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    867 results match your criteria BMC Medical Genomics [Journal]

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    Calculating the statistical significance of rare variants causal for Mendelian and complex disorders.
    BMC Med Genomics 2018 Jun 13;11(1):53. Epub 2018 Jun 13.
    Department of Human Genetics, University of California, Los Angeles, California, Los Angeles, USA.
    Background: With the expanding use of next-gen sequencing (NGS) to diagnose the thousands of rare Mendelian genetic diseases, it is critical to be able to interpret individual DNA variation. To calculate the significance of finding a rare protein-altering variant in a given gene, one must know the frequency of seeing a variant in the general population that is at least as damaging as the variant in question.

    Methods: We developed a general method to better interpret the likelihood that a rare variant is disease causing if observed in a given gene or genic region mapping to a described protein domain, using genome-wide information from a large control sample. Read More

    RNA sequencing-based longitudinal transcriptomic profiling gives novel insights into the disease mechanism of generalized pustular psoriasis.
    BMC Med Genomics 2018 Jun 5;11(1):52. Epub 2018 Jun 5.
    Department of Dermatology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
    Background: 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.

    Methods: To better understand the disease mechanism of GPP, we performed a transcriptome analysis to profile the gene expression of peripheral blood mononuclear cells (PBMCs) from patients enrolled at the time of diagnosis and receiving follow-up treatment for up to 6 months. Read More

    African ancestry is associated with cluster-based childhood asthma subphenotypes.
    BMC Med Genomics 2018 May 31;11(1):51. Epub 2018 May 31.
    Division of Asthma Research, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, 3333 Burnet Ave, Cincinnati, OH, 45229, USA.
    Background: Childhood asthma is a syndrome composed of heterogeneous phenotypes; furthermore, intrinsic biologic variation among racial/ethnic populations suggests possible genetic ancestry variation in childhood asthma. The objective of the study is to identify clinically homogeneous asthma subphenotypes in a diverse sample of asthmatic children and to assess subphenotype-specific genetic ancestry in African-American asthmatic children.

    Methods: A total of 1211 asthmatic children including 813 in the Childhood Asthma Management Program and 398 in the Childhood Asthma Research and Education program were studied. Read More

    Burden of de novo mutations and inherited rare single nucleotide variants in children with sensory processing dysfunction.
    BMC Med Genomics 2018 May 25;11(1):50. Epub 2018 May 25.
    Department of Neurology, University of California, San Francisco, 675 Nelson Rising Lane, San Francisco, CA, 9415, USA.
    Background: 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 neurodevelopmental genes is unknown and in need of investigation. We hypothesize that children with SPD may have pathogenic variants in genes that have been identified as causing other neurodevelopmental disorders including ASD. This genetic information may provide important insight into the etiology of sensory processing dysfunction and guide clinical evaluation and care. Read More

    Chromosomal microarray analysis in developmental delay and intellectual disability with comorbid conditions.
    BMC Med Genomics 2018 May 24;11(1):49. Epub 2018 May 24.
    Department of Pediatric Endocrinology/Genetics, Xinhua Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, 1665 Kongjiang Road, Shanghai, 200092, China.
    Background: Developmental delay (DD) and intellectual disability (ID) are frequently associated with a broad spectrum of additional phenotypes. Chromosomal microarray analysis (CMA) has been recommended as a first-tier test for DD/ID in general, whereas the diagnostic yield differs significantly among DD/ID patients with different comorbid conditions.

