriminative power.
    BMC Med Genomics 2018 Feb 6;11(1):10. Epub 2018 Feb 6.
    Cancer Research Center of Marseille, INSERM U1068, F-13009, Marseille, France.
    Background: Oncology drugs are only effective in a small proportion of cancer patients. Our current ability to identify these responsive patients before treatment is still poor in most cases. Thus, there is a pressing need to discover response markers for marketed and research oncology drugs. Read More

    Methylation of the genes ROD1, NLRC5, and HKR1 is associated with aging in Hainan centenarians.
    BMC Med Genomics 2018 Feb 2;11(1). Epub 2018 Feb 2.
    Hainan branch of PLA General Hospital, Sanya, 572000, China.
    Background: Human aging is a hot topic in biology, and it has been associated with DNA methylation changes at specific genomic sites. We aimed to study the changes of DNA methylation at a single-CpG-site resolution using peripheral blood samples from centenarians.

    Methods: Using Illumina 450 K Methylation BeadChip microarray assays, we carried out a pool-based, epigenome-wide investigation of DNA methylation of blood samples from 12 centenarians and 12 healthy controls. Read More

    Efficient strategy for the molecular diagnosis of intractable early-onset epilepsy using targeted gene sequencing.
    BMC Med Genomics 2018 Feb 1;11(1). Epub 2018 Feb 1.
    Divison of Pediatric Neurology, Department of Pediatrics, Severance Children's Hospital, Yonsei University College of Medicine, Epilepsy Research Institute, 50-1 Yonsei-ro, Seodaemun-Gu, Seoul, 03722, South Korea.
    Background: We intended to evaluate diagnostic utility of a targeted gene sequencing by using next generation sequencing (NGS) panel in patients with intractable early-onset epilepsy (EOE) and find the efficient analytical step for increasing the diagnosis rate.

    Methods: We assessed 74 patients with EOE whose seizures started before 3 years of age using a customized NGS panel that included 172 genes. Single nucleotide variants (SNVs) and exonic and chromosomal copy number variations (CNVs) were intensively examined with our customized pipeline and crosschecked with commercial or pre-built software. Read More

    Impacts of incorporating personal genome sequencing into graduate genomics education: a longitudinal study over three course years.
    BMC Med Genomics 2018 Jan 30;11(1). Epub 2018 Jan 30.
    Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
    Background: To address the need for more effective genomics training, beginning in 2012 the Icahn School of Medicine at Mount Sinai has offered a unique laboratory-style graduate genomics course, "Practical Analysis of Your Personal Genome" (PAPG), in which students optionally sequence and analyze their own whole genome. We hypothesized that incorporating personal genome sequencing (PGS) into the course pedagogy could improve educational outcomes by increasing student motivation and engagement. Here we extend our initial study of the pilot PAPG cohort with a report on student attitudes towards genome sequencing, decision-making, psychological wellbeing, genomics knowledge and pedagogical engagement across three course years. Read More

    Deleterious genetic variants in ciliopathy genes increase risk of ritodrine-induced cardiac and pulmonary side effects.
    BMC Med Genomics 2018 Jan 24;11(1). Epub 2018 Jan 24.
    Department of Obstetrics and Gynecology, College of Medicine, Ewha Womans University Mok Dong Hospital, Seoul, 07985, Korea.
    Background: 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 whether such adverse reactions are associated with pharmacogenomic variants in patients. Read More

    Are minor alleles more likely to be risk alleles?
    BMC Med Genomics 2018 Jan 19;11(1). Epub 2018 Jan 19.
    Institute for Computational Health Sciences, University of California, 550 16th Street, San Francisco, CA, 94158, USA.
    Background: Genome-wide association studies (GWASs) have revealed relationships between over 57,000 genetic variants and diseases. However, unlike Mendelian diseases, complex diseases arise from the interplay of multiple genetic and environmental factors. Natural selection has led to a high tendency of risk alleles to be enriched in minor alleles in Mendelian diseases. Read More