    Methods: To investigate the genotype-phenotype correlation, we examined the characteristics of identified pathogenic copy number variations (pCNVs) and compared the diagnostic yields among patient subgroups with different co-occurring conditions. Read More

    Erythrocyte microRNA sequencing reveals differential expression in relapsing-remitting multiple sclerosis.
    BMC Med Genomics 2018 May 21;11(1):48. Epub 2018 May 21.
    School of Medicine and Public Health, University of Newcastle, Callaghan, NSW, 2308, Australia.
    Background: 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 haemorheological features. Several studies have identified an abundance of erythrocyte miRNAs and variable profiles associated with disease states, such as sickle cell disease and malaria. The aim of this study was to compare the erythrocyte miRNA profile of relapsing-remitting MS (RRMS) patients to healthy sex- and age-matched controls. Read More

    Genome-wide association study identifies two loci influencing plasma neurofilament light levels.
    BMC Med Genomics 2018 May 10;11(1):47. Epub 2018 May 10.
    Department of Neurology, The First Affiliated Hospital of Wenzhou Medical University, Nanbaixiang Road, Wenzhou, 325000, Zhejiang Province, China.
    Background: Plasma neurofilament light (NFL) is a promising biomarker for Alzheimer disease (AD), which increases in the early stage of AD and is associated with the progression of AD. We performed a genome-wide association study (GWAS) of plasma NFL in Alzheimer's Disease Neuroimaging Initiative 1 (ADNI-1) cohort to identify novel variants associated with AD.

    Methods: This study included 179 cognitively healthy controls (HC), 176 patients with mild cognitive impairment (MCI), and 172 patients with AD. Read More

    Clinical providers' experiences with returning results from genomic sequencing: an interview study.
    BMC Med Genomics 2018 May 8;11(1):45. Epub 2018 May 8.
    Department of Pediatrics, Baylor College of Medicine, 1102 Bates St. FC 1200, Houston, TX, 77030, USA.
    Background: 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 and research participants has not been thoroughly examined and there are no established best practices.

    Methods: We conducted semi-structured interviews with 21 genetic and non-genetic clinicians returning results of GS as part of the NIH funded Clinical Sequencing Exploratory Research (CSER) Consortium projects. Read More

    DNA methylation in the APOE genomic region is associated with cognitive function in African Americans.
    BMC Med Genomics 2018 May 8;11(1):43. Epub 2018 May 8.
    Department of Epidemiology, School of Public Health, University of Michigan, 1415 Washington Heights, 4602 SPH Tower, Ann Arbor, MI, 48109-2029, USA.
    Background: Genetic variations in apolipoprotein E (APOE) and proximal genes (PVRL2, TOMM40, and APOC1) are associated with cognitive function and dementia, particularly Alzheimer's disease. Epigenetic mechanisms such as DNA methylation play a central role in the regulation of gene expression. Recent studies have found evidence that DNA methylation may contribute to the pathogenesis of dementia, but its association with cognitive function in populations without dementia remains unclear. Read More

    A child with multiple congenital anomalies due to partial trisomy 7q22.1 → qter resulting from a maternally inherited balanced translocation: a case report and review of literature.
    BMC Med Genomics 2018 May 8;11(1):44. Epub 2018 May 8.
    Human Genetics Unit, Faculty of Medicine, University of Colombo, Kynsey Road, Colombo, 00800, Sri Lanka.
    Background: Parental balanced reciprocal translocations can result in partial aneuploidies in the offspring due to unbalanced meiotic segregation during gametogenesis. Herein, we report the phenotypic and molecular cytogenetic characterization of a 2 years and 4 months old female child with partial trisomy 7q22 → qter. This is the first such reported case resulting from a parental balanced translocation involving the long arms of chromosomes 7 and 14. Read More

    Integrative analyses of genes and microRNA expressions in human trisomy 21 placentas.
    BMC Med Genomics 2018 May 9;11(1):46. Epub 2018 May 9.
    Laboratory of Medical Genetics, Medical Research Institute, Cheil General Hospital and Women's Healthcare Center, Seoul, South Korea.
    Background: The most frequent chromosomal aneuploidy is trisomy 21 (T21) that is caused by an extra copy of chromosome 21. The imbalance of whole genome including genes and microRNAs contributes to the various phenotypes of T21. However, the integrative association between genes and microRNAs in the T21 placenta has yet to be determined. Read More