    Insights into the genetics of blood pressure in black South African individuals: the Birth to Twenty cohort.
    BMC Med Genomics 2018 Jan 17;11(1). Epub 2018 Jan 17.
    School of Molecular & Cell Biology, Faculty of Science, University of the Witwatersrand, Johannesburg, South Africa.
    Background: Cardiovascular diseases (CVDs) are the leading cause of non-communicable disease deaths globally, with hypertension being a major risk factor contributing to CVDs. Blood pressure is a heritable trait, with relatively few genetic studies having been performed in Africans. This study aimed to identify genetic variants associated with variance in systolic (SBP) and diastolic (DBP) blood pressure in black South Africans. Read More

    Peripheral blood gene expression signatures which reflect smoking and aspirin exposure are associated with cardiovascular events.
    BMC Med Genomics 2018 Jan 12;11(1). Epub 2018 Jan 12.
    Center for Applied Genomics & Precision Medicine, Department of Medicine, Duke University, 101 Science Drive, 2187 CIEMAS, Durham, NC, 27708, UK.
    Background: 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 the molecular underpinnings of risk factors for cardiovascular events. Smoking and aspirin have known opposing effects on platelet reactivity and MACE, however their effects on each other and on MACE are not well described. Read More

    Predicting binary, discrete and continued lncRNA-disease associations via a unified framework based on graph regression.
    BMC Med Genomics 2017 Dec 21;10(Suppl 4):65. Epub 2017 Dec 21.
    Department of Computer Science, the University of Hong Kong, Hong Kong, 999077, China.
    Background: In human genomes, long non-coding RNAs (lncRNAs) have attracted more and more attention because their dysfunctions are involved in many diseases. However, the associations between lncRNAs and diseases (LDA) still remain unknown in most cases. While identifying disease-related lncRNAs in vivo is costly, computational approaches are promising to not only accelerate the possible identification of associations but also provide clues on the underlying mechanism of various lncRNA-caused diseases. Read More

    Classifying cancer genome aberrations by their mutually exclusive effects on transcription.
    BMC Med Genomics 2017 Dec 21;10(Suppl 4):66. Epub 2017 Dec 21.
    Department of Biology, Brigham Young University, Provo, UT, 84602, USA.
    Background: Malignant tumors are typically caused by a conglomeration of genomic aberrations-including point mutations, small insertions, small deletions, and large copy-number variations. In some cases, specific chemotherapies and targeted drug treatments are effective against tumors that harbor certain genomic aberrations. However, predictive aberrations (biomarkers) have not been identified for many tumor types and treatments. Read More

    Identification of prognostic signature in cancer based on DNA methylation interaction network.
    BMC Med Genomics 2017 Dec 21;10(Suppl 4):63. Epub 2017 Dec 21.
    College of Informatics, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.
    Background: The identification of prognostic biomarkers for cancer patients is essential for cancer research. These days, DNA methylation has been proved to be associated with cancer prognosis. However, there are few methods which identify the prognostic markers based on DNA methylation data systematically, especially considering the interaction among DNA methylation sites. Read More

    Differential responses of innate immunity triggered by different subtypes of influenza a viruses in human and avian hosts.
    BMC Med Genomics 2017 Dec 21;10(Suppl 4):70. Epub 2017 Dec 21.
    Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, University of Chinese Academy of Sciences, Shanghai, China.
    Background: Innate immunity provides first line of defense against viral infections. The interactions between hosts and influenza A virus and the response of host innate immunity to viral infection are critical determinants for the pathogenicity or virulence of influenza A viruses. This study was designed to investigate global changes of gene expression and detailed responses of innate immune systems in human and avian hosts during the course of infection with various subtypes of influenza A viruses, using collected and self-generated transcriptome sequencing data from human bronchial epithelial (HBE), human tracheobronchial epithelial (HTBE), and A549 cells infected with influenza A virus subtypes, namely H1N1, H3N2, H5N1 HALo mutant, and H7N9, and from ileum and lung of chicken and quail infected with H5N1, or H5N2. Read More

    Subtype identification from heterogeneous TCGA datasets on a genomic scale by multi-view clustering with enhanced consensus.
    BMC Med Genomics 2017 Dec 21;10(Suppl 4):75. Epub 2017 Dec 21.
    School of Mathematics and Statistics, Xi'an Jiaotong University, Xianning West 28, Xi'an, China.
    Background: The Cancer Genome Atlas (TCGA) has collected transcriptome, genome and epigenome information for over 20 cancers from thousands of patients. The availability of these diverse data types makes it necessary to combine these data to capture the heterogeneity of biological processes and phenotypes and further identify homogeneous subtypes for cancers such as breast cancer. Many multi-view clustering approaches are proposed to discover clusters across different data types. Read More

    Analysis of viral diversity for vaccine target discovery.
    BMC Med Genomics 2017 Dec 21;10(Suppl 4):78. Epub 2017 Dec 21.
    Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD, 21205, USA.
    Background: Viral vaccine target discovery requires understanding the diversity of both the virus and the human immune system. The readily available and rapidly growing pool of viral sequence data in the public domain enable the identification and characterization of immune targets relevant to adaptive immunity. A systematic bioinformatics approach is necessary to facilitate the analysis of such large datasets for selection of potential candidate vaccine targets. Read More

    Tensor decomposition-based unsupervised feature extraction identifies candidate genes that induce post-traumatic stress disorder-mediated heart diseases.
    BMC Med Genomics 2017 Dec 21;10(Suppl 4):67. Epub 2017 Dec 21.
    Department of Physics, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo, 112-8551, Japan.
    Background: Although post-traumatic stress disorder (PTSD) is primarily a mental disorder, it can cause additional symptoms that do not seem to be directly related to the central nervous system, which PTSD is assumed to directly affect. PTSD-mediated heart diseases are some of such secondary disorders. In spite of the significant correlations between PTSD and heart diseases, spatial separation between the heart and brain (where PTSD is primarily active) prevents researchers from elucidating the mechanisms that bridge the two disorders. Read More

    Predicting drug-disease interactions by semi-supervised graph cut algorithm and three-layer data integration.
    BMC Med Genomics 2017 Dec 28;10(Suppl 5):79. Epub 2017 Dec 28.
    State Key Laboratory of Software Engineering, School of Computer Science, Wuhan University, Wuhan, 430072, People's Republic of China.
    Background: Prediction of drug-disease interactions is promising for either drug repositioning or disease treatment fields. The discovery of novel drug-disease interactions, on one hand can help to find novel indictions for the approved drugs; on the other hand can provide new therapeutic approaches for the diseases. Recently, computational methods for finding drug-disease interactions have attracted lots of attention because of their far more higher efficiency and lower cost than the traditional wet experiment methods. Read More

    Reverse-engineering of gene networks for regulating early blood development from single-cell measurements.
    BMC Med Genomics 2017 Dec 28;10(Suppl 5):72. Epub 2017 Dec 28.
    School of Mathematical Sciences, Monash University, Melbourne, VIC 3800, Australia.
    Background: Recent advances in omics technologies have raised great opportunities to study large-scale regulatory networks inside the cell. In addition, single-cell experiments have measured the gene and protein activities in a large number of cells under the same experimental conditions. However, a significant challenge in computational biology and bioinformatics is how to derive quantitative information from the single-cell observations and how to develop sophisticated mathematical models to describe the dynamic properties of regulatory networks using the derived quantitative information. Read More

    Disease named entity recognition from biomedical literature using a novel convolutional neural network.
    BMC Med Genomics 2017 Dec 28;10(Suppl 5):73. Epub 2017 Dec 28.
    College of Computer Science and Technology, Dalian University of Technology, Dalian, 116023, China.
    Background: Automatic disease named entity recognition (DNER) is of utmost importance for development of more sophisticated BioNLP tools. However, most conventional CRF based DNER systems rely on well-designed features whose selection is labor intensive and time-consuming. Though most deep learning methods can solve NER problems with little feature engineering, they employ additional CRF layer to capture the correlation information between labels in neighborhoods which makes them much complicated. Read More