    Splice-site mutation causing partial retention of intron in the FLCN gene in Birt-Hogg-Dubé syndrome: a case report.
    BMC Med Genomics 2018 May 2;11(1):42. Epub 2018 May 2.
    Department of Diagnostic Pathology, Chiba University Graduate School of Medicine, Chiba, Japan.
    Background: 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 is a frameshift mutation within a coding exon. Read More

    LDSplitDB: a database for studies of meiotic recombination hotspots in MHC using human genomic data.
    BMC Med Genomics 2018 Apr 20;11(Suppl 2):27. Epub 2018 Apr 20.
    School of Computer Science and Engineering, Nanyang Technological University, Nanyang Ave, Singapore, 639798, Singapore.
    Background: Meiotic recombination happens during the process of meiosis when chromosomes inherited from two parents exchange genetic materials to generate chromosomes in the gamete cells. The recombination events tend to occur in narrow genomic regions called recombination hotspots. Its dysregulation could lead to serious human diseases such as birth defects. Read More

    EAGLE: Explicit Alternative Genome Likelihood Evaluator.
    BMC Med Genomics 2018 Apr 20;11(Suppl 2):28. Epub 2018 Apr 20.
    Artificial Intelligence Research Center, AIST, 2-3-26 Aomi, Koto-ku, Tokyo, 135-0064, Japan.
    Background: Reliable detection of genome variations, especially insertions and deletions (indels), from single sample DNA sequencing data remains challenging, partially due to the inherent uncertainty involved in aligning sequencing reads to the reference genome. In practice a variety of ad hoc quality filtering methods are employed to produce more reliable lists of putative variants, but the resulting lists typically still include numerous false positives. Thus it would be desirable to be able to rigorously evaluate the degree to which each putative variant is supported by the data. Read More

    Exact association test for small size sequencing data.
    BMC Med Genomics 2018 Apr 20;11(Suppl 2):30. Epub 2018 Apr 20.
    Department of Statistics, Seoul National University, Seoul, South Korea.
    Background: Recent statistical methods for next generation sequencing (NGS) data have been successfully applied to identifying rare genetic variants associated with certain diseases. However, most commonly used methods (e.g. Read More

    CAS-viewer: web-based tool for splicing-guided integrative analysis of multi-omics cancer data.
    BMC Med Genomics 2018 Apr 20;11(Suppl 2):25. Epub 2018 Apr 20.
    Department of Biomedical Informatics, University of Utah, University of Utah School of Medicine, Salt Lake City, UT, 84108, USA.
    Background: The Cancer Genome Atlas (TCGA) project is a public resource that provides transcriptomic, DNA sequence, methylation, and clinical data for 33 cancer types. Transforming the large size and high complexity of TCGA cancer genome data into integrated knowledge can be useful to promote cancer research. Alternative splicing (AS) is a key regulatory mechanism of genes in human cancer development and in the interaction with epigenetic factors. Read More

    Fuzzy set-based generalized multifactor dimensionality reduction analysis of gene-gene interactions.
    BMC Med Genomics 2018 Apr 20;11(Suppl 2):32. Epub 2018 Apr 20.
    Department of Statistics, Seoul National University, Seoul, 08826, South Korea.
    Background: Gene-gene interactions (GGIs) are a known cause of missing heritability. Multifactor dimensionality reduction (MDR) is one of most commonly used methods for GGI detection. The generalized multifactor dimensionality reduction (GMDR) method is an extension of MDR method that is applicable to various types of traits, and allows covariate adjustments. Read More

    Population-based statistical inference for temporal sequence of somatic mutations in cancer genomes.
    BMC Med Genomics 2018 Apr 20;11(Suppl 2):29. Epub 2018 Apr 20.
    Cancer Research Institute, College of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul, 06591, Republic of Korea.
    Background: It is well recognized that accumulation of somatic mutations in cancer genomes plays a role in carcinogenesis; however, the temporal sequence and evolutionary relationship of somatic mutations remain largely unknown.