    Stable solution to l-based robust inductive matrix completion and its application in linking long noncoding RNAs to human diseases.
    BMC Med Genomics 2017 Dec 28;10(Suppl 5):77. Epub 2017 Dec 28.
    Department of Computer Science and Engineering, University of Texas at Arlington, Arlington, 76019, Texas, USA.
    Backgrounds: A large number of long intergenic non-coding RNAs (lincRNAs) are linked to a broad spectrum of human diseases. The disease association with many other lincRNAs still remain as puzzle. Validation of such links between the two entities through biological experiments are expensive. Read More

    Probability-based collaborative filtering model for predicting gene-disease associations.
    BMC Med Genomics 2017 Dec 28;10(Suppl 5):76. Epub 2017 Dec 28.
    School of Computer Science and Technology, Tianjin University, Tianjin, China.
    Background: Accurately predicting pathogenic human genes has been challenging in recent research. Considering extensive gene-disease data verified by biological experiments, we can apply computational methods to perform accurate predictions with reduced time and expenses.

    Methods: We propose a probability-based collaborative filtering model (PCFM) to predict pathogenic human genes. Read More

    iOPTICS-GSO for identifying protein complexes from dynamic PPI networks.
    BMC Med Genomics 2017 Dec 28;10(Suppl 5):80. Epub 2017 Dec 28.
    School of Mathematical Sciences, Nankai University, Tianjin, China.
    Background: Identifying protein complexes plays an important role for understanding cellular organization and functional mechanisms. As plenty of evidences have indicated that dense sub-networks in dynamic protein-protein interaction network (DPIN) usually correspond to protein complexes, identifying protein complexes is formulated as density-based clustering.

    Methods: In this paper, a new approach named iOPTICS-GSO is developed, which is the improved Ordering Points to Identify the Clustering Structure (OPTICS) algorithm with Glowworm swarm optimization algorithm (GSO) to optimize the parameters in OPTICS when finding dense sub-networks. Read More

    Measuring disease similarity and predicting disease-related ncRNAs by a novel method.
    BMC Med Genomics 2017 Dec 28;10(Suppl 5):71. Epub 2017 Dec 28.
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150001, China.
    Background: Similar diseases are always caused by similar molecular origins, such as diasease-related protein-coding genes (PCGs). And the molecular associations reflect their similarity. Therefore, current methods for calculating disease similarity often utilized functional interactions of PCGs. Read More

    Platform-independent gene expression signature differentiates sessile serrated adenomas/polyps and hyperplastic polyps of the colon.
    BMC Med Genomics 2017 Dec 28;10(1):81. Epub 2017 Dec 28.
    Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA.
    Background: Sessile serrated adenomas/polyps are distinguished from hyperplastic colonic polyps subjectively by their endoscopic appearance and histological morphology. However, hyperplastic and sessile serrated polyps can have overlapping morphological features resulting in sessile serrated polyps diagnosed as hyperplastic. While sessile serrated polyps can progress into colon cancer, hyperplastic polyps have virtually no risk for colon cancer. Read More

    Chromosome 9p copy number gains involving PD-L1 are associated with a specific proliferation and immune-modulating gene expression program active across major cancer types.
    BMC Med Genomics 2017 Dec 6;10(1):74. Epub 2017 Dec 6.
    German Cancer Consortium (DKTK), Berlin and Heidelberg partner sites, and German Cancer Research Center (DKFZ), Heidelberg, Germany.
    Background: 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 subpopulations of patients emphasizing the need for powerful biomarkers that adequately reflect the complex interaction between the tumor and the immune system. Recently, recurrent copy number gains (CNG) in chromosome 9p involving PD-L1 were detected in many cancer types including lung cancer, melanoma, bladder cancer, head and neck cancer, cervical cancer, soft tissue sarcoma, prostate cancer, gastric cancer, ovarian cancer, and triple-negative breast cancer. Read More

    Correction to: FLAGS, frequently mutated genes in public exomes.
    BMC Med Genomics 2017 11 29;10(1):69. Epub 2017 Nov 29.
    Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Vancouver, BC, Canada.
    Correction: Unfortunately, the original article [1] contained an error. The additional files were included incorrectly. The correct additional files 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 and 14 are published in this correction. Read More

    High resolution chromosomal microarray analysis in paediatric obsessive-compulsive disorder.
    BMC Med Genomics 2017 Nov 28;10(1):68. Epub 2017 Nov 28.
    Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital of Psychiatry Zurich, University of Zurich, Neumünsterallee 9, 8032, Zürich, Switzerland.
    Background: Obsessive-Compulsive Disorder (OCD) is a common and chronic disorder in which a person has uncontrollable, reoccurring thoughts and behaviours. It is a complex genetic condition and, in case of early onset (EO), the patients manifest a more severe phenotype, and an increased heritability. Large (>500 kb) copy number variations (CNVs) previously associated with autism and schizophrenia have been reported in OCD. Read More

    Bioinformatics prediction of miR-30a targets and its inhibition of cell proliferation of osteosarcoma by up-regulating the expression of PTEN.
    BMC Med Genomics 2017 Nov 15;10(1):64. Epub 2017 Nov 15.
    Department of Orthopedics, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, 200233, China.
    Background: MiRNAs are frequently abnormally expressed in the progression of human osteosarcoma. Phosphatase and tensin homologue deleted on chromosome 10 (PTEN) is one of the tumor suppressors in various types of human cancer. In the present study, we detected how hsa-miR-30a-3p regulated PTEN and further tested the role of hsa-miR-30a-3p in the cell proliferation of osteosarcoma cells. Read More

    Targeted/exome sequencing identified mutations in ten Chinese patients diagnosed with Noonan syndrome and related disorders.
    BMC Med Genomics 2017 Oct 30;10(1):62. Epub 2017 Oct 30.
    Department of Pediatric Endocrinology/Genetics, Xin Hua Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, 1665 Kongjiang Road, Shanghai, 200092, China.
    Background: Noonan syndrome (NS) and Noonan syndrome with multiple lentigines (NSML) are autosomal dominant developmental disorders. NS and NSML are caused by abnormalities in genes that encode proteins related to the RAS-MAPK pathway, including PTPN11, RAF1, BRAF, and MAP2K. In this study, we diagnosed ten NS or NSML patients via targeted sequencing or whole exome sequencing (TS/WES). Read More

    A method to reduce ancestry related germline false positives in tumor only somatic variant calling.
    BMC Med Genomics 2017 Oct 19;10(1):61. Epub 2017 Oct 19.
    Department of Translational Genomics, University of Southern California, Los Angeles, CA, USA.
    Background: Significant clinical and research applications are driving large scale adoption of individualized tumor sequencing in cancer in order to identify tumors-specific mutations. When a matched germline sample is available, somatic mutations may be identified using comparative callers. However, matched germline samples are frequently not available such as with archival tissues, which makes it difficult to distinguish somatic from germline variants. Read More

    The establishment and application of preimplantation genetic haplotyping in embryo diagnosis for reciprocal and Robertsonian translocation carriers.
    BMC Med Genomics 2017 Oct 17;10(1):60. Epub 2017 Oct 17.
    Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology Hospital, Fudan University, 588 Fangxie Rd, Shanghai, 200011, China.
    Background: Preimplantation genetic diagnosis (PGD) is now widely used to select embryos free of chromosomal copy number variations (CNV) from chromosome balanced translocation carriers. However, it remains a difficulty to distinguish in embryos between balanced and structurally normal chromosomes efficiently.