    Methods: In this study, we built a population-based statistical framework to infer the temporal sequence of acquisition of somatic mutations. Using the model, we analyzed the mutation profiles of 1954 tumor specimens across eight tumor types. Read More

    IMPACT web portal: oncology database integrating molecular profiles with actionable therapeutics.
    BMC Med Genomics 2018 Apr 20;11(Suppl 2):26. Epub 2018 Apr 20.
    Division of Medical Oncology, Department of Medicine, Translational Bioinformatics and Cancer Systems Biology Laboratory, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
    Background: With the advancement of next generation sequencing technology, researchers are now able to identify important variants and structural changes in DNA and RNA in cancer patient samples. With this information, we can now correlate specific variants and/or structural changes with actionable therapeutics known to inhibit these variants. We introduce the creation of the IMPACT Web Portal, a new online resource that connects molecular profiles of tumors to approved drugs, investigational therapeutics and pharmacogenetics associated drugs. Read More

    Identifying statistically significant combinatorial markers for survival analysis.
    BMC Med Genomics 2018 Apr 20;11(Suppl 2):31. Epub 2018 Apr 20.
    Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan.
    Background: Survival analysis methods have been widely applied in different areas of health and medicine, spanning over varying events of interest and target diseases. They can be utilized to provide relationships between the survival time of individuals and factors of interest, rendering them useful in searching for biomarkers in diseases such as cancer. However, some disease progression can be very unpredictable because the conventional approaches have failed to consider multiple-marker interactions. Read More

    An integrated clinical and genomic information system for cancer precision medicine.
    BMC Med Genomics 2018 Apr 20;11(Suppl 2):34. Epub 2018 Apr 20.
    Ewha Research Center for Systems Biology (ERCSB), Ewha Womans University, Seoul, Korea.
    Background: Increasing affordability of next-generation sequencing (NGS) has created an opportunity for realizing genomically-informed personalized cancer therapy as a path to precision oncology. However, the complex nature of genomic information presents a huge challenge for clinicians in interpreting the patient's genomic alterations and selecting the optimum approved or investigational therapy. An elaborate and practical information system is urgently needed to support clinical decision as well as to test clinical hypotheses quickly. Read More

    Mut2Vec: distributed representation of cancerous mutations.
    BMC Med Genomics 2018 Apr 20;11(Suppl 2):33. Epub 2018 Apr 20.
    Department of Computer Science and Engineering, Korea University, Seoul, Korea.
    Background: Embedding techniques for converting high-dimensional sparse data into low-dimensional distributed representations have been gaining popularity in various fields of research. In deep learning models, embedding is commonly used and proven to be more effective than naive binary representation. However, yet no attempt has been made to embed highly sparse mutation profiles into densely distributed representations. Read More

    WISARD: workbench for integrated superfast association studies for related datasets.
    BMC Med Genomics 2018 Apr 20;11(Suppl 2):39. Epub 2018 Apr 20.
    Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, South Korea.
    Background: A Mendelian transmission produces phenotypic and genetic relatedness between family members, giving family-based analytical methods an important role in genetic epidemiological studies-from heritability estimations to genetic association analyses. With the advance in genotyping technologies, whole-genome sequence data can be utilized for genetic epidemiological studies, and family-based samples may become more useful for detecting de novo mutations. However, genetic analyses employing family-based samples usually suffer from the complexity of the computational/statistical algorithms, and certain types of family designs, such as incorporating data from extended families, have rarely been used. Read More

    Integrative bioinformatics analysis characterizing the role of EDC3 in mRNA decay and its association to intellectual disability.
    BMC Med Genomics 2018 Apr 23;11(1):41. Epub 2018 Apr 23.
    Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Schwabachanlage 10, 91054, Erlangen, Germany.
    Background: Decapping of mRNA is an important step in the regulation of mRNA turnover and therefore of gene expression, which is a key process controlling development and homeostasis of all organisms. It has been shown that EDC3 plays a role in mRNA decapping, however its function is not well understood. Previously, we have associated a homozygous variant in EDC3 with autosomal recessive intellectual disability. Read More