    Methods: For this purpose, genome wide preimplantation genetic haplotyping (PGH) analysis was utilized based on single nucleotide polymorphism (SNP) microarray. Read More

    Differential gene expression in disease: a comparison between high-throughput studies and the literature.
    BMC Med Genomics 2017 Oct 11;10(1):59. Epub 2017 Oct 11.
    Biogen, Cambridge, MA, USA.
    Background: Differential gene expression is important to understand the biological differences between healthy and diseased states. Two common sources of differential gene expression data are microarray studies and the biomedical literature.

    Methods: With the aid of text mining and gene expression analysis we have examined the comparative properties of these two sources of differential gene expression data. Read More

    RNA sequencing identifies novel non-coding RNA and exon-specific effects associated with cigarette smoking.
    BMC Med Genomics 2017 Oct 6;10(1):58. Epub 2017 Oct 6.
    Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Ave, Boston, MA, USA.
    Background: Cigarette smoking is the leading modifiable risk factor for disease and death worldwide. Previous studies quantifying gene-level expression have documented the effect of smoking on mRNA levels. Using RNA sequencing, it is possible to analyze the impact of smoking on complex regulatory phenomena (e. Read More

    Clinical utility of the low-density Infinium QC genotyping Array in a genomics-based diagnostics laboratory.
    BMC Med Genomics 2017 Oct 6;10(1):57. Epub 2017 Oct 6.
    Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA.
    Background: With 15,949 markers, the low-density Infinium QC Array-24 BeadChip enables linkage analysis, HLA haplotyping, fingerprinting, ethnicity determination, mitochondrial genome variations, blood groups and pharmacogenomics. It represents an attractive independent QC option for NGS-based diagnostic laboratories, and provides cost-efficient means for determining gender, ethnic ancestry, and sample kinships, that are important for data interpretation of NGS-based genetic tests.

    Methods: We evaluated accuracy and reproducibility of Infinium QC genotyping calls by comparing them with genotyping data of the same samples from other genotyping platforms, whole genome/exome sequencing. Read More

    Genomic diversity and phylogeography of norovirus in China.
    BMC Med Genomics 2017 Oct 3;10(Suppl 3):51. Epub 2017 Oct 3.
    Key Laboratory of Medical Molecular Virology of MoE & MoH and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, 138 Yi Xue Yuan Rd, Shanghai, 200032, People's Republic of China.
    Background: Little is known about the phylogeography of norovirus (NoV) in China. In norovirus, a clear understanding for the characteristics of tree topology, migration patterns and its demographic dynamics in viral circulation are needed to identify its prevalence trends, which can help us better prepare for its epidemics as well as develop useful control strategies. The aim of this study was to explore the genetic diversity, temporal distribution, demographic dynamics and migration patterns of NoV that circulated in China. Read More

    A systematic review and integrative approach to decode the common molecular link between levodopa response and Parkinson's disease.
    BMC Med Genomics 2017 Sep 19;10(1):56. Epub 2017 Sep 19.
    Genomics and Molecular Medicine Unit, Institute of Genomics and Integrative Biology (IGIB), Council of Scientific and Industrial Research (CSIR), Mall Road, New Delhi, -110007, India.
    Background: 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 predictive genetic biomarkers for levodopa response (LR) and determine common molecular link with disease susceptibility. Read More

    Assessing the activity of nonsense-mediated mRNA decay in lung cancer.
    BMC Med Genomics 2017 Sep 6;10(1):55. Epub 2017 Sep 6.
    State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China.
    Background: Inhibition of nonsense-mediated mRNA decay (NMD) in tumor cells can suppress tumor growth through expressing new antigens whose mRNAs otherwise are degraded by NMD. Thus NMD inhibition is a promising approach for developing cancer therapies. Apparently, the success of this approach relies on the basal NMD activity in cancer cells. Read More

    A streamlined method for analysing genome-wide DNA methylation patterns from low amounts of FFPE DNA.
    BMC Med Genomics 2017 Aug 31;10(1):54. Epub 2017 Aug 31.
    Department of Pathology, Dunedin School of Medicine, University of Otago, 270 Great King Street, P.O. Box 56, Dunedin, 9054, New Zealand.
    Background: 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 nucleic acid crosslinking. FFPE tissue particularly possesses challenges for methylation analysis and for preparing sequencing-based libraries relying on bisulfite conversion. Read More