    A meta-analysis of public microarray data identifies biological regulatory networks in Parkinson's disease.
    BMC Med Genomics 2018 Apr 13;11(1):40. Epub 2018 Apr 13.
    Department of Biology of Basic Medical Science College, Hebei North University, Zhangjiakou, 075000, Hebei, China.
    Background: Parkinson's disease (PD) is a long-term degenerative disease that is caused by environmental and genetic factors. The networks of genes and their regulators that control the progression and development of PD require further elucidation.

    Methods: We examine common differentially expressed genes (DEGs) from several PD blood and substantia nigra (SN) microarray datasets by meta-analysis. Read More

    Genetic analysis of Wnt/PCP genes in neural tube defects.
    BMC Med Genomics 2018 Apr 4;11(1):38. Epub 2018 Apr 4.
    Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering at School of Life Sciences, Institute of Reproduction and Development, Fudan University, Shanghai, 200011, China.
    Background: 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 closure (NTC). Knockout mice that are heterozygotes of single PCP genes likely fail to produce NTD phenotypes, yet damaging variants detected in human NTDs are almost always heterozygous, suggesting that other deleterious interacting variants are likely to be present. Nonetheless, the Wnt/PCP pathway remains a genetic hotspot. Read More

    Patient with multiple acyl-CoA dehydrogenase deficiency disease and ETFDH mutations benefits from riboflavin therapy: a case report.
    BMC Med Genomics 2018 Apr 3;11(1):37. Epub 2018 Apr 3.
    Department of Endocrinology, Tan Tock Seng Hospital, 11 Jalan Tan Tock Seng, Singapore, 308433, Singapore.
    Background: 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 known to occur secondary to mutations in electron transfer flavoprotein dehydrogenase (ETFDH) gene. Whole exome sequencing (WES) with clinical correlations can be useful in identifying genomic alterations for targeted therapy. Read More

    HLA and proteasome expression body map.
    BMC Med Genomics 2018 Mar 27;11(1):36. Epub 2018 Mar 27.
    TRON gGmbH - Translational Oncology at Johannes Gutenberg, University Medical Center gGmbH, Freiligrathstr 12, Mainz, Germany.
    Background: The presentation of HLA peptide complexes to T cells is a highly regulated and tissue specific process involving multiple transcriptionally controlled cellular components. The extensive polymorphism of HLA genes and the complex composition of the proteasome make it difficult to map their expression profiles across tissues.

    Methods: Here we applied a tailored gene quantification pipeline to 4323 publicly available RNA-Seq datasets representing 55 normal tissues and cell types to examine expression profiles of (classical and non-classical) HLA class I, class II and proteasomal genes. Read More

    Performance of in silico prediction tools for the classification of rare BRCA1/2 missense variants in clinical diagnostics.
    BMC Med Genomics 2018 Mar 27;11(1):35. Epub 2018 Mar 27.
    Center for Familial Breast and Ovarian Cancer, Center for Integated Oncology (CIO), Medical Faculty, University Hospital Cologne, Kerpener Straße 34, Cologne, 50931, Germany.
    Background: The use of next-generation sequencing approaches in clinical diagnostics has led to a tremendous increase in data and a vast number of variants of uncertain significance that require interpretation. Therefore, prediction of the effects of missense mutations using in silico tools has become a frequently used approach. Aim of this study was to assess the reliability of in silico prediction as a basis for clinical decision making in the context of hereditary breast and/or ovarian cancer. Read More