    De novo assembly and characterization of breast cancer transcriptomes identifies large numbers of novel fusion-gene transcripts of potential functional significance.
    BMC Med Genomics 2017 Aug 29;10(1):53. Epub 2017 Aug 29.
    Integrated Cancer Research Center, School of Biological Sciences, and Parker H. Petit Institute of Bioengineering and Biosciences, Georgia Institute of Technology, 315 Ferst Dr, Atlanta, GA, 30332, USA.
    Background: Gene-fusion or chimeric transcripts have been implicated in the onset and progression of a variety of cancers. Massively parallel RNA sequencing (RNA-Seq) of the cellular transcriptome is a promising approach for the identification of chimeric transcripts of potential functional significance. We report here the development and use of an integrated computational pipeline for the de novo assembly and characterization of chimeric transcripts in 55 primary breast cancer and normal tissue samples. Read More

    Integrative model of leukocyte genomics and organ dysfunction in heart failure patients requiring mechanical circulatory support: a prospective observational study.
    BMC Med Genomics 2017 Aug 29;10(1):52. Epub 2017 Aug 29.
    Department of Medicine, Division of Cardiology, University of California Los Angeles, 100 UCLA Medical Plaza, Suite 630, Los Angeles, California, 90095, USA.
    Background: The implantation of mechanical circulatory support devices in heart failure patients is associated with a systemic inflammatory response, potentially leading to death from multiple organ dysfunction syndrome. Previous studies point to the involvement of many mechanisms, but an integrative hypothesis does not yet exist. Using time-dependent whole-genome mRNA expression in circulating leukocytes, we constructed a systems-model to improve mechanistic understanding and prediction of adverse outcomes. Read More

    Consensus strategy in genes prioritization and combined bioinformatics analysis for preeclampsia pathogenesis.
    BMC Med Genomics 2017 Aug 8;10(1):50. Epub 2017 Aug 8.
    Faculty of Pharmacy, University of Porto, Porto, Portugal.
    Background: Preeclampsia is a multifactorial disease with unknown pathogenesis. Even when recent studies explored this disease using several bioinformatics tools, the main objective was not directed to pathogenesis. Additionally, consensus prioritization was proved to be highly efficient in the recognition of genes-disease association. Read More

    Secure searching of biomarkers through hybrid homomorphic encryption scheme.
    BMC Med Genomics 2017 Jul 26;10(Suppl 2):42. Epub 2017 Jul 26.
    Department of Mathematical Sciences, Seoul National University, GwanAkRo 1, Seoul, 08826, Republic of Korea.
    Background: As genome sequencing technology develops rapidly, there has lately been an increasing need to keep genomic data secure even when stored in the cloud and still used for research. We are interested in designing a protocol for the secure outsourcing matching problem on encrypted data.

    Method: We propose an efficient method to securely search a matching position with the query data and extract some information at the position. Read More

    PRESAGE: PRivacy-preserving gEnetic testing via SoftwAre Guard Extension.
    BMC Med Genomics 2017 Jul 26;10(Suppl 2):48. Epub 2017 Jul 26.
    Department of Biomedical Informatics, University of California San Diego, La Jolla, 92093, CA, USA.
    Background: Advances in DNA sequencing technologies have prompted a wide range of genomic applications to improve healthcare and facilitate biomedical research. However, privacy and security concerns have emerged as a challenge for utilizing cloud computing to handle sensitive genomic data.