    Integrated analysis of DNA-methylation and gene expression using high-dimensional penalized regression: a cohort study on bone mineral density in postmenopausal women.
    BMC Med Genomics 2018 Mar 7;11(1):24. Epub 2018 Mar 7.
    University of Oslo, Department of Mathematics, P.O Box 1053, Oslo, 0316, Norway.
    Background: Using high-dimensional penalized regression we studied genome-wide DNA-methylation in bone biopsies of 80 postmenopausal women in relation to their bone mineral density (BMD). The women showed BMD varying from severely osteoporotic to normal. Global gene expression data from the same individuals was available, and since DNA-methylation often affects gene expression, the overall aim of this paper was to include both of these omics data sets into an integrated analysis. Read More

    Whole exome sequencing in three families segregating a pediatric case of sarcoidosis.
    BMC Med Genomics 2018 Mar 6;11(1):23. Epub 2018 Mar 6.
    AP-HP Pediatric pulmonology and Reference Center for rare lung diseases RespiRare, Hôpital Trousseau, INSERM UMR-S933, Sorbonne University, Paris, France.
    Background: Sarcoidosis (OMIM 181000) is a multi-systemic granulomatous disorder of unknown origin. Despite multiple genome-wide association (GWAS) studies, no major pathogenic pathways have been identified to date. To find out relevant sarcoidosis predisposing genes, we searched for de novo and recessive mutations in 3 young probands with sarcoidosis and their healthy parents using a whole-exome sequencing (WES) methodology. Read More

    A combined linkage, microarray and exome analysis suggests MAP3K11 as a candidate gene for left ventricular hypertrophy.
    BMC Med Genomics 2018 Mar 5;11(1):22. Epub 2018 Mar 5.
    Genetic Epidemiology Unit, Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands.
    Background: Electrocardiographic measures of left ventricular hypertrophy (LVH) are used as predictors of cardiovascular risk. We combined linkage and association analyses to discover novel rare genetic variants involved in three such measures and two principal components derived from them.

    Methods: The study was conducted among participants from the Erasmus Rucphen Family Study (ERF), a Dutch family-based sample from the southwestern Netherlands. Read More

    Computational master-regulator search reveals mTOR and PI3K pathways responsible for low sensitivity of NCI-H292 and A427 lung cancer cell lines to cytotoxic action of p53 activator Nutlin-3.
    BMC Med Genomics 2018 Feb 13;11(Suppl 1):12. Epub 2018 Feb 13.
    Institute of Chemical Biology and Fundamental Medicine, SBRAN, Novosibirsk, Russia.
    Background: Small molecule Nutlin-3 reactivates p53 in cancer cells by interacting with the complex between p53 and its repressor Mdm-2 and causing an increase in cancer cell apoptosis. Therefore, Nutlin-3 has potent anticancer properties. Clinical and experimental studies of Nutlin-3 showed that some cancer cells may lose sensitivity to this compound. Read More

    Cumulative prognostic power of laminin genes in colorectal cancer.
    BMC Med Genomics 2018 Feb 13;11(Suppl 1). Epub 2018 Feb 13.
    SRC Bioclinicum, Ugreshskaya str 2/85, 115088, Moscow, Russia.
    Background: Laminins are a major family of extracellular matrix proteins and the main component of basement membranes. Laminins are involved in many if not all stages of cancer progression, and expression of laminin genes has prognostic value in various types of cancer, including colorectal. Only single laminin genes or components of a single laminin trimer with significant differential expression have been regarded as potential biomarkers to date. Read More

    Novel candidate genes important for asthma and hypertension comorbidity revealed from associative gene networks.
    BMC Med Genomics 2018 Feb 13;11(Suppl 1):15. Epub 2018 Feb 13.
    Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia.
    Background: Hypertension and bronchial asthma are a major issue for people's health. As of 2014, approximately one billion adults, or ~ 22% of the world population, have had hypertension. As of 2011, 235-330 million people globally have been affected by asthma and approximately 250,000-345,000 people have died each year from the disease. Read More

    Targeted sequencing reveals complex, phenotype-correlated genotypes in cystic fibrosis.
    BMC Med Genomics 2018 Feb 13;11(Suppl 1):13. Epub 2018 Feb 13.
    Moscow Institute of Physics and Technology, Department of Biological and Medical Physics, Dolgoprudny, Moscow Region, Russian Federation, 141700.
    Background: Cystic fibrosis (CF) is one of the most common life-threatening genetic disorders. Around 2000 variants in the CFTR gene have been identified, with some proportion known to be pathogenic and 300 disease-causing mutations have been characterized in detail by CFTR2 database, which complicates its analysis with conventional methods.

    Methods: We conducted next-generation sequencing (NGS) in a cohort of 89 adult patients negative for p. Read More

    Circadian succession of molecular processes in living tissues.
    BMC Med Genomics 2018 Feb 13;11(Suppl 1):14. Epub 2018 Feb 13.
    Sidra Medicine, PO Box 26999, Doha, Qatar.
    Background: Oscillations of different origin, period and amplitude play an important role in the regulation of cellular processes. Most widely studied is the circadian or approximately daily variation in gene expression activity. Timing of gene expression is controlled by internal molecular clock keeping steady periodic expression. Read More

    Analysis of microbial sequences in plasma cell-free DNA for early-onset breast cancer patients and healthy females.
    BMC Med Genomics 2018 Feb 13;11(Suppl 1):16. Epub 2018 Feb 13.
    Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang District, Taipei, 115, Taiwan.
    Background: Cell-free circulating DNA (cfDNA) is becoming a useful biopsy for noninvasive diagnosis of diseases. Microbial sequences in plasma cfDNA may provide important information to improve prognosis and treatment. We have developed a stringent method to identify microbial species via microbial cfDNA in the blood plasma of early-onset breast cancer (EOBC) patients and healthy females. Read More

    Exome analysis of carotid body tumor.
    BMC Med Genomics 2018 Feb 13;11(Suppl 1):17. Epub 2018 Feb 13.
    Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
    Background: Carotid body tumor (CBT) is a form of head and neck paragangliomas (HNPGLs) arising at the bifurcation of carotid arteries. Paragangliomas are commonly associated with germline and somatic mutations involving at least one of more than thirty causative genes. However, the specific functionality of a number of these genes involved in the formation of paragangliomas has not yet been fully investigated. Read More

    Primary microcephaly case from the Karachay-Cherkess Republic poses an additional support for microcephaly and Seckel syndrome spectrum disorders.
    BMC Med Genomics 2018 Feb 13;11(Suppl 1). Epub 2018 Feb 13.
    Research Centre for Medical Genetics, Moscow, Russia.
    Background: Primary microcephaly represents an example of clinically and genetically heterogeneous condition. Here we describe a case of primary microcephaly from the Karachay-Cherkess Republic, which was initially diagnosed with Seckel syndrome.

    Case Presentation: Clinical exome sequencing of the proband revealed a novel homozygous single nucleotide deletion in ASPM gene, c. Read More

    Impaired type I interferon regulation in the blood transcriptome of recurrent asthma exacerbations.
    BMC Med Genomics 2018 Feb 27;11(1):21. Epub 2018 Feb 27.
    Division of Pulmonary, Critical Care & Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA.
    Background: Asthma exacerbations are an important cause of morbidity in asthma. Respiratory infections are often involved in asthma exacerbations in both children and adults. Some individuals with asthma have increased susceptibility to viral infections and as a result increased rates of asthma exacerbations. Read More

    Whole transcriptome analysis reveals differential gene expression profile reflecting macrophage polarization in response to influenza A H5N1 virus infection.
    BMC Med Genomics 2018 Feb 23;11(1):20. Epub 2018 Feb 23.
    HKU-Pasteur Research Pole and Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong, China.
    Background: Avian influenza A H5N1 virus can cause lethal disease in humans. The virus can trigger severe pneumonia and lead to acute respiratory distress syndrome. Data from clinical, in vitro and in vivo suggest that virus-induced cytokine dysregulation could be a contributory factor to the pathogenesis of human H5N1 disease. Read More

    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

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