    Methods: We present one of the first implementations of Software Guard Extension (SGX) based securely outsourced genetic testing framework, which leverages multiple cryptographic protocols and minimal perfect hash scheme to enable efficient and secure data storage and computation outsourcing. Read More

    Aftermath of bustamante attack on genomic beacon service.
    BMC Med Genomics 2017 Jul 26;10(Suppl 2):43. Epub 2017 Jul 26.
    Department of Computer Science, University of Manitoba, Winnipeg, Canada.
    Background: With the enormous need for federated eco-system for holding global genomic and clinical data, Global Alliance for Genomic and Health (GA4GH) has created an international website called beacon service which allows a researcher to find out whether a specific dataset can be utilized to his or her research beforehand. This simple webservice is quite useful as it allows queries like whether a certain position of a target chromosome has a specific nucleotide. However, the increased integration of individuals genomic data into clinical practice and research raised serious privacy concern. Read More

    Efficient and secure outsourcing of genomic data storage.
    BMC Med Genomics 2017 Jul 26;10(Suppl 2):46. Epub 2017 Jul 26.
    Laboratory for Communications and Applications - LCA 1, École Polytechnique Fédérale de Lausanne, Route Cantonale, Lausanne, 1015, Switzerland.
    Background: Cloud computing is becoming the preferred solution for efficiently dealing with the increasing amount of genomic data. Yet, outsourcing storage and processing sensitive information, such as genomic data, comes with important concerns related to privacy and security. This calls for new sophisticated techniques that ensure data protection from untrusted cloud providers and that still enable researchers to obtain useful information. Read More

    Secure approximation of edit distance on genomic data.
    BMC Med Genomics 2017 Jul 26;10(Suppl 2):41. Epub 2017 Jul 26.
    Department of Computer Science, University of Manitoba, Winnipeg, Canada.
    Background: Edit distance is a well established metric to quantify how dissimilar two strings are by counting the minimum number of operations required to transform one string into the other. It is utilized in the domain of human genomic sequence similarity as it captures the requirements and leads to a better diagnosis of diseases. However, in addition to the computational complexity due to the large genomic sequence length, the privacy of these sequences are highly important. Read More

    BLOOM: BLoom filter based oblivious outsourced matchings.
    BMC Med Genomics 2017 Jul 26;10(Suppl 2):44. Epub 2017 Jul 26.
    Communication and Distributed Systems (COMSYS), RWTH Aachen University, Ahornstrasse 55, Aachen, 52074, Germany.
    Background: Whole genome sequencing has become fast, accurate, and cheap, paving the way towards the large-scale collection and processing of human genome data. Unfortunately, this dawning genome era does not only promise tremendous advances in biomedical research but also causes unprecedented privacy risks for the many. Handling storage and processing of large genome datasets through cloud services greatly aggravates these concerns. Read More

    Controlling the signal: Practical privacy protection of genomic data sharing through Beacon services.
    BMC Med Genomics 2017 Jul 26;10(Suppl 2):39. Epub 2017 Jul 26.
    Department of Electrical Engineering and Computer Science, Vanderbilt University, 2525 West End Avenue, Suite 800, 37203, Nashville, TN, USA.
    Background: Genomic data is increasingly collected by a wide array of organizations. As such, there is a growing demand to make summary information about such collections available more widely. However, over the past decade, a series of investigations have shown that attacks, rooted in statistical inference methods, can be applied to discern the presence of a known individual's DNA sequence in the pool of subjects. Read More

    Private queries on encrypted genomic data.
    BMC Med Genomics 2017 Jul 26;10(Suppl 2):45. Epub 2017 Jul 26.
    Princeton University, 304 Washington Rd, Princeton, NJ 08544, USA.
    Background: One of the tasks in the iDASH Secure Genome Analysis Competition in 2016 was to demonstrate the feasibility of privacy-preserving queries on homomorphically encrypted genomic data. More precisely, given a list of up to 100,000 mutations, the task was to encrypt the data using homomorphic encryption in a way that allows it to be stored securely in the cloud, and enables the data owner to query the dataset for the presence of specific mutations, without revealing any information about the dataset or the queries to the cloud.

    Methods: We devise a novel string matching protocol to enable privacy-preserving queries on homomorphically encrypted data. Read More

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